TY - BLOG TI - Loss, Grief, and the Humanities in the Time of Pandemic AU - Booker, M. T2 - Humanities in Action DA - 2020/4// PY - 2020/4// PB - National Humanities Center UR - https://action.nationalhumanitiescenter.org/loss-grief-humanities-pandemic/ ER - TY - CHAP TI - Integrating History into the Restoration of Coho Salmon in the Siuslaw River, Oregon AU - Booker, Matthew T2 - Sustainable Fisheries Management PY - 2020/2/10/ DO - 10.1201/9780429104411-46 SP - 625-636 PB - CRC Press UR - http://dx.doi.org/10.1201/9780429104411-46 ER - TY - CHAP TI - Why Do People Care for Sourdough? AU - Booker, Matthew AB - Using one family’s story and survey responses from hundreds of Sourdough Project participants, Matthew Booker will speculate about why people carry sourdough cultures with them around the world and down through generations. PY - 2020/4/23/ DO - 10.52750/533004 UR - https://doi.org/10.52750/533004 ER - TY - BOOK TI - Down By the Bay: San Francisco's History Between the Tides DA - 2020/6/30/ PY - 2020/6/30/ UR - https://www.ucpress.edu/book/9780520355569/down-by-the-bay ER - TY - JOUR TI - Efficacy of Selected Insecticides for Managing Brown Stink Bug in Corn, 2019 AU - Babu, Arun AU - Reisig, Dominic D T2 - Arthropod Management Tests DA - 2020/1/1/ PY - 2020/1/1/ DO - 10.1093/amt/tsaa030 UR - https://doi.org/10.1093/amt/tsaa030 ER - TY - JOUR TI - Efficacy of Selected Insecticides for Managing Aphids in Cotton, 2019 AU - Babu, Arun AU - Reisig, Dominic D T2 - Arthropod Management Tests DA - 2020/1/1/ PY - 2020/1/1/ DO - 10.1093/amt/tsaa031 UR - https://doi.org/10.1093/amt/tsaa031 ER - TY - ER - TY - JOUR TI - Genetic Variation and Potential for Resistance Development to the tTA Overexpression Lethal System in Insects AU - Knudsen, Katherine E AU - Reid, William R AU - Barbour, Traci M AU - Bowes, Laci M AU - Duncan, Juliana AU - Philpott, Elaina AU - Potter, Samantha AU - Scott, Maxwell J T2 - G3 Genes|Genomes|Genetics AB - Release of insect pests carrying the dominant lethal tetracycline transactivator (tTA) overexpression system has been proposed as a means for population suppression. High levels of the tTA transcription factor are thought to be toxic due to either transcriptional squelching or interference with protein ubiquitination. Here we utilized the Drosophila melanogaster Genetic Reference Panel (DGRP) to examine the influence of genetic variation on the efficacy of a female-specific tTA overexpression system. The level of female lethality between DGRP lines varied from 11 to 97% with a broad sense heritability of 0.89. A genome-wide association analysis identified 192 allelic variants associated with high or low lethality (P < 10-5), although none were significant when corrected for multiple testing. 151 of the variants fell within 108 genes that were associated with several biological processes including transcription and protein ubiquitination. In four lines with high female lethality, tTA RNA levels were similar or higher than in the parental tTA overexpression strain. In two lines with low lethality, tTA levels were about two fold lower than in the parental strain. However, in two other lines with low lethality, tTA levels were similar or approximately 30% lower. RNAseq analysis identified genes that were up or downregulated in the four low female lethal lines compared to the four high lethal lines. For example, genes associated with RNA processing and rRNA maturation were significantly upregulated in low lethal lines. Our data suggest that standing genetic variation in an insect population could provide multiple mechanisms for resistance to the tTA overexpression system. DA - 2020/4/1/ PY - 2020/4/1/ DO - 10.1534/g3.120.400990 VL - 10 IS - 4 SP - 1271-1281 LA - en OP - SN - 2160-1836 UR - http://dx.doi.org/10.1534/g3.120.400990 DB - Crossref ER - TY - JOUR TI - Development and testing of a novel killer–rescue self-limiting gene drive system in Drosophila melanogaster AU - Webster, Sophia H. AU - Vella, Michael R. AU - Scott, Maxwell J. T2 - Proceedings of the Royal Society B: Biological Sciences AB - Here we report the development and testing of a novel self-limiting gene drive system, Killer–Rescue (K–R), in Drosophila melanogaster . This system is composed of an autoregulated Gal4 Killer (K) and a Gal4-activated Gal80 Rescue (R). Overexpression of Gal4 is lethal, but in the presence of R activation of Gal80 leads to much lower levels of Gal4 and rescue of lethality. We demonstrate that with a single 2 : 1 engineered to wild-type release, K drives R through the population and after nine generations, more than 98% of the population carry R and less than 2% of the population are wild-type flies. We discuss how this simple K–R gene drive system may be readily adapted for population replacement in a human health pest, Aedes aegypti , or for population suppression in an agricultural pest, Drosophila suzukii . DA - 2020/4/15/ PY - 2020/4/15/ DO - 10.1098/rspb.2019.2994 VL - 287 IS - 1925 SP - 20192994 J2 - Proc. R. Soc. B. LA - en OP - SN - 0962-8452 1471-2954 UR - http://dx.doi.org/10.1098/rspb.2019.2994 DB - Crossref ER - TY - JOUR TI - Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions AU - Broeck, Lisa Van AU - Spurney, Ryan J. AU - Fisher, Adam P. AU - Schwartz, Michael AU - Clark, Natalie M. AU - Nguyen, Thomas T. AU - Madison, Imani AU - Gobble, Mariah AU - Long, Terri AU - Sozzani, Rosangela AB - Abstract Stem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WOX5 and SHR, regulate divisions in the root stem cell niche (SCN). However, how these proteins coordinately function to establish systemic behavior is not well understood. We propose a non-cell autonomous role for WOX5 in the CEI and identify a regulator, AN3/GIF1, that coordinates CEI divisions. Here we show with a multiscale hybrid model integrating ODEs and agent-based modeling that QC and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behavior, which led us to predict cell-type-specific expression dynamics of SHR, SCR, WOX5, AN3, and CYCD6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions. Thumbnail image DA - 2020/12/1/ PY - 2020/12/1/ DO - 10.1101/2020.11.30.404426 UR - https://doi.org/10.1101/2020.11.30.404426 ER - TY - JOUR TI - Adding Epidemiologically Important Meteorological Data to Peanut Rx, the Risk Assessment Framework for Spotted Wilt of Peanut AU - Chappell, Thomas M. AU - Codod, Clarence B. AU - Williams, Blake W. AU - Kemerait, Robert C. AU - Culbreath, Albert K. AU - Kennedy, George G. T2 - Phytopathology® AB - Management of disease affecting peanut in the southeastern United States has benefited from extensive field research identifying disease-associated risk factors since the 1990s. An assessment of risk factors associated with tomato spotted wilt (TSW), caused by tomato spotted wilt virus and spread exclusively by thrips, is available to growers through Peanut Rx, a tool developed to inform peanut management decisions. Peanut Rx provides an assessment of relative TSW risk as an index. The assessment provides information about the relative degree to which a field characterized by a specified suite of practices is at risk of crop loss caused by TSW. Loss results when infection occurs, and infection rates are determined, in part, by factors outside a grower's control, primarily the abundance of dispersing, viruliferous thrips. In this study, we incorporated meteorological variables useful for predicting thrips dispersal, increasing the robustness of the Peanut Rx framework in relation to variation in the weather. We used data from field experiments and a large grower survey to estimate the relationships between weather and TSW risk mediated by thrips vectors, and developed an addition to Peanut Rx that proved informative and easy to implement. The expected temporal occurrence of major thrips flights, as a function of heat and precipitation, was translated into the existing risk-point system of Peanut Rx. Results from the grower survey further demonstrated the validity of Peanut Rx for guiding growers' decisions to minimize risk of TSW. DA - 2020/6// PY - 2020/6// DO - 10.1094/PHYTO-11-19-0438-R VL - 110 IS - 6 SP - 1199-1207 J2 - Phytopathology® LA - en OP - SN - 0031-949X 1943-7684 UR - http://dx.doi.org/10.1094/PHYTO-11-19-0438-R DB - Crossref ER - TY - JOUR TI - Understanding the potential impact of continued seed treatment use for resistance management in Cry51Aa2.834_16 Bt cotton against Frankliniella fusca AU - Huseth, Anders S. AU - D’Ambrosio, Damon A. AU - Kennedy, George G. T2 - PLOS ONE AB - Transgenic cotton expressing Cry51Aa2.834_16 Bt toxin (hereafter referred to as MON 88702) has the potential to be an important tool for pest management due to its unique activity against tobacco thrips, Frankliniella fusca. Unlike other Bt toxins targeting lepidopteran cotton pests, MON 88702 does not cause direct mortality but has an antixenotic effect that suppresses F. fusca oviposition. Previous work has shown neonicotinoid seed treated (NST) crops have similar behavioral effects on thrips. This study used non-choice and common garden experiments to examine how the presence of MON 88702 cotton and soybean (another F. fusca host) with and without NSTs might alter F. fusca infestation distributions. In a no-choice environment, significant larval establishment differences were observed, with untreated soybean plants becoming most heavily infested. In choice experiments, plants expressing MON 88702 or were neonicotinoid treated had significantly lower larval establishment. Larval density decreased as dispersal distance increased, suggesting reproductive decisions were negatively related to distance from the release point. Understanding how F. fusca responds to MON 88702 in an environment where adults can choose among multiple host plants will provide valuable context for projections regarding design of MON 88702 resistance refuges. Reduced larval establishment on NST cotton and soybean suggests that area-wide use of NSTs could reduce the number of susceptible F. fusca generated in unstructured crop refuges for MON 88702. These results also suggest that although the presence of NST MON 88702 could suppress reproduction and resistance selection, over time this benefit could erode resulting in increased larval establishment on NST cotton and soybean due to increased frequency of neonicotinoid resistant F. fusca populations. DA - 2020/10/1/ PY - 2020/10/1/ DO - 10.1371/journal.pone.0239910 VL - 15 IS - 10 SP - e0239910 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0239910 DB - Crossref ER - TY - CHAP TI - Responsibilities to the Public—Professional Engineering Societies AU - Herkert, Joseph AU - Borenstein, Jason T2 - The Routledge Handbook of the Philosophy of Engineering AB - This chapter focuses on the collective social responsibilities of the engineering profession to the public from the perspective of both traditional professional engineering societies and quasi-professional engineering organizations. Traditional professional engineering societies usually have direct ties to a specific engineering discipline or the engineering profession as a whole, while quasi-professional engineering societies are organized outside of traditional professional institutions and focus on a specific issue or kind of activity. The views of traditional professional engineering societies on social responsibilities of engineers are often revealed in their formulation and consideration of public policy including issuance of formal position statements, as well as in the promulgation and enforcement of codes of ethics and in the creation of technical standards. Issues of concern to engineering societies that highlight social responsibility and public policy include such topics as privacy and security; social and environmental justice; and autonomous weapons systems. Humanitarian and social justice-oriented quasi-professional engineering societies often address such issues, but these groups lack the influence of the larger, more mainstream engineering societies. Emerging technologies raise social and ethical concerns, which highlight the need, and opportunities, for traditional professional societies to assume leadership roles in addressing such concerns. PY - 2020/12/29/ DO - 10.4324/9781315276502-52 SP - 592-606 PB - Routledge UR - http://dx.doi.org/10.4324/9781315276502-52 ER - TY - JOUR TI - Autonomous Vehicles and the Ethical Tension Between Occupant and Non-Occupant Safety AU - Borenstein, Jason AU - Herkert, Joseph AU - Miller, Keith T2 - Journal of Sociotechnical Critique DA - 2020/// PY - 2020/// DO - 10.25779/5G55-HW09 UR - https://digitalcommons.odu.edu/sociotechnicalcritique/vol1/iss1/6/ ER - TY - RPRT TI - Complete list of requirements for a nano-specific risk governance framework AU - Jensen, K.A. AU - Porcari, A. AU - Pizzol, L. AU - Kelly, S. AU - Bakker, M. AU - Spurgeon, D. AU - Grieger, K. AU - Chakravarty, S. A3 - caLIBRAte European project, Horizon 2020 research and innovation program DA - 2020/// PY - 2020/// M3 - Deliverable PB - caLIBRAte European project, Horizon 2020 research and innovation program ER - TY - CHAP TI - Nanomaterials: Regulation and Risk Assessment AU - Hansen, S.F. AU - Grieger, K. AU - Baun, A. T2 - Managing Human and Social Systems PY - 2020/// ET - 2nd PB - CRC Press ER - TY - JOUR TI - Pandemics Call for Systems Approaches to Research and Funding AU - Cummings, C.L. AU - Kuzma, J. AU - Grieger, K. AU - Brown, Z.S. T2 - Issues in Science and Technology DA - 2020/4// PY - 2020/4// UR - https://issues.org/pandemics-call-for-systems-approaches/ ER - TY - JOUR TI - Accessing Legacy Phosphorus in Soils AU - Doydora, Sarah AU - Gatiboni, Luciano AU - Grieger, Khara AU - Hesterberg, Dean AU - Jones, Jacob L. AU - McLamore, Eric S. AU - Peters, Rachel AU - Sozzani, Rosangela AU - Van den Broeck, Lisa AU - Duckworth, Owen W. T2 - Soil Systems AB - Repeated applications of phosphorus (P) fertilizers result in the buildup of P in soil (commonly known as legacy P), a large fraction of which is not immediately available for plant use. Long-term applications and accumulations of soil P is an inefficient use of dwindling P supplies and can result in nutrient runoff, often leading to eutrophication of water bodies. Although soil legacy P is problematic in some regards, it conversely may serve as a source of P for crop use and could potentially decrease dependence on external P fertilizer inputs. This paper reviews the (1) current knowledge on the occurrence and bioaccessibility of different chemical forms of P in soil, (2) legacy P transformations with mineral and organic fertilizer applications in relation to their potential bioaccessibility, and (3) approaches and associated challenges for accessing native soil P that could be used to harness soil legacy P for crop production. We highlight how the occurrence and potential bioaccessibility of different forms of soil inorganic and organic P vary depending on soil properties, such as soil pH and organic matter content. We also found that accumulation of inorganic legacy P forms changes more than organic P species with fertilizer applications and cessations. We also discuss progress and challenges with current approaches for accessing native soil P that could be used for accessing legacy P, including natural and genetically modified plant-based strategies, the use of P-solubilizing microorganisms, and immobilized organic P-hydrolyzing enzymes. It is foreseeable that accessing legacy P will require multidisciplinary approaches to address these limitations. DA - 2020/12/18/ PY - 2020/12/18/ DO - 10.3390/soilsystems4040074 VL - 4 IS - 4 SP - 74 J2 - Soil Systems LA - en OP - SN - 2571-8789 UR - http://dx.doi.org/10.3390/soilsystems4040074 DB - Crossref ER - TY - JOUR TI - Scale development for stakeholder responses in crises: Centering on stakeholders in the United Airlines crisis AU - Shen, H.M. AU - Cheng, Y. T2 - Public Relations Journal DA - 2020/// PY - 2020/// VL - 13 IS - 2 SP - 1–17 ER - TY - CHAP TI - Public Relations, Social Media, and Public Opinion in China AU - Cheng, Y. AU - Huang, Y.H. AU - Chan, C.M. T2 - China in the Era of Social Media: An Unprecedented Force for An Unprecedented Social Change A2 - Hong, Junhao PY - 2020/// SP - 171-186 PB - Rowman & Littlefield SN - 9781793608741 9781793608758 ER - TY - CHAP TI - Agenda Setting AU - Cheng, Yang T2 - The SAGE International Encyclopedia of Mass Media and Society PY - 2020/// DO - 10.4135/9781483375519.n23 PB - SAGE Publications, Inc. UR - http://dx.doi.org/10.4135/9781483375519.n23 ER - TY - JOUR TI - United Airlines crisis from the stakeholder perspective: Exploring customers’ ethical judgment, trust and distrust, and behavioral intentions AU - Cheng, Yang AU - Shen, Hongmei T2 - Public Relations Review AB - In the context of the United Airlines crisis, this study investigated the relationships among customers’ ethical judgment, trust and distrust toward United Airlines, and post-crisis behavioral intentions. Results from an online survey (N = 579) demonstrated that customers’ negative ethical judgment was positively associated with the level of trust and negatively predicted their distrust toward the corporation. Distrust had a bigger impact on stakeholders’ behavioral intentions such as information seeking, mobilizing, and consulting than trust. Findings indicated the important role of customers in corporate crisis management. Theoretical and practical implications were discussed. DA - 2020/6// PY - 2020/6// DO - 10.1016/j.pubrev.2020.101908 VL - 46 IS - 2 SP - 101908 J2 - Public Relations Review LA - en OP - SN - 0363-8111 UR - http://dx.doi.org/10.1016/j.pubrev.2020.101908 DB - Crossref ER - TY - ER - TY - JOUR TI - Genetic variation for plant growth traits in a common wheat population is dominated by known variants and novel QTL AU - DeWitt, Noah AU - Guedira, Mohammed AU - Lauer, Edwin AU - Murphy, J. Paul AU - Marshall, David AU - Mergoum, Mohamed AU - Johnson, Jerry AU - Holland, James B. AU - Brown-Guedira, Gina AB - Abstract Genetic variation in growth over the course of the season is a major source of grain yield variation in wheat, and for this reason variants controlling heading date and plant height are among the best-characterized in wheat genetics. While the major variants for these traits have been cloned, the importance of these variants in contributing to genetic variation for plant growth over time is not fully understood. Here we develop a biparental population segregating for major variants for both plant height and flowering time to characterize the genetic architecture of the traits and identify additional novel QTL. We find that additive genetic variation for both traits is almost entirely associated with major and moderate-effect QTL, including four novel heading date QTL and four novel plant height QTL. FT2 and Vrn-A3 are proposed as candidate genes underlying QTL on chromosomes 3A and 7A, while Rht8 is mapped to chromosome 2D. These mapped QTL also underlie genetic variation in a longitudinal analysis of plant growth over time. The oligogenic architecture of these traits is further demonstrated by the superior trait prediction accuracy of QTL-based prediction models compared to polygenic genomic selection models. In a population constructed from two modern wheat cultivars adapted to the southeast U.S., almost all additive genetic variation in plant growth traits is associated with known major variants or novel moderate-effect QTL. Major transgressive segregation was observed in this population despite the similar plant height and heading date characters of the parental lines. This segregation is being driven primarily by a small number of mapped QTL, instead of by many small-effect, undetected QTL. As most breeding populations in the southeast U.S. segregate for known QTL for these traits, genetic variation in plant height and heading date in these populations likely emerges from similar combinations of major and moderate effect QTL. We can make more accurate and cost-effective prediction models by targeted genotyping of key SNPs. DA - 2020/12/16/ PY - 2020/12/16/ DO - 10.1101/2020.12.16.422696 UR - https://doi.org/10.1101/2020.12.16.422696 ER - TY - CONF TI - Addressing the speculative "you": Contextualizing the readers of documentation AU - Swarts, J. AB - The poster presents a corpus analysis of a stylistic feature of topic-based documentation: the speculative “you.” The feature signals important information to help readers adapt the content for their situated uses. The feature is illustrated with examples and the author offers recommendations for amplifying this information. C2 - 2020/// C3 - SIGDOC 2020 - Proceedings of the 38th ACM International Conference on Design of Communication DA - 2020/// DO - 10.1145/3380851.3416749 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85094963020&partnerID=MN8TOARS ER - TY - CHAP TI - Writing about structure in DITA AU - Swarts, J. T2 - Teaching Content Management in Technical and Professional Communication PY - 2020/// SP - 155-175 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85088625088&partnerID=MN8TOARS ER - TY - JOUR TI - Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa AU - Matthews, Megan L. AU - Wang, Jack P. AU - Sederoff, Ronald AU - Chiang, Vincent L. AU - Williams, Cranos M. T2 - PLOS Computational Biology AB - Accurate manipulation of metabolites in monolignol biosynthesis is a key step for controlling lignin content, structure, and other wood properties important to the bioenergy and biomaterial industries. A crucial component of this strategy is predicting how single and combinatorial knockdowns of monolignol specific gene transcripts influence the abundance of monolignol proteins, which are the driving mechanisms of monolignol biosynthesis. Computational models have been developed to estimate protein abundances from transcript perturbations of monolignol specific genes. The accuracy of these models, however, is hindered by their inability to capture indirect regulatory influences on other pathway genes. Here, we examine the manifestation of these indirect influences on transgenic transcript and protein abundances, identifying putative indirect regulatory influences that occur when one or more specific monolignol pathway genes are perturbed. We created a computational model using sparse maximum likelihood to estimate the resulting monolignol transcript and protein abundances in transgenic Populus trichocarpa based on targeted knockdowns of specific monolignol genes. Using in-silico simulations of this model and root mean square error, we showed that our model more accurately estimated transcript and protein abundances, in comparison to previous models, when individual and families of monolignol genes were perturbed. We leveraged insight from the inferred network structure obtained from our model to identify potential genes, including PtrHCT, PtrCAD, and Ptr4CL, involved in post-transcriptional and/or post-translational regulation. Our model provides a useful computational tool for exploring the cascaded impact of single and combinatorial modifications of monolignol specific genes on lignin and other wood properties. DA - 2020/4/10/ PY - 2020/4/10/ DO - 10.1371/journal.pcbi.1007197 UR - https://doi.org/10.1371/journal.pcbi.1007197 ER - TY - JOUR TI - Computer vision approach to characterize size and shape phenotypes of horticultural crops using high-throughput imagery AU - Haque, Samiul AU - Lobaton, Edgar AU - Nelson, Natalie AU - Yencho, G Craig AU - Pecota, Kenneth V AU - Mierop, Russell AU - Kudenov, Michael W AU - Boyette, Mike AU - Williams, Cranos M AB - Abstract For many horticultural crops, variation in quality (e.g., shape and size) contribute significantly to the crop’s market value. Metrics characterizing less subjective harvest quantities (e.g., yield and total biomass) are routinely monitored. In contrast, metrics quantifying more subjective crop quality characteristics such as ideal size and shape remain difficult to characterize objectively at the production-scale due to the lack of modular technologies for high-throughput sensing and computation. Several horticultural crops are sent to packing facilities after having been harvested, where they are sorted into boxes and containers using high-throughput scanners. These scanners capture images of each fruit or vegetable being sorted and packed, but the images are typically used solely for sorting purposes and promptly discarded. With further analysis, these images could offer unparalleled insight on how crop quality metrics vary at the industrial production-scale and provide further insight into how these characteristics translate to overall market value. At present, methods for extracting and quantifying quality characteristics of crops using images generated by existing industrial infrastructure have not been developed. Furthermore, prior studies that investigated horticultural crop quality metrics, specifically of size and shape, used a limited number of samples, did not incorporate deformed or non-marketable samples, and did not use images captured from high-throughput systems. In this work, using sweetpotato (SP) as a use case, we introduce a computer vision algorithm for quantifying shape and size characteristics in a high-throughput manner. This approach generates 3D model of SPs from two 2D images captured by an industrial sorter 90 degrees apart and extracts 3D shape features in a few hundred milliseconds. We applied the 3D reconstruction and feature extraction method to thousands of image samples to demonstrate how variations in shape features across sweetptoato cultivars can be quantified. We created a sweetpotato shape dataset containing sweetpotato images, extracted shape features, and qualitative shape types (U.S. No. 1 or Cull). We used this dataset to develop a neural network-based shape classifier that was able to predict Cull vs. U.S. No. 1 sweetpotato with 84.59% accuracy. In addition, using univariate Chi-squared tests and random forest, we identified the most important features for determining qualitative shape (U.S. No. 1 or Cull) of the sweetpotatoes. Our study serves as the first step towards enabling big data analytics for sweetpotato agriculture. The methodological framework is readily transferable to other horticultural crops, particularly those that are sorted using commercial imaging equipment. DA - 2020/7/26/ PY - 2020/7/26/ DO - 10.1101/2020.07.24.199539 VL - 7 UR - https://doi.org/10.1101/2020.07.24.199539 ER - TY - JOUR TI - Combination of plant-growth-promoting and fluoranthene-degrading microbes enhances phytoremediation efficiency in the ryegrass rhizosphere AU - Li, Weiming AU - Zhang, Zhen AU - Sun, Bin AU - Hu, Shuijin AU - Wang, Dongsheng AU - Hu, Feng AU - Li, Huixin AU - Xu, Li AU - Jiao, Jiaguo T2 - ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH DA - 2020/// PY - 2020/// DO - 10.1007/s11356-020-10937-3 KW - Microbe-assisted phytoremediation KW - Polycyclic aromatic hydrocarbons KW - Microbial functional diversity KW - Biolog Eco-plates KW - Ryegrass KW - Plant-growth-promoting rhizobacteria ER - TY - JOUR TI - Assessing Rate-Reducing Foliar Resistance to Anthracnose Crown Rot and Fruit Rot in Strawberry AU - Jacobs, Raymond L. AU - Adhikari, Tika B. AU - Pattison, Jeremy AU - Yencho, G. Craig AU - Fernandez, Gina E. AU - Louws, Frank J. T2 - Plant Disease AB - Anthracnose fruit rot and anthracnose crown rot (ACR) caused by two species complexes of the fungus referred to as Colletotrichum acutatum and Colletotrichum gloeosporioides, respectively, are major pathogens of strawberry in North Carolina. Anthracnose epidemics are common when susceptible cultivars and asymptomatic planting stocks carrying quiescent Colletotrichum infection or hemibiotrophic infection (HBI) are planted. The main objective of this study was to assess resistance to HBI and ACR in strawberry. Strawberry cultivars and breeding lines were spray inoculated with isolates of C. acutatum or C. gloeosporioides. Four epidemiological parameters providing estimates of rate-reducing resistance to HBI and ACR in strawberry cultivars and lines were evaluated in repeated experiments in controlled environments in a greenhouse. HBI severity, measured as the percentage of total leaf area covered by acervuli, was estimated visually and by image analysis. ACR severity was rated weekly for wilt symptoms, and relative area under disease progress curve scores were calculated for comparing strawberry cultivars and lines. Significant differences (P ≤ 0.005) in HBI severity were found among strawberry genotypes; however, the correlations were not remarkable between Colletotrichum species (r = 0.4251). Although significant variation in resistance was observed for ACR, this was also weakly correlated (r = 0.2430) with resistance to C. gloeosporioides HBI. Overall, rate-reducing resistance to HBI and ACR in strawberry identified in this study could be utilized in breeding programs to develop durable resistance to anthracnose in North Carolina. DA - 2020/2// PY - 2020/2// DO - 10.1094/PDIS-04-19-0687-RE VL - 104 IS - 2 SP - 398-407 J2 - Plant Disease LA - en OP - SN - 0191-2917 1943-7692 UR - http://dx.doi.org/10.1094/PDIS-04-19-0687-RE DB - Crossref KW - etiology KW - fungi KW - fruit KW - pathogen detection KW - small fruits KW - techniques ER - TY - JOUR TI - Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations AU - Zhou, Chenxi AU - Olukolu, Bode AU - Gemenet, Dorcus C. AU - Wu, Shan AU - Gruneberg, Wolfgang AU - Cao, Minh Duc AU - Fei, Zhangjun AU - Zeng, Zhao-Bang AU - George, Andrew W. AU - Khan, Awais AU - Yencho, G. Craig AU - Coin, Lachlan J. M. T2 - Nature Genetics DA - 2020/10/30/ PY - 2020/10/30/ DO - 10.1038/s41588-020-00717-7 VL - 52 IS - 11 SP - 1256-1264 J2 - Nat Genet LA - en OP - SN - 1061-4036 1546-1718 UR - http://dx.doi.org/10.1038/s41588-020-00717-7 DB - Crossref ER - TY - JOUR TI - Use of unconventional mixed Acetone-Butanol-Ethanol solvents for anthocyanin extraction from Purple-Fleshed sweetpotatoes AU - Zuleta-Correa, Ana AU - Chinn, Mari Sum AU - Alfaro-Córdoba, Marcela AU - Truong, Van-Den AU - Yencho, George Craig AU - Bruno-Bárcena, José Manuel T2 - Food Chemistry AB - Anthocyanins from purple-fleshed sweetpotatoes constitute highly valued natural colorants and functional ingredients. In the past, anthocyanin extraction conditions and efficiencies using a single acidified solvent have been assessed. However, the potential of solvent mixes that can be generated by fermentation of biomass-derived sugars have not been explored. In this study, the effects of single and mixed solvent, time, temperature, sweetpotato genotype and preparation, on anthocyanin and phenolic extraction were evaluated. Results indicated that unconventional diluted solvent mixes containing acetone, butanol, and ethanol were superior or equally efficient for extracting anthocyanins when compared to commonly used concentrated extractants. In addition, analysis of anthocyanidins concentrations including cyanidin (cy), peonidin (pe), and pelargonidin (pl), indicated that different ratios of pn/cy were obtained depending on the solvent used. These results could be useful when selecting processing conditions that better suit particular end-use applications and more environmentally friendly process development for purple sweetpotatoes. DA - 2020/6// PY - 2020/6// DO - 10.1016/j.foodchem.2019.125959 VL - 314 SP - 125959 J2 - Food Chemistry LA - en OP - SN - 0308-8146 UR - http://dx.doi.org/10.1016/j.foodchem.2019.125959 DB - Crossref KW - Ipomoea batatas KW - Anthocyanidins KW - Phenolics KW - Cyanidin KW - Peonidin KW - Temperature KW - Flour ER - TY - JOUR TI - Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs AU - Gemenet, Dorcus C. AU - Kitavi, Mercy N. AU - David, Maria AU - Ndege, Dorcah AU - Ssali, Reuben T. AU - Swanckaert, Jolien AU - Makunde, Godwill AU - Yencho, G. Craig AU - Gruneberg, Wolfgang AU - Carey, Edward AU - Mwanga, Robert O. AU - Andrade, Maria I. AU - Heck, Simon AU - Campos, Hugo T2 - PLOS ONE AB - Quality assurance and control (QA/QC) is an essential element of a breeding program’s optimization efforts towards increased genetic gains. Due to auto-hexaploid genome complexity, a low-cost marker platform for routine QA/QC in sweetpotato breeding programs is still unavailable. We used 662 parents of the International Potato Center (CIP)’s global breeding program spanning Peru, Uganda, Mozambique and Ghana, to develop a low-density highly informative single nucleotide polymorphism (SNP) marker set to be deployed for routine QA/QC. Segregation of the selected 30 SNPs (two SNPs per base chromosome) in a recombined breeding population was evaluated using 282 progeny from some of the parents above. The progeny were replicated from in-vitro, screenhouse and field, and the selected SNP-set was confirmed to identify relatively similar mislabeling error rates as a high density SNP-set of 10,159 markers. Six additional trait-specific markers were added to the selected SNP set from previous quantitative trait loci mapping studies. The 36-SNP set will be deployed for QA/QC in breeding pipelines and in fingerprinting of advanced clones or released varieties to monitor genetic gains in famers’ fields. The study also enabled evaluation of CIP’s global breeding population structure and the effect of some of the most devastating stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato. DA - 2020/4/24/ PY - 2020/4/24/ DO - 10.1371/journal.pone.0232173 VL - 15 IS - 4 SP - e0232173 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0232173 DB - Crossref ER - TY - JOUR TI - Assessment of the potential of wild Ipomoea spp. for the improvement of drought tolerance in cultivated sweetpotato Ipomoea batatas (L.) Lam AU - Nhanala, Stella E. C. AU - Yencho, G. Craig T2 - Crop Science AB - Abstract Sweetpotato [ Ipomoea batatas (L.) Lam] is cultivated worldwide, and it is a staple food in many developing countries. In some regions (e.g., Africa) drought is a major production constraint that results in significant yield loss. Climate change is predicted to result in even greater losses due to long periods of drought and elevated temperatures. The goal of this study was to assess the potential of wild Ipomoea spp. as a source of drought tolerance in cultivated sweetpotato. We evaluated the drought tolerance of I. batatas , I. cynanchifolia , I. leucantha , I. trifida and I. triloba in a randomized complete block design, with five levels of simulated drought: control (daily irrigation), and no irrigation for 7, 9, 21 and 50 days. We observed that post drought re‐irrigation of the wild species subjected to 21 days of stress resulted in plant recovery and an increase of the stomatal conductance of up to 99% in I. leucantha . However, under extreme stress (50 d) the wild plants did not respond to re‐irrigation, resulting in up to 89% ( I. leucantha ) plant mortality. The wild species did not produce storage roots, while the I. batatas cultivars produced storage roots. Under 50 days of stress I. batatas had a survival rate between 44% (cv. Tanzania) and 89% (cv. Beauregard). We concluded that the wild genotypes screened may not be a valuable source of germplasm for drought tolerance and that significant levels of drought tolerance may exist in cultivated sweetpotato. DA - 2020/11/18/ PY - 2020/11/18/ DO - 10.1002/csc2.20363 VL - 61 IS - 1 SP - 234-249 J2 - Crop Sci. LA - en OP - SN - 0011-183X 1435-0653 UR - http://dx.doi.org/10.1002/csc2.20363 DB - Crossref ER - TY - JOUR TI - Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population AU - da Silva Pereira, Guilherme AU - Gemenet, Dorcus C AU - Mollinari, Marcelo AU - Olukolu, Bode A AU - Wood, Joshua C AU - Diaz, Federico AU - Mosquera, Veronica AU - Gruneberg, Wolfgang J AU - Khan, Awais AU - Buell, C Robin AU - Yencho, G Craig AU - Zeng, Zhao-Bang T2 - Genetics AB - Abstract Genetic analysis in autopolyploids is a very complicated subject due to the enormous number of genotypes at a locus that needs to be considered. For instance, the number of... In developing countries, the sweetpotato, Ipomoea batatas (L.) Lam. (2n=6x=90), is an important autopolyploid species, both socially and economically. However, quantitative trait loci (QTL) mapping has remained limited due to its genetic complexity. Current fixed-effect models can fit only a single QTL and are generally hard to interpret. Here, we report the use of a random-effect model approach to map multiple QTL based on score statistics in a sweetpotato biparental population (‘Beauregard’ × ‘Tanzania’) with 315 full-sibs. Phenotypic data were collected for eight yield component traits in six environments in Peru, and jointly adjusted means were obtained using mixed-effect models. An integrated linkage map consisting of 30,684 markers distributed along 15 linkage groups (LGs) was used to obtain the genotype conditional probabilities of putative QTL at every centiMorgan position. Multiple interval mapping was performed using our R package QTLpoly and detected a total of 13 QTL, ranging from none to four QTL per trait, which explained up to 55% of the total variance. Some regions, such as those on LGs 3 and 15, were consistently detected among root number and yield traits, and provided a basis for candidate gene search. In addition, some QTL were found to affect commercial and noncommercial root traits distinctly. Further best linear unbiased predictions were decomposed into additive allele effects and were used to compute multiple QTL-based breeding values for selection. Together with quantitative genotyping and its appropriate usage in linkage analyses, this QTL mapping methodology will facilitate the use of genomic tools in sweetpotato breeding as well as in other autopolyploids. DA - 2020/7/1/ PY - 2020/7/1/ DO - 10.1534/genetics.120.303080 VL - 215 IS - 3 SP - 579-595 LA - en OP - SN - 1943-2631 UR - http://dx.doi.org/10.1534/genetics.120.303080 DB - Crossref KW - multiple interval mapping KW - polyploid QTL model KW - restricted maximum likelihood KW - variance components KW - yield components KW - heritability ER - TY - JOUR TI - Evaluation of Educator Self-Efficacy in Informal Science Centers AU - Ennes, M. AU - Jones, M.G. AU - Chesnutt, K. T2 - Journal of Museum Education AB - There is increasing recognition that significant amounts of science learning take place over the course of one’s lifetime and much of this learning takes place outside of the formal educational settings. This learning is often facilitated by educators in these informal science settings. While much is known about educators in formal classroom settings, the research on informal science educators is nascent. This study aims to add to the literature through a survey of informal science educators’ levels of self-efficacy related to their work. The participants in this study (n = 400) completed a 35-item survey the survey which included 32 Likert scale questions on perceived levels of self-efficacy in different aspects of teaching in an informal science setting. When examining the results, the areas where the respondents felt less than skillful fell in areas related to facilitation and teaching about physical sciences concepts. Identifying areas where informal science educators feel less than skillful can help improve professional development opportunities by tailoring them to cover specific skills. DA - 2020/// PY - 2020/// DO - 10.1080/10598650.2020.1771993 VL - 45 IS - 3 SP - 327-339 KW - Informal science KW - museum KW - educators KW - self-efficacy KW - science KW - professional development ER - TY - SOUND TI - Society Equity Perspectives: A Balanced Discussion on Law Enforcement Budgeting AU - Berry-James, R.M. DA - 2020/// PY - 2020/// PB - National Academy of Public Administration ER - TY - SOUND TI - Does Responsible Innovation Really Matter? Examining Cultural Perceptions of Biotechnology in Food Systems AU - Berry-James, R.M. DA - 2020/9/8/ PY - 2020/9/8/ M3 - Podcast ER - TY - CONF TI - Conducting Social Equity, Diversity and Inclusion Research AU - Berry-James, R.M. T2 - 3rd Annual Social Equity, Diversity, and Inclusion (SEDI) Workshop at the American Society for Public Administration, 2020 Vision for Politics, Policy and Administration Annual Conference C2 - 2020/4/4/ CY - Anaheim, CA (Conference Cancelled) DA - 2020/4/4/ PY - 2020/4/4/ ER - TY - CONF TI - Book Signing: Why Research Methods Matter: Essential Skills for Decision-making AU - Berry-James, R.M. AU - Gooden, S. T2 - American Society for Public Administration, 2020 Vision for Politics, Policy and Administration Annual Conference, C2 - 2020/4/4/ CY - Anaheim, CA (Conference Cancelled) DA - 2020/4/4/ PY - 2020/4/4/ ER - TY - CONF TI - The Places and Spaces Where Race and Gender Intersect in Public Administration on SWPA Social Equity Panel: Public Administration’s Response to Gender in the 21st Century: A Social Equity Perspective AU - Berry-James, R.M. T2 - American Society for Public Administration, 2020 Vision for Politics, Policy and Administration Annual Conference C2 - 2020/4/3/ CY - Anaheim, CA (Conference Cancelled) DA - 2020/4/3/ PY - 2020/4/3/ ER - TY - SOUND TI - COMPA Students/Young Professional Virtual Town Hall AU - Berry-James, R.M. DA - 2020/7/1/ PY - 2020/7/1/ ER - TY - CONF TI - Dissertations Focused on Social Equity and Social Justice AU - Berry-James, R.M. T2 - ASPA Student and New Professional Webinar C2 - 2020/1/30/ DA - 2020/1/30/ PY - 2020/1/30/ ER - TY - SOUND TI - Online Roundtable on Social Equity AU - Berry-James, R.M. AU - Birdsell, D. AU - Wooldridge, B. DA - 2020/6/29/ PY - 2020/6/29/ ER - TY - SOUND TI - Graduate student recommendations for Northam Administration’s Health Equity Team AU - Berry-James, R.M. DA - 2020/6/17/ PY - 2020/6/17/ ER - TY - SOUND TI - The Intersection of Positive Momentum: Racial Equity & Justice AU - Berry-James, R.M. DA - 2020/6/23/ PY - 2020/6/23/ ER - TY - SOUND TI - Addressing COVID-19: Fostering Equity In and Out of the Classroom AU - Berry-James, R.M. DA - 2020/6/4/ PY - 2020/6/4/ ER - TY - SOUND TI - Teaching Online During COVID-19 AU - Berry-James, R.M. DA - 2020/4/9/ PY - 2020/4/9/ ER - TY - CONF TI - Examining Social Equity in the Evidence-building Process: A Case Study of Food Wealth and Good Health in North Carolina AU - Berry-James, R.M. T2 - APPAM, Virtual Fall Research Conference C2 - 2020/11/13/ CY - Washington, D.C. DA - 2020/11/13/ PY - 2020/11/13/ ER - TY - SOUND TI - Diversity Accountability and Talent Management AU - Berry-James, R.M. DA - 2020/1/30/ PY - 2020/1/30/ ER - TY - SOUND TI - Leveraging Talent: Research and Best Practices in Public Administration AU - Berry-James, R.M. DA - 2020/1/23/ PY - 2020/1/23/ ER - TY - CONF TI - Big Data, Artificial Intelligence and The Equitable Use of Technology. Why Research Methods Matter: Artificial Intelligence and Inequities AU - Johnson, C. AU - Berry-James, R.M. T2 - American Society for Public Administration, 2020 Vision for Politics, Policy and Administration Annual Conference C2 - 2020/// CY - Anaheim, CA (Conference Cancellled) DA - 2020/// PY - 2020/4/6/ ER - TY - SOUND TI - ASPA Book Talk Webinar Series. Why Research Methods Matter: Essential Skills for Decision Making AU - Berry-James, R.M. DA - 2020/12/9/ PY - 2020/12/9/ ER - TY - SOUND TI - Looking Back and Looking Forward: Next Steps for Ethics Education in PA AU - Berry-James, R.M. AU - Jacobs, R. AU - Meyer, S. DA - 2020/11/10/ PY - 2020/11/10/ ER - TY - SOUND TI - Center Stage Session: The Future of Work: Are You Ready? AU - Berry-James, R.M. DA - 2020/10/29/ PY - 2020/10/29/ ER - TY - SOUND TI - Conducting SEDI Research: Why Research Methods Matter AU - Berry-James, R.M. DA - 2020/10/1/ PY - 2020/10/1/ ER - TY - SOUND TI - Dismantling Inequities and injustices in Health Care and Public Health AU - Berry-James, R.M. AU - Golembeski, C. AU - Lopez-Littleton, V. AU - Sampson, C.J. DA - 2020/9/30/ PY - 2020/9/30/ ER - TY - RPRT TI - Annual Evaluation of the North Carolina Farm to Early Care and Education Evaluation Report: Year 3 AU - Berry-James, R.M. A3 - W. K. Kellogg Foundation/Center for Environmental Systems DA - 2020/10// PY - 2020/10// PB - W. K. Kellogg Foundation/Center for Environmental Systems ER - TY - SOUND TI - Cultural Perceptions regarding GMO: Engaging, Sampling and Inclusion Strategies AU - Berry-James, R.M. DA - 2020/9/25/ PY - 2020/9/25/ ER - TY - CONF TI - Mindful Movers Breaking the Cycle AU - Berry-James, R.M. AU - Ishak, A. T2 - Break the Cycle 15 of Health Disparities: Exploring Social, Economic, and Environmental Determinants of Health Online Conference C2 - 2020/4/20/ CY - Atlanta, GA DA - 2020/4/20/ PY - 2020/4/20/ ER - TY - SOUND TI - The Impact on COVID-19 on Faculty, Students and Staff AU - Berry-James, R.M. AU - Wooldridge, B. AU - Smith-Mason, J. DA - 2020/9/24/ PY - 2020/9/24/ ER - TY - SOUND TI - Building a Successful Mentor-Mentee Relationship AU - Berry-James, R.M. DA - 2020/12/10/ PY - 2020/12/10/ ER - TY - RPRT TI - Promoting Social Equity in an Evidence-Based Policy Environment: An Action Plan for 2021 AU - Simms, M. AU - Berry-James, R.M. AU - Glickman, G. AU - Nightingale, D. A3 - National Academy of Public Administration Election 2020 Work Group: Foster Social Equity DA - 2020/6// PY - 2020/6// PB - National Academy of Public Administration Election 2020 Work Group: Foster Social Equity UR - https://napawash.org/uploads/Election_2020_Social_Equity.pdf ER - TY - RPRT TI - Improving Child Well-being & Reducing Food Insecurity: An Action Plan for 2021 AU - Simms, M. AU - Berry-James, R.M. AU - Glickman, G. AU - Nightingale, D. A3 - National Academy of Public Administration Election 2020 Work Group: Foster Social Equity DA - 2020/6// PY - 2020/6// PB - National Academy of Public Administration Election 2020 Work Group: Foster Social Equity UR - https://napawash.org/uploads/Election_2020_Social_Equity_Food_Insecurity.pdf ER - TY - CONF TI - Fostering Social Equity in the Face of Housing, Food, and Voting Insecurities AU - Berry-James, R.M. AU - Johnson, C.C. AU - Nwakpuda, E. AU - Jackson-Leftwich, C. AU - Foxworth, R. AU - Boulding, C. T2 - APPAM, Virtual Fall Research Conference C2 - 2020/11/13/ CY - Washington, D.C. DA - 2020/11/13/ PY - 2020/11/13/ ER - TY - JOUR TI - Symposium Introduction: The Pursuit of Civil Rights and Public Sector Values in the 21st Century: Examining Dr. Martin Luther King Jr.’s Vision in the Trump Era AU - Johnson, Richard Greggory, III AU - Gooden, Susan T. AU - Berry‐James, RaJade M. T2 - Public Administration Review AB - Public Administration ReviewVolume 80, Issue 6 p. 1035-1037 Symposium Introduction: The Pursuit of Civil Rights and Public Sector Values in the 21st Century: Examining Dr. Martin Luther King Jr.'s Vision in the Trump Era Symposium Introduction: The Pursuit of Civil Rights and Public Sector Values in the 21st Century: Examining Dr. Martin Luther King Jr.’s Vision in the Trump Era Richard Greggory Johnson III, Corresponding Author Richard Greggory Johnson III Symposium Editor rgjohnsoniii@usfca.edu Search for more papers by this authorSusan T. Gooden, Susan T. Gooden Symposium EditorSearch for more papers by this authorRaJade M. Berry-James PhD, RaJade M. Berry-James PhD Symposium EditorSearch for more papers by this author Richard Greggory Johnson III, Corresponding Author Richard Greggory Johnson III Symposium Editor rgjohnsoniii@usfca.edu Search for more papers by this authorSusan T. Gooden, Susan T. Gooden Symposium EditorSearch for more papers by this authorRaJade M. Berry-James PhD, RaJade M. Berry-James PhD Symposium EditorSearch for more papers by this author First published: 22 December 2020 https://doi.org/10.1111/puar.13314Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume80, Issue6November/December 2020Pages 1035-1037 RelatedInformation DA - 2020/11// PY - 2020/11// DO - 10.1111/puar.13314 VL - 80 IS - 6 SP - 1035–1037 SN - 0033-3352 1540-6210 UR - http://dx.doi.org/10.1111/puar.13314 ER - TY - JOUR TI - Stepping up to the plate: Making social equity a priority in public administration’s troubled times AU - Berry-James, RaJade M. AU - Blessett, Brandi AU - Emas, Rachel AU - McCandless, Sean AU - Nickels, Ashley E. AU - Norman-Major, Kristen AU - Vinzant, Parisa T2 - Journal of Public Affairs Education AB - The United States is built on and reinforced by exploitation and oppression, especially the genocide “of Native Americans, and the theft of their lands, and the extensive enslavement of Africans” (... DA - 2020/9/22/ PY - 2020/9/22/ DO - 10.1080/15236803.2020.1820289 VL - 27 IS - 1 SP - 5-15 J2 - Journal of Public Affairs Education LA - en OP - SN - 1523-6803 2328-9643 UR - http://dx.doi.org/10.1080/15236803.2020.1820289 DB - Crossref ER - TY - CHAP TI - RiboSimR: A Tool for Simulation and Power Analysis of Ribo-seq Data AU - Perkins, Patrick AU - Stepanova, Anna AU - Alonso, Jose AU - Heber, Steffen T2 - Computational Advances in Bio and Medical Sciences A2 - Măndoiu, I. A2 - Murali, T. A2 - Narasimhan, G. A2 - Rajasekaran, S. A2 - Skums, P. A2 - Zelikovsky, A. T3 - Lecture Notes in Computer Science AB - RNA-seq and Ribo-seq are widespread quantitative methods for assessing transcription and translation. They can be used to detect differential expression, differential translation, and differential translation efficiency between conditions. The statistical power to detect differential genes is affected by multiple factors, such as the number of replicates, sequencing depth, magnitude of differential expression and translation, distribution of gene counts, and method for estimating biological variance. As power estimation of translational efficiency involves the combination of both RNA-seq measurements and Ribo-seq measurements, this task is particularly challenging. Here we propose a power assessment tool, called RiboSimR, based purely on data simulation. RiboSimR, produces semi-parametric simulations that generate data based on real RNA and Ribo-seq experiments, with customizable choices on baseline parameters and tool configurations. We demonstrate the usefulness of our tool by simulating data based on two published Ribo-seq datasets and analyzing various aspects of experimental design. PY - 2020/// DO - 10.1007/978-3-030-46165-2_10 SP - 121–133 PB - Springer International Publishing SN - 9783030461645 9783030461652 SV - 12029 UR - http://dx.doi.org/10.1007/978-3-030-46165-2_10 ER - TY - JOUR TI - Life in hot acid: a genome‐based reassessment of the archaeal order Sulfolobales AU - Counts, James A. AU - Willard, Daniel J. AU - Kelly, Robert M. T2 - Environmental Microbiology AB - Summary The order Sulfolobales was one of the first named Archaeal lineages, with globally distributed members from terrestrial thermal acid springs (pH < 4; T > 65°C). The Sulfolobales represent broad metabolic capabilities, ranging from lithotrophy, based on inorganic iron and sulfur biotransformations, to autotrophy, to chemoheterotrophy in less acidophilic species. Components of the 3‐hydroxypropionate/4‐hydroxybutyrate carbon fixation cycle, as well as sulfur oxidation, are nearly universally conserved, although dissimilatory sulfur reduction and disproportionation ( Acidianus , Stygiolobus and Sulfurisphaera ) and iron oxidation ( Acidianus , Metallosphaera , Sulfurisphaera , Sulfuracidifex and Sulfodiicoccus ) are limited to fewer lineages. Lithotrophic marker genes appear more often in highly acidophilic lineages. Despite the presence of facultative anaerobes and one confirmed obligate anaerobe, oxidase complexes ( fox , sox , dox and a new putative cytochrome bd) are prevalent in many species (even facultative/obligate anaerobes), suggesting a key role for oxygen among the Sulfolobales . The presence of fox genes tracks with a putative antioxidant OsmC family peroxiredoxin, an indicator of oxidative stress derived from mixing reactive metals and oxygen. Extreme acidophily appears to track inversely with heterotrophy but directly with lithotrophy. Recent phylogenetic re‐organization efforts are supported by the comparative genomics here, although several changes are proposed, including the expansion of the genus Saccharolobus . DA - 2020/9/7/ PY - 2020/9/7/ DO - 10.1111/1462-2920.15189 VL - 9 J2 - Environ Microbiol LA - en OP - SN - 1462-2912 1462-2920 UR - http://dx.doi.org/10.1111/1462-2920.15189 DB - Crossref ER - TY - JOUR TI - Mosquitoes Bite: A Zika Story of Vector Management and Gene Drives AU - Berube, David M. T2 - SYNTHETIC BIOLOGY 2020: FRONTIERS IN RISK ANALYSIS AND GOVERNANCE DA - 2020/// PY - 2020/// DO - 10.1007/978-3-030-27264-7_7 SP - 143-163 ER - TY - JOUR TI - Biology Without Borders: Need for Collective Governance? AU - Kuiken, Todd T2 - SYNTHETIC BIOLOGY 2020: FRONTIERS IN RISK ANALYSIS AND GOVERNANCE AB - “College students try to hack a gene – and set a science fair abuzz” (Swetlitz 2016); “Amateurs Are New Fear in Creating Mutant Virus”(Zimmer 2015); “DIY Gene Editing: Someone Is Going to Get Hurt” (Baumgaertner 2018); and “In Attics and Closets, Biohackers Discover Their Inner Frankenstein (Whalen 2009)”—these are the headlines the public reads in major publications like the New York Times, Wall Street Journal, and others about the increasing accessibility to biotechnologies. Read aloud; they sound like the opening trailers for horror movies. Have there been missteps? Stunts? Individuals that spark controversy? Of course. But pandemics? Environmental disasters? Of course not. What has occurred though, and the story that is rarely told, are the tens of thousands of students and everyday citizens that have been introduced to biology, biotechnology, and science more broadly, who might not otherwise have had the opportunity to explore it. As with any broad reaching loosely affiliated community, there will always be those pushing the boundaries and trying to steal the spotlight with hyperbole and stunts. And with the help of some in the press, have misbranded and misrepresented the entire community of citizens interested in biology. Unfortunately these stories overshadow the educational opportunities this community provides and dismisses the safety, security, ethical, and responsible innovation practices and programs they have established. DA - 2020/// PY - 2020/// DO - 10.1007/978-3-030-27264-7_12 SP - 269-295 ER - TY - JOUR TI - The complex nature of willpower and conceptual mapping of its normative significance in research on stress, addiction, and dementia AU - Dubljevic, Veljko AU - Neupert, Shevaun D. T2 - BEHAVIORAL AND BRAIN SCIENCES AB - Abstract Willpower (as suppression, resolve, and habit) has ramifications for autonomy and mental time-travel. Autonomy presupposes mature powers of volition and the capacity to anticipate future events and consequences of one's actions. Ainslie's study is useful to clarify basic autonomy in addiction and dementia. Furthermore, we show how our study on coping with stress can be applied to suppression and resolve. DA - 2020/8/26/ PY - 2020/8/26/ DO - 10.1017/S0140525X20000886 VL - 44 SP - SN - 1469-1825 ER - TY - CONF TI - Perspectives on the new USDA regulations for GM crops AU - Delborne, J. T2 - Genetic Engineering and Society Colloquium C2 - 2020/6/5/ CY - North Carolina State University, Raleigh, NC DA - 2020/6/5/ PY - 2020/6/5/ ER - TY - CONF TI - Public and Stakeholder Engagement in the Governance of Emerging Biotechnologies AU - Delborne, J. T2 - International Plant and Animal Genome XXVIII Conference C2 - 2020/1/13/ CY - San Diego, CA DA - 2020/1/13/ PY - 2020/1/13/ ER - TY - CONF TI - Public Engagement When Biotechnology Goes ‘Wild’ AU - Delborne, J. T2 - Midwest Fish and Wildlife Conference C2 - 2020/1/27/ CY - Springfield, IL DA - 2020/1/27/ PY - 2020/1/27/ ER - TY - SOUND TI - Stakeholder Engagement and Governance of Emerging Biotechnologies AU - Delborne, J. DA - 2020/1/29/ PY - 2020/1/29/ ER - TY - CONF TI - Navigating GMO Misinformation: Frustrations, Controversy, and a Glance in the Mirror AU - Delborne, J. T2 - Symposium: Addressing Misinformation on the Web in Science, Engineering, and Health. National Academies of Sciences C2 - 2020/2/20/ CY - Washington, DC DA - 2020/2/20/ PY - 2020/2/20/ ER - TY - SOUND TI - Engaging Stakeholders with Complex and Sometimes Controversial Technologies AU - Delborne, J. DA - 2020/3/9/ PY - 2020/3/9/ ER - TY - SOUND TI - The Potential for Biotechnology to Address Forest Health AU - Delborne, J. DA - 2020/3/21/ PY - 2020/3/21/ ER - TY - SOUND TI - Values and Beliefs Influencing Genetic Interventions in the Environment AU - Delborne, J. DA - 2020/6/2/ PY - 2020/6/2/ ER - TY - SOUND TI - Emerging Technology in the Field of Island Conservation AU - Delborne, J. DA - 2020/6/9/ PY - 2020/6/9/ ER - TY - CONF TI - GBIRd Stakeholder Beliefs and Values: Landscape Analysis and Workshop AU - Delborne, J. T2 - Intended Consequences Workshop C2 - 2020/6/23/ DA - 2020/6/23/ PY - 2020/6/23/ PB - Revive & Restore ER - TY - SOUND TI - Public Engagement when Biotechnology Goes "Wild" AU - Delborne, J. DA - 2020/10/7/ PY - 2020/10/7/ ER - TY - SOUND TI - Public Engagement when Biotechnology “Goes Wild" AU - Delborne, J. DA - 2020/11/17/ PY - 2020/11/17/ ER - TY - JOUR TI - Forum: Regulating Gene Drives AU - Delborne, J. T2 - Issues in Science and Technology DA - 2020/// PY - 2020/// VL - 36 IS - 3 UR - https://issues.org/forum36-3/ ER - TY - BLOG TI - The Gene Drive Conundrum AU - Delborne, J. T2 - Switzer Network Leadership Story DA - 2020/5/27/ PY - 2020/5/27/ PB - Robert and Patricia Switzer Foundation UR - https://www.switzernetwork.org/leadership-story/jason-delborne-gene-drive-conundrum ER - TY - SOUND TI - Sustainability and wood pellets, and science controversies AU - Delborne, J. DA - 2020/4/20/ PY - 2020/4/20/ PB - North Carolina State University ER - TY - JOUR TI - Stereotypes of scientists: Seeds of progress and recommendations for elementary teachers AU - Carrier, S. AU - Jones, M.G. AU - Ennes, M. AU - Lee, T. AU - Madden, L. AU - Cayton, E. AU - Chesnutt, K. AU - Huff, P. AU - Phillips, L. AU - Bellino, M. T2 - Science Educator DA - 2020/// PY - 2020/// VL - 27 IS - 2 SP - 114-120 ER - TY - CHAP TI - Challenges in nanoscience education AU - Jones, M.G. AU - Blonder, R. AU - Kähkönen, A. T2 - 21st Century Nanoscience - A Handbook: Public policy, education, and global trends PY - 2020/// VL - 10 PB - Taylor and Francis SN - 9780429351631 9780815357094 ER - TY - JOUR TI - Core commitments for field trials of gene drive organisms AU - Long, Kanya C. AU - Alphey, Luke AU - Annas, George J. AU - Bloss, Cinnamon S. AU - Campbell, Karl J. AU - Champer, Jackson AU - Chen, Chun-Hong AU - Choudhary, Amit AU - Church, George M. AU - Collins, James P. AU - Cooper, Kimberly L. AU - Delborne, Jason A. AU - Edwards, Owain R. AU - Emerson, Claudia I. AU - Esvelt, Kevin AU - Evans, Sam Weiss AU - Friedman, Robert M. AU - Gantz, Valentino M. AU - Gould, Fred AU - Hartley, Sarah AU - Heitman, Elizabeth AU - Hemingway, Janet AU - Kanuka, Hirotaka AU - Kuzma, Jennifer AU - Lavery, James V. AU - Lee, Yoosook AU - Lorenzen, Marce AU - Lunshof, Jeantine E. AU - Marshall, John M. AU - Messer, Philipp W. AU - Montell, Craig AU - Oye, Kenneth A. AU - Palmer, Megan J. AU - Papathanos, Philippos Aris AU - Paradkar, Prasad N. AU - Piaggio, Antoinette J. AU - Rasgon, Jason L. AU - Rašić, Gordana AU - Rudenko, Larisa AU - Saah, J. Royden AU - Scott, Maxwell J. AU - Sutton, Jolene T. AU - Vorsino, Adam E. AU - Akbari, Omar S. T2 - Science AB - We must ensure that trials are scientifically, politically, and socially robust, publicly accountable, and widely transparent DA - 2020/12/17/ PY - 2020/12/17/ DO - 10.1126/science.abd1908 VL - 370 IS - 6523 SP - 1417-1419 J2 - Science LA - en OP - SN - 0036-8075 1095-9203 UR - http://dx.doi.org/10.1126/science.abd1908 DB - Crossref ER - TY - JOUR TI - Identifying interest, risks, and impressions of organic peanut production: A survey of conventional farmers in the Virginia-Carolina region AU - Kaufman, Amanda A. AU - Jordan, David L. AU - Reberg-Horton, Chris AU - Dean, Lisa L. AU - Shew, Barbara B. AU - Brandenburg, Rick L. AU - Anco, Dan AU - Mehl, Hillary AU - Taylor, Sally AU - Balota, Maria AU - Goodell, L. Suzanne AU - Allen, Jonathan T2 - CROP FORAGE & TURFGRASS MANAGEMENT AB - Crop, Forage & Turfgrass ManagementVolume 6, Issue 1 e20042 CROP MANAGEMENT—BRIEFS Identifying interest, risks, and impressions of organic peanut production: A survey of conventional farmers in the Virginia–Carolina region Amanda A. Kaufman, Amanda A. Kaufman Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Box 7624, Raleigh, NC, 27695 USASearch for more papers by this authorDavid L. Jordan, Corresponding Author David L. Jordan david_jordan@ncsu.edu orcid.org/0000-0003-4786-2727 Department of Crop and Soil Sciences, North Carolina State University, Box 7620, Raleigh, NC, 27695 USA Correspondence Department of Crop and Soil Sciences, North Carolina State University, Box 7620, Raleigh, NC 27695 Email: david_jordan@ncsu.eduSearch for more papers by this authorChris Reberg-Horton, Chris Reberg-Horton Department of Crop and Soil Sciences, North Carolina State University, Box 7620, Raleigh, NC, 27695 USASearch for more papers by this authorLisa L. Dean, Lisa L. Dean Market Quality and Handling Research Unit, ARS, SEA, USDA, Raleigh, NC, 27695 USASearch for more papers by this authorBarbara B. Shew, Barbara B. Shew Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, Raleigh, NC, 27695 USASearch for more papers by this authorRick L. Brandenburg, Rick L. Brandenburg Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, Raleigh, NC, 27695 USASearch for more papers by this authorDan Anco, Dan Anco Edisto Research and Extension Center, Clemson University, 64 Research Road, Blackville, SC, 29817 USASearch for more papers by this authorHillary Mehl, Hillary Mehl Tidewater Agricultural Research and Extension Center, 6321 Holland Road, Suffolk, VA, 23437 USASearch for more papers by this authorSally Taylor, Sally Taylor Tidewater Agricultural Research and Extension Center, 6321 Holland Road, Suffolk, VA, 23437 USASearch for more papers by this authorMaria Balota, Maria Balota orcid.org/0000-0003-4626-0193 Tidewater Agricultural Research and Extension Center, 6321 Holland Road, Suffolk, VA, 23437 USASearch for more papers by this authorL. Suzanne Goodell, L. Suzanne Goodell Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Box 7624, Raleigh, NC, 27695 USASearch for more papers by this authorJonathan Allen, Jonathan Allen Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Box 7624, Raleigh, NC, 27695 USASearch for more papers by this author Amanda A. Kaufman, Amanda A. Kaufman Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Box 7624, Raleigh, NC, 27695 USASearch for more papers by this authorDavid L. Jordan, Corresponding Author David L. Jordan david_jordan@ncsu.edu orcid.org/0000-0003-4786-2727 Department of Crop and Soil Sciences, North Carolina State University, Box 7620, Raleigh, NC, 27695 USA Correspondence Department of Crop and Soil Sciences, North Carolina State University, Box 7620, Raleigh, NC 27695 Email: david_jordan@ncsu.eduSearch for more papers by this authorChris Reberg-Horton, Chris Reberg-Horton Department of Crop and Soil Sciences, North Carolina State University, Box 7620, Raleigh, NC, 27695 USASearch for more papers by this authorLisa L. Dean, Lisa L. Dean Market Quality and Handling Research Unit, ARS, SEA, USDA, Raleigh, NC, 27695 USASearch for more papers by this authorBarbara B. Shew, Barbara B. Shew Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, Raleigh, NC, 27695 USASearch for more papers by this authorRick L. Brandenburg, Rick L. Brandenburg Department of Entomology and Plant Pathology, North Carolina State University, Box 7613, Raleigh, NC, 27695 USASearch for more papers by this authorDan Anco, Dan Anco Edisto Research and Extension Center, Clemson University, 64 Research Road, Blackville, SC, 29817 USASearch for more papers by this authorHillary Mehl, Hillary Mehl Tidewater Agricultural Research and Extension Center, 6321 Holland Road, Suffolk, VA, 23437 USASearch for more papers by this authorSally Taylor, Sally Taylor Tidewater Agricultural Research and Extension Center, 6321 Holland Road, Suffolk, VA, 23437 USASearch for more papers by this authorMaria Balota, Maria Balota orcid.org/0000-0003-4626-0193 Tidewater Agricultural Research and Extension Center, 6321 Holland Road, Suffolk, VA, 23437 USASearch for more papers by this authorL. Suzanne Goodell, L. Suzanne Goodell Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Box 7624, Raleigh, NC, 27695 USASearch for more papers by this authorJonathan Allen, Jonathan Allen Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Box 7624, Raleigh, NC, 27695 USASearch for more papers by this author First published: 14 June 2020 https://doi.org/10.1002/cft2.20042Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Volume6, Issue12020e20042 RelatedInformation DA - 2020/// PY - 2020/// DO - 10.1002/cft2.20042 VL - 6 IS - 1 SP - SN - 2374-3832 ER - TY - JOUR TI - "Yes, and ... " continuing the scholarly conversation about pandemic pedagogy AU - Rudick, C. Kyle AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - Deanna: “Ok, we’ve got 3 years and 12 issues ahead of us. The sky's the limit … let's go BIG! What wicked problems do we want to tackle?” Kyle: “well, there's the obvious—the election … DACA … hate... DA - 2020/10/1/ PY - 2020/10/1/ DO - 10.1080/03634523.2020.1809167 VL - 69 IS - 4 SP - 540-544 SN - 1479-5795 ER - TY - JOUR TI - Community-led governance for gene-edited crops A post-market certification process could promote transparency and trust AU - Kuzma, Jennifer AU - Grieger, Khara T2 - SCIENCE AB - A post–market certification process could promote transparency and trust DA - 2020/11/20/ PY - 2020/11/20/ DO - 10.1126/science.abd1512 VL - 370 IS - 6519 SP - 916-918 SN - 1095-9203 ER - TY - JOUR TI - Ode to light: a swan song AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - Raising the curtain to look back on my life as an editor, with hopes and goals and intentions and lessons learned taking center stage; this manuscript wanders through intersecting sounds, places, melodies, and scenes emblematic of my journey through and reflections on editorial work. DA - 2020/10/1/ PY - 2020/10/1/ DO - 10.1080/03634523.2020.1812189 VL - 69 IS - 4 SP - 549-557 SN - 1479-5795 KW - Communication KW - teaching KW - learning KW - editorial work ER - TY - JOUR TI - Be our guest INTRODUCTION AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - *[brackets denote speaker notes] [breathe] Distinguished audience, my name is Deanna Dannels and I have the honor of standing before you, for the last time, as Editor of Communication Education. I ... DA - 2020/10/1/ PY - 2020/10/1/ DO - 10.1080/03634523.2020.1804128 VL - 69 IS - 4 SP - 402-404 SN - 1479-5795 ER - TY - JOUR TI - Genome-enabled insights into the biology of thrips as crop pests (vol 18, 142, 2020) AU - Rotenberg, Dorith AU - Baumann, Aaron A. AU - Ben-Mahmoud, Sulley AU - Christiaens, Olivier AU - Dermauw, Wannes AU - Ioannidis, Panagiotis AU - Jacobs, Chris G. C. AU - Jentzsch, Iris M. Vargas AU - Oliver, Jonathan E. AU - Poelchau, Monica F. AU - Rajarapu, Swapna Priya AU - Schneweis, Derek J. AU - Snoeck, Simon AU - Taning, Clauvis N. T. AU - Wei, Dong AU - Gamage, Shirani M. K. Widana AU - Hughes, Daniel S. T. AU - Murali, Shwetha C. AU - Bailey, Samuel T. AU - Bejerman, Nicolas E. AU - Holmes, Christopher J. AU - Jennings, Emily C. AU - Rosendale, Andrew J. AU - Rosselot, Andrew AU - Hervey, Kaylee AU - Schneweis, Brandi A. AU - Cheng, Sammy AU - Childers, Christopher AU - Simao, Felipe A. AU - Dietzgen, Ralf G. AU - Chao, Hsu AU - Dinh, Huyen AU - Doddapaneni, Harsha Vardhan AU - Dugan, Shannon AU - Han, Yi AU - Lee, Sandra L. AU - Muzny, Donna M. AU - Qu, Jiaxin AU - Worley, Kim C. AU - Benoit, Joshua B. AU - Friedrich, Markus AU - Jones, Jeffery W. AU - Panfilio, Kristen A. AU - Park, Yoonseong AU - Robertson, Hugh M. AU - Smagghe, Guy AU - Ullman, Diane E. AU - Zee, Maurijn AU - Van Leeuwen, Thomas AU - Veenstra, Jan A. AU - Waterhouse, Robert M. AU - Weirauch, Matthew T. AU - Werren, John H. AU - Whitfield, Anna E. AU - Zdobnov, Evgeny M. AU - Gibbs, Richard A. AU - Richards, Stephen T2 - BMC BIOLOGY AB - An amendment to this paper has been published and can be accessed via the original article. DA - 2020/11/16/ PY - 2020/11/16/ DO - 10.1186/s12915-020-00915-z VL - 18 IS - 1 SP - SN - 1741-7007 ER - TY - JOUR TI - Efficacy and Spatial Extent of Yard-Scale Control of Aedes (Stegomyia) albopictus (Diptera: Culicidae) Using Barrier Sprays and Larval Habitat Management AU - Hollingsworth, B. AU - Hawkins, P. AU - Lloyd, A. L. AU - Reiskind, M. H. T2 - J. Med. Entomol. DA - 2020/2/13/ PY - 2020/2/13/ VL - 57 SP - 1104–-1110 ER - TY - JOUR TI - Gene Drive Dynamics in Natural Populations: The Importance of Density Dependence, Space, and Sex AU - Dhole, Sumit AU - Lloyd, Alun L. AU - Gould, Fred T2 - ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 51, 2020 AB - The spread of synthetic gene drives is often discussed in the context of panmictic populations connected by gene flow and described with simple deterministic models. Under such assumptions, an entire species could be altered by releasing a single individual carrying an invasive gene drive, such as a standard homing drive. While this remains a theoretical possibility, gene drive spread in natural populations is more complex and merits a more realistic assessment. The fate of any gene drive released in a population would be inextricably linked to the population's ecology. Given the uncertainty often involved in ecological assessment of natural populations, understanding the sensitivity of gene drive spread to important ecological factors is critical. Here we review how different forms of density dependence, spatial heterogeneity, and mating behaviors can impact the spread of self-sustaining gene drives. We highlight specific aspects of gene drive dynamics and the target populations that need further research. DA - 2020/// PY - 2020/// DO - 10.1146/annurev-ecolsys-031120-101013 VL - 51 IS - 1 SP - 505-531 SN - 1545-2069 KW - genetic pest management KW - underdominance KW - CRISPR KW - spatial dynamics KW - density dependence KW - population alteration ER - TY - RPRT TI - Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces AU - Wang, Li AU - Josephs, Emily B. AU - Lee, Kristin M. AU - Roberts, Lucas M. AU - Rellán-Álvarez, Rubén AU - Ross-Ibarra, Jeffrey AU - Hufford, Matthew B. AB - Abstract Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal strong evidence of parallel adaptation at the level of individual SNPs, genes and pathways in four independent highland maize populations, even though most SNPs show unique patterns of local adaptation. The majority of selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients. C6 - 227629 DA - 2020/8/2/ PY - 2020/8/2/ DO - 10.1101/2020.07.31.227629 M1 - 227629 M3 - bioRxiv preprint SN - 227629 UR - http://dx.doi.org/10.1101/2020.07.31.227629 ER - TY - JOUR TI - Gene regulatory effects of a large chromosomal inversion in highland maize AU - Crow, Taylor AU - Ta, James AU - Nojoomi, Saghi AU - Aguilar-Rangel, M. Rocío AU - Torres Rodríguez, Jorge Vladimir AU - Gates, Daniel AU - Rellán-Álvarez, Rubén AU - Sawers, Ruairidh AU - Runcie, Daniel T2 - PLOS Genetics AB - Chromosomal inversions play an important role in local adaptation. Inversions can capture multiple locally adaptive functional variants in a linked block by repressing recombination. However, this recombination suppression makes it difficult to identify the genetic mechanisms underlying an inversion’s role in adaptation. In this study, we used large-scale transcriptomic data to dissect the functional importance of a 13 Mb inversion locus ( Inv4m ) found almost exclusively in highland populations of maize ( Zea mays ssp. mays ). Inv4m was introgressed into highland maize from the wild relative Zea mays ssp. mexicana , also present in the highlands of Mexico, and is thought to be important for the adaptation of these populations to cultivation in highland environments. However, the specific genetic variants and traits that underlie this adaptation are not known. We created two families segregating for the standard and inverted haplotypes of Inv4m in a common genetic background and measured gene expression effects associated with the inversion across 9 tissues in two experimental conditions. With these data, we quantified both the global transcriptomic effects of the highland Inv4m haplotype, and the local cis-regulatory variation present within the locus. We found diverse physiological effects of Inv4m across the 9 tissues, including a strong effect on the expression of genes involved in photosynthesis and chloroplast physiology. Although we could not confidently identify the causal alleles within Inv4m , this research accelerates progress towards understanding this inversion and will guide future research on these important genomic features. DA - 2020/12/3/ PY - 2020/12/3/ DO - 10.1371/journal.pgen.1009213 VL - 16 IS - 12 SP - e1009213 J2 - PLoS Genet LA - en OP - SN - 1553-7404 UR - http://dx.doi.org/10.1371/journal.pgen.1009213 DB - Crossref ER - TY - JOUR TI - Gibberellin-mediated RGA-LIKE1 degradation regulates embryo sac development in Arabidopsis AU - Dolores Gomez, Maria AU - Barro-Trastoy, Daniela AU - Fuster-Almunia, Clara AU - Tornero, Pablo AU - Alonso, Jose M. AU - Perez-Amador, Miguel A. T2 - JOURNAL OF EXPERIMENTAL BOTANY AB - Abstract Ovule development is essential for plant survival, as it allows correct embryo and seed development upon fertilization. The female gametophyte is formed in the central area of the nucellus during ovule development, in a complex developmental programme that involves key regulatory genes and the plant hormones auxins and brassinosteroids. Here we provide novel evidence of the role of gibberellins (GAs) in the control of megagametogenesis and embryo sac development, via the GA-dependent degradation of RGA-LIKE1 (RGL1) in the ovule primordia. YPet-rgl1Δ17 plants, which express a dominant version of RGL1, showed reduced fertility, mainly due to altered embryo sac formation that varied from partial to total ablation. YPet-rgl1Δ17 ovules followed normal development of the megaspore mother cell, meiosis, and formation of the functional megaspore, but YPet-rgl1Δ17 plants had impaired mitotic divisions of the functional megaspore. This phenotype is RGL1-specific, as it is not observed in any other dominant mutants of the DELLA proteins. Expression analysis of YPet-rgl1Δ17 coupled to in situ localization of bioactive GAs in ovule primordia led us to propose a mechanism of GA-mediated RGL1 degradation that allows proper embryo sac development. Taken together, our data unravel a novel specific role of GAs in the control of female gametophyte development. DA - 2020/12/31/ PY - 2020/12/31/ DO - 10.1093/jxb/eraa395 VL - 71 IS - 22 SP - 7059-7072 SN - 1460-2431 KW - Arabidopsis KW - DELLA KW - development KW - embryo sac KW - gibberellin KW - megagametogenesis KW - ovule KW - RGL1 ER - TY - JOUR TI - Susceptibility of Palmer amaranth (Amaranthus palmeri) to herbicides in accessions collected from the North Carolina Coastal Plain AU - Mahoney, Denis J. AU - Jordan, David L. AU - Roma-Burgos, Nilda AU - Jennings, Katherine M. AU - Leon, Ramon G. AU - Vann, Matthew C. AU - Everman, Wesley J. AU - Cahoon, Charles W. T2 - WEED SCIENCE AB - Abstract Palmer amaranth ( Amaranthus palmeri S. Watson) populations resistant to acetolactate synthase (ALS)-inhibiting herbicides and glyphosate are fairly common throughout the state of North Carolina (NC). This has led farm managers to rely more heavily on herbicides with other sites of action (SOA) for A. palmeri control, especially protoporphyrinogen oxidase and glutamine synthetase inhibitors. In the fall of 2016, seeds from A. palmeri populations were collected from the NC Coastal Plain, the state’s most prominent agricultural region. In separate experiments, plants with 2 to 4 leaves from the 110 populations were treated with field use rates of glyphosate, glufosinate-ammonium, fomesafen, mesotrione, or thifensulfuron-methyl. Percent visible control and survival were evaluated 3 wk after treatment. Survival frequencies were highest following glyphosate (99%) or thifensulfuron-methyl (96%) treatment. Known mutations conferring resistance to ALS inhibitors were found in populations surviving thifensulfuron-methyl application (Ala-122-Ser, Pro-197-Ser, Trp-574-Leu, and/or Ser-653-Asn), in addition to a new mutation (Ala-282-Asp) that requires further investigation. Forty-two populations had survivors after mesotrione application, with one population having 17% survival. Four populations survived fomesafen treatment, while none survived glufosinate. Dose–response studies showed an increase in fomesafen needed to kill 50% of two populations (LD 50 ); however, these rates were far below the field use rate (less than 5 g ha −1 ). In two populations following mesotrione dose–response studies, a 2.4- to 3.3-fold increase was noted, with LD 90 values approaching the field use rate (72.8 and 89.8 g ha −1 ). Screening of the progeny of individuals surviving mesotrione confirmed the presence of resistance alleles, as there were a higher number of survivors at the 1X rate compared with the parent population, confirming resistance to mesotrione. These data suggest A. palmeri resistant to chemistries other than glyphosate and thifensulfuron-methyl are present in NC, which highlights the need for weed management approaches to mitigate the evolution and spread of herbicide-resistant populations. DA - 2020/11// PY - 2020/11// DO - 10.1017/wsc.2020.67 VL - 68 IS - 6 SP - 582-593 SN - 1550-2759 KW - Herbicide resistance KW - multiple resistance ER - TY - JOUR TI - Core Committments for Field Trials of Gene Drive ORganisms T2 - Science DA - 2020/12/20/ PY - 2020/12/20/ ER - TY - JOUR TI - Community Led Governance for Gene Edited Crops T2 - Science DA - 2020/11/20/ PY - 2020/11/20/ ER - TY - JOUR TI - Soil acidification alters root morphology, increases root biomass but reduces root decomposition in an alpine grassland AU - Wang, Peng AU - Guo, Jin AU - Xu, Xinyu AU - Yan, Xuebin AU - Zhang, Kangcheng AU - Qiu, Yunpeng AU - Zhao, Qingzhou AU - Huang, Kailing AU - Luo, , Xi AU - Yang, Fei AU - Guo, Hui AU - Hu, Shuijin T2 - ENVIRONMENTAL POLLUTION AB - Soil acidification has been expanding in many areas of Asia due to increasing reactive nitrogen (N) inputs and industrial activities. While the detrimental effects of acidification on forests have been extensively studied, less attention has been paid to grasslands, particularly alpine grasslands. In a soil pH manipulation experiment in the Qinghai-Tibet Plateau, we examined the effects of soil acidification on plant roots, which account for the major part of alpine plants. After three years of manipulation, soil pH decreased from 6.0 to 4.7 with the acid-addition gradient, accompanied by significant changes in the availability of soil nitrogen, phosphorus and cations. Plant composition shifted with the soil acidity, with graminoids replacing forbs. Differing from findings in forests, soil acidification in the alpine grassland increased root biomass by increasing the fraction of coarse roots and the production of fine roots, corresponding to enhanced sedge and grass biomass, respectively. In addition, litter decomposability decreased with altered root morphological and chemical traits, and soil acidification slowed root decomposition by reducing soil microbial activity and litter quality. Our results showed that acidification effect on root dynamics in our alpine grassland was significantly different from that in forests, and supported similar results obtained in limited studies in other grassland ecosystems. These results suggest an important role of root morphology in mediating root dynamics, and imply that soil acidification may lead to transient increase in soil carbon stock as root standing biomass and undecomposed root litter. These changes may reduce nutrient cycling and further constrain ecosystem productivity in nutrient-limiting alpine systems. DA - 2020/10// PY - 2020/10// DO - 10.1016/j.envpol.2020.115016 VL - 265 SP - SN - 1873-6424 KW - Acid deposition KW - Alpine meadow KW - Root dynamics KW - Root functional traits KW - Soil carbon stock KW - Soil pH ER - TY - CHAP TI - Norms of advocacy AU - Goodwin, Jean T2 - Rigour and Reason : Essays in Honour of Hans Vilhelm Hansen A2 - Blair, J. Anthony A2 - Tindale, Christopher W. T3 - Windsor Studies in Argumentation AB - Built in the centre of Copenhagen, and noted for its equestrian stairway, the Rundetaarn (Round Tower), was intended as an astronomical observatory. Part of a complex of buildings that once included a university library, it affords expansive views of the city in every direction, towering above what surrounds it. The metaphor of the towering figure, who sees what others might not, whose vantage point allows him to visualize how things fit together, and who has an earned-stature of respect and authority, fits another Danish stalwart, Hans Vilhelm Hansen, whose contributions to the fields of informal logic and argument theory have earned the gratitude of his colleagues, and inspired this collection of essays, written to express the appreciation of its authors and of the many, many colleagues they represent. PY - 2020/6/4/ DO - 10.22329/wsia.10.2020 SP - 111–142 PB - University of Windsor SV - 10 ER - TY - CHAP TI - The Threat of Late Blight to Global Food Security AU - Ristaino, J.B. AU - Cooke, D.C. AU - Acuna, I. AU - Munoz, M. T2 - Emerging Plant Disease and Global Food Security A2 - Ristaino, J.B. A2 - Records, A. PY - 2020/// PB - American Phytopathological Society Press SN - 9780890546376 ER - TY - BOOK TI - Emerging Plant Disease and Global Food Security A3 - Ristaino, J.B. A3 - Records, A. DA - 2020/// PY - 2020/// PB - American Phytopathological Society Press SN - 9780890546376 ER - TY - JOUR TI - Qu-2, a robust poplar suspension cell line for molecular biology AU - Liu, Caixia AU - Li, Kailong AU - Wang, Meng AU - Fan, Erqin AU - Yang, Chuanping AU - Wang, Junhui AU - Fu, Pengyue AU - Ge, Xiaolan AU - Sederoff, Heike AU - Sederoff, Ronald R. AU - Chiang, Vincent L. AU - Wang, Sui AU - Qu, Guanzheng T2 - JOURNAL OF FORESTRY RESEARCH AB - Abstract Populus spp. have long been used as model woody plant species for molecular biology research. However, tissues of poplar are often recalcitrant to experimental procedures for molecular studies. We generated a hormone autotrophic poplar suspension cell line from a hybrid of Populus alba × P. berolinensis ‘Yinzhong’, named Qu-2. Qu-2 cells are suitable as a model biological system for studying woody plants. Qu-2 cells have many advantages over suspension cell lines derived so far from