TY - JOUR TI - The social-mediated crisis communication research: Revisiting dialogue between organizations and publics in crises of China 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 - 2019/5// PY - 2019/5// DO - 10.1016/j.pubrev.2019.04.003 UR - http://dx.doi.org/10.1016/j.pubrev.2019.04.003 ER - TY - JOUR TI - Corporate dialogue in crises of China: Examining dialogic strategies and communicative outcomes in a child abuse scandal 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 - 2019/7// PY - 2019/7// DO - 10.1016/j.pubrev.2019.101816 UR - http://dx.doi.org/10.1016/j.pubrev.2019.101816 ER - TY - CONF TI - Beyond Despair: Theory and Practice in Environmental Humanities AU - Booker, M. T2 - National Humanities Center C2 - 2019/// C3 - National Humanities Center CY - Durham, NC DA - 2019/// PY - 2019/// ER - TY - CHAP TI - Introduction AU - Ludington, Charles C. AU - Booker, Matthew Morse T2 - Food Fights AB - Food is a contentious topic in the contemporary United States. But our debates surrounding food are hardly new. The chapters in Food Fights constitute a series of debates about food, emphasizing the historical background to our current arguments. All the authors share the assumption that knowing how we got the food and foodways we have today will help us appreciate both the triumphs and failures, strengths and weaknesses of our current food system, and thereby build some common understanding between those who only condemn its problems and those who see only its virtues. PY - 2019/11/11/ DO - 10.5149/northcarolina/9781469652894.003.0001 SP - 1-12 PB - University of North Carolina Press UR - http://dx.doi.org/10.5149/northcarolina/9781469652894.003.0001 ER - TY - CHAP TI - Who Should Be Responsible for Food Safety? Oysters as a Case Study AU - Booker, Matthew Morse T2 - Food Fights: How History Matters to Contemporary Food Debates PY - 2019/11// PB - Ludington and Matthew Morse Booker, University of North Carolina Press UR - https://uncpress.org/book/9781469652894/food-fights/ ER - TY - TI - Sourdough Cultures DA - 2019/8/29/ PY - 2019/8/29/ UR - https://seeingthewoods.org/2019/08/29/sourdough-cultures/ ER - TY - BOOK TI - Food Fights: How History Matters to Contemporary Food Debates DA - 2019/11/11/ PY - 2019/11/11/ UR - https://uncpress.org/book/9781469652894/food-fights/ 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 - 2019/11/12/ PY - 2019/11/12/ DO - 10.1007/s00438-019-01622-3 VL - 295 IS - 2 SP - 287-298 J2 - Mol Genet Genomics LA - en OP - SN - 1617-4615 1617-4623 UR - http://dx.doi.org/10.1007/s00438-019-01622-3 DB - Crossref ER - TY - JOUR TI - Novel mechanism of thrips suppression by Cry51Aa2.834_16 Bt toxin expressed in cotton AU - Huseth, Anders S AU - D′Ambrosio, Damon A 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 - 2019/11/23/ PY - 2019/11/23/ DO - 10.1002/ps.5664 VL - 76 IS - 4 SP - 1492-1499 J2 - Pest Management Science LA - en OP - SN - 1526-498X 1526-4998 UR - http://dx.doi.org/10.1002/ps.5664 DB - Crossref ER - TY - ER - TY - BLOG TI - Lessons Learned for Risk Governance of Synthetic Biology, Nanomaterials, and Other Emerging Technologies in a Post-2020 World AU - Grieger, K.D. AU - Kuiken, T. T2 - Genetic Engineering and Society Center DA - 2019/// PY - 2019/// UR - https://research.ncsu.edu/ges/2019/12/lessons-learned-risk-governance-synbio-nano-post2020-world/ ER - TY - CHAP TI - Sustainable Environmental Remediation Using NZVI by Managing Benefit-Risk Trade-Offs AU - Grieger, Khara AU - Hjorth, Rune AU - Carpenter, Alexis Wells AU - Klaessig, Frederick AU - Lefevre, Emilie AU - Gunsch, Claudia AU - Soratana, Kullapa AU - Landis, Amy E. AU - Wickson, Fern AU - Hristozov, Danail AU - Linkov, Igor T2 - Nanoscale Zerovalent Iron Particles for Environmental Restoration A2 - Phenrat, T. A2 - Lowry, G.V. AB - Ensuring the sustainable development and use of NZVI for in situ remediation requires the incorporation of a multitude of factors and criteria, including those related to technology performance, cost, potential impacts to the environment and human health, as well as ethical, social, and legal concerns. This chapter provides an overview of these factors in order to help guide the sustainable development of NZVI. Among other main results, we find that while there are promising findings regarding its performance and effectiveness as a remediation technique, there are also growing concerns regarding its impacts to the environment and health. To date, most of this research has focused on the potential (eco)toxicological effects of NZVI with limited research on broader issues such as social or ethical implications. In fact, the social implications of NZVI, including the ability for a range of stakeholders and members of the public to be active participants in decision-making processes, have either been minimal or nonexistent. We also find that marketplace limitations appear to be serious obstacles to ensuring the sustainable development and use of NZVI as an environmental remediation technology, including questions pertaining to the validity of its cost-competitiveness. In order to balance the potential benefits, risks, and uncertainty characteristics of NZVI, there are a number of decision support frameworks and risk analysis tools which may be applied, including multi-criteria decision analysis, life cycle assessment, as well as diverse risk characterization or screening tools (e.g., NanoRiskCat). While several of these frameworks and tools may be suited for NZVI in theory, very few of them have been applied to NZVI in practice. In conclusion, these results indicate that while NZVI has potential to reduce environmental contaminants through in situ remediation, its development and use, particularly at field-scale sites, has not proceeded in the most sustainable manner possible thus far. In light of this, we provide specific recommendations to help ensure the sustainable development and use of NZVI, including recommendations specific for diverse stakeholder groups such as researchers, academics, industry, and government officials. PY - 2019/// DO - 10.1007/978-3-319-95340-3_15 SP - 511-562 PB - Springer International Publishing SN - 9783319953380 9783319953403 UR - http://dx.doi.org/10.1007/978-3-319-95340-3_15 ER - TY - JOUR TI - Emerging risk governance for stratospheric aerosol injection as a climate management technology AU - Grieger, Khara D. AU - Felgenhauer, Tyler AU - Renn, Ortwin AU - Wiener, Jonathan AU - Borsuk, Mark T2 - Environment Systems and Decisions DA - 2019/4/30/ PY - 2019/4/30/ DO - 10.1007/s10669-019-09730-6 VL - 39 IS - 4 SP - 371-382 J2 - Environ Syst Decis LA - en OP - SN - 2194-5403 2194-5411 UR - http://dx.doi.org/10.1007/s10669-019-09730-6 DB - Crossref ER - TY - BOOK TI - Review of "Advertising and consumer culture in China," by H.M. Li AU - Cheng, Y. AU - Li, H.M. DA - 2019/// PY - 2019/// VL - 13 SE - 459–461 ER - TY - JOUR TI - When CSR meets mobile SNA users in mainland China: An examination of gratifications sought, CSR motives, and relational outcomes in natural disasters AU - Cheng, Y. AU - Chen, Y.R. AU - Hung-Baesecke, R. AU - Jin, Y. T2 - International Journal of Communication DA - 2019/// PY - 2019/// VL - 13 SP - 319–341 UR - https://ijoc.org/index.php/ijoc/article/view/10169 ER - TY - JOUR TI - Spatial and temporal variations of PM2.5 mass closure and inorganic PM2.5 in the Southeastern U.S. AU - Cheng, Bin AU - Wang-Li, Lingjuan AU - Meskhidze, Nicholas AU - Classen, John AU - Bloomfield, Peter T2 - Environmental Science and Pollution Research DA - 2019/9/13/ PY - 2019/9/13/ DO - 10.1007/s11356-019-06437-8 VL - 26 IS - 32 SP - 33181-33191 J2 - Environ Sci Pollut Res LA - en OP - SN - 0944-1344 1614-7499 UR - http://dx.doi.org/10.1007/s11356-019-06437-8 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 & 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 - 2019/10/9/ PY - 2019/10/9/ DO - 10.1108/JPBM-12-2018-2145 VL - 29 IS - 2 SP - 188-198 J2 - JPBM LA - en OP - SN - 1061-0421 1061-0421 UR - http://dx.doi.org/10.1108/JPBM-12-2018-2145 DB - Crossref ER - TY - JOUR TI - Humanistic communication in information centric workplaces AU - Ranade, Nupoor AU - Swarts, Jason T2 - Communication Design Quarterly AB - Professional writers adapt their skills to suit expanded professional roles that involve production and management of information, but preparation through mere skill-based training is problematic because that communication work is messy in ways that are not addressable through simple skills training. We must understand how skills "influence and shape the discursive activities surrounding their use" (Selber, 1994). This paper reports the results of a study of people trained in humanities disciplines like communication, English, writing studies, technical communication, etc., on how they have found means to employ their training in their workplace and keep what is humanistic about writing and communicating at the foreground of their interactions with information technologies. Instead of focusing on technology alone, this research encourages a unified approach to preparing students for the workplace. DA - 2019/// PY - 2019/// DO - 10.1145/3363790.3363792 VL - 7 IS - 4 SP - 17–31 SN - 2166-1642 UR - http://dx.doi.org/10.1145/3363790.3363792 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. AB - Abstract Accurate manipulation of metabolites in the monolignol biosynthetic pathway 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 the inability to capture indirect regulatory influences on other pathway genes. Here, we examine the manifestation of these indirect influences collectively 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 desired single or combinatorial knockdowns of specific monolignol genes. Using in-silico simulations of this model and root mean square error, we show that our model more accurately estimates transcript and protein abundances in differentiating xylem tissue when individual and families of monolignol genes were perturbed. This approach 