any other woody plants. Qu-2 cells are very easy to cultivate and can grow on several common plant culture media without the addition of any plant hormone. They show exceptionally high growth rates, reaching an approximately 150-fold increase in biomass after one week of culturing. Another important unique characteristic of Qu-2 cells is that they can be cryopreserved and readily reactivated. Qu-2 cells are suitable for molecular manipulations such as protoplast production, transient transformation, and RNA-seq analysis. Therefore, Qu-2 cells have the great potential to be an excellent model cell line in tree molecular biological research, ranging from physiology to gene function. The Qu-2 cells will be made available to the plant community for research. DA - 2020/// PY - 2020/// DO - 10.1007/s11676-020-01266-9 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85097191965&partnerID=MN8TOARS KW - Qu-2 cell line KW - Suspension cell KW - Poplar KW - Protoplast isolation KW - Transient transformation ER - TY - JOUR TI - The presumed influence of digital misinformation: examining US public’s support for governmental restrictions versus corrective action in the COVID-19 pandemic AU - Cheng, Yang AU - Luo, Yunjuan T2 - Online Information Review AB - Purpose Informed by the third-person effects (TPE) theory, this study aims to analyze restrictive versus corrective actions in response to the perceived TPE of misinformation on social media in the USA. Design/methodology/approach The authors conducted an online survey among 1,793 adults in the USA in early April. All participants were randomly enrolled in this research through a professional survey company. The structural equation modeling via Amos 20 was adopted for hypothesis testing. Findings Results indicated that individuals also perceived that others were more influenced by misinformation about COVID-19 than they were. Further, such a perceptual gap was associated with public support for governmental restrictions and corrective action. Negative affections toward health misinformation directly affected public support for governmental restrictions rather than corrective action. Support for governmental restrictions could further facilitate corrective action. Originality/value This study examined the applicability of TPE theory in the context of digital health misinformation during a unique global crisis. It explored the significant role of negative affections in influencing restrictive and corrective actions. Practically, this study offered implications for information and communication educators and practitioners. Peer review The peer review history for this article is available at: https://publons.com/publon/10.1108/OIR-08-2020-0386 DA - 2020/12/2/ PY - 2020/12/2/ DO - 10.1108/OIR-08-2020-0386 VL - 45 IS - 4 SP - 834-852 J2 - OIR LA - en OP - SN - 1468-4527 UR - http://dx.doi.org/10.1108/OIR-08-2020-0386 DB - Crossref KW - COVID-19 KW - Health misinformation KW - Social media KW - Mass communication KW - Governmental restrictions KW - Correction action KW - Third-person effects (TPE) ER - TY - JOUR TI - Encountering misinformation online: antecedents of trust and distrust and their impact on the intensity of Facebook use AU - Cheng, Yang AU - Chen, Zifei Fay T2 - Online Information Review AB - Purpose This study focused on the impact of misinformation on social networking sites. Through theorizing and integrating literature from interdisciplinary fields such as information behavior, communication and relationship management, this study explored how misinformation on Facebook influences users' trust, distrust and intensity of Facebook use. Design/methodology/approach This study employed quantitative survey research and collected panel data via an online professional survey platform. A total of 661 participants in the USA completed this study, and structural equation modeling (SEM) was used to test the theoretical model using Amos 20. Findings Based on data from an online questionnaire ( N = 661) in the USA, results showed that information trustworthiness and elaboration, users' self-efficacy of detecting misinformation and prescriptive expectancy of the social media platform significantly predicted both trust and distrust toward Facebook, which in turn jointly influenced users' intensity of using this information system. Originality/value This study contributes to the growing body of literature on information and relationship management and digital communication from several important aspects. First, this study disclosed the underlying cognitive psychological and social processing of online misinformation and addressed the strategies for future system design and behavioral intervention of misinformation. Second, this study systematically examined both trust and distrust as cognitive and affective dimensions of the human mindsets, encompassed the different components of the online information behavior and enriched one’s understanding of how misinformation affected publics' perceptions of the information system where it appeared. Last but not least, this study advanced the relationship management literature and demonstrated that a trustful attitude exerted a stronger influence on the intensity of Facebook use than distrust did. Peer review The peer review history for this article is available at: https://publons.com/publon/10.1108/OIR-04-2020-0130 DA - 2020/12/4/ PY - 2020/12/4/ DO - 10.1108/OIR-04-2020-0130 VL - 45 IS - 2 SP - 372-388 J2 - OIR LA - en OP - SN - 1468-4527 UR - http://dx.doi.org/10.1108/OIR-04-2020-0130 DB - Crossref KW - Misinformation KW - Relationship management KW - Trust KW - Distrust KW - Social media intensity KW - Digital platform ER - TY - JOUR TI - Genome-wide association analysis of the strength of the MAMP-elicited defense response and resistance to target leaf spot in sorghum AU - Samira, Rozalynne AU - Kimball, Jennifer A. AU - Samayoa, Luis Fernando AU - Holland, James B. AU - Jamann, Tiffany M. AU - Brown, Patrick J. AU - Stacey, Gary AU - Balint-Kurti, Peter J. T2 - SCIENTIFIC REPORTS AB - Plants have the capacity to respond to conserved molecular features known as microbe-associated molecular patterns (MAMPs). The goal of this work was to assess variation in the MAMP response in sorghum, to map loci associated with this variation, and to investigate possible connections with variation in quantitative disease resistance. Using an assay that measures the production of reactive oxygen species, we assessed variation in the MAMP response in a sorghum association mapping population known as the sorghum conversion population (SCP). We identified consistent variation for the response to chitin and flg22-an epitope of flagellin. We identified two SNP loci associated with variation in the flg22 response and one with the chitin response. We also assessed resistance to Target Leaf Spot (TLS) disease caused by the necrotrophic fungus Bipolaris cookei in the SCP. We identified one strong association on chromosome 5 near a previously characterized disease resistance gene. A moderately significant correlation was observed between stronger flg22 response and lower TLS resistance. Possible reasons for this are discussed. DA - 2020/11/30/ PY - 2020/11/30/ DO - 10.1038/s41598-020-77684-w VL - 10 IS - 1 SP - SN - 2045-2322 ER - TY - JOUR TI - Sweet Corn Sentinel Monitoring for Lepidopteran Field-Evolved Resistance to Bt Toxins AU - Dively, G P AU - Kuhar, T P AU - Taylor, S AU - Doughty, H B AU - Holmstrom, K AU - Gilrein, D AU - Nault, B A AU - Ingerson-Mahar, J AU - Whalen, J AU - Reisig, D AU - Frank, Daniel L AU - Fleischer, S J AU - Owens, David AU - Welty, C AU - Reay-Jones, F P F AU - Porter, P AU - Smith, J L AU - Saguez, J AU - Murray, S AU - Wallingford, A AU - Byker, H AU - Jensen, B AU - Burkness, E AU - Hutchison, W D AU - Hamby, K A T2 - Journal of Economic Entomology AB - As part of an insect resistance management plan to preserve Bt transgenic technology, annual monitoring of target pests is mandated to detect susceptibility changes to Bt toxins. Currently Helicoverpa zea (Boddie) monitoring involves investigating unexpected injury in Bt crop fields and collecting larvae from non-Bt host plants for laboratory diet bioassays to determine mortality responses to diagnostic concentrations of Bt toxins. To date, this monitoring approach has not detected any significant change from the known range of baseline susceptibility to Bt toxins, yet practical field-evolved resistance in H. zea populations and numerous occurrences of unexpected injury occur in Bt crops. In this study, we implemented a network of 73 sentinel sweet corn trials, spanning 16 U.S. states and 4 Canadian provinces, for monitoring changes in H. zea susceptibility to Cry and Vip3A toxins by measuring differences in ear damage and larval infestations between isogenic pairs of non-Bt and Bt hybrids over three years. This approach can monitor susceptibility changes and regional differences in other ear-feeding lepidopteran pests. Temporal changes in the field efficacy of each toxin were evidenced by comparing our current results with earlier published studies, including baseline data for each Bt trait when first commercialized. Changes in amount of ear damage showed significant increases in H. zea resistance to Cry toxins and possibly lower susceptibility to Vip3a. Our findings demonstrate that the sentinel plot approach as an in-field screen can effectively monitor phenotypic resistance and document field-evolved resistance in target pest populations, improving resistance monitoring for Bt crops. DA - 2020/12/4/ PY - 2020/12/4/ DO - 10.1093/jee/toaa264 VL - 12 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/toaa264 DB - Crossref KW - Bt toxin KW - insect resistance monitoring KW - sentinel sweet corn ER - TY - JOUR TI - Location of Helicoverpa zea (Lepidoptera: Noctuidae) larvae on different plant parts of determinate and indeterminate soybean AU - Reisig, Dominic D. AU - Cook, Don AU - Greene, Jeremy AU - Caprio, Michael AU - Gore, Jeff AU - Musser, Fred AU - Reay-Jones, Francis T2 - Bulletin of Entomological Research AB - Abstract Helicoverpa zea (Boddie) is a damaging pest of many crops including soybean, Glycine max (L.), especially in the southern United States. Previous studies have concluded that oviposition and development of H. zea larvae mirror the phenology of soybean, with oviposition occurring during full bloom, younger larvae developing on blooms and leaves, intermediate aged larvae developing on varying tissue types, and older larvae developing on flowers and pods. In a field trial, we investigated the presence of natural infestations of H. zea larvae by instar in determinate and indeterminate soybean varieties. In complementary experiments, we artificially infested H. zea and allowed them to oviposit on plants within replicated cages (one with a determinate variety and two with an indeterminate variety). Plants were sampled weekly during the time larvae were present. In the natural infestation experiment, most larvae were found on blooms during R3 and were early to middle instars; by R4, most larvae were found on leaves and were middle to late instars. In contrast, in the cage study, most larvae were found on leaves regardless of soybean growth stage or larval stage. Determinate and indeterminate growth habit did not impact larval preference for different soybean tissue types. Our studies suggest H. zea larvae prefer specific tissue types, but also provide evidence that experimental design can influence the results. Finally, our finding of larval preference for leaves contrasts with findings from previous studies. DA - 2020/6/2/ PY - 2020/6/2/ DO - 10.1017/S0007485320000280 VL - 110 IS - 6 SP - 725-731 J2 - Bull. Entomol. Res. LA - en OP - SN - 0007-4853 1475-2670 UR - http://dx.doi.org/10.1017/S0007485320000280 DB - Crossref KW - Blooms KW - development KW - leaves KW - pods KW - preference ER - TY - JOUR TI - Vertical and temporal distribution of Helicoverpa zea (Lepidoptera: Noctuidae) larvae in determinate and indeterminate soybean AU - Reisig, Dominic D. AU - Cook, Don AU - Greene, Jeremy K. AU - Caprio, Michael AU - Gore, Jeff AU - Musser, Fred AU - Reay-Jones, Francis T2 - Bulletin of Entomological Research AB - Most oviposition by Helicoverpa zea (Boddie) occurs near the top of the canopy in soybean, Glycine max (L.) Merr, and larval abundance is influenced by the growth habit of plants. However, the vertical distribution of larvae within the canopy is not as well known. We evaluated the vertical distribution of H. zea larvae in determinate and indeterminate varieties, hypothesizing that larval distribution in the canopy would vary between these two growth habits and over time. We tested this hypothesis in a naturally infested replicated field experiment and two experimentally manipulated cage experiments. In the field experiment, flowering time was synchronized between the varieties by manipulating planting date, while infestation timing was manipulated in the cage experiments. Larvae were recovered using destructive sampling of individual soybean plants, and their vertical distribution by instar was recorded from three sampling points over time in each experiment. While larval population growth and development varied between the determinate and indeterminate varieties within and among experiments, we found little evidence that larvae have preference for different vertical locations in the canopy. This study lends support to the hypothesis that larval movement and location within soybean canopies do not result entirely from oviposition location and nutritional requirements. DA - 2020/9/18/ PY - 2020/9/18/ DO - 10.1017/S0007485320000619 VL - 9 SP - 1-7 J2 - Bull. Entomol. Res. LA - en OP - SN - 0007-4853 1475-2670 UR - http://dx.doi.org/10.1017/S0007485320000619 DB - Crossref KW - Canopy KW - growth habit KW - movement KW - ovipositional location KW - preference ER - TY - JOUR TI - Proposal to change the conserved type of Ipomoea, nom. cons. (Convolvulaceae) AU - Eserman, Lauren A. AU - Sosef, Marc S. M. AU - Simao-Bianchini, Rosangela AU - Utteridge, Timothy M. A. AU - Barbosa, Juliana C. J. AU - Buril, Maria Teresa AU - Chatrou, Lars W. AU - Clay, Keith AU - Delgado, Geadelande AU - Desquilbet, Thibaut E. AU - Ferreira, Priscila P. A. AU - Grande Allende, Jose R. AU - Hernandez, Alexis L. AU - Huerta-Ramos, Guillermo AU - Jarret, Robert L. AU - Kojima, Roberta K. AU - Landrein, Sven AU - Lourenco, Juliana A. A. M. AU - De Man, Ine AU - Miller, Richard E. AU - More, Sushant AU - Moreira, Andre L. C. AU - Mwanga-Mwanga, Ithe AU - Nhanala, Stella AU - Pastore, Mayara AU - Petrongari, Fernanda S. AU - Pisuttimarn, Ponprom AU - Pornpongrungrueng, Pimwadee AU - Rifkin, Joanna AU - Santos, Francisco D. S. AU - Shimpale, Vinod B. AU - Silva, Simone S. AU - Stinchcombe, John R. AU - Traiperm, Paweena AU - Vasconcelos, Liziane V. AU - Wang, Ming Li AU - Villordon, Arthur AU - Yang, Jun AU - Yencho, G. Craig AU - Heider, Bettina AU - Simoes, Ana Rita G. T2 - TAXON AB - (2786) Ipomoea L., Sp. Pl.: 159. 1 Mai 1753 [Convolvul.], nom. cons. Typus: I. triloba L., typ. cons. prop. Ipomoea L. is the largest (650–900 species, depending on the concept adopted) and most iconic genus in Convolvulaceae, a family of c. 1880 species (data from Staples, Convolvulaceae Unlimited, 2012 at: http//convolvulaceae.myspecies.info), including the important crop sweetpotato, Ipomoea batatas (L.) Lam. (Tabl. Encycl. 1: 465. 1793), and several ornamental species commonly known as “bindweeds” or “morning glories” (Wilkin in Kew Bull. 54: 853–876. 1999; Mabberley, Mabberley's Plant-book. 2008). The genus has a long history of taxonomic and nomenclatural problems, mainly for the lack of a clear morphological circumscription and overlap with other genera. In his Species plantarum (1753), Linnaeus distinguished two genera, Convolvulus L. and Ipomoea, whose species suffered numerous re-arrangements, between Ipomoea and Convolvulus, but especially into numerous more recently described genera, which amount today to a total of 60 (Staples in World Checklist of Vascular Plants, v.2.0. 2020, http://wcvp.science.kew.org/ retrieved 2 Apr 2020). Linnaeus included 17 species in Ipomoea. However, of these, only the first, I. quamoclit L., truly matched his earlier generic description published in 1737 (Gen. Pl.: 47; “Petalum infundibuliforme; Tubus sere cylindraceus, longissimus”). Linnaeus actually replaced the name Quamoclit of Tournefort (Inst. Rei Herb., ed. 3, 2: t. 39. 1719) with his own Ipomoea (see Manitz in Taxon 25: 193–194. 1976). Hence, I. quamoclit would be the logical type of Ipomoea. However, in the past, some argued for a separation between the genus Quamoclit Mill. and Ipomoea (Roberty in Candollea 14: 11–65. 1952) that would result in an unfortunate recombination of hundreds of Ipomoea names, and which led Manitz (l.c.) to propose to conserve the name Ipomoea with another, conserved, type, I. pes-tigridis L., which was accepted (see Taxon 30: 145. 1981, 31: 310. 1982). More recently, molecular phylogenetic analyses have greatly assisted in obtaining a better understanding of the classification and phylogeny of the family as a whole and a much more stable taxonomy is now emerging. These studies have also shown that within the tribe Ipomoeeae Hall. f. s.l., Ipomoea is paraphyletic with 10 genera nested within it: Argyreia Lour., Astripomoea A. Meeuse, Blinkworthia Choisy, Lepistemon Blume, Lepistemonopsis Dammer, Mina Cerv., Paralepistemon Lejoly & Lisowski, Rivea Choisy, Stictocardia Hall. f., and Turbina Raf. (Wilkin, l.c.; Manos & al. in Syst. Bot. 26: 585–602. 2001; Miller & al. in Syst. Biol. 51: 740–753. 2002; Stefanović & al. in Amer. J. Bot. 89: 1510–1522. 2002, in Syst. Bot. 28: 701–806. 2003; Eserman & al. in Amer. J. Bot. 101: 92–103. 2014; Simões & al. in Bot. J. Linn. Soc. 179: 374–387. 2015). This furthered the debate about the actual identity of Ipomoea. Wilkin (l.c.) proposed the inclusion of all genera of Ipomoeeae into an Ipomoea s.l. This was recently taken up by Munõz-Rodríguez & al. (in Nature, Pl. 5: 1136–1154. 2019), soaring the genus to c. 900 species, without proposing any infrageneric classification and allowing huge morphological variation. As molecular phylogenetic results have also demonstrated, tribe Ipomoeeae can be subdivided into two main clades (Stefanović & al., l.c. 2003; Wood & al. in Phytokeys 143: 1–823. 2020) with the informal names “Astripomoeinae” and “Argyreiinae”. While the first concentrates a large diversity of the Neotropical Ipomoea, the latter is more widely distributed throughout Africa, Asia, Australia, and many of the Pacific islands, and is mostly absent from the Neotropics. Unfortunately, “Argyreiinae” includes the presently conserved type of Ipomoea, I. pes-tigridis L. Hence, implementing a new classification with the distinction of several clades at genus level would result in around 600 name changes for the Ipomoea within the “Astripomoeinae” clade, affecting mostly the American species of the genus, many of which have ornamental value. Moreover, the most economically important species, I. batatas (L.) Lam., also does not belong to the clade including the type; therefore, a potential segregation of Ipomoea s.l. into smaller genera would result in the renaming of sweetpotato. With an annual production of over 90 million metric tons (data from Shahbandeh, Global sweet potato production volume 2010–2018. 2020, https://www.statista.com/statistics/812343/global-sweet-potato-production) and hundreds if not thousands of registered cultivars (in Asia and the Pacific region alone, there exists an estimated 12,000 landraces, while in 1994 the International Potato Center (CIP) in Peru held a total of 6500 sweetpotato accessions; Takagi & al. in Flach & Rumawas, PROSEA 9, Plants Yielding Non-seed Carbohydrates: 102–107. 1999), a name change in sweetpotato would certainly result in a very costly and extreme effort by the commercial enterprises involved. As shown above (Wilkin, l.c.; Munõz-Rodriguez & al., l.c.), some authors regard the presence of the type of Ipomoea in the “Argyreiinae” clade as an obstacle towards a most useful renewal of the re-circumscription of the genera in tribe Ipomoeeae because of the sheer amount of necessary name changes and have preferred to advocate the inclusion of all the taxonomic diversity into a mega-genus Ipomoea. We think nomenclature should not block the development of a more stable and logical classification and here propose to replace the conserved type of the genus with a species included in the “Astripomoeinae” clade. This would permit those who wish to create a new classification to do so with far fewer nomenclatorial consequences. Thus, the generic name Ipomoea would be retained for the clade with the highest taxonomic diversity (c. 600 species), while preventing a name change in the economically important I. batatas. There are numerous examples of changes in nomenclature that are rejected by the scientific community when they cause significant destabilization. For example, the recent taxonomic changes in “monkeyflowers” (Mimulus, Phrymaceae; Barker & al. in Phytoneuron 39: 1–60. 2012, Lowry & al. in Taxon 68: 617–623. 2019, Nesom & al. in Taxon 68: 624–627. 2019) were rejected by the evolutionary biology community and have brought to the forefront discussions about when nomenclatural changes are appropriate. Most scientists recognize the importance of naming groups based on evolutionary lineages, but to what extent this is applied must be done with the utmost consideration. As it concerns Ipomoea, it is a priority to allow the possibility to subdivide the genus into smaller genera, while maintaining maximal nomenclatural stability. Manitz (l.c.), in proposing to conserve Ipomoea with a conserved type, identified the early confusion in the circumscription of Ipomoea and Convolvulus and acknowledged the need to stabilize nomenclature. His argument followed previous authors, especially House (in Ann. New York Acad. Sci. 18: 181–263. 1908) in considering that, although I. quamoclit would be the “historically correct” species to be selected, its morphological particularities (red tubular corolla) might have blocked those who wanted to regard Quamoclit as a distinct genus because of the very high number of new names that would then be needed to accommodate the remainder of the Ipomoea species. What Manitz did not know, was that the type House had already proposed, Ipomoea pes-tigridis L., and which he selected for conservation, would later lead to almost the same situation. In view of the recent molecular and systematic works that suggest the phylogenetic position of I. pes-tigridis as distantly related to the largest part of the genus Ipomoea, we would propose alternatively I. triloba L. as the conserved type for the genus. The broad-scale molecular phylogenetic study of Wood & al. (l.c.) demonstrated with ample sampling that I. triloba is one of the most closely related species to I. batatas. A range of important ornamental species are also fairly closely related to I. batatas and I. triloba, when considering a broader clade (e.g., I. nil (L.) Roth, I. tricolor Cav., and I. purpurea (L.) Roth). Therefore, our proposed type will allow future studies to re-assess the generic delimitation within tribe Ipomoeeae, without the fear of destabilizing the nomenclature of the group, in particular the species with greatest economic importance. LAE, https://orcid.org/0000-0002-0208-6632 MSMS, https://orcid.org/0000-0002-6997-5813 RS-B, https://orcid.org/0000-0001-9738-9494 TMAU, https://orcid.org/0000-0003-2823-0337 JCJB, https://orcid.org/0000-0002-8753-4915 MTB, https://orcid.org/0000-0001-9615-2057 LWC, https://orcid.org/0000-0003-0131-0302 KC, https://orcid.org/0000-0002-3956-0887 GD, https://orcid.org/0000-0002-6693-1540 TED, https://orcid.org/0000-0002-2119-4524 PPAF, https://orcid.org/0000-0003-1134-7918 JRGA, https://orcid.org/0000-0002-7066-0608 ALH, https://orcid.org/0000-0003-2172-6356 GH-R, https://orcid.org/0000-0002-8209-0366 RLJ, https://orcid.org/0000-0002-0426-6186 RKK, https://orcid.org/0000-0002-8538-8694 SL, https://orcid.org/0000-0003-0028-2450 JAAML, https://orcid.org/0000-0003-4741-1723 IDM, https://orcid.org/0000-0002-7567-470X REM, https://orcid.org/0000-0002-5802-2267 SM, https://orcid.org/0000-0002-7712-7785 ALCM, https://orcid.org/0000-0003-0862-0135 IM-M, https://orcid.org/0000-0003-0203-5795 SN, https://orcid.org/0000-0002-1829-7290 MP, https://orcid.org/0000-0002-2936-8920 FSP, https://orcid.org/0000-0002-8380-843X PPi, https://orcid.org/0000-0003-1746-1439 PPo, https://orcid.org/0000-0002-7998-2064 JR, https://orcid.org/0000-0003-1980-5557 FDSS, https://orcid.org/0000-0002-0053-1333 VBS, https://orcid.org/0000-0002-7028-1114 SSS, https://orcid.org/0000-0002-6318-3137 JRS, https://orcid.org/0000-0003-3349-2964 PT, https://orcid.org/0000-0001-8051-5722 LVV, https://orcid.org/0000-0003-1724-2068 MLW, https://orcid.org/0000-0001-9406-8951 AV, https://orcid.org/0000-0002-2844-723X JY, https://orcid.org/0000-0002-0371-8814 CY, https://orcid.org/0000-0001-6583-0628 BH, https://orcid.org/0000-0002-9792-8512 ARGS, https://orcid.org/0000-0001-7267-8353 We are thankful for useful comments from Dr. Mihai Costea (Wilfrid Laurier University, Canada) and Dr. Saša Stefanović (University of Toronto Mississauga, Canada). DA - 2020/12// PY - 2020/12// DO - 10.1002/tax.12400 VL - 69 IS - 6 SP - 1369-1371 SN - 1996-8175 ER - TY - JOUR TI - Data integration, analysis, and interpretation of eight academic CLARITY-BPA studies AU - Heindel, Jerrold J. AU - Belcher, Scott AU - Flaws, Jodi A. AU - Prins, Gail S. AU - Ho, Shuk-Mei AU - Mao, Jiude AU - Patisaul, Heather B. AU - Ricke, William AU - Rosenfeld, Cheryl S. AU - Soto, Ana M. AU - Saal, Frederick S. AU - Zoeller, R. Thomas T2 - REPRODUCTIVE TOXICOLOGY AB - "Consortium Linking Academic and Regulatory Insights on BPA Toxicity" (CLARITY-BPA) was a comprehensive "industry-standard" Good Laboratory Practice (GLP)-compliant 2-year chronic exposure study of bisphenol A (BPA) toxicity that was supplemented by hypothesis-driven independent investigator-initiated studies. The investigator-initiated studies were focused on integrating disease-associated, molecular, and physiological endpoints previously found by academic scientists into an industry standard guideline-compliant toxicity study. Thus, the goal of this collaboration was to provide a more comprehensive dataset upon which to base safety standards and to determine whether industry-standard tests are as sensitive and predictive as molecular and disease-associated endpoints. The goal of this report is to integrate the findings from the investigator-initiated studies into a comprehensive overview of the observed impacts of BPA across the multiple organs and systems analyzed. For each organ system, we provide the rationale for the study, an overview of methodology, and summarize major findings. We then compare the results of the CLARITY-BPA studies across organ systems with the results of previous peer-reviewed studies from independent labs. Finally, we discuss potential influences that contributed to differences between studies. Developmental exposure to BPA can lead to adverse effects in multiple organs systems, including the brain, prostate gland, urinary tract, ovary, mammary gland, and heart. As published previously, many effects were at the lowest dose tested, 2.5μg/kg /day, and many of the responses were non-monotonic. Because the low dose of BPA affected endpoints in the same animals across organs evaluated in different labs, we conclude that these are biologically - and toxicologically - relevant. DA - 2020/12// PY - 2020/12// DO - 10.1016/j.reprotox.2020.05.014 VL - 98 SP - 29-60 SN - 1873-1708 KW - CLARITY-BPA KW - Guideline study KW - Bisphenol A KW - EDC KW - Endocrine disruptor KW - GLP KW - Systemic effects ER - TY - JOUR TI - The Coupled Influence of Thermal Physiology and Biotic Interactions on the Distribution and Density of Ant Species along an Elevational Gradient AU - Chick, Lacy D. AU - Lessard, Jean-Philippe AU - Dunn, Robert R. AU - Sanders, Nathan J. T2 - DIVERSITY-BASEL AB - A fundamental tenet of biogeography is that abiotic and biotic factors interact to shape the distributions of species and the organization of communities, with interactions being more important in benign environments, and environmental filtering more important in stressful environments. This pattern is often inferred using large databases or phylogenetic signal, but physiological mechanisms underlying such patterns are rarely examined. We focused on 18 ant species at 29 sites along an extensive elevational gradient, coupling experimental data on critical thermal limits, null model analyses, and observational data of density and abundance to elucidate factors governing species’ elevational range limits. Thermal tolerance data showed that environmental conditions were likely to be more important in colder, more stressful environments, where physiology was the most important constraint on the distribution and density of ant species. Conversely, the evidence for species interactions was strongest in warmer, more benign conditions, as indicated by our observational data and null model analyses. Our results provide a strong test that biotic interactions drive the distributions and density of species in warm climates, but that environmental filtering predominates at colder, high-elevation sites. Such a pattern suggests that the responses of species to climate change are likely to be context-dependent and more specifically, geographically-dependent. DA - 2020/12// PY - 2020/12// DO - 10.3390/d12120456 VL - 12 IS - 12 SP - SN - 1424-2818 KW - ants KW - community structure KW - physiology KW - interactions KW - temperature ER - TY - JOUR TI - BAM1/2 receptor kinase signaling drives CLE peptide-mediated formative cell divisions in Arabidopsis roots AU - Crook, Ashley D. AU - Willoughby, Andrew C. AU - Hazak, Ora AU - Okuda, Satohiro AU - VanDerMolen, Kylie R. AU - Soyars, Cara L. AU - Cattaneo, Pietro AU - Clark, Natalie M. AU - Sozzani, Rosangela AU - Hothorn, Michael AU - Hardtke, Christian S. AU - Nimchuk, Zachary L. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Cell division is often regulated by extracellular signaling networks to ensure correct patterning during development. In Arabidopsis, the SHORT-ROOT (SHR)/SCARECROW (SCR) transcription factor dimer activates CYCLIND6;1 (CYCD6;1) to drive formative divisions during root ground tissue development. Here, we show plasma-membrane-localized BARELY ANY MERISTEM1/2 (BAM1/2) family receptor kinases are required for SHR-dependent formative divisions and CYCD6;1 expression, but not SHR-dependent ground tissue specification. Root-enriched CLE ligands bind the BAM1 extracellular domain and are necessary and sufficient to activate SHR-mediated divisions and CYCD6;1 expression. Correspondingly, BAM-CLE signaling contributes to the restriction of formative divisions to the distal root region. Additionally, genetic analysis reveals that BAM-CLE and SHR converge to regulate additional cell divisions outside of the ground tissues. Our work identifies an extracellular signaling pathway regulating formative root divisions and provides a framework to explore this pathway in patterning and evolution. DA - 2020/12/22/ PY - 2020/12/22/ DO - 10.1073/pnas.2018565117 VL - 117 IS - 51 SP - 32750-32756 SN - 0027-8424 KW - Arabidopsis KW - receptor kinase KW - cell cycle KW - SHORT-ROOT KW - CLE peptide ER - TY - JOUR TI - An early female lethal system of the New World screwworm, Cochliomyia hominivorax, for biotechnology-enhanced SIT AU - Concha, Carolina AU - Yan, Ying AU - Arp, Alex AU - Quilarque, Evelin AU - Sagel, Agustin AU - de León, Adalberto Pérez AU - McMillan, W. Owen AU - Skoda, Steven AU - Scott, Maxwell J. T2 - BMC Genetics AB - Abstract Background The New World Screwworm fly (NWS), Cochliomyia hominivorax , is an ectoparasite of warm-blooded animals and a major pest of livestock in parts of South America and the Caribbean where it remains endemic. In North and Central America it was eradicated using the Sterile Insect Technique (SIT). A control program is managed cooperatively between the governments of the United States and Panama to prevent the northward spread of NWS from infested countries in South America. This is accomplished by maintaining a permanent barrier through the release of millions of sterile male and female flies in the border between Panama and Colombia. Our research team demonstrated the utility of biotechnology-enhanced approaches for SIT by developing a male-only strain of the NWS. The strain carried a single component tetracycline repressible female lethal system where females died at late larval/pupal stages. The control program can be further improved by removing females during embryonic development as larval diet costs are significant. Results The strains developed carry a two-component system consisting of the Lucilia sericata bottleneck gene promoter driving expression of the tTA gene and a tTA-regulated Lshid proapoptotic effector gene. Insertion of the sex-specifically spliced intron from the C. hominivorax transformer gene within the Lshid gene ensures that only females die when insects are reared in the absence of tetracycline. In several double homozygous two-component strains and in one “All-in-one” strain that had both components in a single construct, female lethality occurred at the embryonic and/or first instar larval stages when raised on diet without tetracycline. Laboratory evaluation for phenotypes that are relevant for mass rearing in a production facility revealed that most strains had fitness characteristics similar to the wild type J06 strain that is currently reared for release in the permanent barrier. Testing of an “All in one” strain under mass rearing conditions showed that the strain maintained the fitness characteristics observed in small-scale rearing. Conclusions The early female lethal strains described here could be selected by the NWS Control Program for testing at large scale in the production facility to enhance the efficiency of the NWS eradication program. DA - 2020/12// PY - 2020/12// DO - 10.1186/s12863-020-00948-x VL - 21 IS - S2 SP - J2 - BMC Genet LA - en OP - SN - 1471-2156 UR - http://dx.doi.org/10.1186/s12863-020-00948-x DB - Crossref KW - Transgenic sexing strain KW - Pest control KW - Female lethal strain ER - TY - JOUR TI - Tomato Spotted Wilt Virus Benefits Its Thrips Vector by Modulating Metabolic and Plant Defense Pathways in Tomato AU - Nachappa, Punya AU - Challacombe, Jean AU - Margolies, David C. AU - Nechols, James R. AU - Whitfield, Anna E. AU - Rotenberg, Dorith T2 - FRONTIERS IN PLANT SCIENCE AB - Several plant viruses modulate vector fitness and behavior in ways that may enhance virus transmission. Previous studies have documented indirect, plant-mediated effects of tomato spotted wilt virus (TSWV) infection on the fecundity, growth and survival of its principal thrips vector, Frankliniella occidentalis , the western flower thrips. We conducted thrips performance and preference experiments combined with plant gene expression, phytohormone and total free amino acid analyses to determine if systemically-infected tomato plants modulate primary metabolic and defense-related pathways to culminate into a more favorable environment for the vector. In a greenhouse setting, we documented a significant increase in the number of offspring produced by F. occidentalis on TSWV-infected tomato plants compared to mock-inoculated plants, and in choice test assays, females exhibited enhanced settling on TSWV-infected leaves. Microarray analysis combined with phytohormone signaling pathway analysis revealed reciprocal modulation of key phytohormone pathways under dual attack, possibly indicating a coordinated and dampening defense against the vector on infected plants. TSWV infection, alone or in combination with thrips, suppressed genes associated with photosynthesis and chloroplast function thereby significantly impacting primary metabolism of the host plant, and hierarchical cluster and network analyses revealed that many of these genes were co-regulated with phytohormone defense signaling genes. TSWV infection increased expression of genes related to protein synthesis and degradation which was reflected in the increased total free amino acid content in virus-infected plants that harbored higher thrips populations. These results suggest coordinated gene networks that regulate plant primary metabolism and defense responses rendering virus-infected plants more conducive for vector colonization, an outcome that is potentially beneficial to the vector and the virus when considered within the context of the complex transmission biology of TSWV. To our knowledge this is the first study to identify global transcriptional networks that underlie the TSWV-thrips interaction as compared to a single mechanistic approach. Findings of this study increase our fundamental knowledge of host plant-virus-vector interactions and identifies underlying mechanisms of induced host susceptibility to the insect vector. DA - 2020/12/18/ PY - 2020/12/18/ DO - 10.3389/fpls.2020.575564 VL - 11 SP - SN - 1664-462X KW - tomato spotted wilt virus KW - Frankliniella occidentalis KW - defense crosstalk KW - cell wall organization KW - photosynthesis KW - nutrition KW - phytohormones ER - TY - JOUR TI - Editorial overview: Directionality and precision - how signaling and gene regulation drive plant development and growth AU - Van Norman, Jaimie M. AU - Strader, Lucia C. AU - Sozzani, Rosangela T2 - CURRENT OPINION IN PLANT BIOLOGY DA - 2020/10// PY - 2020/10// DO - 10.1016/j.pbi.2020.11.001 VL - 57 SP - A1-A3 SN - 1879-0356 ER - TY - JOUR TI - Building a transgenic sexing strain for genetic control of the Australian sheep blow fly Lucilia cuprina using two lethal effectors AU - Yan, Ying AU - Scott, Maxwell J. T2 - BMC Genetics AB - Abstract Background The sterile insect technique (SIT) has been successfully used in many pest management programs worldwide. Some SIT programs release both sexes due to the lack of genetic sexing strains or efficient sex separation methods but sterile females are ineffective control agents. Transgenic sexing strains (TSS) using the tetracycline-off control system have been developed in a variety of insect pests, from which females die by either of two commonly used lethal effectors: overexpression of the transcription factor tetracycline transactivator (tTA) or ectopic expression of a proapoptotic gene, such as head involution defective ( hid ). The lethality from tTA overexpression is thought to be due to “transcriptional squelching”, while hid causes lethality by induction of apoptosis. This study aims to create and characterize a TSS of Lucilia cuprina , which is a major pest of sheep, by combining both lethal effectors in a single transgenic strain. Results Here a stable TSS of L. cuprina (DH6) that carries two lethal effectors was successfully generated, by crossing FL3#2 which carries a female-specific tTA overexpression cassette, with EF1#12 which carries a tTA-regulated Lshid Ala2 cassette. Females with one copy of the FL3#2 transgene are viable but up to 99.8% of homozygous females die at the pupal stage when raised on diet that lacks tetracycline. Additionally, the female lethality of FL3#2 was partially repressed by supplying tetracycline to the parental generation. With an additional Lshid Ala2 effector, the female lethality of DH6 is 100% dominant and cannot be repressed by maternal tetracycline. DH6 females die at the late-larval stage. Several fitness parameters important for mass rearing such as hatching rate, adult emergence and sex ratio were comparable to those of the wild type strain. Conclusions Compared to the parental FL3#2 strain, the DH6 strain shows stronger female lethality and lethality occurs at an earlier stage of development. The combination of two tTA-dependent lethal effectors could improve strain stability under mass rearing and could reduce the risk of resistance in the field if fertile males are released. Our approach could be easily adapted for other pest species for an efficient, safe and sustainable genetic control program. DA - 2020/12// PY - 2020/12// DO - 10.1186/s12863-020-00947-y VL - 21 IS - S2 SP - J2 - BMC Genet LA - en OP - SN - 1471-2156 UR - http://dx.doi.org/10.1186/s12863-020-00947-y DB - Crossref KW - Sterile insect technique (SIT) KW - Tetracycline transactivator (tTA) KW - Head involution defective (hid) KW - Genetic pest management ER - TY - JOUR TI - Network isomorphism?: A network perspective on the symbolic performance of purpose-oriented networks AU - Yang, Zheng AU - Nowell, Branda T2 - INTERNATIONAL PUBLIC MANAGEMENT JOURNAL AB - While there has been increasing interest in understanding network performance in public and nonprofit sectors, the existing literature on network performance has primarily focused on the internal functioning of networks, paying less attention to the external environment. In this study, we address this gap by adopting a network domain perspective in combination with social network analysis technique to examine both internal and external stakeholder assessments of network’s symbolic performance. Examining a case where multiple networks exist in one county who all focused on the health domain, the study aims to test competing hypotheses built upon institutional theory and strategic management literature on the relationship between network isomorphism and networks’ symbolic performance. Our findings aim to contribute to both the public network literature as well as advance institutional theory within networked environments. DA - 2020/// PY - 2020/// DO - 10.1080/10967494.2020.1824949 ER - TY - JOUR TI - Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain AU - Diepenbrock, Christine H. AU - Ilut, Daniel C. AU - Magallanes-Lundback, Maria AU - Kandianis, Catherine B. AU - Lipka, Alexander E. AU - Bradbury, Peter J. AU - Holland, James B. AU - Hamilton, John P. AU - Wooldridge, Edmund AU - Vaillancourt, Brieanne AU - Góngora-Castillo, Elsa AU - Wallace, Jason G. AU - Cepela, Jason AU - Mateos-Hernandez, Maria AU - Owens, Brenda F. AU - Tiede, Tyler AU - Buckler, Edward S. AU - Rocheford, Torbert AU - Buell, C. Robin AU - Gore, Michael A. AU - DellaPenna, Dean AB - ABSTRACT Vitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize is a food staple. Extensive natural variation exists for carotenoids in maize grain; to understand its genetic basis, we conducted a joint linkage and genome-wide association study in the U.S. maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were correlated expression and effect QTL (ceeQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six ceeQTL also had the largest percent phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these ceeQTL had strongly correlated QTL allelic effect estimates across multiple traits. These findings provide the most comprehensive genome-level understanding of the genetic and molecular control of carotenoids in any plant system, and a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extendable to other cereals. DA - 2020/7/15/ PY - 2020/7/15/ DO - 10.1101/2020.07.15.203448 VL - 7 UR - https://doi.org/10.1101/2020.07.15.203448 ER - TY - JOUR TI - Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species AU - Halawani, Omar AU - Dunn, Robert R. AU - Grunden, Amy M. AU - Smith, Adrian A. T2 - PEERJ AB - Social insects have co-existed with microbial species for millions of years and have evolved a diversity of collective defenses, including the use of antimicrobials. While many studies have revealed strategies that ants use against microbial entomopathogens, and several have shown ant-produced compounds inhibit environmental bacterial growth, few studies have tested whether exposure to environmental bacteria represents a health threat to ants. We compare four ant species’ responses to exposure to Escherichia coli and Staphylococcus epidermidis bacteria in order to broaden our understanding of microbial health-threats to ants and their ability to defend against them. In a first experiment, we measure worker mortality of Solenopsis invicta , Brachymyrmex chinensis , Aphaenogaster rudis , and Dorymyrmex bureni in response to exposure to E. coli and S. epidermidis . We found that exposure to E. coli was lethal for S. invicta and D. bureni , while all other effects of exposure were not different from experimental controls. In a second experiment, we compared the antimicrobial ability of surface extracts from bacteria-exposed and non-exposed S. invicta and B. chinensis worker ants, to see if exposure to E. coli or S. epidermidis led to an increase in antimicrobial compounds. We found no difference in the inhibitory effects from either treatment group in either species. Our results demonstrate the susceptibility to bacteria is varied across ant species. This variation may correlate with an ant species’ use of surface antimicrobials, as we found significant mortality effects in species which also were producing antimicrobials. Further exploration of a wide range of both bacteria and ant species is likely to reveal unique and nuanced antimicrobial strategies and deepen our understanding of how ant societies respond to microbial health threats. DA - 2020/12/3/ PY - 2020/12/3/ DO - 10.7717/peerj.10412 VL - 8 SP - SN - 2167-8359 KW - Entomopathogen KW - Metapleural gland KW - Social immunity KW - Bacterial exposure KW - Social insects KW - Sociobiology KW - Antimicrobial ER - TY - JOUR TI - Realizing Present and Future Promise of DIY Biology and Medicine through a Trust Architecture AU - Rasmussen, Lisa M. AU - Guerrini, Christi J. AU - Kuiken, Todd AU - Nebeker, Camille AU - Pearlman, Alex AU - Ware, Sarah B. AU - Wexler, Anna AU - Zettler, Patricia J. T2 - HASTINGS CENTER REPORT AB - The speed and scale of the COVID-19 pandemic has highlighted the limits of current health systems and the potential promise of non-establishment research such as "DIY" research. We consider one example of how DIY research is responding to the pandemic, discuss the challenges faced by DIY research more generally, and suggest that a "trust architecture" should be developed now to contribute to successful future DIY efforts. DA - 2020/11// PY - 2020/11// DO - 10.1002/hast.1194 VL - 50 IS - 6 SP - 10-14 SN - 1552-146X KW - citizen science KW - DIY biology KW - DIY bio KW - research ethics KW - Covid-19 KW - pandemic KW - community bio KW - biohacking KW - DIY medicine KW - trust architecture KW - participant-led research KW - personal science ER - TY - JOUR TI - Physiological and molecular correlates of the screwworm fly attraction to wound and animal odors AU - Hickner, Paul V. AU - Mittapalli, Omprakash AU - Subramoniam, Anjana AU - Sagel, Agustin AU - Watson, Wes AU - Scott, Maxwell J. AU - Arp, Alex P. AU - de León, Adalberto A. Pérez AU - Syed, Zainulabeuddin T2 - Scientific Reports AB - Abstract The screwworm fly, Cochliomyia hominivorax (Coquerel), was successfully eradicated from the United States by the sterile insect technique (SIT). However, recent detection of these flies in the Florida Keys, and increased risk of introductions to the other areas warrant novel tools for management of the flies. Surveillance, a key component of screwworm control programs, utilizes traps baited with rotting liver or a blend of synthetic chemicals such as swormlure-4 . In this work, we evaluated the olfactory physiology of the screwworm fly and compared it with the non-obligate ectoparasitic secondary screwworm flies, C. macellaria, that invade necrotic wound and feed on dead tissue. These two species occur in geographically overlapping regions. C. macellaria , along with other blowflies such as the exotic C. megacephala , greatly outnumber C. hominivorax in the existing monitoring traps. Olfactory responses to swormlure-4 constituents between sex and mating status (mated vs unmated) in both species were recorded and compared. Overall, responses measured by the antennograms offered insights into the comparative olfactory physiology of the two fly species. We also present detailed analyses of the antennal transcriptome by RNA-Sequencing that reveal significant differences between male and female screwworm flies. The differential expression patterns were confirmed by quantitative PCR. Taken together, this integrated study provides insights into the physiological and molecular correlates of the screwworm’s attraction to wounds, and identifies molecular targets that will aid in the development of odorant-based fly management strategies. DA - 2020/11/27/ PY - 2020/11/27/ DO - 10.1038/s41598-020-77541-w VL - 10 IS - 1 J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-020-77541-w DB - Crossref ER - TY - JOUR TI - Tolerance of pintoi peanut to PRE and POST herbicides AU - Martin, Logan J. AU - Dias, Jose Luiz C. S. AU - Sellers, Brent A. AU - Ferrell, Jason A. AU - Leon, Ramon G. AU - Vendramini, Joao M. B. T2 - WEED TECHNOLOGY AB - Abstract Pintoi peanut is a warm-season perennial legume that shows promise as a forage crop for the southeastern United States, however, little is known about the proper methods of weed management during establishment for this species. The objective of this study was to determine the ability of pintoi peanut to tolerate applications of PRE and POST herbicides during the year of and year after planting. The effects of herbicide treatments on percentage of visual estimates of injury and stand counts of pintoi peanut were investigated at Ona and Marianna, FL, in 2015 and 2016. All PRE herbicides did not result in significant injury or stand reduction. Pintoi peanut’s tolerance to POST herbicides was higher when plants were emerged for at least 2 wk prior to herbicide application. Stands of pintoi peanut that were planted the previous year appear to tolerate all herbicides examined in this work, except sulfosulfuron. Results of this study indicate that at the year of planting pintoi peanut is tolerant to PRE applications of pendimethalin, imazethapyr, and imazapic. Pintoi peanut appears to tolerate applications of 2,4-D, carfentrazone, imazapic and imazethapyr the year after planting at the rates utilized in this study. Future research should evaluate the effects of multiple herbicide applications and tank-mixes to obtain satisfactory weed control and selectivity in pintoi peanut swards. DA - 2020/12// PY - 2020/12// DO - 10.1017/wet.2020.82 VL - 34 IS - 6 SP - 870-875 SN - 1550-2740 KW - 2,4-D KW - carfentrazone KW - imazapic KW - imazethapyr KW - pendimethalin KW - sulfosulfuron KW - pintoi peanut KW - Arachis pintoi Krap. and Greg. KW - 'Amarillo' ER - TY - JOUR TI - How Do AI-driven Chatbots Impact User Experience? Examining Gratifications, Perceived Privacy Risk, Satisfaction, Loyalty, and Continued Use AU - Cheng, Yang AU - Jiang, Hua T2 - Journal of Broadcasting & Electronic Media AB - This study examined how artificial intelligence (AI)-driven chatbots impact user experience. It collected survey data from 1,064 consumers who used any chatbot service from the top 30 brands in the U.S. Results indicated that utilitarian (information), hedonic (entertainment), technology (media appeal), and social (social presence) gratifications obtained from chatbot use positively predicted users’ satisfaction with chatbot services of their selected brand. In contrast, perceived privacy risk associated with chatbot use reduced user satisfaction. Data also demonstrated that user satisfaction positively affected both the continued use intention of chatbot services and customer loyalty. Implications of this study are discussed. DA - 2020/10/1/ PY - 2020/10/1/ DO - 10.1080/08838151.2020.1834296 VL - 64 IS - 4 SP - 592-614 J2 - Journal of Broadcasting & Electronic Media LA - en OP - SN - 0883-8151 1550-6878 UR - http://dx.doi.org/10.1080/08838151.2020.1834296 DB - Crossref ER - TY - JOUR TI - Carbon Neutral: The Failure of Dung Beetles (Coleoptera: Scarabaeidae) to Affect Dung-Generated Greenhouse Gases in the Pasture AU - Fowler, Fallon AU - Denning, Steve AU - Hu, Shuijin AU - Watson, Wes AU - Schmidt, Jason T2 - ENVIRONMENTAL ENTOMOLOGY AB - Abstract Research suggests dung beetles can churn, aerate, and desiccate dung in ways that influence the dung and soil microbes producing greenhouse gases (GHGs). We examined the impacts of the tunneling beetle, Onthophagus taurus (Schreber), and the dwelling beetle, Labarrus pseudolividus (Balthasar), on the carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) emitted from pasture-laid bovine dung as well as their sum-total (CO2 + CH4 + N2O) effect on global warming, or their carbon dioxide equivalent (CO2e). Despite dung beetles potential effects on CH4 and N2O, the existing literature shows no ultimate CO2e reductions. We hypothesized that more dung beetles would degrade pats faster and reduce CO2e, and so we increased the average dung beetle biomass per dung volume 6.22× above previously published records, and visually documented any dung damage. However, the time effects were 2–5× greater for any GHG and CO2e (E = 0.27–0.77) than dung beetle effects alone (E = 0.09–0.24). This suggests that dung beetle communities cannot adequately reduce GHGs unless they can accelerate dung decomposition faster than time alone. DA - 2020/10// PY - 2020/10// DO - 10.1093/ee/nvaa094 VL - 49 IS - 5 SP - 1105-1116 SN - 1938-2936 KW - dung beetle KW - tunneling KW - dwelling KW - greenhouse gas KW - dung decomposition ER - TY - JOUR TI - Pest pressure relates to similarity of crops and native plants AU - Kennedy, George G. AU - Huseth, Anders S. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Errors in clinical decision-making are disturbingly common. Here, we show that structured information–sharing networks among clinicians significantly reduce diagnostic errors, and improve treatment recommendations, as compared to groups of ...Errors in clinical decision-making are disturbingly common. Recent studies have found that 10 to 15% of all clinical decisions regarding diagnoses and treatment are inaccurate. Here, we experimentally study the ability of structured information–sharing ... DA - 2020/11/24/ PY - 2020/11/24/ DO - 10.1073/pnas.2020945117 VL - 117 IS - 47 SP - 29260-29262 SN - 0027-8424 KW - pesticides KW - pest management KW - phylogenetic ecology KW - agricultural ecology ER - TY - JOUR TI - Sustainable Swine Manure Management: A Tale of Two Agreements AU - Deviney, Alison AU - Classen, John AU - Bruce, Jackie AU - Sharara, Mahmoud T2 - Sustainability AB - Intensification and concentration of swine farming has provided economic benefit to rural communities but also negative environmental and human health impacts, particularly from the use of the lagoon-sprayfield system for manure management. Although cost effective, this system is susceptible to poor management, unpleasant odor and other emissions, and inundation during extreme weather events. Competition for manure-spreading acres with other livestock or encroaching development can also pose a problem. This study examines two agreements between industry and government designed to develop and implement improved manure management technologies for swine farms: a voluntary agreement between the attorney general of North Carolina and Smithfield Foods and a consent judgment between the State of Missouri and Premium Standard Farms. Individuals involved in executing these agreements were interviewed to gain insight from their perspective on those processes and lessons they learned from their experience. Common themes among participant responses to support transition processes included the need to involve multiple stakeholder groups, clearly define goals, understand the system, allow time for incremental change, and provide adequate “protected space” for technology development and implementation. Viewing these themes through the lens of multi-level perspective theory identifies leverage points throughout the system to support transitioning farms to a more sustainable path of manure management. DA - 2020/12/22/ PY - 2020/12/22/ DO - 10.3390/su13010015 VL - 13 IS - 1 SP - 15 J2 - Sustainability LA - en OP - SN - 2071-1050 UR - http://dx.doi.org/10.3390/su13010015 DB - Crossref KW - case study KW - industrial agriculture KW - swine manure KW - multi-level perspective theory KW - sustainability KW - systems thinking ER - TY - JOUR TI - Identifying Candidate Genetic Markers of CDV Cross-Species Pathogenicity in African Lions AU - Weckworth, Julie K. AU - Davis, Brian W. AU - Roelke-Parker, Melody E. AU - Wilkes, Rebecca P. AU - Packer, Craig AU - Eblate, Ernest AU - Schwartz, Michael K. AU - Mills, L. Scott T2 - PATHOGENS AB - Canine distemper virus (CDV) is a multi-host pathogen with variable clinical outcomes of infection across and within species. We used whole-genome sequencing (WGS) to search for viral markers correlated with clinical distemper in African lions. To identify candidate markers, we first documented single-nucleotide polymorphisms (SNPs) differentiating CDV strains associated with different clinical outcomes in lions in East Africa. We then conducted evolutionary analyses on WGS from all global CDV lineages to identify loci subject to selection. SNPs that both differentiated East African strains and were under selection were mapped to a phylogenetic tree representing global CDV diversity to assess if candidate markers correlated with documented outbreaks of clinical distemper in lions (n = 3). Of 54 SNPs differentiating East African strains, ten were under positive or episodic diversifying selection and 20 occurred in the clinical strain despite strong purifying selection at those loci. Candidate markers were in functional domains of the RNP complex (n = 19), the matrix protein (n = 4), on CDV glycoproteins (n = 5), and on the V protein (n = 1). We found mutations at two loci in common between sequences from three CDV outbreaks of clinical distemper in African lions; one in the signaling lymphocytic activation molecule receptor (SLAM)-binding region of the hemagglutinin protein and another in the catalytic center of phosphodiester bond formation on the large polymerase protein. These results suggest convergent evolution at these sites may have a functional role in clinical distemper outbreaks in African lions and uncover potential novel barriers to pathogenicity in this species. DA - 2020/11// PY - 2020/11// DO - 10.3390/pathogens9110872 VL - 9 IS - 11 SP - SN - 2076-0817 KW - canine distemper virus KW - African lion KW - cross-species pathogenicity KW - multi-host pathogen KW - evolutionary genetics KW - viral genomics KW - spillover ER - TY - JOUR TI - Emerging lanthanum (III)-containing materials for phosphate removal from water: A review towards future developments AU - Zhi, Yue AU - Zhang, Chuhui AU - Hjorth, Rune AU - Baun, Anders AU - Duckworth, Owen W. AU - Call, Douglas F. AU - Knappe, Detlef R. U. AU - Jones, Jacob L. AU - Grieger, Khara T2 - ENVIRONMENT INTERNATIONAL AB - The last two decades have seen a rise in the development of lanthanum (III)-containing materials (LM) for controlling phosphate in the aquatic environment. >70 papers have been published on this topic in the peer-reviewed literature, but mechanisms of phosphate removal by LM as well as potential environmental impacts of LM remain unclear. In this review, we summarize peer-reviewed scientific articles on the development and use of 80 different types of LM in terms of prospective benefits, potential ecological impacts, and research needs. We find that the main benefits of LM for phosphate removal are their ability to strongly bind phosphate under diverse environmental conditions (e.g., over a wide pH range, in the presence of diverse aqueous constituents). The maximum phosphate uptake capacity of LM correlates primarily with the La content of LM, whereas reaction kinetics are influenced by LM formulation and ambient environmental conditions (e.g., pH, presence of co-existing ions, ligands, organic matter). Increased La solubilization can occur under some environmental conditions, including at moderately acidic pH values (i.e., < 4.5–5.6), highly saline conditions, and in the presence of organic matter. At the same time, dissolved La will likely undergo hydrolysis, bind to organic matter, and combine with phosphate to precipitate rhabdophane (LaPO4·H2O), all of which reduce the bioavailability of La in aquatic environments. Overall, LM use presents a low risk of adverse effects in water with pH > 7 and moderate-to-high bicarbonate alkalinity, although caution should be applied when considering LM use in aquatic systems with acidic pH values and low bicarbonate alkalinity. Moving forward, we recommend additional research dedicated to understanding La release from LM under diverse environmental conditions as well as long-term exposures on ecological organisms, particularly primary producers and benthic organisms. Further, site-specific monitoring could be useful for evaluating potential impacts of LM on both biotic and abiotic systems post-application. DA - 2020/12// PY - 2020/12// DO - 10.1016/j.envint.2020.106115 VL - 145 SP - SN - 1873-6750 KW - Lanthanum KW - Lanthanum-containing materials KW - Phosphate KW - Surface water restoration KW - Eutrophication control KW - Phosphorus inactivation ER - TY - JOUR TI - Using Moderate Transgene Expression to Improve the Genetic Sexing System of the Australian Sheep Blow Fly Lucilia cuprina AU - Yan, Ying AU - Williamson, Megan E. AU - Scott, Maxwell J. T2 - Insects AB - The sterile insect technique (SIT) is a promising strategy to control the Australian sheep blow fly Lucilia cuprina, a major pest of sheep. We have previously developed a transgenic embryonic sexing system (TESS) for this pest to facilitate the potential SIT application. TESS carry two transgenes, a tetracycline transactivator (tTA) driver and a tTA-activated pro-apoptotic effector. TESS females die at the embryonic stage unless tetracycline is supplied in the diet. However, undesired female sterility was observed in some TESS strains without tetracycline due to expression of tTA in ovaries. Here we investigate if TESS that combine transgenes with relatively low/moderate expression/activity improves the fertility of TESS females. tTA driver lines were evaluated for tTA expression by quantitative real time PCR and/or by crossing with a tTA-activated RFPex effector line. Fertility and lethality tests showed that a TESS strain containing a driver line with moderate tTA expression and an effector line showing moderate pro-apoptotic activity could recover the fertility of parental females and eliminated all female offspring at the embryonic stage. Consequently, such a strain could be further evaluated for an SIT program for L. cuprina, and such a “moderate strategy” could be considered for the TESS development in other pest species. DA - 2020/11/13/ PY - 2020/11/13/ DO - 10.3390/insects11110797 VL - 11 IS - 11 SP - 797 J2 - Insects LA - en OP - SN - 2075-4450 UR - http://dx.doi.org/10.3390/insects11110797 DB - Crossref KW - livestock pest KW - Lucilia cuprina KW - genetic control KW - pro-apoptotic gene KW - sterile insect technique KW - genetic sexing KW - tetracycline-off system KW - insect transgenesis ER - TY - JOUR TI - Estimations of Fine-Scale Species Distributions of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) in Eastern Florida AU - Hopperstad, Kristen A AU - Sallam, Mohamed F AU - Reiskind, Michael H T2 - Journal of Medical Entomology AB - Abstract Many species distribution maps indicate the ranges of Aedes aegypti (Linnaeus) and Aedes albopictus (Skuse) overlap in Florida despite the well-documented range reduction of Ae. aegypti. Within the last 30 yr, competitive displacement of Ae. aegypti by Ae. albopictus has resulted in partial spatial segregation of the two species, with Ae. aegypti persisting primarily in urban refugia. We modeled fine-scale distributions of both species, with the goal of capturing the outcome of interspecific competition across space by building habitat suitability maps. We empirically parameterized models by sampling 59 sites in south and central Florida over time and incorporated climatic, landscape, and human population data to identify predictors of habitat suitability for both species. Our results show human density, precipitation, and urban land cover drive Ae. aegypti habitat suitability, compared with exclusively climatic variables driving Ae. albopictus habitat suitability. Remotely sensed variables (macrohabitat) were more predictive than locally collected metrics (microhabitat), although recorded minimum daily temperature showed significant, inverse relationships with both species. We detected minor Aedes habitat segregation; some periurban areas that were highly suitable for Ae. albopictus were unsuitable for Ae. aegypti. Fine-scale empirical models like those presented here have the potential for precise risk assessment and the improvement of operational applications to control container-breeding Aedes mosquitoes. DA - 2020/10/31/ PY - 2020/10/31/ DO - 10.1093/jme/tjaa216 VL - 10 UR - http://dx.doi.org/10.1093/jme/tjaa216 KW - habitat suitability model KW - maximum entropy model KW - MaxEnt KW - Aedes aegypti KW - Aedes albopictus ER - TY - JOUR TI - Efficacy and Spatial Extent of Yard-Scale Control of Aedes (Stegomyia) albopictus (Diptera: Culicidae) Using Barrier Sprays and Larval Habitat Management AU - Hollingsworth, Brandon AU - Hawkins, Pete AU - Lloyd, Alun L AU - Reiskind, Michael H T2 - Journal of Medical Entomology AB - Abstract The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse), is a peridomestic, container-ovipositing mosquito commonly found throughout the southeastern United States. In the United States, Ae. albopictus is typically considered a nuisance pest; however, it is capable of transmitting multiple pathogens. Ae. albopictus is an important pest species and the target of numerous mosquito control efforts in the United States. Here, we evaluate the effectiveness and spatial extent of Ae. albopictus population reduction using a bifenthrin (AI Bifen IT, 7.9%) barrier spray and larval habitat management (LHM) in a temperate, suburban setting. Sixteen pairs of adjoining neighbors were randomly assigned to treatment groups with one neighbor receiving a treatment and the other monitored for evidence of a spillover effect of the treatments. Ae. albopictus populations in both yards were monitored for 33 d, with treatments occurring on the eighth day. Barrier sprays, both alone and combined with LHM, resulted in a significant reduction in Ae. albopictus abundance posttreatment. While LHM alone did not result in a significant reduction over the entire posttreatment period, Ae. albopictus populations were observed to be in decline during this period. No treatments were observed to have any reduction in efficacy 25 d posttreatment, with treatments involving LHM having a significantly increased efficacy. Yards neighboring treated yards were also observed to have reduced population sizes posttreatment, but these differences were rarely significant. These results provide insights into the population dynamics of Ae. albopictus following two common treatments and will be useful for integrated pest management plans. DA - 2020/7/4/ PY - 2020/7/4/ DO - 10.1093/jme/tjaa016 VL - 57 IS - 4 SP - 1104-1110 UR - http://dx.doi.org/10.1093/jme/tjaa016 KW - Aedes albopictus KW - mosquito control KW - pyrethroid KW - larval habitat reduction ER - TY - JOUR TI - Context-Dependent Accuracy of the BG-Counter Remote Mosquito Surveillance Device in North Carolina AU - Day, Corey A. AU - Richards, Stephanie L. AU - Reiskind, Michael H. AU - Doyle, Michael S. AU - Byrd, Brian D. T2 - Journal of the American Mosquito Control Association AB - ABSTRACT There is a clear need for improved vector surveillance approaches that are affordable, labor efficient, and safer than traditional methods. The BG-Counter (Biogents USA, Moorefield, WV) is a device for remotely monitoring mosquito activity in combination with the BG-Sentinel (Biogents USA), a widely used trap for the collection of host-seeking mosquitoes. The BG-Counter uses a wireless connection to provide real-time counts of mosquitoes captured by the BG-Sentinel, allowing users to remotely monitor mosquito populations. This study tested the effectiveness of the BG-Counter in 5 North Carolina counties. A total of 96 trap-days resulted in the collection of &gt;45,000 individual mosquitoes representing 35 species. Aedes albopictus was the most common species collected in all counties, except for New Hanover County where Culex nigripalpus was the most common. The mean daily accuracy ranged from 80.1% (New Hanover County) to 9.4% (Jackson County). There was a significant linear relationship between the actual number of mosquitoes collected and the device counts at all sites except Jackson County, the site with the lowest relative mosquito abundance compared with nontarget organisms. A linear regression of daily BG-Counter accuracy and the daily proportion of mosquitoes to the total number of arthropods collected revealed a significant positive linear relationship, supporting the premise that the BG-Counter is less effective when the relative abundance of mosquitoes is low. Mosquito surveillance programs using the BG-Counter should recognize its context-dependent accuracy and routinely evaluate the accuracy of the device based on local conditions. DA - 2020/6/1/ PY - 2020/6/1/ DO - 10.2987/19-6903.1 VL - 36 IS - 2 SP - 74-80 UR - http://dx.doi.org/10.2987/19-6903.1 ER - TY - JOUR TI - Effects of Prenatal Exposure to a Mixture of Organophosphhate Flame Ritardants on Placental Gene Expression and Serotonergic Innervaion in the Fetal Rat Brain AU - Rock, Kylie D. AU - St Armour, Genevieve AU - Horman, Brian AU - Phillips, Allison AU - Ruis, Matthew AU - Stewart, Allison K. AU - Jima, Dereje AU - Muddiman, David C. AU - Stapleton, Heather M. AU - Patisaul, Heather B. T2 - TOXICOLOGICAL SCIENCES AB - There is a growing need to understand the potential neurotoxicity of organophosphate flame retardants (OPFRs) and plasticizers because use and, consequently, human exposure, is rapidly expanding. We have previously shown in rats that developmental exposure to the commercial flame retardant mixture Firemaster 550 (FM 550), which contains OPFRs, results in sex-specific behavioral effects, and identified the placenta as a potential target of toxicity. The placenta is a critical coordinator of fetal growth and neurodevelopment, and a source of neurotransmitters for the developing brain. We have shown in rats and humans that flame retardants accumulate in placental tissue, and induce functional changes, including altered neurotransmitter production. Here, we sought to establish if OPFRs (triphenyl phosphate and a mixture of isopropylated triarylphosphate isomers) alter placental function and fetal forebrain development, with disruption of tryptophan metabolism as a primary pathway of interest. Wistar rat dams were orally exposed to OPFRs (0, 500, 1000, or 2000 μg/day) or a serotonin (5-HT) agonist 5-methoxytryptamine for 14 days during gestation and placenta and fetal forebrain tissues collected for analysis by transcriptomics and metabolomics. Relative abundance of genes responsible for the transport and synthesis of placental 5-HT were disrupted, and multiple neuroactive metabolites in the 5-HT and kynurenine metabolic pathways were upregulated. In addition, 5-HTergic projections were significantly longer in the fetal forebrains of exposed males. These findings suggest that OPFRs have the potential to impact the 5-HTergic system in the fetal forebrain by disrupting placental tryptophan metabolism. DA - 2020/7// PY - 2020/7// DO - 10.1093/toxsci/kfaa046 VL - 176 IS - 1 SP - 203-223 SN - 1096-0929 KW - endocrine disruptors KW - endocrine toxicology KW - flame retardants KW - metabolome KW - neurotoxicity KW - developmental KW - neurotoxicology KW - neurotransmitter KW - developmental toxicity KW - prenatal KW - reproductive and developmental toxicology KW - developmental/teratology ER - TY - JOUR TI - Short-term effects of bioenergy cropping on soil carbon and nitrogen dynamics in a Florida Ultisol AU - Silveira, M. L. AU - Brandani, C. B. AU - Kohmann, M. M. AU - Erickson, J. E. AU - Reyes-Cabrera, J. AU - Leon, R. G. AU - Sollenberger, L. E. AU - Piotto, V. AU - Quadros, D. G. AU - Mello, S. Q. S. T2 - SOIL SCIENCE SOCIETY OF AMERICA JOURNAL AB - Abstract Although perennial bioenergy crops provide a potential for soil C sequestration, high fertilizer inputs are required to sustain yields. Land application of bioenergy byproducts can be an effective strategy to reduce the use of inorganic fertilizer. This study examined the impacts of elephantgrass [ Pennisetum purpureum (L.) Schum.] bioenergy cropping and conventional pasture on soil C and N responses. Treatments included (a) bahiagrass + 50 kg N ha −1 yr −1 (BHG), (b) elephantgrass + 50 kg N ha −1 yr −1 (E50), (c) elephantgrass + 50 kg N ha −1 yr −1 + fermentation residual (E50FR), (d) elephantgrass + 50 kg N ha −1 yr −1 + biochar (E50BC), and (e) elephantgrass + 250 kg N ha −1 yr −1 (E250). Soil C and N responses occurred mainly at the 0‐ to 10‐cm depth. Biochar resulted in the largest increase in soil C stocks at the 0‐ to 10‐cm depth (5.8 Mg C ha −1 in 2012 vs. 40 Mg C ha −1 in 2016), but no differences were observed among the other treatments. Conversely, greater soil N stocks at the 0‐ to 10‐cm depth were associated with the BHG (0.8 and 0.34 Mg N ha −1 for other treatments). Biochar favored N and C accumulation in the mineral‐associated (<53 μm) fraction, possibly from the accumulation of fine biochar fragments. In contrast, fermentation residual promoted C accumulation in unprotected light fraction. These results are supported by the δ 13 C signature and C/N ratios of the fractions. Results underscore the value of recycling biochar in bioenergy cropping systems as a means of improving C in coarse‐textured soils. DA - 2020/// PY - 2020/// DO - 10.1002/saj2.20081 VL - 84 IS - 4 SP - 1233-1246 SN - 1435-0661 ER - TY - JOUR TI - Reevaluating the Economic Injury Level for Brown Stink Bug (Hemiptera: Pentatomidae) at Various Growth Stages of Maize AU - Bryant, Tim B AU - Dorman, Seth J AU - Reisig, Dominic D AU - Dillard, DeShae AU - Schürch, Roger AU - Taylor, Sally V T2 - Journal of Economic Entomology AB - Abstract Economic yield loss and reduction in grain quality from brown stink bug, Euschistus servus (Say), feeding injury in early and late stages of maize, Zea mays (Poales: Poaceae, Linnaeus), development was assessed in Virginia and North Carolina in 2018 and 2019. Varying levels of stink bug infestations were introduced to seedling maize (V2—early stage), and a range of late-stages of maize, including 1) the last stage of vegetative development (V12/V14), 2) prior to tasseling, 3) at tasseling (VT), and 4) across all tested late growth stages. Euschistus servus infestation levels included 33, 67, and 100% of maize seedlings, and 25, 50, 100, and 200% of plants during later stages. Infestations were maintained on seedling maize for 7 d, and 8 or 16 d in reproductive stages. Infestation level in seedling maize had an impact on grain yield. Infestation level and growth stage both had an impact on grain yield in reproductive maize. The percentage of discolored kernels was also affected by infestation level, but not growth stage. Regression analysis between grain yield and infestation level indicated that the average economic injury level is 7% in seedling maize (7 bugs/100 plants) and 12% (12 bugs/100 plants) from the last vegetative stages (V12/V14) through pollination (VT). The economic injury level in the late vegetative stages is only applicable when infestations are present for an extended period of time (16 d), emphasizing the need for continued scouting of maize throughout the season to make informed management decisions. DA - 2020/8/25/ PY - 2020/8/25/ DO - 10.1093/jee/toaa173 VL - 113 IS - 5 SP - 2250-2258 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/toaa173 DB - Crossref KW - brown stink bug KW - economic thresholds KW - maize KW - economic injury level ER - TY - JOUR TI - Decline in Sublethal Effects of Bt Corn on Corn Earworm (Lepidoptera: Noctuidae) Linked to Increasing Levels of Resistance AU - Reay-Jones, Francis P F AU - Bilbo, Thomas R AU - Reisig, Dominic D T2 - Journal of Economic Entomology AB - Abstract As part of an ongoing longitudinal study in North and South Carolina, this study reports the recovery of Helicoverpa zea (Boddie) pupae in field trials with genetically engineered corn, Zea mays L., hybrids that produce insecticidal toxins from Bacillus thuringiensis (Bt) in 2017–2019. In total, 10,400 corn ears were collected, which led to 3,927 H. zea pupae (2,215 in South Carolina and 1,712 in North Carolina). Late-planted corn led to a 3.39-fold increase in recovery of pupae compared to early-planted corn. Bt corn expressing Cry1F + Cry1Ab and Cry1A.105 + Cry2Ab2 had 1.67-fold and 2.51-fold fewer pupae than non-Bt near-isolines, respectively. Only six pupae were recovered from the hybrid expressing Cry1F + Cry1Ab + Vip3Aa20. Averaged across trials, Bt corn expressing either Cry1A.105 + Cry2Ab2 or Cry1F + Cry1Ab significantly reduced pupal weight compared to non-Bt near-isolines in North and South Carolina. Combining our data with a previous study at the same locations (Bilbo et al. 2018), reduction in pupal weight between Bt and non-Bt near-isolines significantly declined from 2014 to 2019 for Cry1Ab + Cry1F in North and South Carolina. This decline in levels of a sublethal effect of Bt corn expressing Cry1Ab + Cry1F on H. zea at both locations is likely correlated with resistance development. DA - 2020/8/2/ PY - 2020/8/2/ DO - 10.1093/jee/toaa163 VL - 113 IS - 5 SP - 2241-2249 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/toaa163 DB - Crossref KW - Helicoverpa zea KW - transgenic crops KW - Bacillus thuringiensis KW - maize ER - TY - JOUR TI - Three-dimensional imaging of intact porcine cochlea using tissue clearing and custom-built light-sheet microscopy AU - Moatti, Adele AU - Cai, Yuheng AU - Li, Chen AU - Sattler, Tyler AU - Edwards, Laura AU - Piedrahita, Jorge AU - Ligler, Frances S. AU - Greenbaum, Alon T2 - BIOMEDICAL OPTICS EXPRESS AB - Hearing loss is a prevalent disorder that affects people of all ages. On top of the existing hearing aids and cochlear implants, there is a growing effort to regenerate functional tissues and restore hearing. However, studying and evaluating these regenerative medicine approaches in a big animal model (e.g. pigs) whose anatomy, physiology, and organ size are similar to a human is challenging. In big animal models, the cochlea is bulky, intricate, and veiled in a dense and craggy otic capsule. These facts complicate 3D microscopic analysis that is vital in the cochlea, where structure-function relation is time and again manifested. To allow 3D imaging of an intact cochlea of newborn and juvenile pigs with a volume up to ∼ 250 mm 3 , we adapted the BoneClear tissue clearing technique, which renders the bone transparent. The transparent cochleae were then imaged with cellular resolution and in a timely fashion, which prevented bubble formation and tissue degradation, using an adaptive custom-built light-sheet fluorescence microscope. The adaptive light-sheet microscope compensated for deflections of the illumination beam by changing the angles of the beam and translating the detection objective while acquiring images. Using this combination of techniques, macroscopic and microscopic properties of the cochlea were extracted, including the density of hair cells, frequency maps, and lower frequency limits. Consequently, the proposed platform could support the growing effort to regenerate cochlear tissues and assist with basic research to advance cures for hearing impairments. DA - 2020/11/1/ PY - 2020/11/1/ DO - 10.1364/BOE.402991 VL - 11 IS - 11 SP - 6181-6196 SN - 2156-7085 ER - TY - JOUR TI - Yes, and horizontal ellipsis : continuing the scholarly conversation about undue donor influence on higher education AU - Rudick, C. Kyle AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - I (Dannels), in my role as Associate Dean of Academic Affairs, have participated in meetings with potential donors when donors have expressed interest in initiatives related to student success. 