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. Additionally, these results can be used to guide future experiments to elucidate the mechanisms responsible for the indirect influences. Author summary Engineering trees to have desirable lignin and wood traits is of significant interest to the bioenergy and biomaterial industries. Genetically modifying the expression of the genes that drive the monolignol biosynthetic pathway is a useful method for obtaining new traits. Modifying the expression of one gene affects not only the abundance of its encoded protein, but can also indirectly impact the amount of other transcripts and proteins. These proteins drive the monolignol biosynthetic pathway. Having an accurate representation of their abundances is key to understanding how lignin and wood traits are altered. We developed a computational model to estimate how the abundance of monolignol transcripts and proteins are changed when one or more monolignol genes are knocked down. Specifying only the abundances of the targeted genes as input, our model estimates how the levels of the other, untargeted, transcripts and proteins are altered. Our model captures indirect regulatory influences at the transcript and protein levels observed in experimental data. The model is an important addition to current models of lignin biosynthesis. By incorporating our approach into the existing models, we expect to improve our ability to explore how new combinations of gene knockdowns impact lignin and many other wood properties. DA - 2019/6/19/ PY - 2019/6/19/ DO - 10.1101/677047 VL - 6 UR - https://doi.org/10.1101/677047 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 - 2019/// PY - 2019/// DO - 10.1111/gcb.14841 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 - 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 - 2019/// PY - 2019/// DO - 10.1111/nph.16266 KW - drought KW - fine roots KW - plant functional type KW - precipitation increase KW - rainfall KW - root biomass KW - root production 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 - 2019/// PY - 2019/// DO - 10.1111/1462-2920.14719 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 - 2019/// PY - 2019/// DO - 10.1111/geb.13030 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 - Adaptability of a U.S. purple-fleshed sweetpotato breeding population in Uganda AU - Musabyemungu, Anastasie AU - Wasswa, Peter AU - Alajo, Agnes AU - Chelagat, Doreen M. AU - Otema, Milton A. AU - Musana, Paul AU - Rukundo, Placide AU - Gibson, Paul AU - Edema, Richard AU - Pecota, Kenneth V. AU - Yencho, G. Craig AU - Yada, Benard T2 - Australian Journal of Crop Science AB - Purple-fleshed sweetpotato varieties are important for their nutraceutical value due primarily to their high anthocyanin content. These varieties also often have high dry matter content preferred by consumers and processors in sub-Saharan Africa. However, improved purple-fleshed sweetpotatoes are not available in Uganda. This study was conducted to evaluate the adaptability of purple-fleshed sweetpotato genotypes for storage root yield, dry matter and anthocyanin content in Uganda. A bi-parental population of 159 clones from the cross NCP06-020 NC09-188 introduced to Uganda from North Carolina State University was evaluated with three local checks in two sites and two seasons in Uganda. The trials were planted in two locations using alpha lattice design with two replicates and five sweetpotato vine cuttings per genotype. Storage roots and vines were harvested after five months and the agronomic characteristics were recorded. Dry matter and anthocyanin content of storage roots were analysed after harvesting. The mean storage root yield of clones across the two locations was 37.8 t/ha and 24.2 t/ha in the first season (2015A) and second season (2015B); respectively, with an overall mean of 31.0 t/ha. Storage root dry matter content ranged from 21.5 to 33.7% across locations and seasons with an overall mean of 29.1%. Storage root anthocyanin content across the two locations ranged from 0 to 12.6 mg/100g FW with the overall mean of 3.9 mg/100g FW. A total of ten genotypes showed significantly stable performance (P <= 0.001) across two locations and two seasons. Highly significant difference between genotypes for dry matter content, anthocyanin content and total storage root yields revealed significant genetic variability among the tested genotypes, which can be exploited for future crop improvement. DA - 2019/1/20/ PY - 2019/1/20/ DO - 10.21475/ajcs.19.13.01.p1023 VL - 13 IS - 01 SP - 17-25 J2 - Aust J Crop Sci OP - SN - 1835-2693 1835-2707 UR - http://dx.doi.org/10.21475/ajcs.19.13.01.p1023 DB - Crossref ER - TY - JOUR TI - Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.] AU - Gemenet, Dorcus C. AU - da Silva Pereira, Guilherme AU - De Boeck, Bert AU - Wood, Joshua C. AU - Mollinari, Marcelo AU - Olukolu, Bode A. AU - Diaz, Federico AU - Mosquera, Veronica AU - Ssali, Reuben T. AU - David, Maria AU - Kitavi, Mercy N. AU - Burgos, Gabriela AU - Felde, Thomas Zum AU - Ghislain, Marc AU - Carey, Edward AU - Swanckaert, Jolien AU - Coin, Lachlan J. M. AU - Fei, Zhangjun AU - Hamilton, John P. AU - Yada, Benard AU - Yencho, G. Craig AU - Zeng, Zhao-Bang AU - Mwanga, Robert O. M. AU - Khan, Awais AU - Gruneberg, Wolfgang J. AU - Buell, C. Robin T2 - Theoretical and Applied Genetics AB - β-Carotene content in sweetpotato is associated with the Orange and phytoene synthase genes; due to physical linkage of phytoene synthase with sucrose synthase, β-carotene and starch content are negatively correlated. In populations depending on sweetpotato for food security, starch is an important source of calories, while β-carotene is an important source of provitamin A. The negative association between the two traits contributes to the low nutritional quality of sweetpotato consumed, especially in sub-Saharan Africa. Using a biparental mapping population of 315 F1 progeny generated from a cross between an orange-fleshed and a non-orange-fleshed sweetpotato variety, we identified two major quantitative trait loci (QTL) on linkage group (LG) three (LG3) and twelve (LG12) affecting starch, β-carotene, and their correlated traits, dry matter and flesh color. Analysis of parental haplotypes indicated that these two regions acted pleiotropically to reduce starch content and increase β-carotene in genotypes carrying the orange-fleshed parental haplotype at the LG3 locus. Phytoene synthase and sucrose synthase, the rate-limiting and linked genes located within the QTL on LG3 involved in the carotenoid and starch biosynthesis, respectively, were differentially expressed in Beauregard versus Tanzania storage roots. The Orange gene, the molecular switch for chromoplast biogenesis, located within the QTL on LG12 while not differentially expressed was expressed in developing roots of the parental genotypes. We conclude that these two QTL regions act together in a cis and trans manner to inhibit starch biosynthesis in amyloplasts and enhance chromoplast biogenesis, carotenoid biosynthesis, and accumulation in orange-fleshed sweetpotato. Understanding the genetic basis of this negative association between starch and β-carotene will inform future sweetpotato breeding strategies targeting sweetpotato for food and nutritional security. DA - 2019/10/8/ PY - 2019/10/8/ DO - 10.1007/s00122-019-03437-7 VL - 133 IS - 1 SP - 23-36 J2 - Theor Appl Genet LA - en OP - SN - 0040-5752 1432-2242 UR - http://dx.doi.org/10.1007/s00122-019-03437-7 DB - Crossref ER - TY - RPRT TI - Evaluation of the Coalition of NC Farm to School NC Awards Initiative AU - Berry-James, R.M. A3 - Center for Environmental Systems DA - 2019/// PY - 2019/// PB - Center for Environmental Systems ER - TY - RPRT TI - Annual Evaluation of the North Carolina Farm to Early Care and Education Evaluation Report: Year 2 AU - Berry-James, R.M. A3 - W. K. Kellogg Foundation/Center for Environmental Systems DA - 2019/5// PY - 2019/5// PB - W. K. Kellogg Foundation/Center for Environmental Systems ER - TY - CONF TI - Institutionalizing Social Equity into the Public Policy Decision Process: Examining Trends and Disproportionality in Juvenile Justice AU - Berry-James, R.M. T2 - National Academy of Public Administration (NAPA) Fall Meeting C2 - 2019/11/7/ CY - Washington, DC DA - 2019/11/7/ PY - 2019/11/7/ ER - TY - CONF TI - NASPAA Accreditation Training AU - Berry-James, R.M. T2 - NASPAA Accreditation Institute C2 - 2019/10/16/ CY - Los Angeles, CA DA - 2019/10/16/ PY - 2019/10/16/ ER - TY - CONF TI - NC Farm to Early Care and Education Collaborative: Clarifying Program Theory through Life of the Program AU - Berry-James, R.M. T2 - Farm to ECE Community of Practice Meeting/Kellogg Foundation C2 - 2019/9/24/ CY - Washington, DC DA - 2019/9/24/ PY - 2019/9/24/ ER - TY - CONF TI - Responsible Innovation: Cultural Perceptions of Biotechnology in Food Systems AU - Berry-James, R.M. T2 - NC State 2019 University Research Symposium C2 - 2019/3/21/ CY - Raleigh, NC DA - 2019/3/21/ PY - 2019/3/21/ ER - TY - CONF TI - Leading Change in Social Equity through Planning, Research, and the Dissemination of Information AU - Berry-James, R.M. T2 - American Society for Public Administration C2 - 2019/3/12/ CY - Washington, DC DA - 2019/3/12/ PY - 2019/3/12/ ER - TY - SOUND TI - Educating Future Public Administrators and City Managers at Managing the City: Honoring the Career of Professor Sylvester Murray Conference AU - Berry-James, R.M. DA - 2019/3/25/ PY - 2019/3/25/ ER - TY - SOUND TI - #MeToo The Role of Universities in the Me Too Movement AU - Berry-James, R.M. DA - 2019/3/11/ PY - 2019/3/11/ ER - TY - SOUND TI - Diversity in Education: Research on Diversity, Cultural Competence and Social Equity. African American History Month (AAHM) AU - Berry-James, R.M. DA - 2019/2/14/ PY - 2019/2/14/ ER - TY - CONF TI - Social Determinants of Health Starts with Food Wealth: Examining Emerging Practices, Best Practices and Breakthrough Practices AU - Berry-James, R.M. T2 - American Society of Public