1 I... DA - 2020/7/2/ PY - 2020/7/2/ DO - 10.1080/03634523.2020.1769904 VL - 69 IS - 3 SP - 395-398 SN - 1479-5795 ER - TY - JOUR TI - Determining the Effect of Postharvest Cold Storage Treatment on the Survival of Immature Drosophila suzukii (Diptera: Drosophilidae) in Small Fruits AU - Kraft, Laura J. AU - Yeh, D. Adeline AU - Gomez, Miguel I AU - Burrack, Hannah J. T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - Abstract We evaluated the effect of postharvest cold storage temperature (0.0–2.2°C) and duration (3–5 d) on pupal emergence of single life stage populations of laboratory-generated Drosophila suzukii (Matsumura) and mixed-age populations collected in the field from blackberries, blueberries, strawberries, and raspberries. For field-infested fruit, cold storage at any temperature and duration resulted in less pupal emergence compared with the control held at 20°C, but D. suzukii subjected to higher temperatures and shorter storage durations in caneberries had higher survival. When a single life stage of D. suzukii was exposed to cold storage, pupal emergence was significantly reduced across all fruit types held at 0°C and for most life stages and fruit types held at 1.5 and 2.2°C, dependent on the substrate. Freshly laid eggs exposed to cold storage produced the lowest pupal emergence. Our results suggest using cold storage treatment is an effective postharvest management strategy for small-fruit growers to use on-farm as part of an integrated program to manage D. suzukii infestation. An economic assessment was made to examine the profit implications of an investment in cold storage units to counter pest pressure. Results suggest that investment in a cold storage unit would breakeven in about 4 yr. On farms that already have cold storage installed, we estimated a $0.11/kg decrease in blueberry market price for holding fruit for 3 d. Together, this cost assessment will provide growers with the knowledge to make decisions based on infestation risk and the seasonal sale price of blueberries. DA - 2020/10// PY - 2020/10// DO - 10.1093/jee/toaa185 VL - 113 IS - 5 SP - 2427-2435 SN - 1938-291X KW - postharvest KW - cold storage ER - TY - JOUR TI - History and Domestication of Saccharomyces cerevisiae in Bread Baking AU - Lahue, Caitlin AU - Madden, Anne A. AU - Dunn, Robert R. AU - Smukowski Heil, Caiti T2 - FRONTIERS IN GENETICS AB - The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field. DA - 2020/11/11/ PY - 2020/11/11/ DO - 10.3389/fgene.2020.584718 VL - 11 SP - SN - 1664-8021 KW - Saccharomyces cerevisiae (Baker’ KW - s yeast) KW - bread KW - baking KW - domestication KW - industrial KW - yeast ER - TY - JOUR TI - Systems Approach to Evaluate Tarnished Plant Bug (Hemiptera: Miridae) Management Practices in Virginia and North Carolina Cotton AU - Dorman, Seth J AU - Reisig, Dominic D AU - Malone, Sean AU - Taylor, Sally V T2 - Journal of Economic Entomology AB - Abstract Economically damaging infestations of Lygus lineolaris (Palisot de Beauvois), tarnished plant bug, were sporadic in Virginia and North Carolina cotton before 2010. Given the sudden rise of L. lineolaris as an economic pest in these states, regionally specific management practices (i.e., chemical and cultural control) are needed to help producers protect yield potential while minimizing input costs. Field experiments were conducted in Virginia and North Carolina in 2018 and 2019 to 1) determine the effects of various management practices on L. lineolaris density, plant injury (i.e., square retention, internal boll injury), and lint yield, 2) calculate the economic trade-offs between integrated pest management (IPM) systems approach and current management practices for L. lineolaris in these states, and 3) evaluate economic benefits associated with various sampling thresholds. Lygus lineolaris populations peaked mid-season (i.e., August) during cotton flowering in both states. Weekly scouting and applying foliar insecticides when the current University Extension recommended economic threshold was reached was the most critical management treatment in maximizing economic returns. Additional costs among various IPM practices did not translate into significant yield protection and economic gains. Moreover, there were additional economic benefits associated with protecting glabrous and longer maturing varieties in Virginia. Lygus lineolaris density varied significantly between states; therefore, management recommendations should be modified based on the growing region. Results from this study will be used to create an IPM strategy to help cotton producers effectively manage this insect pest in the Southeast. DA - 2020/7/1/ PY - 2020/7/1/ DO - 10.1093/jee/toaa142 VL - 113 IS - 5 SP - 2223-2234 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/toaa142 DB - Crossref KW - tarnished plant bug KW - cotton KW - economic threshold KW - IPM ER - TY - JOUR TI - Disease control across urban–rural gradients AU - Wells, Konstans AU - Lurgi, Miguel AU - Collins, Brendan AU - Lucini, Biagio AU - Kao, Rowland R. AU - Lloyd, Alun L. AU - Frost, Simon D. W. AU - Gravenor, Mike B. T2 - Journal of The Royal Society Interface AB - Controlling the regional re-emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after its initial spread in ever-changing personal contact networks and disease landscapes is a challenging task. In a landscape context, contact opportunities within and between populations are changing rapidly as lockdown measures are relaxed and a number of social activities re-activated. Using an individual-based metapopulation model, we explored the efficacy of different control strategies across an urban–rural gradient in Wales, UK. Our model shows that isolation of symptomatic cases or regional lockdowns in response to local outbreaks have limited efficacy unless the overall transmission rate is kept persistently low. Additional isolation of non-symptomatic infected individuals, who may be detected by effective test-and-trace strategies, is pivotal to reducing the overall epidemic size over a wider range of transmission scenarios. We define an ‘urban–rural gradient in epidemic size' as a correlation between regional epidemic size and connectivity within the region, with more highly connected urban populations experiencing relatively larger outbreaks. For interventions focused on regional lockdowns, the strength of such gradients in epidemic size increased with higher travel frequencies, indicating a reduced efficacy of the control measure in the urban regions under these conditions. When both non-symptomatic and symptomatic individuals are isolated or regional lockdown strategies are enforced, we further found the strongest urban–rural epidemic gradients at high transmission rates. This effect was reversed for strategies targeted at symptomatic individuals only. Our results emphasize the importance of test-and-trace strategies and maintaining low transmission rates for efficiently controlling SARS-CoV-2 spread, both at landscape scale and in urban areas. DA - 2020/12// PY - 2020/12// DO - 10.1098/rsif.2020.0775 VL - 17 IS - 173 SP - 20200775 UR - https://doi.org/10.1098/rsif.2020.0775 KW - disease spread KW - epidemiological metapopulation dynamics KW - pandemic control KW - source-sink dynamics ER - TY - JOUR TI - Relative utility of agronomic, phenological, and morphological traits for assessing genotype-by-environment interaction in maize inbreds AU - Falcon, C.M. AU - Kaeppler, S.M. AU - Spalding, E.P. AU - Miller, N.D. AU - Haase, N. AU - AlKhalifah, N. AU - Bohn, M. AU - Buckler, E.S. AU - Campbell, D.A. AU - Ciampitti, I. AU - Coffey, L. AU - Edwards, J. AU - Ertl, D. AU - Flint-Garcia, S. AU - Gore, M.A. AU - Graham, C. AU - Hirsch, C.N. AU - Holland, J.B. AU - Jarquín, D. AU - Knoll, J. AU - Lauter, N. AU - Lawrence-Dill, C.J. AU - Lee, E.C. AU - Lorenz, A. AU - Lynch, J.P. AU - Murray, S.C. AU - Nelson, R. AU - Romay, M.C. AU - Rocheford, T. AU - Schnable, P.S. AU - Scully, B. AU - Smith, M. AU - Springer, N. AU - Tuinstra, M.R. AU - Walton, R. AU - Weldekidan, T. AU - Wisser, R.J. AU - Xu, W. AU - Leon, N. T2 - Crop Science AB - Abstract Plant breeders face the challenge of genotype × environment interaction (G × E) in comprehensively breeding for expanded geographic regions. An improved understanding of G × E sensitivity of traits and the environmental features that effectively discriminate among genotypes will enable more efficient breeding efforts. In this study of 31 maize ( Zea mays L.) inbreds grown in 36 environments that are part of the Genomes to Fields Initiative, we measured 14 traits, including flowering date, height, and yield components (i.e., ear and kernel dimensions) to (i) identify traits that are the most sensitive indicators of G × E; (ii) determine how geographic location and weather factors influence environments’ discriminability of inbreds; and (iii) detect patterns of stability in better and worse discriminating environments. Genotype × environment interaction explained between 9.0–20.4% of the phenotypic variance with greater effects in the yield‐component traits. Discriminability of environments varied by trait. Midwest locations (where 26 of the 31 inbreds were developed) were among the most discriminating environments for more traits, while environments in the West and East tended to be less discriminating. Weather factors during silking were significantly different between the most and least discriminating environments more often than average weather across the season or during the period from planting to silking. Stability of genotypes varied by trait, and performance was usually not correlated with stability. The dissection of complex traits, such as yield into component traits, appears to be a useful approach to understand how environmental factors differentially affect phenotype. DA - 2020/// PY - 2020/// DO - 10.1002/csc2.20035 VL - 60 IS - 1 SP - 62-81 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85078817946&partnerID=MN8TOARS ER - TY - JOUR TI - Maize genomes to fields (G2F): 2014-2017 field seasons: Genotype, phenotype, climatic, soil, and inbred ear image datasets AU - McFarland, B.A. AU - Alkhalifah, N. AU - Bohn, M. AU - Bubert, J. AU - Buckler, E.S. AU - Ciampitti, I. AU - Edwards, J. AU - Ertl, D. AU - Gage, J.L. AU - Falcon, C.M. AU - Flint-Garcia, S. AU - Gore, M.A. AU - Graham, C. AU - Hirsch, C.N. AU - Holland, J.B. AU - Hood, E. AU - Hooker, D. AU - Jarquin, D. AU - Kaeppler, S.M. AU - Knoll, J. AU - Kruger, G. AU - Lauter, N. AU - Lee, E.C. AU - Lima, D.C. AU - Lorenz, A. AU - Lynch, J.P. AU - McKay, J. AU - Miller, N.D. AU - Moose, S.P. AU - Murray, S.C. AU - Nelson, R. AU - Poudyal, C. AU - Rocheford, T. AU - Rodriguez, O. AU - Romay, M.C. AU - Schnable, J.C. AU - Schnable, P.S. AU - Scully, B. AU - Sekhon, R. AU - Silverstein, K. AU - Singh, M. AU - Smith, M. AU - Spalding, E.P. AU - Springer, N. AU - Thelen, K. AU - Thomison, P. AU - Tuinstra, M. AU - Wallace, J. AU - Walls, R. AU - Wills, D. AU - Wisser, R.J. AU - Xu, W. AU - Yeh, C.-T. AU - De Leon, N. T2 - BMC Research Notes AB - Abstract Objectives Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F’s genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014–2017. Data description Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported. The 2014 and 2015 datasets are updated versions from the previously released files [1] while 2016 and 2017 datasets are newly available to the public. DA - 2020/// PY - 2020/// DO - 10.1186/s13104-020-4922-8 VL - 13 IS - 1 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85079338248&partnerID=MN8TOARS KW - Maize KW - Genome KW - Genotype KW - GBS KW - G x E KW - Hybrid KW - Inbred KW - Phenotype KW - Environment KW - Field metadata ER - TY - JOUR TI - Association mapping and genomic prediction for ear rot disease caused by Fusarium verticillioides in a tropical maize germplasm AU - Kuki, Mauricio Carlos AU - Barth Pinto, Ronald Jose AU - Bengosi Bertagna, Filipe Augusto AU - Tessmann, Dauri Jose AU - Amaral Junior, Antonio Teixeira AU - Scapim, Carlos Alberto AU - Holland, James Brendan T2 - CROP SCIENCE AB - Abstract Fusarium ear rot (FER), caused by Fusarium verticillioides (Sacc.) Nirenberg, is one of the major ear diseases that affect both yield and grain quality in maize ( Zea mays L.), especially in tropical environments. Fusarium genetic resistance is a complex trait, controlled by several small‐effect genes and strongly influenced by the environment. We applied a comprehensive genome‐wide association study and genomic prediction for ear rot and starburst symptoms, using 291,633 high‐quality single nucleotide polymorphism (SNPs) markers in 320 tropical maize inbred lines, in two distinct locations in Brazil's southern region. Three SNPs were significantly associated with starburst symptoms, each associated with 6–8% of the phenotypic variance, and with gene models that have expression levels in ears, pericarp, and kernels, corresponding to disease infection period and suggesting some role in FER resistance. No significant SNP was associated with FER, which is an indication that the genetic architecture for this trait is highly polygenic, with potentially many variants having small effects that are not detectable in the association mapping analysis. We observed genomic prediction accuracies ranging from 0.34 to 0.4 for FER and starburst, respectively. Further research is required to validate these significant SNPs and their relationship to genes affecting FER resistance, and also to improve genomic prediction accuracies across different genetic backgrounds. DA - 2020/// PY - 2020/// DO - 10.1002/csc2.20272 VL - 60 IS - 6 SP - 2867-2881 SN - 1435-0653 UR - https://doi.org/10.1002/csc2.20272 ER - TY - JOUR TI - Heterosis of leaf and rhizosphere microbiomes in field‐grown maize AU - Wagner, Maggie R. AU - Roberts, Joseph H. AU - Balint‐Kurti, Peter AU - Holland, James B. T2 - New Phytologist AB - Summary Macroorganisms’ genotypes shape their phenotypes, which in turn shape the habitat available to potential microbial symbionts. This influence of host genotype on microbiome composition has been demonstrated in many systems; however, most previous studies have either compared unrelated genotypes or delved into molecular mechanisms. As a result, it is currently unclear whether the heritability of host‐associated microbiomes follows similar patterns to the heritability of other complex traits. We take a new approach to this question by comparing the microbiomes of diverse maize inbred lines and their F 1 hybrid offspring, which we quantified in both rhizosphere and leaves of field‐grown plants using 16S‐v4 and ITS1 amplicon sequencing. We show that inbred lines and hybrids differ consistently in the composition of bacterial and fungal rhizosphere communities, as well as leaf‐associated fungal communities. A wide range of microbiome features display heterosis within individual crosses, consistent with patterns for nonmicrobial maize phenotypes. For leaf microbiomes, these results were supported by the observation that broad‐sense heritability in hybrids was substantially higher than narrow‐sense heritability. Our results support our hypothesis that at least some heterotic host traits affect microbiome composition in maize. DA - 2020/11// PY - 2020/11// DO - 10.1111/nph.16730 VL - 228 IS - 3 SP - 1055-1069 UR - https://doi.org/10.1111/nph.16730 KW - heterosis KW - hybridization KW - maize KW - microbiome KW - phyllosphere KW - rhizosphere ER - TY - JOUR TI - Genetic variation for response to mixed triazole and strobilurin application in diverse maize AU - Woore, Matthew Smith AU - Holland, James Brendan T2 - Agrosystems, Geosciences & Environment AB - Abstract Strobilurin and triazole classes of fungicides have been reported to have growth‐regulating effects on crops in the absence of their target pathogens and to increase maize yield. Because the response of maize ( Zea mays L.) plants to a commercially marketed mixture of strobilurin and triazole may not be uniform across genotypes, it may be possible to breed selectively for higher yield responses to application of this chemical treatment. To test this hypothesis, diverse samples of maize inbred lines and hybrids were evaluated for response to a combined mixture of a treatment of strobilurin and triazole. Main effects of treatment and genotype and treatment × genotype interactions were measured on agronomic traits including grain yield and several yield components, lodging, and delayed leaf senescence. Hybrid and inbred genotype main effect variation was significant for all measured traits. Favorable main effects of strobilurin and triazole treatment were observed only for leaf senescence and foliar disease, and genotype × treatment interactions were not significant for yield or yield components. Yield was significantly increased only in two inbred varieties and did not correlate with any known pedigree or genetic relationships. These results suggest that breeding to enhance the response to strobilurin and triazole treatment is not likely to be effective in maize. DA - 2020/1// PY - 2020/1// DO - 10.1002/agg2.20054 VL - 3 IS - 1 UR - https://doi.org/10.1002/agg2.20054 ER - TY - JOUR TI - Genomic prediction for resistance to Fusarium ear rot and fumonisin contamination in maize AU - Holland, James B. AU - Marino, Thiago P. AU - Manching, Heather C. AU - Wisser, Randall J. T2 - CROP SCIENCE AB - Abstract Fusarium ear rot (FER) disease of maize ( Zea mays L.) is caused by Fusarium verticillioides (Sacc.) Nirenberg, which produces fumonisin (FUM), a mycotoxin linked to human and animal health risks. Extensive field trials, laborious inoculations and ear evaluations, and expensive antibody assays are required to reliably assess resistances to FER and FUM contamination in breeding populations. To evaluate the potential utility of genomic selection (GS) to improve FER and FUM in maize, we genotyped 6086 single nucleotide polymorphisms (SNPs) on 449 S 0:1 lines from a recurrent selection population. Two different partitions of the S 0:1 evaluation data were made to test the ability of models trained on 251 or 201 lines evaluated at three locations in 2014–2015 to predict FER and FUM of 198 or 248 different lines evaluated at three locations in 2016. Single‐stage univariate and multivariate genomic best linear unbiased predictor (GBLUP) models and two‐stage GBLUP, Bayes Cπ, Bayesian LASSO, and extreme gradient boosting models were compared for prediction. Maximum prediction accuracy for untested lines in a new year was 0.46 for FER and 0.67 for FUM. Bayesian models optimized for predicting traits influenced by major‐effect loci were best for FUM in one set, despite no evidence for significant individual SNP–trait associations from genome‐wide association study (GWAS) in the training sets; otherwise, GBLUP models were best. These results suggest that GS can help improve resistance to FER and FUM contamination in an applied breeding program. DA - 2020/// PY - 2020/// DO - 10.1002/csc2.20163 VL - 60 IS - 4 SP - 1863-1875 SN - 1435-0653 UR - https://doi.org/10.1002/csc2.20163 ER - TY - CHAP TI - Neuroenhancement at work: Addressing the ethical, legal and social implications AU - Dubljević, V. AU - McCall, I.C. AU - Illes, J. T2 - Organizational Neuroethics A2 - Trempe-Martineau, J. A2 - Racine, E. AB - Neuroenhancement is associated with a wide range of existing, emerging, and future biomedical technologies that are intended to improve human cognitive performance and mitigate—if not reverse—human error. Neuroenhancement in classrooms, universities, and the military has been discussed at length, but the workplace has been largely omitted from the conversation until now. By providing examples from branches of the commercial market that are rarely linked with cognitive enhancement in the literature, we argue that neuroenhancement at work is likely to become a major challenge in the labor market. Therefore, we focus here on the specific application of neuroenhancements to the workplace. Central issues involve both drugs and devices, some of which are well-trodden ethical concerns while others are novel challenges. We conclude with a brief discussion and outline of a discourage-use policy that has the potential to mitigate the challenges of neuroenhancement at work. PY - 2020/// DO - 10.1007/978-3-030-27177-0_7 SP - 87–103 PB - Springer SN - 9783030271763 ER - TY - JOUR TI - Genotype by environment interaction for gene expression in Drosophila melanogaster AU - Huang, Wen AU - Carbone, Mary Anna AU - Lyman, Richard F. AU - Anholt, Robert R. H. AU - Mackay, Trudy F. C. T2 - NATURE COMMUNICATIONS AB - The genetics of phenotypic responses to changing environments remains elusive. Using whole-genome quantitative gene expression as a model, here we study how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed in different environments (25 °C and 18 °C). We find a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. Genetic variance in expression increases at 18 °C relative to 25 °C for most genes that have a change in genetic variance. Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments are shared and have similar effects, analysis of the environment-specific eQTLs reveals enrichment of binding sites for two transcription factors. Finally, although genotype by environment interaction in gene expression could potentially disrupt genetic networks, the co-expression networks are highly conserved across environments. Genes with higher network connectivity are under stronger stabilizing selection, suggesting that stabilizing selection on expression plays an important role in promoting network robustness. DA - 2020/10/28/ PY - 2020/10/28/ DO - 10.1038/s41467-020-19131-y VL - 11 IS - 1 SP - SN - 2041-1723 ER - TY - CHAP TI - Engineered Gene Drives: Ecological, environmental, and societal concerns AU - Kuzma, J. T2 - GMOs: Implications for Biodiversity Conservation and Ecological Processes A2 - Chaurasia, Anurag A2 - Hawksworth, David L. A2 - Pessoa de Miranda, Manoela PY - 2020/// PB - Springer ER - TY - BOOK TI - Discovery Engineering in Biology: Case studies for grades 6-12 AU - Hite, R. AU - Childers, G. AU - Ennes, M. AU - Jones, M.G. DA - 2020/// PY - 2020/// PB - National Science Teachers Association Press ER - TY - CHAP TI - Connecting underrepresented families to their local environment AU - Ennes, M. AU - Jones, M.G. T2 - Building Community: Twelve Principles for a Healthy Future A2 - Gruber, James PY - 2020/// SP - 249-251 PB - New Society Publishers ER - TY - JOUR TI - Reactions to the National Academies/Royal Society Report on Heritable Human Genome Editing AU - Angrist, Misha AU - Barrangou, Rodolphe AU - Baylis, Francoise AU - Brokowski, Carolyn AU - Burgio, Gaetan AU - Caplan, Arthur AU - Chapman, Carolyn Riley AU - Church, George M. AU - Cook-Deegan, Robert AU - Cwik, Bryan AU - Doudna, Jennifer A. AU - Evans, John H. AU - Greely, Henry T. AU - Hercher, Laura AU - Hurlbut, J. Benjamin AU - Hynes, Richard O. AU - Ishii, Tetsuya AU - Kiani, Samira AU - Lee, LaTasha Hoskins AU - Levrier, Guillaume AU - Liu, David R. AU - Lunshof, Jeantine E. AU - Macintosh, Kerry Lynn AU - Mathews, Debra J. H. AU - Meslin, Eric M. AU - Mills, Peter H. R. AU - Montoliu, Lluis AU - Musunuru, Kiran AU - Nicol, Dianne AU - O'Neill, Helen AU - Qiu, Renzong AU - Ranisch, Robert AU - Sherkow, Jacob S. AU - Soni, Sheetal AU - Terry, Sharon AU - Topol, Eric AU - Williamson, Robert AU - Zhang, Feng AU - Davies, Kevin T2 - CRISPR JOURNAL AB - In September 2020, a detailed report on Heritable Human Genome Editing was published. The report offers a translational pathway for the limited approval of germline editing under limited circumstances and assuming various criteria have been met. In this perspective, some three dozen experts from the fields of genome editing, medicine, bioethics, law, and related fields offer their candid reactions to the National Academies/Royal Society report, highlighting areas of support, omissions, disagreements, and priorities moving forward. DA - 2020/10// PY - 2020/10// DO - 10.1089/crispr.2020.29106.man VL - 3 IS - 5 SP - 332-349 SN - 2573-1602 ER - TY - JOUR TI - In Vitro Validation of Transgene Expression in Gene-Edited Pias Using CRISPR Transcriptional Activators AU - Polkoff, Kathryn M. AU - Chung, Jaewook AU - Simpson, Sean G. AU - Gleason, Katherine AU - Piedrahita, Jorge A. T2 - CRISPR JOURNAL AB - The use of CRISPR-Cas and RNA-guided endonucleases has drastically changed research strategies for understanding and exploiting gene function, particularly for the generation of gene-edited animal models. This has resulted in an explosion in the number of gene-edited species, including highly biomedically relevant pig models. However, even with error-free DNA insertion or deletion, edited genes are occasionally not expressed and/or translated as expected. Therefore, there is a need to validate the expression outcomes gene modifications in vitro before investing in the costly generation of a gene-edited animal. Unfortunately, many gene targets are tissue specific and/or not expressed in cultured primary cells, making validation difficult without generating an animal. In this study, using pigs as a proof of concept, we show that CRISPR-dCas9 transcriptional activators can be used to validate functional transgene insertion in nonexpressing easily cultured cells such as fibroblasts. This is a tool that can be used across disciplines and animal species to save time and resources by verifying expected outcomes of gene edits before generating live animals. DA - 2020/10// PY - 2020/10// DO - 10.1089/crispr.2020.0037 VL - 3 IS - 5 SP - 409-418 SN - 2573-1602 ER - TY - JOUR TI - How Public Opinion Can Inform Cognitive Enhancement Regulation AU - McCall, Iris Coates AU - McIntosh, Tristan AU - Dubljević, Veljko T2 - AJOB Neuroscience AB - In the target article “Public Opinion on Cognitive Enhancement Varies Across Different Situations,” the authors explore the effect of metaphor framing, the cognitive enhancement (CE) context (stude... DA - 2020/10/1/ PY - 2020/10/1/ DO - 10.1080/21507740.2020.1830881 UR - https://doi.org/10.1080/21507740.2020.1830881 ER - TY - JOUR TI - Microbial Interactions Within Multiple-Strain Biological Control Agents Impact Soil-Borne Plant Disease AU - Niu, Ben AU - Wang, Weixiong AU - Yuan, Zhibo AU - Sederoff, Ronald R. AU - Sederoff, Heike AU - Chiang, Vincent L. AU - Borriss, Rainer T2 - FRONTIERS IN MICROBIOLOGY AB - Major losses of crop yield and quality caused by soil-borne plant diseases have long threatened the ecology and economy of agriculture and forestry. Biological control using beneficial microorganisms has become more popular for management of soil-borne pathogens as an environmentally friendly method for protecting plants. Two major barriers limiting the disease-suppressive functions of biocontrol microbes are inadequate colonization of hosts and inefficient inhibition of soil-borne pathogen growth, due to biotic and abiotic factors acting in complex rhizosphere environments. Use of a consortium of microbial strains with disease inhibitory activity may improve the biocontrol efficacy of the disease-inhibiting microbes. The mechanisms of biological control are not fully understood. In this review, we focus on bacterial and fungal biocontrol agents to summarize the current state of the use of single strain and multi-strain biological control consortia in the management of soil-borne diseases. We discuss potential mechanisms used by microbial components to improve the disease suppressing efficacy. We emphasize the interaction-related factors to be considered when constructing multiple-strain biological control consortia and propose a workflow for assembling them by applying a reductionist synthetic community approach. DA - 2020/10/9/ PY - 2020/10/9/ DO - 10.3389/fmicb.2020.585404 VL - 11 SP - SN - 1664-302X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85094139988&partnerID=MN8TOARS KW - microbial interaction KW - biological control agents KW - soil-borne disease KW - consortia KW - microbiome and community ER - TY - JOUR TI - A Five-Year Engagement AU - Kinchy, Abby J. AU - Parthasarathy, Shobita AU - Delborne, Jason T2 - Engaging Science, Technology, and Society AB - In this editorial essay, Abby Kinchy, Shobita Parthasarathy, and Jason Delborne look back at the editorial and publishing practices of the first five years of the journal Engaging Science, Technology, and Society (ESTS), the open access journal of The Society for Social Studies of Science (4S). As three members of the inaugural ESTS Editorial Board, Kinchy, Parthasarathy, and Delborne reflect on what they value in academic practice, including publishing, and consider some of the highlights and accomplishments of ESTS’s first five years (2015-2020). DA - 2020/10/24/ PY - 2020/10/24/ DO - 10.17351/ests2020.749 VL - 6 SP - 411 J2 - Engaging STS OP - SN - 2413-8053 UR - http://dx.doi.org/10.17351/ests2020.749 DB - Crossref ER - TY - JOUR TI - Development of a genetic framework to improve the efficiency of bioactive delivery from blueberry AU - Mengist, Molla F. AU - Burtch, Haley AU - Debelo, Hawi AU - Pottorff, Marti AU - Bostan, Hamed AU - Nunn, Candace AU - Corbin, Sydney AU - Kay, Colin D. AU - Bassil, Nahla AU - Hummer, Kim AU - Lila, Mary Ann AU - Ferruzzi, Mario G. AU - Iorizzo, Massimo T2 - SCIENTIFIC REPORTS AB - In the present study, we applied a novel high-throughput in vitro gastrointestinal digestion model to phenotype bioaccessibility of phenolics in a diverse germplasm collection representing cultivated highbush blueberries. Results revealed significant (P < 0.05) differences between accessions, years, and accession by year interaction for relative and absolute bioaccessibility of flavonoids and phenolic acids. Broad sense heritability estimates revealed low to moderate inheritances of relative and absolute bioaccessibility, suggesting that besides environmental variables, genetics factors could control bioaccessibility of phenolics. Acylated anthocyanins had significantly higher relative bioaccessibility than non-acylated anthocyanins. Correlation analysis indicated that relative bioaccessibility did not show significant association with fruit quality or raw concentration of metabolites. The study also identified accessions that have high relative and absolute bioaccessibility values. Overall, combining the bioaccessibility of phenolics with genetic and genomic approaches will enable the identification of genotypes and genetic factors influencing these traits in blueberry. DA - 2020/10/14/ PY - 2020/10/14/ DO - 10.1038/s41598-020-74280-w VL - 10 IS - 1 SP - SN - 2045-2322 ER - TY - JOUR TI - Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid AU - Brandt, Katelyn AU - Barrangou, Rodolphe T2 - BMC Microbiology AB - Abstract Background Microbiome and metagenomic studies have given rise to a new understanding of microbial colonization of various human tissues and their ability to impact our health. One human microbiome growing in notoriety, the vaginal microbiome, stands out given its importance for women’s health, and is peculiar in terms of its relative bacterial composition, including its simplicity and typical domination by a small number of Lactobacillus species. The loss of Lactobacillus dominance is associated with disorders such as bacterial vaginosis, and efforts are now underway to understand the ability of Lactobacillus species to colonize the vaginal tract and adapt to this dynamic and acidic environment. Here, we investigate how various Lactobacillus species often isolated from the vaginal and intestinal cavities genomically and transcriptionally respond to iterative growth in simulated vaginal fluid. Results We determined the genomes and transcriptomes of L. acidophilus, L. crispatus, L. fermentum, L. gasseri, and L. jensenii and compared profiles after 50, 100, 500, and 1000 generations of iterative passages in synthetic vaginal fluid. In general, we identified relatively few genetic changes consisting of single nucleotide polymorphisms, with higher counts occurring more frequently in non-vaginal isolated species. Transcriptional profiles were more impacted over time and tended to be more extensive for species that typically do not dominate the vaginal tract, reflecting a more extensive need to adapt to a less familiar environment. Conclusions This study provides insights into how vaginal and non-vaginal Lactobacillus species respond and adapt to a simulated vaginal environment. Overall, trends indicate high genomic stability for all species involved, with more variability in the transcriptome especially for non-dominant species of the vaginal tract. DA - 2020/12// PY - 2020/12// DO - 10.1186/s12866-020-02027-8 VL - 20 IS - 1 UR - https://doi.org/10.1186/s12866-020-02027-8 KW - Lactobacillus KW - Vaginal KW - Passages KW - Probiotics ER - TY - JOUR TI - Genome-enabled insights into the biology of thrips as crop pests AU - Rotenberg, Dorith AU - Baumann, Aaron A. AU - Ben-Mahmoud, Sulley AU - Christiaens, Olivier AU - Dermauw, Wannes AU - Ioannidis, Panagiotis AU - Jacobs, Chris G. C. AU - Vargas Jentzsch, Iris M. AU - Oliver, Jonathan E. AU - Poelchau, Monica F. AU - Rajarapu, Swapna Priya AU - Schneweis, Derek J. AU - Snoeck, Simon AU - Taning, Clauvis N. T. AU - Wei, Dong AU - Widana Gamage, Shirani M. K. AU - Hughes, Daniel S. T. AU - Murali, Shwetha C. AU - Bailey, Samuel T. AU - Bejerman, Nicolas E. AU - Holmes, Christopher J. AU - Jennings, Emily C. AU - Rosendale, Andrew J. AU - Rosselot, Andrew AU - Hervey, Kaylee AU - Schneweis, Brandi A. AU - Cheng, Sammy AU - Childers, Christopher AU - Simao, Felipe A. AU - Dietzgen, Ralf G. AU - Chao, Hsu AU - Dinh, Huyen AU - Doddapaneni, Harsha Vardhan AU - Dugan, Shannon AU - Han, Yi AU - Lee, Sandra L. AU - Muzny, Donna M. AU - Qu, Jiaxin AU - Worley, Kim C. AU - Benoit, Joshua B. AU - Friedrich, Markus AU - Jones, Jeffery W. AU - Panfilio, Kristen A. AU - Park, Yoonseong AU - Robertson, Hugh M. AU - Smagghe, Guy AU - Ullman, Diane E. AU - Zee, Maurijn AU - Van Leeuwen, Thomas AU - Veenstra, Jan A. AU - Waterhouse, Robert M. AU - Weirauch, Matthew T. AU - Werren, John H. AU - Whitfield, Anna E. AU - Zdobnov, Evgeny M. AU - Gibbs, Richard A. AU - Richards, Stephen T2 - BMC BIOLOGY AB - Abstract Background The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. Conclusions Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species. DA - 2020/10/19/ PY - 2020/10/19/ DO - 10.1186/s12915-020-00862-9 VL - 18 IS - 1 SP - SN - 1741-7007 KW - Thysanoptera KW - Western flower thrips KW - Hemipteroid assemblage KW - Insect genomics KW - Tospovirus KW - Salivary glands KW - Chemosensory receptors KW - Opsins KW - Detoxification KW - Innate immunity ER - TY - JOUR TI - Large losses of ammonium-nitrogen from a rice ecosystem under elevated CO2 AU - Xu, Chenchao AU - Zhang, Kaihang AU - Zhu, Wanying AU - Xiao, Jing AU - Zhu, Chen AU - Zhang, Naifang AU - Yu, Fangjian AU - Li, Shuyao AU - Zhu, Chunwu AU - Tu, Qichao AU - Chen, Xin AU - Zhu, Jianguo AU - Hu, Shuijin AU - Koide, Roger T. AU - Firestone, Mary K. AU - Cheng, Lei T2 - SCIENCE ADVANCES AB - Carbon dioxide enrichment facilitates nitrogen loss through anaerobic oxidation of ammonium coupled to the reduction of iron. DA - 2020/10// PY - 2020/10// DO - 10.1126/sciadv.abb7433 VL - 6 IS - 42 SP - SN - 2375-2548 ER - TY - JOUR TI - Mechanisms of Soybean Host-Plant Resistance Against Megacopta cribraria (Hemiptera: Plataspidae) AU - Lahiri, S AU - Reisig, D D AU - Dean, Lisa L AU - Reay-Jones, F P F AU - Greene, J K AU - Carter, T E, Jr AU - Mian, R AU - Fallen, B D T2 - Environmental Entomology AB - Abstract A number of soybean varieties traditionally bred for resistance to various soybean arthropod pests have been identified as resistant to Megacopta cribraria (F.) (Hemiptera: Plataspidae). However, the mechanisms of host-plant resistance (HPR) in this system are not understood. The goal of this study was to identify the mechanisms of resistance by examining the role of plant volatile organic compounds (VOCs) and free amino acids (FAAs) among 16 soybean varieties. Choice and no-choice cage experiments identified several soybean varieties that demonstrated antixenosis as well as antibiosis. However, resistance varied over time in certain soybean varieties, such as N02-7002 and PI567352B. Mean nymph number from choice experiments had positive correlations with the FAAs asparagine, tryptophan, alanine, phenylanaline, and serine; negative correlation with leucine and threonine. Four plant volatiles, hexanal, 2-pentylfuran, beta-cyclocitral, and cis-9-hexadecenal, were positively correlated with subsequent nymph development, whereas n-hexadecenoic acid was negatively correlated with nymph number only, in adult choice cage experiments. This study contributes to understanding the mechanisms of HPR through associations with plant VOCs and FAAs in relation to M. cribraria development and provides useful knowledge for developing soybean varieties for M. cribraria management. DA - 2020/7/5/ PY - 2020/7/5/ DO - 10.1093/ee/nvaa075 VL - 49 IS - 4 SP - 876-885 LA - en OP - SN - 0046-225X 1938-2936 UR - http://dx.doi.org/10.1093/ee/nvaa075 DB - Crossref KW - antixenosis KW - antibiosis KW - volatile organic compounds KW - free amino acids ER - TY - JOUR TI - Integrating emergence and phenology models to determine windows of action for weed control: A case study using Senna obtusifolia AU - Piskackova, Theresa A. Reinhardt AU - Reberg-Horton, Chris AU - Richardson, Robert J. AU - Jennings, Katie M. AU - Leon, Ramon G. T2 - FIELD CROPS RESEARCH AB - The success of integrated weed management strategies is contingent on the accuracy of control actions in both time and space. While emphasis has been given to spatial accuracy, timing accuracy has been largely neglected. Weed control timing must consider not only the total duration of weed interference with the crop, as done by the traditional critical period of weed control (CPWC) based on yield protection only, but also weed growth, size, and susceptible phenological stages. In this study, we expand upon the idea of using weed emergence models for timing weed control by integrating them with phenology probability models for key weed growth stages to optimize timing of control actions, here referred as Critical Control Windows (CCW). Combining the CCW with thresholds for yield loss due to weed interference and thresholds for weed survival risk makes it possible determining the frequency with which control actions should be implemented to maintain crop yield and weed populations at desired levels. Using Senna obtusifolia as a study case, vegetative and reproductive phenological stages were modeled as a function of seedling emergence for different cohorts. Chronological and thermal-time models provided robust predictions of S. obtusifolia phenology. CCW did not always coincided with CPWC for several crops when considering 10-cm tall plants as the threshold for control. In general, for summer row crops, CCW required 2 postemergence control actions and sometimes 1 action outside the CPWC. The results of the present research illustrate how predictive models can be used to develop CCW that will complement the traditional CPWC. These two concepts when used complementary can increase not only timing accuracy, but also efficiency of weed control. DA - 2020/11/1/ PY - 2020/11/1/ DO - 10.1016/j.fcr.2020.107959 VL - 258 SP - SN - 1872-6852 KW - Weed predictive modeling KW - Thermal time KW - Hydrothermal time KW - Vulnerable stages KW - Integrated weed management KW - Critical period of weed control ER - TY - JOUR TI - Carrot Anthocyanins Genetics and Genomics: Status and Perspectives to Improve Its Application for the Food Colorant Industry AU - Iorizzo, Massimo AU - Curaba, Julien AU - Pottorff, Marti AU - Ferruzzi, Mario G. AU - Simon, Philipp AU - Cavagnaro, Pablo F. T2 - GENES AB - Purple or black carrots (Daucus carota ssp. sativus var. atrorubens Alef) are characterized by their dark purple- to black-colored roots, owing their appearance to high anthocyanin concentrations. In recent years, there has been increasing interest in the use of black carrot anthocyanins as natural food dyes. Black carrot roots contain large quantities of mono-acylated anthocyanins, which impart a measure of heat-, light- and pH-stability, enhancing the color-stability of food products over their shelf-life. The genetic pathway controlling anthocyanin biosynthesis appears well conserved among land plants; however, different variants of anthocyanin-related genes between cultivars results in tissue-specific accumulations of purple pigments. Thus, broad genetic variations of anthocyanin profile, and tissue-specific distributions in carrot tissues and organs, can be observed, and the ratio of acylated to non-acylated anthocyanins varies significantly in the purple carrot germplasm. Additionally, anthocyanins synthesis can also be influenced by a wide range of external factors, such as abiotic stressors and/or chemical elicitors, directly affecting the anthocyanin yield and stability potential in food and beverage applications. In this study, we critically review and discuss the current knowledge on anthocyanin diversity, genetics and the molecular mechanisms controlling anthocyanin accumulation in carrots. We also provide a view of the current knowledge gaps and advancement needs as regards developing and applying innovative molecular tools to improve the yield, product performance and stability of carrot anthocyanin for use as a natural food colorant. DA - 2020/8// PY - 2020/8// DO - 10.3390/genes11080906 VL - 11 IS - 8 SP - SN - 2073-4425 KW - anthocyanins KW - carrots KW - natural colorant KW - genetics ER - TY - JOUR TI - Evolutionary dynamics of Tomato spotted wilt virus within and between alternate plant hosts and thrips AU - Ruark-Seward, Casey L. AU - Bonville, Brian AU - Kennedy, George AU - Rasmussen, David A. T2 - Scientific Reports AB - Abstract Tomato spotted wilt virus (TSWV) is a generalist pathogen with one of the broadest known host ranges among RNA viruses. To understand how TSWV adapts to different hosts, we experimentally passaged viral populations between two alternate hosts, Emilia sochifolia and Datura stramonium , and an obligate vector in which it also replicates, western flower thrips ( Frankliniella occidentalis ). Deep sequencing viral populations at multiple time points allowed us to track the evolutionary dynamics of viral populations within and between hosts. High levels of viral genetic diversity were maintained in both plants and thrips between transmission events. Rapid fluctuations in the frequency of amino acid variants indicated strong host-specific selection pressures on proteins involved in viral movement (NSm) and replication (RdRp). While several genetic variants showed opposing fitness effects in different hosts, fitness effects were generally positively correlated between hosts indicating that positive rather than antagonistic pleiotropy is pervasive. These results suggest that high levels of genetic diversity together with the positive pleiotropic effects of mutations have allowed TSWV to rapidly adapt to new hosts and expand its host range. DA - 2020/9/25/ PY - 2020/9/25/ DO - 10.1038/s41598-020-72691-3 VL - 10 IS - 1 SP - J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-020-72691-3 DB - Crossref ER - TY - JOUR TI - Contingent organization-public relationship (COPR) matters: reconciling the contingency theory of accommodation into the relationship management paradigm AU - Cheng, Yang T2 - Journal of Public Relations Research AB - Although the relational approach has been a focus in many published public relations studies, the dynamic and longitudinal aspects of relationships deserve more exploration. Through explicating and examining the concept of contingent organization-public relationship (COPR) in two empirical studies, this article investigates relationships between corporations and activist publics, and provides dynamic instances of the value of COPR and its six modes in conflictual situations. By tracking the stances of each corporation and its activists longitudinally through content analysis, results generate the occurrence and changes of relationship modes over time. Findings show that COPR is equally applicable in both resolved and unresolved U.S. conflicts. Regardless of whether the problems were resolved or not, competing relationships occurred more frequently than cooperating relationships, which strengthens the argument that both parties maintain competing relationships for self-interests and may adopt strategies to achieve mutual benefits as well. The integrating of the contingency theory of accommodation into the relationship management paradigm shows great promise reflected in current findings as well as future directions. DA - 2020/7/3/ PY - 2020/7/3/ DO - 10.1080/1062726X.2020.1830405 VL - 32 IS - 3-4 SP - 140-154 J2 - Journal of Public Relations Research LA - en OP - SN - 1062-726X 1532-754X UR - http://dx.doi.org/10.1080/1062726X.2020.1830405 DB - Crossref KW - Contingent organization-public relationship (COPR) KW - content analysis KW - conflict KW - activists KW - corporations KW - relationship mode KW - dynamism ER - TY - JOUR TI - SPARSE BAYESIAN ADDITIVE NONPARAMETRIC REGRESSION WITH APPLICATION TO HEALTH EFFECTS OF PESTICIDES MIXTURES AU - Wei, Ran AU - Reich, Brian J. AU - Hoppin, Jane A. AU - Ghosal, Subhashis T2 - STATISTICA SINICA DA - 2020/1// PY - 2020/1// DO - 10.5705/ss.202017.0315 VL - 30 IS - 1 SP - 55-79 SN - 1996-8507 KW - Additive nonparametric regression KW - Bayesian variable selection KW - continuous shrinkage prior KW - environmental epidemiology KW - posterior consistency ER - TY - JOUR TI - Ethical Aspects of BCI Technology: What Is the State of the Art? AU - Coin, Allen AU - Mulder, Megan AU - Dubljević, Veljko T2 - Philosophies AB - Brain–Computer Interface (BCI) technology is a promising research area in many domains. Brain activity can be interpreted through both invasive and non-invasive monitoring devices, allowing for novel, therapeutic solutions for individuals with disabilities and for other non-medical applications. However, a number of ethical issues have been identified from the use of BCI technology. In this paper, we review the academic discussion of the ethical implications of BCI technology in the last five years. We conclude that some emerging applications of BCI technology—including commercial ventures that seek to meld human intelligence with AI—present new and unique ethical concerns. Further, we seek to understand how academic literature on the topic of BCIs addresses these novel concerns. Similar to prior work, we use a limited sample to identify trends and areas of concern or debate among researchers and ethicists. From our analysis, we identify two key areas of BCI ethics that warrant further research: the physical and psychological effects of BCI technology. Additionally, questions of BCI policy have not yet become a frequent point of discussion in the relevant literature on BCI ethics, and we argue this should be addressed in future work. We provide guiding questions that will help ethicists and policy makers grapple with the most important issues associated with BCI technology. DA - 2020/10/24/ PY - 2020/10/24/ DO - 10.3390/philosophies5040031 UR - https://doi.org/10.3390/philosophies5040031 KW - brain– KW - computer interface (BCI) KW - brain– KW - machine interface (BMI) KW - ethical KW - legal and social Issues (ELSI) KW - neuroethics KW - narrative review ER - TY - JOUR TI - Quantitative trait locus mapping for common scab resistance in a tetraploid potato full-sib population AU - Silva Pereira, Guilherme AU - Mollinari, Marcelo AU - Qu, Xinshun AU - Thill, Christian AU - Zeng, Zhao-Bang AU - Haynes, Kathleen AU - Yencho, G. Craig AB - Abstract Despite the negative impact of common scab ( Streptomyces spp.) to the potato industry, little is known about the genetic architecture of resistance to this bacterial disease in the crop. We evaluated a mapping population (~150 full-sibs) derived from a cross between two tetraploid potatoes (‘Atlantic’ × B1829-5) in three environments (MN11, PA11, ME12) under natural common scab pressure. Three measures to common scab reaction were assessed, namely percentage of scabby tubers, and disease area and lesion indices, which were highly correlated (>0.76). Due to large environmental effect, heritability values were zero for all three traits in MN11, but moderate to high in PA11 and ME12 (0.44~0.79). We identified a single quantitative trait locus (QTL) for lesion index in PA11, ME12 and joint analyses on linkage group 3, explaining 22~30% of the total variation. The identification of QTL haplotypes and candidate genes contributing to disease resistance can support genomics-assisted breeding approaches. DA - 2020/10/25/ PY - 2020/10/25/ DO - 10.1101/2020.10.24.353557 VL - 10 UR - https://doi.org/10.1101/2020.10.24.353557 ER - TY - JOUR TI - Simulation Models on the Ecology and Management of Arable Weeds: Structure, Quantitative Insights, and Applications AU - Bagavathiannan, Muthukumar V. AU - Beckie, Hugh J. AU - Chantre, Guillermo R. AU - Gonzalez-Andujar, Jose L. AU - Leon, Ramon G. AU - Neve, Paul AU - Poggio, Santiago L. AU - Schutte, Brian J. AU - Somerville, Gayle J. AU - Werle, Rodrigo AU - Acker, Rene Van T2 - Agronomy AB - In weed science and management, models are important and can be used to better understand what has occurred in management scenarios, to predict what will happen and to evaluate the outcomes of control methods. To-date, perspectives on and the understanding of weed models have been disjointed, especially in terms of how they have been applied to advance weed science and management. This paper presents a general overview of the nature and application of a full range of simulation models on the ecology, biology, and management of arable weeds, and how they have been used to provide insights and directions for decision making when long-term weed population trajectories are impractical to be determined using field experimentation. While research on weed biology and ecology has gained momentum over the past four decades, especially for species with high risk for herbicide resistance evolution, knowledge gaps still exist for several life cycle parameters for many agriculturally important weed species. More research efforts should be invested in filling these knowledge gaps, which will lead to better models and ultimately better inform weed management decision making. DA - 2020/10/21/ PY - 2020/10/21/ DO - 10.3390/agronomy10101611 VL - 10 IS - 10 SP - 1611 UR - https://doi.org/10.3390/agronomy10101611 KW - weed seedling emergence KW - crop-weed competition KW - weed population dynamics KW - gene flow KW - herbicide resistance KW - decision-support tools KW - predictive models ER - TY - JOUR TI - Complete Genome Sequence of Lactobacillus johnsonii NCK2677, Isolated from Mice AU - O'Flaherty, Sarah AU - Foley, Matthew H. AU - Rivera, Alissa J. AU - Theriot, Casey M. AU - Barrangou, Rodolphe T2 - Microbiology Resource Announcements AB - We report the closed genome sequence of a Lactobacillus johnsonii strain (NCK2677) that was isolated from a cefoperazone-treated mouse model designed for the study of Clostridioides difficile infection. Illumina and Nanopore sequencing reads were assembled into a circular 1,951,416-bp chromosome with a G+C content of 34.7%, containing 1,865 genes. DA - 2020/10/22/ PY - 2020/10/22/ DO - 10.1128/MRA.00918-20 VL - 9 IS - 43 UR - https://doi.org/10.1128/MRA.00918-20 ER - TY - JOUR TI - After the honeymoon, the divorce: Unexpected outcomes of disease control measures against endemic infections AU - Hollingsworth, Brandon AU - Okamoto, Kenichi W. AU - Lloyd, Alun L. T2 - PLOS Computational Biology AB - The lack of effective vaccines for many endemic diseases often forces policymakers to rely on non-immunizing control measures, such as vector control, to reduce the massive burden of these diseases. Controls can have well-known counterintuitive effects on endemic infections, including the honeymoon effect, in which partially effective controls cause not only a greater initial reduction in infection than expected, but also large outbreaks during control resulting from accumulation of susceptibles. Unfortunately, many control measures cannot be maintained indefinitely, and the results of cessation are poorly understood. Here, we examine the results of stopped or failed non-immunizing control measures in endemic settings. By using a mathematical model to compare the cumulative number of cases expected with and without control, we show that deployment of control can lead to a larger total number of infections, counting from the time that control started, than without any control–the divorce effect. This result is directly related to the population-level loss of immunity resulting from non-immunizing controls and is seen in a variety of models when non-immunizing controls are used against an infection that confers immunity. Finally, we examine three control plans for minimizing the magnitude of the divorce effect in seasonal infections and show that they are incapable of eliminating the divorce effect. While we do not suggest stopping control programs that rely on non-immunizing controls, our results strongly argue that the accumulation of susceptibility should be considered before deploying such controls against endemic infections when indefinite use of the control is unlikely. We highlight that our results are particularly germane to endemic mosquito-borne infections, such as dengue virus, both for routine management involving vector control and for field trials of novel control approaches, and in the context of non-pharmaceutical interventions aimed at COVID-19. DA - 2020/10/19/ PY - 2020/10/19/ DO - 10.1371/journal.pcbi.1008292 VL - 16 IS - 10 SP - e1008292 UR - https://doi.org/10.1371/journal.pcbi.1008292 ER - TY - JOUR TI - Crop rotation mitigates impacts of corn rootworm resistance to transgenic Bt corn AU - Carriere, Yves AU - Brown, Zachary AU - Aglasan, Serkan AU - Dutilleul, Pierre AU - Carroll, Matthew AU - Head, Graham AU - Tabashnik, Bruce E. AU - Jorgensen, Peter Sogaard AU - Carroll, Scott P. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Significance The western corn rootworm, a major insect pest in the Midwestern United States, has evolved resistance to genetically engineered corn that produces insecticidal proteins derived from the bacterium Bacillus thuringiensis (Bt). To evaluate tactics for reducing the damage caused by resistant rootworms, we analyzed field data for 2011 to 2016 from Illinois, Iowa, and Minnesota. The frequency of corn fields with severe rootworm damage was reduced by rotating corn with other crops and by not planting the same type of Bt corn year after year in the same field. These results support the EPA’s recommendations to decrease the negative impacts of rootworm resistance to Bt corn by rotating corn with other crops and diversifying the type of Bt corn planted. DA - 2020/8/4/ PY - 2020/8/4/ DO - 10.1073/pnas.2003604117 VL - 117 IS - 31 SP - 18385-18392 SN - 0027-8424 KW - resistance management KW - resistance mitigation KW - landscape analysis ER - TY - JOUR TI - Can the scaling of plant nitrogen to phosphorus be altered by global change? An empirical test AU - Long, Min AU - Zhang, Juanjuan AU - Liu, Zhengyi AU - Zhou, Luyao AU - Su, Fanglong AU - Xiao, Rui AU - Wang, Yi AU - Guo, Hui AU - Hu, Shuijin T2 - JOURNAL OF PLANT ECOLOGY AB - Abstract Aims Global change may cause unparalleled supplies of soil nutrients and further lead to stoichiometric imbalance of nitrogen (N) and phosphorus (P) in terrestrial plants. While previous studies had reported the effects of global change factors on plant N, P contents and their ratios, few had examined whether or how these factors may influence the scaling of these two elements. Methods Taking advantage of a manipulative experiment with altered precipitation, warming and N addition, and using the general scaling function N = βPα, we examined how the scaling of plant N to P may respond to global change factors in a Loess grassland in northwestern China. Important Findings We found that precipitation reduction (PR) and warming decreased plant P concentrations, while N addition increased plant N concentrations, resulting in increased N:P ratios. The slopes of the linear regressions between plant N and P (i.e. log-transformed N versus P) did not change significantly, whereas the intercepts increased significantly under PR, warming and N addition. These results indicate that global change factors may not affect the synergistic variation of plant N and P, showing a closely coupled relationship between them. Our findings may help to better understand plant nutrient dynamics and element balance in a changing world. DA - 2020/8// PY - 2020/8// DO - 10.1093/jpe/rtaa032 VL - 13 IS - 4 SP - 442-449 SN - 1752-993X KW - climate change KW - element coupling KW - N addition KW - nutrient cycling KW - stoichiometry ER - TY - JOUR TI - Editorial: Interdisciplinary Approaches to Improve Quality of Soft Fruit Berries AU - Farneti, Brian AU - Emanuelli, Francesco AU - Giongo, Lara AU - Toivonen, Peter AU - Iorizzo, Massimo AU - Folta, Kevin AU - Finn, Chad T2 - FRONTIERS IN PLANT SCIENCE AB - EDITORIAL article Front. Plant Sci., 10 September 2020Sec. Crop and Product Physiology Volume 11 - 2020 | https://doi.org/10.3389/fpls.2020.592222 DA - 2020/9/10/ PY - 2020/9/10/ DO - 10.3389/fpls.2020.592222 VL - 11 SP - SN - 1664-462X KW - quality KW - breeding KW - omics analyses KW - vaccinium KW - rubus KW - fragaria KW - postharvest KW - nutraceutical ER - TY - JOUR TI - Short-Term, Large-Area Survey of ContainerAedes spp. (Diptera: Culicidae): Presence and Abundance is Associated with Fine-scale Landscape Factors in North Carolina, USA AU - Reiskind, Michael H. AU - Styers, Diane M. AU - Hayes, Isaac AU - Richards, Stephanie L. AU - Doyle, Michael S. AU - Reed, Emily M. X. AU - Hollingsworth, Brandon AU - Byrd, Brian D. T2 - ENVIRONMENTAL HEALTH INSIGHTS AB - Container Aedes mosquitoes are responsible for the transmission of anthroponotic and zoonotic viruses to people. The surveillance and control of these mosquitoes is an important part of public health protection and prevention of mosquito-borne disease. In this study, we surveyed 327 sites over 2 weeks in late June and early July in 2017 in North Carolina, USA for the presence and abundance of Aedes spp. eggs in an effort to better target potential Ae. aegypti collections. We examined the ability of 2 types of landscape data, Light Detection And Ranging (LIDAR) and National Land Cover Database (NLCD) to explain the presence and abundance of eggs using principal component analysis to deal with collinearity, followed by generalized linear regression. We explained variation of both egg presence and abundance for Aedes albopictus (Skuse) and Aedes triseriatus (Say) using both NLCD and LIDAR data. However, the ability to make robust predictions was limited by variation in the data. Increased sampling time and better landscape data would likely improve the predictive ability of our models, as would a better understanding of oviposition behavior. DA - 2020/9// PY - 2020/9// DO - 10.1177/1178630220952806 VL - 14 SP - SN - 1178-6302 UR - http://dx.doi.org/10.1177/1178630220952806 KW - Light detection and ranging KW - LIDAR KW - Aedes albopictus KW - mosquito ecology ER - TY - JOUR TI - Social science and infrastructure networks and the human-technology interface AU - Berube, D. M. AU - Bogomoletc, E. AU - Eng, N. AU - Jones, J. L. AU - Jokerst, N. T2 - JOURNAL OF NANOPARTICLE RESEARCH DA - 2020/9/23/ PY - 2020/9/23/ DO - 10.1007/s11051-020-05022-2 VL - 22 IS - 9 SP - SN - 1572-896X UR - https://doi.org/10.1007/s11051-020-05022-2 KW - Assessment KW - Societal and ethical implications KW - Nanotechnology infrastructure network KW - National Nanotechnology Coordinating Infrastructure (NNCI) KW - Research Triangle Nanotechnology Network (RTNN) KW - Deep assessment KW - Grounded theory ER - TY - JOUR TI - Derivation of stable embryonic stem cell-like, but transcriptionally heterogenous, induced pluripotent stem cells from non-permissive mouse strains AU - Garbutt, Tiffany A. AU - Konganti, Kranti AU - Konneker, Thomas AU - Hillhouse, Andrew AU - Phelps, Drake AU - Jones, Alexis AU - Aylor, David AU - Threadgill, David W. T2 - MAMMALIAN GENOME AB - Genetic background is known to play a role in the ability to derive pluripotent, embryonic stem cells (ESC), a trait referred to as permissiveness. Previously we demonstrated that induced pluripotent stem cells (iPSC) can be readily derived from non-permissive mouse strains by addition of serum-based media supplemented with GSK3B and MEK inhibitors, termed 2iS media, 3 days into reprogramming. Here, we describe the derivation of second type of iPSC colony from non-permissive mouse strains that can be stably maintained independently of 2iS media. The resulting cells display transcriptional heterogeneity similar to that observed in ESC from permissive genetic backgrounds derived in conventional serum containing media supplemented with leukemia inhibitor factor. However, unlike previous studies that report exclusive subpopulations, we observe both exclusive and simultaneous expression of naive and primed cell surface markers. Herein, we explore shifts in pluripotency in the presence of 2iS and characterize heterogenous subpopulations to determine their pluripotent state and role in heterogenous iPSCs derived from the non-permissive NOD/ShiLtJ strain. We conclude that heterogeneity is a naturally occurring, necessary quality of stem cells that allows for the maintenance of pluripotency. This study further demonstrates the efficacy of the 2iS reprogramming technique. It is also the first study to derive stable ESC-like stem cells from the non-permissive NOD/ShiLtJ and WSB/EiJ strains, enabling easier and broader research possibilities into pluripotency for these and similar non-permissive mouse strains and species. DA - 2020/12// PY - 2020/12// DO - 10.1007/s00335-020-09849-x VL - 31 IS - 9-12 SP - 263-286 SN - 1432-1777 ER - TY - JOUR TI - AI‐Powered mental health chatbots: Examining users’ motivations, active communicative action and engagement after mass‐shooting disasters AU - Cheng, Yang AU - Jiang, Hua T2 - Journal of Contingencies and Crisis Management AB - Abstract Chatbots are gaining their popularity in society and have triggered heated discussions in academia as well. Currently, few studies explored the applications of AI‐powered mental health chatbots in a mass‐shooting disaster context. Via integrating literature from multi‐disciplines such as crisis management, mental health and digital communication, this quantitative study intends to contribute to close this gap and explore the associations between perceived gratifications and protection motivations of using mental health chatbot services, active communicative action, and online and offline engagement behaviours of solving mental health problems after disasters. This study surveyed 1,114 US participants who ever used chatbot services from top healthcare companies. Implications of the results enhance theoretical discussions on how artificial intelligence has shaped individuals’ motivations, communicative action and engagement behaviour to treat mental health problems. This study also benefits professionals who want to learn more about chatbots for mental healthcare, crisis management and customer engagement. DA - 2020/9// PY - 2020/9// DO - 10.1111/1468-5973.12319 VL - 28 IS - 3 SP - 339-354 J2 - J Contingencies and Crisis Management LA - en OP - SN - 0966-0879 1468-5973 UR - http://dx.doi.org/10.1111/1468-5973.12319 DB - Crossref KW - artificial intelligence(AI) KW - chatbots KW - crises KW - engagement KW - mass shootings KW - mental health KW - situational theory of problem-solving (STOPS) ER - TY - JOUR TI - Transitioning Machine Learning from Theory to Practice in Natural Resources Management AU - Saia, Sheila M. AU - Nelson, Natalie AU - Huseth, Anders S. AU - Grieger, Khara AU - Reich, Brian J. T2 - ECOLOGICAL MODELLING DA - 2020/11/1/ PY - 2020/11/1/ DO - 10.1016/j.ecolmodel.2020.109257 VL - 435 SP - SN - 1872-7026 KW - Machine learning KW - Natural resources management KW - Stakeholders KW - Decision-support tools KW - Decision-making KW - Process-based modeling ER - TY - JOUR TI - Resistance to natural and synthetic gene drive systems AU - Price, Tom A. R. AU - Windbichler, Nikolai AU - Unckless, Robert L. AU - Sutter, Andreas AU - Runge, Jan-Niklas AU - Ross, Perran A. AU - Pomiankowski, Andrew AU - Nuckolls, Nicole L. AU - Montchamp-Moreau, Catherine AU - Mideo, Nicole AU - Martin, Oliver Y. AU - Manser, Andri AU - Legros, Mathieu AU - Larracuente, Amanda M. AU - Holman, Luke AU - Godwin, John AU - Gemmell, Neil AU - Courret, Cecile AU - Buchman, Anna AU - Barrett, Luke G. AU - Lindholm, Anna K. T2 - JOURNAL OF EVOLUTIONARY BIOLOGY AB - Scientists are rapidly developing synthetic gene drive elements intended for release into natural populations. These are intended to control or eradicate disease vectors and pests, or to spread useful traits through wild populations for disease control or conservation purposes. However, a crucial problem for gene drives is the evolution of resistance against them, preventing their spread. Understanding the mechanisms by which populations might evolve resistance is essential for engineering effective gene drive systems. This review summarizes our current knowledge of drive resistance in both natural and synthetic gene drives. We explore how insights from naturally occurring and synthetic drive systems can be integrated to improve the design of gene drives, better predict the outcome of releases and understand genomic conflict in general. DA - 2020/10// PY - 2020/10// DO - 10.1111/jeb.13693 VL - 33 IS - 10 SP - 1345-1360 SN - 1420-9101 KW - CRISPR-Cas9 KW - fitness costs KW - meiotic drive KW - population suppression KW - selfish genetic elements KW - sex ratio distorter KW - transposable element KW - Wolbachia ER - TY - JOUR TI - Civil Rights, Social Equity, and Census 2020 AU - Berry‐James, RaJade M. AU - Gooden, Susan T. AU - Johnson, Richard Greggory, III T2 - Public Administration Review AB - This article examines Census 2020 relative to civil rights and social equity. Mandated by the U.S. Constitution, the Census is directly related to civil rights as Census totals are used to determine voting representation, and results impact billions of dollars of federal, state, and local funding across multiple areas including education, health care, and housing. Census undercounts impact marginalized communities, and this is a heightened concern for Census 2020 along two core social equity dimensions: (1) race and ethnicity, and (2) immigration and citizenship. The implementation of Census 2020 is the responsibility of public administrators and poses challenges in the areas of social equity, leadership, and administrative infrastructure. Practitioner Points Census 2020 matters. Data from the U.S. Census is fundamental to apportioning political power as well as more than $800 billion each year for governmental services. In each state, population totals will determine the House of Representative seats. Every state will use population totals to redraw legislative districts, allocate resources, and provide public services. Racial categories and undercounts have been fundamental concerns since the first U.S. Census in 1790. These undercounts pose on‐going challenges to political participation, representation, and resources. The citizenship question controversy of Census 2020 will likely lead to lower completion levels for noncitizens. Implementation of Census 2020 is the responsibility of public administrators, and there are important challenges relative to civil rights and social equity. DA - 2020/9/23/ PY - 2020/9/23/ DO - 10.1111/puar.13285 VL - 80 IS - 6 SP - 1100-1108 J2 - Public Administration Review LA - en OP - SN - 0033-3352 1540-6210 UR - http://dx.doi.org/10.1111/puar.13285 DB - Crossref ER - TY - JOUR TI - Association between lone star tick bites and increased alpha-gal sensitization: evidence from a prospective cohort of outdoor workers AU - Mitchell, Cedar L. AU - Lin, Feng-Chang AU - Vaughn, Meagan AU - Apperson, Charles S. AU - Meshnick, Steven R. AU - Commins, Scott P. T2 - PARASITES & VECTORS AB - Abstract Background Alpha-gal is an oligosaccharide implicated in delayed anaphylaxis following red meat consumption. Exposure to tick bites has been correlated with development of an allergic response to alpha-gal. However, evidence prospectively linking exposure to a single tick species and an immune response to alpha-gal is lacking. Methods We used serum samples from a prior study cohort of outdoor workers in North Carolina, USA, with high exposure to the lone star tick, Amblyomma americanum , to prospectively evaluate the relationship between tick bites and anti-alpha-gal IgE antibodies. Results Individuals who reported exposure to one or more tick bites were significantly more likely to have a positive change in anti-alpha-gal IgE compared to individuals with no reported tick bites. This relationship was not dependent on time. A trend toward increasing number of tick bites and increased anti-alpha-gal IgE levels was observed but not statistically significant. Conclusion To our knowledge, this is the first study to prospectively link documented exposure to A. americanum bites and increased sensitization to alpha-gal in a cohort of outdoor workers. Our results support the role of A. americanum as likely agents for eliciting an allergic response to red meat, and highlight the importance of preventing tick bites. DA - 2020/9/14/ PY - 2020/9/14/ DO - 10.1186/s13071-020-04343-4 VL - 13 IS - 1 SP - SN - 1756-3305 KW - Alpha-gal KW - Amblyomma americanum KW - Red meat allergy ER - TY - JOUR TI - Antimicrobial resistance and virulence factors profile of Salmonella spp. and Escherichia coli isolated from different environments exposed to anthropogenic activity AU - Balbin, Michelle M. AU - Hull, Dawn AU - Guest, Chloe AU - Nichols, Lauren AU - Dunn, Robert AU - Thakur, Siddhartha T2 - JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE AB - The study aimed to identify the antimicrobial resistance (AMR) determinants and virulence factors in Salmonella spp. and Escherichia coli recovered from different anthropogenic areas in North Carolina. Soil samples were collected from different anthropogenic areas, urban and natural. The minimum inhibitory concentration (MIC) was determined by using the broth microdilution method. Whole-genome sequencing (WGS) and analysis were done to identify the AMR determinants and virulence factors. A higher prevalence of Salmonella spp. and E. coli was detected in the urban environment. The Salmonella spp. isolates showed resistance to sulfisoxazole and streptomycin, whereas E. coli was resistant to sulfisoxazole, cefoxitin and ampicillin. Salmonella serotypes Schwarzengrund and Mississippi were identified based on WGS analysis. Aminoglycoside resistance genes and IncFIB and IncFIC(FII) plasmids were detected among Salmonella spp. In general, E. coli was predominated by isolates from phylogroups B1, B2 and D. The multidrug transporter mdfA gene was detected in most of the E. coli from both the urban (100%) and natural (84.5%) environments. The FosA7 gene was detected in an isolate from a residential yard. The pCoo and pB171 plasmids were detected in an urban environment; col(156) and pHN7A8 plasmids were detected in natural environments. The detection of AMR determinants and virulence factors in these bacteria is significant in understanding the occurrence and even the development of AMR. The presence of these determinants in different anthropogenic areas suggests the need to conduct longitudinal studies for comparing the profile of pathogens across different environments. DA - 2020/9// PY - 2020/9// DO - 10.1016/j.jgar.2020.05.016 VL - 22 SP - 578-583 SN - 2213-7173 KW - Anthropogenic areas KW - Whole-genome sequencing KW - FosA7 gene KW - pHN7A8 (F33:A-:B-plasmid) ER - TY - JOUR TI - Nitrogen-induced acidification, not N-nutrient, dominates suppressive N effects on arbuscular mycorrhizal fungi AU - Pan, Shang AU - Wang, Yang AU - Qiu, Yunpeng AU - Chen, Dima AU - Zhang, Lin AU - Ye, Chenglong AU - Guo, Hui AU - Zhu, Weixing AU - Chen, Aiqun AU - Xu, Guohua AU - Zhang, Yi AU - Bai, Yongfei AU - Hu, Shuijin T2 - GLOBAL CHANGE BIOLOGY AB - Abstract Arbuscular mycorrhizal fungi (AMF) form symbiosis with most terrestrial plant roots, obtaining photosynthates in return for mineral nutrients. Ecological theories based on the economics of trading partnership predict that nutrient enrichment would suppress AMF. Experimental results from nitrogen (N) and phosphorus (P) additions, however, were highly variable, and the underlying mechanisms remain unclear. Here we show distinct AMF responses to soil N:P stoichiometry manipulations via gradients of long‐term N and P additions in a Mongolian steppe. A complementary experiment with an acid addition gradient was designed to help tease apart the effect of N‐induced acidification from N nutrient. AMF root colonization and extraradical fungal biomass progressively decreased along the P gradient under two distinct host plant species, suggesting a carbon (C)‐P tradeoff. In contrast, low to moderate N inputs increased both AMF parameters, corresponding to the increasing N:P ratio. Yet, high N inputs reduced AMF colonization and biomass, and the magnitudes of N‐led inhibition were similar to those under acid additions that induced comparable changes in soil pH. Structural equation modeling further showed that while soil N:P stoichiometry primarily controlled the effect of P addition on AMF, N‐induced soil acidity overtook the N:P stoichiometry under high N inputs and dominated the effects of reactive N on AMF. In addition, AMF community composition in roots was more dependent on host plants and unresponsive to changes in soil nutrients. We further proposed a comprehensive framework that integrates biological and geochemical effects of reactive N and P inputs on AMF. Together, these results indicate that while the C‐P tradeoff controls P suppression of AMF, N‐induced acidification dominates the N inhibition. Our findings suggest that incorporation of geochemical impacts of N and P inputs would facilitate modeling efforts to project mycorrhizal impact on plant interactions and soil C balance under future nutrient enrichment scenarios. DA - 2020/11// PY - 2020/11// DO - 10.1111/gcb.15311 VL - 26 IS - 11 SP - 6568-6580 SN - 1365-2486 KW - arbuscular mycorrhizal fungi KW - extraradical hyphae KW - Mongolian steppe KW - N and P enrichment KW - root colonization KW - soil N KW - P ER - TY - JOUR TI - Freedom and Unavoidable Judgments A Commentary on "Nondomination and the Limits of Relational Autonomy" by Danielle M. Wenner AU - Harwood, Karey T2 - INTERNATIONAL JOURNAL OF FEMINIST APPROACHES TO BIOETHICS DA - 2020/8// PY - 2020/8// DO - 10.3138/ijfab.13.2.07 VL - 13 IS - 2 SP - 56-59 SN - 1937-4577 UR - http://dx.doi.org/10.3138/ijfab.13.2.07 ER - TY - JOUR TI - Which "New Eugenics"? Expanding Access to Art, Respecting Procreative Liberty, and Protecting the Moral Equality of All Persons in an Era of Neoliberal Choice AU - Harwood, Karey T2 - INTERNATIONAL JOURNAL OF FEMINIST APPROACHES TO BIOETHICS AB - In The New Eugenics: Selective Breeding in an Era of Reproductive Technologies, Judith Daar (2017) advocates for increased access to assisted reproductive technologies (ART) and minimizes concerns about the potential “eugenic logic” of some procreative choices. Although Daar’s goal of expanded access is laudable, her argument suggests an unresolved tension between the moral equality of persons and individual reproductive freedom. Exploring that tension, this paper argues that efforts to expand access to ART must still grapple with the “eugenic mentality” of quality control that some forms of reproductive and genetic technologies enable. DA - 2020/8// PY - 2020/8// DO - 10.3138/ijfab.13.2.17 VL - 13 IS - 2 SP - 148-173 SN - 1937-4577 UR - http://dx.doi.org/10.3138/ijfab.13.2.17 KW - assisted reproductive technologies (ART) KW - disability rights KW - eugenics KW - preimplantation genetic diagnosis (PGD) KW - reproductive justice ER - TY - JOUR TI - Technical Communication is a Social Medium AU - Swarts, Jason T2 - TECHNICAL COMMUNICATION QUARTERLY AB - Technical communicators can manage the content users share in online communities, but this is only feasible if the users act like a community with a shared understanding of what the software does. When they do not, users discuss technologies as unsettled objects and rely on technical communication to socially construct them. This research describes such uses of technical communication and argues how professional technical communicators can help. DA - 2020/// PY - 2020/// DO - 10.1080/10572252.2020.1774659 VL - 29 IS - 4 SP - 427-439 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85087111844&partnerID=MN8TOARS ER - TY - JOUR TI - Bahiagrass pasture and elephantgrass bioenergy cropping systems differ in root traits AU - Reyes-Cabrera, Joel AU - Erickson, John E. AU - Leon, Ramon G. AU - Quadros, Danilo G. AU - Silveira, Maria L. AU - Sollenberger, Lynn E. T2 - AGRONOMY JOURNAL AB - Abstract Root morphology and production are important for soil nutrient acquisition and C sequestration, but these traits are poorly understood in the bioenergy crop elephantgrass [ Pennisetum purpureum (L.) Schum.]. Our objective was to characterize root traits of elephantgrass receiving different nutrient management practices in comparison with bahiagrass ( Paspalum notatum Flüggé) pasture grown in the southeastern U.S. Treatments were bahiagrass + 50 kg N ha −1 (BHG), and elephantgrass receiving either: 50 kg N ha −1 (E50), 50 kg N ha −1 + biochar (E50BC), 50 kg N ha −1 + lignocellulosic fermentation residual (E50FR), or 250 kg N ha −1 (E250). Roots were sampled annually for 4 yr (2013‐2016). Root C and N concentration were measured at termination (2016) of the study. Both crop species exhibited similar root length density (RLD) and root mass density (RMD) across all depths in 2014 and 2015. BHG root diameter was 55% greater than all elephantgrass treatments. By 2016, E50FR increased elephantgrass RLD and RMD in the shallow soil layers (< 0.2 m). Root N content was 15–39% lower for all elephantgrass treatments than BHG in the 0‐0.1 m depth, and 22–25% lower for E50 and E50BC in the 0.1‐ to 0.2‐m depth compared with BHG. Additionally, roots C content was 6% higher in the 0‐0.1 m compared with the 0.1‐ to 0.2‐m soil depth irrespective of treatment. Application of biochar and lignocellulosic fermentation residual as amendments produced a stimulatory effect on elephantgrass root growth in soil shallow layers, which could affect nutrient and water acquisition. DA - 2020/// PY - 2020/// DO - 10.1002/agj2.20382 VL - 112 IS - 6 SP - 4810-4821 SN - 1435-0645 UR - https://doi.org/10.1002/agj2.20382 ER - TY - JOUR TI - Weed Management Guide for Florida Lawns AU - Unruh, J. Bryan AU - Trenholm, Laurie AU - Harlow, Erin AU - Leon, Ramon G. T2 - EDIS AB - Weeds can be defined as unwanted plants or plants growing out of place. Proper identification and some understanding of how and why weeds are present in a lawn are important when selecting the best control strategy. Knowing if weeds were previously present in an area also helps homeowners prepare control measures in the future. Weed control should be a carefully planned and coordinated program.https://edis.ifas.ufl.edu/ep141 Previous version: Unruh, Joseph, Ramon Leon, Barry Brecke, and Laurie Trenholm. 2013. “Weed Management Guide for Florida Lawns”. EDIS 2013 (7). https://journals.flvc.org/edis/article/view/121086. DA - 2020/9/21/ PY - 2020/9/21/ DO - 10.32473/edis-ep141-2019 UR - https://doi.org/10.32473/edis-ep141-2019 ER - TY - JOUR TI - The Internal, External and Extended Microbiomes of Hominins (vol 8, 25, 2020) AU - Dunn, Robert R. AU - Amato, Katherine R. AU - Archie, Elizabeth A. AU - Arandjelovic, Mimi AU - Crittenden, Alyssa N. AU - Nichols, Lauren M. T2 - FRONTIERS IN ECOLOGY AND EVOLUTION AB - Error in Figure/TableIn the original article, there was a mistake in Figure 1 as published. Colobus monkeys and Langur monkeys were misclassified as omnivores rather than as folivores; and “Sykes monkeys” was misspelled and misclassified as an herbivore rather than as an omnivore. The corrected Figure 1 appears below. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated. DA - 2020/8/19/ PY - 2020/8/19/ DO - 10.3389/fevo.2020.00236 VL - 8 SP - SN - 2296-701X KW - fermentation KW - primates KW - prosocial microbes KW - feces KW - food KW - armpits KW - alcohol ER - TY - JOUR TI - Assessing Insecticide Resistance in Adult Mosquitoes: Perspectives on Current Methods AU - Richards, Stephanie L. AU - Byrd, Brian D. AU - Reiskind, Michael H. AU - White, Avian V T2 - ENVIRONMENTAL HEALTH INSIGHTS AB - Mosquito insecticide resistance (IR) is a growing global issue that must be addressed to protect public health. Vector control programs (VCPs) should regularly monitor local mosquito populations for IR and plan control measures accordingly. In some cases, state/federal resources financially support this testing with expertise and/or training programs. Standardization of methods (eg, Centers for Disease Control and Prevention bottle bioassay, World Health Organization tube testing, dose-mortality bioassay) for monitoring IR must be prioritized. One solution is regional hubs of IR monitoring at the state or other level. Training programs on methodology and interpretation of results should be developed and routinely offered to local VCPs conducting IR testing in mosquitoes. Here, current methods for assessing mosquito IR are discussed and insights into a variety of questions from VCPs are considered. It is critical that methods for IR monitoring and data interpretation are standardized through routine training, with the goal of evidence-driven decision making to improve control of mosquitoes and mosquito-borne disease. DA - 2020/9// PY - 2020/9// DO - 10.1177/1178630220952790 VL - 14 SP - 117863022095279 UR - http://dx.doi.org/10.1177/1178630220952790 ER - TY - JOUR TI - Responsible Innovation in Biotechnology: Stakeholder Attitudes and Implications for Research Policy AU - Roberts, J.P. AU - Herkert, J. AU - Kuzma, J. T2 - Elementa: Science of the Anthropocene AB - This article explores attitudes of stakeholders involved in biotechnology towards the Responsible Innovation (RI) framework. As a framework for governance, RI has received increasing scholarly attention but has yet to be successfully integrated into U.S. research and innovation policy. Using a mixed methods approach, we analyzed the attitudes of different biotechnology stakeholders, particularly those working in areas related to genetically modified organisms (GMOs) in agriculture and the environment, towards the principles and practices of RI. Homogenous focus groups (organized by stakeholder affiliation) and pre- and post-focus group surveys were used to measure attitudes towards RI. We designed the survey questions according to the Advocacy Coalition Framework (ACF) and examined the agreement of stakeholders with policy core beliefs (general principles of RI) and secondary beliefs (implementation practices of RI). Although all stakeholder groups had neutral to positive attitudes towards RI general principles, we found significant differences in their reactions to the scholarly definitions of RI and in their attitudes towards practices to implement RI. In comparison to government and advocacy groups, stakeholders promoting biotechnology innovations–industry, trade organizations, and academics–had more negative reactions to social science definitions of RI and to RI practices that relinquish control to people outside of technology development pipelines. Qualitative analysis of focus-groups revealed barriers for implementing RI practices. For example, innovators were cynical about including external voices in innovation pathways due to inflexible funding programs and were concerned about potential delays to innovation given the highly competitive environments for financing and patents. In order to help address these tensions, we call for the co-design of RI practices between biotechnology innovators and other stakeholders. The opening-up of biotechnology innovation to RI practices of anticipation, inclusion, responsiveness and reflexivity will likely be important for future, public legitimacy of emerging genetic engineering applications such as gene editing and gene drives. DA - 2020/8/31/ PY - 2020/8/31/ DO - 10.1525/elementa.446 VL - 8 IS - 1 SP - 47 SN - 2325-1026 UR - http://dx.doi.org/10.1525/elementa.446 KW - Responsible innovation KW - Biotechnology KW - Governance KW - GMOs ER - TY - JOUR TI - Molecular Characterizations of Double-Stranded RNA Degrading Nuclease Genes from Ostrinia nubilalis AU - Cooper, Anastasia M. W. AU - Song, Huifang AU - Shi, Xuekai AU - Yu, Zhitao AU - Lorenzen, Marcé AU - Silver, Kristopher AU - Zhang, Jianzhen AU - Zhu, Kun Yan T2 - Insects AB - Variable RNA interference (RNAi) efficiencies limit RNAi-based pest management strategies for many pests. Previous efforts to understand mechanisms contributing to low RNAi efficiency indicate that double-stranded RNA (dsRNA) is degraded in the European corn borer (ECB), Ostrinia nubilalis, due to nuclease activity. To investigate the contribution of dsRNA-degrading endonucleases (dsRNases) and lepidopteran-specific RNAi efficiency-related nucleases (REases) to dsRNA instability and low RNAi efficiency in ECB, five complementary DNAs putatively encoding four dsRNases (OndsRNase1, 2, 3, and 4) and one REase (OnREase) were sequenced. Characterization of these transcripts revealed that substrate specificity might vary among the four dsRNases due to different amino acid combinations in the substrate-binding sites. Gene expression analysis indicated that OndsRNase2 and OnREase were highly expressed in the larval gut, and OndsRNase1 showed the highest expression in hemolymph, especially in older developmental stages. Transcript level analysis after dsRNA exposure revealed that expression of OnREase rapidly increased upon dsRNA ingestion or injection, whereas OndsRNase4 expression only increased after long-term ingestion of dsRNA. While the biological function of these nucleases remains to be verified, our results suggest that OnREase and OndsRNase2, and OndsRNase1 and OndsRNase4 may be responsible for degradation of dsRNAs in the ECB gut and hemolymph, respectively, thereby contributing to low RNAi efficiency. DA - 2020/9/23/ PY - 2020/9/23/ DO - 10.3390/insects11100652 VL - 11 IS - 10 SP - 652 J2 - Insects LA - en OP - SN - 2075-4450 UR - http://dx.doi.org/10.3390/insects11100652 DB - Crossref KW - dsRNase KW - European corn borer KW - gene expression KW - REase KW - RNAi efficiency KW - substrate specificity ER - TY - JOUR TI - 2020 taxonomic update for phylumNegarnaviricota(Riboviria:Orthornavirae), including the large ordersBunyaviralesandMononegavirales AU - Kuhn, Jens H. AU - Adkins, Scott AU - Alioto, Daniela AU - Alkhovsky, Sergey V. AU - Amarasinghe, Gaya K. AU - Anthony, Simon J. AU - Avsic-Zupanc, Tatjana AU - Ayllon, Maria A. AU - Bahl, Justin AU - Balkema-Buschmann, Anne AU - Ballinger, Matthew J. AU - Bartonicka, Tomas AU - Basler, Christopher AU - Bavari, Sina AU - Beer, Martin AU - Bente, Dennis A. AU - Bergeron, Eric AU - Bird, Brian H. AU - Blair, Carol AU - Blasdell, Kim R. AU - Bradfute, Steven B. AU - Breyta, Rachel AU - Briese, Thomas AU - Brown, Paul A. AU - Buchholz, Ursula J. AU - Buchmeier, Michael J. AU - Bukreyev, Alexander AU - Burt, Felicity AU - Buzkan, Nihal AU - Calisher, Charles H. AU - Cao, Mengji AU - Casas, Inmaculada AU - Chamberlain, John AU - Chandran, Kartik AU - Charrel, Remi N. AU - Chen, Biao AU - Chiumenti, Michela AU - Choi, Il-Ryong AU - Clegg, J. Christopher S. AU - Crozier, Ian AU - Graca, John V. AU - Dal Bo, Elena AU - Davila, Alberto M. R. AU - Torre, Juan Carlos AU - Lamballerie, Xavier AU - Swart, Rik L. AU - Di Bello, Patrick L. AU - Di Paola, Nicholas AU - Di Serio, Francesco AU - Dietzgen, Ralf G. AU - Digiaro, Michele AU - Dolja, Valerian V. AU - Dolnik, Olga AU - Drebot, Michael A. AU - Drexler, Jan Felix AU - Duerrwald, Ralf AU - Dufkova, Lucie AU - Dundon, William G. AU - Duprex, W. Paul AU - Dye, John M. AU - Easton, Andrew J. AU - Ebihara, Hideki AU - Elbeaino, Toufic AU - Ergunay, Koray AU - Fernandes, Jorlan AU - Fooks, Anthony R. AU - Formenty, Pierre B. H. AU - Forth, Leonie F. AU - Fouchier, Ron A. M. AU - Freitas-Astua, Juliana AU - Gago-Zachert, Selma AU - Gao, George Fu AU - Garcia, Maria Laura AU - Garcia-Sastre, Adolfo AU - Garrison, Aura R. AU - Gbakima, Aiah AU - Goldstein, Tracey AU - Gonzalez, Jean-Paul J. AU - Griffiths, Anthony AU - Groschup, Martin H. AU - Guenther, Stephan AU - Guterres, Alexandro AU - Hall, Roy A. AU - Hammond, John AU - Hassan, Mohamed AU - Hepojoki, Jussi AU - Hepojoki, Satu AU - Hetzel, Udo AU - Hewson, Roger AU - Hoffmann, Bernd AU - Hongo, Seiji AU - Hoeper, Dirk AU - Horie, Masayuki AU - Hughes, Holly R. AU - Hyndman, Timothy H. AU - Jambai, Amara AU - Jardim, Rodrigo AU - Jiang, Daohong AU - Jin, Qi AU - Jonson, Gilda B. AU - Junglen, Sandra AU - Karadag, Serpil AU - Keller, Karen E. AU - Klempa, Boris AU - Klingstrom, Jonas AU - Kobinger, Gary AU - Kondo, Hideki AU - Koonin, Eugene V. AU - Krupovic, Mart AU - Kurath, Gael AU - Kuzmin, Ivan V. AU - Laenen, Lies AU - Lamb, Robert A. AU - Lambert, Amy J. AU - Langevin, Stanley L. AU - Lee, Benhur AU - Lemos, Elba R. S. AU - Leroy, Eric M. AU - Li, Dexin AU - Li, Jianrong AU - Liang, Mifang AU - Liu, Wenwen AU - Liu, Yan AU - Lukashevich, Igor S. AU - Maes, Piet AU - Souza, William AU - Marklewitz, Marco AU - Marshall, Sergio H. AU - Martelli, Giovanni P. AU - Martin, Robert R. AU - Marzano, Shin-Yi L. AU - Massart, Sebastien AU - McCauley, John W. AU - Mielke-Ehret, Nicole AU - Minafra, Angelantonio AU - Minutolo, Maria AU - Mirazimi, Ali AU - Muehlbach, Hans-Peter AU - Muhlberger, Elke AU - Naidu, Rayapati AU - Natsuaki, Tomohide AU - Navarro, Beatriz AU - Navarro, Jose A. AU - Netesov, Sergey V. AU - Neumann, Gabriele AU - Nowotny, Norbert AU - Nunes, Marcio R. T. AU - Nylund, Are AU - Okland, Arnfinn L. AU - Oliveira, Renata C. AU - Palacios, Gustavo AU - Pallas, Vicente AU - Palyi, Bernadett AU - Papa, Anna AU - Parrish, Colin R. AU - Pauvolid-Correa, Alex AU - Paweska, Janusz T. AU - Payne, Susan AU - Perez, Daniel R. AU - Pfaff, Florian AU - Radoshitzky, Sheli R. AU - Rahman, Aziz-ul AU - Ramos-Gonzalez, Pedro L. AU - Resende, Renato O. AU - Reyes, Carina A. AU - Rima, Bertus K. AU - Romanowski, Victor AU - Robles Luna, Gabriel AU - Rota, Paul AU - Rubbenstroth, Dennis AU - Runstadler, Jonathan A. AU - Ruzek, Daniel AU - Sabanadzovic, Sead AU - Salat, Jiri AU - Sall, Amadou Alpha AU - Salvato, Maria S. AU - Sarpkaya, Kamil AU - Sasaya, Takahide AU - Schwemmle, Martin AU - Shabbir, Muhammad Z. AU - Shi, Xiaohong AU - Shi, Zhengli AU - Shirako, Yukio AU - Simmonds, Peter AU - Sirmarova, Jana AU - Sironi, Manuela AU - Smither, Sophie AU - Smura, Teemu AU - Song, Jin-Won AU - Spann, Kirsten M. AU - Spengler, Jessica R. AU - Stenglein, Mark D. AU - Stone, David M. AU - Strakova, Petra AU - Takada, Ayato AU - Tesh, Robert B. AU - Thornburg, Natalie J. AU - Tomonaga, Keizo AU - Tordo, Noel AU - Towner, Jonathan S. AU - Turina, Massimo AU - Tzanetakis, Ioannis AU - Ulrich, Rainer G. AU - Vaira, Anna Maria AU - Hoogen, Bernadette AU - Varsani, Arvind AU - Vasilakis, Nikos AU - Verbeek, Martin AU - Wahl, Victoria AU - Walker, Peter J. AU - Wang, Hui AU - Wang, Jianwei AU - Wang, Xifeng AU - Wang, Lin-Fa AU - Wei, Taiyun AU - Wells, Heather AU - Whitfield, Anna E. AU - Williams, John V. AU - Wolf, Yuri I. AU - Wu, Zhiqiang AU - Yang, Xin AU - Yang, Xinglou AU - Yu, Xuejie AU - Yutin, Natalya AU - Zerbini, F. Murilo AU - Zhang, Tong AU - Zhang, Yong-Zhen AU - Zhou, Guohui AU - Zhou, Xueping T2 - ARCHIVES OF VIROLOGY AB - In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. DA - 2020/12// PY - 2020/12// DO - 10.1007/s00705-020-04731-2 VL - 165 IS - 12 SP - 3023-3072 SN - 1432-8798 ER - TY - JOUR TI - Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops AU - Gemenet, Dorcus C. AU - Lindqvist-Kreuze, Hannele AU - De Boeck, Bert AU - da Silva Pereira, Guilherme AU - Mollinari, Marcelo AU - Zeng, Zhao-Bang AU - Craig Yencho, G. AU - Campos, Hugo T2 - Theoretical and Applied Genetics AB - Polypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture. The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F1 population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations. DA - 2020/9/2/ PY - 2020/9/2/ DO - 10.1007/s00122-020-03673-2 VL - 133 IS - 12 SP - 3345-3363 J2 - Theor Appl Genet LA - en OP - SN - 0040-5752 1432-2242 UR - http://dx.doi.org/10.1007/s00122-020-03673-2 DB - Crossref ER - TY - JOUR TI - Consumer response to fake news about brands on social media: the effects of self-efficacy, media trust, and persuasion knowledge on brand trust AU - Chen, Zifei Fay AU - Cheng, Yang T2 - JOURNAL OF PRODUCT AND BRAND MANAGEMENT AB - Purpose Drawing on theoretical insights from the persuasion knowledge model (PKM), this study aims to propose and test a model that maps out the antecedents, process and consequences to explain how consumers process and respond to fake news about brands on Facebook. Design/methodology/approach Contextualizing the fake news about Coca-Cola’s recall of Dasani water, an online survey was conducted via Qualtrics with consumers in the USA ( N = 468). Data were analyzed using covariance-based structural equation modeling. Findings Results showed that self-efficacy and media trust significantly predicted consumers’ persuasion knowledge of the fake news. Persuasion knowledge of the fake news significantly influenced consumers’ perceived diagnosticity of the fake news and subsequent brand trust. Furthermore, persuasion knowledge of the fake news mediated the effects from self-efficacy on perceived diagnosticity of the fake news and brand trust, respectively. Originality/value This study contributes to the literature of brand management by examining how consumers process and respond to fake news about a brand. It also extends the persuasion knowledge model by applying it to the context of fake news about brands on social media, and incorporating antecedents (self-efficacy and media trust) and consequences (perceived diagnosticity and brand trust) of persuasion knowledge in this particular context. Practically, this study provides insights to key stakeholders of brands to better understand consumers’ information processing of fake news about brands on social media. DA - 2020/// PY - 2020/// DO - 10.1108/JPBM-12-2018-2145 VL - 29 IS - 2 SP - 188-198 SN - 2054-1643 KW - Brand trust KW - Social media KW - Self-efficacy KW - Persuasion knowledge KW - Fake news ER - TY - JOUR TI - Should Climate Scientists Fly? AU - Goodwin, Jean T2 - Informal Logic AB - I inquire into argument at the system level, exploring the controversy over whether climate scientists should fly. I document participants’ knowledge of a skeptical argument that because scientists fly, they cannot testify credibly about the climate emergency. I show how this argument has been managed by pro-climate action arguers, and how some climate scientists have developed parallel reasoning, articulating a sophisticated case why they will be more effective in the controversy if they fly less. Finally, I review some strategies arguers deploy to use the arguments of others against them. I argue that only by attending to argument-making at the system level can we understand how arguers come to know the resources for argument available in a controversy and to think strategically about how to use them. I call for more work on argument at the system level DA - 2020/7/6/ PY - 2020/7/6/ DO - 10.22329/il.v40i2.6327 VL - 40 IS - 2 SP - 157-203 J2 - IL OP - SN - 2293-734X 0824-2577 UR - http://dx.doi.org/10.22329/il.v40i2.6327 DB - Crossref KW - argument KW - argumentation KW - argumentation theory KW - argumentative content knowledge KW - argument strategy KW - climate controversy KW - controversy KW - ethos KW - polylogue KW - systems thinking ER - TY - CHAP TI - MAGIC: Live imaging of cellular division in plant seedlings using lightsheet microscopy AU - Madison, Imani AU - Melvin, Charles AU - Buckner, Eli AU - Williams, Cranos AU - Sozzani, Rosangela AU - Long, Terri T2 - Methods in Cell Biology AB - Imaging technologies have been used to understand plant genetic and developmental processes, from the dynamics of gene expression to tissue and organ morphogenesis. Although the field has advanced incredibly in recent years, gaps remain in identifying fine and dynamic spatiotemporal intervals of target processes, such as changes to gene expression in response to abiotic stresses. Lightsheet microscopy is a valuable tool for such studies due to its ability to perform long-term imaging at fine intervals of time and at low photo-toxicity of live vertically oriented seedlings. In this chapter, we describe a detailed method for preparing and imaging Arabidopsis thaliana seedlings for lightsheet microscopy via a Multi-Sample Imaging Growth Chamber (MAGIC), which allows simultaneous imaging of at least four samples. This method opens new avenues for acquiring imaging data at a high temporal resolution, which can be eventually probed to identify key regulatory time points and any spatial dependencies of target developmental processes. PY - 2020/// DO - 10.1016/bs.mcb.2020.04.004 VL - 160 SP - 405-418 OP - PB - Elsevier SN - 9780128215333 UR - http://dx.doi.org/10.1016/bs.mcb.2020.04.004 DB - Crossref ER - TY - CHAP TI - BioVision Tracker: A semi-automated image analysis software for spatiotemporal gene expression tracking in Arabidopsis thaliana AU - Buckner, Eli AU - Madison, Imani AU - Melvin, Charles AU - Long, Terri AU - Sozzani, Rosangela AU - Williams, Cranos T2 - Methods in Cell Biology AB - Fluorescence microscopy can produce large quantities of data that reveal the spatiotemporal behavior of gene expression at the cellular level in plants. Automated or semi-automated image analysis methods are required to extract data from these images. These data are helpful in revealing spatial and/or temporal-dependent processes that influence development in the meristematic region of plant roots. Tracking spatiotemporal gene expression in the meristem requires the processing of multiple microscopy imaging channels (one channel used to image root geometry which serves as a reference for relating locations within the root, and one or more channels used to image fluorescent gene expression signals). Many automated image analysis methods rely on the staining of cell walls with fluorescent dyes to capture cellular geometry and overall root geometry. However, in long time-course imaging experiments, dyes may fade which hinders spatial assessment in image analysis. Here, we describe a procedure for analyzing 3D microscopy images to track spatiotemporal gene expression signals using the MATLAB-based BioVision Tracker software. This software requires either a fluorescence image or a brightfield image to analyze root geometry and a fluorescence image to capture and track temporal changes in gene expression. PY - 2020/// DO - 10.1016/bs.mcb.2020.04.017 VL - 160 SP - 419-436 OP - PB - Elsevier SN - 9780128215333 UR - http://dx.doi.org/10.1016/bs.mcb.2020.04.017 DB - Crossref ER - TY - JOUR TI - Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division AU - Clark, Natalie M. AU - Fisher, Adam P. AU - Berckmans, Barbara AU - Van den Broeck, Lisa AU - Nelson, Emily C. AU - Nguyen, Thomas T. AU - Bustillo-Avendaño, Estefano AU - Zebell, Sophia G. AU - Moreno-Risueno, Miguel A. AU - Simon, Rüdiger AU - Gallagher, Kimberly L. AU - Sozzani, Rosangela T2 - Proceedings of the National Academy of Sciences AB - Stem cells divide and differentiate to form all of the specialized cell types in a multicellular organism. In the Arabidopsis root, stem cells are maintained in an undifferentiated state by a less mitotically active population of cells called the quiescent center (QC). Determining how the QC regulates the surrounding stem cell initials, or what makes the QC fundamentally different from the actively dividing initials, is important for understanding how stem cell divisions are maintained. Here we gained insight into the differences between the QC and the cortex endodermis initials (CEI) by studying the mobile transcription factor SHORTROOT (SHR) and its binding partner SCARECROW (SCR). We constructed an ordinary differential equation model of SHR and SCR in the QC and CEI which incorporated the stoichiometry of the SHR-SCR complex as well as upstream transcriptional regulation of SHR and SCR. Our model prediction, coupled with experimental validation, showed that high levels of the SHR-SCR complex are associated with more CEI division but less QC division. Furthermore, our model prediction allowed us to propose the putative upstream SHR regulators SEUSS and WUSCHEL-RELATED HOMEOBOX 5 and to experimentally validate their roles in QC and CEI division. In addition, our model established the timing of QC and CEI division and suggests that SHR repression of QC division depends on formation of the SHR homodimer. Thus, our results support that SHR-SCR protein complex stoichiometry and regulation of SHR transcription modulate the division timing of two different specialized cell types in the root stem cell niche. DA - 2020/6/15/ PY - 2020/6/15/ DO - 10.1073/pnas.2002166117 VL - 117 IS - 26 SP - 15332-15342 J2 - Proc Natl Acad Sci USA LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.2002166117 DB - Crossref KW - protein complex stoichiometry KW - intercellular protein movement KW - mathematical modeling KW - expression dynamics KW - transcription factor ER - TY - JOUR TI - Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big AU - Clark, Natalie M. AU - Van den Broeck, Lisa AU - Guichard, Marjorie AU - Stager, Adam AU - Tanner, Herbert G. AU - Blilou, Ikram AU - Grossmann, Guido AU - Iyer-Pascuzzi, Anjali S. AU - Maizel, Alexis AU - Sparks, Erin E. AU - Sozzani, Rosangela T2 - Annual Review of Plant Biology AB - The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale. DA - 2020/4/29/ PY - 2020/4/29/ DO - 10.1146/annurev-arplant-050718-100038 VL - 71 IS - 1 SP - 789-816 J2 - Annu. Rev. Plant Biol. LA - en OP - SN - 1543-5008 1545-2123 UR - http://dx.doi.org/10.1146/annurev-arplant-050718-100038 DB - Crossref KW - Forster resonance energy transfer KW - scanning fluorescent correlation spectroscopy KW - microfluid devices KW - light sheet microscopy KW - imaging of macroscopic traits KW - multiscale imaging techniques ER - TY - JOUR TI - Key questions for modelling COVID-19 exit strategies AU - Thompson, Robin N. AU - Hollingsworth, T. Deirdre AU - Isham, Valerie AU - Arribas-Bel, Daniel AU - Ashby, Ben AU - Britton, Tom AU - Challenor, Peter AU - Chappell, Lauren H. K. AU - Clapham, Hannah AU - Cunniffe, Nik J. AU - Dawid, A. Philip AU - Donnelly, Christl A. AU - Eggo, Rosalind M. AU - Funk, Sebastian AU - Gilbert, Nigel AU - Glendinning, Paul AU - Gog, Julia R. AU - Hart, William S. AU - Heesterbeek, Hans AU - House, Thomas AU - Keeling, Matt AU - Kiss, Istvan Z. AU - Kretzschmar, Mirjam E. AU - Lloyd, Alun L. AU - McBryde, Emma S. AU - McCaw, James M. AU - McKinley, Trevelyan J. AU - Miller, Joel C. AU - Morris, Martina AU - Philip D. O'Neill, AU - Parag, Kris V AU - Pearson, Carl A. B. AU - Pellis, Lorenzo AU - Pulliam, Juliet R. C. AU - Ross, Joshua V AU - Tomba, Gianpaolo Scalia AU - Silverman, Bernard W. AU - Struchiner, Claudio J. AU - Tildesley, Michael J. AU - Trapman, Pieter AU - Webb, Cerian R. AU - Mollison, Denis AU - Restif, Olivier T2 - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES AB - Combinations of intense non-pharmaceutical interventions ('lockdowns') were introduced in countries worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement lockdown exit strategies that allow restrictions to be relaxed while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, will allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. The roadmap requires a global collaborative effort from the scientific community and policy-makers, and is made up of three parts: i) improve estimation of key epidemiological parameters; ii) understand sources of heterogeneity in populations; iii) focus on requirements for data collection, particularly in Low-to-Middle-Income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health. DA - 2020/8/12/ PY - 2020/8/12/ DO - 10.1098/rspb.2020.1405 VL - 287 IS - 1932 SP - SN - 1471-2954 KW - COVID-19 KW - SARS-CoV-2 KW - exit strategy KW - mathematical modelling KW - epidemic control KW - uncertainty ER - TY - JOUR TI - The small home ranges and large local ecological impacts of pet cats AU - Kays, R. AU - Dunn, R. R. AU - Parsons, A. W. AU - Mcdonald, B. AU - Perkins, T. AU - Powers, S. A. AU - Shell, L. AU - McDonald, J. L. AU - Cole, H. AU - Kikillus, H. AU - Woods, L. AU - Tindle, H. AU - Roetman, P. T2 - ANIMAL CONSERVATION AB - Abstract Domestic cats ( Felis catus ) are a conservation concern because they kill billions of native prey each year, but without spatial context the ecological importance of pets as predators remains uncertain. We worked with citizen scientists to track 925 pet cats from six countries, finding remarkably small home ranges (3.6 ± 5.6 ha). Only three cats ranged > 1 km 2 and we found no relationship between home range size and the presence of larger native predators (i.e. coyotes, Canis latrans ). Most (75%) cats used primarily (90%) disturbed habitats. Owners reported that their pets killed an average of 3.5 prey items/month, leading to an estimated ecological impact per cat of 14.2‐38.9 prey ha −1 yr −1 . This is similar or higher than the per‐animal ecological impact of wild carnivores but the effect is amplified by the high density of cats in neighborhoods. As a result, pet cats around the world have an ecological impact greater than native predators but concentrated within ~100 m of their homes. DA - 2020/10// PY - 2020/10// DO - 10.1111/acv.12563 VL - 23 IS - 5 SP - 516-523 SN - 1469-1795 KW - citizen science KW - domestic cats KW - GPS tracking KW - predation KW - urban ecology KW - home rage KW - carnivores KW - Felis catus ER - TY - JOUR TI - First documentation of major Vip3Aa resistance alleles in field populations of Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) in Texas, USA AU - Yang, Fei AU - González, José C. Santiago AU - Little, Nathan AU - Reisig, Dominic AU - Payne, Gregory AU - Dos Santos, Rafael Ferreira AU - Jurat-Fuentes, Juan Luis AU - Kurtz, Ryan AU - Kerns, David L. T2 - Scientific Reports AB - Abstract The corn earworm, Helicoverpa zea , is a major target pest of the insecticidal Vip3Aa protein used in pyramided transgenic Bt corn and cotton with Cry1 and Cry2 proteins in the U.S. The widespread resistance to Cry1 and Cry2 proteins in H. zea will challenge the long-term efficacy of Vip3Aa technology. Determining the frequency of resistant alleles to Vip3Aa in field populations of H. zea is critically important for resistance management. Here, we provided the first F 2 screen study to estimate the resistance allele frequency for Vip3Aa in H. zea populations in Texas, U.S. In 2019, 128 H. zea neonates per isofamily for a total of 114 F 2 families were screened with a diagnostic concentration of 3.0 μg/cm 2 of Vip3Aa39 protein in diet-overlay bioassays. The F 2 screen detected two families carrying a major Vip3Aa resistance allele. The estimated frequency of major resistance alleles against Vip3Aa39 in H. zea in Texas from this study was 0.0065 with a 95% CI of 0.0014–0.0157. A Vip3Aa-resistant strain (RR) derived from the F 2 screen showed a high level of resistance to Vip3Aa39 protein, with a resistance ratio of >588.0-fold relative to a susceptible population (SS) based on diet-overlay bioassays. We provide the first documentation of a major resistance allele conferring high levels of Vip3Aa resistance in a field-derived strain of H. zea in the U.S. Data generated from this study contribute to development of management strategies for the sustainable use of the Vip3Aa technology to control H. zea in the U.S. DA - 2020/4/3/ PY - 2020/4/3/ DO - 10.1038/s41598-020-62748-8 VL - 10 IS - 1 SP - 5867 SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-020-62748-8 ER - TY - JOUR TI - Transcriptome analysis of life stages of the house cricket, Acheta domesticus, to improve insect crop production AU - Oppert, Brenda AU - Perkin, Lindsey C. AU - Lorenzen, Marcé AU - Dossey, Aaron T. T2 - Scientific Reports AB - Abstract To develop genetic resources for the improvement of insects as food, we sequenced transcripts from embryos, one-day hatchlings, three nymphal stages, and male and female adults of the house cricket, Acheta domesticus . A draft transcriptome was assembled from more than 138 million sequences combined from all life stages and sexes. The draft transcriptome assembly contained 45,866 contigs, and more than half were similar to sequences at NCBI (e value < e −3 ). The highest sequence identity was found in sequences from the termites Cryptotermes secundus and Zootermopsis nevadensis . Sequences with identity to Gregarina niphandrodes suggest that these crickets carry the parasite. Among all life stages, there were 5,042 genes with differential expression between life stages (significant at p < 0.05). An enrichment analysis of gene ontology terms from each life stage or sex highlighted genes that were important to biological processes in cricket development. We further characterized genes that may be important in future studies of genetically modified crickets for improved food production, including those involved in RNA interference, and those encoding prolixicin and hexamerins. The data represent an important first step in our efforts to provide genetically improved crickets for human consumption and livestock feed. DA - 2020/2/26/ PY - 2020/2/26/ DO - 10.1038/s41598-020-59087-z VL - 10 IS - 1 SP - J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-020-59087-z DB - Crossref ER - TY - JOUR TI - Sustainable atmospheric-pressure plasma treatment of cellulose triacetate (CTA) films for electronics AU - Sun, Xiaohang AU - Bourham, Mohamed AU - Barrett, Devin G. AU - Pal, Lokendra AU - McCord, Marian T2 - JOURNAL OF APPLIED PHYSICS AB - Surface treatments of cellulose triacetate (CTA) films via atmospheric pressure plasmas containing helium and either O2 or C3F6 as plasma reactive gas were performed to study their effects on moisture barrier, transmittance, thermal, surface chemistry, and morphological properties. Plasma treated CTA films were characterized using X-ray photoelectron spectroscopy (XPS), attenuated total reflectance-Fourier transform infrared spectroscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS), differential scanning calorimetry, thermogravimetric analysis, and scanning electron microscopy analytical techniques. Both surface chemical and morphological changes were correlated with water vapor transmission rates (WVTRs) and contact angle measurements. XPS spectra showed that the relative chemical composition of the C 1s spectra after O2 plasma treatments exhibits an increase in the relative amount of C—C bonds, which may be due to a change in surface cross-linking. ToF-SIMS spectra showed the depth of treatment of atmospheric plasma treatment of CTA films at about 100 nm. The WVTR of the CTA film was reduced up to 20% after sustainable atmospheric O2/helium plasma, while no significant changes were observed in light transmittance. Thus, the use of sustainable atmospheric plasmas to enhance moisture barrier while maintaining other critical properties such as light transmittance, thermal stability, and morphology of a CTA film could provide significant benefits to the electronics industry. DA - 2020/8/21/ PY - 2020/8/21/ DO - 10.1063/5.0013633 VL - 128 IS - 7 SP - SN - 1089-7550 ER - TY - JOUR TI - Sharing the CRISPR Toolbox with an Expanding Community AU - LaManna, Caroline M. AU - Pyhtila, Brook AU - Barrangou, Rodolphe T2 - CRISPR JOURNAL AB - Over the past 8 years, the widespread adoption of CRISPR-based technologies has fueled the global genome editing revolution. This platform is based on Cas molecular machines such as Cas9, Cas12, Cas13, as well as other CRISPR effector proteins that are able to alter the genome, transcriptome, and epigenome of virtually any species. Technological improvements have rendered these tools more efficient and precise, and enabled functional diversification and specialization, as recently illustrated by the rise of base editing and the quickly growing demand for prime editing constructs. Here, we discuss the continued adoption of CRISPR tools and constructs distributed by the nonprofit organization Addgene, highlight the trends in the global demand for the CRISPR toolbox, and consider the widespread attitude changes around open sharing that are having a transformative effect on speeding up science. DA - 2020/8// PY - 2020/8// DO - 10.1089/crispr.2020.0075 VL - 3 IS - 4 SP - 248-252 SN - 2573-1602 ER - TY - JOUR TI - Distribution of Meloidogyne enterolobii in Eastern North Carolina and Comparison of Four Isolates AU - Schwarz, Tanner AU - Li, Chunying AU - Ye, Weimin AU - Davis, Eric T2 - PLANT HEALTH PROGRESS AB - The guava root-knot nematode (RKN), Meloidogyne enterolobii, is a particularly aggressive pathogen with limited known distribution in the United States. In 2011, M. enterolobii was identified on field crops in North Carolina for the first time. In collaboration with the North Carolina Department of Agriculture and Consumer Services Nematode Assay Laboratory, RKN-positive samples from the eastern half of North Carolina submitted to the laboratory were analyzed for Meloidogyne species identification using polymerase chain reaction (PCR) of individual nematodes. PCR primers specific for Meloidogyne incognita, M. javanica, M. arenaria, M. hapla, and M. enterolobii were used to analyze DNA from 203 RKN-positive samples representing a variety of field and vegetable crops grown in counties in the eastern half of North Carolina. M. incognita was the predominant species identified (32% of samples), and M. enterolobii was identified in 6% of samples including ones from sweetpotato, tobacco, and soybean crops. New detections of M. enterolobii were found in Nash, Greene, Sampson, and Harnett counties in addition to the previously identified locations in Johnston, Wayne, Columbus, and Wilson counties. Four isolates of M. enterolobii populations were collected from soybean and sweetpotato crops in Johnston, Greene, and Wilson counties and reared on ‘Rutgers’ tomato plants in the greenhouse. Potential differences in virulence among the four M. enterolobii populations were not detected in greenhouse infection assays on six selected resistant and susceptible sweetpotato genotypes in two independent tests. DA - 2020/// PY - 2020/// DO - 10.1094/PHP-12-19-0093-RS VL - 21 IS - 2 SP - 91-96 SN - 1535-1025 KW - root-knot nematodes KW - molecular identification KW - virulence ER - TY - JOUR TI - Evaluating how Swedish hunters determine which species belong in nature AU - Peterson, M. Nils AU - Chen, Alyssa AU - Essen, Erica AU - Hansen, Hans Peter T2 - EUROPEAN JOURNAL OF WILDLIFE RESEARCH DA - 2020/8/27/ PY - 2020/8/27/ DO - 10.1007/s10344-020-01418-6 VL - 66 IS - 5 SP - SN - 1439-0574 KW - Belonging KW - Exotic KW - Hunters KW - Introduced species KW - Invasive KW - Native ER - TY - JOUR TI - Multiple Known Mechanisms and a Possible Role of an Enhanced Immune System in Bt-Resistance in a Field Population of the Bollworm, Helicoverpa zea: Differences in Gene Expression with RNAseq AU - Lawrie, Roger D. AU - Mitchell III, Robert D. AU - Deguenon, Jean Marcel AU - Ponnusamy, Loganathan AU - Reisig, Dominic AU - Pozo-Valdivia, Alejandro Del AU - Kurtz, Ryan W. AU - Roe, R. Michael T2 - International Journal of Molecular Sciences AB - Several different agricultural insect pests have developed field resistance to Bt (Bacillus thuringiensis) proteins (ex. Cry1Ac, Cry1F, etc.) expressed in crops, including corn and cotton. In the bollworm, Helicoverpa zea, resistance levels are increasing; recent reports in 2019 show up to 1000-fold levels of resistance to Cry1Ac, a major insecticidal protein in Bt-crops. A common method to analyze global differences in gene expression is RNA-seq. This technique was used to measure differences in global gene expression between a Bt-susceptible and Bt-resistant strain of the bollworm, where the differences in susceptibility to Cry1Ac insecticidal proteins were 100-fold. We found expected gene expression differences based on our current understanding of the Bt mode of action, including increased expression of proteases (trypsins and serine proteases) and reduced expression of Bt-interacting receptors (aminopeptidases and cadherins) in resistant bollworms. We also found additional expression differences for transcripts that were not previously investigated, i.e., transcripts from three immune pathways-Jak/STAT, Toll, and IMD. Immune pathway receptors (ex. PGRPs) and the IMD pathway demonstrated the highest differences in expression. Our analysis suggested that multiple mechanisms are involved in the development of Bt-resistance, including potentially unrecognized pathways. DA - 2020/9/7/ PY - 2020/9/7/ DO - 10.3390/ijms21186528 VL - 21 IS - 18 SP - 6528 J2 - IJMS LA - en OP - SN - 1422-0067 UR - http://dx.doi.org/10.3390/ijms21186528 DB - Crossref KW - Helicoverpa zea KW - bollworm KW - Bt-resistance KW - insect immunity KW - Cry1Ac resistance ER - TY - JOUR TI - COVID-19 control across urban-rural gradients AU - Wells, Konstans AU - Lurgi, Miguel AU - Collins, Brendan AU - Lucini, Biagio AU - Kao, Rowland R. AU - Lloyd, Alun L. AU - Frost, Simon D.W. AU - Gravenor, Mike B. AB - Abstract Controlling the regional re-emergence of SARS-CoV-2 after its initial spread in ever-changing personal contact networks and disease landscapes is a challenging task. In a landscape context, contact opportunities within and between populations are changing rapidly as lockdown measures are relaxed and a number of social activities re-activated. Using an individual-based metapopulation model, we explored the efficacy of different control strategies across an urban-rural gradient in Wales, UK. Our model shows that isolation of symptomatic cases, or regional lockdowns in response to local outbreaks, have limited efficacy unless the overall transmission rate is kept persistently low. Additional isolation of non-symptomatic infected individuals, who may be detected by effective test and trace strategies, is pivotal to reduce the overall epidemic size over a wider range of transmission scenarios. We define an ‘urban-rural gradient in epidemic size’ as a correlation between regional epidemic size and connectivity within the region, with more highly connected urban populations experiencing relatively larger outbreaks. For interventions focused on regional lockdowns, the strength of such gradients in epidemic size increased with higher travel frequencies, indicating a reduced efficacy of the control measure in the urban regions under these conditions. When both non-symptomatic and symptomatic individuals are isolated or regional lockdown strategies are enforced, we further found the strongest urban-rural epidemic gradients at high transmission rates. This effect was reversed for strategies targeted at symptomatics only. Our results emphasise the importance of test-and-tracing strategies and maintaining low transmission rates for efficiently controlling COVID19 spread, both at landscape scale and in urban areas. Author summary The spread of infectious diseases is the outcome of contact patterns and involves source-sink dynamics of how infectious individuals spread the disease through pools of susceptible individuals. Control strategies that aim to reduce disease spread often need to accept ongoing transmission chains and therefore, may not work equally well in different scenarios of how individuals and populations are connected to each other. To understand the efficacy of different control strategies to contain the spread of COVID19 across gradients of urban and rural populations, we simulated a large range of different control strategies in response to regional COVID19 outbreaks, involving regional lockdown and the isolation individuals that express symptoms and those that developed not symptoms but may contribute to disease transmission. Our results suggest that isolation of asymptomatic individuals through intensive test-and-tracing is important for efficiently reducing the epidemic size. Regional lockdowns and the isolation of symptomatic cases only are of limited efficacy for reducing the epidemic size, unless overall transmission rate is kept persistently low. Moreover, we found high overall transmission rates to result in relatively larger epidemics in urban than in rural communities for these control strategies, emphasising the importance of keeping transmission rates constantly low in addition to regional measures to avoid the disease spread at large scale. DA - 2020/9/9/ PY - 2020/9/9/ DO - 10.1101/2020.09.07.20189597 VL - 9 UR - https://doi.org/10.1101/2020.09.07.20189597 ER - TY - JOUR TI - Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs AU - Scott, Maxwell J. AU - Benoit, Joshua B. AU - Davis, Rebecca J. AU - Bailey, Samuel T. AU - Varga, Virag AU - Martinson, Ellen O. AU - Hickner, Paul V. AU - Syed, Zainulabeuddin AU - Cardoso, Gisele A. AU - Torres, Tatiana T. AU - Weirauch, Matthew T. AU - Scholl, Elizabeth H. AU - Phillippy, Adam M. AU - Sagel, Agustin AU - Vasquez, Mario AU - Quintero, Gladys AU - Skoda, Steven R. T2 - Communications Biology AB - Abstract The New World Screwworm fly, Cochliomyia hominivorax , is a major pest of livestock in South America and Caribbean. However, few genomic resources have been available for this species. A genome of 534 Mb was assembled from long read PacBio DNA sequencing of DNA from a highly inbred strain. Analysis of molecular evolution identified 40 genes that are likely under positive selection. Developmental RNA-seq analysis identified specific genes associated with each stage. We identify and analyze the expression of genes that are likely important for host-seeking behavior (chemosensory), development of larvae in open wounds in warm-blooded animals (heat shock protein, immune response) and for building transgenic strains for genetic control programs including gene drive (sex determination, germline). This study will underpin future experiments aimed at understanding the parasitic lifestyle of the screwworm fly and greatly facilitate future development of strains for efficient systems for genetic control of screwworm. DA - 2020/8/4/ PY - 2020/8/4/ DO - 10.1038/s42003-020-01152-4 VL - 3 IS - 1 SP - J2 - Commun Biol LA - en OP - SN - 2399-3642 UR - http://dx.doi.org/10.1038/s42003-020-01152-4 DB - Crossref ER - TY - JOUR TI - Mycorrhizal nitrogen uptake of wheat is increased by earthworm activity only under no-till and straw removal conditions AU - Yang, Haishui AU - Zhou, Jiajia AU - Weih, Martin AU - Li, Yifan AU - Zhai, Silong AU - Zhang, Qian AU - Chen, Weiping AU - Liu, Jian AU - Liu, Ling AU - Hu, Shuijin T2 - APPLIED SOIL ECOLOGY AB - A large part of crop nutrient uptake occurs through the interaction of roots with symbiotic arbuscular mycorrhizal fungi (AMF). However, it is still an open question how straw management and earthworm activity affect AMF community structure and their nitrogen-transferring function in wheat. A split-plot field experiment was conducted to address this question. Three straw management regimes including different tillage treatments (no-till with no straw, NTNS; rotary tillage with straw return, RTSR and ditch-buried straw return, DBSR), and two earthworm treatments (no earthworm, −E; and earthworm addition, +E) were conducted. The AMF community structure in the wheat roots was characterized with high-throughput sequencing, and its function in terms of N acquisition was measured with 15N isotope tracing through hyphal in-growth cores. Our results showed that both the DBSR and RTSR treatments significantly changed AMF community composition and enhanced the mycorrhiza-mediated plant N uptake when compared to NTNS. The effect of earthworm activity on AMF community composition and mycorrhiza-mediated N uptake strongly depended on the straw management regimes. While earthworm presence increased AMF dominance (+32.9%) and mycorrhizal N uptake (+2.05-fold) under straw removal, they decreased AMF dominance (−30.4% and −41.9% respectively) and mycorrhizal N uptake (−37.3% and −34.3% respectively) under both DBSR and RTSR treatments in comparison with the absence of earthworms. It is concluded that straw addition shifts the AMF community structure and increases N uptake by the host plants; and that the effect of earthworms on AMF community structure and functioning depends on the straw management regime. The results suggest that straw management and its interaction with earthworms can affect mycorrhiza-mediated plant N uptake, possibly through altering some dominant AMF taxa. DA - 2020/11// PY - 2020/11// DO - 10.1016/j.apsoil.2020.103672 VL - 155 SP - SN - 1873-0272 KW - Arbuscular mycorrhizal fungi KW - Crop residue incorporation KW - Wheat KW - Nitrogen uptake ER - TY - JOUR TI - Metabolically engineeredCaldicellulosiruptor besciias a platform for producing acetone and hydrogen from lignocellulose AU - Straub, Christopher T. AU - Bing, Ryan G. AU - Otten, Jonathan K. AU - Keller, Lisa M. AU - Zeldes, Benjamin M. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - BIOTECHNOLOGY AND BIOENGINEERING AB - The production of volatile industrial chemicals utilizing metabolically engineered extreme thermophiles offers the potential for processes with simultaneous fermentation and product separation. An excellent target chemical for such a process is acetone (Tb = 56°C), ideally produced from lignocellulosic biomass. Caldicellulosiruptor bescii (Topt 78°C), an extremely thermophilic fermentative bacterium naturally capable of deconstructing and fermenting lignocellulose, was metabolically engineered to produce acetone. When the acetone pathway construct was integrated into a parent strain containing the bifunctional alcohol dehydrogenase from Clostridium thermocellum, acetone was produced at 9.1 mM (0.53 g/L), in addition to minimal ethanol 3.3 mM (0.15 g/L), along with net acetate consumption. This demonstrates that C. bescii can be engineered with balanced pathways in which renewable carbohydrate sources are converted to useful metabolites, primarily acetone and H2 , without net production of its native fermentation products, acetate and lactate. DA - 2020/12// PY - 2020/12// DO - 10.1002/bit.27529 VL - 117 IS - 12 SP - 3799-3808 SN - 1097-0290 KW - acetone KW - Caldicellulosiruptor bescii KW - extreme thermophiles KW - metabolic engineering ER - TY - JOUR TI - Predominant role of soil moisture in regulating the response of ecosystem carbon fluxes to global change factors in a semi-arid grassland on the Loess Plateau AU - Su, Fanglong AU - Wang, Fuwei AU - Li, Zhen AU - Wei, Yanan AU - Li, Shijie AU - Bai, Tongshuo AU - Wang, Yi AU - Guo, Hui AU - Hu, Shuijin T2 - SCIENCE OF THE TOTAL ENVIRONMENT AB - Climate warming, altered precipitation and nitrogen deposition may critically affect plant growth and ecosystem carbon fluxes. However, the underlying mechanisms are not fully understood. We conducted a 2-yr, multi-factor experiment (warming (W), altered precipitation (+30% and − 30%) and nitrogen addition (N)) in a semi-arid grassland on the Loess Plateau to study how these factors affect ecosystem carbon fluxes. Surprisingly, no interactive effects of warming, altered precipitation and nitrogen addition were detected on parameters of ecosystem carbon fluxes, including net ecosystem CO2 exchange (NEE), ecosystem respiration (ER), gross ecosystem productivity (GEP) and soil respiration (SR). Warming marginally reduced NEE and GEP mainly due to its negative effects on them in July and August. Altered precipitation significantly affected all parameters of carbon fluxes with precipitation reduction decreasing NEE, ER and GEP, whereas precipitation addition increasing SR. In contrast, nitrogen addition had little effect on any parameters of carbon fluxes. Soil moisture was the most important driver and positively correlated with ecosystem carbon fluxes and warming impacted ecosystem carbon fluxes indirectly by decreasing soil moisture. While plant community cover did not show significant association with carbon fluxes, semi-shrubs cover was positively related to NEE, ER and GEP. Together, these results suggest that soil water availability, rather than soil temperature and nitrogen availability, may dominate the effect of the future multi-faceted global changes on semi-arid grassland carbon fluxes on the Loess Plateau. DA - 2020/10/10/ PY - 2020/10/10/ DO - 10.1016/j.scitotenv.2020.139746 VL - 738 SP - SN - 1879-1026 KW - Carbon fluxes KW - Global change KW - Plant cover KW - Soil moisture KW - Soil temperature ER - TY - JOUR TI - Engineering the cellulolytic extreme thermophile Caldicellulosiruptor bescii to reduce carboxylic acids to alcohols using plant biomass as the energy source AU - Rubinstein, Gabriel M AU - Lipscomb, Gina L AU - Williams-Rhaesa, Amanda M AU - Schut, Gerrit J AU - Kelly, Robert M AU - Adams, Michael W W T2 - Journal of Industrial Microbiology and Biotechnology AB - Abstract Caldicellulosiruptor bescii is the most thermophilic cellulolytic organism yet identified (Topt 78 °C). It grows on untreated plant biomass and has an established genetic system thereby making it a promising microbial platform for lignocellulose conversion to bio-products. Here, we investigated the ability of engineered C. bescii to generate alcohols from carboxylic acids. Expression of aldehyde ferredoxin oxidoreductase (aor from Pyrococcus furiosus) and alcohol dehydrogenase (adhA from Thermoanaerobacter sp. X514) enabled C. bescii to generate ethanol from crystalline cellulose and from biomass by reducing the acetate produced by fermentation. Deletion of lactate dehydrogenase in a strain expressing the AOR–Adh pathway increased ethanol production. Engineered strains also converted exogenously supplied organic acids (isobutyrate and n-caproate) to the corresponding alcohol (isobutanol and hexanol) using both crystalline cellulose and switchgrass as sources of reductant for alcohol production. This is the first instance of an acid to alcohol conversion pathway in a cellulolytic microbe. DA - 2020/8/1/ PY - 2020/8/1/ DO - 10.1007/s10295-020-02299-z VL - 47 IS - 8 SP - 585-597 LA - en OP - SN - 1476-5535 1367-5435 UR - http://dx.doi.org/10.1007/s10295-020-02299-z DB - Crossref KW - Thermophile KW - Biofuels KW - Lignocellulose KW - Metabolic engineering KW - Caldicellulosiruptor ER - TY - JOUR TI - Incorporating environmental factors to describe wild radish (Raphanus raphanistrum) seedling emergence and plant phenology AU - Piskackova, Theresa Reinhardt AU - Reberg-Horton, S. Chris AU - Richardson, Robert J. AU - Jennings, Katie M. AU - Leon, Ramon G. T2 - Weed Science AB - Abstract Wild radish ( Raphanus raphanistrum L.) is a weed found globally in agricultural systems. The facultative winter annual nature of this plant and high genetic variability makes modeling its growth and phenology difficult. In the present study, R. raphanistrum natural seedbanks exhibited a biphasic pattern of emergence, with emergence peaks occurring in both fall and spring. Traditional sigmoidal models were inadequate to fit this pattern, regardless of the predictive environmental variable, and a corresponding biphasic model (sigmoidal + Weibull) was used to describe emergence based on the best parameters. Each best-fit chronological, thermal, and hydrothermal model accounted for at least 85% of the variation of the validation data. Observations on phenology progression from four cohorts were used to create a common model that described all cohorts adequately. Different phenological stages were described using chronological, thermal, hydrothermal, daylength-dependent thermal time, and daylength-dependent hydrothermal time. Integrating daylength and temperature into the models was important for predicting reproductive stages of R. raphanistrum . DA - 2020/11/26/ PY - 2020/11/26/ DO - 10.1017/wsc.2020.64 VL - 8 SP - 1-12 UR - https://doi.org/10.1017/wsc.2020.64 KW - Hydrothermal time KW - integrated weed management KW - predictive models KW - thermal time KW - weed growth ER - TY - JOUR TI - The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. ‘Atlantic’-derived F1 population AU - Silva Pereira, Guilherme AU - Mollinari, Marcelo AU - Schumann, Mitchell J. AU - Clough, Mark E. AU - Zeng, Zhao-Bang AU - Yencho, G. Craig AB - Abstract There are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato, Solanum tuberosum (2 n = 4 x = 48). The development of new analytical methods has made it valuable to re-analyze an F1 population ( n = 156) derived from a cross involving ‘Atlantic’, a widely grown chipping variety in the USA. A fully integrated genetic map with 4,285 single nucleotide polymorphisms, spanning 1,630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0∼72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2∼39.2%). Seven traits were evaluated over four years (2006-8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified as QTL for maturity, plant yield, specific gravity and internal heat necrosis resistance over different years were co-located. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity ( StCDF1 ) and tuber formation ( POTH1 ). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species. DA - 2020/8/24/ PY - 2020/8/24/ DO - 10.1101/2020.08.24.265397 VL - 8 UR - https://doi.org/10.1101/2020.08.24.265397 ER - TY - JOUR TI - Building biosecurity for synthetic biology AU - Trump, Benjamin D. AU - Galaitsi, S. E. AU - Appleton, Evan AU - Bleijs, Diederik A. AU - Florin, Marie-Valentine AU - Gollihar, Jimmy D. AU - Hamilton, R. Alexander AU - Kuiken, Todd AU - Lentzos, Filippa AU - Mampuys, Ruth AU - Merad, Myriam AU - Novossiolova, Tatyana AU - Oye, Kenneth AU - Perkins, Edward AU - Garcia-Reyero, Natalia AU - Rhodes, Catherine AU - Linkov, Igor T2 - MOLECULAR SYSTEMS BIOLOGY AB - Commentary21 July 2020Open Access Building biosecurity for synthetic biology Benjamin D Trump Corresponding Author [email protected] orcid.org/0000-0002-4097-733X US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author SE Galaitsi US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author Evan Appleton Harvard University, Cambridge, MA, USA Search for more papers by this author Diederik A Bleijs Biosecurity Office, Netherlands National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands Search for more papers by this author Marie-Valentine Florin International Risk Governance Center, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Search for more papers by this author Jimmy D Gollihar US Army Research Laboratory (ARL), Adelphi, MD, USA Search for more papers by this author R Alexander Hamilton United Nations Interregional Crime and Justice Research Institute (UNICRI), Turin, Italy Search for more papers by this author Todd Kuiken orcid.org/0000-0001-7851-6232 Genetic Engineering & Society Center at North Carolina State University, Raleigh, NC, USA Search for more papers by this author Filippa Lentzos King's College London, London, UK Search for more papers by this author Ruth Mampuys Netherlands Commission on Genetic Modification (COGEM), Bilthoven, The Netherlands Search for more papers by this author Myriam Merad French National Centre for Scientific Research, Paris, France Search for more papers by this author Tatyana Novossiolova Center for the Study of Democracy, Sofia, Bulgaria Search for more papers by this author Kenneth Oye International Risk Governance Center, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Massachusetts Institute of Technology, Cambridge, MA, USA Search for more papers by this author Edward Perkins US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author Natàlia Garcia-Reyero US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author Catherine Rhodes University of Cambridge, Cambridge, UK Search for more papers by this author Igor Linkov orcid.org/0000-0002-0823-8107 US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author Benjamin D Trump Corresponding Author [email protected] orcid.org/0000-0002-4097-733X US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author SE Galaitsi US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author Evan Appleton Harvard University, Cambridge, MA, USA Search for more papers by this author Diederik A Bleijs Biosecurity Office, Netherlands National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands Search for more papers by this author Marie-Valentine Florin International Risk Governance Center, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Search for more papers by this author Jimmy D Gollihar US Army Research Laboratory (ARL), Adelphi, MD, USA Search for more papers by this author R Alexander Hamilton United Nations Interregional Crime and Justice Research Institute (UNICRI), Turin, Italy Search for more papers by this author Todd Kuiken orcid.org/0000-0001-7851-6232 Genetic Engineering & Society Center at North Carolina State University, Raleigh, NC, USA Search for more papers by this author Filippa Lentzos King's College London, London, UK Search for more papers by this author Ruth Mampuys Netherlands Commission on Genetic Modification (COGEM), Bilthoven, The Netherlands Search for more papers by this author Myriam Merad French National Centre for Scientific Research, Paris, France Search for more papers by this author Tatyana Novossiolova Center for the Study of Democracy, Sofia, Bulgaria Search for more papers by this author Kenneth Oye International Risk Governance Center, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Massachusetts Institute of Technology, Cambridge, MA, USA Search for more papers by this author Edward Perkins US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author Natàlia Garcia-Reyero US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author Catherine Rhodes University of Cambridge, Cambridge, UK Search for more papers by this author Igor Linkov orcid.org/0000-0002-0823-8107 US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA Search for more papers by this author Author Information Benjamin D Trump *,1, SE Galaitsi1, Evan Appleton2, Diederik A Bleijs3, Marie-Valentine Florin4, Jimmy D Gollihar5, R Alexander Hamilton6, Todd Kuiken7, Filippa Lentzos8, Ruth Mampuys9, Myriam Merad10, Tatyana Novossiolova11, Kenneth Oye4,12, Edward Perkins1, Natàlia Garcia-Reyero1, Catherine Rhodes13 and Igor Linkov1 1US Army Corps of Engineers, Engineer Research and Development Center, Vicksburg, MS, USA 2Harvard University, Cambridge, MA, USA 3Biosecurity Office, Netherlands National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands 4International Risk Governance Center, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland 5US Army Research Laboratory (ARL), Adelphi, MD, USA 6United Nations Interregional Crime and Justice Research Institute (UNICRI), Turin, Italy 7Genetic Engineering & Society Center at North Carolina State University, Raleigh, NC, USA 8King's College London, London, UK 9Netherlands Commission on Genetic Modification (COGEM), Bilthoven, The Netherlands 10French National Centre for Scientific Research, Paris, France 11Center for the Study of Democracy, Sofia, Bulgaria 12Massachusetts Institute of Technology, Cambridge, MA, USA 13University of Cambridge, Cambridge, UK *Corresponding author. E-mail: [email protected] Mol Syst Biol (2020)16:e9723https://doi.org/10.15252/msb.20209723 PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info The fast-paced field of synthetic biology is fundamentally changing the global biosecurity framework. Current biosecurity regulations and strategies are based on previous governance paradigms for pathogen-oriented security, recombinant DNA research, and broader concerns related to genetically modified organisms (GMOs). Many scholarly discussions and biosecurity practitioners are therefore concerned that synthetic biology outpaces established biosafety and biosecurity measures to prevent deliberate and malicious or inadvertent and accidental misuse of synthetic biology's processes or products. This commentary proposes three strategies to improve biosecurity: Security must be treated as an investment in the future applicability of the technology; social scientists and policy makers should be engaged early in technology development and forecasting; and coordination among global stakeholders is necessary to ensure acceptable levels of risk. All technology has dual-use aspects: It can be used for beneficial and harmful purposes. The Internet is a source of limitless information and interaction but it also enables much criminal behavior under the guise of anonymity. Similarly, synthetic biology (SB) has great potential for beneficial and valuable applications and products but could also be misused to harm humans or the environment. Governance regimes must therefore balance mitigating the risk of misuse with supporting opportunities for innovation and development. However, biosecurity efforts remain mired in uncertainty about the capabilities of SB and its practitioners’ motivations in the growing number of contexts in which it is applied. Two decades into the 21st century, governments are still imposing old rules on a new technology, an insufficient strategy to provide security in the future. Though it lacks a universal definition, SB has been described as “designing and constructing biological modules, biological systems, and biological machines or, re-design of existing biological systems for useful purposes” (Nakano et al, 2013). The Engineering Biology Research Consortium (EBRC) puts SB in an evolutionary context that “builds on the advances in molecular, cell, and systems biology” to design and construct genetic circuits, metabolic pathways, or other constructs to address defined objectives. Building an effective biosecurity strategy that covers these SB design approaches and technologies requires understanding the novel threats that these technologies create, along with the structural vulnerabilities products stemming from these technologies can exploit and the likely causes of inadequate biosecurity practices. New concerns arise from SB's broad scope, wider availability, complexity, and uncertainty over current and future capabilities. One very critical technology is gene editing to precisely modify genomes. One of its applications, gene drive, has raised particular concerns as it can quickly propagate a specific suite of genes or alleles through a population by circumventing Mendelian inheritance and thereby increasing the probability that these genes are passed on to offspring. Gene editing has enormous potential for improving human health, agriculture, and the environment, but it can also cause substantial and irreversible harms. Such harms might include the uncontrolled diffusion of gene-edited material in the environment, off-target effects from genome editing, or the disruption of ecologies with genetically altered organisms, especially with engineered gene drive systems. Harms may also arise through the deliberate use of these techniques to target humans and/or the environment. Such intentional misuse of SB techniques requires two circumstances: the availability of techniques and know-how that could be exploited for irresponsible or nefarious purposes (“information hazard”); and the ability to use such knowledge and tools to generate and disseminate harmful engineered organisms. Such knowledge includes the publication of a method for synthesizing horsepox; some critics argue that this information might reasonably enable a nefarious actor to reconstitute smallpox or to synthetize other viruses. Additionally, the widely publicized sequence and recreation of the 1918 Spanish Influenza virus, which killed some 50 million people at the close of the First World War (Evans & Selgelid, 2015), could enable other actors to cause harm. Even non-pathogenic approaches have been described as dual-use research, ranging from the disruption of local ecologies via gene drives to the manipulation or destruction of inorganic materials through engineered bacteria. Potential misusers These and other cases show that interested actors or parties can acquire information and apply existing tools for advanced genetic engineering with limited to no oversight. Those who may choose to misuse SB could possess a broad diversity of backgrounds, motivations, strategic goals, and resources. From a top-down perspective, classical global biosecurity has focused on state actors with the scientific and technological know-how to pursue offensive biological research, including infamous examples such as Imperial Japan's Unit 731 during World War II, as well as postwar biological weapons programs in the UK, the USSR, and the USA. Typically, such offensive biological weapons capabilities were framed as “first strike” options or avenues to destabilize enemy ground forces that would not easily be deterred by conventional ordnance, such as the Hussein Government's development of bioweapons during the Iran-Iraq War via anthrax, botulinum toxin, and aflatoxin. In each instance, states developed scientific and materiel capability to construct, package, and deploy biological weapons for strategic measures. More recently, the pursuit of biological weapons has extended to non-state organizations. For example, al-Qaeda (anthrax) and Aum Shinrikyo (anthrax, botulinum toxin) both demonstrated an interest in bioweapons but with very limited success given the technological constraints at the time. However, even individuals or small cells have increased in number and destructive potential. Among the most infamous examples is Bruce Edwards Ivins, who according to the US Department of Justice, leveraged institutional resources as the sole actor responsible for the 2001 deployment of anthrax in letters to Congress and the media. Other actors could be disgruntled employees of sophisticated scientific laboratories or vengeful academics. As advances in genetic engineering become more accessible to private persons, a question remains regarding the rate-limiting steps (e.g., technical knowledge or inspiration) for such individual actors or small groups to pursue more sophisticated biological weapons. Currently, significant barriers remain for independent actors to access critical equipment and materials, but oversight organizations are not prepared for a future when intangible transfers reduce or overcome these obstacles. In 1975, the US National Institutes of Health (NIH) established compliance measures for genome engineering that were enforced through funding restrictions; however, much SB research now operates without NIH funding, approval or even awareness, and NIH does not oversee research in other countries. Today, the financial costs, time limitations, and skill requirements needed to use SB tools have scaled down to become even more broadly accessible. Furthermore, the requisite baseline knowledge will diminish over time as SB processes become more streamlined. While such broad access to sophisticated genetic engineering knowledge and equipment can accelerate scientific breakthroughs, it also places the responsibility of biosecurity on a near-infinite number of unsupervised actors across the globe (Fig 1). Indeed, in 2018, the States Parties to the Biological Weapons Convention (BWC) noted that access to technologies such as gene editing, gene drives, and gene synthesis is increasingly being conferred to actors with limited or no oversight from established industry or governmental organizations, raising concerns about potential violations of the BWC. Figure 1.Increasing number of global users able to access genetic engineering (blue) and synthetic biology (orange) technologies over time. Download figure Download PowerPoint Lack of oversight It is helpful to forecast and understand looming threats and potential mitigation strategies at various scales, but international treaties are not structured to oversee bottom-up efforts related to SB below the national scale. One response may be more engagement by overseeing agencies such as the NIH. Another option is the Responsible Research and Innovation (RRI) approach to assess societal implications of emerging research to better align processes and expected outcomes with the needs and values of society. Where top-down governance proves insufficient, other actors such as universities, non-profits, and companies will need to act as gatekeepers and watchdogs to protect against nefarious actors. Top-down governance may then support such initiatives, which will require harmonization and communication at the international level. Long-standing biosecurity policy practices appear to have gaps in biosecurity oversight for SB. These policies include the framing of security as a cost or undesirable expense; the siloing of scholarship and practice across disciplinary domains and between academia, government, industry, and civil society; and the narrow framing of security issues that ignore technology developments. Each of these concerns could be addressed by policy solutions that both support technological development and mitigate security threats while facilitating public engagement in SB and investment in its products. These policies must be scalable, transferrable, and adaptable to incorporate emerging technical and social challenges. Security must be an investment, not a cost Investment implies allocating resources with the expectation of greater gains in the future. To incentivize investments in biosecurity, the entity that provides the initial resources must therefore have a share in future benefits. At present, however, biosecurity is framed as an obligation for individual scientists, organizations, and companies to use institutional funds to comply with unstated and often ambiguous needs for general security. This is an unstable balance of costs and benefits, and thus, few institutions prefer to minimize expenditures associated with fulfilling basic oversight requirements (Gillum et al, 2018). Yet, the best argument in favor of investing in biosecurity is that SB's development requires public acceptance, which remains tentative at present (Oliver, 2018). Such acceptance could drop precipitously if the public is inadvertently exposed to harm as a result of a lack of oversight. Biosecurity therefore requires an approach that incentivizes managers to keep abreast of risks and concerns. Biosecurity can signal to the general public that SB products have been appropriately screened to assure beneficial uses. The US Nuclear Regulatory Commission (nrc.gov) performs this for research and test reactors, mostly in universities or colleges, but there is no analogous commission for biosecurity. The members of the International Gene Synthesis Consortium (IGSC)—which are most of the DNA synthesis companies—devote company resources to screening customers and their requests for potential security issues: This is in the best interests of the companies, despite the fact that no legal mandate requires them to do so. Similarly, in January 2020, the Nuclear Threat Initiative (NTI) and the World Economic Forum recommended in a report the establishment of a Technical Consortium to develop a common DNA sequence screening mechanism, following up on work and conclusions by the IGSC. Across such efforts, Industry has realized that companies stand to gain from aligning themselves with the risk aversion of the public and to invest accordingly in security. This was the lesson for the chemical industry that initially lobbied against the 1925 Geneva Protocol against chemical weapons and prevented its ratification for 50 years in the USA (Tucker, 2007). Today's chemical industry is a strong advocate of chemical arms control (e.g., The Responsible Care Programme). Bridges are needed between biosecurity experts, social scientists, and practitioners Many emerging technologies develop out of sight of social scientists and policy commentators (Linkov et al, 2018). Institutional incentives to advance science and technology usually do not create opportunities for inquiry and discussion between developers, risk assessors, ethicists, and policy analysts at the early stages of research. As a result, social science discussions, especially those that the public may relate to such as concerns related to ethics, morals, and risk to health, are often relegated to an afterthought and isolated within institutions or organizations. To address the problem, the RRI programs in the UK and the EU involve experts from diverse fields to assess scientific advancement with the aim of mitigating risk, upholding core morals and values, and achieving research commodification in equitable and sustainable means. Measures such as RRI are not intended to block research or publication of results, but to reduce downstream harms that might place developers, companies, and governments potentially responsible for expensive cleanup and/or insurance efforts. More social inquiry alongside significant funding for SB will improve deliberation into potential biosecurity threats and reduce the potential for unexpected dual-use publications or developments. The lack of transparency within the process of technical development removes an essential opportunity to consider whether an idea or goal presents a biosecurity hazard that broader society will not condone. A recent example includes Dr. Jiankui He's work to produce the world's first genome-edited babies in late 2018. His experiments were widely condemned by leading biologists around the world, yet the small circle of people and institutions that engaged with his experiment while it was underway did nothing to stop him (Cohen, 2019). Broader engagement may have shifted or even halted Dr. He's work to better align with global norms and expectations for human experimentation. The future of biosecurity must be a collective global effort Neither “synthetic biology” nor “biosecurity” has a universally accepted definition, leaving states and organizations to include or exclude lines of research depending on their risk tolerance or incentives in pursuing specific goals. Though conventions such as the BWC and Chemical Weapons Convention (CWC) provide common ground related to weaponry, the ethics and practices that support their objectives are not necessarily taught or enforced within all institutions. Institutional, political, and economic influences shape local attitudes toward the perception, management, and communication of risk from emerging technologies, requiring that biosecurity measures are tailored to different national and institutional contexts. However, biosecurity equally represents a global public good, requiring international dialogue and collaboration to achieve minimum biosecurity standards. Where some governments or industries may adopt a precautionary approach to manage uncertain biological threats, others may be more risk tolerant and thereby more vulnerable to certain threats. Countries may also avoid disclosing information about their activities or committing themselves to any restrictions on behaviors. Challenges stemming from diverging practices of SB biosecurity governance are exacerbated by the increasingly globalized, dispersed, and distributed nature of the technology and its research. Advanced biological research is no longer dominated by the Western world, and this may require different approaches to or priorities for biosecurity. Russia's Federal Research Programme for Genetic Technologies Development for 2019–2027 intends to “implement a comprehensive solution to the task of the accelerated development of genetic technologies, including genetic editing…” Saudi Arabia is funding research to develop microbial cell factories to produce fuels and chemicals, while Singapore is investing considerable resources into life and environmental sciences research. The Chinese Academy of Sciences is establishing an Institute of Synthetic Biology, which is tasked with the dual responsibilities of fostering roadmaps for future development while establishing safety and security norms for researchers at Chinese institutions. There are no top-down efforts beyond existing mechanisms like the BWC or the CWC to standardize global governance and usage of SB, and bottom-up efforts are not coordinated in their reach or messaging. Newcomers to SB may have differing tolerances and understandings of risk than more experienced technology developers. The implications, though vast, can be grouped into two general areas. One includes diverging safety and security practices at various points of an international supply chain that forms the backbone of an increasingly globalized economy. Another includes the potential for small-scale experiments to escape national biosecurity control and spill across political boundaries. While one country may find the environmental risk of a particular SB application acceptable, its spread across borders into another country may disrupt those local ecologies or expose vulnerable human, animal, and plant populations to irreversible consequences. The nature of certain SB applications, in particular gene drive, makes it impossible for risk-averse countries to wholly quarantine themselves from another country's decisions. This is also an issue of equity: Risk-tolerant countries will reap the rewards when beneficial technologies emerge, while risk-averse countries may bear their neighbor's risks without any means to capture potential rewards. An environment of competing and incongruent risk architectures causes individual states, organizations, or industries to arrive at differing definitions of security threats or acceptable levels of loss in pursuit of a technology's gains. For a technology as uncertain as SB, this may set governments, companies, and other research organizations down vastly differing policy paths and impede consensus to assure security for anyone. Increasing monetary and non-monetary benefits and reducing risks Many individuals and organizations are actively tackling the biosecurity challenge. The International Genetically Engineered Machine (iGEM) synthetic biology competition, which began in 2004, mandates that organizational leaders and judges conduct rigorous reviews of the materials and planned experiments of each team. Safety and security concerns receive further scrutiny from iGEM's Safety and Security Committee (SSC) and are screened for potential hazards by a commercial partner; all of this is part of the competition's guidance for participating students (Millett et al, 2019). Biosecurity precautions are also incorporated in the “Do-It-Yourself” (DIY) biology community's code of ethics in North America and Europe (DIYbio.org), the statement of shared purpose from MIT's Bio Summit 2.0 (www.biosummit.org), the priority of the States Parties to the BWC to establish a code of conduct (Meeting of the States Parties, 2018), the construction of biosecurity norms practices by the African Union for transgenic insects and genetically modified crops (Glover et al, 2018), and Australian foreign policy. There is a growing demand for an update to international biosecurity norms and practices akin to the Cartagena Protocol on Biosafety, to increase transparency, cooperation, and collective security in pursuit of SB. Yet, a question remains of how to invest and incentivize biosecurity with private actors? Such an answer requires focus not only on bench scientists, but also on various gatekeepers, overseers, and watchdogs involved in biotechnology research and development (e.g., the World Organisation for Animal Health's Guideline for Responsible Conduct in Veterinary Research). For example, the furtherance of dual-use research might be better controlled by training journal editors on what constitutes a potential information hazard within article submissions. Such considerations extend to the grant review process, where funders can require an up-to-date understanding of possible information and security hazards that may ensue over the course of the proposed work. In these and other instances, top-down and bottom-up collaboration is necessary to raise biosecurity awareness and to identify security threats, while bottom-up organizations, agencies, and universities conduct on-the-ground passive surveillance of possible dual-use security threats. One example of this fusion includes the US Federal Bureau of Investigation (FBI), which has sponsored and been working with iGEM to increase awareness of risks and to gain an understanding of possible or developing threats. Though no biosecurity effort will eliminate all threats—nor is such an environment desirable if it means universally forbidding research and innovation that can greatly benefit society—a layering of strengths and capabilities by government and private institutions will provide a more unified effort for biosecurity and might disincentivize actors from leveraging gaps in oversight to develop a biological weapon. Conclusions SB is a transformative technology poised to have at least as much impact as the digital revolution. As with scientific breakthroughs of the past two centuries, the potential for its misuse is globally present and warrants scrutiny at the highest levels of policy discourse. While some protection may be provided by developing specific countermeasures, preventative action may be more reliable. Biosecurity policies and practices must be updated to accommodate the novel challenges associated with SB and acknowledge the globalized and diverse nature of its threat space. Effective global biosecurity will not happen quickly nor will it be enthusiastically adopted by all governments or non-governmental organizations. Incentives to misuse synthetic biology with harmful consequences remain high for certain negligent actors, and the coming years may see such events affecting human, animal, or environmental health. Successful biosecurity implementation must be adaptable to quickly incorporate uncertainty as well as new capabilities. Urgent steps are required to place such notions into practice before a major threat incident, both to prevent the damage and subsequent policy reactions that could limit or ban technology platforms entirely. Now is the time to take steps to apply biosecurity to maximize technological benefits while minimizing its dual-use potential by improving the framing, prioritization, and governance of biosecurity risks. Disclaimer The statements herein are the author's opinions only and not necessarily representative of their host institutions. Acknowledgements The authors are grateful for the participation and support of attendees to the NATO Science for Peace and Security Programme Advanced Research Workshop (G5489) in July 2019. Additional acknowledgements are due to the International Risk Governance Center at École polytechnique fédérale de Lausanne, the US Office of Naval Research Global, and the US Army Engineer Research and Development Center. The authors and workshop organizers thank Patrick Rose for his support. The authors thank George Siharulidze for his assistance with figure development. The authors are grateful for the financial support of the NATO Science for Peace and Security Programme (Advanced Research Workshop G5489). Conflict of interest The authors declare that they have no conflict of interest. References Cohen J (2019) The untold story of the ‘circle of trust’ behind the world's first gene-edited babies. Science. https://doi.org/10.1126/science.aay9400Google Scholar Evans NG, Selgelid MJ (2015) Biosecurity and open-source biology: the promise and peril of distributed synthetic biological technologies. Sci Eng Ethics 21: 1065–1083CrossrefPubMedWeb of Science®Google Scholar Gillum D, Carrera LAO, Mendoza IA, Bates P, Bowens D, Jetson Z, Maldonado J, Mancini C, Miraldi M, Moritz R (2018) The 2017 Arizona biosecurity workshop: an open dialogue about biosecurity. 