Administration C2 - 2019/3/12/ CY - Washington, DC DA - 2019/3/12/ PY - 2019/3/12/ ER - TY - CONF TI - Naming Privilege, Social Justice, and Racism through Reflective Pedagogy and Student Experiences: A Case Study at North Carolina State University AU - Berry-James, R.M. T2 - NASPAA Annual Conference: Reconstructing Governance for the Next 50 Years C2 - 2019/10/16/ CY - Los Angeles, CA DA - 2019/10/16/ PY - 2019/10/16/ ER - TY - CONF TI - Institutionalizing Social Equity into the Public Policy Decision Process AU - Birdsell, D. AU - Berry-James, R.M. AU - Poethig, E. AU - Katzen, S. T2 - National Academy of Public Administration, Standing Panel on Social Equity in Governance, Fall 2019 Annual Meeting C2 - 2019/// C3 - Proceedings of the National Academy of Public Administration DA - 2019/// PY - 2019/11// ER - TY - ER - TY - DATA TI - Gene regulatory effects of a large chromosomal inversion in highland maize AB - Abstract 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 that underlie an inversion’s role in adaption. In this study, we explore how large-scale transcriptomic data can be used 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 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. First, using a large publicly available association mapping panel, we confirmed that Inv4m is associated with locally adaptive agronomic phenotypes, but only in highland fields. Second, we created two families segregating for standard and inverted haplotypess of Inv4m in a isogenic B73 background, and measured gene expression variation association with Inv4m 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 , and speculate that the genetic basis of its effects on adaptive traits is distributed across many separate functional variants. Author Summary Chromosomal inversions are an important type of genomic structural variant. However, mapping causal alleles within their boundaries is difficult because inversions suppress recombination between homologous chromosomes. This means that inversions, regardless of their size, are inherited as a unit. We leveraged the high-dimensional phenotype of gene expression as a tool to study the genetics of a large chromosomal inversion found in highland maize populations in Mexico - Inv4m . We grew plants carrying multiple versions of Inv4m in a common genetic background, and quantified the transcriptional reprogramming induced by alternative alleles at the locus. Inv4m has been shown in previous studies to have a large effect on flowering, but we show that the functional variation within Inv4m affects many developmental and physiological processes. Author Contributions T. Crow, R. Rellan-Alvarez, R. Sawers and D. Runcie conceived and designed the experiment. M. Aguilar-Rangel, J. Rodrǵuez, R. Rellan-Alvarez and R. Sawers generated the segregating families. T. Crow, J. Ta, S. Nojoomi, M. Aguilar-Rangel, J. Rodrǵuez D. Gates, D. Runcie performed the experiment. T. Crow, D. Gates, D. Runcie analyzed the data. T. Crow, D. Runcie wrote the original manuscript, and R. Rellan-Alvarez and R. Sawers provided review and editing. DA - 2019/12/2/ PY - 2019/12/2/ DO - 10.1101/861583 UR - http://dx.doi.org/10.1101/861583 ER - TY - SOUND TI - Public Engagement and Genetic Biocontrol Technologies for Invasive Species AU - Delborne, J. DA - 2019/6/26/ PY - 2019/6/26/ ER - TY - SOUND TI - Communicating Biotechnology with the Public AU - Delborne, J. DA - 2019/10/9/ PY - 2019/10/9/ PB - Cornell University ER - TY - SOUND TI - Approaching the Genetically Engineered Chestnut AU - Delborne, J. DA - 2019/10/10/ PY - 2019/10/10/ ER - TY - SOUND TI - Design Choices for Public Engagement AU - Delborne, J. DA - 2019/10/11/ PY - 2019/10/11/ ER - TY - CONF TI - Mapping the Landscape of Interests and Engaging Stakeholders to Inform Research and Development of Gene Drives for Conservation AU - Delborne, J. T2 - Genetic Biocontrol of Invasive Rodents (GBIRd) International Partnership Meeting C2 - 2019/11/13/ CY - Raleigh, NC DA - 2019/11/13/ PY - 2019/11/13/ ER - TY - CONF TI - Suspect screening and prioritization of chemicals of concern (COCs) in a comprehensive, field-scale study of a forested water reuse system AU - Hedgespeth, M.L. AU - Rashash, D. AU - Shea, D. AU - Strynar, M.J. AU - Delborne, J.A. AU - Nichols, E.G. T2 - 2019 WRRI Annual Conference C2 - 2019/3/21/ CY - Raleigh, NC DA - 2019/3/21/ PY - 2019/3/21/ ER - TY - CONF TI - Innovations, Interruptions, and Regenerations of Chestnut Restoration: Reciprocal Restoration as a Framework for Reflexivity in Chestnut Restoration Narratives AU - Barnhill-Dilling, S.K. AU - Delborne, J.A. T2 - Annual Meeting of the Society for Social Studies of Science C2 - 2019/9/5/ CY - New Orleans, LA DA - 2019/9/5/ PY - 2019/9/5/ ER - TY - CONF TI - Creating Space for Reflexivity: Facilitating Dialogue Between Scientists and Stakeholders AU - Costantini, D. AU - George, D. AU - Delborne, J.A. T2 - Annual Meeting of the Society for Social Studies of Science C2 - 2019/9/5/ CY - New Orleans, LA DA - 2019/9/5/ PY - 2019/9/5/ ER - TY - CONF TI - Mapping Engagement for Emerging Technologies: Decision Phases, Stakeholders, and the Genetically Engineered American Chestnut Tree AU - George, D. AU - Delborne, J.A. T2 - Annual Meeting of the Society for Social Studies of Science C2 - 2019/9/5/ CY - New Orleans, LA DA - 2019/9/5/ PY - 2019/9/5/ ER - TY - CONF TI - Kingdoms of Engagement: Reflecting on Stakeholder Engagement Exercises Focused on GE Algae, Trees, and Mice AU - Delborne, J.A. T2 - Annual Meeting of the Society for Social Studies of Science C2 - 2019/9/5/ CY - New Orleans, LA DA - 2019/9/5/ PY - 2019/9/5/ ER - TY - CONF TI - Communicating about Biotechnology with Public Audiences AU - Delborne, J.A. T2 - NC Cooperative Extension State Conference C2 - 2019/10/30/ DA - 2019/10/30/ PY - 2019/10/30/ ER - TY - CONF TI - Discussion of the Documentary Human Nature AU - Delborne, J. AU - Barrangou, R. AU - Charo, R.Alta AU - Goodwin, Sarah AU - Kirschner, Elliot T2 - Board on Life Sciences 2019 Spring Meeting, National Academies of Sciences, Engineering, and Medicine C2 - 2019/4/26/ CY - Washington, DC DA - 2019/4/26/ PY - 2019/4/26/ ER - TY - SOUND TI - Gene Editing in the Food System AU - Delborne, J. AU - Brown, Z. AU - Burrack, Hannah AU - Sederoff, Heike AU - Sozzani, Ross DA - 2019/9/25/ PY - 2019/9/25/ ER - TY - SOUND TI - Genetic Arts Intervening in the Anthropocene: Climate, Geoengineering, and Ecosystems AU - Delborne, J. AU - Ellison, Aaron AU - Ong, Joel AU - Davis, Jon AU - Kirchner, Erin AU - Rusk, Rachel DA - 2019/10/18/ PY - 2019/10/18/ UR - https://research.ncsu.edu/ges/arts-work-in-biotech/ ER - TY - CHAP TI - A potential new tool for the toolbox: assessing gene drives for eradicating invasive rodent populations AU - Campbell, K.J. AU - Saah, J.R. AU - Brown, P.R. AU - Godwin, J. AU - Gould, F. AU - Howald, G.R. AU - Piaggio, A. AU - Thomas, P. AU - Tompkins, D.M. AU - Threadgill, D. AU - Delborne, J. AU - Kanavy, D.M. AU - Kuiken, T. AU - Packard, H. AU - Serr, M. AU - Shiels, A. T2 - Island Invasives: Scaling up to meet the challenge A2 - Veitch, C.R. A2 - Clout, M.N. A2 - Martin, A.R. A2 - Russell, J.C. A2 - West, C.J. T3 - Occasional Paper SSC PY - 2019/// SP - 6–14 PB - IUCN SV - 62 ER - TY - CHAP TI - Governance of synthetic biology and biodiversity conservation AU - Slobodian, L. AU - Winter, G. AU - Thizy, D. AU - Oliva, M.J. AU - Kingiri, A. AU - Kokotovich, A. AU - Delborne, J. T2 - Genetic Frontiers for Conservation: An Assessment of Synthetic Biology and Biodiversity Conservation A2 - Redford, K.H. A2 - Brooks, T.M. A2 - Macfarlane, N.B.W. A2 - Adams, J.S. PY - 2019/// SP - 19-48 PB - IUCN SN - 9782831719733 9782831719740 ER - TY - CHAP TI - Summing Up and Looking Forward AU - Redford, K.H. AU - Brooks, T.M. AU - Macfarlane, N.B.W. AU - Delborne, J. AU - Adams, J.S. T2 - Genetic Frontiers for Conservation: An Assessment of Synthetic Biology and Biodiversity Conservation A2 - Redford, K.H. A2 - Brooks, T.M. A2 - Macfarlane, N.B.W. A2 - Adams, J.S. PY - 2019/// SP - 119-126 PB - IUCN SN - 9782831719733 9782831719740 ER - TY - CHAP TI - Evidence in the Context of Synthetic Biology and Biodiversity Conservation AU - Delborne, J. AU - Kokotovich, A. AU - Kolodziejczyk, B. T2 - Genetic Frontiers for Conservation A2 - Redford, K.H. A2 - Brooks, T.M. A2 - Macfarlane, N.B.W. A2 - Adams, J.S. PY - 2019/// SP - 49-58 PB - IUCN SN - 9782831719733 9782831719740 ER - TY - RPRT TI - Exploring Stakeholder Perspectives on the Development of a Gene Drive Mouse for Biodiversity Protection on Islands: Summary Report of Stakeholder Interviews AU - Delborne, J. AU - Shapiro, J. AU - Farooque, M. AU - Ford, T. AU - George, D. AU - Dermer, S. DA - 2019/3/7/ PY - 2019/3/7/ UR - http://go.ncsu.edu/ges-gene-drive-landscape ER - TY - RPRT TI - Exploring Stakeholder Perspectives on the Development of a Gene Drive Mouse for Biodiversity Protection on Islands AU - Farooque, M. AU - Barnhill-Dilling, S.K. AU - Shapiro, J. AU - Delborne, J. DA - 2019/2// PY - 2019/2// M3 - Workshop Report UR - http://go.ncsu.edu/ges-gene-drive-workshop ER - TY - SOUND TI - Forest Health and Biotechnology: Possibilities and Considerations AU - Delborne, J. AU - Offut, S. AU - DiFazio, S. AU - Ibanez, I. DA - 2019/1/8/ PY - 2019/1/8/ ER - TY - CONF TI - Exploring Stakeholder Perspectives on the Development of a Gene Drive Mouse for Biodiversity Protection AU - Delborne, J. AU - Farooque, M. AU - Shapiro, J. T2 - North Carolina State University C2 - 2019/3/7/ CY - Raleigh, NC DA - 2019/3/7/ PY - 2019/3/7/ PB - DARPA Safe Genes Program ER - TY - CONF TI - Workshop on the Impacts and Management of Free-Ranging Cats in U.S. National Parks AU - Delborne, J. AU - Kokotovich, A. AU - Redford, K. T2 - National Park Service C2 - 2019/3/19/ CY - Alexandria, VA DA - 2019/3/19/ PY - 2019/3/19/ ER - TY - CONF TI - Reflecting on Reflexivity in Practice: Responsible Innovation, Engagement, and Governance AU - Delborne, J. AU - George, D. AU - Kokotovich, A. T2 - Annual Meeting of the Society for