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World Organization for Animal Health (2019) Guidelines for responsible conduct in veterinary research. https://www.oie.int/fileadmin/Home/eng/Our_scientific_expertise/docs/pdf/BTR/A_GUIDELINES_VETERINARY_RESEARCH.pdf Previous ArticleNext Article Read MoreAbout the coverClose modalView large imageVolume 16,Issue 7,July 2020This month's cover highlights the article LymphoAtlas: a dynamic and integrated phosphoproteomic resource of TCR signaling in primary T cells by Marie Locard-Paulet, Guillaume Voisinne, Anne Gonzalez de Peredo, Romain Roncagalli and colleagues. The study presents LymphoAtlas, a phosphoproteomic dataset enabling the identification and visualization of phosphorylation dynamics during the first 10 minutes after TCR stimulation of primary mouse T cells. (Scientific image by Scistories LLC, www.scistories.com). Volume 16Issue 71 July 2020In this issue FiguresReferencesRelatedDetailsLoading ... DA - 2020/7// PY - 2020/7// DO - 10.15252/msb.20209723 VL - 16 IS - 7 SP - SN - 1744-4292 ER - TY - JOUR TI - Preserving connectivity under climate and land-use change: No one-size-fits-all approach for focal species in similar habitats AU - Costanza, Jennifer K. AU - Watling, James AU - Sutherland, Ron AU - Belyea, Curtis AU - Dilkina, Bistra AU - Cayton, Heather AU - Bucklin, David AU - Romanach, Stephanie S. AU - Haddad, Nick M. T2 - BIOLOGICAL CONSERVATION AB - Habitat connectivity is essential for maintaining populations of wildlife species, especially as climate changes. Knowledge about the fate of existing habitat networks in a changing climate and in light of land-use change is critical for determining which types of conservation actions must be taken to maintain those networks. However, information is lacking about how multiple focal species that use similar habitats overlap in the degree and geographic patterns of threats to linkages among currently suitable habitat patches. We sought to address that gap. We assessed climate change threat to existing linkages in the southeastern United States for three wildlife species that use similar habitats but differ in the degree to which their ranges are limited by climate, habitat specificity, and dispersal ability. Linkages for the specialist species (timber rattlesnake), whose range is climate-restricted, were more likely to serve as climate change refugia – that is, they were more likely to be climate-stable – by the middle of the 21st century. This contrasts with the two more generalist species (Rafinesque's big-eared bat and American black bear), whose linkages were threatened by climate change and thus required adaptation measures. Further incorporation of projected land-use change and current protection status for important linkages narrows down our recommended conservation actions for each species. Our results highlight the surprising ways in which even species that use similar habitats will experience differences in the degree and geographic patterns of threats to connectivity. Taking action before these projected changes occur will be critical for successful conservation. DA - 2020/8// PY - 2020/8// DO - 10.1016/j.biocon.2020.108678 VL - 248 SP - SN - 1873-2917 KW - Climate adaptation KW - Climate refugia KW - Corridor KW - Land-use change KW - Landscape conservation KW - Protection status ER - TY - JOUR TI - Measurement of Novel, Drinking Water-Associated PFAS in Blood from Adults and Children in Wilmington, North Carolina AU - Kotlarz, Nadine AU - McCord, James AU - Collier, David AU - Lea, C. Suzanne AU - Strynar, Mark AU - Lindstrom, Andrew B. AU - Wilkie, Adrien A. AU - Islam, Jessica Y. AU - Matney, Katelyn AU - Tarte, Phillip AU - Polera, M. E. AU - Burdette, Kemp AU - DeWitt, Jamie AU - May, Katlyn AU - Smart, Robert C. AU - Knappe, Detlef R. U. AU - Hoppin, Jane A. T2 - ENVIRONMENTAL HEALTH PERSPECTIVES AB - Vol. 128, No. 7 ResearchOpen AccessMeasurement of Novel, Drinking Water-Associated PFAS in Blood from Adults and Children in Wilmington, North Carolinais corrected byErratum: “Measurement of Novel, Drinking Water-Associated PFAS in Blood from Adults and Children in Wilmington, North Carolina” Nadine Kotlarz, James McCord, David Collier, C. Suzanne Lea, Mark Strynar, Andrew B. Lindstrom, Adrien A. Wilkie, Jessica Y. Islam, Katelyn Matney, Phillip Tarte, M.E. Polera, Kemp Burdette, Jamie DeWitt, Katlyn May, Robert C. Smart, Detlef R.U. Knappe, and Jane A. Hoppin Nadine Kotlarz Department of Civil, Construction, and Environmental Engineering, North Carolina State University (NCSU), Raleigh, North Carolina, USA Department of Biological Sciences, NCSU, Raleigh, North Carolina, USA Center for Human Health and the Environment, NCSU, Raleigh, North Carolina, USA Search for more papers by this author , James McCord Center for Environmental Measurement and Modeling, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA Search for more papers by this author , David Collier Center for Human Health and the Environment, NCSU, Raleigh, North Carolina, USA Department of Pediatrics, Brody School of Medicine, East Carolina University (ECU), Greenville, North Carolina, USA Search for more papers by this author , C. Suzanne Lea Center for Human Health and the Environment, NCSU, Raleigh, North Carolina, USA Department of Public Health, ECU, Greenville, North Carolina, USA Search for more papers by this author , Mark Strynar Center for Environmental Measurement and Modeling, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA Search for more papers by this author , Andrew B. Lindstrom Center for Environmental Measurement and Modeling, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA Search for more papers by this author , Adrien A. Wilkie Department of Biological Sciences, NCSU, Raleigh, North Carolina, USA Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, North Carolina, USA Search for more papers by this author , Jessica Y. Islam Department of Biological Sciences, NCSU, Raleigh, North Carolina, USA Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, North Carolina, USA Search for more papers by this author , Katelyn Matney New Hanover County Health Department, Wilmington, North Carolina, USA Search for more papers by this author , Phillip Tarte New Hanover County Health Department, Wilmington, North Carolina, USA Search for more papers by this author , M.E. Polera Cape Fear River Watch, Wilmington, North Carolina, USA Search for more papers by this author , Kemp Burdette Cape Fear River Watch, Wilmington, North Carolina, USA Search for more papers by this author , Jamie DeWitt Center for Human Health and the Environment, NCSU, Raleigh, North Carolina, USA Department of Pharmacology and Toxicology, ECU, Greenville, North Carolina, USA Search for more papers by this author , Katlyn May Center for Human Health and the Environment, NCSU, Raleigh, North Carolina, USA Search for more papers by this author , Robert C. Smart Department of Biological Sciences, NCSU, Raleigh, North Carolina, USA Center for Human Health and the Environment, NCSU, Raleigh, North Carolina, USA Search for more papers by this author , Detlef R.U. Knappe Department of Civil, Construction, and Environmental Engineering, North Carolina State University (NCSU), Raleigh, North Carolina, USA Center for Human Health and the Environment, NCSU, Raleigh, North Carolina, USA Search for more papers by this author , and Jane A. Hoppin Address correspondence to Jane A. Hoppin, Department of Biological Sciences, Campus Box 7633, NC State University, Raleigh, NC 27695-7633 USA. Telephone: (919) 515-2918. Email: E-mail Address: [email protected] Department of Biological Sciences, NCSU, Raleigh, North Carolina, USA Center for Human Health and the Environment, NCSU, Raleigh, North Carolina, USA Search for more papers by this author Published:22 July 2020CID: 077005https://doi.org/10.1289/EHP6837Cited by:26AboutSectionsPDF Supplemental Materials ToolsDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmail AbstractBackground:From 1980 to 2017, a fluorochemical manufacturing facility discharged wastewater containing poorly understood per- and polyfluoroalkyl substances (PFAS) to the Cape Fear River, the primary drinking water source for Wilmington, North Carolina, residents. Those PFAS included several fluoroethers including HFPO-DA also known as GenX. Little is known about the bioaccumulation potential of these fluoroethers.Objective:We determined levels of fluoroethers and legacy PFAS in serum samples from Wilmington residents.Methods:In November 2017 and May 2018, we enrolled 344 Wilmington residents ≥6 years of age into the GenX Exposure Study and collected blood samples. Repeated blood samples were collected from 44 participants 6 months after enrollment. We analyzed serum for 10 fluoroethers and 10 legacy PFAS using liquid chromatography–high-resolution mass spectrometry.Results:Participants’ ages ranged from 6 to 86 y, and they lived in the lower Cape Fear Region for 20 y on average (standard deviation: 16 y). Six fluoroethers were detected in serum; Nafion by-product 2, PFO4DA, and PFO5DoA were detected in >85% of participants. PFO3OA and NVHOS were infrequently detected. Hydro-EVE was present in a subset of samples, but we could not quantify it. GenX was not detected above our analytical method reporting limit (2 ng/mL). In participants with repeated samples, the median decrease in fluoroether levels ranged from 28% for PFO5DoA to 65% for PFO4DA in 6 months due to wastewater discharge control. Four legacy PFAS (PFHxS, PFOA, PFOS, PFNA) were detected in most (≥97%) participants; these levels were higher than U.S. national levels for the 2015–2016 National Health and Nutrition Examination Survey. The sum concentration of fluoroethers contributed 24% to participants’ total serum PFAS (median: 25.3 ng/mL).Conclusion:Poorly understood fluoroethers released into the Cape Fear River by a fluorochemical manufacturing facility were detected in blood samples from Wilmington, North Carolina, residents. Health implications of exposure to these novel PFAS have not been well characterized. https://doi.org/10.1289/EHP6837IntroductionPer- and polyfluoroalkyl substances (PFAS) are a broad class of synthetic chemicals used to manufacture fluoropolymers, stain repellents, paper coatings, and fire-fighting foams (Kissa 2001). In addition to the PFAS produced for commercial purposes, other PFAS can be formed as by-products or impurities of fluorochemical production (Dinglasan et al. 2004; James and Franklin 1966; Liang et al. 1998; Moore et al. 1966). Many PFAS have high aqueous solubility and are persistent in the environment. As a result, PFAS are stable in water and can travel over long distances in freshwater and marine ecosystems (Banzhaf et al. 2017; Möller et al. 2010). PFAS releases into the environment can therefore impact drinking water sources both near and far from the source of contamination (Hu et al. 2016; Ingelido et al. 2018; Mak et al. 2009; Pan et al. 2018; Sharma et al. 2016; Sun et al. 2016).PFAS are not substantially removed by most conventional drinking-water treatment processes, including coagulation, flocculation, sedimentation, filtration, and disinfection (Rahman et al. 2014). Elevated concentrations of PFAS have been reported in the finished drinking water of community water systems that source water from areas with industrial facilities producing or using PFAS (Graber et al. 2019; Hu et al. 2016). Notably, perfluorooctanoic acid (PFOA) releases from a fluorochemical plant near Parkersburg, West Virginia, resulted in parts-per-billion levels of PFOA in drinking water sourced from contaminated wells; in the community, tap water consumption was a significant predictor of serum PFOA levels (Emmett et al. 2006; Hoffman et al. 2011). Human exposure to PFAS [PFOA and perfluorooctane sulfonate (PFOS) are the most studied to date] has been associated with thyroid disease, ulcerative colitis, elevated cholesterol levels, developmental delays, liver disease, kidney and testicular cancer, and immunosuppression (ATSDR 2018; DeWitt et al. 2009; Steenland et al. 2010; Sunderland et al. 2019).In North Carolina, a 2,150-acre fluorochemical manufacturing facility (i.e., Fayetteville Works) (Figure 1) discharged process wastewater to the Cape Fear River as early as 1980 (Wagner and Buckland 2017). Several poorly understood PFAS, including hexafluoropropylene oxide dimer acid (HFPO-DA or GenX), have been detected in water samples collected downriver of the facility’s effluent discharge point (Hopkins et al. 2018; McCord and Strynar 2019; McCord et al. 2018; Strynar et al. 2015; Sun et al. 2016; Zhang et al. 2019). These PFAS are collectively referred to as fluoroethers because they have the traditional perfluoroalkyl carbon chains characteristic of legacy PFAS, such as PFOA, but the chains are interrupted by ether oxygen(s) (see Figure S1) (Strynar et al. 2015). The released fluoroethers, including GenX, were generated as by-products of fluoropolymer production at Fayetteville Works facility (Hopkins et al. 2018; McCord and Strynar 2019). Human exposure to by-products of fluorochemical manufacturing has not been studied to date.Figure 1. Cape Fear River Basin, North Carolina, United States. Note: PFAS, per- and polyfluoroalkyl substances.Approximately 80 miles downriver of Fayetteville Works is the raw water intake for the Cape Fear Public Utility Authority (CFPUA), which provides drinking water to approximately 200,000 people in New Hanover County, home to Wilmington, North Carolina. Raw water concentrations of the fluoroethers were similar to treated water concentrations because the fluoroethers were not measurably removed by CFPUA’s water treatment processes, which included several advanced steps (i.e., raw and settled water ozonation, biofiltration, and ultraviolet light disinfection) (Hopkins et al. 2018). In early June 2017, the public became aware of the presence of GenX in their drinking water (Hagerty 2017). Community concern and subsequent action by the North Carolina Department of Environmental Quality (NC DEQ) resulted in the fluorochemical manufacturer reducing its wastewater discharges to the Cape Fear River on 21 June 2017, and by September 2017, the facility stopped discharging process wastewater containing PFAS into the Cape Fear River (NC DEQ 2017). As a result, the GenX concentration in Wilmington’s drinking water source dropped from approximately 700 ng/L before discharge control to approximately 100 ng/L 1 week later (Hopkins et al. 2018; Sun et al. 2016; Zhang et al. 2019).We initiated The GenX Exposure Study in November 2017 to answer community members’ questions about their exposure to GenX and other PFAS. We included in our analysis fluoroethers that were by-products of fluorochemical manufacturing at Fayetteville Works as well as legacy PFAS historically used throughout the Cape Fear River Basin. We report here the initial findings for serum PFAS levels measured in a Wilmington, North Carolina, population.MethodsStudy PopulationIn November 2017 and May 2018, we recruited individuals from New Hanover County, North Carolina, to participate in the GenX Exposure Study. We partnered with Cape Fear River Watch, a local nongovernmental organization focusing on water quality in the region; the New Hanover County Health Department; the New Hanover County NAACP; and informal community partners to inform the public about the study. Press releases, news stories, public service announcements, recruitment flyers, social media platforms, and the study website ( https://genxstudy.ncsu.edu/) were used to promote the study.CFPUA distributes drinking water to the City of Wilmington and unincorporated areas of New Hanover County not served by privately owned systems. CFPUA operates three treatment plants with separate distribution systems: One plant sources water from the lower Cape Fear River, and the other two from various groundwater sources (CFPUA 2020b). Most (153,200 or 80%) of the 190,500 people served by CFPUA receive water from the lower Cape Fear River (NC Drinking Water Watch 2020). The Richardson and Monterey Heights groundwater treatment plants serve 37,250 people collectively.Study participants were required to be current residents of New Hanover County, ≥6 years of age, and to have lived in a home served with CFPUA drinking water for at least 12 months prior to November 2017 (the start of enrollment). Up to four individuals per household were allowed to participate. We excluded pregnant women and people who were human immunodeficiency virus- or hepatitis C-positive. Individuals were recruited in both English and Spanish. The majority of our participants were recruited in November 2017, with a smaller, targeted recruitment in May 2018. In November, interested individuals contacted the study office to be screened for eligibility. Eligible individuals were scheduled for a clinic visit at the New Hanover County Health Department during the weekend of 10–12 November 2017. We conducted a second recruitment of participants in May 2018, aimed at increasing participation of African Americans. We joined the annual health fair at the MLK Center in Wilmington, hosted by the New Hanover County NAACP. Recruitment, enrollment, and biological sample collection took place at the MLK Center on 5 May 2018. We also scheduled repeat blood and urine collection from a random sample of the November 2017 participants.All study participants provided written informed consent to participate. All phases of the study were conducted in compliance with the North Carolina State University Institutional Review Board.Data CollectionDuring clinic visits, we consented participants, administered a questionnaire, collected biological samples (blood and urine), and measured height and weight. Study staff administered a questionnaire to each participant at the clinic visit to collect information on demographics, drinking water habits, residential history, health history, and PFAS exposures other than drinking water. Children completed a shortened version of the adult questionnaire. Parents provided the residential history for their children.Trained phlebotomists collected nonfasting blood samples from participants. For participants who were ≥11 years of age, four tubes of blood (two red-top tubes for serum, two ethylenediaminetetraacetic acid (EDTA) tubes for whole blood or plasma) were collected. For children 6–10 years of age, two red-top tubes for serum were collected. Serum tubes were spun at 1,300×g for 10 min in a Sorvall RT 600D centrifuge at room temperature. Serum was aliquoted into transfer tubes. One EDTA tube was processed for plasma; the remainder was saved as whole blood. Spot urine samples were provided by study participants during the clinic visit. Urine and blood samples were stored on dry ice and transported to East Carolina University (Greenville, NC) and stored at −80°C. A 2-mL aliquot of serum was shipped on dry ice to the U.S. Environmental Protection Agency (EPA) in Research Triangle Park, North Carolina, where they were stored at −80°C until analysis.PFAS Analysis in BloodAnalytical standards.Native standards for GenX, perfluorobutanoic acid (PFBA), perfluoropentanoic acid (PFPeA), perfluorohexanoic acid (PFHxA), perfluoroheptanoic acid (PFHpA), PFOA, perfluorononanoic acid (PFNA), perfluorobutane sulfonic acid (PFBS), perfluorohexane sulfonic acid (PFHxS), PFOS, and 6:2 fluorotelomer sulfonate (6:2 FTS) and mass-labeled standards for GenX, PFBA, PFHxA, PFOA, PFNA, PFHxS, PFOS, and 6:2 FTS were purchased dissolved in methanol from Wellington Laboratories (see Table S1). Analytical standards for perfluoro-2-methoxyacetic acid (PFMOAA), perfluoro-2-methoxypropanoic acid, 2,3,3,3-tetrafluoro-2-(pentafluoroethoxy)propanoic acid, perfluoro-2-ethoxypropanoic acid (PEPA), perfluoro-3,5-dioxahexanoic acid (PFO2HxA), perfluoro-3,5,7-trioxaoctanoic acid (PFO3OA), perfluoro-3,5,7,9-tetraoxadecanoic acid (PFO4DA), perfluoro-3,5,7,9,11-pentaoxadodecanoic acid (PFO5DoA), and 1,1,2,2-tetrafluoro-2-(1,2,2,2-tetrafluoroethoxy)ethanesulfonic acid (NVHOS) and for perfluoro-3,6-dioxa-4-methyl-7-octene-1-sulfonic acid (Nafion by-product 1), and perfluoro-2-{[perfluoro-3-(perfluoroethoxy)-2-proanyl]oxy}ethanesulfonic acid (Nafion by-product 2) were acquired as aqueous solutions (1,000 ng/μL) from the Chemours Company because there were no commercial sources. The identity of each standard was confirmed by high-resolution mass spectrometry (HRMS). A mixed PFAS standard stock solution was prepared in methanol at 0.1 ng/μL.Sample preparation.Fifty microliters of serum was transferred into 2-mL polypropylene tubes and 100μL0.1M formic acid containing mass-labeled standards (6.25 ng/mL) was added to denature serum proteins. Each sample was then vortex mixed and 450μL cold (−20°C) acetonitrile was added to precipitate proteins. The sample was vortex mixed again and centrifuged at 12,500×g for 5 min in an IEC CL31R Multispeed Centrifuge (Thermo Scientific) at room temperature. Finally, a 100-μL aliquot of the acetonitrile supernatant was placed into a liquid chromatography (LC) vial with 100μL0.4 mM ammonium formate buffer (1:1 mixture).Sample analysis.Measurements for 20 PFAS, 10 fluoroethers, and 10 legacy PFAS (Table 1) in serum were conducted using LC-HRMS. Each serum sample was analyzed using a Thermo Vanquish ultra-performance liquid chromatograph coupled to a Thermo Orbitrap Fusion mass spectrometer. Using a 25-μL injection volume, PFAS were separated on an Accucore Vanquish C18+LC column (100×2.1mm, 1.5μL particle diameter). The mobile phases were 95:5% vol/vol water:acetonitrile with 0.4 mM ammonium formate (Eluent A) and 5:95% vol/vol water:acetonitrile with 0.4 mM ammonium formate (Eluent B), with a flow rate of 300μL/min. The LC method used a 3-min pre-equilibration time at 10% B followed by a linear gradient from 10% to 100% over 10 min with a 3-min hold at 100% B. The mass spectrometer was run in full scan mode with a mass range of 100–700 Da and 120,000 resolving power at m/z 200.Table 1 Ten fluoroethers and 10 legacy PFAS measured for in serum samples in the GenX exposure study.Table 1 has eight columns, namely, Short name, U.S. EPA registry name, Formula, CAS number (hyperlinked to U.S. EPA Chemicals Dashboard superscript a), DTXSID superscript b, Monoisotopic mass, deprotonated, number of fluorinated carbons, and Chain length superscript c.Short nameU.S. EPA registry nameFormulaCASN (hyperlinked to U.S. EPA Chemicals Dashboarda)DTXSIDbMonoisotopic mass, deprotonated# of fluorinated carbonsChain lengthcFluoroethers HFPO-DA (GenX)Hexafluoropropylene oxide dimer acidC6HF11O3 13252-13-670880215328.967757 PMPAPerfluoro-2-methoxypropanoic acidC4HF7O3 13140-29-980528474228.974135 PEPAPerfluoro-2-ethoxypropanoic acidC5HF9O3 267239-61-260896486278.970946 PFO2HxAPerfluoro-3,5-dioxahexanoic acidC4HF7O4 39492-88-150892351244.969136 PFO3OAPerfluoro-3,5,7-trioxaoctanoic acidC5HF9O5 39492-89-220892348310.960848 PFO4DAPerfluoro-3,5,7,9-tetraoxadecanoic acidC6HF11O6 39492-90-590723993376.9525510 PFO5DoAPerfluoro-3,5,7,9,11-pentaoxadodecanoic acidC7HF13O7 39492-91-650723994442.9442612 NVHOS1,1,2,2-Tetrafluoro-2-(1,2,2,2-tetrafluoroethoxy)ethanesulfonic acidC4H2F8O4S 801209-99-480904754296.947346 Nafion by-product 1Perfluoro-3,6-dioxa-4-methyl-7-octene-1-sulfonic acidC7HF13SO5 29311-67-930892354442.9264710 Nafion by-product 2Perfluoro-2-{[perfluoro-3-(perfluoroethoxy)-2-propanyl]oxy}ethanesulfonic acidC7H2F14SO5 749836-20-210892352462.9327710Legacy PFAS PFBAPerfluorobutanoic acidC4HF7O2 375-22-44059916212.979234 PFPeAPerfluoropentanoic acidC5HF9O2 2706-90-36062599262.976045 PFHxAPerfluorohexanoic acidC6HF11O2 307-24-43031862312.972856 PFHpAPerfluoroheptanoic acidC7HF13O2 375-85-91037303362.969667 PFOAPerfluorooctanoic acidC8HF15O2 335-67-18031865412.966478 PFNAPerfluorononanoic acidC9HF17O2 375-95-18031863462.963289 PFBSPerfluorobutane sulfonic acidC4HF9SO3 375-73-55030030298.942945 PFHxSPerfluorohexane sulfonic acidC6HF13SO3 355-46-47040150398.936667 PFOSPerfluorooctane sulfonic acidC8HF17SO3 1763-23-13031864498.930289 6:2 FTS6:2 fluorotelomer sulfonateC8H5F13SO3 27619-97-26067331426.967969Note: CASN, Chemical Abstracts Services Number; EPA, Environmental Protection Agency; GenX, hexafluoropropylene oxide dimer acid.aU.S. EPA CompTox Chemistry Dashboard ( https://comptox.epa.gov/dashboard).bDTXSID is a unique substance identifier used in the U.S. EPA CompTox Chemistry Dashboard (Williams et al. 2017).cIncludes carbon, oxygen, and sulfur atoms in the fluoroalkyl chain but does not include oxygen atoms in the anionic group (i.e., does not include O in carboxylic acid).Extracted ion chromatograms for 6:2 FTS (426.9679±5 ppm) yielded a doublet peak that was selected for follow-up MS/MS investigation with higher-energy C-trap dissociation (HCD) normalized collision energy of 45. Standards of 6:2 FTS (Schultz et al. 2004) and a polyfluoroalkyl ether carboxylic acid 2,2,3,3-tetrafluoro-3-((1,1,1,2,3,3-hexafluoro-3-(1,2,2,2-tetrafluoroethoxy)propan-2-yl)oxy)propanoic acid (known as Hydro-EVE) (Chemical Abstracts Services Number 773804-62-9) (U.S. EPA 2020) were prepared and analyzed by LC-HRMS/MS; annotated MS/MS spectra were compared with spectra collected from 10 serum samples randomly selected from our Wilmington cohort samples.Calibration standards ranging in concentration from 0.1 ng/mL to 25 ng/mL were prepared in newborn calf serum (ThermoFisher Scientific) by spiking PFAS standard stock solution into the serum; calibration standards were processed using the protocol for human serum samples described above. Compounds were quantified using a relative response ratio of the native standard and isotopically labeled internal standard; the [M-H]− or [M-H-CO2]− ions were used. Integration of PFAS isomers was consistent with U.S. EPA Method 537.1 (U.S. EPA 2018); that is, for compounds with branched and linear isomers (PFOA, PFOS, PFHxS), peaks for the branched and linear isomers were integrated together to report total concentration.Serum samples were run in batches of approximately 50 samples. Each batch contained in-house spiked newborn calf serum samples for continuing calibration checks. National Institutes of Standards and Technology (NIST) standard reference material (SRM) 1957 human serum was analyzed for calibration verification (acceptance criteria were ≤30% difference from consensus value). Mean concentrations of legacy PFAS (PFHpA, PFHxS, PFOA, PFOS, and PFNA) in SRM 1957 were within 10% difference of reference values determined by an interlaboratory analysis (see Table S2). We calculated the precision between replicate analyses by taking the difference divided by the average. Intrarun replicate analysis precision for duplicate analyses was less than 30% for most PFAS (see Table S3). As expected, lower replicate precision was observed at lower concentrations.The study sera were run in batches across eight analytical runs. Each analyte was assigned a batch-specific method reporting limit (MRL) defined as the first point of the standard curve for which the regression equation yielded a calculated value within 30% of the true value. For analytes with significant background signal in calf serum blanks, the MRL was designated as three times the maximum response in newborn calf serum blanks (i.e., in the 0-ng/mL standard), if higher than the MRL from the calibration curve. Higher instrument background levels for PFPeA, PFO2HxA, and GenX were observed on some analytical runs and resulted in higher batch-specific MRLs for those PFAS (see Table S4). In addition, the mass spectrometer had a high background response for the mass corresponding to PFMOAA, making it difficult to distinguish PFMOAA standards. We prioritized the method development for PFAS with longer alkyl (ether) chain length (e.g., PFO5DoA), which we suspected were more likely to be detected in blood (Ng and Hungerbühler 2014). Thus, we moved forward without measuring samples for PFMOAA.Statistical MethodsTo calculate summary statistics, we used the first blood sample collected from each participant (i.e., the blood sample collected when the participant was enrolled; that is, the November 2017 sample for most participants and the May 2018 sample for new enrollees in May). We present results for PFAS detected in 60% or more of 344 serum samples. For samples analyzed in duplicate, average values were used in the analyses. Sample results below the MRL were assigned a fill value of the MRL divided by the square root of 2 (Calafat et al. 2007; Daly et al. 2018). However, when we summed the mass concentration of all detectable PFAS to determine total PFAS in serum, we added 0 to the total for PFAS that were below the MRL so that we did not bias the sum upward because of multiple nondetected chemicals. We assessed correlation of PFAS serum concentrations using Spearman correlation coefficients; values greater than or equal to 0.70 were considered highly correlated.To compare differences between participants served with treated Cape Fear River water or another drinking water source, we used a Wilcoxon rank sum test. Two study participants who were enrolled in the early stages of the recruitment effort and who shared the same residence did not meet the study eligibility criterion of residing in the CFPUA service area. Their residence, however, was in Wilmington, and their drinking water source was not the Cape Fear River. Therefore, we included these two participants as part of the group with drinking water not sourced from the Cape Fear River.For participants who provided repeat samples, we calculated percentage change over time using serum PFAS concentrations in November 2017 and May 2018. Percentage change was calculated as ConcentrationNovember 2017−ConcentrationMay 2018ConcentrationNovember 2017×100% [1] We also used a Wilcoxon test for paired samples to evaluate differences in serum PFAS concentrations between November 2017 and May 2018. All statistical analyses were conducted in R (version 3.5.1; R Development Core Team). The significance level for all statistical analyses was p<0.05.Comparison DataTo determine whether fluoroethers were detectable in people living remote from the fluorochemical manufacturing site, we analyzed 20 stored serum samples collected in 2008–2009 from 30- to 44-y-old women participating in an unrelated research study, and living in the Raleigh, Durham, and Chapel Hill, North Carolina, area (Crawford et al. 2017) (Figure 1).ResultsStudy PopulationIn November 2017 and May 2018, we enrolled 344 participants, including 289 adults and 55 children; 310 enrolled in November 2017 and 34 enrolled in May 2018. We collected repeat blood samples from 44 participants (Table 2, Figure 2). Participants ranged in age from 6 to 86 y, with a median age of 50 y. The average years lived in the lower Cape Fear Region was 20 y [standard deviation (SD): 16 y], and 72% of participants reported residing in the region for >10y. In 75 of the 231 participating households (32%), at least 2 household members participated in the study. Most participants (97%) had drinking water sourced from the lower Cape Fear River, but 9 participants had another drinking water source.Table 2 Demographic characteristics of the 344 Wilmington, North Carolina, GenX exposure study participants.Table 2 has four columns, namely, Characteristic, November 2017 (n equals 310) (n, percentage), November 2017 Resampled May 2018 (n equals 44) (n, percentage), and May 2018 (n equals 34) (n, percentage).CharacteristicNovember 2017 (n=310) [n (%)]November 2017 (resampled May 2018) (n=44) [n (%)]May 2018 (n=34) [n (%)]Adult/child Adult (≥18y)256 (82.6)42 (95.5)33 (97.1) Child54 (17.4)2 (4.6)1 (2.94)Age group (y)a 6–1754 (17.5)2 (4.6)1 (3.1) 18–2912 (3.9)1 (2.3)2 (6.3) 30–3937 (12.0)4 (9.1)2 (6.3) 40–4957 (18.4)10 (22.7)2 (6.3) 50–5951 (16.5)9 (20.5)4 (12.5) 60–6962 (20.1)9 (20.5)13 (40.6) 70–8636 (11.7)9 (20.5)8 (25.0)Gender Female189 (61.0)28 (63.6)27 (79.4) Male120 (38.7)16 (36.4)7 (20.6) Transgender1 (0.3)00Race/ethnicityb Black, non–Hispanic8 (2.6)027 (79.4) Hispanic, regardless of race33 (10.7)3 (7.0)0 White, non–Hispanic261 (84.7)40 (93.0)4 (11.8) Otherc6 (2.0)03 Spanish speaker17 (5.5)00Residence in lower Cape Fear Region (y)d 1–988 (28.5)10 (22.7)6 (18.8) 10–19112 (36.3)18 (40.9)7 (21.9) 20–3976 (24.6)6 (13.6)6 (18.8) 40–4916 (5.2)5 (11.4)3 (9.4) 50–7317 (5.5)5 (11.4)10 (31.3)Drinking water sourcee CFPUA groundwater5 (1.6)1 (2.3)2 (5.9) CFPUA Cape Fear River301 (97.7)42 (97.7)32 (94.1) Not served by CFPUA2 (0.7)00Number of households2013530Participants per household 1130 (64.7)28 (80.0)26 (86.7) 246 (22.9)6 (17.4)4 (13.3) 312 (6.0)00 413 (6.5)1 (2.9)0Note: CFPUA, Cape Fear Public Utility Authority; GenX, hexafluoropropylene oxide dimer acid.aMissing age for three participants.bMissing race/ethnicity for two participants.cOther includes mixed-race individuals Native American/Pacific Islander, black or African American and Native American/Pacific Islander and white and other, Native American/Pacific Islander and white. May 2018: Other includes: American Indian/Alaska Native and Black or African American, black or African American and Native American/Pacific Islander and white, black or African American and white.dMissing years lived in lower Cape Fear River Region for 1 participant for the November 2017/May 2018 repeaters and 2 participants for the May 201 DA - 2020/7// PY - 2020/7// DO - 10.1289/EHP6837 VL - 128 IS - 7 SP - SN - 1552-9924 ER - TY - JOUR TI - S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM AU - Klotz, Courtney AU - Goh, Yong Jun AU - Sarah, O’Flaherty AU - Barrangou, Rodolphe T2 - BMC Microbiology AB - Abstract Background Surface layers (S-layers) are two-dimensional crystalline arrays of repeating proteinaceous subunits that form the outermost layer of many bacterial cell envelopes. Within the Lactobacillus genus, S-layer presence is frequently associated with probiotic-relevant properties such as improved adherence to host epithelial cells and modulation of the immune response. However, recent studies have demonstrated that certain S-layer functions may be supplemented by a novel subset of proteins embedded within its lattice, termed S-layer associated proteins (SLAPs). In the following study, four Lactobacillus acidophilus NCFM SLAPs (LBA0046, LBA0864, LBA1426, and LBA1539) were selected for in silico and phenotypic assessment. Results Despite lacking any sequence similarity or catalytic domains that may indicate function, the genes encoding the four proteins of interest were shown to be unique to S-layer-forming, host-adapted lactobacilli species. Likewise, their corresponding deletion mutants exhibited broad, host-relevant phenotypes including decreased inflammatory profiles and reduced adherence to Caco-2 intestinal cells, extracellular matrices, and mucin in vitro. Conclusions Overall, the data presented in this study collectively links several previously uncharacterized extracellular proteins to roles in the underlying host adaptive mechanisms of L. acidophilus . DA - 2020/12// PY - 2020/12// DO - 10.1186/s12866-020-01908-2 VL - 20 IS - 1 UR - https://doi.org/10.1186/s12866-020-01908-2 KW - Lactobacillus KW - S-layer KW - Probiotics KW - Cell surface ER - TY - JOUR TI - Modeling multiple reasons for adopting precision technologies: Evidence from US cotton producers AU - Paudel, Krishna P. AU - Mishra, Ashok K. AU - Pandit, Mahesh AU - Larkin, Sherry AU - Rejesus, Rodrick AU - Velandia, Margarita T2 - COMPUTERS AND ELECTRONICS IN AGRICULTURE AB - Before deciding to adopt a particular technology, an individual should assess the reasons for its adoption. The major reasons for adoption could be to profitability, environmental benefit, or to be at the forefront of the technology. Using Monte Carlo simulations, this study determined that seemingly unrelated ordered probit (SUOP) method performs better than a single ordered probit (UOP) method for analyzing factors affecting multiple reasons for adopting precision farming (PF) technologies. Results indicated that profit was the most important reason, and environmental benefits were the second most important reason for adopting PF technologies. Findings revealed that educated, experienced, and farmers with farm planning and computers chose PF technologies for profit reasons. Younger farmers and farmers using university publication information are more likely to indicate the importance of environmental quality benefits. Finally, farmers located in the Delta, Appalachia, and Southeast regions of the US are more likely to adopt PF technologies for environmental benefits reason, compared to farmers in the Southern Plains region. DA - 2020/8// PY - 2020/8// DO - 10.1016/j.compag.2020.105625 VL - 175 SP - SN - 1872-7107 KW - Precision farming technologies KW - Seemingly unrelated ordered probit KW - Cotton KW - Profitability KW - Monte Carlo simulations ER - TY - JOUR TI - Cotton thrips infestation predictor: a practical tool for predicting tobacco thrips (Frankliniella fusca) infestation of cotton seedlings in the south-eastern United States AU - Chappell, Thomas M AU - Ward, Rebecca V AU - DePolt, Kelley T AU - Roberts, Phillip M AU - Greene, Jeremy K AU - Kennedy, George G T2 - Pest Management Science AB - Abstract Background Thrips (order Thysanoptera) infestations of cotton seedlings result in plant injury, increasing the detrimental consequences of other challenges to production agriculture, such as abiotic stress or infestation by other pests. Using Frankliniella fusca as a thrips species of focus, we empirically developed a composite model of thrips phenology and cotton seedling susceptibility to predict site‐specific infestation risk so that monitoring and other resources can be allocated efficiently, to optimize the timing of thrips control measures to maximize effectiveness, and to inform stakeholders about the dynamics of thrips infestation and cotton seedling injury at a time when thrips are evolving resistance to commonly‐used pesticides. Results A mixture distribution model of thrips infestation potential, fit to data describing F. fusca adult dispersal in time, proved best for predicting infestations of F. fusca on cotton seedlings. Thrips generations occurring each year as a function of weather are represented as a probability distribution. A model of cotton seedling growth was also developed to predict susceptibility as a function of weather. Combining these two models resulted in a model of seedling injury, which was validated and developed for implementation as a software tool. Conclusions Experimental validation of the implemented model demonstrated the utility of its output in predicting infestation risk. Successful implementation and use of the software tool derived from this model was enabled by close cooperation with university extension personnel, agricultural consultants, and growers, underscoring the importance of stakeholder and expert input to the success of applied analytical research. © 2020 Society of Chemical Industry DA - 2020/7/20/ PY - 2020/7/20/ DO - 10.1002/ps.5954 VL - 76 IS - 12 SP - 4018–4028 SN - 1526-498X 1526-4998 UR - http://dx.doi.org/10.1002/ps.5954 KW - cotton KW - thrips KW - management KW - forecasting KW - decision support KW - Gossypium hirsutum KW - Frankliniella fusca ER - TY - JOUR TI - Snow-mediated plasticity does not prevent camouflage mismatch AU - Kumar, Alexander V AU - Zimova, Marketa AU - Sparks, James R. AU - Mills, L. Scott T2 - OECOLOGIA AB - Global reduction in snow cover duration is one of the most consistent and widespread climate change outcomes. Declining snow duration has severe negative consequences for diverse taxa including seasonally color molting species, which rely on snow for camouflage. However, phenotypic plasticity may facilitate adaptation to reduced snow duration. Plastic responses could occur in the color molt phenology or through behavior that minimizes coat color mismatch or its consequences. We quantified molt phenology of 200 wild snowshoe hares (Lepus americanus), and measured microhabitat choice and local snow cover. Similar to other studies, we found that hares did not show behavioral plasticity to minimize coat color mismatch via background matching; instead they preferred colder, snow free areas regardless of their coat color. Furthermore, hares did not behaviorally mitigate the negative consequences of mismatch by choosing resting sites with denser vegetation cover when mismatched. Importantly, we demonstrated plasticity in the initiation and the rate of the molt and established the direct effect of snow on molt phenology; greater snow cover was associated with whiter hares and this association was not due to whiter hares preferring snowier areas. However, despite the observed snow-mediated plasticity in molt phenology, camouflage mismatch with white hares on brown snowless ground persisted and was more frequent during early snowmelt. Thus, we find no evidence that phenotypic plasticity in snowshoe hares is sufficient to facilitate adaptive rescue to camouflage mismatch under climate change. DA - 2020/11// PY - 2020/11// DO - 10.1007/s00442-020-04680-2 VL - 194 IS - 3 SP - 301-310 SN - 1432-1939 KW - Adaptive rescue KW - Phenotypic plasticity KW - Behavioral plasticity KW - Climate change KW - Molt phenology ER - TY - JOUR TI - Clinical xenotransplantation of the heart: At the watershed AU - Platt, Jeffrey L. AU - Piedrahita, Jorge A. AU - Cascalho, Marilia T2 - JOURNAL OF HEART AND LUNG TRANSPLANTATION AB - See Related Article, page 751 See Related Article, page 751 Transplantation has been the preferred treatment for severe failure of the heart and other organs for more than 3 decades. But, for these decades and longer transplantation could be offered to few who could benefit because donated human organs were scarce. The most obvious solution to the scarcity of human hearts and other organs today, 30 years ago and decades before has been to use animals instead of humans as the source of organs, that is xenotransplantation. Yet, if xenotransplantation has been the most obvious solution, it also has seemed the most frustrating, a proverbial carrot on a stick, held just beyond reach by 3 barriers—immunity, physiologic incompatibility, and infection—of which immunity appeared most daunting.1Cascalho M Platt JL The immunological barrier to xenotransplantation.Immunity. 2001; 14: 437-446Abstract Full Text Full Text PDF PubMed Scopus (154) Google Scholar The past 3 decades brought some dramatic advances in concept and technologies that might address the barriers to xenotransplantation. Yet, these advances were countered at every turn by discovery of new antigens, more incompatibilities and longer lists of zoonotic organisms. But in the current issue of Journal of Heart and Lung Transplantation, and in a previous report in another journal,2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar,3Längin M Mayr T Reichart B et al.Consistent success in life-supporting porcine cardiac xenotransplantation.Nature. 2018; 564: 430-433Crossref PubMed Scopus (142) Google Scholar Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar report > 3-month survival and function of orthotopic pig cardiac xenografts in baboons given clinically acceptable immunosuppression. The results “fulfill for the first time the preclinical efficacy” standard an International Society for Heart and Lung Transplantation (ISHLT) committee proposed as a premise for launching clinical trials in cardiac xenotransplantation.2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar,4Cooper DK Keogh AM Brink J et al.Report of the Xenotransplantation Advisory Committee of the International Society for Heart and Lung Transplantation: the present status of xenotransplantation and its potential role in the treatment of end-stage cardiac and pulmonary diseases.J Heart Lung Transplant. 2000; 19: 1125-1165Abstract Full Text Full Text PDF PubMed Scopus (136) Google Scholar Did Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar finally capture the carrot and take, what they call “the final step toward clinical xenotransplantation” or did they just advance the stick, with unenumerated barriers keeping clinical application beyond reach? In 2000, an advisory committee of the ISHLT reported on the status of research into the barriers to clinical cardiac and pulmonary xenotransplantation and recommended that “a clinical trial should be considered when approximately 60% survival of life-supporting pig organs in non-human primates for a minimum of 3 months [has been achieved in] at least 10 animals.”4Cooper DK Keogh AM Brink J et al.Report of the Xenotransplantation Advisory Committee of the International Society for Heart and Lung Transplantation: the present status of xenotransplantation and its potential role in the treatment of end-stage cardiac and pulmonary diseases.J Heart Lung Transplant. 2000; 19: 1125-1165Abstract Full Text Full Text PDF PubMed Scopus (136) Google Scholar The report culminated a decade of high profile discovery and debate. Key immune, physiologic, and infectious barriers to xenotransplantation had been identified and dramatic advances had been reported in genetic engineering, reproductive cloning, and development of biologic technologies for suppressing immunity and inducing tolerance (see Cascalho and Platt1Cascalho M Platt JL The immunological barrier to xenotransplantation.Immunity. 2001; 14: 437-446Abstract Full Text Full Text PDF PubMed Scopus (154) Google Scholar for review). But, the exciting advances that made clinical application seem so close also fueled concern about a long-known but little-understood endogenous retrovirus of pigs (porcine endogenous retrovirus) and about novel organisms that might develop in and spread beyond the immunosuppressed recipient. Although the need for organs for transplantation was urgent and increasing the ISHLT committee suggested only "consideration" of clinical trials because the proposed standard was still far from being achieved. Only 1 of numerous heterotopic cardiac xenografts in non-human primates had survived 3 months, and this graft suffered severe immune and inflammatory injury. Thus, the ISHLT committee correctly asserted that as of 2000, the “immune barriers [had] not yet been overcome.”4Cooper DK Keogh AM Brink J et al.Report of the Xenotransplantation Advisory Committee of the International Society for Heart and Lung Transplantation: the present status of xenotransplantation and its potential role in the treatment of end-stage cardiac and pulmonary diseases.J Heart Lung Transplant. 2000; 19: 1125-1165Abstract Full Text Full Text PDF PubMed Scopus (136) Google Scholar Equally important was that only 1 orthotopic porcine cardiac xenograft had as yet supported the life of a non-human primate treated with clinically acceptable immunosuppression regimen and that for 39 days.5Vial CM Ostlie DJ Bhatti FN et al.Life supporting function for over one month of a transgenic porcine heart in a baboon.J Heart Lung Transplant. 2000; 19: 224-229Abstract Full Text Full Text PDF PubMed Scopus (97) Google Scholar In 2016, the prospects for clinical application of xenotransplantation changed dramatically. Mohiuddin et al6Mohiuddin MM Singh AK Corcoran PC et al.Chimeric 2C10R4 anti-CD40 antibody therapy is critical for long-term survival of GTKO.hCD46.hTBM pig-to-primate cardiac xenograft.Nat Commun. 2016; 7: 11138Crossref PubMed Scopus (190) Google Scholar reported that heterotopic porcine cardiac xenografts expressing a human complement regulator (CD46) and human thrombomodulin and lacking Galα1-3Gal (owing targeting of α1,3-galactosyltransferase) could survive more than a year (up to 945 days) in baboons treated with a clinically-acceptable regimen that included anti-rhesus monkey CD40. Because the xenografts were heterotopic, the potential for providing physiologic support remained uncertain but this success in overcoming immune barriers reinvigorated discussion about whether and how xenotransplantation might be applied in patients. In 2018, Längin et al3Längin M Mayr T Reichart B et al.Consistent success in life-supporting porcine cardiac xenotransplantation.Nature. 2018; 564: 430-433Crossref PubMed Scopus (142) Google Scholar reported 4 successful orthotopic porcine xenografts in baboons that functioned until the recipients were euthanized, per protocol on days 90, 90, 182, and 195. The xenografts were from pigs with the same or similar genetic modifications as those used by Mohiuddin et al,6Mohiuddin MM Singh AK Corcoran PC et al.Chimeric 2C10R4 anti-CD40 antibody therapy is critical for long-term survival of GTKO.hCD46.hTBM pig-to-primate cardiac xenograft.Nat Commun. 2016; 7: 11138Crossref PubMed Scopus (190) Google Scholar and the baboons were treated with immunosuppression similar to that of Mohiuddin et al6Mohiuddin MM Singh AK Corcoran PC et al.Chimeric 2C10R4 anti-CD40 antibody therapy is critical for long-term survival of GTKO.hCD46.hTBM pig-to-primate cardiac xenograft.Nat Commun. 2016; 7: 11138Crossref PubMed Scopus (190) Google Scholar (plus an mammalian target of rapamycin inhibitor to limit myocardial remodeling7Kushwaha SS Raichlin E Sheinin Y et al.Sirolimus affects cardiomyocytes to reduce left ventricular mass in heart transplant recipients.Eur Heart J. 2008; 29: 2742-2750Crossref PubMed Scopus (41) Google Scholar). The present report2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar adds 4 orthotopic xenografts to the series. The xenografts in 2 recipients exhibited no evidence of significant rejection but systemic complications in the baboons with grafts harboring Cytomegalovirus (porcine cytomegalovirus [pCMV]) necessitated termination on Days 15 and 27. Two other xenografts functioned at 90 days, when the recipients were euthanized per protocol. Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar portray the 6 of 8 orthotopic xenografts functioning 3 months or longer as “well exceeding the key requirement of the ISHLT of the ISHLT International Advisory Board.” Some might questionwhether 6 of 8 xenografts functioning 3 months or more well exceeds or meets the ISHLT standard (60% of at least 10 life-supporting xenografts functioning 3 months4Cooper DK Keogh AM Brink J et al.Report of the Xenotransplantation Advisory Committee of the International Society for Heart and Lung Transplantation: the present status of xenotransplantation and its potential role in the treatment of end-stage cardiac and pulmonary diseases.J Heart Lung Transplant. 2000; 19: 1125-1165Abstract Full Text Full Text PDF PubMed Scopus (136) Google Scholar). We think giving more than passing mention to this standard formulated more than 15 years before the immunologic barriers had been overcome, obscures the significance of Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar’s accomplishment. If a porcine cardiac xenograft can support a non-human primate treated with a clinically acceptable regimen of immunosuppression; then, we must urgently consider what more, if anything, is needed to offer a cardiac xenograft to a dying human patient. And, we must explain why those facing imminent death for want of a transplant cannot be permitted xenotransplantation instead. Yet, after repeatedly claiming to have met or exceeded the standard for clinical application of xenotransplantation,2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar,3Längin M Mayr T Reichart B et al.Consistent success in life-supporting porcine cardiac xenotransplantation.Nature. 2018; 564: 430-433Crossref PubMed Scopus (142) Google Scholar Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar now demurs, saying only that “more experiments will be necessary.” But, the justification for more experiments is unpersuasive. The authors assert more experiments would “address the efficacy of humanized anti-CD40/CD40L,” but orthotopic cardiac xenografts are extraordinarily inefficient, complex, and insensitive system for testing the efficacy of immune modifiers; indeed, the efficacy of anti-CD40/CD40L was established using heterotopic xenografts.6Mohiuddin MM Singh AK Corcoran PC et al.Chimeric 2C10R4 anti-CD40 antibody therapy is critical for long-term survival of GTKO.hCD46.hTBM pig-to-primate cardiac xenograft.Nat Commun. 2016; 7: 11138Crossref PubMed Scopus (190) Google Scholar Eight orthotopic xenografts are certainly too few to firmly establish the frequency of success and durability of function porcine cardiac xenografts in baboons. But, larger numbers of xenografts in baboons will reveal little more about the efficacy and durability xenografts might have in humans. The ISHLT committee wisely avoided stipulating a standard error for 60% survival or an end-point beyond 90 days because experimental transplants in non-human primates do not model and potentially misrepresent some key variables in clinical cardiac transplantation.8Platt JL Cascalho M Piedrahita JA Xenotransplantation: progress along paths uncertain from models to application.ILAR J. 2018; 59: 286-308Crossref PubMed Scopus (5) Google Scholar That is not to say experimentation in this model or in others should cease. Clinical cardiac xenotransplantation is likely to raise questions and challenges not foreseen today, and an experimental model could prove invaluable for addressing these. There is another perhaps more pressing reason to question what more experiments can accomplish. We suspect porcine cardiac xenografts in non-human primates might overestimate or misrepresent the barriers to clinical xenotransplantation.8Platt JL Cascalho M Piedrahita JA Xenotransplantation: progress along paths uncertain from models to application.ILAR J. 2018; 59: 286-308Crossref PubMed Scopus (5) Google Scholar The xenografts reported by Mohiuddin et al6Mohiuddin MM Singh AK Corcoran PC et al.Chimeric 2C10R4 anti-CD40 antibody therapy is critical for long-term survival of GTKO.hCD46.hTBM pig-to-primate cardiac xenograft.Nat Commun. 2016; 7: 11138Crossref PubMed Scopus (190) Google Scholar and Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar were from pigs engineered to express human CD46 and human thrombomodulin to better regulate complement and coagulation in recipients. Yet, these and other proteins interact inefficiently with cognatepartners in baboons.9Lawson JH Platt JL Molecular barriers to xenotransplantation.Transplantation. 1996; 62: 303-310Crossref PubMed Scopus (162) Google Scholar Still more important is the possibility that the human proteins might elicit cellular and/or humoral immunity in baboons. Such immunity developing over time, perhaps when immunosuppression decreases to maintenance, might block regulatory functions or initiate injury to the grafts. Perhaps the anti-CD40 antibodies Mohiuddin et al6Mohiuddin MM Singh AK Corcoran PC et al.Chimeric 2C10R4 anti-CD40 antibody therapy is critical for long-term survival of GTKO.hCD46.hTBM pig-to-primate cardiac xenograft.Nat Commun. 2016; 7: 11138Crossref PubMed Scopus (190) Google Scholar considers essential are needed to disrupt immunity to the human proteins. Since intensity of immunosuppression could limit clinical application of xenotransplantation, it would be ironic if humans were found to need less intense regimens than baboons because humans are tolerant to the products of these transgenes. Of course, clinical trials might reveal higher or different barriers to xenotransplantation in humans than in baboons. But, that possibility has eluded detection in Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar’s model, and it would seem unlikely that more experiments would overcome the deficiency. Nor will the conduct of more porcine xenografts in baboons reveal much about the barrier posed by infection. The microorganisms of pigs known to be capable of infecting humans have been identified almost entirely by investigation of humans and pigs. Indeed, concerns about porcine endogenous retrovirus arose from investigation of human and pig cells in culture and the waning of those concerns from investigation of human contact with pig organs and xenografts.10Paradis K Langford G Long Z et al.Search for cross-species transmission of porcine endogenous retrovirus in patients treated with living pig tissue. The XEN 111 Study Group.Science. 1999; 285: 1236-1241Crossref PubMed Scopus (631) Google Scholar Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar associate the demise of 2 baboon recipients with the presence of pCMV in in cardiac xenografts, but the paper provides no evidence that pCMV was transmitted to the recipients or directly caused multiorgan failure that forced termination of the experiments. Perhaps a yet unidentified organism harbored by the baboons compromised innate immune control of pCMV. Regardless, pCMV will be excluded from potential sources of xenografts and since pCMV has not been shown to infect humans, Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar’s experience might reflect an instance in which non-human primates misrepresent a biologic barrier. In 2018, Längin et al3Längin M Mayr T Reichart B et al.Consistent success in life-supporting porcine cardiac xenotransplantation.Nature. 2018; 564: 430-433Crossref PubMed Scopus (142) Google Scholar called the first 4 successful orthotopic cardiac xenografts in baboons a milestone. If those xenografts and the 2 successful xenografts now reported2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar are a milestone, it is because they erase serious doubt about whether a porcine heart can survive and function for months in a non-human primate recipient receiving a clinically acceptable (if not yet optimal) immunosuppression regimen. But, the experiments do not prove clinical xenotransplantation will succeed—only clinical xenotransplants can prove that. If this regimen were used successfully in clinical xenotransplants, the clinical xenotransplants would be appropriately called a milestone, if the regimen failed some other term might be used. Reichart et al2Reichart B, Längin M, Radan J, et al. Pig-to-non-human primate heart transplantation: the final step toward clinical xenotransplantation [e-pub ahead of print]?J Heart Lung Transplant, https://doi.org/10.1016/j.healun.2020.05.004. Accessed July 6, 2020.Google Scholar’s report brings into focus an impending watershed in management heart failure. When clinical trials in cardiac xenotransplantation do begin, whether soon or after many more experiments, interest in the multitude of pre-clinical experiments and committee deliberations concerning the feasibility of xenotransplantation will fade. And, the central question will be whether the essential but intrusive immune modifiers and/or the less than optimal genetic background of engineered pigs8Platt JL Cascalho M Piedrahita JA Xenotransplantation: progress along paths uncertain from models to application.ILAR J. 2018; 59: 286-308Crossref PubMed Scopus (5) Google Scholar can be omitted or changed so that xenotransplantation can approach or even surpass the safety and efficacy of allotransplantation and become the preferred treatment for organ failure. That shift in focus as difficult to imagine as it may be will fuel identification and surmounting of barriers unapparent in today's pre-clinical models. If this impending change in interest in xenotransplantation seems fanciful, it just recapitulates how interest in allotransplantation changed 60 years ago. The authors have no conflicts of interest to declare. The work be the authors pertinent to this communication was supported by the National Institutes of Health (AI122369; OD023138) Pig-to-non-human primate heart transplantation: The final step toward clinical xenotransplantation?The Journal of Heart and Lung TransplantationVol. 39Issue 8PreviewThe demand for donated human hearts far exceeds the number available. Xenotransplantation of genetically modified porcine organs provides an alternative. In 2000, an Advisory Board of the International Society for Heart and Lung Transplantation set the benchmark for commencing clinical cardiac xenotransplantation as consistent 60% survival of non-human primates after life-supporting porcine heart transplantations. Recently, we reported the stepwise optimization of pig-to-baboon orthotopic cardiac xenotransplantation finally resulting in consistent success, with 4 recipients surviving 90 (n = 2), 182, and 195 days. Full-Text PDF DA - 2020/8// PY - 2020/8// DO - 10.1016/j.healun.2020.06.002 VL - 39 IS - 8 SP - 758-760 SN - 1557-3117 ER - TY - JOUR TI - Beyond resource limitation: an expanded test of the niche dimension hypothesis for multiple types of niche axes AU - Yan, Xuebin AU - Diez, Jeffrey AU - Huang, Kailing AU - Li, Shaopeng AU - Luo, , Xi AU - Xu, Xinyu AU - Su, Fanglong AU - Jiang, Lin AU - Guo, Hui AU - Hu, Shuijin T2 - OECOLOGIA DA - 2020/7// PY - 2020/7// DO - 10.1007/s00442-020-04713-w VL - 193 IS - 3 SP - 689-699 SN - 1432-1939 KW - Niche dimensionality KW - Species diversity KW - Biomass KW - Tibetan plateau KW - Alpine meadow ER - TY - JOUR TI - Targeted suppression of soybean BAG6-induced cell death in yeast by soybean cyst nematode effectors AU - Wang, Jianying AU - Yeckel, Greg AU - Kandoth, Pramod K. AU - Wasala, Lakmini AU - Hussey, Richard S. AU - Davis, Eric L. AU - Baum, Thomas J. AU - Mitchum, Melissa G. T2 - MOLECULAR PLANT PATHOLOGY AB - Abstract While numerous effectors that suppress plant immunity have been identified from bacteria, fungi, and oomycete pathogens, relatively little is known for nematode effectors. Several dozen effectors have been reported from the soybean cyst nematode (SCN). Previous studies suggest that a hypersensitive response‐like programmed cell death is triggered at nematode feeding sites in soybean during an incompatible interaction. However, virulent SCN populations overcome this incompatibility using unknown mechanisms. A soybean BAG6 (Bcl‐2 associated anthanogene 6) gene previously reported by us to be highly up‐regulated in degenerating feeding sites induced by SCN in a resistant soybean line was attenuated in response to a virulent SCN population. We show that GmBAG6‐1 induces cell death in yeast like its Arabidopsis homolog AtBAG6 and also in soybean. This led us to hypothesize that virulent SCN may target GmBAG6‐1 as part of their strategy to overcome soybean defence responses during infection. Thus, we used a yeast viability assay to screen SCN effector candidates for their ability to specifically suppress GmBAG6‐1‐induced cell death. We identified several effectors that strongly suppressed cell death mediated by GmBAG6‐1. Two effectors identified as suppressors showed direct interaction with GmBAG6‐1 in yeast, suggesting that one mechanism of cell death suppression may occur through an interaction with this host protein. DA - 2020/9// PY - 2020/9// DO - 10.1111/mpp.12970 VL - 21 IS - 9 SP - 1227-1239 SN - 1364-3703 KW - BAG6 KW - cell death KW - cyst nematode KW - defence suppression KW - effector KW - Heterodera glycines KW - soybean ER - TY - JOUR TI - Mowing alters nitrogen effects on the community-level plant stoichiometry through shifting plant functional groups in a semi-arid grassland AU - Li, Shijie AU - Wang, Fuwei AU - Chen, Mengfei AU - Liu, Zhengyi AU - Zhou, Luyao AU - Deng, Jun AU - Dong, Changjun AU - Bao, Guocheng AU - Bai, Tongshuo AU - Li, Zhen AU - Guo, Hui AU - Wang, Yi AU - Qiu, Yunpeng AU - Hu, Shuijin T2 - ENVIRONMENTAL RESEARCH LETTERS AB - Abstract Land-use practices such as mowing and nitrogen (N) fertilization can have significant impacts on plant stoichiometry. However, the interactive effects of mowing and N fertilization on the community-level plant stoichiometry and the underlying processes are not well understood. We examined the impacts of mowing (once a year) and N fertilization (12 g N m −2 yr −1 ) on the community-level plant stoichiometry in a semi-arid grassland on the Loess Plateau. Results obtained showed that mowing alone had no effect on the community-level plant N or phosphorus (P) concentration. N fertilization alone significantly reduced the community-level plant P concentration, but did not affect the community-level plant N concentration, leading to an enhancement of plant N:P ratio. However, mowing altered the effects of N fertilization, leading to a higher plant N (and P) concentration than the fertilization-only plots. Also, mowing significantly reduced soil nitrate (NO 3 − ), but increased soil temperature, photosynthetic active radiation, plant diversity, richness and gross ecosystem productivity. In addition, mowing and N fertilization significantly affected plant community composition through shifting dominant plant functional groups (PFGs) (e.g. asteraceae, forbs and grass). Further, our structural equation modeling analysis showed that shifts in PFGs played an important role in regulating plant stoichiometry under mowing and N fertilization. Together, these results illustrate that effective management of mowing and N fertilization may induce changes in soil limiting nutrients and shifts in plant community composition, potentially altering plant N:P stoichiometry at the community level. DA - 2020/7// PY - 2020/7// DO - 10.1088/1748-9326/ab8a87 VL - 15 IS - 7 SP - SN - 1748-9326 KW - Nitrogen fertilization KW - mowing KW - plant stoichiometry KW - plant community structure KW - plant diversity KW - photosynthetic active radiation KW - gross ecosystem productivity ER - TY - JOUR TI - Shutting down RNA-targeting CRISPR AU - Barrangou, Rodolphe AU - Sontheimer, Erik J. T2 - SCIENCE AB - The discovery of an anti-CRISPR reveals viral escape from CRISPR immunity DA - 2020/7/3/ PY - 2020/7/3/ DO - 10.1126/science.abc8243 VL - 369 IS - 6499 SP - 31-32 SN - 1095-9203 ER - TY - JOUR TI - New Technologies for Studying Negative-Strand RNA Viruses in Plant and Arthropod Hosts AU - German, Thomas L. AU - Lorenzen, Marcé D. AU - Grubbs, Nathaniel AU - Whitfield, Anna E. T2 - Molecular Plant-Microbe Interactions® AB - The plant viruses in the phylum Negarnaviricota, orders Bunyavirales and Mononegavirales, have common features of single-stranded, negative-sense RNA genomes and replication in the biological vector. Due to the similarities in biology, comparative functional analysis in plant and vector hosts is helpful for understanding host–virus interactions for negative-strand RNA viruses. In this review, we will highlight recent technological advances that are breaking new ground in the study of these recalcitrant virus systems. The development of infectious clones for plant rhabdoviruses and bunyaviruses is enabling unprecedented examination of gene function in plants and these advances are also being transferred to study virus biology in the vector. In addition, genome and transcriptome projects for critical nonmodel arthropods has enabled characterization of insect response to viruses and identification of interacting proteins. Functional analysis of genes using genome editing will provide future pathways for further study of the transmission cycle and new control strategies for these viruses and their vectors. DA - 2020/3// PY - 2020/3// DO - 10.1094/MPMI-10-19-0281-FI VL - 33 IS - 3 SP - 382-393 J2 - MPMI LA - en OP - SN - 0894-0282 1943-7706 UR - http://dx.doi.org/10.1094/MPMI-10-19-0281-FI DB - Crossref KW - virus-plant interactions ER - TY - JOUR TI - Seasonal polyphenism of spotted-wing Drosophila is affected by variation in local abiotic conditions within its invaded range, likely influencing survival and regional population dynamics AU - Stockton, Dara G. AU - Wallingford, Anna K. AU - Brind'amore, Gabrielle AU - Diepenbrock, Lauren AU - Burrack, Hannah AU - Leach, Heather AU - Isaacs, Rufus AU - Iglesias, Lindsy E. AU - Liburd, Oscar AU - Drummond, Francis AU - Ballman, Elissa AU - Guedot, Christelle AU - Van Zoeren, Janet AU - Loeb, Greg M. T2 - ECOLOGY AND EVOLUTION AB - Abstract Overwintering Drosophila often display adaptive phenotypic differences beneficial for survival at low temperatures. However, it is unclear which morphological traits are the best estimators of abiotic conditions, how those traits are correlated with functional outcomes in cold tolerance, and whether there are regional differences in trait expression. We used a combination of controlled laboratory assays, and collaborative field collections of invasive Drosophila suzukii in different areas of the United States, to study the factors affecting phenotype variability of this temperate fruit pest now found globally. Laboratory studies demonstrated that winter morph (WM) trait expression is continuous within the developmental temperature niche of this species (10–25°C) and that wing length and abdominal melanization are the best predictors of the larval abiotic environment. However, the duration and timing of cold exposure also produced significant variation in development time, morphology, and survival at cold temperatures. During a stress test assay conducted at −5°C, although cold tolerance was greater among WM flies, long‐term exposure to cold temperatures as adults significantly improved summer morph (SM) survival, indicating that these traits are not controlled by a single mechanism. Among wild D. suzukii populations, we found that regional variation in abiotic conditions differentially affects the expression of morphological traits, although further research is needed to determine whether these differences are genetic or environmental in origin and whether thermal susceptibility thresholds differ among populations within its invaded range. DA - 2020/7// PY - 2020/7// DO - 10.1002/ece3.6491 VL - 10 IS - 14 SP - 7669-7685 SN - 2045-7758 KW - cold tolerance KW - Drosophila KW - overwintering KW - phenotypic plasticity KW - polymorphism KW - SWD KW - winter morph ER - TY - JOUR TI - The Boeing 737 MAX: Lessons for Engineering Ethics AU - Herkert, Joseph AU - Borenstein, Jason AU - Miller, Keith T2 - SCIENCE AND ENGINEERING ETHICS AB - The crash of two 737 MAX passenger aircraft in late 2018 and early 2019, and subsequent grounding of the entire fleet of 737 MAX jets, turned a global spotlight on Boeing’s practices and culture. Explanations for the crashes include: design flaws within the MAX’s new flight control software system designed to prevent stalls; internal pressure to keep pace with Boeing’s chief competitor, Airbus; Boeing’s lack of transparency about the new software; and the lack of adequate monitoring of Boeing by the FAA, especially during the certification of the MAX and following the first crash. While these and other factors have been the subject of numerous government reports and investigative journalism articles, little to date has been written on the ethical significance of the accidents, in particular the ethical responsibilities of the engineers at Boeing and the FAA involved in designing and certifying the MAX. Lessons learned from this case include the need to strengthen the voice of engineers within large organizations. There is also the need for greater involvement of professional engineering societies in ethics-related activities and for broader focus on moral courage in engineering ethics education. DA - 2020/12// PY - 2020/12// DO - 10.1007/s11948-020-00252-y VL - 26 IS - 6 SP - 2957-2974 SN - 1471-5546 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85087828587&partnerID=MN8TOARS KW - Engineering ethics KW - Airline safety KW - Engineering design KW - Corporate culture KW - Regulation KW - Software engineering ER - TY - JOUR TI - Conservation Hospice: A Better Metaphor for the Conservation and Care of Terminal Species AU - Peterson, M. Nils AU - Bruskotter, Jeremy T. AU - Rodriguez, Shari L. T2 - FRONTIERS IN ECOLOGY AND EVOLUTION AB - The extinction crisis creates a need to increase conservation funding, and use it more efficiently. Most conservation resources are allocated through inefficient political processes, that seem ill-equipped for dealing with the crisis. In response, conservation triage emerged as a metaphor for thinking about the optimization of resource allocation. Since triage operates primarily as a metaphor, not means for allocating resources, its metaphorical implications are of particular importance. Of particular concern, the triage metaphor justifies abandoning some species, while acquiescing to inadequate conservation funding. We argue conservation hospice provides an alternative medical metaphor for thinking about the extinction crisis. Hospice is based on the underlying principle of caring for all [species], and places particular emphasis on expected survival time, symptom burden and relief, treatments, ability to ‘stay at home’ (i.e., in-situ conservation), and maintaining support for related species and landscapes. Ultimately, application of hospice principles may be ethically obligated for a society that accepts the idea that least some organisms are intrinsically valuable and may help place emphasis on resource allocation issues without providing implicit justification for abandoning species to extinction. DA - 2020/6/17/ PY - 2020/6/17/ DO - 10.3389/fevo.2020.00143 VL - 8 SP - SN - 2296-701X KW - conservation triage KW - climate change KW - endangered species KW - extinction KW - conservation ethics ER - TY - JOUR TI - Toward Implementing the ADC Model of Moral Judgment in Autonomous Vehicles AU - Dubljevic, Veljko T2 - SCIENCE AND ENGINEERING ETHICS DA - 2020/10// PY - 2020/10// DO - 10.1007/s11948-020-00242-0 VL - 26 IS - 5 SP - 2461-2472 SN - 1471-5546 KW - Agent-deed-consequence (ADC) model KW - Autonomous vehicles (AVs) KW - Artificial intelligence (AI) KW - Artificial neural networks KW - Artificial morality KW - Neuroethics ER - TY - JOUR TI - Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads T2 - Ecology and Evolution AB - Abstract Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads ( Spea multiplicata ). Spea tadpoles normally develop into an “omnivore” morph that is favored in long‐lasting, low‐density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a “carnivore” morph that is favored in ephemeral, high‐density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with each morph (carnivores vs. omnivores) and loci associated with adaptive phenotypic plasticity (adaptive vs. maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might mediate adaptive plasticity. DA - 2020/7/24/ PY - 2020/7/24/ DO - 10.1002/ece3.6602 UR - http://dx.doi.org/10.1002/ece3.6602 KW - assessment KW - ddRADseq KW - outlier loci KW - phenotypic plasticity KW - population genomics KW - spadefoot toad ER - TY - JOUR TI - Testing trade-offs and the dominance-impoverishment rule among ant communities AU - Sheard, Julie K. AU - Nelson, Annika S. AU - Berggreen, Jeppe D. AU - Boulay, Raphael AU - Dunn, Robert R. AU - Sanders, Nathan J. T2 - JOURNAL OF BIOGEOGRAPHY AB - Abstract Aim Ant communities are believed to be structured by competition, with dominant species competitively excluding subordinates (the dominance–impoverishment rule). However, a high number of seemingly similar species coexist, possibly due to interspecific trade‐offs. Here, we examine the evidence for the dominance–impoverishment rule across a broad latitudinal gradient and explore whether trade‐offs explain coexistence within and among ant communities. Location 40 sites in 19 countries across Europe, western North America and northern South America. Taxon Formicidae. Methods We conducted 2‐hr baiting experiments at each site. Three dominance scores were calculated for each species at each site where it occurred. We then examined the relationship between ant dominance and diversity and tested for the generality of three trade‐offs (dominance–discovery, dominance–thermal tolerance and dominance–generalism) within and among ant communities along with the possible effects of environmental variables on these trade‐offs. Results We found no support for the dominance–impoverishment rule. Instead, overall species richness at baits was positively correlated with the number of dominant species and exhibited a unimodal relationship with the relative abundance of dominant ants. Moreover, we found little consistent evidence for the three interspecific trade‐offs. Main conclusion Although total species richness at baits is positively correlated with species richness of dominant species and, to a point, increasing worker numbers of dominants, trade‐offs among species do not appear to shape broad‐scale patterns of coexistence among ants. Species richness declines only when the numbers of dominant workers are very high. Together, these results suggest that while trade‐offs and the dominance–impoverishment rule might promote coexistence or shape ant communities in some locations, the evidence for their being general across communities is scant. DA - 2020/9// PY - 2020/9// DO - 10.1111/jbi.13911 VL - 47 IS - 9 SP - 1899-1909 SN - 1365-2699 KW - biogeography KW - competition KW - discovery KW - dominance KW - formicidae KW - resource use KW - thermal tolerance ER - TY - JOUR TI - Interactive global change factors mitigate soil aggregation and carbon change in a semi-arid grassland AU - Bai, Tongshuo AU - Wang, Peng AU - Hall, Steven J. AU - Wang, Fuwei AU - Ye, Chenglong AU - Li, Zhen AU - Li, Shijie AU - Zhou, Luyao AU - Qiu, Yunpeng AU - Guo, Jiuxin AU - Guo, Hui AU - Wang, Yi AU - Hu, Shuijin T2 - GLOBAL CHANGE BIOLOGY AB - Abstract The ongoing global change is multi‐faceted, but the interactive effects of multiple drivers on the persistence of soil carbon (C) are poorly understood. We examined the effects of warming, reactive nitrogen (N) inputs (12 g N m −2 year −1 ) and altered precipitation (+ or − 30% ambient) on soil aggregates and mineral‐associated C in a 4 year manipulation experiment with a semi‐arid grassland on China's Loess Plateau. Our results showed that in the absence of N inputs, precipitation additions significantly enhanced soil aggregation and promoted the coupling between aggregation and both soil fungal biomass and exchangeable Mg 2+ . However, N inputs negated the promotional effects of increased precipitation, mainly through suppressing fungal growth and altering soil pH and clay‐Mg 2+ ‐OC bridging. Warming increased C content in the mineral‐associated fraction, likely by increasing inputs of root‐derived C, and reducing turnover of existing mineral‐associated C due to suppression of fungal growth and soil respiration. Together, our results provide new insights into the potential mechanisms through which multiple global change factors control soil C persistence in arid and semi‐arid grasslands. These findings suggest that the interactive effects among global change factors should be incorporated to predict the soil C dynamics under future global change scenarios. DA - 2020/9// PY - 2020/9// DO - 10.1111/gcb.15220 VL - 26 IS - 9 SP - 5320-5332 SN - 1365-2486 KW - aggregate stability KW - carbonate KW - global change KW - mineral-associated C KW - N-induced acidification KW - soil respiration ER - TY - JOUR TI - Simulated warming enhances the responses of microbial N transformations to reactive N input in a Tibetan alpine meadow AU - Zhang, Yi AU - Zhang, Nan AU - Yin, Jingjing AU - Zhao, Yexin AU - Yang, Fei AU - Jiang, Zhongquan AU - Tao, Jinjin AU - Yan, Xuebin AU - Qiu, Yunpeng AU - Guo, Hui AU - Hu, Shuijin T2 - ENVIRONMENT INTERNATIONAL AB - Alpine ecosystems worldwide are characterized with high soil organic carbon (C) and low mineral nitrogen (N). Climate warming has been predicted to stimulate microbial decomposition and N mineralization in these systems. However, experimental results are highly variable, and the underlying mechanisms remain unclear. We examined the effects of warming, N input, and their combination on soil N pools and N-cycling microbes in a field manipulation experiment. Special attention was directed to the ammonia-oxidizing bacteria and archaea, and their mediated N-cycling processes (transformation rates and N2O emissions) in the third plant growing season after the treatments were initiated. Nitrogen input (12 g m−2 y−1) alone significantly increased soil mineral N pools and plant N uptake, and stimulated the growth of AOB and N2O emissions in the late growing season. While warming (by 1.4 °C air temperature) alone did not have significant effects on most parameters, it amplified the effects of N input on soil N concentrations and AOB abundance, eliciting a chain reaction that increased nitrification potential (+83%), soil NO3−-N (+200%), and N2O emissions (+412%) across the whole season. Also, N input reduced AOB diversity but increased the dominance of genus Nitrosospira within the AOB community, corresponding to the increased N2O emissions. These results showed that a small temperature increase in soil may significantly enhance N losses through NO3− leaching and N2O emissions when mineral N becomes available. These findings suggest that interactions among global change factors may predominantly affect ammonia-oxidizing microbes and their mediated N-cycling processes in alpine ecosystems under future climate change scenarios. DA - 2020/8// PY - 2020/8// DO - 10.1016/j.envint.2020.105795 VL - 141 SP - SN - 1873-6750 KW - Alpine meadow KW - Climate warming KW - Nitrogen addition KW - N2O emission KW - Ammonia-oxidizing archaea KW - Ammonia-oxidizing bacteria ER - TY - JOUR TI - Baseline Flight Potential of Euschistus servus (Hemiptera: Pentatomidae) and Its Implications on Local Dispersal AU - Babu, Arun AU - Del Pozo-Valdivia, Alejandro I AU - Reisig, Dominic D T2 - Environmental Entomology AB - The brown stink bug, Euschistus servus (Say), is a damaging pest of multiple crops in the southeastern United States. In addition to crops, both the weedy field borders and wooded areas of a typical farmscape in this region harbor E. servus host plants, many of which are temporally and spatially limiting in availability or nutritional suitability. Therefore, local dispersal is required so that individuals efficiently track and utilize host resources. This research sought to establish the baseline flight capacity of adult E. servus across the season in relation to body weight, sex, and plant host use with a flight mill system. Across this 2-yr study, among the individuals with a flight response in the flight mill, 90.1% of individuals flew in a range of >0-1 km, with an individual maximum flight distance of 15.9 km. In 2017, mean total distance flown varied across the season. Except for the individuals collected from corn in 2019, during both 2017 and 2019, the highest numerical mean flight potential occurred soon after overwintering emergence and a relatively low flight potential occurred during the cropping season. Individuals collected from wheat, corn, and early season weeds lost a higher proportion of body weight after flight than did individuals from soybean and late season weeds. The baseline dispersal potential information generated from this study can be extrapolated to the farmscape level aiming to develop, plan, and implement E. servus management programs. DA - 2020/4/20/ PY - 2020/4/20/ DO - 10.1093/ee/nvaa041 VL - 49 IS - 3 SP - 699-708 LA - en OP - SN - 0046-225X 1938-2936 UR - http://dx.doi.org/10.1093/ee/nvaa041 DB - Crossref KW - arm-pivoting flight mill KW - stink bug KW - plant host use KW - body weight ER - TY - JOUR TI - Response of agronomic crops to planting date and double-cropping with wheat AU - Hare, Andrew T. AU - Jordan, David L. AU - Edmisten, Keith L. AU - Leon, Ramon G. AU - Post, Angela R. AU - Vann, Rachel AU - Dunphy, E. James AU - Heiniger, Ronnie AU - Collins, Guy AU - Washburn, Derek T2 - AGRONOMY JOURNAL AB - Abstract Planting date can affect crop yield and is an important management decision for practitioners. Although wheat ( Triticum aestivum L.) and soybean [ Glycine max (L.) Merr.] can be effectively double‐cropped in North Carolina, if commodity prices and projected economic returns are higher for crops other than soybean, growers might consider a nontraditional, double‐crop system. Direct comparisons of major agronomic crops with different planting dates or in a double‐crop system with wheat are limited in North Carolina. Therefore, research was conducted in North Carolina from 2013 through 2017 to determine yield potential of corn ( Zea mays L.), cotton ( Gossypium hirsutum L.), grain sorghum [ Sorghum bicolor (L.) Moench], peanut ( Arachis hypogaea L.), and soybean planted at two dates within the recommended planting window for full‐season production versus planting these crops after wheat harvest. The experimental design was a split plot, with summer crop serving as the whole plot unit and planting date within a crop serving as the subplot unit. Yield of corn, cotton, grain sorghum, peanut, and soybean in full‐season production exceeded that of double‐cropping with wheat in 5, 5, 2, 4, and 5 yr out of 5 yr of the study, respectively. Estimated economic returns were generated using the 10‐yr average (2008–2017) summer crop prices with the 10‐yr average wheat price. When considering all possible combinations of years and crops (n = 25), in only 20% of the possible combinations was the economic return of the double‐cropping system greater than economic return of full‐season crop production when compared with at least one of the planting dates within the traditional planting window. DA - 2020/// PY - 2020/// DO - 10.1002/agj2.20164 VL - 112 IS - 3 SP - 1972-1980 SN - 1435-0645 ER - TY - JOUR TI - Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling AU - Van den Broeck, Lisa AU - Gordon, Max AU - Inzé, Dirk AU - Williams, Cranos AU - Sozzani, Rosangela T2 - Frontiers in Genetics AB - Plant responses to environmental and intrinsic signals are tightly controlled by multiple transcription factors (TFs). These TFs and their regulatory connections form gene regulatory networks (GRNs), which provide a blueprint of the transcriptional regulations underlying plant development and environmental responses. This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs. Additionally, this review describes network inference techniques that leverage gene expression data to predict regulatory interactions. These computational and experimental methodologies yield complex networks that can identify new regulatory interactions, driving novel hypotheses. Biological