Social Studies of Science C2 - 2019/9/5/ CY - New Orleans, LA DA - 2019/9/5/ PY - 2019/9/5/ ER - TY - CONF TI - Having Conversations about the USDA’s New GMO Labelling Standard AU - Delborne, J. AU - Bloom, D. AU - Dankbar, H. AU - Stout, R. AU - Cruz, A. AU - Goodwin, J. AU - Mugwanya, N. AU - Barnhill-Dilling, S.K. T2 - NC Cooperative Extension State Conference C2 - 2019/10/30/ DA - 2019/10/30/ PY - 2019/10/30/ ER - TY - JOUR TI - An Important Community in Restoration Efforts to Protect the American Chestnut Tree AU - Barnhill-Dilling, S.K. AU - Delborne, J.A. T2 - Science Trends DA - 2019/5/13/ PY - 2019/5/13/ UR - https://sciencetrends.com/an-important-community-in-restoration-efforts-to-protect-the-american-chestnut-tree/ ER - TY - SOUND TI - Forest Biotech AU - Delborne, J. DA - 2019/// PY - 2019/// UR - https://academicminute.org/2019/07/jason-delborne-north-carolina-state-university-forest-biotech/ ER - TY - CONF TI - The Potential for Biotechnology to Address Forest Health (NASEM Report) AU - Delborne, J. T2 - Genetic Engineering and Society Colloquium C2 - 2019/2/19/ CY - North Carolina State University, Raleigh, NC DA - 2019/2/19/ PY - 2019/2/19/ ER - TY - SOUND TI - Forest Biotechnology and Public Values AU - Delborne, J. DA - 2019/1/17/ PY - 2019/1/17/ ER - TY - CONF TI - Rooting Innovation in Forest Biotechnology in Public Engagement AU - Delborne, J. T2 - American Association for the Advancement of Science Annual Meeting C2 - 2019/2/16/ CY - Washington, DC DA - 2019/2/16/ PY - 2019/2/16/ ER - TY - SOUND TI - Listening and Talking about GMOs AU - Delborne, J. DA - 2019/2/27/ PY - 2019/2/27/ ER - TY - CONF TI - Promises and Fears of New Biotechnologies: Making Decisions with Stakeholder and Community Participation AU - Delborne, J. T2 - Science History Institute, Joseph Priestly Society C2 - 2019/3/14/ CY - Philadelphia, PA DA - 2019/3/14/ PY - 2019/3/14/ ER - TY - CONF TI - Engagement – Motivations and Methods AU - Delborne, J. T2 - Workshop on the impacts and management of Free-Ranging Cats in U.S. National Parks C2 - 2019/3/20/ CY - River Farm, Alexandria, VA DA - 2019/3/20/ PY - 2019/3/20/ ER - TY - CONF TI - Interdisciplinary Research AU - Delborne, J. T2 - University Research Symposium, hosted by the Research Leadership Academy C2 - 2019/3/21/ CY - North Carolina State University, Raleigh, NC DA - 2019/3/21/ PY - 2019/3/21/ ER - TY - SOUND TI - Biotechnology in Social and Political Contexts AU - Delborne, J. DA - 2019/4/24/ PY - 2019/4/24/ ER - TY - CONF TI - Wicked, Post-Normal, Complex: Using Social Science to Enhance Academies Work in the Life Sciences AU - Delborne, J. T2 - Board on Life Sciences Spring 2019 Meeting, National Academies of Sciences, Engineering, and Medicine C2 - 2019/4/26/ CY - Washington, DC DA - 2019/4/26/ PY - 2019/4/26/ ER - TY - CONF TI - Public Engagement when Biotechnology Goes ‘Wild’ AU - Delborne, J. T2 - Genetics and Genomics Initiative Annual Retreat C2 - 2019/8/19/ CY - Park Alumni Center, North Carolina State University DA - 2019/8/19/ PY - 2019/8/19/ ER - TY - CONF TI - Bioethics and Public Outreach – Starting the Conversation AU - Palmer, Clare AU - Delborne, J. T2 - Enabling Discovery through Genomic Tools, National Science Foundation 1st Annual EDGE Investigator Meeting C2 - 2019/4/29/ CY - Alexandria, VA DA - 2019/4/29/ PY - 2019/4/29/ ER - TY - SOUND TI - Communicating Biotechnology with the Public AU - Delborne, J. DA - 2019/12/3/ PY - 2019/12/3/ ER - TY - CONF TI - Decision Points in the Design of Deliberative Forums AU - Delborne, J. T2 - Public Deliberation on Gene Editing in the Wild Working Group C2 - 2019/6/20/ CY - The Hastings Center, Garrison, NY DA - 2019/6/20/ PY - 2019/6/20/ ER - TY - BOOK TI - Forest Health and Biotechnology: Possibilities and Considerations AU - Offutt, S.E. AU - Chhatre, V.E. AU - Delborne, J. AU - DiFazio, S. AU - Gordon, D. AU - Ibanez, I. AU - Jaffe, G. AU - Needham, M.D. AU - Palmer, C. AU - Romero-Severson, J. AU - Sederoff, R.R. AU - Six, D.L. DA - 2019/// PY - 2019/// PB - National Academies Press ER - TY - CHAP TI - Genetic Engineering and Society AU - Barnes, Jessica Cavin AU - Pitts, Elizabeth A. AU - Barnhill-Dilling, S. Kathleen AU - Delborne, Jason A. T2 - Science, Technology, and Society AB - Genetic engineering disrupts assumed distinctions between nature and culture, between human and nonhuman, and between the production of knowledge and the production of commercially viable products. As a result, this area of technological development continues to inspire science and technology studies (STS) researchers not only to rethink theoretical paradigms, but also to test and retest a variety of ways to intervene in science and society. PY - 2019/11/21/ DO - 10.1017/9781316691489.009 SP - 203-233 OP - PB - Cambridge University Press SN - 9781316691489 9781107165120 9781316616895 UR - http://dx.doi.org/10.1017/9781316691489.009 DB - Crossref 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 - 2019/11/5/ PY - 2019/11/5/ DO - 10.1080/08941920.2019.1685145 