properties that contribute to the complexity of GRNs are also described in this review. These include network topology, network size, transient binding of TFs to DNA, and competition between multiple upstream regulators. Finally, this review highlights the potential of machine learning approaches to leverage gene expression data to predict phenotypic outputs. DA - 2020/5/25/ PY - 2020/5/25/ DO - 10.3389/fgene.2020.00457 VL - 11 SP - J2 - Front. Genet. OP - SN - 1664-8021 UR - http://dx.doi.org/10.3389/fgene.2020.00457 DB - Crossref KW - gene regulatory network KW - network properties KW - network inference KW - machine learning KW - experimental methodologies ER - TY - JOUR TI - Extracting Uranium's futures: Nuclear wastes, toxic temporalities, and uncertain decisions AU - Kinsella, William J. T2 - EXTRACTIVE INDUSTRIES AND SOCIETY-AN INTERNATIONAL JOURNAL AB - Civilian and military uses of nuclear energy have produced a legacy of high-level radioactive wastes posing threats of millennial duration, and their production continues despite the absence of viable disposal solutions. These materials extend the impact of decisions made today into a far distant future, raising difficult questions regarding intergenerational and intragenerational social justice, ethical responsibility, and collective decision-making. This essay critically reviews those challenges using resources from the fields of communication and rhetoric, sociologies and philosophies of temporality and risk, and science and technology studies. The essay argues that modern notions of prediction, control, and decision-making are inadequate for addressing such highly complex phenomena and long temporal durations. Nuclear waste disposal is then examined as an activity that seeks not only to contain material hazards, but also to symbolically purify the system of nuclear production and consumption. The proposed U.S. nuclear waste repository at Yucca Mountain provides an example in which predictive models, which warrant both epistemic and political authority, are nevertheless insufficient bases for collective decision-making. The essay then considers the situation in the United States, where a new political economy of nuclear waste appears to be emerging, and offers summary conclusions regarding nuclear power and social justice. DA - 2020/4// PY - 2020/4// DO - 10.1016/j.exis.2020.01.003 VL - 7 IS - 2 SP - 524-534 SN - 2214-7918 KW - Nuclear waste KW - Temporality KW - Nuclear risk KW - Intergenerational justice KW - Yucca Mountain ER - TY - JOUR TI - Amaranthus palmeri a New Invasive Weed in Spain with Herbicide Resistant Biotypes AU - Torra, Joel AU - Royo-Esnal, Aritz AU - Romano, Yolanda AU - Osuna, María AU - León, Ramón AU - Recasens, Jordi T2 - Agronomy AB - Amaranthus palmeri is the most prominent invasive weed in agricultural land from North America, partly due to its propensity to evolve resistance to multiple herbicide sites of action. In the last two decades, reports of this species have increased throughout the American continent and occasionally in other continents. In 2007, A. palmeri populations were found in three localities in northeastern Spain, and they are still present today. To determine whether these three populations resulted from a common or independent introduction events—and when and from where they could have occurred—research was carried out aiming to characterize the resistance profile and mechanisms to 5-enolpyruvylshikimate-3-phosphate synthase-and acetolactate synthase (ALS)-inhibiting herbicides and to analyze the relationship between these three populations using inter simple sequence repeat DNA fingerprinting. Dose–response trials confirmed that the three populations were susceptible to glyphosate but resistant to nicosulfuron-methyl. Resistance to ALS inhibitors was due to several amino acid substitutions in positions Pro197, Trp574 and Ser653. Moreover, the substitutions Ser653Ile and Pro197Thr are described for the first time in this species. At field-labeled rates, all populations were fully controlled with alternative herbicides with other sites of action. Amaranthus palmeri individuals were clustered in three groups based on unweighted pair group method with arithmetic mean analysis, which corresponded to the three sampled populations, with a 67% of genetic relationship among them. Considering this high genetic variability and the different positions and amino acid substations found between populations, it was hypothesized that different colonization events occurred from the American continent probably prior to the introduction of glyphosate resistant crops. Prevention from new introductions is warranted because new herbicide resistance traits could arrive, complicating the management of this invasive weed species, while managing or eradicating the already established populations. DA - 2020/7/10/ PY - 2020/7/10/ DO - 10.3390/agronomy10070993 VL - 10 IS - 7 SP - 993 UR - https://doi.org/10.3390/agronomy10070993 KW - alien plant KW - ALS inhibitors KW - dendrogram KW - glyphosate KW - inter simple sequence repeat (ISSR) DNA fingerprinting KW - maize KW - nicosulfuron-methyl KW - target-site resistance ER - TY - CHAP TI - Disease and wellness across the lifespan: A global perspective on the mental health burden of dementia AU - Dubljević, Veljko T2 - Global Mental Health and Neuroethics AB - Dementia, and especially behavioral variant frontotemporal dementia (bvFTD), reverses the hard won freedoms and rights that are enjoyed by most adult human beings. The deficits in cognition and decision-making lead to a legitimate reduction in autonomy and rights. The prognosis for dementia is poor and it ultimately ends in death. These facts, along with the widespread fear of dementia, lead to social exclusion and stigmatization of both persons living with dementia and their family members, which contributes to significant mental health burdens. This chapter explores the perspectives of persons living with dementia, caregivers, and people at risk of developing dementia in order to give a human face and voice to a marginalized population that is increasing globally. Perspectives and challenges of early and later stage patients and care-givers are contrasted to preconceived notions of older adults as well as media representations of dementia in order to explore the social discourses of labeling persons as “demented.” The mental health burden of dementia is a global problem which can only be solved after innovative policies across the world are assessed for enabling healthcare delivery and empowering patients to lead as dignified lives as possible. PY - 2020/// DO - 10.1016/b978-0-12-815063-4.00014-9 SP - 225-235 OP - PB - Elsevier SN - 9780128150634 UR - http://dx.doi.org/10.1016/b978-0-12-815063-4.00014-9 DB - Crossref ER - TY - CONF TI - Toward Implementing the Agent-Deed-Consequence Model of Moral Judgment in Autonomous Vehicles AU - Dubljevic, Veljko T2 - AIES '20: AAAI/ACM Conference on AI, Ethics, and Society AB - Autonomous vehicles (AVs) and accidents they are involved in attest to the urgent need to consider the ethics of AI. The question dominating the discussion has been whether we want AVs to behave in a 'selfish' or utilitarian manner. Rather than considering modeling self-driving cars on a single moral system like utilitarianism, one possible way to approach programming for AI would be to reflect recent work in neuroethics. The Agent-Deed-Consequence (ADC) model [1-4] provides a promising account while also lending itself well to implementation in AI. The ADC model explains moral judgments by breaking them down into positive or negative intuitive evaluations of the Agent, Deed, and Consequence in any given situation. These intuitive evaluations combine to produce a judgment of moral acceptability. This explains the considerable flexibility and stability of human moral judgment that has yet to be replicated in AI. This paper examines the advantages and disadvantages of implementing the ADC model and how the model could inform future work on ethics of AI in general. C2 - 2020/2/7/ C3 - Proceedings of the AAAI/ACM Conference on AI, Ethics, and Society DA - 2020/2/7/ DO - 10.1145/3375627.3375853 PB - ACM SN - 9781450371100 UR - http://dx.doi.org/10.1145/3375627.3375853 DB - Crossref ER - TY - JOUR TI - Is the insect apocalypse upon us? How to find out AU - Montgomery, Graham A. AU - Dunn, Robert R. AU - Fox, Richard AU - Jongejans, Eelke AU - Leather, Simon R. AU - Saunders, Manu E. AU - Shortall, Chris R. AU - Tingley, Morgan W. AU - Wagner, David L. T2 - Biological Conservation AB - In recent decades, entomologists have documented alarming declines in occurrence, taxonomic richness, and geographic range of insects around the world. Additionally, some recent studies have reported that insect abundance and biomass, often of common species, are rapidly declining, which has led some to dub the phenomenon an “Insect Apocalypse”. Recent reports are sufficiently robust to justify immediate actions to protect insect biodiversity worldwide. We caution, however, that we do not yet have the data to assess large-scale spatial patterns in the severity of insect trends. Most documented collapses are from geographically restricted studies and, alone, do not allow us to draw conclusions about insect declines on continental or global scales, especially with regards to future projections of total insect biomass, abundance, and extinction. There are many challenges to understanding insect declines: only a small fraction of insect species have had any substantial population monitoring, millions of species remain unstudied, and most of the long-term population data for insects come from human-dominated landscapes in western and northern Europe. But there are still concrete steps we can take to improve our understanding of potential declines. Here, we review the challenges scientists face in documenting insect population and diversity trends, including communicating their findings, and recommend research approaches needed to address these challenges. DA - 2020/1// PY - 2020/1// DO - 10.1016/j.biocon.2019.108327 VL - 241 SP - 108327 J2 - Biological Conservation LA - en OP - SN - 0006-3207 UR - http://dx.doi.org/10.1016/j.biocon.2019.108327 DB - Crossref KW - Insect declines KW - Biodiversity crisis KW - Biomass KW - Monitoring KW - Entomology ER - TY - JOUR TI - Current outlook and future research needs for harvest weed seed control in North American cropping systems AU - Shergill, Lovreet S AU - Schwartz‐Lazaro, Lauren M AU - Leon, Ramon AU - Ackroyd, Victoria J AU - Flessner, Michael L AU - Bagavathiannan, Muthukumar AU - Everman, Wesley AU - Norsworthy, Jason K AU - VanGessel, Mark J AU - Mirsky, Steven B T2 - Pest Management Science AB - Abstract Harvest weed seed control (HWSC) comprises a set of tools and tactics that prevents the addition of weed seed to the soil seed bank, attenuating weed infestations and providing a method to combat the development and spread of herbicide‐resistant weed populations. Initial HWSC research efforts in North America are summarized and, combined with the vast area of crops suitable for HWSC, clearly indicate strong potential for this technology. However, potential limitations exist that are not present in Australian cropping systems where HWSC was developed. These include rotations with crops that are not currently amenable to HWSC (e.g. corn), high moisture content at harvest, untimely harvest, and others. Concerns about weeds becoming resistant to HWSC (i.e. adapting) exist, as do shifts in weed species composition, particularly with the diversity of weeds in North America. Currently the potential of HWSC vastly outweighs any drawbacks, necessitating further research. Such expanded efforts should foremost include chaff lining and impact mill commercial scale evaluation, as this will address potential limitations as well as economics. Growers must be integrated into large‐scale, on‐farm research and development activities aimed at alleviating the problems of using HWSC systems in North America and drive greater adoption subsequently. © 2020 Society of Chemical Industry DA - 2020/12// PY - 2020/12// DO - 10.1002/ps.5986 UR - https://doi.org/10.1002/ps.5986 KW - herbicide resistance management KW - integrated weed management KW - soil seed bank ER - TY - JOUR TI - Resistance monitoring to four insecticides and mechanisms of resistance in Lygus lineolaris Palisot de Beauvois (Hemiptera: Miridae) populations of southeastern USA cotton AU - Dorman, Seth J AU - Gross, Aaron D AU - Musser, Fred R AU - Catchot, Beverly D AU - Smith, Ronald H AU - Reisig, Dominic D AU - Reay‐Jones, Francis PF AU - Greene, Jeremy K AU - Roberts, Phillip M AU - Taylor, Sally V T2 - Pest Management Science AB - Abstract BACKGROUND Economically damaging infestations of the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), have become more frequent in Virginia and North Carolina cotton since 2013 and 2010, respectively. Foliar insecticide use has increased dramatically in response. Efficacy data (LC 50 ) are needed to evaluate L. lineolaris susceptibility and resistance levels (RR 50 ) to commonly used and recommended insecticides for managing this pest in the southeastern USA. RESULTS Elevated resistance levels to acephate and bifenthrin were measured in L. lineolaris populations collected from wild and cultivated hosts in Virginia, North Carolina and northern Alabama when compared to a susceptible laboratory population. High levels of bifenthrin resistance were observed in 2018 and 2019. Mixed‐function oxidase and esterase (EST) inhibitors, piperonyl butoxide and S , S , S ‐Tributyl phosphotrithioate, respectively, had a synergistic effect on bifenthrin with resistant populations of L. lineolaris . Bifenthrin‐resistant L. lineolaris populations expressed elevated levels of cytochrome P450 (CYP 450 ) monooxygenase and general EST activity. Results suggest that insecticide resistance is present in some locations and that CYP 450 and EST activity in L. lineolaris contribute to pyrethroid resistance in the southeastern USA. CONCLUSIONS Results can serve as a baseline for continued monitoring of L. lineolaris insecticide resistance and inform insecticide resistance management strategies that help southeastern USA cotton producers to minimize inputs and slow resistance development. © 2020 Society of Chemical Industry DA - 2020/6/22/ PY - 2020/6/22/ DO - 10.1002/ps.5940 VL - 76 IS - 12 SP - 3935-3944 J2 - Pest Manag Sci LA - en OP - SN - 1526-498X 1526-4998 UR - http://dx.doi.org/10.1002/ps.5940 DB - Crossref KW - tarnished plant bug KW - Gossypium hirsutumL KW - insecticide resistance KW - general esterase KW - cytochrome P450 monooxygenase ER - TY - JOUR TI - Soil acidification reduces the effects of short-term nutrient enrichment on plant and soil biota and their interactions in grasslands AU - Xiao, Hong AU - Wang, Bing AU - Lu, Shunbao AU - Chen, Dima AU - Wu, Ying AU - Zhu, Yuhe AU - Hu, Shuijin AU - Bai, Yongfei T2 - GLOBAL CHANGE BIOLOGY AB - Abstract Soil nitrogen (N) and phosphorus (P) contents, and soil acidification have greatly increased in grassland ecosystems due to increased industrial and agricultural activities. As major environmental and economic concerns worldwide, nutrient enrichment and soil acidification can lead to substantial changes in the diversity and structure of plant and soil communities. Although the separate effects of N and P enrichment on soil food webs have been assessed across different ecosystems, the combined effects of N and P enrichment on multiple trophic levels in soil food webs have not been studied in semiarid grasslands experiencing soil acidification. Here we conducted a short‐term N and P enrichment experiment in non‐acidified and acidified soil in a semiarid grassland on the Mongolian Plateau. We found that net primary productivity was not affected by N or P enrichment alone in either non‐acidified or acidified soil, but was increased by combined N and P enrichment in both non‐acidified and acidified soil. Nutrient enrichment decreased the biomass of most microbial groups in non‐acidified soil (the decrease tended to be greatest with combined N and P enrichment) but not in acidified soil, and did not affect most soil nematode variables in non‐acidified or acidified soil. Nutrient enrichment also changed plant and microbial community structure in non‐acidified but not in acidified soil, and had no effect on nematode community structure in non‐acidified or acidified soil. These results indicate that the responses to short‐term nutrient enrichment were weaker for higher trophic groups (nematodes) than for lower trophic groups (microorganisms) and primary producers (plants). The findings increase our understanding of the effects of nutrient enrichment on multiple trophic levels of soil food webs, and highlight that soil acidification, as an anthropogenic stressor, reduced the responses of plants and soil food webs to nutrient enrichment and weakened plant–soil interactions. DA - 2020/8// PY - 2020/8// DO - 10.1111/gcb.15167 VL - 26 IS - 8 SP - 4626-4637 SN - 1365-2486 KW - environmental context KW - interaction of nutrient additions KW - multiple trophic levels KW - nitrogen and phosphorus enrichments KW - plant-soil interactions KW - soil food webs ER - TY - JOUR TI - Global forensic geolocation with deep neural networks AU - Grantham, Neal S. AU - Reich, Brian J. AU - Laber, Eric B. AU - Pacifici, Krishna AU - Dunn, Robert R. AU - Fierer, Noah AU - Gebert, Matthew AU - Allwood, Julia S. AU - Faith, Seth A. T2 - JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS AB - Summary An important problem in modern forensic analyses is identifying the provenance of materials at a crime scene, such as biological material on a piece of clothing. This procedure, which is known as geolocation, is conventionally guided by expert knowledge of the biological evidence and therefore tends to be application specific, labour intensive and often subjective. Purely data-driven methods have yet to be fully realized in this domain, because in part of the lack of a sufficiently rich source of data. However, high throughput sequencing technologies can identify tens of thousands of fungi and bacteria taxa by using DNA recovered from a single swab collected from nearly any object or surface. This microbial community, or microbiome, may be highly informative of the provenance of the sample, but data on the spatial variation of microbiomes are sparse and high dimensional and have a complex dependence structure that render them difficult to model with standard statistical tools. Deep learning algorithms have generated a tremendous amount of interest within the machine learning community for their predictive performance in high dimensional problems. We present DeepSpace: a new algorithm for geolocation that aggregates over an ensemble of deep neural network classifiers trained on randomly generated Voronoi partitions of a spatial domain. The DeepSpace algorithm makes remarkably good point predictions; for example, when applied to the microbiomes of over 1300 dust samples collected across continental USA, more than half of geolocation predictions produced by this model fall less than 100 km from their true origin, which is a 60% reduction in error from competing geolocation methods. Moreover, we apply DeepSpace to a novel data set of global dust samples collected from nearly 30 countries, finding that dust-associated fungi alone predict a sample's country of origin with nearly 90% accuracy. DA - 2020/8// PY - 2020/8// DO - 10.1111/rssc.12427 VL - 69 IS - 4 SP - 909-929 SN - 1467-9876 KW - Citizen science KW - Machine learning KW - Microbiome KW - Non-homogeneous Poisson process KW - Spatial point pattern ER - TY - JOUR TI - Role of long non-coding RNA in DEET- and fipronil-mediated alteration of transcripts associated with Phase I and Phase II xenobiotic metabolism in human primary hepatocytes AU - Lawrie, Roger D. AU - Mitchell, Robert D., III AU - Dhammi, Anirudh AU - Wallace, Andrew AU - Hodgson, Ernest AU - Roe, R. Michael T2 - PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY AB - Human exposure to environmental chemicals both individually and in combination occurs frequently world-wide most often with unknown consequences. Use of molecular approaches to aide in the assessment of risk involved in chemical exposure is a growing field in toxicology. In this study, we examined the impact of two environmental chemicals used in and around homes, the insect repellent DEET (N,N-diethyl-m-toluamide) and the phenylpyrazole insecticide fipronil (fluocyanobenpyrazole) on transcript levels of enzymes potentially involved in xenobiotic metabolism and on long non-coding RNAs (lncRNAs). Primary human hepatocytes were treated with these two chemicals both individually and in combination. Using RNA-Seq, we found that 10 major enzyme categories involved in phase 1 and phase 2 xenobiotic metabolism were significantly (α = 0.05) up- and down-regulated (i.e., 100 μM DEET–19 transcripts, 89% up and 11% down; 10 μM fipronil–52 transcripts, 53% up and 47% down; and 100 μM DEET +10 μM fipronil–69 transcripts, 43% up and 57% down). The altered genes were then mapped to the human genome and their proximity (within 1,000,000 bp) to lncRNAs examined. Unique proximities were discovered between altered lncRNA and altered P450s (CYP) and other enzymes (DEET, 2 CYP; Fipronil, 6 CYP and 15 other; and DEET + fipronil, 7 CYP and 21 other). Many of the altered P450 transcripts were in multiple clusters in the genome with proximal altered lncRNAs, suggesting a regulator function for the lncRNA. At the gene level there was high percent identity for lncRNAs near P450 clusters, but this relationship was not found at the transcript level. The role of these altered lncRNAs associated with xenobiotic induction, human diseases and chemical mixtures is discussed. DA - 2020/7// PY - 2020/7// DO - 10.1016/j.pestbp.2020.104607 VL - 167 SP - SN - 1095-9939 KW - Long non-coding RNA KW - DEET KW - Fipronil KW - Xenobiotic metabolism KW - Environmental chemicals KW - Cytochrome P450 ER - TY - JOUR TI - Structure–Function Analysis of Interallelic Complementation in ROOTY Transheterozygotes AU - Brumos, Javier AU - Bobay, Benjamin G. AU - Clark, Cierra A. AU - Alonso, Jose M. AU - Stepanova, Anna N. T2 - Plant Physiology AB - Auxin is a crucial plant growth regulator. Forward genetic screens for auxin-related mutants have led to the identification of key genes involved in auxin biosynthesis, transport, and signaling. Loss-of-function mutations in genes involved in glucosinolate biosynthesis, a metabolically related route that produces defense compounds, result in auxin overproduction. We identified an allelic series of fertile, hypomorphic Arabidopsis (Arabidopsis thaliana) mutants for the essential glucosinolate biosynthetic gene ROOTY (RTY) that exhibit a range of phenotypic defects characteristic of enhanced auxin production. Genetic characterization of these lines uncovered phenotypic suppression by cyp79b2 cyp79b3, wei2, and wei7 mutations and revealed the phenomenon of interallelic complementation in several RTY transheterozygotes. Structural modeling of RTY elucidated the relationships between structure and function in the RTY homo- and heterodimers, and unveiled the likely structural basis of interallelic complementation. This work underscores the importance of employing true null mutants in genetic complementation studies. DA - 2020/7// PY - 2020/7// DO - 10.1104/pp.20.00310 VL - 183 IS - 3 SP - 1110-1125 UR - https://doi.org/10.1104/pp.20.00310 ER - TY - JOUR TI - Perspective: enhancing economic evaluations and impacts of integrated pest management Farmer Field Schools (IPM-FFS) in low-income countries AU - Rejesus, Roderick M. AU - Jones, Michael S. T2 - PEST MANAGEMENT SCIENCE AB - Abstract Over the last few decades, the use of Farmer Field Schools (FFS) have been considered one of the best approaches to disseminate integrated pest management (IPM) practices that aim to reduce reliance on and misuse of chemical pest control methods in agriculture. However, the published empirical literature has been decidedly mixed in terms of the effectiveness of the IPM‐FFS approach to improve economic outcomes in the short‐term (e.g. reduce chemical use, improve profits), and the potential for scaling‐up and IPM dissemination in the medium‐term. This article briefly explores the empirical IPM‐FFS literature and draws implications for future research directions that can potentially enhance IPM knowledge diffusion methods (including IPM‐FFS) and increase the economic impact of IPM techniques in low‐income countries. We find that promising research directions to improve understanding of IPM dissemination and IPM impacts will need to involve: (i) interdisciplinary long‐run studies using rigorous evaluation methods; (ii) in‐depth assessments of spillover effects; (iii) careful examination of IPM and IPM‐FFS impact heterogeneity; (iv) evaluation of novel IPM packages with herbicide‐ and genetics‐centered components; (v) piloting and impact assessments of alternative IPM knowledge diffusion structures; and (vi) piloting and impact analysis of IPM dissemination and learning programs with private sector involvement. © 2020 Society of Chemical Industry DA - 2020/11// PY - 2020/11// DO - 10.1002/ps.5912 VL - 76 IS - 11 SP - 3527-3536 SN - 1526-4998 KW - economic evaluations KW - economic impacts KW - Farmer Field Schools KW - future research directions KW - integrated pest management (IPM) KW - interdisciplinary research ER - TY - JOUR TI - Bioengineering horizon scan 2020 AU - Kemp, Luke AU - Adam, Laura AU - Boehm, Christian R. AU - Breitling, Rainer AU - Casagrande, Rocco AU - Dando, Malcolm AU - Djikeng, Appolinaire AU - Evans, Nicholas G. AU - Hammond, Richard AU - Hills, Kelly AU - Holt, Lauren A. AU - Kuiken, Todd AU - Markotic, Alemka AU - Millett, Piers AU - Napier, Johnathan A. AU - Nelson, Cassidy AU - Oheigeartaigh, Sean S. AU - Osbourn, Anne AU - Palmer, Megan J. AU - Patron, Nicola J. AU - Perello, Edward AU - Piyawattanametha, Wibool AU - Restrepo-Schild, Vanessa AU - Rios-Rojas, Clarissa AU - Rhodes, Catherine AU - Roessing, Anna AU - Scott, Deborah AU - Shapira, Philip AU - Simuntala, Christopher AU - Smith, Robert D. J. AU - Sundaram, Lalitha S. AU - Takano, Eriko AU - Uttmark, Gwyn AU - Wintle, Bonnie C. AU - Zahra, Nadia B. AU - Sutherland, William J. T2 - ELIFE AB - Horizon scanning is intended to identify the opportunities and threats associated with technological, regulatory and social change. In 2017 some of the present authors conducted a horizon scan for bioengineering (Wintle et al., 2017). Here we report the results of a new horizon scan that is based on inputs from a larger and more international group of 38 participants. The final list of 20 issues includes topics spanning from the political (the regulation of genomic data, increased philanthropic funding and malicious uses of neurochemicals) to the environmental (crops for changing climates and agricultural gene drives). The early identification of such issues is relevant to researchers, policy-makers and the wider public. DA - 2020/5/29/ PY - 2020/5/29/ DO - 10.7554/elife.54489 VL - 9 SP - SN - 2050-084X ER - TY - JOUR TI - The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication AU - Chen, Qiuyue AU - Samayoa, Luis Fernando AU - Yang, Chin Jian AU - Bradbury, Peter J. AU - Olukolu, Bode A. AU - Neumeyer, Michael A. AU - Romay, Maria Cinta AU - Sun, Qi AU - Lorant, Anne AU - Buckler, Edward S. AU - Ross-Ibarra, Jeffrey AU - Holland, James B. AU - Doebley, John F. T2 - PLOS GENETICS AB - The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is "missing" in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect. DA - 2020/5// PY - 2020/5// DO - 10.1371/journal.pgen.1008791 VL - 16 IS - 5 SP - SN - 1553-7404 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85085904066&partnerID=MN8TOARS ER - TY - JOUR TI - A typology of beliefs and misperceptions about the influenza disease and vaccine among older adults in Singapore AU - Cummings, Christopher L. AU - Kong, Wei Yi AU - Orminski, Jeanette T2 - PLOS ONE AB - Access to the influenza vaccine pose little barriers in developed countries such as Singapore and vaccination against influenza is highly recommended for at-risk populations including older adults. However, vaccination rates are much lower than recommended despite the significant morbidity and mortality associated with the disease among this vulnerable population. Given timely goals to increase vaccine acceptance and uptake, we explored Singaporean older adults’ misperceptions about influenza disease and vaccine. Qualitative semi-structured interviews were conducted among 76 Singaporean adults aged 65 and above with no focus on a specific area in Singapore. Data were analyzed with grounded theory methods to understand participants’ attitudes, perceptions, and knowledge. We developed in vivo codes that reflect the verbiage used by participants and exhaustively catalogued themes through a constant comparison coding method. Focusing specifically on older adults’ misperceptions, seven main themes about influenza disease or vaccine emerged from our data analysis: familiarity with influenza, misperceptions about influenza, personal susceptibility to influenza, familiarity with the influenza vaccine, misperceptions about the influenza vaccine, misperceptions about influenza vaccine usage, and opinions about and barriers to influenza vaccine uptake. Notably, there is a lack of adequate knowledge and motivation in vaccinating against influenza among older adults in Singapore. Health communication needs to be more tailored toward older adults’ message processing systems and engage health professionals’ involvement in addressing the influenza disease and vaccine misperceptions identified in this study. DA - 2020/5/6/ PY - 2020/5/6/ DO - 10.1371/journal.pone.0232472 VL - 15 IS - 5 SP - SN - 1932-6203 ER - TY - JOUR TI - Disturbances drive changes in coral community assemblages and coral calcification capacity AU - Courtney, Travis A. AU - Barnes, Brian B. AU - Chollett, Iliana AU - Elahi, Robin AU - Gross, Kevin AU - Guest, James R. AU - Kuffner, Ilsa B. AU - Lenz, Elizabeth A. AU - Nelson, Hannah R. AU - Rogers, Caroline S. AU - Toth, Lauren T. AU - Andersson, Andreas J. T2 - ECOSPHERE AB - Abstract Anthropogenic environmental change has increased coral reef disturbance regimes in recent decades, altering the structure and function of many coral reefs globally. In this study, we used coral community survey data collected from 1996 to 2015 to evaluate reef‐scale coral calcification capacity (CCC) dynamics with respect to recorded pulse disturbances for 121 reef sites in the Main Hawaiian Islands and Mo'orea (French Polynesia) in the Pacific and the Florida Keys Reef Tract and St. John (U.S. Virgin Islands) in the western Atlantic. CCC remained relatively high in the Main Hawaiian Islands in the absence of recorded widespread disturbances; declined and subsequently recovered in Mo'orea following a crown‐of‐thorns sea star outbreak, coral bleaching, and major cyclone; decreased and remained low following coral bleaching in the Florida Keys Reef Tract; and decreased following coral bleaching and disease in St. John. Individual coral taxa have variable calcification rates and susceptibility to disturbances because of their differing life‐history strategies. As a result, temporal changes in CCC in this study were driven by shifts in both overall coral cover and coral community composition. Analysis of our results considering coral life‐history strategies showed that weedy corals generally increased their contributions to CCC over time while the contribution of competitive corals decreased. Shifts in contributions by stress‐tolerant and generalist corals to CCC were more variable across regions. The increasing frequency and intensity of disturbances under 21st century global change therefore has the potential to drive lower and more variable CCC because of the increasing dominance of weedy and some stress‐tolerant corals. DA - 2020/4// PY - 2020/4// DO - 10.1002/ecs2.3066 VL - 11 IS - 4 SP - SN - 2150-8925 KW - carbonate budgets KW - climate change KW - coral bleaching KW - coral disease KW - ecological traits KW - environmental monitoring KW - resilience KW - scleractinians ER - TY - JOUR TI - Diurnal and Seasonal Activity Patterns of Drosophilid Species (Diptera: Drosophilidae) Present in Blackberry Agroecosystems With a Focus on Spotted-Wing Drosophila AU - Swoboda-Bhattarai, Katharine A. AU - Burrack, Hannah J. T2 - ENVIRONMENTAL ENTOMOLOGY AB - Abstract Drosophilid species with different life histories have been shown to exhibit similar behavioral patterns related to locating and utilizing resources such as hosts, mates, and food sources. Drosophila suzukii (Matsumura) is an invasive species that differs from other frugivorous drosophilids in that females lay eggs in ripe and ripening fruits instead of overripe or rotten fruits. We hypothesized that there may be diurnal and/or seasonal patterns associated with the movement of drosophilid species into and out of crop fields and their attraction to fermentation-odor-based monitoring traps, and that D. suzukii would conform to similar patterns. To test these hypotheses, we deployed passive, 2-headed Malaise traps between crop fields and wooded edges to simultaneously catch flies moving into and out of crop fields. We also deployed monitoring traps with a fermentation-based bait between crop fields and wooded edges and within crop rows. Traps were deployed weekly in June–August in 2014 and 2015 at two commercial blackberry farm in Cleveland County, NC, and were checked hourly for 24 h, except during darkness. Both D. suzukii and other drosophilid species moved between crop fields and wooded edges and were attracted to monitoring traps primarily during the morning and evening hours. Whereas other drosophilids were captured in traps throughout the season, few D. suzukii were caught in traps until early to mid-July in both years and increased as the season progressed. Understanding D. suzukii movement and activity patterns is essential for the development of effective management strategies. DA - 2020/4// PY - 2020/4// DO - 10.1093/ee/nvz161 VL - 49 IS - 2 SP - 277-287 SN - 1938-2936 KW - invasive species KW - pest phenology KW - Drosophila suzukii KW - Rubus ER - TY - JOUR TI - Impacts of drought and nitrogen enrichment on leaf nutrient resorption and root nutrient allocation in four Tibetan plant species AU - Zhao, Qingzhou AU - Guo, Jin AU - Shu, Meng AU - Wang, Peng AU - Hu, Shuijin T2 - SCIENCE OF THE TOTAL ENVIRONMENT AB - Plant nutrient resorption, a process by which plant withdraws nutrients from senescing structures to developing tissues, can significantly affect plant growth, litter decomposition and nutrient cycling. Global change factors, such as nitrogen (N) deposition and altered precipitation, may mediate plant nutrient resorption and allocation. The ongoing global change is accompanied with increased N inputs and drought frequency in many regions. However, the interactive effects of increased N availability and drought on plant nutrient-responses remain largely unclear. In a pot experiment, we examined the impacts of N enrichment and drought on leaf N and phosphorous (P) resorption and root nutrient allocation in four species from the Qinghai-Tibet Plateau, including two graminoid species (Kobresia capillifolia and Elymus nutans) and two forb species (Delphinium kamaonense and Aster diplostephioides). Our results showed divergent resorption patterns within the two functional groups. E. nutans and D. kamaonense showed stronger N resorption than K. capillifolia and A. diplostephioides. N addition did not alter their N resorption efficiencies, but decreased the N resorption proficiencies of the former two species. In contrast, drought did not affect N or P resorption proficiencies, but decreased N resorption efficiency of K. capillifolia. Besides, N addition facilitated P resorption in K. capillifolia and D. kamaonense, and drought did the same in A. diplostephioides, suggesting that P resorption plays an important role in nutrient conservation in these species. Moreover, species with stronger N resorption allocated more biomass C or N to aboveground and enhanced their litter quality under N enrichment, while species with weaker resorption allocated more biomass C and/or N to belowground part under drought. Together, these results show that the responses of nutrient resorption and allocation to N enrichment and drought are highly species-specific. Future studies should take these differential responses into consideration to better predict litter decomposition and ecosystem nutrient cycling. DA - 2020/6/25/ PY - 2020/6/25/ DO - 10.1016/j.scitotenv.2020.138106 VL - 723 SP - SN - 1879-1026 KW - Global change KW - Nitrogen retranslocation KW - Nutrient cycling KW - Nutrient conservation KW - Nutrient distribution KW - Qinghai-Tibet Plateau ER - TY - JOUR TI - Developmental Exposure to the Flame Retardant Mixture Firemaster 550 Compromises Adult Bone Integrity in Male but not Female Rats AU - Macari, Soraia AU - Rock, Kylie D. AU - Santos, Mariana S. AU - Lima, Virginia T. M. AU - Szawka, Raphael E. AU - Moss, Jamal AU - Horman, Brian AU - Patisaul, Heather B. T2 - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES AB - Flame retardants (FRs) are used in a variety of common items from furniture to carpet to electronics to reduce flammability and combustion, but the potential toxicity of these compounds is raising health concerns globally. Organophosphate FRs (OPFRs) are becoming more prevalent as older, brominated FRs are phased out, but the toxicity of these compounds, and the FR mixtures that contain them, is poorly understood. Work in a variety of in vitro model systems has suggested that FRs may induce metabolic reprogramming such that bone density is compromised at the expense of increasing adiposity. To address this hypothesis, the present studies maternally exposed Wistar rat dams orally across gestation and lactation to 1000 µg daily of the FR mixture Firemaster 550 (FM 550) which contains a mixture of brominated FRs and OPFRs. At six months of age, the offspring of both sexes were examined for evidence of compromised bone composition. Bone density, composition, and marrow were all significantly affected, but only in males. The fact that the phenotype was observed months after exposure suggests that FM 550 altered some fundamental aspect of mesenchymal stem cell reprogramming. The severity of the phenotype and the human-relevance of the dose employed, affirm this is an adverse outcome meriting further exploration. DA - 2020/4// PY - 2020/4// DO - 10.3390/ijms21072553 VL - 21 IS - 7 SP - SN - 1422-0067 KW - obesogen KW - endocrine disrupting chemicals KW - sex difference KW - adipose KW - trabecular KW - cortical bone KW - ppar gamma ER - TY - JOUR TI - Entangled Life: How Fungi Make Our Worlds, Change Our Minds, and Shape Our Futures AU - Dunn, Rob T2 - SCIENCE AB - An ode to an underappreciated life form reminds readers that the mundane can be sublime DA - 2020/5/15/ PY - 2020/5/15/ DO - 10.1126/science.abb5841 VL - 368 IS - 6492 SP - 722-722 SN - 1095-9203 ER - TY - JOUR TI - Island area, not isolation, drives taxonomic, phylogenetic and functional diversity of ants on land-bridge islands AU - Zhao, Yuhao AU - Dunn, Robert R. AU - Zhou, Haonan AU - Si, Xingfeng AU - Ding, Ping T2 - JOURNAL OF BIOGEOGRAPHY AB - Abstract Aim To explore the impact of island area and isolation on multiple dimensions of ant biodiversity (taxonomic, phylogenetic and functional diversity) and the underlying processes of community assembly on islands. Location Thousand Island Lake, Zhejiang, China, created by dam construction in 1959. Taxon Ants. Methods We sampled ants on 33 islands, built a species‐level phylogenetic tree and measured five morphological traits of all species collected to estimate taxonomic, phylogenetic and functional diversity. We used multiple linear regression models and null models to examine the relationships between diversity metrics and island variables (area and isolation). Results We recorded 97 ant species on the study islands. We verified positive diversity–area relationships for species richness, phylogenetic diversity and functional diversity. However, although functional and phylogenetic community structure were indistinguishable from random communities, phylogenetic structure tended to be clustered, whereas functional structure tended to be overdispersed. Additionally, we found the structure of ant communities shifted from phylogenetic and functional clustering on smaller islands to phylogenetic and functional overdispersion on larger islands. Main conclusions Our results support the hypothesis that environmental filtering is the dominant process structuring ant communities on smaller islands, and that competitive exclusion becomes more important on larger islands. Thus, island area acts as an important filter even though ant community structure on the study islands was indistinguishable from random communities. Moreover, our results show that environmental filtering influences phylogenetic community structure of ants, whereas competitive exclusion influences functional community structure of ants. These findings highlight the need to examine both phylogenetic and functional diversity in order to understand the mechanisms that govern the assembly of natural communities on islands. DA - 2020/8// PY - 2020/8// DO - 10.1111/jbi.13860 VL - 47 IS - 8 SP - 1627-1637 SN - 1365-2699 KW - ants KW - community structure KW - competitive exclusion KW - environmental filtering KW - island biogeography KW - morphological traits KW - phylogeny KW - Thousand Island Lake ER - TY - JOUR TI - Relationships of virus titers and transmission rates among sympatric and allopatric virus isolates and thrips vectors support local adaptation AU - Linak, Jessica A. AU - Jacobson, Alana L. AU - Sit, Tim L. AU - Kennedy, George G. T2 - Scientific Reports AB - Abstract Plant viruses rely on insect vectors for transmission among plant hosts, but many of the specifics of virus-vector interactions are not fully understood. Thrips tabaci , which transmits Tomato spotted wilt virus (TSWV) in a persistent and propagative manner, varies greatly in its ability to transmit different isolates of TSWV. Similarly, TSWV isolates are transmitted at different efficiencies by different populations of T. tabaci . This study characterizes differences in virus titers in the vector among TSWV isolate- T. tabaci isoline pairings in relation to differences in transmission rates, and demonstrates that although transmission rates were higher for sympatric than allopatric TSWV isolate- T. tabaci isoline pairings, virus titers in the thrips vector were significantly lower in the sympatric pairings. Results further demonstrate that TSWV titers in the vector were unrelated to virus titers in the leaf tissue from which they acquired the virus and provide evidence for the importance of specific vector-virus interactions and local adaptation in determining transmission efficiency of TSWV by T. tabaci . DA - 2020/5/6/ PY - 2020/5/6/ DO - 10.1038/s41598-020-64507-1 VL - 10 IS - 1 SP - J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-020-64507-1 DB - Crossref ER - TY - JOUR TI - The Individual-Level Origins of Congressional Corruption Scandals AU - Taylor, Andrew J. AU - Cobb, Michael D. T2 - AMERICAN POLITICS RESEARCH AB - To date, the literature on corruption scandals in Congress focuses exclusively on their consequences. Using theory that directs analyses of the causes of corruption scandals at the jurisdictional level in the American states and other countries, we test a variety of hypotheses about which kinds of members of the House are more likely to be caught in these episodes. We derive our hypotheses from three basic propositions about individual-level corruption—opportunity, culture, and target. There is evidence to support them all. Members with cultivated relationships, in positions of power, and elected from districts with traditions of or perceived tolerance for corruption are disproportionately scandalous. So, interestingly, are some potentially marginalized legislators, particularly racial minorities. We explore the finding that Black members are frequently associated with corruption scandals. DA - 2020/7// PY - 2020/7// DO - 10.1177/1532673X19850093 VL - 48 IS - 4 SP - 442-454 ER - TY - JOUR TI - Keeping up with the fast-moving world of crisis management AU - Rice, Charles W. AU - Schoen, Robin AU - Aristidou, Aristos AU - Burgess, Shane C. AU - Capalbo, Susan AU - Czarnecki-Maulden, Gail AU - Dunham, Bernadette AU - Ejeta, Gibesa AU - Famigilietti, Jay S. AU - Gould, Fred AU - Hamer, John AU - Jackson-Smith, Douglas B. AU - Jones, James W. AU - Kebreab, Ermias AU - Kelley, Stephen S. AU - Leach, Jan E. AU - Lougee, Robin AU - McCluskey, Jill J. AU - Plaut, Karen I. AU - Salvador, Ricardo J. AU - Sample, V. Alaric T2 - AGRICULTURE AND HUMAN VALUES AB - Author(s): Rice, Charles W; Schoen, Robin; Aristidou, Aristos; Burgess, Shane C; Capalbo, Susan; Czarnecki-Maulden, Gail; Dunham, Bernadette; Ejeta, Gibesa; Famigilietti, Jay S; Gould, Fred; Hamer, John; Jackson-Smith, Douglas B; Jones, James W; Kebreab, Ermias; Kelley, Stephen S; Leach, Jan E; Lougee, Robin; McCluskey, Jill J; Plaut, Karen I; Salvador, Ricardo J; Sample, V Alaric DA - 2020/9// PY - 2020/9// DO - 10.1007/s10460-020-10045-5 VL - 37 IS - 3 SP - 531-533 SN - 1572-8366 ER - TY - JOUR TI - Coevolutionary Governance of Antibiotic and Pesticide Resistance AU - Jorgensen, Peter Sogaard AU - Folke, Carl AU - Henriksson, Patrik J. G. AU - Malmros, Karin AU - Troell, Max AU - Zorzet, Anna AU - Aktipis, Athena AU - Brown, Zachary AU - Carriere, Yves AU - Downes, Sharon AU - Dunn, Robert R. AU - Epstein, Graham AU - Frisvold, George AU - Grohn, Yrjo AU - Gujar, Govind Tikaramsa AU - Hawthorne, David AU - Jasovsky, Dusan AU - Klein, Eili Y. AU - Klein, Franziska AU - Lhermie, Guillaume AU - Mota-Sanchez, David AU - Omoto, Celso AU - Scott, H. Morgan AU - Wemli, Didier AU - Carroll, Scott P. T2 - TRENDS IN ECOLOGY & EVOLUTION AB - Development of new biocides has dominated human responses to evolution of antibiotic and pesticide resistance. Increasing and uniform biocide use, the spread of resistance genes, and the lack of new classes of compounds indicate the importance of navigating toward more sustainable coevolutionary dynamics between human culture and species that evolve resistance. To inform this challenge, we introduce the concept of coevolutionary governance and propose three priorities for its implementation: (i) new norms and mental models for lowering use, (ii) diversifying practices to reduce directional selection, and (iii) investment in collective action institutions to govern connectivity. We highlight the availability of solutions that facilitate broader sustainable development, which for antibiotic resistance include improved sanitation and hygiene, strong health systems, and decreased meat consumption. DA - 2020/6// PY - 2020/6// DO - 10.1016/j.tree.2020.01.011 VL - 35 IS - 6 SP - 484-494 SN - 1872-8383 ER - TY - JOUR TI - Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize AU - Ramstein, Guillaume P. AU - Larsson, Sara J. AU - Cook, Jason P. AU - Edwards, Jode W. AU - Ersoz, Elhan S. AU - Flint-Garcia, Sherry AU - Gardner, Candice A. AU - Holland, James B. AU - Lorenz, Aaron J. AU - McMullen, Michael D. AU - Millard, Mark J. AU - Rocheford, Torbert R. AU - Tuinstra, Mitchell R. AU - Bradbury, Peter J. AU - Buckler, Edward S. AU - Romay, M. Cinta T2 - GENETICS AB - Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize. DA - 2020/5// PY - 2020/5// DO - 10.1534/genetics.120.303025 VL - 215 IS - 1 SP - 215-230 SN - 1943-2631 UR - https://doi.org/10.1534/genetics.120.303025 KW - dominance KW - genomic features KW - functional enrichment KW - genomic prediction KW - hybrid maize ER - TY - JOUR TI - Cross-species transmission and evolutionary dynamics of canine distemper virus during a spillover in African lions of Serengeti National Park AU - Weckworth, Julie K. AU - Davis, Brian W. AU - Dubovi, Edward AU - Fountain-Jones, Nicholas AU - Packer, Craig AU - Cleaveland, Sarah AU - Craft, Meggan E. AU - Eblate, Ernest AU - Schwartz, Michael AU - Mills, L. Scott AU - Roelke-Parker, Melody T2 - MOLECULAR ECOLOGY AB - Abstract The outcome of pathogen spillover from a reservoir to a novel host population can range from a “dead‐end” when there is no onward transmission in the recipient population, to epidemic spread and even establishment in new hosts. Understanding the evolutionary epidemiology of spillover events leading to discrete outcomes in novel hosts is key to predicting risk and can lead to a better understanding of the mechanisms of emergence. Here we use a Bayesian phylodynamic approach to examine cross‐species transmission and evolutionary dynamics during a canine distemper virus (CDV) spillover event causing clinical disease and population decline in an African lion population ( Panthera leo ) in the Serengeti Ecological Region between 1993 and 1994. Using 21 near‐complete viral genomes from four species we found that this large‐scale outbreak was likely ignited by a single cross‐species spillover event from a canid reservoir to noncanid hosts <1 year before disease detection and explosive spread of CDV in lions. Cross‐species transmission from other noncanid species probably fuelled the high prevalence of CDV across spatially structured lion prides. Multiple lines of evidence suggest that spotted hyenas ( Crocuta crocuta ) could have acted as the proximate source of CDV exposure in lions. We report 13 nucleotide substitutions segregating CDV strains found in canids and noncanids. Our results are consistent with the hypothesis that virus evolution played a role in CDV emergence in noncanid hosts following spillover during the outbreak, suggest that host barriers to clinical infection can limit outcomes of CDV spillover in novel host species. DA - 2020/11// PY - 2020/11// DO - 10.1111/mec.15449 VL - 29 IS - 22 SP - 4308-4321 SN - 1365-294X KW - African lion KW - canine distemper virus KW - carnivore conservation KW - evolutionary epidemiology KW - pathogen spillover KW - Serengeti ER - TY - JOUR TI - Psychometric properties of the Italian version of the sense of community responsibility scale AU - Prati, Gabriele AU - Procentese, Fortuna AU - Albanesi, Cinzia AU - Cicognani, Elvira AU - Fedi, Angela AU - Gatti, Flora AU - Mannarini, Terri AU - Rochira, Alessia AU - Tartaglia, Stefano AU - Boyd, Neil AU - Nowell, Branda AU - Gattino, Silvia T2 - JOURNAL OF COMMUNITY PSYCHOLOGY AB - Abstract The central aim of the present research was to examine the psychometric properties of adapted versions of the sense of community (SOC) responsibility scale in three Italian samples. We examined the psychometric properties of three modified versions of the sense of community responsibility (SOC‐R) scale. Consistent with the original scale, exploratory and confirmatory factor analyses demonstrated that the scale was unidimensional and exhibited excellent internal consistency. In addition, factor analyses revealed that SOC responsibility and SOC are two separate, albeit related, constructs. The results also provided evidence of the discriminant validity of SOC and SOC‐R on key outcomes. Taken together, these results provide support for the Community Experience Model , which posits that community experiences are a function of resource and responsibility components, as well as for the adaptable nature of the SOC‐R scale to the Italian context. DA - 2020/8// PY - 2020/8// DO - 10.1002/jcop.22366 VL - 48 IS - 6 SP - 1770-1790 SN - 1520-6629 KW - cross-cultural validation KW - measurement KW - reliability KW - sense of community KW - sense of community responsibility KW - validity ER - TY - JOUR TI - The Use and Misuse of Historical Controls in Regulatory Toxicology: Lessons from the CLARITY-BPA Study AU - Vandenberg, Laura N. AU - Prins, Gail S. AU - Patisaul, Heather B. AU - Zoeller, R. Thomas T2 - ENDOCRINOLOGY AB - Abstract For many endocrine-disrupting chemicals (EDCs) including Bisphenol A (BPA), animal studies show that environmentally relevant exposures cause harm; human studies are consistent with these findings. Yet, regulatory agencies charged with protecting public health continue to conclude that human exposures to these EDCs pose no risk. One reason for the disconnect between the scientific consensus on EDCs in the endocrinology community and the failure to act in the regulatory community is the dependence of the latter on so-called “guideline studies” to evaluate hazards, and the inability to incorporate independent scientific studies in risk assessment. The Consortium Linking Academic and Regulatory Insights on Toxicity (CLARITY) study was intended to bridge this gap, combining a “guideline” study with independent hypothesis-driven studies designed to be more appropriate to evaluate EDCs. Here we examined an aspect of “guideline” studies, the use of so-called “historical controls,” which are essentially control data borrowed from prior studies to aid in the interpretation of current findings. The US Food and Drug Administration authors used historical controls to question the plausibility of statistically significant BPA-related effects in the CLARITY study. We examined the use of historical controls on 5 outcomes in the CLARITY “guideline” study: mammary neoplasms, pituitary neoplasms, kidney nephropathy, prostate inflammation and adenomas, and body weight. Using US Food and Drug Administration–proposed historical control data, our evaluation revealed that endpoints used in “guideline” studies are not as reproducible as previously held. Combined with other data comparing the effects of ethinyl estradiol in 2 “guideline” studies including CLARITY-BPA, we conclude that near-exclusive reliance on “guideline” studies can result in scientifically invalid conclusions. DA - 2020/5// PY - 2020/5// DO - 10.1210/endocr/bqz014 VL - 161 IS - 5 SP - SN - 1945-7170 KW - adenocarcinoma KW - Food and Drug Administration KW - gavage KW - lymphocyte infiltration KW - National Toxicology Program KW - obesity ER - TY - JOUR TI - A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel AU - Stagnati, Lorenzo AU - Rahjoo, Vahid AU - Samayoa, Luis F. AU - Holland, James B. AU - Borrelli, Virginia M. G. AU - Busconi, Matteo AU - Lanubile, Alessandra AU - Marocco, Adriano T2 - G3-GENES GENOMES GENETICS AB - Abstract Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population using 226,446 SNP markers. Phenotypes were scored on artificially infected kernels applying the rolled towel assay screening method and three traits related to disease response were measured in inoculated and not-inoculated seedlings: plant seedling length (PL), plant seedling weight (PW) and germination rate (GERM). Overall, GWAS resulted in 42 SNPs significantly associated with the examined traits. Two and eleven SNPs were associated with PL in inoculated and not-inoculated samples, respectively. Additionally, six and one SNPs were associated with PW and GERM traits in not-inoculated kernels, and further nine and thirteen SNPs were associated to the same traits in inoculated kernels. Five genes containing the significant SNPs or physically closed to them were proposed for Fusarium resistance, and 18 out of 25 genes containing or adjacent to significant SNPs identified by GWAS in the current research co-localized within QTL regions previously reported for resistance to Fusarium seed rot, Fusarium ear rot and fumonisin accumulation. Furthermore, linkage disequilibrium analysis revealed an additional gene not directly observed by GWAS analysis. These findings could aid to better understand the complex interaction between maize and F. verticillioides. DA - 2020/5// PY - 2020/5// DO - 10.1534/g3.119.400987 VL - 10 IS - 5 SP - 1685-1696 SN - 2160-1836 UR - https://doi.org/10.1534/g3.119.400987 KW - GWAS KW - SNPs KW - Artificial inoculation KW - Fusarium verticillioides KW - Maize ER - TY - JOUR TI - Modification of the glycolytic pathway in Pyrococcus furiosus and the implications for metabolic engineering AU - Straub, Christopher T. AU - Schut, Gerritt AU - Otten, Jonathan K. AU - Keller, Lisa M. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - EXTREMOPHILES DA - 2020/7// PY - 2020/7// DO - 10.1007/s00792-020-01172-2 VL - 24 IS - 4 SP - 511-518 SN - 1433-4909 KW - Pyrococcus KW - Thermophile KW - Central metabolism KW - Glycolysis ER - TY - JOUR TI - Analysis of neurotransmitters in rat placenta exposed to flame retardants using IR-MALDESI mass spectrometry imaging AU - Pace, Crystal L. AU - Horman, Brian AU - Patisaul, Heather AU - Muddiman, David C. T2 - ANALYTICAL AND BIOANALYTICAL CHEMISTRY AB - Chemical exposures can adversely impact fetal development. For many compounds, including common flame retardants, the mechanisms by which this occurs remain unclear, but emerging evidence suggests that disruption at the level of the placenta may play a role. Understanding how the placenta might be vulnerable to chemical exposures is challenging due to its complex structure. The primary objective of this study was to develop a method for detecting placental neurotransmitters and related metabolites without chemical derivatization so changes in the abundance and spatial distribution of neurotransmitters in rat placenta following chemical exposure could be determined using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging. Without chemical derivatization, 49 neurotransmitters and their related metabolites were putatively identified in untreated rat placenta sections using mass measurement accuracy and spectral accuracy. A few neurotransmitters were less abundant in placentas that were exposed to various flame retardants and were further investigated by KEGG metabolic pathway analysis. Many of these downregulated neurotransmitters shared the same enzyme responsible for metabolism, aromaticl-amino acid decarboxylase, suggesting a mechanistic role. These data constitute a new approach that could help identify novel mechanisms of toxicity in complex tissues. Graphical abstract. DA - 2020/6// PY - 2020/6// DO - 10.1007/s00216-020-02626-4 VL - 412 IS - 15 SP - 3745-3752 SN - 1618-2650 KW - IR-MALDESI KW - Mass spectrometry imaging KW - Neurotransmitters KW - Exposomics ER - TY - JOUR TI - Creating Predictive Weed Emergence Models Using Repeat Photography and Image Analysis AU - Piskackova, Theresa Reinhardt AU - Reberg-Horton, Chris AU - Richardson, Robert J AU - Austin, Robert AU - Jennings, Katie M AU - Leon, Ramon G T2 - Plants AB - Weed emergence models have the potential to be important tools for automating weed control actions; however, producing the necessary data (e.g., seedling counts) is time consuming and tedious. If similar weed emergence models could be created by deriving emergence data from images rather than physical counts, the amount of generated data could be increased to create more robust models. In this research, repeat RGB images taken throughout the emergence period of Raphanus raphanistrum L. and Senna obtusifolia (L.) Irwin and Barneby underwent pixel-based spectral classification. Relative cumulative pixels generated by the weed of interest over time were used to model emergence patterns. The models that were derived from cumulative pixel data were validated with the relative emergence of true seedling counts. The cumulative pixel model for R. raphanistrum and S. obtusifolia accounted for 92% of the variation in relative emergence of true counts. The results demonstrate that a simple image analysis approach based on time-dependent changes in weed cover can be used to generate weed emergence predictive models equivalent to those produced based on seedling counts. This process will help researchers working on weed emergence models, providing a new low-cost and technologically simple tool for data collection. DA - 2020/5/15/ PY - 2020/5/15/ DO - 10.3390/plants9050635 VL - 9 IS - 5 SP - 635 UR - https://doi.org/10.3390/plants9050635 KW - emergence models KW - sigmoidal models KW - RGB KW - maximum likelihood analysis KW - supervised classification ER - TY - JOUR TI - Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium AU - Pan, Meichen AU - Nethery, Matthew A. AU - Hidalgo-Cantabrana, Claudio AU - Barrangou, Rodolphe T2 - Microorganisms AB - The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated cas) systems constitute the adaptive immune system in prokaryotes, which provides resistance against bacteriophages and invasive genetic elements. The landscape of applications in bacteria and eukaryotes relies on a few Cas effector proteins that have been characterized in detail. However, there is a lack of comprehensive studies on naturally occurring CRISPR-Cas systems in beneficial bacteria, such as human gut commensal Bifidobacterium species. In this study, we mined 954 publicly available Bifidobacterium genomes and identified CRIPSR-Cas systems in 57% of these strains. A total of five CRISPR-Cas subtypes were identified as follows: Type I-E, I-C, I-G, II-A, and II-C. Among the subtypes, Type I-C was the most abundant (23%). We further characterized the CRISPR RNA (crRNA), tracrRNA, and PAM sequences to provide a molecular basis for the development of new genome editing tools for a variety of applications. Moreover, we investigated the evolutionary history of certain Bifidobacterium strains through visualization of acquired spacer sequences and demonstrated how these hypervariable CRISPR regions can be used as genotyping markers. This extensive characterization will enable the repurposing of endogenous CRISPR-Cas systems in Bifidobacteria for genome engineering, transcriptional regulation, genotyping, and screening of rare variants. DA - 2020/5/12/ PY - 2020/5/12/ DO - 10.3390/microorganisms8050720 VL - 8 IS - 5 SP - 720 UR - https://doi.org/10.3390/microorganisms8050720 KW - Bifidobacterium KW - CRISPR-Cas KW - genomics ER - TY - JOUR TI - ImergardTMWP: A Non-Chemical Alternative for an Indoor Residual Spray, Effective against Pyrethroid-Resistant Anopheles gambiae (s.l.) in Africa AU - Deguenon, Jean M. AU - Azondekon, Roseric AU - Agossa, Fiacre A.R. AU - Padonou, Gil G. AU - Anagonou, Rodrigue AU - Ahoga, Juniace AU - Boris, N’dombidje AU - Akinro, Bruno AU - Stewart, David A. AU - Wang, Bo AU - Gittins, David AU - Tihomirov, Larissa AU - Apperson, Charles S. AU - McCord, Marian G. AU - Akogbeto, Martin C. AU - Roe, Richard T2 - Insects AB - Malaria is the deadliest mosquito-borne disease and kills predominantly people in sub-Saharan Africa (SSA). The now widespread mosquito resistance to pyrethroids, with rapidly growing resistance to other insecticide classes recommended by the World Health Organization (WHO), may overturn the successes gained in mosquito control in recent years. It is of utmost importance to search for new, inexpensive, and safe alternatives, with new modes of action, that might improve the efficacy of current insecticides. The efficacy of a novel mechanical insecticidal mineral derived from volcanic rock, ImergardTMWP, was investigated to determine its efficacy as a stand-alone residual wall spray and as a mixture with deltamethrin (K-Othrine® Polyzone) in experimental huts in Cove, Benin. The evaluation was conducted with susceptible (Kisumu) and wild-type Anopheles gambiae (s.l.). Deltamethrin applied alone demonstrated 40–45% mortality (at 72 h post-exposure) during the first four months, which declined to 25% at six months for wild An. gambiae from Cove. ImergardTMWP alone and mixed with deltamethrin, under the same assay conditions, produced 79–82% and 73–81% mortality, respectively, during the same six-month period. ImergardTMWP met the 80% WHO bio-efficacy threshold for residual activity for the first five months with 78% residual activity at six months. ImergardTMWP can be used as a mixture with chemical insecticides or as a stand-alone pesticide for mosquito control in Africa. DA - 2020/5// PY - 2020/5// DO - 10.3390/insects11050322 UR - https://www.mdpi.com/2075-4450/11/5/322 KW - mosquito KW - Anopheles gambiae (sl) KW - malaria KW - Imergard(TM)WP KW - mechanical insecticide KW - pyrethroid resistance KW - Africa KW - Benin KW - residual wall spray ER - TY - JOUR TI - Use of standardized bioinformatics for the analysis of fungal DNA signatures applied to sample provenance AU - Allwood, Julia S. AU - Fierer, Noah AU - Dunn, Robert R. AU - Breen, Matthew AU - Reich, Brian J. AU - Laber, Eric B. AU - Clifton, Jesse AU - Grantham, Neal S. AU - Faith, Seth A. T2 - FORENSIC SCIENCE INTERNATIONAL AB - The use of environmental trace material to aid criminal investigations is an ongoing field of research within forensic science. The application of environmental material thus far has focused upon a variety of different objectives relevant to forensic biology, including sample provenance (also referred to as sample attribution). The capability to predict the provenance or origin of an environmental DNA sample would be an advantageous addition to the suite of investigative tools currently available. A metabarcoding approach is often used to predict sample provenance, through the extraction and comparison of the DNA signatures found within different environmental materials, such as the bacteria within soil or fungi within dust. Such approaches are combined with bioinformatics workflows and statistical modelling, often as part of large-scale study, with less emphasis on the investigation of the adaptation of these methods to a smaller scale method for forensic use. The present work was investigating a small-scale approach as an adaptation of a larger metabarcoding study to develop a model for global sample provenance using fungal DNA signatures collected from dust swabs. This adaptation was to facilitate a standardized method for consistent, reproducible sample treatment, including bioinformatics processing and final application of resulting data to the available prediction model. To investigate this small-scale method, 76 DNA samples were treated as anonymous test samples and analyzed using the standardized process to demonstrate and evaluate processing and customized sequence data analysis. This testing included samples originating from countries previously used to train the model, samples artificially mixed to represent multiple or mixed countries, as well as outgroup samples. Positive controls were also developed to monitor laboratory processing and bioinformatics analysis. Through this evaluation we were able to demonstrate that the samples could be processed and analyzed in a consistent manner, facilitated by a relatively user-friendly bioinformatic pipeline for sequence data analysis. Such investigation into standardized analyses and application of metabarcoding data is of key importance for the future use of applied microbiology in forensic science. DA - 2020/5// PY - 2020/5// DO - 10.1016/j.forsciint.2020.110250 VL - 310 SP - SN - 1872-6283 KW - Forensic microbiology KW - Bioinformatics KW - Metabarcoding KW - Sample provenance ER - TY - JOUR TI - Olive Fruit Fly, Bactrocera oleae (Diptera: Tephritidae), Attraction to Volatile Compounds Produced by Host and Insect-Associated Yeast Strains AU - Vitanovic, Elda AU - Aldrich, Jeffrey R. AU - Boundy-Mills, Kyria AU - Cagalj, Marin AU - Ebeler, Susan E. AU - Burrack, Hannah AU - Zalom, Frank G. T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - Abstract The olive fruit fly, Bactrocera oleae (Rossi), is one of the most damaging insect pests of olives worldwide, requiring the use of insecticides for fruit protection in many orchards. Olive fruit flies are attracted to volatile composunds, including a female-produced pheromone, and host-plant and bacterial volatiles. Preliminary laboratory bioassays were conducted for olive fruit fly attraction to over 130 yeast strains from among 400 that were isolated from B. oleae adults and larvae or other insects, infested olives, and potential feeding sites. Kuraishia capsulata, Scheffersomyces ergatensis, Peterozyma xylosa, Wickerhamomyces subpelliculosus, and Lachancea thermotolerans appeared to attract B. oleae as well or better than did torula yeast pellets (Cyberlindnera jadinii; syn. Candida utilis). Volatile compounds emitted by these yeast strains were chemically identified, and included isobutanol, isoamyl alcohol, 2-phenethyl alcohol, isobutyl acetate, and 2-phenethyl acetate. The behavioral response of B. oleae adults to these volatile compounds at three concentrations was tested in a laboratory Y-tube olfactometer. The same volatile compounds were also tested in the field. Isoamyl alcohol was more attractive than the other compounds tested in both laboratory and field bioassays. Isobutanol was not attractive to B. oleae in either laboratory bioassay or field bioassay. Identifying yeast volatiles attractive to the olive fruit fly may lead to development of a more effective lure for detection, monitoring, and possibly control of B. oleae. DA - 2020/4// PY - 2020/4// DO - 10.1093/jee/toz341 VL - 113 IS - 2 SP - 752-759 SN - 1938-291X KW - HS-SPME/GC/MS KW - insect behavior KW - pest control KW - Torula KW - Y-tube olfactometer ER - TY - JOUR TI - The Influence of Presumed Fake News Influence: Examining Public Support for Corporate Corrective Response, Media Literacy Interventions, and Governmental Regulation AU - Cheng, Yang AU - Chen, Zifei Fay T2 - Mass Communication and Society AB - In today’s society with polarized opinions, fake news has significantly affected people’s trust in online news. Informed by the third-person effect (TPE) and influence of presumed influence (IPI) theories, this study examined atheoretical model to understand the antecedents and consequences of the presumed effects of fake news on others (PFNE3). Data were collected from 661 respondents through survey research based on fake news about acompany shared on Facebook. Results showed the significant impacts of self-efficacy, social undesirability, and consumer involvement on PFNE3. Furthermore, PFNE3 positively predicted public support for corporate corrective actions, media literacy interventions, and governmental regulation. Findings demonstrated the mediating role of PFNE3 in the model. Theoretical and practical implications were discussed. DA - 2020/5/1/ PY - 2020/5/1/ DO - 10.1080/15205436.2020.1750656 VL - 23 IS - 5 SP - 705-729 J2 - Mass Communication and Society LA - en OP - SN - 1520-5436 1532-7825 UR - http://dx.doi.org/10.1080/15205436.2020.1750656 DB - Crossref ER - TY - JOUR TI - Applications of CRISPR-Cas systems in lactic acid bacteria AU - Roberts, Avery AU - Barrangou, Rodolphe T2 - FEMS Microbiology Reviews AB - ABSTRACT As a phenotypically and phylogenetically diverse group, lactic acid bacteria are found in a variety of natural environments and occupy important roles in medicine, biotechnology, food and agriculture. The widespread use of lactic acid bacteria across these industries fuels the need for new and functionally diverse strains that may be utilized as starter cultures or probiotics. Originally characterized in lactic acid bacteria, CRISPR-Cas systems and derived molecular machines can be used natively or exogenously to engineer new strains with enhanced functional attributes. Research on CRISPR-Cas biology and its applications has exploded over the past decade with studies spanning from the initial characterization of CRISPR-Cas immunity in Streptococcus thermophilus to the use of CRISPR-Cas for clinical gene therapies. Here, we discuss CRISPR-Cas classification, overview CRISPR biology and mechanism of action, and discuss current and future applications in lactic acid bacteria, opening new avenues for their industrial exploitation and manipulation of microbiomes. DA - 2020/9/1/ PY - 2020/9/1/ DO - 10.1093/femsre/fuaa016 VL - 44 IS - 5 SP - 523-537 UR - https://doi.org/10.1093/femsre/fuaa016 KW - Lactic acid bacteria KW - CRISPR KW - Cas KW - genome editing KW - probiotics KW - genomics ER - TY - JOUR TI - The basic reproductive number for disease systems with multiple coupled heterogeneities T2 - Mathematical Biosciences AB - In mathematical epidemiology, a well-known formula describes the impact of heterogeneity on the basic reproductive number, R0, for situations in which transmission is separable and for which there is one source of variation in susceptibility and one source of variation in infectiousness. This formula is written in terms of the magnitudes of the heterogeneities, as quantified by their coefficients of variation, and the correlation between them. A natural question to ask is whether analogous results apply when there are multiple sources of variation in susceptibility and/or infectiousness. In this paper we demonstrate that with three or more coupled heterogeneities, R0 under separable transmission depends on details of the distribution of the heterogeneities in a way that is not seen in the well-known simpler situation. We provide explicit formulae for the cases of multivariate normal and multivariate log-normal distributions, showing that R0 can again be expressed in terms of the magnitudes of the heterogeneities and the pairwise correlations between them. The formulae, however, differ between the two multivariate distributions, demonstrating that no formula of this type applies generally when there are three or more coupled heterogeneities. We see that the results of the formulae are approximately equal when heterogeneities are relatively small and show that an earlier result in the literature (Koella, 1991) should be viewed in this light. We provide numerical illustrations of our results and discuss a setting in which coupled heterogeneities are likely to have a major impact on the value of R0. We also describe a rather surprising result: in a system with three heterogeneities, R0 can exhibit non-monotonic behavior with increasing levels of heterogeneity, in marked contrast to the familiar two heterogeneity setting in which R0 either increases or decreases with increasing heterogeneity. DA - 2020/3// PY - 2020/3// DO - 10.1016/j.mbs.2019.108294 UR - http://dx.doi.org/10.1016/j.mbs.2019.108294 KW - Disease transmission model KW - Heterogeneity KW - Basic reproductive number KW - Coupled heterogeneities ER - TY - JOUR TI - Bidirectional contact tracing dramatically improves COVID-19 control AU - Bradshaw, William J. AU - Alley, Ethan C. AU - Huggins, Jonathan H. AU - Lloyd, Alun L. AU - Esvelt, Kevin M. AB - Abstract Contact tracing is critical to controlling COVID-19, but most protocols only “forward-trace” to notify people who were recently exposed. Using a stochastic branching-process model, we show that “bidirectional” tracing to identify infector individuals and their other infectees robustly improves outbreak control, reducing the effective reproduction number ( R eff ) by at least ∼0.3 while dramatically increasing resilience to low case ascertainment and test sensitivity. Adding smartphone-based exposure notification can further reduce R eff by 0.25, but only if nearly all smartphones can detect exposure events. Our results suggest that with or without digital approaches, implementing bidirectional tracing will enable health agencies to control COVID-19 more effectively without requiring high-cost interventions. DA - 2020/5/10/ PY - 2020/5/10/ DO - 10.1101/2020.05.06.20093369 VL - 5 UR - https://doi.org/10.1101/2020.05.06.20093369 ER - TY - JOUR TI - Strain-Dependent Inhibition of Clostridioides difficile by Commensal Clostridia Carrying the Bile Acid-Inducible ( bai ) Operon AU - Reed, A. D. AU - Nethery, M. A. AU - Stewart, A. AU - Barrangou, R. AU - Theriot, C. M. T2 - Journal of Bacteriology AB - ABSTRACT Clostridioides difficile is one of the leading causes of antibiotic-associated diarrhea. Gut microbiota-derived secondary bile acids and commensal Clostridia that carry the bile acid-inducible ( bai ) operon are associated with protection from C. difficile infection (CDI), although the mechanism is not known. In this study, we hypothesized that commensal Clostridia are important for providing colonization resistance against C. difficile due to their ability to produce secondary bile acids, as well as potentially competing against C. difficile for similar nutrients. To test this hypothesis, we examined the abilities of four commensal Clostridia carrying the bai operon ( Clostridium scindens VPI 12708, C. scindens ATCC 35704, Clostridium hiranonis , and Clostridium hylemonae ) to convert cholate (CA) to deoxycholate (DCA) in vitro, and we determined whether the amount of DCA produced was sufficient to inhibit the growth of a clinically relevant C. difficile strain. We also investigated the competitive relationships between these commensals and C. difficile using an in vitro coculture system. We found that inhibition of C. difficile growth by commensal Clostridia supplemented with CA was strain dependent, correlated with the production of ∼2 mM DCA, and increased the expression of bai operon genes. We also found that C. difficile was able to outcompete all four commensal Clostridia in an in vitro coculture system. These studies are instrumental in understanding the relationship between commensal Clostridia and C. difficile in the gut, which is vital for designing targeted bacterial therapeutics. Future studies dissecting the regulation of the bai operon in vitro and in vivo and how this affects CDI will be important. IMPORTANCE Commensal Clostridia carrying the bai operon, such as C. scindens, have been associated with protection against CDI; however, the mechanism for this protection is unknown. Herein, we show four commensal Clostridia that carry the bai operon and affect C. difficile growth in a strain-dependent manner, with and without the addition of cholate. Inhibition of C. difficile by commensals correlated with the efficient conversion of cholate to deoxycholate, a secondary bile acid that inhibits C. difficile germination, growth, and toxin production. Competition studies also revealed that C. difficile was able to outcompete the commensals in an in vitro coculture system. These studies are instrumental in understanding the relationship between commensal Clostridia and C. difficile in the gut, which is vital for designing targeted bacterial therapeutics. DA - 2020/5/11/ PY - 2020/5/11/ DO - 10.1128/JB.00039-20 VL - 202 IS - 11 UR - https://doi.org/10.1128/JB.00039-20 KW - 7 alpha-dehydroxylation KW - Clostridia KW - Clostridioides difficile KW - bile acids KW - cholate KW - deoxycholate ER - TY - JOUR TI - Pruning of small fruit crops can affect habitat suitability for Drosophila suzukii AU - Schoneberg, Torsten AU - Arsenault-Benoit, Arielle AU - Taylor, Christopher M. AU - Butler, Bryan R. AU - Dalton, Daniel T. AU - Walton, Vaughn M. AU - Petran, Andrew AU - Rogers, Mary A. AU - Diepenbrock, Lauren M. AU - Burrack, Hannah J. AU - Leach, Heather AU - Van Timmeren, Steven AU - Fanning, Philip D. AU - Isaacs, Rufus AU - Gress, Brian E. AU - Bolda, Mark P. AU - Zalom, Frank G. AU - Roubos, Craig R. AU - Evans, Richard K. AU - Sial, Ashfaq A. AU - Hamby, Kelly A. T2 - AGRICULTURE ECOSYSTEMS & ENVIRONMENT AB - Insect activity, survival, and development are affected by climatic conditions that elicit effects at multiple scales. Pruning small fruit crop canopies alters the microclimate, which in turn may influence insect pest activity. We investigated the effect of three canopy density treatments (high, medium, low) on Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) fruit infestation in blueberries and caneberries using a two-year, multi-state experiment. We quantified the effect of canopy density on canopy microclimate, fruit quality (total soluble solids, fruit firmness), and yield. To better understand heterogeneity in canopy microclimate, parameters were further separated by canopy location (exterior vs. interior) in Maryland. In both crops, meta-analyses reveal small magnitude effects of the plant canopy on microclimate, whereas analysis of variance did not separate these effects, with mean canopy differences of 0.1–0.7 °C and 0.5–1.3 % relative humidity (RH) between caneberry canopy densities and locations. In caneberry multi-state trials, 0.14 fewer D. suzukii larvae (g fruit)−1 occurred on average in the low canopy density treatment, and 0.2 fewer D. suzukii larvae (g fruit)−1 occurred in exterior raspberries in Maryland compared with the canopy interior. Artificially infested blueberry fruit indicated immature D. suzukii survival within fruit can vary across canopy densities and locations. Although lower total yield was produced in low density canopies, canopy density did not influence berry quality or marketable yield. Microhabitats provide important shelter from extreme environmental conditions; the availability of shelter and ability to locate it affects insect pest populations and distributions. Understanding how crop canopy microclimate affects D. suzukii infestation can inform efforts to develop habitat manipulation tactics and improve the efficiency of fruit production. DA - 2020/6/1/ PY - 2020/6/1/ DO - 10.1016/j.agee.2020.106860 VL - 294 SP - SN - 1873-2305 KW - Spotted-wing drosophila KW - Blackberry KW - Blueberry KW - Raspberry KW - Canopy microclimate KW - Cultural management ER - TY - JOUR TI - Peanut nitrogen credits to winter wheat are negligible under conservation tillage management in the southeastern USA AU - Jani, Arun D. AU - Mulvaney, Michael J. AU - Erickson, John E. AU - Leon, Ramon G. AU - Wood, C. Wesley AU - Rowland, Diane L. AU - Enloe, Heather A. T2 - FIELD CROPS RESEARCH AB - Agricultural extension services in many peanut (Arachis hypogaea L.)-producing regions recommend that farmers reduce nitrogen (N) fertilization rates, or apply N credits, to crops planted after peanut but do not typically specify how peanut residue management or planting schedules of subsequent crops affect the magnitude of peanut N credits. The objective of this study was to quantify peanut N credits to winter wheat (Triticum aestivum L.) in a conservation tillage cropping system in different subtropical growing environments. A five site-year study was conducted in Florida, USA beginning in 2016. A split-plot experimental design was arranged in which summer crop [peanut, cotton (Gossypium hirsutum L.), and weed-free fallow] was the main plot factor, while N rate (0, 34, 67, and 101 kg N ha−1) to winter wheat was the split plot factor. Peanut and cotton were planted under strip-tillage, while winter wheat was drilled into peanut and cotton residues and weed-free fallow plots without tillage. Although peanut residues accumulated 54–93 kg N ha−1, plant available N at winter wheat planting in the 0–15 cm soil depth range of former peanut plots was only higher than in former cotton or fallow plots for one site-year. A previous peanut crop did not affect winter wheat grain yield, but there were cases of lower grain yield, grain N removal, and agronomic efficiency following cotton relative to peanut depending on site. Nonlinear regression procedures predicted that N rates required to optimize grain yields following peanut would exceed 94 kg N ha−1, further indicating the absence of detectible peanut N credits in this study. These results suggest that assuming peanut provides N credits to subsequent crops in the southeastern USA is not justified and, if assumed, will reduce the productivity of subsequent crops. DA - 2020/4/1/ PY - 2020/4/1/ DO - 10.1016/j.fcr.2020.107739 VL - 249 SP - SN - 1872-6852 KW - Peanut (Arachis hypogaea L.) KW - Winter wheat (Triticum aestivum L.) KW - Nitrogen credits KW - Conservation tillage ER - TY - JOUR TI - Combining omics technologies with CRISPR-based genome editing to study food microbes AU - Pan, Meichen AU - Barrangou, Rodolphe T2 - CURRENT OPINION IN BIOTECHNOLOGY AB - The implementation of omics technologies such as genomics, proteomics and transcriptomics has revolutionized our understanding of microbiomes, and shed light on the functional attributes and mechanisms of action underlying the ability of probiotics to impact host health and starter cultures to drive food fermentation. Recently, molecular machines from CRISPR-Cas systems have redefined the gene editing toolbox and democritized our ability to alter the genome of food microorganisms. An integrated approach in which CRISPR-based genome editing is informed by omics studies is poised to enable the engineering of microorganisms and the formulation of microbiomes impacting the food supply chain. Here, we highlight the current applications of omics technologies in food microorganisms and CRISPR-based genome editing technologies in bacteria, and discuss how this integrated approach enables effective engineering of food microbes to generate enhanced probiotic strains, develop novel biotherapeutics and alter microbial communities in food matrices. DA - 2020/2// PY - 2020/2// DO - 10.1016/j.copbio.2019.12.027 VL - 61 SP - 198-208 SN - 1879-0429 ER - TY - JOUR TI - Genomic characterization of Lactobacillus fermentum DSM 20052 AU - Brandt, Katelyn AU - Nethery, Matthew A. AU - Sarah, O’Flaherty AU - Barrangou, Rodolphe T2 - BMC Genomics AB - Abstract Background Lactobacillus fermentum, a member of the lactic acid bacteria complex, has recently garnered increased attention due to documented antagonistic properties and interest in assessing the probiotic potential of select strains that may provide human health benefits. Here, we genomically characterize L. fermentum using the type strain DSM 20052 as a canonical representative of this species. Results We determined the polished whole genome sequence of this type strain and compared it to 37 available genome sequences within this species. Results reveal genetic diversity across nine clades, with variable content encompassing mobile genetic elements, CRISPR-Cas immune systems and genomic islands, as well as numerous genome rearrangements. Interestingly, we determined a high frequency of occurrence of diverse Type I, II, and III CRISPR-Cas systems in 72% of the genomes, with a high level of strain hypervariability. Conclusions These findings provide a basis for the genetic characterization of L. fermentum strains of scientific and commercial interest. Furthermore, our study enables genomic-informed selection of strains with specific traits for commercial product formulation, and establishes a framework for the functional characterization of features of interest. DA - 2020/12// PY - 2020/12// DO - 10.1186/s12864-020-6740-8 VL - 21 IS - 1 UR - https://doi.org/10.1186/s12864-020-6740-8 KW - Lactobacillus KW - Fermentum KW - Comparative genomics KW - CRISPR ER - TY - JOUR TI - Sense of community, sense of community responsibility, organizational commitment and identification, and public service motivation: a simultaneous test of affective states on employee well-being and engagement in a public service work context AU - Boyd, Neil M. AU - Nowell, Branda T2 - PUBLIC MANAGEMENT REVIEW AB - ABSTRACT The present study has two aims. First, we examine sense of community, sense of community responsibility, organizational commitment and identification, and PSM in predicting measures of employee engagement and well-being. Second, we examine if PSM acts as a direct or indirect predictor of the employee measures. The findings highlight that community experiences are powerful predictors and that the role of PSM is more indirect than direct. The study provides a step forward in understanding the utility of psychological predictors when simultaneously compared, and offers hope for future studies where we continue to conduct comparative analyses beyond the boundary of public management. DA - 2020/// PY - 2020/// DO - 10.1080/14719037.2020.1740301 VL - 22 IS - 7 SP - 1024-1050 SN - 1471-9045 KW - Sense of community KW - sense of community responsibility KW - affective organizational commitment KW - organizational identification KW - public service motivation ER - TY - JOUR TI - Deletion of S-Layer Associated Ig-Like Domain Protein Disrupts the Lactobacillus acidophilus Cell Surface AU - Klotz, Courtney AU - Goh, Yong Jun AU - O'Flaherty, Sarah AU - Johnson, Brant AU - Barrangou, Rodolphe T2 - FRONTIERS IN MICROBIOLOGY AB - Bacterial surface-layers (S-layers) are crystalline arrays of repeating proteinaceous subunits that coat the exterior of many cell envelopes. S-layers have demonstrated diverse functions in growth and survival, maintenance of cell integrity, and mediation of host interactions. Additionally, S-layers can act as scaffolds for the outward display of auxiliary proteins and glycoproteins. These non-covalently bound S-layer associated proteins (SLAPs) have characterized roles in cell division, adherence to intestinal cells, and modulation of the host immune response. Recently, IgdA (LBA0695), a Lactobacillus acidophilus SLAP that possesses a Group 3 immunoglobulin (Ig)-like domain and GW (Gly-Tryp) dipeptide surface anchor, was recognized for its high conservation among S-layer-forming lactobacilli, constitutive expression, and surface localization. These findings prompted its selection for examination within the present study. Although IgdA and corresponding orthologs were shown to be unique to host-adapted lactobacilli, the Ig domain itself was specific to vertebrate-adapted species suggesting a role in vertebrate adaptation. Using a counterselective gene replacement system, igdA was deleted from the L. acidophilus NCFM chromosome. The resultant mutant, NCK2532, exhibited a visibly disrupted cell surface which likely contributed to its higher salt sensitivity, severely reduced adhesive capacity, and altered immunogenicity profile. Transcriptomic analyses revealed the induction of several stress response genes and secondary surface proteins. Due to the broad impact of IgdA on the cellular physiology and probiotic attributes of L. acidophilus, identification of similar proteins in alternative bacterial species may help pinpoint next-generation host-adapted probiotic candidates. DA - 2020/3/17/ PY - 2020/3/17/ DO - 10.3389/fmicb.2020.00345 VL - 11 SP - SN - 1664-302X KW - Lactobacillus KW - probiotic KW - S-layer KW - cell surface KW - S-layer associated protein KW - Ig-like domain ER - TY - JOUR TI - Optimizing the deployment of ultra-low volume and targeted indoor residual spraying for dengue outbreak response AU - Cavany, Sean M. AU - España, Guido AU - Lloyd, Alun L. AU - Waller, Lance A. AU - Kitron, Uriel AU - Astete, Helvio AU - Elson, William H. AU - Vazquez-Prokopec, Gonzalo M. AU - Scott, Thomas W. AU - Morrison, Amy C. AU - Reiner, Robert C., Jr. AU - Perkins, T. Alex T2 - PLOS Computational Biology AB - Recent years have seen rising incidence of dengue and large outbreaks of Zika and chikungunya, which are all caused by viruses transmitted by Aedes aegypti mosquitoes. In most settings, the primary intervention against Aedes-transmitted viruses is vector control, such as indoor, ultra-low volume (ULV) spraying. Targeted indoor residual spraying (TIRS) has the potential to more effectively impact Aedes-borne diseases, but its implementation requires careful planning and evaluation. The optimal time to deploy these interventions and their relative epidemiological effects are, however, not well understood. We used an agent-based model of dengue virus transmission calibrated to data from Iquitos, Peru to assess the epidemiological effects of these interventions under differing strategies for deploying them. Specifically, we compared strategies where spray application was initiated when incidence rose above a threshold based on incidence in recent years to strategies where spraying occurred at the same time(s) each year. In the absence of spraying, the model predicted 361,000 infections [inter-quartile range (IQR): 347,000-383,000] in the period 2000-2010. The ULV strategy with the fewest median infections was spraying twice yearly, in March and October, which led to a median of 172,000 infections [IQR: 158,000-183,000], a 52% reduction from baseline. Compared to spraying once yearly in September, the best threshold-based strategy utilizing ULV had fewer median infections (254,000 vs. 261,000), but required more spraying (351 vs. 274 days). For TIRS, the best strategy was threshold-based, which led to the fewest infections of all strategies tested (9,900; [IQR: 8,720-11,400], a 94% reduction), and required fewer days spraying than the equivalent ULV strategy (280). Although spraying twice each year is likely to avert the most infections, our results indicate that a threshold-based strategy can become an alternative to better balance the translation of spraying effort into impact, particularly if used with a residual insecticide. DA - 2020/4/20/ PY - 2020/4/20/ DO - 10.1371/journal.pcbi.1007743 VL - 16 IS - 4 SP - e1007743 UR - https://doi.org/10.1371/journal.pcbi.1007743 ER - TY - JOUR TI - Cotton response to preplant applications of 2,4-D or dicamba AU - Price, Katilyn AU - Li, Xiao AU - Leon, Ramon G. AU - Price, Andrew T2 - WEED TECHNOLOGY AB - Abstract Sensitive cotton varieties planted into soil treated with 2,4-D or dicamba utilized in burndowns can result in stunting and stand loss if use rate is too high and the plant-back interval is too short. The objective of this study was to evaluate cotton stunting and yield responses resulting from 2,4-D or dicamba residues in soil after preplant burndown applications at three locations in 2016 and 2017. Treatments with 2,4-D included 532 and 1,063 g ae ha −1 applied 3 wk before planting (WBP) and 53, 160, 266, 532, 1,063 g ae ha −1 applied at planting. Dicamba treatments included 560 and 1,120 g ae h −1 applied 3 WBP and 56, 168, 280, 560, 1,120 g ae ha −1 applied at planting. Dicamba or 2,4-D treatments applied 3 WBP resulted in no adverse effects on cotton stand, plant height, or yield. Dicamba 560 g ae h −1 applied at planting reduced cotton stand by 36% at 21 to 24 d after planting (DAP) over all locations in 2016. In 2017, stands were reduced by dicamba at 168, 280, 560, and 1,120 g ae ha −1 by 17% to 25% at 20 to 23 DAP. Moreover, cotton stands were not affected by 2,4-D in 2016, and only 266, 532, and 1,063 g ae ha −1 of 2,4-D caused stand reductions of 26% to 36% at 20 to 23 DAP over all locations in 2017. Dicamba at 560 g ae ha −1 at planting was the only treatment in this study that reduced plant height. Although stand losses were observed in both years, no yield loss occurred. The data suggest that stunting and stand reduction may occur if susceptible varieties are planted soon after burndown applications with 2,4-D or dicamba, but yield may not be affected after a full growing season. Dicamba showed greater potential to cause stunting and stand reduction than 2,4-D. DA - 2020/2// PY - 2020/2// DO - 10.1017/wet.2019.98 VL - 34 IS - 1 SP - 96-100 SN - 1550-2740 KW - 2 KW - 4-D KW - dicamba KW - cotton KW - Gossypium hirsutum L KW - Stunting KW - stand reduction KW - plant height KW - yield loss ER - TY - JOUR TI - Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models AU - Larson, Gary AU - Thorne, Jeffrey L. AU - Schmidler, Scott T2 - JOURNAL OF COMPUTATIONAL BIOLOGY AB - Evolutionary models of proteins are widely used for statistical sequence alignment and inference of homology and phylogeny. However, the vast majority of these models rely on an unrealistic assumption of independent evolution between sites. Here we focus on the related problem of protein structure alignment, a classic tool of computational biology that is widely used to identify structural and functional similarity and to infer homology among proteins. A site-independent statistical model for protein structural evolution has previously been introduced and shown to significantly improve alignments and phylogenetic inferences compared with approaches that utilize only amino acid sequence information. Here we extend this model to account for correlated evolutionary drift among neighboring amino acid positions. The result is a spatiotemporal model of protein structure evolution, described by a multivariate diffusion process convolved with a spatial birth–death process. This extended site-dependent model (SDM) comes with little additional computational cost or analytical complexity compared with the site-independent model (SIM). We demonstrate that this SDM yields a significant reduction of bias in estimated evolutionary distances and helps further improve phylogenetic tree reconstruction. We also develop a simple model of site-dependent sequence evolution, which we use to demonstrate the bias resulting from the application of standard site-independent sequence evolution models. DA - 2020/3/1/ PY - 2020/3/1/ DO - 10.1089/cmb.2019.0500 VL - 27 IS - 3 SP - 361-375 SN - 1557-8666 KW - diffusion process KW - dynamic programming KW - evolution KW - phylogeny KW - protein structure ER - TY - JOUR TI - Mosquito diversity and dog heartworm prevalence in suburban areas AU - Spence Beaulieu, Meredith R. AU - Federico, Jennifer L. AU - Reiskind, Michael H. T2 - PARASITES & VECTORS AB - Abstract Background Urbanization is occurring rapidly on a global scale and is altering mosquito communities, creating assemblages that are characteristically less diverse. Despite high rates of urbanization and ample examples of vector-borne diseases transmitted by multiple species, the effects of urbanization-driven mosquito diversity losses on disease transmission has not been well explored. We investigated this question using the dog heartworm, a filarial parasite vectored by numerous mosquito species. Methods We trapped host-seeking mosquitoes in undeveloped areas and neighborhoods of different ages in Wake County, North Carolina, USA, analyzing captured mosquitoes for heartworm DNA. We compared within-mosquito heartworm infection across land-use types by Kruskal–Wallis and likelihood ratio tests. Using zip code level data acquired from dogs in a local shelter, we performed linear regressions of within-host heartworm prevalence by within-mosquito heartworm prevalence as well as by three mosquito diversity measures. We also determined the best predictor of host-level prevalence among models including within-mosquito infection, mosquito diversity and abundance, and socioeconomic status as variables. Results Suburban areas had lower within-mosquito heartworm prevalence and lower likelihood of heartworm-positive mosquitoes than did undeveloped field sites, although no differences were seen between suburban and undeveloped wooded sites. No relationships were noted between within-mosquito and within-host heartworm prevalence. However, mosquito diversity metrics were positively correlated with host heartworm prevalence. Model selection revealed within-host prevalence was best predicted by a positive relationship with mosquito Shannon–Wiener diversity and a negative relationship with household income. Conclusions Our results demonstrate that decreases in mosquito diversity due to urbanization alter vector-borne disease risk. With regard to dog heartworm disease, this loss of mosquito diversity is associated with decreased heartworm prevalence within both the vector and the host. Although the response is likely different for diseases transmitted by one or few species, mosquito diversity losses leading to decreased transmission could be generalizable to other pathogens with multiple vectors. This study contributes to better understanding of the effects of urbanization and the role of vector diversity in multi-vectored pathosystems. DA - 2020/1/10/ PY - 2020/1/10/ DO - 10.1186/s13071-019-3874-0 VL - 13 IS - 1 SP - SN - 1756-3305 KW - Mosquito KW - Heartworm KW - Urbanization KW - Diversity KW - Vector KW - Landscape KW - Disease ecology ER - TY - JOUR TI - Nitrogen deposition differentially affects soil gross nitrogen transformations in organic and mineral horizons AU - Cheng, Yi AU - Wang, Jing AU - Wang, Jinyang AU - Wang, Shenqiang AU - Chang, Scott X. AU - Cai, Zucong AU - Zhang, Jinbo AU - Niu, Shuli AU - Hu, Shuijin T2 - EARTH-SCIENCE REVIEWS AB - Reactive nitrogen (N) input can profoundly alter soil N transformations and long-term productivity of forest ecosystems. However, critical knowledge gaps exist in our understanding of N deposition effects on internal soil N cycling in forest ecosystems. It is well established that N addition enhances soil N availability based on traditional net mineralization rate assays. Yet, experimental additions of inorganic N to soils broadly show a suppression of microbial activity and protein depolymerization. Here we show, from a global meta-analysis of 15N-labelled studies that gross N transformation rates in forest soil organic and mineral horizons differentially respond to N addition. In carbon (C)-rich organic horizons, N addition significantly enhanced soil gross rates of N mineralization, nitrification and microbial NO3¯ immobilization rates, but decreased gross microbial NH4+ immobilization rates. In C-poor mineral soils, in contrast, N addition did not change gross N transformation rates except for increasing gross nitrification rates. An initial soil C/N threshold of approx. 14.6, above which N addition enhanced gross N mineralization rates, could explain why gross N mineralization was increased by N deposition in organic horizons alone. Enhancement of gross N mineralization by N deposition was also largely attributed to enhanced N mineralization activity per unit microbial biomass. Our results indicate that the net effect of N input on forest soil gross N transformations are highly stratified by soil C distribution along the soil profile, and thus challenge the perception that N availability ubiquitously limits N mineralization. These findings suggest that these differences should be integrated into models to better predict forest ecosystem N cycle and C sequestration potential under future N deposition scenarios. DA - 2020/2// PY - 2020/2// DO - 10.1016/j.earscirev.2019.103033 VL - 201 SP - SN - 1872-6828 KW - Net N mineralization KW - Gross mineralization KW - Gross nitrification KW - Gross NH4(+) and NO3(-) immobilization KW - Nitrogen deposition KW - Microbial biomass ER - TY - JOUR TI - Associations between urine phthalate metabolites and thyroid function in pregnant women and the influence of iodine status AU - Villanger, Gro D. AU - Drover, Samantha S. M. AU - Nethery, Rachel C. AU - Thomsen, Cathrine AU - Sakhi, Amrit K. AU - Overgaard, Kristin R. AU - Zeiner, Pal AU - Hoppin, Jane A. AU - Reichborn-Kjennerud, Ted AU - Aase, Heidi AU - Engel, Stephanie M. T2 - ENVIRONMENT INTERNATIONAL AB - Human populations, including susceptible subpopulations such as pregnant women and their fetuses, are continuously exposed to phthalates. Phthalates may affect the thyroid hormone system, causing concern for pregnancy health, birth outcomes and child development. Few studies have investigated the joint effect of phthalates on thyroid function in pregnant women, although they are present as a mixture with highly inter-correlated compounds. Additionally, no studies have investigated if the key nutrient for thyroid health, iodine, modifies these relationships. In this study, we examined the cross-sectional relationships between concentrations of 12 urinary phthalate metabolites and 6 plasma thyroid function biomarkers measured mid-pregnancy (~17 week gestation) in pregnant women (N = 1072), that were selected from a population-based prospective birth cohort, The Norwegian Mother, Father and Child Cohort study (MoBa). We investigated if the phthalate metabolite-thyroid function biomarker associations differed by iodine status by using a validated estimate of habitual dietary iodine intake based on a food frequency questionnaire from the 22nd gestation week. We accounted for the phthalate metabolite mixture by factor analyses, ultimately reducing the exposure into two uncorrelated factors. These factors were used as predictors in multivariable adjusted linear regression models with thyroid function biomarkers as the outcomes. Factor 1, which included high loadings for mono-iso-butyl phthalate (MiBP), mono-n-butyl phthalate (MnBP), and monobenzyl phthalate (MBzP), was associated with increased total triiodothyronine (TT3) and free T3 index (fT3i). These associations appeared to be driven primarily by women with low iodine intake (<150 µg/day, ~70% of our sample). Iodine intake significantly modified (p-interaction < 0.05) the association of factor 1 with thyroid stimulating hormone (TSH), total thyroxine (TT4) and free T4 index (fT4i), such that only among women in the high iodine intake category (≥150 µg/day, i.e. sufficient) was this factor associated with increased TSH and decreased TT4 and FT4i, respectively. In contrast, factor 2, which included high loadings for di-2-ethylhexyl phthalate metabolites (∑DEHP) and di-iso-nonyl phthalate metabolites (∑DiNP), was associated with a decrease in TT3 and fT3i, which appeared fairly uniform across iodine intake categories. We find that phthalate exposure is associated with thyroid function in mid-pregnancy among Norwegian women, and that iodine intake, which is essential for thyroid health, could influence some of these relationships. DA - 2020/4// PY - 2020/4// DO - 10.1016/j.envint.2020.105509 VL - 137 SP - SN - 1873-6750 KW - Phthalates KW - Thyroid hormones KW - Pregnancy KW - Iodine KW - The Norwegian Mother KW - Father and Child Cohort study KW - MoBa ER - TY - JOUR TI - Context-dependent genetic architecture of Drosophila life span AU - Huang, Wen AU - Campbell, Terry AU - Carbone, Mary Anna AU - Jones, W. Elizabeth AU - Unselt, Desiree AU - Anholt, Robert R. H. AU - Mackay, Trudy F. C. T2 - PLOS BIOLOGY AB - Understanding the genetic basis of variation in life span is a major challenge that is difficult to address in human populations. Evolutionary theory predicts that alleles affecting natural variation in life span will have properties that enable them to persist in populations at intermediate frequencies, such as late-life–specific deleterious effects, antagonistic pleiotropic effects on early and late-age fitness components, and/or sex- and environment-specific or antagonistic effects. Here, we quantified variation in life span in males and females reared in 3 thermal environments for the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and an advanced intercross outbred population derived from a subset of DGRP lines. Quantitative genetic analyses of life span and the micro-environmental variance of life span in the DGRP revealed significant genetic variance for both traits within each sex and environment, as well as significant genotype-by-sex interaction (GSI) and genotype-by-environment interaction (GEI). Genome-wide association (GWA) mapping in both populations implicates over 2,000 candidate genes with sex- and environment-specific or antagonistic pleiotropic allelic effects. Over 1,000 of these genes are associated with variation in life span in other D. melanogaster populations. We functionally assessed the effects of 15 candidate genes using RNA interference (RNAi): all affected life span and/or micro-environmental variance of life span in at least one sex and environment and exhibited sex-and environment-specific effects. Our results implicate novel candidate genes affecting life span and suggest that variation for life span may be maintained by variable allelic effects in heterogeneous environments. DA - 2020/3// PY - 2020/3// DO - 10.1371/journal.pbio.3000645 VL - 18 IS - 3 SP - SN - 1545-7885 ER - TY - JOUR TI - Corporate dialogue in crises of China: Examining dialogic strategies and communicative outcomes in a child abuse scandal AU - Cheng, Yang AU - Shen, Hongmei AU - Jiang, Qiaolei T2 - Public Relations Review AB - Although dialogue has become a key concept in the field of public relations, little research has dealt with corporate dialogic strategies and communicative outcomes in crises of a non-Western context. Applying a mixed-method approach including both quantitative survey research and qualitative content analysis, this study analyzed both corporate dialogic strategies and public reactions in a social-mediated crisis in mainland China. Results demonstrated the corporation utilized both concertative and transformative dialogic strategies as the crisis progressed. After the crisis, concerned publics perceived low trust and moderate distrust towards the organization and reported five different communicative action intentions (i.e., mobilizing, information seeking, threatening, persuasion, and partnering). Trust and distrust exerted different impacts on publics’ post-crisis communicative action intentions and distrust was a stronger driver. Theoretical and practical implications of these findings are discussed. DA - 2020/3// PY - 2020/3// DO - 10.1016/j.pubrev.2019.101816 VL - 46 IS - 1 SP - 101816 J2 - Public Relations Review LA - en OP - SN - 0363-8111 UR - http://dx.doi.org/10.1016/j.pubrev.2019.101816 DB - Crossref KW - Organizational dialogic strategies KW - Crisis KW - Public communicative action intentions KW - Social media KW - China KW - Trust KW - Distrust ER - TY - JOUR TI - Feeding behavior of Frankliniella fusca on seedling cotton expressing Cry51Aa2.834_16 Bt toxin AU - D'Ambrosio, Damon A AU - Kennedy, George G AU - Huseth, Anders S T2 - Pest Management Science AB - Abstract BACKGROUND Tobacco thrips, Frankliniella fusca (Hinds), is a pest of cotton. Currently, growers rely on neonicotinoid seed treatments to control F. fusca. However, the occurrence of neonicotinoid‐resistant F. fusca populations has created new challenges for their management. Development of thrips‐active Cry51Aa2.834_16 Bacillus thuringiensis ( Bt ) toxin expressed in MON 88702 cotton will be an important new tactic for thrips management. Previous studies have shown that MON 88702 causes limited mortality of F. fusca adults and larvae but reduces infestations on seedling cotton by suppressing oviposition from colonizing adults. This suggests that the toxin affects host preference of adult F. fusca. Knowledge of the effect of this trait on F. fusca feeding behavior provides a more complete understanding of MON 88702 activity. Using electropenetrography, we compared the feeding behaviors of adult F. fusca females on MON 88702 cotton and a non‐ Bt isoline cotton over 2 h. The number of probes, proportion of probes resulting in ingestion, total duration of ingestion, and duration of ingestion per event were measured. RESULTS On MON 88702 seedlings, F. fusca probed and ingested fewer times than those on non‐ Bt cotton. Probes on MON 88702 were less likely to lead to ingestion than on non‐ Bt cotton. The total duration of ingestion and duration of ingestion per event did not differ between treatments. CONCLUSION The results show that MON 88702 has an antifeedant effect on F. fusca , which provides insight into behavioral responses driving MON 88702 aversion and anti‐oviposition documented in previous studies. © 2020 Society of Chemical Industry DA - 2020/4/7/ PY - 2020/4/7/ DO - 10.1002/ps.5825 VL - 76 IS - 8 SP - 2781-2786 J2 - Pest Management Science LA - en OP - SN - 1526-498X 1526-4998 UR - http://dx.doi.org/10.1002/ps.5825 DB - Crossref KW - tobacco thrips KW - Gossypium hirsutum KW - electropenetrography KW - Bacillus thuringiensis KW - MON 88702 KW - antixenosis ER - TY - JOUR TI - Temporal and bidirectional influences of estradiol on voluntary wheel running in adult female and male rats AU - Krentzel, Amanda A. AU - Proano, Stephanie AU - Patisaul, Heather B. AU - Meitzen, John T2 - HORMONES AND BEHAVIOR AB - The sex steroid hormone 17β-estradiol (estradiol) regulates animal behavior as both a non-rapid hormone signal and as a rapid-acting neuromodulator. By practical necessity, estradiol's divergent temporal actions on rodent behavior are typically studied singularly and in one sex. We hypothesized that estradiol simultaneously acts through both temporal mechanisms to sex-specifically modulate a single behavior; and furthermore, that estradiol action in one temporal domain may regulate action in another. To test this hypothesis, we utilized one of the most robust rat behaviors exhibiting sex differences and estradiol-responsiveness, voluntary wheel running. Adult female and male rats were gonadectomized and exposed to daily repeated estradiol benzoate (EB) injections. Estradiol-sensitive running behavior was continually assessed in both the rapid and non-rapid temporal domains. We found that in female rats, estradiol rapidly decreased voluntary wheel running, but only after prior daily EB injections, supporting the hypothesis that non-rapid estradiol action influences rapid estradiol actions. Males exhibited a similar but less robust response, demonstrating sex-responsiveness. This rapid estradiol-induced decrease in running contrasted to non-rapid estradiol action which overall increased running in both sexes, revealing a bidirectional nature of estradiol's temporal influence. Non-rapid estradiol action also demonstrated sex-responsiveness, as a higher dose of EB was required to induce increased running in males compared to females. These findings indicate that estradiol rapidly, non-rapidly, and bidirectionally modulates wheel running in a sex-responsive manner, and that rapid estradiol action is modulated by non-rapid estradiol action. Overall, these data illustrate estradiol as a pleiotropic sex-responsive neuromodulator of a single behavior across temporal domains. DA - 2020/4// PY - 2020/4// DO - 10.1016/j.yhbeh.2020.104694 VL - 120 SP - SN - 1095-6867 KW - Estradiol KW - Sex differences KW - Voluntary wheel running KW - Locomotion KW - Motivation ER - TY - JOUR TI - Localization of viral and host RNA within soybean cyst nematode via fluorescence in situ hybridization AU - Ruark-Seward, Casey L. AU - Davis, Eric L. AU - Sit, Tim L. T2 - EXPERIMENTAL PARASITOLOGY AB - Nematode-infecting RNA viruses have recently been discovered via transcriptome sequencing. In soybean cyst nematode (SCN; Heterodera glycines), seven single-stranded RNA viruses have been identified from transcriptome data and experimentally confirmed with qRT-PCR and Sanger sequencing. Presently, there is still much unknown about the relationship between these viruses and the nematode host. In this study, we localize three viruses within the soybean cyst nematode: SCN socyvirus-1 (SbCNV-1), SCN nyami-like virus (NLV), and SCN bunya-like virus (BLV). To visually locate the viruses, whole-mount fluorescence in situ hybridization (FISH) methodology was developed for SCN pre-parasitic second-stage juveniles (ppJ2s). Two SCN populations with differing viral titers (LY1 and MM21) were used as a comparison for viral probe fluorescence intensity. Viral RNAs for all three viruses were abundant in cells throughout the SCN ppJ2 body of the high titer (LY1) population but absent within the majority of the intestinal tract. A significant reduction in viral fluorescence intensity was observed in a similar body pattern in ppJ2 of the low-titer (MM21) SCN, highlighting the specificity of the FISH method. As controls, viral RNAs were colocalized with host mRNA glyceraldehyde 3-phosphate dehydrogenase (GAPDH) for full body localization and a secretory ubiquitin protein (4G06) expressed specifically within the subventral esophageal glands. In addition, viral replication was confirmed in SCN eggs and ppJ2s via qRT-PCR detection of the anti-genomic RNA strands. DA - 2020/4// PY - 2020/4// DO - 10.1016/j.exppara.2020.107866 VL - 211 SP - SN - 1090-2449 ER - TY - JOUR TI - The social-mediated crisis communication research: Revisiting dialogue between organizations and publics in crises of China AU - Cheng, Yang T2 - Public Relations Review AB - The rapid diffusion of social media is ushering in a new era of crisis communication. To enhance our understanding of the social-mediated dialogue between organizations and their publics in crises of China, this study conducts a content analysis of 61 relevant journal articles published in 2006–2018. Results of this research present an overview of ongoing research trends such as theoretical frameworks and methodological preferences. This research also explores how the unique Chinese social media characteristics affect the dialogue between types of organizations and their publics. Contextual factors such as face and favor, relationship (Guanxi) and sentiment (Renqing), and the centralized political system that may facilitate/inhibit dialogue in crises of China are identified as well. Finally, this study suggests promising new directions such as a scholarly assessment tool for the social-mediated crisis communication research in China. DA - 2020/3// PY - 2020/3// DO - 10.1016/j.pubrev.2019.04.003 VL - 46 IS - 1 SP - 101769 J2 - Public Relations Review LA - en OP - SN - 0363-8111 UR - http://dx.doi.org/10.1016/j.pubrev.2019.04.003 DB - Crossref KW - Social media KW - Crisis communication KW - Weibo KW - Dialogue KW - Mediator KW - China KW - Public relations ER - TY - JOUR TI - Gene expression networks in the Drosophila Genetic Reference Panel AU - Everett, Logan J. AU - Huang, Wen AU - Zhou, Shanshan AU - Carbone, Mary Anna AU - Lyman, Richard F. AU - Arya, Gunjan H. AU - Geisz, Matthew S. AU - Ma, Junwu AU - Morgante, Fabio AU - St Armour, Genevieve AU - Turlapati, Lavanya AU - Anholt, Robert R. H. AU - Mackay, Trudy F. C. T2 - GENOME RESEARCH AB - A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. This question is best addressed in a genetic mapping population in which all molecular polymorphisms are known and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable elements, and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, as well as genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses. DA - 2020/3// PY - 2020/3// DO - 10.1101/gr.257592.119 VL - 30 IS - 3 SP - 485-496 SN - 1549-5469 ER - TY - JOUR TI - Systems genetics of the Drosophila metabolome AU - Zhou, Shanshan AU - Morgante, Fabio AU - Geisz, Matthew S. AU - Ma, Junwu AU - Anholt, Robert R. H. AU - Mackay, Trudy F. C. T2 - GENOME RESEARCH AB - How effects of DNA sequence variants are transmitted through intermediate endophenotypes to modulate organismal traits remains a central question in quantitative genetics. This problem can be addressed through a systems approach in a population in which genetic polymorphisms, gene expression traits, metabolites, and complex phenotypes can be evaluated on the same genotypes. Here, we focused on the metabolome, which represents the most proximal link between genetic variation and organismal phenotype, and quantified metabolite levels in 40 lines of the Drosophila melanogaster Genetic Reference Panel. We identified sex-specific modules of genetically correlated metabolites and constructed networks that integrate DNA sequence variation and variation in gene expression with variation in metabolites and organismal traits, including starvation stress resistance and male aggression. Finally, we asked to what extent SNPs and metabolites can predict trait phenotypes and generated trait- and sex-specific prediction models that provide novel insights about the metabolomic underpinnings of complex phenotypes. DA - 2020/3// PY - 2020/3// DO - 10.1101/gr.243030.118 VL - 30 IS - 3 SP - 392-405 SN - 1549-5469 ER - TY - JOUR TI - Prenatal pesticide exposure and respiratory health outcomes in the first year of life: Results from the infants' Environmental Health (ISA) study AU - Mora, Ana M. AU - Hoppin, Jane A. AU - Cordoba, Leonel AU - Cano, Juan C. AU - Soto-Martinez, Manuel AU - Eskenazi, Brenda AU - Lindh, Christian H. AU - Joode, Berna T2 - INTERNATIONAL JOURNAL OF HYGIENE AND ENVIRONMENTAL HEALTH AB - Growing evidence suggests that pesticide exposure may influence respiratory health, but data in young children are very limited. We examined the association of prenatal pesticide exposure with lower respiratory tract infections (LRTIs) and wheeze at one year of age in children from the Infants' Environmental Health (ISA) study in Costa Rica. We measured seven pesticide metabolites, including ethylenethiourea (ETU, metabolite of mancozeb), in maternal urine samples collected repeatedly during pregnancy. For each woman, we averaged pesticide concentrations during each half of pregnancy (≤20 and >20 weeks of gestation) and across repeated samples collected over the course of pregnancy. We collected information about LRTIs (n = 355) and wheezing (n = 272) during the first year of life from mothers when their children were 11–19 months old. We fit multivariable logistic regression models using high (quartile 4) vs. low (quartiles 1–3) urinary pesticide concentrations as exposures and adjusted models for maternal age, education, parity, gestational age at birth, and child sex. Ten percent of the children had at least one LRTI and 39% had at least one episode of wheezing during their first year of life. Median (25-75th percentile) specific gravity-corrected urinary ETU concentrations during the first half, second half, and over the course of pregnancy were 3.4 (2.1–5.0), 3.3 (2.2–4.7), and 3.4 (2.4–5.0) ng/mL, respectively. We observed that high urinary ETU concentrations during the first half of pregnancy were associated with increased odds of LRTI (OR = 2.45; 95% CI: 0.96, 6.26), whereas high urinary ETU concentrations during the second half of pregnancy were associated with decreased odds of wheezing (OR = 0.50; 95% CI: 0.26, 0.96). We found that the association between high urinary ETU concentrations during the first half of pregnancy and LRTIs persisted among mother-child pairs with either high or low ETU concentrations during the second half. In contrast, the association of high urinary ETU concentrations during the second half of pregnancy with wheezing was attenuated when we simultaneously adjusted for urinary ETU concentrations during the first half. We observed null associations between other pesticide metabolites measured during pregnancy and respiratory outcomes. Our data indicate that exposure to mancozeb/ETU during the first half of pregnancy may be associated with respiratory outcomes in the first year of life. DA - 2020/4// PY - 2020/4// DO - 10.1016/j.ijheh.2020.113474 VL - 225 SP - SN - 1618-131X KW - Pesticides KW - Mancozeb KW - Respiratory outcomes KW - Infants KW - Costa Rica ER - TY - JOUR TI - Input use under cost-of-production crop insurance: Theory and evidence AU - He, Juan AU - Zheng, Xiaoyong AU - Rejesus, Roderick AU - Yorobe, Jose, Jr. T2 - AGRICULTURAL ECONOMICS AB - Abstract There have been a number of previous studies that examined the effects of yield‐ or revenue‐based crop insurance products on input use of farmers. However, no study has specifically investigated the input use impacts of a cost‐of‐production (COP) crop insurance policy, even though this type of crop insurance is the predominant one used in several other countries outside of the United States (such as the Philippines and China). This article aims to theoretically and empirically examine the effect of a COP crop insurance product on farmers’ chemical input use. Our theoretical model suggests that the effect of COP insurance on input use can either be positive or negative, with the resulting impact depending on the strengths of (a) the traditional moral hazard effect of insurance (i.e., an input use decreasing effect); versus (b) the marginal incentives to apply more inputs due to input levels being the main determinant for expected indemnity amounts in this type of insurance (i.e., an input use increasing effect). A survey data set from corn farmers in the Philippines is then used to empirically illustrate how a particular COP insurance product influences input use in a real‐life context. In this case, we find that COP insurance increases the use of chemical inputs (e.g., fertilizers and total chemical expenditure), implying that the positive marginal incentive to apply more inputs dominates the negative moral hazard effect. DA - 2020/5// PY - 2020/5// DO - 10.1111/agec.12558 VL - 51 IS - 3 SP - 343-357 SN - 1574-0862 KW - cost-of-production crop insurance KW - moral hazard ER - TY - JOUR TI - "Yes, and ... *" continuing the scholarly conversation about student precarity in higher education AU - Rudick, C. Kyle AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - You’ll see here the cost of tuition, room, and board here. We take pride in being a university that works very hard to address all unmet need for the cost of attendance here. We do not want money t... DA - 2020/4/2/ PY - 2020/4/2/ DO - 10.1080/03634523.2020.1724374 VL - 69 IS - 2 SP - 276-280 SN - 1479-5795 ER - TY - JOUR TI - AI in the headlines: the portrayal of the ethical issues of artificial intelligence in the media AU - Ouchchy, Leila AU - Coin, Allen AU - Dubljevic, Veljko T2 - AI & SOCIETY AB - Abstract As artificial intelligence (AI) technologies become increasingly prominent in our daily lives, media coverage of the ethical considerations of these technologies has followed suit. Since previous research has shown that media coverage can drive public discourse about novel technologies, studying how the ethical issues of AI are portrayed in the media may lead to greater insight into the potential ramifications of this public discourse, particularly with regard to development and regulation of AI. This paper expands upon previous research by systematically analyzing and categorizing the media portrayal of the ethical issues of AI to better understand how media coverage of these issues may shape public debate about AI. Our results suggest that the media has a fairly realistic and practical focus in its coverage of the ethics of AI, but that the coverage is still shallow. A multifaceted approach to handling the social, ethical and policy issues of AI technology is needed, including increasing the accessibility of correct information to the public in the form of fact sheets and ethical value statements on trusted webpages (e.g., government agencies), collaboration and inclusion of ethics and AI experts in both research and public debate, and consistent government policies or regulatory frameworks for AI technology. DA - 2020/12// PY - 2020/12// DO - 10.1007/s00146-020-00965-5 VL - 35 IS - 4 SP - 927-936 SN - 1435-5655 KW - Artificial intelligence (AI) KW - Ethics KW - Media KW - News KW - Public discourse KW - Public policy ER - TY - JOUR TI - The Principle of Autonomy and Behavioral Variant Frontotemporal Dementia AU - Dubljević, V. T2 - Journal of Bioethical Inquiry DA - 2020/6// PY - 2020/6// DO - 10.1007/s11673-020-09972-z VL - 17 IS - 2 SP - 271-282 SN - 1872-4353 KW - Autonomy KW - Behavioural variant frontotemporal dementia KW - Moral responsibility KW - Legal issues KW - Informed consent ER - TY - JOUR TI - Gender differences in respiratory health outcomes among farming cohorts around the globe: findings from the AGRICOH consortium AU - Fix, Jonathan AU - Annesi-Maesano, Isabella AU - Baldi, Isabelle AU - Boulanger, Mathilde AU - Cheng, Soo AU - Cortes, Sandra AU - Dalphin, Jean-Charles AU - Dalvie, Mohamed Aqiel AU - Degano, Bruno AU - Douwes, Jeroen AU - Eduard, Wijnand AU - Elholm, Grethe AU - Ferreccio, Catterina AU - Harding, Anne-Helen AU - Jeebhay, Mohamed AU - Kelly, Kevin M. AU - Kromhout, Hans AU - MacFarlane, Ewan AU - Maesano, Cara Nichole AU - Mitchell, Diane Catherine AU - Mwanga, Hussein AU - Naidoo, Saloshni AU - Negatu, Beyene AU - Ngajilo, Dorothy AU - Nordby, Karl-Christian AU - Parks, Christine G. AU - Schenker, Marc B. AU - Shin, Aesun AU - Sisgaard, Torben AU - Sim, Malcolm AU - Soumagne, Thibaud AU - Thorne, Peter AU - Yoo, Keun-Young AU - Hoppin, Jane T2 - JOURNAL OF AGROMEDICINE AB - Purpose: Respiratory hazards of farming have been identified for centuries, with little focus on gender differences. We used data from the AGRICOH consortium, a collective of prospective cohorts of agricultural workers, to assess respiratory disease prevalence among adults in 18 cohorts representing over 200,000 farmers, farm workers, and their spouses from six continents.Methods: Cohorts collected data between 1992 and 2016 and ranged in size from 200 to >128,000 individuals; 44% of participants were female. Farming practices varied from subsistence farming to large-scale industrial agriculture. All cohorts provided respiratory outcome information for their cohort based on their study definitions. The majority of outcomes were based on self-report using standard respiratory questionnaires; the greatest variability in assessment methods was associated with chronic obstructive pulmonary disease (COPD).Results: For all three respiratory symptoms (cough, phlegm, and wheeze), the median prevalence in men was higher than in women, with the greatest difference for phlegm (17% vs. 10%). For asthma, women had a higher prevalence (7.8% vs 6.5%), with the difference associated with allergic asthma. The relative proportion of allergic asthma varied among cohorts. In two of eight cohorts for women and two of seven cohorts for men, allergic asthma was more common than non-allergic asthma.Conclusions: These findings indicate that respiratory outcomes are common among farmers around the world despite differences in agricultural production. As women in the general population are at higher risk of asthma, exploring gender differences in occupational studies is critical for a deeper understanding of respiratory disease among agricultural workers. DA - 2020/// PY - 2020/// DO - 10.1080/1059924X.2020.1713274 KW - Farmers KW - Respiratory Health KW - Gender KW - Farmworkers KW - Occupational Exposure ER - TY - JOUR TI - Social license and synthetic biology: the trouble with mining terms AU - Delborne, Jason A. AU - Kokotovich, Adam E. AU - Lunshof, Jeantine E. T2 - Journal of Responsible Innovation AB - ABSTRACT In the wake of controversies over first-generation biotechnologies, the growing field of synthetic biology appears cognizant of the need to attend to the social, political, cultural, and ethical dimensions of innovation. Public engagement has emerged as an important means for attending to these dimensions. Here, we call attention to the problematic nature of one paradigm being drawn upon to conceptualize this public engagement for synthetic biology: social license to operate (SLO). After reviewing SLO’s emergence in the resource extraction context and the existing critiques of SLO, we examine its current use in the synthetic biology literature. We argue that an SLO-derived model of engagement is especially inadequate for synthetic biology due to unique challenges posed by synthetic biology and the limited conception of engagement provided by SLO. We conclude by discussing alternative public engagement paradigms and examples better suited to inform synthetic biology governance. DA - 2020/4/6/ PY - 2020/4/6/ DO - 10.1080/23299460.2020.1738023 VL - 7 IS - 3 SP - 280-297 J2 - Journal of Responsible Innovation LA - en OP - SN - 2329-9460 2329-9037 UR - http://dx.doi.org/10.1080/23299460.2020.1738023 DB - Crossref KW - Community and stakeholder engagement KW - public engagement KW - responsible research and innovation KW - social license to operate KW - synthetic biology ER - TY - JOUR TI - Thermostable endoglucanase gene derived by amplification from the genomic DNA of a cellulose-enriched mixed culture from mudspring water of Mt. Makiling, Laguna, Philippines AU - Tambalo, Richard D. AU - Raymundo, Asuncion K. AU - Grunden, Amy M. T2 - WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY DA - 2020/3/10/ PY - 2020/3/10/ DO - 10.1007/s11274-020-02825-2 VL - 36 IS - 3 SP - SN - 1573-0972 KW - Endoglucanase KW - Saccharolobus KW - Mt KW - Makiling mudspring KW - Lignocellulose hydrolysis KW - Thermophiles ER - TY - JOUR TI - Modulation of Arabidopsis Flavonol Biosynthesis Genes by Cyst and Root-Knot Nematodes AU - Hamamouch, Noureddine AU - Winkel, Brenda S. J. AU - Li, Chunying AU - Davis, Eric L. T2 - PLANTS-BASEL AB - Although it is well established that flavonoid synthesis is induced in diverse plant species during nematode parasitism, little is known about the regulation of genes controlling flavonol biosynthesis during the plant–nematode interaction. In this study, expression of the Arabidopsis thaliana flavonol-specific transcription factor, AtMYB12, the flavonol synthase genes, AtFLS1, 2, 3, 4, and 5, and the gene encoding the central flavonoid enzyme, chalcone synthase (AtCHS), were examined in plant roots during infection by Heterodera schachtii (sugar beet cyst) and Meloidogyne incognita (root-knot) nematodes. These experiments showed that AtMYB12 was transiently upregulated at 9 dpi in syncytia associated with sugar beet cyst nematode infection and that an Atmyb12-deficient line was less susceptible to the parasite. This suggests that, rather than contributing to plant defense, this gene is essential for productive infection. However, the AtCHS and AtFLS1 genes, which are controlled by AtMYB12, did not exhibit a similar transient increase, but rather were expressly downregulated in syncytia relative to adjacent uninfected root tissue. Genetic analyses further indicated that AtFLS1 contributes to plant defense against Cyst nematode infection, while other AtFLS gene family members do not, consistent with prior reports that these other genes encode little or no enzyme activity. Together, these findings indicate a role of AtMyb12 in promoting the early stages of Cyst nematode infection, while flavonols produced through the action of AtFLS1 are essential for plant defense. On the other hand, a transient induction of AtMYB12 was not observed in galls produced during root-knot nematode infection, but this gene was instead substantially downregulated, starting at the 9 dpi sampling point, as were AtCHS and AtFLS1. In addition, both the AtMYB12- and AtFLS1-deficient lines were more susceptible to infection by this parasite. There was again little evidence for contributions from the other AtFLS gene family members, although an AtFLS5-deficient line appeared to be somewhat more susceptible to infection. Taken together, this study shows that sugar-beet cyst and root-knot nematodes modulate differently the genes involved in flavonol biosynthesis in order to successfully infect host roots and that AtFLS1 may be involved in the plant basal defense response against nematode infection. DA - 2020/2// PY - 2020/2// DO - 10.3390/plants9020253 VL - 9 IS - 2 SP - SN - 2223-7747 KW - cyst nematode KW - flavonoids KW - Heterodera schachtii KW - Meloidogyne incognita KW - parasitism KW - root-knot nematode ER - TY - JOUR TI - Use of the lignocellulose-degrading bacterium Caldicellulosiruptor bescii to assess recalcitrance and conversion of wild-type and transgenic poplar AU - Straub, Christopher T. AU - Bing, Ryan G. AU - Wang, Jack P. AU - Chiang, Vincent L. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - BIOTECHNOLOGY FOR BIOFUELS AB - Biological conversion of lignocellulosic biomass is significantly hindered by feedstock recalcitrance, which is typically assessed through an enzymatic digestion assay, often preceded by a thermal and/or chemical pretreatment. Here, we assay 17 lines of unpretreated transgenic black cottonwood (Populus trichocarpa) utilizing a lignocellulose-degrading, metabolically engineered bacterium, Caldicellulosiruptor bescii. The poplar lines were assessed by incubation with an engineered C. bescii strain that solubilized and converted the hexose and pentose carbohydrates to ethanol and acetate. The resulting fermentation titer and biomass solubilization were then utilized as a measure of biomass recalcitrance and compared to data previously reported on the transgenic poplar samples.Of the 17 transgenic poplar lines examined with C. bescii, a wide variation in solubilization and fermentation titer was observed. While the wild type poplar control demonstrated relatively high recalcitrance with a total solubilization of only 20% and a fermentation titer of 7.3 mM, the transgenic lines resulted in solubilization ranging from 15 to 79% and fermentation titers from 6.8 to 29.6 mM. Additionally, a strong inverse correlation (R2 = 0.8) between conversion efficiency and lignin content was observed with lower lignin samples more easily converted and solubilized by C. bescii.Feedstock recalcitrance can be significantly reduced with transgenic plants, but finding the correct modification may require a large sample set to identify the most advantageous genetic modifications for the feedstock. Utilizing C. bescii as a screening assay for recalcitrance, poplar lines with down-regulation of coumarate 3-hydroxylase 3 (C3H3) resulted in the highest degrees of solubilization and conversion by C. bescii. One such line, with a growth phenotype similar to the wild-type, generated more than three times the fermentation products of the wild-type poplar control, suggesting that excellent digestibility can be achieved without compromising fitness of the tree. DA - 2020/3/11/ PY - 2020/3/11/ DO - 10.1186/s13068-020-01675-2 VL - 13 IS - 1 SP - SN - 1754-6834 KW - Caldicellulosiruptor KW - Extreme thermophiles KW - Lignocellulose KW - Biofuel KW - Poplar ER - TY - JOUR TI - CRISPR Shields: Fending Off Diverse Cas Nucleases with Nucleus-like Structures AU - Barrangou, Rodolphe AU - Sontheimer, Erik J. T2 - MOLECULAR CELL AB - Two recent studies have uncovered a novel means by which bacteriophages thwart host immunity. Mendoza et al. (2020) and Malone et al. (2020) demonstrate that a nucleus-like proteinaceous structure shields phage DNA from CRISPR-associated nucleases encompassing Cascade-Cas3, Cas9, and Cas12. DA - 2020/3/5/ PY - 2020/3/5/ DO - 10.1016/j.molcel.2020.02.015 VL - 77 IS - 5 SP - 934-936 SN - 1097-4164 ER - TY - JOUR TI - Detection of Phytophthora infestans by Loop-Mediated Isothermal Amplification, Real-Time LAMP, and Droplet Digital PCR AU - Ristaino, Jean B. AU - Saville, Amanda C. AU - Paul, Rajesh AU - Cooper, Donald C. AU - Wei, Qingshan T2 - PLANT DISEASE AB - Phytophthora infestans is the causal agent of potato late blight, a devastating disease of tomato and potato and a threat to global food security. Early detection and intervention is essential for effective management of the pathogen. We developed a loop-mediated isothermal amplification (LAMP) assay for P. infestans and compared this assay to conventional PCR, real-time LAMP, and droplet digital PCR for detection of P. infestans. The LAMP assay was specific for P. infestans on potato and tomato and did not amplify other potato- or tomato-infecting Phytophthora species or other fungal and bacterial pathogens that infect potato and tomato. The detection threshold for SYBR Green LAMP and real-time LAMP read with hydroxynaphthol blue and EvaGreen was 1 pg/µl. In contrast, detection by conventional PCR was 10 pg/µl. Droplet digital PCR had the lowest detection threshold (100 fg/µl). We adapted the LAMP assay using SYBR Green and a mobile reader (mReader) for use in the field. Detection limits were 584 fg/µl for SYBR Green LAMP read on the mReader, which was more sensitive than visualization with the human eye. The mobile platform records geospatial coordinates and data from positive pathogen detections can be directly uploaded to a cloud database. Data can then be integrated into disease surveillance networks. This system will be useful for real-time detection of P. infestans and will improve the timeliness of reports into surveillance systems such as USABlight or EuroBlight. DA - 2020/3// PY - 2020/3// DO - 10.1094/PDIS-06-19-1186-RE VL - 104 IS - 3 SP - 708-716 SN - 1943-7692 KW - oomycetes KW - pathogen detection KW - Phytophthora infestans KW - vegetables ER - TY - JOUR TI - Genome Sequences of Five Type Strain Members of the Archaeal Family Sulfolobaceae, Acidianus ambivalens, Acidianus infernus, Stygiolobus azoricus, Sulfuracidifex metallicus, and Sulfurisphaera ohwakuensis AU - Counts, James A. AU - Vitko, Nicholas P. AU - Kelly, Robert M. T2 - MICROBIOLOGY RESOURCE ANNOUNCEMENTS AB - Presented are five genomes from the polyextremophilic (optimal temperature of >65°C and optimal pH of <3.5) archaeal family Sulfolobaceae, greatly expanding order-wide genomic diversity. Included are the only obligate anaerobic species, several facultative sulfur utilizers, two metal mobilizers, one facultative chemolithoautotroph with robust metabolic versatility, and some of the most thermophilic thermoacidophiles reported to date. DA - 2020/3// PY - 2020/3// DO - 10.1128/MRA.01490-19 VL - 9 IS - 11 SP - SN - 2576-098X ER - TY - JOUR TI - Brassica carinata genotypes demonstrate potential as a winter biofuel crop in South East United States AU - Kumar, Shivendra AU - Seepaul, Ramdeo AU - Mulvaney, Michael J. AU - Colvin, Blaire AU - George, Sheeja AU - Marois, Jim J. AU - Bennett, Rick AU - Leon, Ramon AU - Wright, David L. AU - Small, Ian M. T2 - Industrial Crops and Products AB - Brassica carinata A. Braun, grown as a winter crop on underutilized agricultural land in the southeast United States (SE US), may provide a new rotation alternative and augment income for producers. Widespread adoption of Brassica carinata as a winter crop in the SE US requires varieties with cold tolerance, acceptable and stable seed yield, oil content, protein content so that the crop will be complementary with the normal cultivation of summer crops such as cotton (Gossypium hirsutum L.), corn (Zea mays L.), soybean (Glycine max L. Merr), sorghum (Sorghum bicolor L. Moench) and peanut (Arachis hypogaea L.). The objective of this study was to evaluate the performance of 11 Brassica carinata genotypes for agronomically important traits including seed yield, oil and protein content, oil quality, days to bolting, flowering and maturity at three locations during two growing seasons (2015–2017) as a winter crop in the SE US. Interactions between genotype and environment played a crucial role in overall agronomic performance. This study provides key information on the effect of environmental conditions, such as precipitation and temperature on the agronomic performance of carinata along with generation of information related to region-specific requirements for the crop in the SE US. Days to maturity ranged from 154 to 165 days. The average yield of the 11 genotypes tested ranged from 2814 kg/ha to 3401 kg/ha, which were improved from earlier studies, demonstrating gain due to regional selection and breeding efforts. Total oil content ranged from 42.0 % to 52.4 %, while the erucic acid (C22:1) content ranged from 40.7 % to 42.9 % on a whole seed basis. Based on these results, specific genotypes with consistently high seed yield, oil, erucic acid and protein content with shorter life cycle irrespective of location or year were identified. Brassica carinata has potential as a viable bioenergy winter crop to be integrated into the cropping systems in the SE US and other regions of the world. DA - 2020/8// PY - 2020/8// DO - 10.1016/j.indcrop.2020.112353 VL - 150 SP - 112353 UR - https://doi.org/10.1016/j.indcrop.2020.112353 KW - Biofuels KW - Renewable KW - Aviation jet fuel KW - Bio-based products KW - Oil seed ER - TY - JOUR TI - The Internal, External and Extended Microbiomes of Hominins AU - Dunn, Robert R. AU - Amato, Katherine R. AU - Archie, Elizabeth A. AU - Arandjelovic, Mimi AU - Crittenden, Alyssa N. AU - Nichols, Lauren M. T2 - FRONTIERS IN ECOLOGY AND EVOLUTION AB - The social structure of primates has recently been shown to influence the composition of their microbiomes. What is less clear is how the microbiome composition of primates might influence their social behavior, either in general or with particular reference to hominins. Here we use a comparative approach to understand how microbiomes of hominins have, or might have, changed since the last common ancestor of chimpanzees and humans, roughly six million years ago. We focus on microbiomes associated with social evolution, namely those hosted or influenced by stomachs, intestines, armpits, and food fermentation. In doing so, we highlight the potential influence of microbiomes in hominin evolution while also offering a series of hypotheses and questions with regard to evolution of human stomach acidity, the factors structuring gut microbiomes, the functional consequences of changes in armpit ecology, and whether Homo erectus was engaged in fermentation. We conclude by briefly considering the possibility that hominin social behavior was influenced by prosocial microbes whose fitness was favored by social interactions among individual hominins. DA - 2020/2/19/ PY - 2020/2/19/ DO - 10.3389/fevo.2020.00025 VL - 8 SP - SN - 2296-701X KW - fermentation KW - primates KW - prosocial microbes KW - feces KW - food KW - armpits KW - alcohol ER - TY - JOUR TI - Ecological clusters based on responses of soil microbial phylotypes to precipitation explain ecosystem functions AU - Wu, Ying AU - Wu, Jianping AU - Saleem, Muhammad AU - Wang, Bing AU - Hu, Shuijin AU - Bai, Yongfei AU - Pan, Qingmin AU - Chen, Dima T2 - SOIL BIOLOGY & BIOCHEMISTRY AB - Ecological classification has been proposed as a way to more tightly link microbial communities and ecosystem functions, but few studies have attempted to relate ecological classifications of microbial communities with specific ecosystem functions. Here, we conducted a 3-year experiment with nine levels of artificial precipitation (100–500 mm) in a typical semi-arid steppe. The first five levels (≤300 mm) were considered a “dry” gradient, and the last five (≥300 mm) were considered a “wet” gradient. Increases in precipitation under dry and wet gradients did not alter the alpha diversities of soil bacterial, soil fungal, or plant communities, except that increases in precipitation under the dry gradient decreased bacterial alpha diversity. Increases in precipitation under the dry and wet gradients altered the composition of the soil bacterial community but did not alter the composition of the fungal or plant communities. Ecological clusters (ECs) based on the relationships between the relative abundance of phylotypes and dry and wet gradients were correlated with soil C or N mineralization rates; these ECs explained 14–28% of the total variance in soil C and N mineralization rates. In contrast, soil C or N mineralization rates were not correlated with the commonly measured properties (e.g., biomass and diversity) of plant, soil bacterial, and soil fungal communities. Our findings indicate that the grouping of soil microorganisms into ECs based on responses to precipitation gradients can provide insights into the relationships between soil organisms and ecosystem functions. DA - 2020/3// PY - 2020/3// DO - 10.1016/j.soilbio.2020.107717 VL - 142 SP - SN - 1879-3428 KW - Alpha diversity KW - Asymmetrical pattern KW - Beta diversity KW - Precipitation change KW - Precipitation gradient KW - Soil function ER - TY - JOUR TI - The Role of Expert Disciplinary Cultures in Assessing Risks and Benefits of Synthetic Biology AU - Ndoh, Christina AU - Cummings, Christopher L. AU - Kuzma, Jennifer T2 - SYNTHETIC BIOLOGY 2020: FRONTIERS IN RISK ANALYSIS AND GOVERNANCE AB - Like other technological fields before it, synthetic biology (SB) has been ascribed different definitions by different scholars (Pauwels 2013; Smith 2013; Wang et al. 2013). One commonly used definition of SB is the extraction of living parts for organisms that are then inserted into other organisms to create a “new” organism with parts from the donor and recipient (Benner and Sismour 2005). Synthetic biology has also been described as “the use of computer assisted, biological engineering to design and construct new synthetic biological part” (Hoffman and Newman 2012). Others like the National Science Foundation and the Engineering and Physical Sciences Research Council have noted that synthetic biology is the identification and application of biology in the design of biological parts and systems for use in the creation or redesign of natural biological systems for useful purposes (Engineering and Physical Sciences Research Council 2009). DA - 2020/// PY - 2020/// DO - 10.1007/978-3-030-27264-7_15 SP - 351-370 UR - http://dx.doi.org/10.1007/978-3-030-27264-7_15 ER - TY - JOUR TI - Synthetic Biology: Perspectives on Risk Analysis, Governance, Communication, and ELSI AU - Trump, Benjamin D. AU - Cummings, Christopher L. AU - Galaitsi, S. E. AU - Kuzma, Jennifer AU - Linkov, Igor T2 - SYNTHETIC BIOLOGY 2020: FRONTIERS IN RISK ANALYSIS AND GOVERNANCE AB - Synthetic biology is a technology with incredible promise yet equally galling uncertainty. The United Nations Convention on Biological Diversity defines synthetic biology as “biotechnology that combines science, technology, and engineering to facilitate and accelerate the understanding, design, redesign, manufacture, and/or modification of genetic materials, living organisms, and biological systems” (Convention of Biological Diversity). Synthetic biology can produce entirely new organisms, some of which may pose risks to naturally existing ecosystems. While humans have been selectively breeding plants and animals for millennia, synthetic biology and its enabling technologies allow combining genetic material from organisms that cannot procreate in nature and grant more deliberate and precise control over the selection of genetic processes. DA - 2020/// PY - 2020/// DO - 10.1007/978-3-030-27264-7_1 SP - 1-18 UR - http://dx.doi.org/10.1007/978-3-030-27264-7_1 ER - TY - BOOK TI - Synthetic Biology 2020: Frontiers in Risk Analysis and Governance T2 - Risk, Systems and Decisions A3 - Trump, Benjamin D. A3 - Cummings, Christopher L. A3 - Kuzma, Jennifer A3 - Linkov, Igor DA - 2020/// PY - 2020/// DO - 10.1007/978-3-030-27264-7 PB - Springer International Publishing SN - 9783030272630 9783030272647 UR - http://dx.doi.org/10.1007/978-3-030-27264-7 ER - TY - JOUR TI - Joint laxity varies in response to partial and complete anterior cruciate ligament injuries throughout skeletal growth AU - Cone, Stephanie G. AU - Lambeth, Emily P. AU - Piedrahita, Jorge A. AU - Spang, Jeffrey T. AU - Fisher, Matthew B. T2 - JOURNAL OF BIOMECHANICS AB - Anterior cruciate ligament (ACL) injuries are increasingly common in the skeletally immature population. As such there is a need to increase our understanding of the biomechanical function of the joint following partial and complete ACL injury during skeletal growth. In this work, we aimed to assess changes in knee kinematics and loading of the remaining soft tissues following both partial and complete ACL injury in a porcine model. To do so, we applied anterior-posterior tibial loads and varus-valgus moments to stifle joints of female pigs ranging from early juvenile to late adolescent ages and assessed both kinematics and in-situ loads carried in the bundles of the ACL and other soft tissues including the collateral ligaments and the menisci. Partial ACL injury led to increased anterior tibial translation only in late adolescence and small increases in varus-valgus rotation at all ages. Complete ACL injury led to substantial increases in translation and rotation at all ages. At all ages, the medial collateral ligament and the medial meniscus combined to resist the majority of applied anterior tibial load following complete ACL transection. Across all ages and flexion angles, the contribution of the MCL ranged from 45 to 90% of the anterior load and the contribution of the medial meniscus ranged from 14 to 35% of the anterior load. These findings add to our current understanding of age-specific functional properties of both healthy and injured knees during skeletal growth. DA - 2020/3/5/ PY - 2020/3/5/ DO - 10.1016/j.jbiomech.2020.109636 VL - 101 SP - SN - 1873-2380 KW - Anterior cruciate ligament KW - Pediatric KW - Injury KW - Joint mechanics KW - Animal model ER - TY - JOUR TI - Influence of timing and intensity of weed management on crop yield and contribution to weed emergence in cotton the following year AU - Hare, Andrew T. AU - Jordan, David L. AU - Leon, Ramon G. AU - Edmisten, Keith L. AU - Post, Angela R. AU - Cahoon, Charles W. AU - Everman, Wesley J. AU - Mahoney, Denis J. AU - Inman, Matthew D. T2 - CROP FORAGE & TURFGRASS MANAGEMENT AB - Abstract Adequate weed control is important in protecting crop yield and allowing efficient harvest in North Carolina. Data in the literature are limited with respect to direct comparisons of weed control and yield across multiple crops. Research is also limited in terms of documenting the impact of weed control in one crop on weed populations in the crop planted the following season. Experiments were conducted in North Carolina to determine weed control and yield of corn ( Zea mays L.), cotton ( Gossypium hirsutum L.), and soybean [ Glycine max (L.) Merr.] in the same experiment when herbicides were applied postemergence at different timings (Year 1) and to determine how weed control translated into weed populations and cotton yield the following year (Year 2). Herbicides were applied 2 or 6 wk after planting (WAP); 2 and 4 WAP; 4 and 6 WAP; and 2, 4, and 6 WAP. At Lewiston‐Woodville, common ragweed ( Ambrosia artemisiifolia L.) and Texas millet ( Urochloa texana L.) were present. At Rocky Mount, Palmer amaranth ( Amanthus palmeri S. Wats) and large crabgrass ( Digitaria sanguinalis L.) were present. A single postemergence application of herbicide protected yield from weed interference in corn, whereas in most instances multiple herbicide applications were needed in cotton and to a degree in soybean. Weed densities in Year 2 in cotton were negatively correlated with weed control the previous year in corn, cotton, and soybean. Densities of common ragweed and Palmer amaranth 3 WAP in Year 2 were higher in cotton when the preceding crop was cotton or soybean rather than corn when herbicides were not applied; no difference was noted when comparing cotton and soybean. In some instances, sequential applications of herbicides resulted in lower weed densities the following year in cotton. These results demonstrate the importance of timely, sequential herbicide applications for weed control in cotton and soybean and in some instances the positive benefits on weed populations the following year in cotton. DA - 2020/// PY - 2020/// DO - 10.1002/cft2.20021 VL - 6 IS - 1 SP - SN - 2374-3832 UR - https://doi.org/10.1002/cft2.20021 ER - TY - JOUR TI - Emerging Technologies for Invasive Insects: The Role of Engagement AU - Kokotovich, Adam E AU - Delborne, Jason A AU - Elsensohn, Johanna AU - Burrack, Hannah T2 - Annals of the Entomological Society of America AB - Abstract Emerging technologies have the potential to offer new applications for managing invasive insects. While scientific and technological advancements are vital to realizing this potential, the successful development and use of these applications will also largely depend on community and stakeholder engagement. To contribute to a relevant and rigorous envisioning of engagement for emerging technologies for invasive insects (ETII), we begin by reviewing key insights on engagement from three scholarly fields: invasive species management, responsible research and innovation, and ecological risk assessment. Across these fields we glean best practices for engagement for ETII: 1) pursue engagement across decision phases and sectors; 2) select context-appropriate participants and methods; and 3) recognize and navigate engagement-related tensions. We illustrate these best practices by describing an ongoing project that uses engagement to inform risk assessment and broader decision making on biotechnologies being developed to address the Spotted-wing Drosophila (Drosophila suzukii) invasive fruit fly. We describe completed and planned engagement activities designed to identify and prioritize potential adverse effects, benefits, management actions, and research actions of the proposed genetically engineered sterile male, gene drive, and RNAi biotechnologies. In the face of broadening calls for engagement on emerging technologies, this article provides theoretical and empirical insights that can guide future engagement for ETII. DA - 2020/3/16/ PY - 2020/3/16/ DO - 10.1093/aesa/saz064 VL - 113 IS - 4 SP - 266-279 LA - en OP - SN - 0013-8746 1938-2901 UR - http://dx.doi.org/10.1093/aesa/saz064 DB - Crossref KW - responsible research and innovation KW - ecological risk assessment KW - invasive species management KW - community and stakeholder engagement KW - Drosophila suzukii ER - TY - JOUR TI - International linkages, technology transfer, and the skilled labor wage share: Evidence from plant-level data in Indonesia AU - Yasar, Mahmut AU - Rejesus, Roderick M. T2 - WORLD DEVELOPMENT AB - This paper examines whether technology transfer through international linkages (such as the importing of intermediate inputs and foreign direct investments) influences skilled labor wage shares in Indonesian plants. Using a variety of specifications, estimators, and robustness checks (including Correlated Random Effects Probit, quantile fixed effects regression, and a moment-based instrumental variable (IV) approach), we find that the import of intermediate inputs and foreign direct investment likely facilitate the transfer of technologies from advanced nations, which then results in skill-biased technological change and increased relative skilled labor wage share. These results indicate that, contrary to standard trade theory predictions, international linkages can lead to increased demand for skilled labor and a potential widening of the skilled-unskilled labor wage gap in Indonesia. Our findings support the theoretical explanation provided by Acemoglu (2003). Since firms in developing countries like Indonesia mainly rely on technologies from advanced nations, trade is likely to increase (rather than decrease) the skilled wage premium. DA - 2020/4// PY - 2020/4// DO - 10.1016/j.worlddev.2019.104847 VL - 128 ER - TY - JOUR TI - Gridlock and beltways: the genetic context of urban invasions T2 - Oecologia DA - 2020/3// PY - 2020/3// DO - 10.1007/s00442-020-04614-y UR - http://dx.doi.org/10.1007/s00442-020-04614-y KW - Synthesis KW - Population genetics KW - Landscape genetics KW - Invasive species KW - Urban ecosystems ER - TY - JOUR TI - Improving Cancer Drug Discovery by Studying Cancer across the Tree of Life AU - Somarelli, Jason A. AU - Boddy, Amy M. AU - Gardner, Heather L. AU - DeWitt, Suzanne Bartholf AU - Tuohy, Joanne AU - Megquier, Kate AU - Sheth, Maya U. AU - Hsu, Shiaowen David AU - Thorne, Jeffrey L. AU - London, Cheryl A. AU - Eward, William C. T2 - MOLECULAR BIOLOGY AND EVOLUTION AB - Abstract Despite a considerable expenditure of time and resources and significant advances in experimental models of disease, cancer research continues to suffer from extremely low success rates in translating preclinical discoveries into clinical practice. The continued failure of cancer drug development, particularly late in the course of human testing, not only impacts patient outcomes, but also drives up the cost for those therapies that do succeed. It is clear that a paradigm shift is necessary if improvements in this process are to occur. One promising direction for increasing translational success is comparative oncology—the study of cancer across species, often involving veterinary patients that develop naturally-occurring cancers. Comparative oncology leverages the power of cross-species analyses to understand the fundamental drivers of cancer protective mechanisms, as well as factors contributing to cancer initiation and progression. Clinical trials in veterinary patients with cancer provide an opportunity to evaluate novel therapeutics in a setting that recapitulates many of the key features of human cancers, including genomic aberrations that underly tumor development, response and resistance to treatment, and the presence of comorbidities that can affect outcomes. With a concerted effort from basic scientists, human physicians and veterinarians, comparative oncology has the potential to enhance the cost-effectiveness and efficiency of pipelines for cancer drug discovery and other cancer treatments. DA - 2020/1// PY - 2020/1// DO - 10.1093/molbev/msz254 VL - 37 IS - 1 SP - 11-17 SN - 1537-1719 KW - veterinary oncology KW - cross-species studies KW - cancer drug discovery KW - evolutionary biology ER - TY - JOUR TI - Identification of an SCPL Gene Controlling Anthocyanin Acylation in Carrot (Daucus carota L.) Root AU - Curaba, Julien AU - Bostan, Hamed AU - Cavagnaro, Pablo F. AU - Senalik, Douglas AU - Mengist, Molla Fentie AU - Zhao, Yunyang AU - Simon, Philipp W. AU - Iorizzo, Massimo T2 - FRONTIERS IN PLANT SCIENCE AB - Anthocyanins are natural health promoting pigments that can be produced in large quantities in some purple carrot cultivars. Decoration patterns of anthocyanins, such as acylation, can greatly influence their stability and biological properties and use in the food industry as nutraceuticals and natural colorants. Despite recent advances made towards understanding the genetic control of anthocyanin accumulation in purple carrot, the genetic mechanism controlling acylation of anthocyanin in carrot root have not been studied yet. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify the genetic factor conditioning the accumulation of non-acylated (Cy3XGG) versus acylated (Cy3XFGG and Cy3XSGG) cyanidin derivatives, in three carrot populations. Segregation and mapping analysis pointed to a single gene with dominant effect controlling anthocyanin acylation in the root, located in a 576kb region containing 29 predicted genes. Orthologous and phylogenetic analyses enabled the identification of a cluster of three SCPL-acyltransferases coding genes within this region. Comparative transcriptome analysis indicated that only one of these three genes, DcSCPL1, was always expressed in association with anthocyanin pigmentation in the root and was co-expressed with DcMYB7, a gene known to activate anthocyanin biosynthetic genes in carrot. DcSCPL1 sequence analysis, in root tissue containing a low level of acylated anthocyanins, demonstrated the presence of an insertion causing an abnormal splicing of the 3rd exon during mRNA editing, likely resulting in the production of a non-functional acyltransferase and explaining the reduced acylation phenotype. This study provides strong linkage-mapping and functional evidences for the candidacy of DcSCPL1 as a primary regulator of anthocyanin acylation in carrot storage root. DA - 2020/1/31/ PY - 2020/1/31/ DO - 10.3389/fpls.2019.01770 VL - 10 SP - SN - 1664-462X KW - Daucus carota L KW - anthocyanins KW - acyltransferase KW - fine mapping KW - transcriptome KW - candidate genes ER - TY - JOUR TI - Soybean Host Plant Resistance to Megacopta cribraria (Hemiptera: Plataspidae) and the Potential Role of Leaf Trichome Density AU - Lahiri, S AU - Reisig, D D AU - Reay-Jones, F P F AU - Greene, J K AU - Carter, T E, Jr AU - Mian, R AU - Fallen, B D T2 - Environmental Entomology AB - Abstract Megacopta cribraria (F.) (Hemiptera: Plataspidae) is an invasive pest of soybean that has spread across the southeastern United States since its initial discovery in 2009 in Georgia. Previous studies in the southeastern states have documented both the population dynamics of this pest and host plant resistance (HPR) among soybean varieties, although the specific mechanisms of HPR remain unknown. The objectives of this study were, therefore, to 1) quantify field resistance to M. cribraria in multiple soybean varieties in two states previously affected by severe M. cribraria infestations, North Carolina (NC) and South Carolina (SC); and 2) study the role of soybean trichome density in imparting resistance against M. cribraria. Soybean variety ‘Camp’ was least attractive to M. cribraria, through time and locations, suggesting consistent resistance. Other varieties showed variable performance among the locations and sampling dates. A significant difference in trichome density was evident. However, there was no correlation between trichome density and M. cribraria infestation. Compared to a previously published study in the same location, when M. cribraria adults emerging from overwintering dispersed into soybeans, in our study only first-generation adults dispersed into soybeans. Considering the current trend of significantly lower M. cribraria infestation rates in North and South Carolina, this pest may be finally succumbing to indigenous natural enemies and should be managed by incorporating integrated pest management tactics, such as HPR, that help conserve natural enemy populations. DA - 2020/1/6/ PY - 2020/1/6/ DO - 10.1093/ee/nvz158 VL - 49 IS - 1 SP - 88-97 LA - en OP - SN - 0046-225X 1938-2936 UR - http://dx.doi.org/10.1093/ee/nvz158 DB - Crossref KW - kudzu bug KW - population dynamics KW - susceptible ER - TY - JOUR TI - Effects of Interspecific Larval Competition on Developmental Parameters in Nutrient Sources Between Drosophila suzukii (Diptera: Drosophilidae) and Zaprionus indianus AU - Shrader, Meredith AU - Burrack, Hannah J. AU - Pfeiffer, Doug T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - Abstract Two invasive drosophilids, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) and Zaprionus indianus (Gupta) (Diptera: Drosophilidae) are expanding their geographic distribution and cohabiting grape production in the Mid-Atlantic. The ecological and economic impact of these two species within vineyards is currently unknown. Zaprionus indianus was presumably not capable of ovipositing directly into grapes because they lack a serrated ovipositor and may use D. suzukii oviposition punctures for depositing their own eggs. Therefore, an interspecific larval competition assay was performed at varying larval densities using commercial medium and four commonly grown wine grapes in Virginia to investigate the impact Z. indianus larvae may have on the mortality and developmental parameters of D. suzukii larvae. Zaprionus indianus did not affect D. suzukii mortality or development parameters even at high interspecific densities when reared in commercial medium, but it did cause higher D. suzukii mortality within grapes. Mortality was also influenced by the variety of grape in which the larvae were reared, with smaller grapes having the highest D. suzukii mortality. Presence of Z. indianus also increased development time to pupariation and adult emergence for most interspecific competition levels compared with the intraspecific D. suzukii controls. Pupal volume was marginally affected at the highest interspecific larval densities. This laboratory study suggests that competition from Z. indianus and grape variety can limit D. suzukii numbers, and the implications on D. suzukii pest management be further verified in the field. DA - 2020/2// PY - 2020/2// DO - 10.1093/jee/toz297 VL - 113 IS - 1 SP - 230-238 SN - 1938-291X KW - interspecific competition KW - intraspecific competition KW - wine grapes KW - medium KW - pupal volume ER - TY - JOUR TI - Dueling metaphors, fueling futures: “Bridge fuel” visions of coal and natural gas in the United States AU - Delborne, Jason A. AU - Hasala, Dresden AU - Wigner, Aubrey AU - Kinchy, Abby T2 - Energy Research & Social Science AB - Since at least the 1970s, the idea that certain fossil fuels represent transitional fuels on the way to a lower-carbon energy future has persisted in energy discourse. In particular, natural gas has come to occupy a new identity in this discourse, shifting from what was once a negligible portion of the energy mix in the United States to one of the nation's most important energy resources. Though the “bridge fuel” metaphor was once fairly unambiguous in its meaning, the term has evolved over time to incorporate many visions of the future roles of coal and natural gas in the energy mix. To probe the variety of these meanings in public discourse, we assess the bridge fuel narrative in news articles and government publications as a means to understand the complexity and context of political debates over the unfolding future of natural gas. Using a qualitative coding scheme, we examine five different interpretations of the bridge fuel metaphor between 1988 and 2016. We argue that with its unique quality of facilitating both consensus-building and contestation, the bridge fuel metaphor's simplicity and accessibility belie its power to reveal changing expectations, values, and visions of the future of American energy. DA - 2020/3// PY - 2020/3// DO - 10.1016/j.erss.2019.101350 VL - 61 SP - 101350 J2 - Energy Research & Social Science LA - en OP - SN - 2214-6296 UR - http://dx.doi.org/10.1016/j.erss.2019.101350 DB - Crossref KW - Fossil fuels KW - Natural gas KW - Energy policy KW - Energy transition KW - Renewable energy KW - Policy metaphor ER - TY - JOUR TI - Green infrastructure site selection in the Walnut Creek wetland community: A case study from southeast Raleigh, North Carolina AU - Hasala, Dresden AU - Supak, Stacy AU - Rivers, Louie T2 - LANDSCAPE AND URBAN PLANNING AB - Recent findings have shown that minority communities are frequently underserved by green infrastructure developments relative to non-minority communities, as local installations of green infrastructure often follow patterns of gentrification. Antipathy from these communities toward existing environmental management efforts present further obstacles related to green infrastructure placement. While hydrologic modeling has been highly utilized in decision support for green infrastructure placement, this technique does not consider ownership, access concerns, or the importance of visibility. Alternatively, participatory geographic information systems (PPGIS) can provide a different perspective from hydrologic models, as they have the potential to forecast community perceptions of green infrastructure utility, rather than hydrological benefit. We use a mixed-methods approach to optimize green infrastructure site-selection that considers hydrologic vulnerabilities in the context of place-based knowledge and historical realities. Residents’ perceptions of the locations of nuisance flooding were reported via participatory mapping within a paper-based survey (n = 95) conducted in the communities surrounding Walnut Creek, a historically African-American community in Raleigh, North Carolina. Hotspot analysis was used to identify statistically significant clustering, which was related to a correspondence between participant-indicated nuisance flooding sites and high flow accumulation cells. Comparison of the participatory and hydrologic hotspot analyses show some geospatial overlap for potential green infrastructure placement. We propose that, when undertaken with community input, green infrastructure installation in these downstream areas may help offset localized flooding patterns while facilitating greater trust with stormwater and environmental practitioners. DA - 2020/4// PY - 2020/4// DO - 10.1016/j.landurbplan.2020.103743 VL - 196 SP - SN - 1872-6062 KW - Green infrastructure KW - Participatory mapping KW - Minority communities KW - Urban planning KW - Flooding KW - Locally undesirable land uses (LULUs) ER - TY - JOUR TI - Highly tunable bioadhesion and optics of 3D printable PNIPAm/cellulose nanofibrils hydrogels AU - Sun, Xiaohang AU - Tyagi, Preeti AU - Agate, Sachin AU - McCord, Marian G. AU - Lucia, Lucian A. AU - Pal, Lokendra T2 - CARBOHYDRATE POLYMERS AB - A hybrid poly(N-isopropylacrylamide) (PNIPAm)/cellulose nanofibrils (CNFs) hydrogel composite was fabricated by inverted stereolithography 3D printing to provide a new platform for regulating lower critical solution temperature (LCST) properties and thus tuning optical and bioadhesive properties. The phenomena of interest in the as-printed PNIPAm/CNF hydrogels may be attributed to the fiber-reinforced composite system between crosslinked PNIPAm and CNFs. The optical tunability was found to be correlated to the micro/nano structures of the PNIPAm/CNF hydrogel films. It was found that PNIPAm/CNF hydrogels exhibit switchable bioadhesivity to bacteria in response to CNF distribution in the hydrogels. After 2.0 wt% CNF was incorporated, it was found that a remarkable 8°C reduction of the LCST was achieved relative to PNIPAm hydrogel crosslinked by TEGDMA without CNF. The prepared PNIPAm/CNF hydrogels possessed highly reversible optical, bioadhesion, and thermal performance, making them suitable to be used as durable temperature-sensitive sensors and functional biomedical devices. DA - 2020/4/15/ PY - 2020/4/15/ DO - 10.1016/j.carbpol.2020.115898 VL - 234 SP - SN - 1879-1344 KW - Stimuli-responsive materials KW - Tunable transparency KW - Switchable bioadhesion KW - Hydrogels KW - Cellulose nanofibrils (CNFs) KW - Poly(N-isopropylacrylamide) (PNIPAm) KW - Inverted stereolithography KW - 3D printing ER - TY - JOUR TI - Achieving Net Zero Energy Greenhouses by Integrating Semitransparent Organic Solar Cells AU - Ravishankar, Eshwar AU - Booth, Ronald E. AU - Saravitz, Carole AU - Sederoff, Heike AU - Ade, Harald W. AU - Brendan T. O'Connor, T2 - JOULE AB - Greenhouses vastly increase agricultural land-use efficiency. However, they also consume significantly more energy than conventional farming due in part to conditioning the greenhouse space. One way to mitigate the increase in energy consumption is to integrate solar modules onto the greenhouse structure. Semitransparent organic solar cells (OSCs) are particularly attractive given that their spectral absorption can be tuned to minimize the attenuation of sunlight over the plants photosynthetically active spectrum. Here, the benefits of integrating OSCs on the net energy demand of greenhouses within the U.S. are determined through a detailed energy balance model. We find that these systems can have an annual surplus of energy in warm and moderate climates. Furthermore, we show that sunlight reduction entering the greenhouse can be minimized with appropriate design. These results demonstrate that OSCs are an excellent candidate for implementing in greenhouses and provide an opportunity to diversify sustainable energy generation technology. DA - 2020/2/19/ PY - 2020/2/19/ DO - 10.1016/j.joule.2019.12.018 VL - 4 IS - 2 SP - 490-506 SN - 2542-4351 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85079138223&partnerID=MN8TOARS ER - TY - JOUR TI - Development of a relative quantification method for infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging of Arabidopsis seedlings AU - Bagley, M. Caleb AU - Stepanova, Anna N. AU - Ekelof, Mans AU - Alonso, Jose M. AU - Muddiman, David C. T2 - RAPID COMMUNICATIONS IN MASS SPECTROMETRY AB - Mass spectrometry imaging of young seedlings is an invaluable tool in understanding how mutations affect metabolite accumulation in plant development. However, due to numerous biological considerations, established methods for the relative quantification of analytes using infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging are not viable options. In this study, we report a method for the quantification of auxin-related compounds using stable-isotope-labelled (SIL) indole-3-acetic acid (IAA) doped into agarose substrate.Wild-type Arabidopsis thaliana seedlings, sur2 and wei8 tar2 loss-of-function mutants, and YUC1 gain-of-function line were grown for 3 days in the dark in standard growth medium. SIL-IAA was doped into a 1% low-melting-point agarose gel and seedlings were gently laid on top for IR-MALDESI imaging with Orbitrap mass spectrometry analysis. Relative quantification was performed post-acquisition by normalization of auxin-related compounds to SIL-IAA in the agarose. Amounts of auxin-related compounds were compared between genotypes to distinguish the effects of the mutations on the accumulation of indolic metabolites of interest.IAA added to agarose was found to remain stable, with repeatability and abundance features of IAA comparable with those of other compounds used in other methods for relative quantification in IR-MALDESI analyses. Indole-3-acetaldoxime was increased in sur2 mutants compared with wild-type and other mutants. Other auxin-related metabolites were either below the limits of quantification or successfully quantified but showing little difference among mutants.Agarose was shown to be an appropriate sampling surface for IR-MALDESI mass spectrometry imaging of Arabidopsis seedlings. SIL-IAA doping of agarose was demonstrated as a viable technique for relative quantification of metabolites in live seedlings or tissues with similar biological considerations. DA - 2020/3/30/ PY - 2020/3/30/ DO - 10.1002/rcm.8616 VL - 34 IS - 6 SP - SN - 1097-0231 ER - TY - JOUR TI - In Vivo Targeting of Clostridioides difficile Using Phage-Delivered CRISPR-Cas3 Antimicrobials AU - Selle, Kurt AU - Fletcher, Joshua R. AU - Tuson, Hannah AU - Schmitt, Daniel S. AU - McMillan, Lana AU - Vridhambal, Gowrinarayani S. AU - Rivera, Alissa J. AU - Montgomery, Stephanie A. AU - Fortier, Louis-Charles AU - Barrangou, Rodolphe AU - Theriot, Casey M. AU - Ousterout, David G. T2 - mBio AB - Clostridioides difficile is an important nosocomial pathogen that causes approximately 500,000 cases of C. difficile infection (CDI) and 29,000 deaths annually in the United States. Antibiotic use is a major risk factor for CDI because broad-spectrum antimicrobials disrupt the indigenous gut microbiota, decreasing colonization resistance against C. difficile Vancomycin is the standard of care for the treatment of CDI, likely contributing to the high recurrence rates due to the continued disruption of the gut microbiota. Thus, there is an urgent need for the development of novel therapeutics that can prevent and treat CDI and precisely target the pathogen without disrupting the gut microbiota. Here, we show that the endogenous type I-B CRISPR-Cas system in C. difficile can be repurposed as an antimicrobial agent by the expression of a self-targeting CRISPR that redirects endogenous CRISPR-Cas3 activity against the bacterial chromosome. We demonstrate that a recombinant bacteriophage expressing bacterial genome-targeting CRISPR RNAs is significantly more effective than its wild-type parent bacteriophage at killing C. difficile both in vitro and in a mouse model of CDI. We also report that conversion of the phage from temperate to obligately lytic is feasible and contributes to the therapeutic suitability of intrinsic C. difficile phages, despite the specific challenges encountered in the disease phenotypes of phage-treated animals. Our findings suggest that phage-delivered programmable CRISPR therapeutics have the potential to leverage the specificity and apparent safety of phage therapies and improve their potency and reliability for eradicating specific bacterial species within complex communities, offering a novel mechanism to treat pathogenic and/or multidrug-resistant organisms.IMPORTANCEClostridioides difficile is a bacterial pathogen responsible for significant morbidity and mortality across the globe. Current therapies based on broad-spectrum antibiotics have some clinical success, but approximately 30% of patients have relapses, presumably due to the continued perturbation to the gut microbiota. Here, we show that phages can be engineered with type I CRISPR-Cas systems and modified to reduce lysogeny and to enable the specific and efficient targeting and killing of C. difficilein vitro and in vivo. Additional genetic engineering to disrupt phage modulation of toxin expression by lysogeny or other mechanisms would be required to advance a CRISPR-enhanced phage antimicrobial for C. difficile toward clinical application. These findings provide evidence into how phage can be combined with CRISPR-based targeting to develop novel therapies and modulate microbiomes associated with health and disease. DA - 2020/4/28/ PY - 2020/4/28/ DO - 10.1128/mBio.00019-20 VL - 11 IS - 2 UR - https://doi.org/10.1128/mBio.00019-20 ER - TY - JOUR TI - Is Science for Me? Promoting Science Identity Following Climate Change Disasters in College Students T2 - figshare DA - 2020/// PY - 2020/// DO - 10.6084/m9.figshare.11908338 ER - TY - JOUR TI - Is Science for Me? Promoting Science Identity Following Climate Change Disasters in College Students T2 - figshare DA - 2020/// PY - 2020/// DO - 10.6084/m9.figshare.11908338.v1 ER - TY - JOUR TI - Can Informal Learning Help Promote Science Identity And Learning In College Students Impacted By Climate Change Disasters? T2 - figshare DA - 2020/// PY - 2020/// DO - 10.6084/m9.figshare.11916759 ER - TY - JOUR TI - Can Informal Learning Help Promote Science Identity And Learning In College Students Impacted By Climate Change Disasters? T2 - figshare DA - 2020/// PY - 2020/// DO - 10.6084/m9.figshare.11916759.v1 ER - TY - JOUR TI - Forests After Florence: Application of 360° Photography and Oral History to Document Hurricane Impacts on Urban Forests and Communities in Coastal North Carolina T2 - figshare DA - 2020/// PY - 2020/// DO - 10.6084/m9.figshare.11908011 ER - TY - JOUR TI - Forests After Florence: Application of 360° Photography and Oral History to Document Hurricane Impacts on Urban Forests and Communities in Coastal North Carolina T2 - figshare DA - 2020/// PY - 2020/// DO - 10.6084/m9.figshare.11908011.v1 ER - TY - JOUR TI - Gene content evolution in the arthropods AU - Thomas, Gregg W. C. AU - Dohmen, Elias AU - Hughes, Daniel S. T. AU - Murali, Shwetha C. AU - Poelchau, Monica AU - Glastad, Karl AU - Anstead, Clare A. AU - Ayoub, Nadia A. AU - Batterham, Phillip AU - Bellair, Michelle AU - Binford, Greta J. AU - Chao, Hsu AU - Chen, Yolanda H. AU - Childers, Christopher AU - Dinh, Huyen AU - Doddapaneni, Harsha Vardhan AU - Duan, Jian J. AU - Dugan, Shannon AU - Esposito, Lauren A. AU - Friedrich, Markus AU - Garb, Jessica AU - Gasser, Robin B. AU - Goodisman, Michael A. D. AU - Gundersen-Rindal, Dawn E. AU - Han, Yi AU - Handler, Alfred M. AU - Hatakeyama, Masatsugu AU - Hering, Lars AU - Hunter, Wayne B. AU - Ioannidis, Panagiotis AU - Jayaseelan, Joy C. AU - Kalra, Divya AU - Khila, Abderrahman AU - Korhonen, Pasi K. AU - Lee, Carol Eunmi AU - Lee, Sandra L. AU - Li, Yiyuan AU - Lindsey, Amelia R. I. AU - Mayer, Georg AU - McGregor, Alistair P. AU - McKenna, Duane D. AU - Misof, Bernhard AU - Munidasa, Mala AU - Munoz-Torres, Monica AU - Muzny, Donna M. AU - Niehuis, Oliver AU - Osuji-Lacy, Nkechinyere AU - Palli, Subba R. AU - Panfilio, Kristen A. AU - Pechmann, Matthias AU - Perry, Trent AU - Peters, Ralph S. AU - Poynton, Helen C. AU - Prpic, Nikola-Michael AU - Qu, Jiaxin AU - Rotenberg, Dorith AU - Schal, Coby AU - Schoville, Sean D. AU - Scully, Erin D. AU - Skinner, Evette AU - Sloan, Daniel B. AU - Stouthamer, Richard AU - Strand, Michael R. AU - Szucsich, Nikolaus U. AU - Wijeratne, Asela AU - Young, Neil D. AU - Zattara, Eduardo E. AU - Benoit, Joshua B. AU - Zdobnov, Evgeny M. AU - Pfrender, Michael E. AU - Hackett, Kevin J. AU - Werren, John H. AU - Worley, Kim C. AU - Gibbs, Richard A. AU - Chipman, Ariel D. AU - Waterhouse, Robert M. AU - Bornberg-Bauer, Erich AU - Hahn, Matthew W. AU - Richards, Stephen T2 - GENOME BIOLOGY AB - Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception.These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity. DA - 2020/1/23/ PY - 2020/1/23/ DO - 10.1186/s13059-019-1925-7 VL - 21 IS - 1 SP - SN - 1474-760X KW - Arthropods KW - Genome assembly KW - Genomics KW - Protein domains KW - Gene content KW - Evolution KW - DNA methylation ER - TY - JOUR TI - Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants AU - Makarova, Kira S. AU - Wolf, Yuri I AU - Iranzo, Jaime AU - Shmakov, Sergey A. AU - Alkhnbashi, Omer S. AU - Brouns, Stan J. J. AU - Charpentier, Emmanuelle AU - Cheng, David AU - Haft, Daniel H. AU - Horvath, Philippe AU - Moineau, Sylvain AU - Mojica, Francisco J. M. AU - Scott, David AU - Shah, Shiraz A. AU - Siksnys, Virginijus AU - Terns, Michael P. AU - Venclovas, Ceslovas AU - White, Malcolm F. AU - Yakunin, Alexander F. AU - Yan, Winston AU - Zhang, Feng AU - Garrett, Roger A. AU - Backofen, Rolf AU - Oost, John AU - Barrangou, Rodolphe AU - Koonin, Eugene V T2 - NATURE REVIEWS MICROBIOLOGY AB - The number and diversity of known CRISPR-Cas systems have substantially increased in recent years. Here, we provide an updated evolutionary classification of CRISPR-Cas systems and cas genes, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015. The new classification includes 2 classes, 6 types and 33 subtypes, compared with 5 types and 16 subtypes in 2015. A key development is the ongoing discovery of multiple, novel class 2 CRISPR-Cas systems, which now include 3 types and 17 subtypes. A second major novelty is the discovery of numerous derived CRISPR-Cas variants, often associated with mobile genetic elements that lack the nucleases required for interference. Some of these variants are involved in RNA-guided transposition, whereas others are predicted to perform functions distinct from adaptive immunity that remain to be characterized experimentally. The third highlight is the discovery of numerous families of ancillary CRISPR-linked genes, often implicated in signal transduction. Together, these findings substantially clarify the functional diversity and evolutionary history of CRISPR-Cas. DA - 2020/2// PY - 2020/2// DO - 10.1038/s41579-019-0299-x VL - 18 IS - 2 SP - 67-83 SN - 1740-1534 ER - TY - JOUR TI - Exploratory behaviour is associated with microhabitat and evolutionary radiation in Lake Malawi cichlids AU - Johnson, Zachary V AU - Moore, Emily C. AU - Wong, Ryan Y. AU - Godwin, John R. AU - Streelman, Jeffrey T. AU - Roberts, Reade B. T2 - ANIMAL BEHAVIOUR AB - Encountering and adaptively responding to unfamiliar or novel stimuli is a fundamental challenge facing animals and is linked to fitness. Behavioural responses to novel stimuli can differ strongly between closely related species; however, the ecological and evolutionary factors underlying these differences are not well understood, in part because most comparative investigations have focused on only two species. In this study, we investigate behavioural responses to novel environments, or exploratory behaviours, sampling from a total of 20 species in a previously untested vertebrate system, Lake Malawi cichlid fishes, which comprises hundreds of phenotypically diverse species that have diverged in the past one million years. We show generally conserved behavioural response patterns to different types of environmental stimuli in Lake Malawi cichlids, spanning multiple assays and paralleling other teleost and rodent lineages. Next, we demonstrate that more specific dimensions of exploratory behaviour vary strongly among Lake Malawi cichlids, and that a large proportion of this variation is explained by species differences. We further show that species differences in open field behaviours are explained by microhabitat and by a major evolutionary split between the mbuna and benthic/utaka radiations in Lake Malawi. Lastly, we track some individuals across a subset of behavioural assays and show that patterns of behavioural covariation across contexts are characteristic of modular complex traits. Taken together, our results tie ecology and evolution to natural behavioural variation, and highlight Lake Malawi cichlids as a powerful system for understanding the biological basis of exploratory behaviours. DA - 2020/2// PY - 2020/2// DO - 10.1016/j.anbehav.2019.11.006 VL - 160 SP - 121-134 SN - 1095-8282 KW - behavioural integration KW - behavioural modularity KW - habitat preference KW - light-dark KW - novel stimuli KW - novel tank KW - open field KW - scototaxis KW - stress response KW - thigmotaxis ER - TY - JOUR TI - The biology and biotechnology of the genus Caldicellulosiruptor: recent developments in 'Caldi World' AU - Lee, Laura L. AU - Crosby, James R. AU - Rubinstein, Gabriel M. AU - Laemthong, Tunyaboon AU - Bing, Ryan G. AU - Straub, Christopher T. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - EXTREMOPHILES DA - 2020/1// PY - 2020/1// DO - 10.1007/s00792-019-01116-5 VL - 24 IS - 1 SP - 1-15 SN - 1433-4909 KW - Caldicellulosiruptor KW - Extreme thermophiles KW - Lignocellulose ER - TY - JOUR TI - Contract elements, growing conditions, and anomalous claims behaviour in US crop insurance AU - Park, Sungkwol AU - Goodwin, Barry K. AU - Zheng, Xiaoyong AU - Rejesus, Roderick M. T2 - GENEVA PAPERS ON RISK AND INSURANCE-ISSUES AND PRACTICE AB - We investigate contract elements and growing conditions associated with anomalous claims behaviour in the U.S. Federal Crop Insurance Program. In this study the measure of “anomalous claims behaviour” is based on the number of producers (in a county) placed on the “Spot Check List” (SCL)—a list generated from government compliance efforts that aim to detect and deter fraud, waste, and abuse in the U.S. Federal Crop Insurance Program. Using county-level data and various econometric approaches that control for features of this data set (e.g., the count nature of the dependent variable, censoring, potential endogeneity, and spatial/temporal dependence), we find that the following crop insurance contract attributes influence the extent of anomalous claims behaviour in a county: (a) the ability to insure individual fields through “optional units”; (b) the coverage level choice; and (c) the total number of acres insured. In addition, our empirical analyses suggest that anomalous claims behaviour significantly increases when extreme weather events occur (e.g., droughts, floods) and when economic conditions are unfavourable (i.e., high input costs that lower profit levels). Results from this study have important implications for addressing potential underwriting vulnerabilities in crop insurance contracts and the frequency of more rigorous compliance inspections. DA - 2020/1// PY - 2020/1// DO - 10.1057/s41288-019-00143-9 VL - 45 IS - 1 SP - 157-183 SN - 1468-0440 KW - Spot Check List KW - Insurance fraud KW - Crop insurance KW - Simulated maximum likelihood estimation KW - Control function approach KW - Block bootstrap ER - TY - JOUR TI - The Development and Validation of a Measure of Science Capital, Habitus, and Future Science Interests AU - Jones, M. Gail AU - Ennes, Megan AU - Weedfall, Drew AU - Chesnutt, Katherine AU - Cayton, Emily T2 - Research in Science Education DA - 2020/1/27/ PY - 2020/1/27/ DO - 10.1007/s11165-020-09916-y VL - 1 J2 - Res Sci Educ LA - en OP - SN - 0157-244X 1573-1898 UR - http://dx.doi.org/10.1007/s11165-020-09916-y DB - Crossref KW - Self-efficacy KW - Science capital KW - Family habitus KW - Career aspirations ER - TY - JOUR TI - Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread AU - Reese, Aspen T. AU - Madden, Anne A. AU - Joossens, Marie AU - Lacaze, Guylaine AU - Dunn, Robert R. T2 - MSPHERE AB - Sourdough starters are complex communities of yeast and bacteria which confer characteristic flavor and texture to sourdough bread. The microbes present in starters can be sourced from ingredients or the baking environment and are typically consistent over time. Herein, we show that even when the recipe and ingredients for starter and bread are identical, different bakers around the globe produce highly diverse starters which then alter bread acidity and flavor. Much of the starter microbial community comes from bread flour, but the diversity is also associated with differences in the microbial community on the hands of bakers. These results indicate that bakers may be a source for yeast and bacteria in their breads and/or that bakers’ jobs are reflected in their skin microbiome. DA - 2020/// PY - 2020/// DO - 10.1128/mSphere.00950-19 VL - 5 IS - 1 SP - SN - 2379-5042 KW - Lactobacillus KW - Saccharomyces KW - skin microbiome KW - sourdough ER - TY - JOUR TI - Achieving CLARITY on bisphenol A, brain and behaviour AU - Patisaul, Heather B. T2 - JOURNAL OF NEUROENDOCRINOLOGY AB - Abstract There is perhaps no endocrine disrupting chemical more controversial than bisphenol A ( BPA ). Comprising a high‐volume production chemical used in a variety of applications, BPA has been linked to a litany of adverse health‐related outcomes, including effects on brain sexual differentiation and behaviour. Risk assessors preferentially rely on classical guideline‐compliant toxicity studies over studies published by academic scientists, and have generally downplayed concerns about the potential risks that BPA poses to human health. It has been argued, however, that, because traditional toxicity studies rarely contain neural endpoints, and only a paucity of endocrine‐sensitive endpoints, they are incapable of fully evaluating harm. To address current controversies on the safety of BPA , the United States National Institute of Environmental Health Sciences, the National Toxicology Program ( NTP ), and the US Food and Drug Administration established the Consortium Linking Academic and Regulatory Insights on BPA Toxicity ( CLARITY ‐ BPA ). CLARITY ‐ BPA performed a classical regulatory‐style toxicology study (Core study) in conjunction with multiple behavioural, molecular and cellular studies conducted by academic laboratories (grantee studies) using a collaboratively devised experimental framework and the same animals and tissues. This review summarises the results from the grantee studies that focused on brain and behaviour. Evidence of altered neuroendocrine development, including age‐ and sex‐specific expression of oestrogen receptor ( ER) α and ERβ, and the abrogation of brain and behavioural sexual dimorphisms, supports the conclusion that developmental BPA exposure, even at doses below what regulatory agencies regard as “safe” for humans, contribute to brain and behavioural change. The consistency and the reproducibility of the effects across CLARITY ‐ BPA and prior studies using the same animal strain and almost identical experimental conditions are compelling. Combined analysis of all of the data from the CLARITY ‐ BPA project is underway at the NTP and a final report expected in late 2019. DA - 2020/1// PY - 2020/1// DO - 10.1111/jne.12730 VL - 32 IS - 1 SP - SN - 1365-2826 KW - amygdala KW - anxiety KW - EDC KW - endocrine disrupting chemical KW - hypothalamus KW - oxytocin ER - TY - JOUR TI - Comparative Analysis of Lactobacillus gasseri and Lactobacillus crispatus Isolated From Human Urogenital and Gastrointestinal Tracts AU - Pan, Meichen AU - Hidalgo-Cantabrana, Claudio AU - Goh, Yong Jun AU - Sanozky-Dawes, Rosemary AU - Barrangou, Rodolphe T2 - FRONTIERS IN MICROBIOLOGY AB - Lactobacillus crispatus and Lactobacillus gasseri are two of the main Lactobacillus species found in the healthy vaginal microbiome and have also previously been identified and isolated from the human gastrointestinal (GI) tract. These two ecological niches are fundamentally different, notably with regards to the epithelial cell type, nutrient availability, environmental conditions, pH and microbiome composition. Given the dramatic differences between these two environments, we characterized strains within the same Lactobacillus species isolated from either the vaginal or intestinal tract to assess whether they are phenotypically and genetically different. We performed a series of comparative phenotypic assays including small intestinal juice and acid resistance, carbohydrate fermentation profiles, lactic acid production, and host interaction with intestinal Caco-2 and vaginal VK2 cell lines. We also developed a simulated vaginal fluid (SVF) to study bacterial growth in a proxy vaginal environment and conducted differential transcriptomic analysis between SVF and standard laboratory MRS medium. Overall, our results show that although strain-specific variation is observed, some phenotypic differences seem associated with the isolation source. We encourage future probiotic formulation to include isolation source and take into consideration genetic and phenotypic features for use at various body sites. DA - 2020/1/22/ PY - 2020/1/22/ DO - 10.3389/fmicb.2019.03146 VL - 10 SP - SN - 1664-302X KW - probiotics KW - niche-specific adaptation KW - Lactobacillus KW - women's health KW - in vitro vaginal fluid model ER - TY - JOUR TI - Regulation of ovule initiation by gibberellins and brassinosteroids in tomato and Arabidopsis: two plant species, two molecular mechanisms AU - Barro‐Trastoy, Daniela AU - Carrera, Esther AU - Baños, Jorge AU - Palau‐Rodríguez, Julia AU - Ruiz‐Rivero, Omar AU - Tornero, Pablo AU - Alonso, José M. AU - López‐Díaz, Isabel AU - Gómez, María Dolores AU - Pérez‐Amador, Miguel A. T2 - The Plant Journal AB - Summary Ovule primordia formation is a complex developmental process with a strong impact on the production of seeds. In Arabidopsis this process is controlled by a gene network, including components of the signalling pathways of auxin, brassinosteroids (BRs) and cytokinins. Recently, we have shown that gibberellins (GAs) also play an important role in ovule primordia initiation, inhibiting ovule formation in both Arabidopsis and tomato. Here we reveal that BRs also participate in the control of ovule initiation in tomato, by promoting an increase on ovule primordia formation. Moreover, molecular and genetic analyses of the co‐regulation by GAs and BRs of the control of ovule initiation indicate that two different mechanisms occur in tomato and Arabidopsis. In tomato, GAs act downstream of BRs. BRs regulate ovule number through the downregulation of GA biosynthesis, which provokes stabilization of DELLA proteins that will finally promote ovule primordia initiation. In contrast, in Arabidopsis both GAs and BRs regulate ovule number independently of the activity levels of the other hormone. Taken together, our data strongly suggest that different molecular mechanisms could operate in different plant species to regulate identical developmental processes even, as for ovule primordia initiation, if the same set of hormones trigger similar responses, adding a new level of complexity. DA - 2020/6// PY - 2020/6// DO - 10.1111/tpj.14684 UR - https://doi.org/10.1111/tpj.14684 KW - Arabidopsis thaliana KW - tomato KW - Solanum lycopersicum KW - gibberellins KW - brassinosteroids KW - ovule KW - reproductive development KW - hormone interaction ER - TY - JOUR TI - High variability within pet foods prevents the identification of native species in pet cats' diets using isotopic evaluation AU - McDonald, Brandon W. AU - Perkins, Troi AU - Dunn, Robert R. AU - McDonald, Jennifer AU - Cole, Holly AU - Feranec, Robert S. AU - Kays, Roland T2 - PEERJ AB - Domestic cats preying on wildlife is a frequent conservation concern but typical approaches for assessing impacts rely on owner reports of prey returned home, which can be biased by inaccurate reporting or by cats consuming prey instead of bringing it home. Isotopes offer an alternative way to quantify broad differences in animal diets. By obtaining samples of pet food from cat owners we predicted that we would have high power to identify cats feeding on wild birds or mammals, given that pet food is thought to have higher C isotope values, due to the pervasive use of corn and/or corn by-products as food ingredients, than native prey. We worked with citizen scientists to quantify the isotopes of 202 cat hair samples and 239 pet food samples from the US and UK. We also characterized the isotopes of 11 likely native prey species from the southeastern US and used mixing models to assess the diet of 47 cats from the same region. Variation in C and N isotope values for cat food was very high, even within the same brand/flavor, suggesting that pet food manufacturers use a wide range of ingredients, and that these may change over time. Cat food and cat hair from the UK had lower C values than the US, presumably reflecting differences in the amount of corn used in the food chains of the two countries. This high variation in pet food reduced our ability to classify cats as hunters of native prey, such that only 43% of the animals could be confidently assigned. If feral or free ranging cats were considered, this uncertainty would be even higher as pet food types would be unknown. Our results question the general assumption that anthropogenic foods always have high C isotope values, because of the high variability we documented within one product type (cat food) and between countries (US vs. UK), and emphasize the need to test a variety of standards before making conclusions from isotope ecology studies. DA - 2020/1/22/ PY - 2020/1/22/ DO - 10.7717/peerj.8337 VL - 8 SP - SN - 2167-8359 KW - Felis catus KW - Carbon KW - Stable isotopes KW - Predation KW - Pet food KW - Nitrogen ER - TY - JOUR TI - Metabotropic glutamate receptor subtype 5 (mGlu(5)) is necessary for estradiol mitigation of light-induced anxiety behavior in female rats AU - Miller, Christiana K. AU - Krentzel, Amanda A. AU - Patisaul, Heather B. AU - Meitzen, John T2 - PHYSIOLOGY & BEHAVIOR AB - Anxiety-related behaviors are influenced by steroid hormones such as 17β-estradiol and environmental stimuli such as acute stressors. For example, rats exhibit increased anxiety-related behaviors in the presence, but not the absence, of light. In females, estradiol potentially mitigates these effects. Experiments across behavioral paradigms and brain regions indicate that estradiol action can be mediated via activation of metabotropic glutamate receptors, including Group I subtype five (mGlu5). mGlu5 has been implicated in mediating estradiol's effects upon psychostimulant-induced behaviors, dopamine release and neuron phenotype in striatal regions. Whether estradiol activation of mGlu5 modulates anxiety or locomotor behavior in the absence of psychostimulants is unknown. Here we test if mGlu5 is necessary for estradiol mitigation of light-induced acute anxiety and locomotor behaviors. Ovariectomized adult female rats were pre-treated with either the mGlu5 antagonist MPEP or saline before estradiol or oil treatment. Anxiety and locomotor behaviors were assessed in the presence or absence of white light to induce high and low acute anxiety behavior phenotypes, respectively. In the presence of white light, estradiol treatment mitigated light-induced anxiety-related behaviors but not overall locomotor activity. MPEP treatment blocked estradiol effects upon light-induced anxiety-related behaviors but did not affect overall locomotor activity. In the absence of white light, estradiol or MPEP treatment did not influence anxiety-related behaviors or locomotor activity, consistent with a low anxiety phenotype. These novel findings indicate that mGlu5 activation is necessary for estradiol mitigation of anxiety-related behaviors induced by an acute stressor. DA - 2020/2/1/ PY - 2020/2/1/ DO - 10.1016/j.physbeh.2019.112770 VL - 214 SP - SN - 0031-9384 KW - Estradiol KW - Metabotropic glutamate receptor 5 KW - Female KW - Anxiety KW - Estrogen ER - TY - JOUR TI - Frankliniella fusca and Frankliniella occidentalis response to thrips-active Cry51Aa2.834_16 Bt cotton with and without neonicotinoid seed treatment AU - Damon A. D'Ambrosio, AU - Kennedy, George G. AU - Huseth, Anders S. T2 - CROP PROTECTION AB - Frankliniella fusca (Hinds) and F. occidentalis (Pergande) are economically important thrips species in cotton production. In the Southeast and Mid-South, F. fusca is an early season seedling pest. In the West, F. occidentalis is a sporadic pest of seedling cotton and a predator of other cotton pests. A novel Bt toxin, Cry51Aa2.834_16 expressed in MON 88702 cotton, has activity against thrips and plant bugs, and will likely become an important management tool for early season pests in cotton. Determining its utility in cotton pest management requires understanding its effects on F. fusca and F. occidentalis. Individual adult female F. fusca and F. occidentalis were exposed to cotyledon disks cut from greenhouse-grown cotton expressing Cry51Aa2.834_16 (MON 88702) or a near-isoline (non-Bt) with or without an imidacloprid seed treatment. Insects were exposed for 72 h and mortality evaluated. Next, individually caged seedlings were infested with five adult female F. fusca or F. occidentalis and egg numbers counted after 72 h. Larval establishment determined after 10 days for F. fusca or 7 days for F. occidentalis. Exposure to MON 88702 in the absence of the imidacloprid seed treatment caused significant adult mortality in F. occidentalis. Exposure to the imidacloprid seed treatment caused significant adult mortality in both species on both MON 88702 and non-Bt cotton plants. Oviposition and larval establishment were reduced by both MON 88702 as well as imidacloprid seed treatment in both species, but the effect size differed between species. In F. fusca, the imidacloprid seed treatment caused the greatest reductions, whereas in F. occidentalis, MON 88702 had the greater effect. DA - 2020/3// PY - 2020/3// DO - 10.1016/j.cropro.2019.105042 VL - 129 SP - SN - 1873-6904 KW - Tobacco thrips KW - Western flower thrips KW - Gossypium hirsutum KW - Imidacloprid KW - MON 88702 ER - TY - BOOK TI - Marriage after Migration: An Ethnography of Money, Romance, and Gender in Globalizing Mexico DA - 2020/// PY - 2020/// UR - https://global.oup.com/academic/product/marriage-after-migration-9780190056018?cc=us&lang=en& ER - TY - JOUR TI - The Future of Environmental DNA in Forensic Science AU - Allwood, Julia S. AU - Fierer, Noah AU - Dunn, Robert R. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - DNA sequencing technologies continue to improve, and there has been a corresponding expansion of DNA-based applications in the forensic sciences. DNA recovered from dust and environmental debris can be used to identify the organisms associated with these sample types, including bacteria, plants, fungi, and insects. Such results can then be leveraged to discern sample origin or geolocation and investigate individual identification. Here, we take a critical look at the current DNA-based technologies using microbiome and environmental sample sources that are focused on the generation of some investigative tools for use in forensic science. We discuss the pitfalls and contentions associated with the use of these techniques and highlight some of the future research required to expand the utility of these methods in the forensic sciences. DA - 2020/1// PY - 2020/1// DO - 10.1128/AEM.01504-19 VL - 86 IS - 2 SP - SN - 1098-5336 KW - environmental DNA KW - forensic science KW - eDNA KW - metabarcoding KW - DNA sequencing ER - TY - JOUR TI - Host and body site-specific adaptation of Lactobacillus crispatus genomes AU - Pan, Meichen AU - Hidalgo-Cantabrana, Claudio AU - Barrangou, Rodolphe T2 - NAR Genomics and Bioinformatics AB - Abstract Lactobacillus crispatus is a common inhabitant of both healthy poultry gut and human vaginal tract, and the absence of this species has been associated with a higher risk of developing infectious diseases. In this study, we analyzed 105 L. crispatus genomes isolated from a variety of ecological niches, including the human vaginal tract, human gut, chicken gut and turkey gut, to shed light on the genetic and functional features that drive evolution and adaptation of this important species. We performed in silico analyses to identify the pan and core genomes of L. crispatus, and to reveal the genomic differences and similarities associated with their origins of isolation. Our results demonstrated that, although a significant portion of the genomic content is conserved, human and poultry L. crispatus isolates evolved to encompass different genomic features (e.g. carbohydrate usage, CRISPR–Cas immune systems, prophage occurrence) in order to thrive in different environmental niches. We also observed that chicken and turkey L. crispatus isolates can be differentiated based on their genomic information, suggesting significant differences may exist between these two poultry gut niches. These results provide insights into host and niche-specific adaptation patterns in species of human and animal importance. DA - 2020/3/1/ PY - 2020/3/1/ DO - 10.1093/nargab/lqaa001 VL - 2 IS - 1 UR - https://doi.org/10.1093/nargab/lqaa001 ER - TY - JOUR TI - Strain-dependent inhibition of Clostridioides difficile by commensal Clostridia encoding the bile acid inducible (bai) operon AU - Reed, A.D. AU - Nethery, M.A. AU - Stewart, A. AU - Barrangou, R. AU - Theriot, C.M. AB - Abstract Clostridioides difficile is one of the leading causes of antibiotic-associated diarrhea. Gut microbiota-derived secondary bile acids and commensal Clostridia that encode the bile acid inducible ( bai ) operon are associated with protection from C. difficile infection (CDI), although the mechanism is not known. In this study we hypothesized that commensal Clostridia are important for providing colonization resistance against C. difficile due to their ability to produce secondary bile acids, as well as potentially competing against C. difficile for similar nutrients. To test this hypothesis, we examined the ability of four commensal Clostridia encoding the bai operon ( C. scindens VPI 12708, C. scindens ATCC 35704, C. hiranonis , and C. hylemonae ) to convert CA to DCA in vitro , and if the amount of DCA produced was sufficient to inhibit growth of a clinically relevant C. difficile strain. We also investigated the competitive relationship between these commensals and C. difficile using an in vitro co-culture system. We found that inhibition of C. difficile growth by commensal Clostridia supplemented with CA was strain-dependent, correlated with the production of ∼2 mM DCA, and increased expression of bai operon genes. We also found that C. difficile was able to outcompete all four commensal Clostridia in an in vitro co-culture system. These studies are instrumental in understanding the relationship between commensal Clostridia and C. difficile in the gut, which is vital for designing targeted bacterial therapeutics. Future studies dissecting the regulation of the bai operon in vitro and in vivo and how this affects CDI will be important. Importance Commensal Clostridia encoding the bai operon such as C. scindens have been associated with protection against CDI, however the mechanism for this protection is unknown. Herein, we show four commensal Clostridia that encode the bai operon effect C. difficile growth in a strain-dependent manner, with and without the addition of cholate. Inhibition of C. difficile by commensals correlated with the efficient conversion of cholate to deoxycholate, a secondary bile acid that inhibits C. difficile germination, growth, and toxin production. Competition studies also revealed that C. difficile was able to outcompete the commensals in an in vitro co-culture system. These studies are instrumental in understanding the relationship between commensal Clostridia and C. difficile in the gut, which is vital for designing targeted bacterial therapeutics. DA - 2020/1/23/ PY - 2020/1/23/ DO - 10.1101/2020.01.22.916304 VL - 1 UR - https://doi.org/10.1101/2020.01.22.916304 ER - TY - JOUR TI - Combination of warming and N inputs increases the temperature sensitivity of soil N2O emission in a Tibetan alpine meadow AU - Zhang, Yi AU - Zhang, Nan AU - Yin, Jingjing AU - Yang, Fei AU - Zhao, Yexin AU - Jiang, Zhongquan AU - Tao, Jinjin AU - Yan, Xuebin AU - Qiu, Yunpeng AU - Guo, Hui AU - Hu, Shuijin T2 - SCIENCE OF THE TOTAL ENVIRONMENT AB - Many high-elevation alpine ecosystems have been experiencing significant increases in air temperature and, to a lesser extent, nitrogen (N) deposition. These changes may affect N-cycling microbes and enhance emissions of nitrous oxide (N2O, a potent greenhouse gas) from soil. However, few studies have investigated whether and how the resulting changes in N-cycling microbes may affect the temperature sensitivity (Q10) of N2O emission and in turn feed back to N2O emissions. We conducted two incubation experiments to examine N2O emissions and their temperature sensitivities in soils that had experienced 3-yr field treatments of warming, N inputs and their combination in a Tibetan alpine meadow. Our results showed that neither N inputs nor warming alone affected the rate or Q10 of soil N2O emission, but combining the two significantly increased both parameters. Also, combined N and warming significantly increased the abundance of ammonia-oxidizing bacteria (AOB), corresponding with high soil N2O emission. In addition, N2O emission from nitrification accounted for 60-80% of total emissions in all soils, indicating that nitrifying microbes dominated the N2O production and its temperature sensitivity. Using random forest (RF) and structural equation model (SEM) analyses, we further evaluated the effects of various soil characteristics on soil N2O emissions and Q10. We identified soil moisture, pH, N mineralization and AOB abundance as the main predictors of the Q10 of N2O emissions. Together, these findings suggest that alterations in soil moisture, pH and ammonia-oxidizing bacteria induced by long-term N inputs and warming may increase temperature sensitivity of soil N2O emissions, leading to a positive climate feedback in this high-altitude alpine ecosystem. DA - 2020/2/20/ PY - 2020/2/20/ DO - 10.1016/j.scitotenv.2019.135450 VL - 704 SP - SN - 1879-1026 KW - Greenhouse gas emission KW - Temperature sensitivity KW - Climate change KW - Alpine ecosystem ER - TY - JOUR TI - An Improved Recombineering Toolset for Plants AU - Brumos, Javier AU - Zhao, Chengsong AU - Gong, Yan AU - Soriano, David AU - Patel, Arjun P. AU - Perez-Amador, Miguel A. AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - The Plant Cell AB - Abstract Gene functional studies often rely on the expression of a gene of interest as transcriptional and translational fusions with specialized tags. Ideally, this is done in the native chromosomal contexts to avoid potential misexpression artifacts. Although recent improvements in genome editing have made it possible to directly modify the target genes in their native chromosomal locations, classical transgenesis is still the preferred experimental approach chosen in most gene tagging studies because of its time efficiency and accessibility. We have developed a recombineering-based tagging system that brings together the convenience of the classical transgenic approaches and the high degree of confidence in the results obtained by direct chromosomal tagging using genome-editing strategies. These simple, scalable, customizable recombineering toolsets and protocols allow a variety of genetic modifications to be generated. In addition, we developed a highly efficient recombinase-mediated cassette exchange system to facilitate the transfer of the desired sequences from a bacterial artificial chromosome clone to a transformation-compatible binary vector, expanding the use of the recombineering approaches beyond Arabidopsis (Arabidopsis thaliana). We demonstrated the utility of this system by generating more than 250 whole-gene translational fusions and 123 Arabidopsis transgenic lines corresponding to 62 auxin-related genes and characterizing the translational reporter expression patterns for 14 auxin biosynthesis genes. DA - 2020/1/10/ PY - 2020/1/10/ DO - 10.1105/tpc.19.00431 UR - https://doi.org/10.1105/tpc.19.00431 ER - TY - JOUR TI - Characterization and applications of Type I CRISPR-Cas systems AU - Hidalgo-Cantabrana, Claudio AU - Barrangou, Rodolphe T2 - Biochemical Society Transactions AB - CRISPR-Cas constitutes the adaptive immune system of bacteria and archaea. This RNA-mediated sequence-specific recognition and targeting machinery has been used broadly for diverse applications in a wide range of organisms across the tree of life. The compact class 2 systems, that hinge on a single Cas effector nuclease have been harnessed for genome editing, transcriptional regulation, detection, imaging and other applications, in different research areas. However, most of the CRISPR-Cas systems belong to class 1, and the molecular machinery of the most widespread and diverse Type I systems afford tremendous opportunities for a broad range of applications. These highly abundant systems rely on a multi-protein effector complex, the CRISPR associated complex for antiviral defense (Cascade), which drives DNA targeting and cleavage. The complexity of these systems has somewhat hindered their widespread usage, but the pool of thousands of diverse Type I CRISPR-Cas systems opens new avenues for CRISPR-based applications in bacteria, archaea and eukaryotes. Here, we describe the features and mechanism of action of Type I CRISPR-Cas systems, illustrate how endogenous systems can be reprogrammed to target the host genome and perform genome editing and transcriptional regulation by co-delivering a minimal CRISPR array together with a repair template. Moreover, we discuss how these systems can also be used in eukaryotes. This review provides a framework for expanding the CRISPR toolbox, and repurposing the most abundant CRISPR-Cas systems for a wide range of applications. DA - 2020/2/28/ PY - 2020/2/28/ DO - 10.1042/BST20190119 VL - 48 IS - 1 SP - 15-23 UR - https://doi.org/10.1042/BST20190119 ER - TY - JOUR TI - Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping AU - Mollinari, Marcelo AU - Olukolu, Bode A AU - S Pereira Guilherme, AU - Khan, Awais AU - Gemenet, Dorcus AU - Yencho, G Craig AU - Zeng, Zhao-Bang T2 - G3 Genes|Genomes|Genetics AB - The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and plays a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly developed software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%), were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato. DA - 2020/1/1/ PY - 2020/1/1/ DO - 10.1534/g3.119.400620 VL - 10 IS - 1 SP - 281-292 UR - https://doi.org/10.1534/g3.119.400620 KW - Polyploidy KW - Genetic Linkage KW - Hexasomic Inheritance KW - Haplotyping KW - Preferential Pairing KW - Multivalent ER - TY - JOUR TI - Scenario analysis on the use of rodenticides and sex-biasing gene drives for the removal of invasive house mice on islands AU - Serr, M.E. AU - Valdez, R.X. AU - Barnhill-Dilling, K.S. AU - Godwin, J. AU - Kuiken, T. AU - Booker, M. T2 - Biological Invasions DA - 2020/// PY - 2020/// DO - 10.1007/s10530-019-02192-6 VL - 22 IS - 4 SP - 1235-1248 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85077527089&partnerID=MN8TOARS KW - Preserving island biodiversity KW - Rodent eradications KW - Synthetic biology KW - Stakeholder engagement KW - Public perceptions ER - TY - JOUR TI - The impact of local population genetic background on the spread of the selfish element Medea-1 in red flour beetles AU - Cash, Sarah A. AU - Robert, Michael A. AU - Lorenzen, Marce D. AU - Gould, Fred T2 - ECOLOGY AND EVOLUTION AB - Selfish genetic elements have been found in the genomes of many species, yet our understanding of their evolutionary dynamics is only partially understood. A number of distinct selfish Medea elements are naturally present in many populations of the red flour beetle (Tribolium castaneum). Although these Medea elements are predicted by models to increase in frequency within populations because any offspring of a Medea-bearing mother that do not inherit at least one Medea allele will die, experiments demonstrating an increase in a naturally occurring Medea element are lacking. Our survey of the specific Medea element, M1, in the United States showed that it had a patchy geographic distribution. From the survey, it could not be determined if this distribution was caused by a slow process of M1 colonization of discrete populations or if some populations lacked M1 because they had genetic factors conferring resistance to the Medea mechanism. We show that populations with naturally low to intermediate M1 frequencies likely represent transient states during the process of Medea spread. Furthermore, we find no evidence that genetic factors are excluding M1 from US populations where the element is not presently found. We also show how a known suppressor of Medea can impair the increase of M1 in populations and discuss the implications of our findings for pest-management applications of Medea elements. DA - 2020/1// PY - 2020/1// DO - 10.1002/ece3.5946 VL - 10 IS - 2 SP - 863-874 SN - 2045-7758 KW - gene drive KW - maternal effect KW - Medea KW - selfish genetic element ER - TY - JOUR TI - Consensus on the key characteristics of endocrine-disrupting chemicals as a basis for hazard identification AU - La Merrill, Michele A. AU - Vandenberg, Laura N. AU - Smith, Martyn T. AU - Goodson, William AU - Browne, Patience AU - Patisaul, Heather B. AU - Guyton, Kathryn Z. AU - Kortenkamp, Andreas AU - Cogliano, Vincent J. AU - Woodruff, Tracey J. AU - Rieswijk, Linda AU - Sone, Hideko AU - Korach, Kenneth S. AU - Gore, Andrea C. AU - Zeise, Lauren AU - Zoeller, R. Thomas T2 - NATURE REVIEWS ENDOCRINOLOGY AB - Abstract Endocrine-disrupting chemicals (EDCs) are exogenous chemicals that interfere with hormone action, thereby increasing the risk of adverse health outcomes, including cancer, reproductive impairment, cognitive deficits and obesity. A complex literature of mechanistic studies provides evidence on the hazards of EDC exposure, yet there is no widely accepted systematic method to integrate these data to help identify EDC hazards. Inspired by work to improve hazard identification of carcinogens using key characteristics (KCs), we have developed ten KCs of EDCs based on our knowledge of hormone actions and EDC effects. In this Expert Consensus Statement, we describe the logic by which these KCs are identified and the assays that could be used to assess several of these KCs. We reflect on how these ten KCs can be used to identify, organize and utilize mechanistic data when evaluating chemicals as EDCs, and we use diethylstilbestrol, bisphenol A and perchlorate as examples to illustrate this approach. DA - 2020/1// PY - 2020/1// DO - 10.1038/s41574-019-0273-8 VL - 16 IS - 1 SP - 45-57 SN - 1759-5037 ER - TY - JOUR TI - Monitoring Ethylene in Plants: Genetically Encoded Reporters and Biosensors AU - Fernandez‐Moreno, Josefina‐Patricia AU - Stepanova, Anna N. T2 - Small Methods AB - Abstract Phytohormone ethylene regulates numerous aspects of plant physiology, from fruit ripening to pathogen responses. The molecular basis of ethylene biosynthesis and action has been investigated for over 40 years, and a combination of biochemistry, genetics, cell, and molecular biology have proven successful at uncovering the core machinery of the ethylene pathway. A number of molecular tools have been developed over the years that enable visualization of the sites of ethylene production and response in the plant. Genetically encoded biosensors take advantage of reporter proteins, i.e., fluorescent, luminescent, or colorimetric markers, to highlight the tissues that make, perceive, or respond to the hormone. This review describes the different types of biosensors currently available to the ethylene community and discusses potential new strategies for developing the next generation of genetically encoded ethylene reporters. DA - 2020/8// PY - 2020/8// DO - 10.1002/smtd.201900260 UR - https://doi.org/10.1002/smtd.201900260 KW - biosensors KW - ethylene KW - hormones KW - reporters KW - signaling ER - TY - JOUR TI - tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks AU - Spurney, Ryan J. AU - Broeck, Lisa AU - Clark, Natalie M. AU - Fisher, Adam P. AU - Balaguer, Maria A. de Luis AU - Sozzani, Rosangela T2 - PLANT JOURNAL AB - Summary Predicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA‐sequencing data analysis, are not automated or are restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet , a user‐friendly platform that can process raw RNA‐sequencing data from any organism with an existing reference genome using a modified tuxedo pipeline ( hisat 2 + cufflinks package) and infer GRNs from these processed data. tuxnet is implemented as a graphical user interface and can mine gene regulations, either by applying a dynamic Bayesian network (DBN) inference algorithm, genist , or a regression tree‐based pipeline, rtp‐star . We obtained time‐course expression data of a PERIANTHIA ( PAN ) inducible line and inferred a GRN using genist to illustrate the use of tuxnet while gaining insight into the regulations downstream of the Arabidopsis root stem cell regulator PAN . Using rtp‐star , we inferred the network of ATHB13 , a downstream gene of PAN, for which we obtained wild‐type and mutant expression profiles. Additionally, we generated two networks using temporal data from developmental leaf data and spatial data from root cell‐type data to highlight the use of tuxnet to form new testable hypotheses from previously explored data. Our case studies feature the versatility of tuxnet when using different types of gene expression data to infer networks and its accessibility as a pipeline for non‐bioinformaticians to analyze transcriptome data, predict causal regulations, assess network topology and identify key regulators. DA - 2020/2// PY - 2020/2// DO - 10.1111/tpj.14558 VL - 101 IS - 3 SP - 716-730 SN - 1365-313X UR - https://doi.org/10.1111/tpj.14558 KW - Arabidopsis thaliana KW - gene regulatory network inference KW - graphical user interface KW - RNA sequencing processing KW - stem cell maintenance KW - technical advance ER - TY - JOUR TI - Distinct fine-root responses to precipitation changes in herbaceous and woody plants: a meta-analysis AU - Wang, Peng AU - Huang, Kailing AU - Hu, Shuijin T2 - NEW PHYTOLOGIST AB - Summary Precipitation is one of the most important factors that determine productivity of terrestrial ecosystems. Precipitation across the globe is predicted to change more intensively under future climate change scenarios, but the resulting impact on plant roots remains unclear. Based on 154 observations from experiments in which precipitation was manipulated in the field and root biomass was measured, we investigated responses in fine‐root biomass of herbaceous and woody plants to alterations in precipitation. We found that root biomass of herbaceous and woody plants responded differently to precipitation change. In particular, precipitation increase consistently enhanced fine‐root biomass of woody plants but had variable effects on herb roots in arid and semi‐arid ecosystems. In contrast, precipitation decrease reduced root biomass of herbaceous plants but not woody plants. In addition, with precipitation alteration, the magnitude of root responses was greater in dry areas than in wet areas. Together, these results indicate that herbaceous and woody plants have different rooting strategies to cope with altered precipitation regimes, particularly in water‐limited ecosystems. These findings suggest that root responses to precipitation change may critically influence root productivity and soil carbon dynamics under future climate change scenarios. DA - 2020/2// PY - 2020/2// DO - 10.1111/nph.16266 VL - 225 IS - 4 SP - 1491-1499 SN - 1469-8137 KW - drought KW - fine roots KW - plant functional type KW - precipitation increase KW - rainfall KW - root biomass KW - root production ER - TY - JOUR TI - Novel mechanism of thrips suppression by Cry51Aa2.834_16 Bt toxin expressed in cotton AU - Huseth, Anders S. AU - Damon A. D'Ambrosio, AU - Yorke, Benjamin T. AU - Head, Graham P. AU - Kennedy, George G. T2 - PEST MANAGEMENT SCIENCE AB - Genetically engineered (GE) crops that express insecticidal traits have improved the sustainability of insect pest management worldwide, but many important pest orders are not controlled by commercially available toxins. Development of the first transgenic thysanopteran- and hemipteran-active Bacillus thuringiensis (Bt) Cry51Aa2.834_16 toxin expressed in MON 88702 cotton will significantly expand the diversity of pests controlled in the crop. Here, we examined MON 88702 cotton activity against two thrips species within the same genera, Frankliniella fusca and Frankliniella occidentalis. We used a multi-component cotton tissue assay approach to understand effects on adult longevity, fecundity, and larval development.We found that in no-choice assays, cotton plants expressing MON 88702 suppress oviposition, when compared to a non-Bt cotton. MON 88702 did not kill a large proportion of F. fusca larvae or adults but killed most F. occidentalis larvae. Time series experiments with F. occidentalis larvae documented significant developmental lags for MON 88702 exposed individuals. We also found that female thrips preferred to oviposit on non-Bt cotton when provided a choice.Together these results describe the activity of MON 88702 against thrips. They document clear differences in toxin performance between different thrips species and throughout the insects' life cycle. Most importantly, we show that MON 88702 was associated with reduced oviposition via behavioral avoidance to the toxin. This is a novel mechanism of action for pest control for a Bt crop plant. Together, these results provide a basis to describe the mechanism of population control for MON 88702 cotton. © 2019 Society of Chemical Industry. DA - 2020/4// PY - 2020/4// DO - 10.1002/ps.5664 VL - 76 IS - 4 SP - 1492-1499 SN - 1526-4998 KW - crop pests KW - Frankliniella fusca KW - Frankliniella occidentalis KW - Gossypium hirsutum KW - MON 88702 ER - TY - JOUR TI - Improved transgenic sexing strains for genetic control of the Australian sheep blow fly Lucilia cuprina using embryo-specific gene promoters AU - Yan, Ying AU - Williamson, Megan E. AU - Davis, Rebecca J. AU - Andere, Anne A. AU - Picard, Christine J. AU - Scott, Maxwell J. T2 - MOLECULAR GENETICS AND GENOMICS DA - 2020/3// PY - 2020/3// DO - 10.1007/s00438-019-01622-3 VL - 295 IS - 2 SP - 287-298 SN - 1617-4623 UR - https://doi.org/10.1007/s00438-019-01622-3 KW - Sterile insect technique KW - Transgenic KW - Lucilia cuprina KW - Genetic control KW - Cellularization gene ER - TY - JOUR TI - Biological controls over the abundances of terrestrial ammonia oxidizers AU - Xiao, Rui AU - Qiu, Yunpeng AU - Tao, Jinjin AU - Zhang, Xuelin AU - Chen, Huaihai AU - Reberg-Horton, S. Chris AU - Shi, Wei AU - Shew, H. David AU - Zhang, Yi AU - Hu, Shuijin T2 - GLOBAL ECOLOGY AND BIOGEOGRAPHY AB - Abstract Aim Ammonia‐oxidizing archaea (AOA) and bacteria (AOB) are the primary agents for nitrification, converting ammonia (NH 4 + ) into nitrate (NO 3 − ) and modulating plant nitrogen (N) utilization and terrestrial N retention. However, there is still lack of a unifying framework describing the patterns of global AOA and AOB distribution. In particular, biotic interactions are rarely integrated into any of the conceptual models. Location World‐wide. Time period 2005–2016. Major taxa studied Ammonia‐oxidizing archaea and ammonia‐oxidizing bacteria. Methods A meta‐analysis and synthesis were conducted to obtain a general picture of global AOA and AOB distribution and identify the primary driving factors. A microcosm experiment was then conducted to assess effects of relative carbon to nitrogen availability for heterotrophic microbes on AOA and AOB in two distinct soils. A mesocosm experiment was further carried out to characterize the effects of plant roots and their arbuscular mycorrhizal fungi (AMF) on AOA and AOB abundances using hyphae‐ or root‐ingrowth techniques. Results Our meta‐analysis showed that soil carbon to nitrogen (C/N) ratios explained the most variance in AOA and AOB abundances, although soil pH had a significant effect. Experimental results demonstrated that high cellulose and mineral N inputs increased total microbial biomass and microbial activities, but inhibited AOA and AOB, suggesting microbial inhibition of AOA and AOB. Also, AMF and roots suppressed AOA and AOB, respectively. Main conclusions Our study provides convincing evidence illustrating that relative carbon to nitrogen availability can predominantly affect the abundances of AOA and AOB. Our experimental results further validate that biotic competition among plants, heterotrophic microbes and ammonia oxidizers for substrate N is the predominant control upon AOA and AOB abundances. Together, these findings provide new insights into the role of abiotic and biotic factors in modulating terrestrial AOA and AOB abundances and their potential applications for management of nitrification in an increasing reactive N world. DA - 2020/2// PY - 2020/2// DO - 10.1111/geb.13030 VL - 29 IS - 2 SP - 384-399 SN - 1466-8238 KW - ammonia-oxidizing archaea KW - ammonia-oxidizing bacteria KW - competition KW - meta-analysis KW - nitrification KW - soil C KW - N ratio ER - TY - JOUR TI - AI Assistants and the Paradox of Internal Automaticity AU - Bauer, William A. AU - Dubljevic, Veljko T2 - NEUROETHICS DA - 2020/10// PY - 2020/10// DO - 10.1007/s12152-019-09423-6 VL - 13 IS - 3 SP - 303-310 SN - 1874-5504 UR - https://doi.org/10.1007/s12152-019-09423-6 KW - AI assistants KW - AI ethics KW - Autonomy KW - Internal automaticity KW - External automaticity KW - Cognition ER - TY - JOUR TI - Auxetic deformation of the weft-knitted Miura-ori fold AU - Luan, Kun AU - West, Andre AU - DenHartog, Emiel AU - McCord, Marian T2 - TEXTILE RESEARCH JOURNAL AB - Negative Poisson’s ratio (NPR) material with unique geometry is rare in nature and has an auxetic response under strain in a specific direction. With this unique property, this type of material is significantly promising in many specific application fields. The curling structure commonly exists in knitted products due to the unbalanced force inside a knit loop. Thus, knitted fabric is an ideal candidate to mimic natural NPR materials, since it possesses such an inherent curly configuration and the flexibility to design and process. In this work, a weft-knitted Miura-ori fold (WMF) fabric was produced that creates a self-folding three-dimensional structure with NPR performance. Also, a finite element analysis model was developed to simulate the structural auxetic response to understand the deformation mechanism of hierarchical thread-based auxetic fabrics. The simulated strain–force curves of four WMF fabrics quantitatively agree with our experimental results. The auxetic morphologies, Poisson’s ratio and damping capacity were discussed, revealing the deformation mechanism of the WMF fabrics. This study thus provides a fundamental framework for mechanical-stimulating textiles. The developed NPR knitted fabrics have a high potential to be employed in areas of tissue engineering, such as artificial blood vessels and artificial folding mucosa. DA - 2020/3// PY - 2020/3// DO - 10.1177/0040517519877468 VL - 90 IS - 5-6 SP - 617-630 SN - 1746-7748 KW - negative Poisson's ratio KW - auxetic structure KW - knitted fabric KW - finite element analysis KW - curling ER - TY - JOUR TI - Rooted in Recognition: Indigenous Environmental Justice and the Genetically Engineered American Chestnut Tree AU - Barnhill-Dilling, S. Kathleen AU - Rivers, Louie AU - Delborne, Jason A. T2 - Society & Natural Resources AB - The restoration plan for the American chestnut tree includes the potential wild release of a genetically engineered tree in close proximity to the sovereign Haudenosaunee communities of Central and Upstate New York. As such, inclusive deliberative frameworks are needed to consider the implications for these communities. Indigenous environmental justice highlights the importance of recognizing tribal sovereignty and Indigenous worldviews as foundational to more just environmental governance. This paper examines how the case of genetically engineered American chestnut tree highlights the importance of recognizing tribal sovereignty and Indigenous worldviews in considering a GE organism for species restoration. DA - 2020/1/2/ PY - 2020/1/2/ DO - 10.1080/08941920.2019.1685145 VL - 33 IS - 1 SP - 83-100 UR - https://doi.org/10.1080/08941920.2019.1685145 KW - Chestnut restoration KW - genetic engineering KW - indigenous environmental justice ER - TY - JOUR TI - Grazing simplifies soil micro-food webs and decouples their relationships with ecosystem functions in grasslands AU - Wang, Bing AU - Wu, Liji AU - Chen, Dima AU - Wu, Ying AU - Hu, Shuijin AU - Li, Linghao AU - Bai, Yongfei T2 - GLOBAL CHANGE BIOLOGY AB - Abstract Livestock grazing often alters aboveground and belowground communities of grasslands and their mediated carbon (C) and nitrogen (N) cycling processes at the local scale. Yet, few have examined whether grazing‐induced changes in soil food webs and their ecosystem functions can be extrapolated to a regional scale. We investigated how large herbivore grazing affects soil micro‐food webs (microbes and nematodes) and ecosystem functions (soil C and N mineralization), using paired grazed and ungrazed plots at 10 locations across the Mongolian Plateau. Our results showed that grazing not only affected plant variables (e.g., biomass and C and N concentrations), but also altered soil substrates (e.g., C and N contents) and soil environment (e.g., soil pH and bulk density). Grazing had strong bottom‐up effects on soil micro‐food webs, leading to more pronounced decreases at higher trophic levels (nematodes) than at lower trophic levels (microbes). Structural equation modeling showed that changes in plant biomass and soil environment dominated grazing effects on microbes, while nematodes were mainly influenced by changes in plant biomass and soil C and N contents; the grazing effects, however, differed greatly among functional groups in the soil micro‐food webs. Grazing reduced soil C and N mineralization rates via changes in plant biomass, soil C and N contents, and soil environment across grasslands on the Mongolian Plateau. Spearman's rank correlation analysis also showed that grazing reduced the correlations between functional groups in soil micro‐food webs and then weakened the correlation between soil micro‐food webs and soil C and N mineralization. These results suggest that changes in soil micro‐food webs resulting from livestock grazing are poor predictors of soil C and N processes at regional scale, and that the relationships between soil food webs and ecosystem functions depend on spatial scales and land‐use changes. DA - 2020/2// PY - 2020/2// DO - 10.1111/gcb.14841 VL - 26 IS - 2 SP - 960-970 SN - 1365-2486 KW - functional groups KW - livestock grazing KW - Mongolian Plateau KW - soil carbon mineralization KW - soil environment KW - soil nitrogen mineralization KW - soil substrates KW - trophic levels ER - TY - JOUR TI - Integration of remote‐weed mapping and an autonomous spraying unmanned aerial vehicle for site‐specific weed management AU - Hunter, Joseph E, III AU - Gannon, Travis W AU - Richardson, Robert J AU - Yelverton, Fred H AU - Leon, Ramon G T2 - Pest Management Science AB - Unmanned aerial vehicles (UAVs) have been used in agriculture to collect imagery for crop and pest monitoring, and for decision-making purposes. Spraying-capable UAVs are now commercially available worldwide for agricultural applications. Combining UAV weed mapping and UAV sprayers into an UAV integrated system (UAV-IS) can offer a new alternative to implement site-specific pest management.The UAV-IS was 0.3- to 3-fold more efficient at identifying and treating target weedy areas, while minimizing treatment on non-weedy areas, than ground-based broadcast applications. The UAV-IS treated 20-60% less area than ground-based broadcast applications, but also missed up to 26% of the target weedy area, while broadcast applications covered almost the entire experimental area and only missed 2-3% of the target weeds. The efficiency of UAV-IS management practices increased as weed spatial aggregation increased (patchiness).Integrating UAV imagery for pest mapping and UAV sprayers can provide a new strategy for integrated pest management programs to improve efficiency and efficacy while reducing the amount of pesticide being applied. The UAV-IS has the potential to improve the detection and control of weed escapes to reduce/delay herbicide resistance evolution. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. DA - 2020/4// PY - 2020/4// DO - 10.1002/ps.5651 UR - https://doi.org/10.1002/ps.5651 KW - UAV KW - precision agriculture KW - site-specific KW - off-target KW - droplet KW - pesticide application KW - resistance KW - detection ER - TY - JOUR TI - Coverage and drift potential associated with nozzle and speed selection for herbicide applications using an unmanned aerial sprayer AU - Hunter, Joseph E., III AU - Gannon, Travis W. AU - Richardson, Robert J. AU - Yelverton, Fred H. AU - Leon, Ramon G. T2 - Weed Technology AB - Abstract In recent years, unmanned aerial vehicle (UAV) technology has expanded to include UAV sprayers capable of applying pesticides. Very little research has been conducted to optimize application parameters and measure the potential of off-target movement from UAV-based pesticide applications. Field experiments were conducted in Raleigh, NC during spring 2018 to characterize the effect of different application speeds and nozzle types on target area coverage and uniformity of UAV applications. The highest coverage was achieved with an application speed of 1 m s −1 and ranged from 30% to 60%, whereas applications at 7 m s −1 yielded 13% to 22% coverage. Coverage consistently decreased as application speed increased across all nozzles, with extended-range flat-spray nozzles declining at a faster rate than air-induction nozzles, likely due to higher drift. Experiments measuring the drift potential of UAV-applied pesticides using extended-range flat spray, air-induction flat-spray, turbo air–induction flat-spray, and hollow-cone nozzles under 0, 2, 4, 7, and 9 m s −1 perpendicular wind conditions in the immediate 1.75 m above the target were conducted in the absence of natural wind. Off-target movement was observed under all perpendicular wind conditions with all nozzles tested but was nondetectable beyond 5 m away from the target. Coverage from all nozzles exhibited a concave-shaped curve in response to the increasing perpendicular wind speed due to turbulence. The maximum target coverage in drift studies was observed when the perpendicular wind was 0 and 8.94 m s −1 , but higher turbulence at the two highest perpendicular wind speeds (6.71 and 8.94 m s −1 ) increased coverage variability, whereas the lowest variability was observed at 2.24 m s −1 wind speed. Results suggested that air-induction flat-spray and turbo air–induction flat-spray nozzles and an application speed of 3 m s −1 provided an adequate coverage of target areas while minimizing off-target movement risk. DA - 2020/4/9/ PY - 2020/4/9/ DO - 10.1017/wet.2019.101 VL - 34 IS - 2 SP - 235-240 UR - https://doi.org/10.1017/wet.2019.101 KW - Bradley Hanson KW - University of California KW - Davis KW - UAV KW - precision agriculture KW - site-specific KW - off-target KW - droplet KW - pesticide application ER - TY - JOUR TI - Arthropod carrion influences plant choice, oviposition, and cannibalism by a specialist predator on a sticky plant AU - Nelson, Peter N. AU - Burrack, Hannah J. AU - Sorenson, Clyde E. T2 - ECOLOGICAL ENTOMOLOGY AB - 1. Dead arthropods, entrapped by trichomes on plant surfaces, are an underappreciated form of plant‐provided food. Specialist predatory arthropods able to manoeuvre on plants covered in trichomes facultatively scavenge on the alternative food resource, increasing their abundance and reducing plant damage by herbivores. 2. This protective mutualism dependent on arthropod carrion has been demonstrated in several plant species, but the mechanisms driving the increase in predator abundance have not been identified. Through a series of greenhouse and laboratory experiments, the effect of arthropod carrion on predator behaviour was assessed. 3. The predator Jalysus wickhami preferred Nicotiana tabacum plants augmented with arthropod carrion, spending significantly more time and laying more eggs on those plants than plants without arthropod carrion. 4. Under low J. wickhami densities, arthropod carrion did not reduce egg cannibalism by adults. Under high densities, egg cannibalism by J. wickhami adults was reduced in the presence of arthropod carrion, but cannibalism by fifth instars was not. 5. Arthropod carrion may be utilised by a wide range of predatory arthropods that facultatively scavenge, and this research demonstrates its potential for influencing arthropod–plant and arthropod–arthropod interactions. DA - 2020/4// PY - 2020/4// DO - 10.1111/een.12787 VL - 45 IS - 2 SP - 182-189 SN - 1365-2311 KW - Arthropod-plant interactions KW - necrophagy KW - phylloplane resource KW - plant-provided food KW - scavenging KW - trichomes ER - TY - JOUR TI - Contrasting the Pb (II) and Cd (II) tolerance of Enterobacter sp. via its cellular stress responses AU - Jiang, Zhongquan AU - Jiang, Liu AU - Zhang, Lin AU - Su, Mu AU - Tian, Da AU - Wang, Tong AU - Sun, Yalin AU - Nong, Ying AU - Hu, Shuijin AU - Wang, Shimei AU - Li, Zhen T2 - ENVIRONMENTAL MICROBIOLOGY AB - Summary Successful application of microorganisms to heavy metal remediation depends on their resistance to toxic metals. This study contrasted the differences of tolerant mechanisms between Pb 2+ and Cd 2+ in Enterobacter sp. Microbial respiration and production of formic acid showed that Enterobacter sp. had a higher tolerant concentration of Pb (>1000 mg l −1 ) than Cd (about 200 mg l −1 ). Additionally, SEM confirmed that most of Pb and Cd nanoparticles (NPs) were adsorbed onto cell membrane. The Cd stress, even at low concentration (50 mg l −1 ), significantly enlarged the sizes of cells. The cellular size raised from 0.4 × 1.0 to 0.9 × 1.6 μm on average, inducing a platelet‐like shape. In contrast, Pb cations did not stimulate such enlargement even up to 1000 mg l −1 . Moreover, Cd NPs were adsorbed homogeneously by almost all the bacterial cells under TEM. However, only a few cells work as ‘hot spots’ on the sorption of Pb NPs. The heterogeneous sorption might result from a ‘self‐sacrifice’ mechanism, i.e., some cells at a special life stage contributed mostly to Pb sorption. This mechanism, together with the lower mobility of Pb cations, caused higher microbial tolerance and removal efficiency towards Pb 2+ . This study sheds evident contrasts of bacterial resistance to the two most common heavy metals. DA - 2020/4// PY - 2020/4// DO - 10.1111/1462-2920.14719 VL - 22 IS - 4 SP - 1507-1516 SN - 1462-2920 ER - TY - JOUR TI - MIMIX: A Bayesian Mixed-Effects Model for Microbiome Data From Designed Experiments AU - Grantham, Neal S. AU - Guan, Yawen AU - Reich, Brian J. AU - Borer, Elizabeth T. AU - Gross, Kevin T2 - JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION AB - Recent advances in bioinformatics have made high-throughput microbiome data widely available, and new statistical tools are required to maximize the information gained from these data. For example, analysis of high-dimensional microbiome data from designed experiments remains an open area in microbiome research. Contemporary analyses work on metrics that summarize collective properties of the microbiome, but such reductions preclude inference on the fine-scale effects of environmental stimuli on individual microbial taxa. Other approaches model the proportions or counts of individual taxa as response variables in mixed models, but these methods fail to account for complex correlation patterns among microbial communities. In this article, we propose a novel Bayesian mixed-effects model that exploits cross-taxa correlations within the microbiome, a model we call microbiome mixed model (MIMIX). MIMIX offers global tests for treatment effects, local tests and estimation of treatment effects on individual taxa, quantification of the relative contribution from heterogeneous sources to microbiome variability, and identification of latent ecological subcommunities in the microbiome. MIMIX is tailored to large microbiome experiments using a combination of Bayesian factor analysis to efficiently represent dependence between taxa and Bayesian variable selection methods to achieve sparsity. We demonstrate the model using a simulation experiment and on a 2 × 2 factorial experiment of the effects of nutrient supplement and herbivore exclusion on the foliar fungal microbiome of Andropogon gerardii, a perennial bunchgrass, as part of the global Nutrient Network research initiative. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement. DA - 2020/4/2/ PY - 2020/4/2/ DO - 10.1080/01621459.2019.1626242 VL - 115 IS - 530 SP - 599-609 SN - 1537-274X KW - Continuous shrinkage prior KW - Factor analysis KW - Microbiome KW - Mixed model KW - Nutrient Network KW - OTU abundance data ER -