VL - 33 IS - 1 SP - 83-100 J2 - Society & Natural Resources LA - en OP - SN - 0894-1920 1521-0723 UR - http://dx.doi.org/10.1080/08941920.2019.1685145 DB - Crossref KW - Chestnut restoration KW - genetic engineering KW - indigenous environmental justice ER - TY - JOUR TI - Mobile Corporate Social Responsibility (mCSR): Examining Publics’ Responses to CSR-Based Initiatives in Natural Disasters AU - Cheng, Yang AU - Jin, Yan AU - Hung-Baesecke, Chun-Ju Flora AU - Chen, Yi-Ru Regina T2 - International Journal of Strategic Communication AB - As social media use on mobile devices has been integrated in people’s daily lives, corporations began to target the publics on corporate social responsibility (CSR) activities on mobile devices. In the context of a natural disaster, this study examines how publics respond to CSR-based initiatives by way of mobile corporate social responsibility (mCSR), including gratifications, social media engagement, perceived CSR motives, and the relationship outcomes as associated with mCSR practice. An online survey was conducted by sampling with 1,433 nationally representative adults in the United States. Findings indicated that four broad types of gratification, such as technological convenience, social interaction, recreation, and information exchange, significantly influenced relationship outcomes such as satisfaction, commitment, distrust, trust, and control mutuality. Results also demonstrated that perceived CSR motives and social media engagement on mobile devices were significantly related to relationship outcomes, providing empirical evidence for the important role that potential mCSR communications can play in engaging publics and cultivating relationships during natural disasters. DA - 2019/1// PY - 2019/1// DO - 10.1080/1553118X.2018.1524382 VL - 13 IS - 1 SP - 76–93 SN - 1553-118X 1553-1198 UR - http://dx.doi.org/10.1080/1553118X.2018.1524382 ER - TY - JOUR TI - Shoot shovel and sanction yourself: Self-policing as a response to wolf poaching among Swedish hunters AU - Peterson, M. Nils AU - von Essen, Erica AU - Hansen, Hans Peter AU - Peterson, Tarla Rai T2 - Ambio AB - Self-policing is essential for addressing wildlife-related crime where illegal activity is extremely diffuse, and limited resources are available for monitoring and enforcement. Emerging research on self-policing suggest key drivers including economics, folk traditions, and socio-political resistance. We build on this research with a case study evaluating potential drivers of self-policing illegal wolf killing among Swedish hunting teams. Swedish hunters marginally leaned toward considering illegal hunting of wolves an expression of resistance (10.30 out of a possible 17 on a resistance scale) and strongly believed outsiders had undue influence over hunting (15.79 out of a possible 21 on an influence scale). Most (73%) Swedish hunters stated they would report illegal wolf killing to authorities, but 20% stated they would handle the infractions through internal sanctions. Viewing illegal hunting of wolves as a form of political resistance, viewing wolf management as being controlled locally, and perceived prevalence of illegal wolf killing among hunting acquaintances were positive predictors of preferring internal sanctions to address illegal wolf killing over reporting the crimes. Resistance and perceived prevalence of wolf killing also predicted preferring no action to address illegal wolf killing. These results suggest that a counterpublic of marginalized ruralism may promote forms of self-policing that rely on internal censure for illegal wolf killing rather than using formal legal channels. Similarly, folk traditions within this counterpublic (e.g., perceptions of prevalence of illegal wolf killing) shape if and how internal sanctions are advocated. Re-engaging marginalized hunting groups and emphasizing the rarity of illegal wolf killing may promote wolf conservation, both in Sweden and in other democratic regimes. DA - 2019/3// PY - 2019/3// DO - 10.1007/S13280-018-1072-5 VL - 48 IS - 3 SP - 230–239 SN - 0044-7447 1654-7209 UR - http://dx.doi.org/10.1007/S13280-018-1072-5 KW - Hunting KW - Poaching KW - Power KW - Predators KW - Resistance KW - Social influence KW - Wolves ER - TY - JOUR TI - Cover Image AU - Yang, Fei AU - Niu, Kechang AU - Collins, Courtney G. AU - Yan, Xuebin AU - Ji, Yangguang AU - Ling, Ning AU - Zhou, Xianhui AU - Du, Guozhen AU - Guo, Hui AU - Hu, Shuijin T2 - Land Degradation & Development AB - The cover image is based on the Research Article Grazing practices affect the soil microbial community composition in a Tibetan alpine meadow, by Fei Yang et al., https://doi.org/10.1002/ldr.3189. DA - 2019/1/15/ PY - 2019/1/15/ DO - 10.1002/LDR.3244 VL - 30 IS - 1 SP - i-i SN - 1085-3278 UR - http://dx.doi.org/10.1002/LDR.3244 ER - TY - JOUR TI - Flux modeling for monolignol biosynthesis AU - Wang, Jack P AU - Matthews, Megan L AU - Naik, Punith P AU - Williams, Cranos M AU - Ducoste, Joel J AU - Sederoff, Ronald R AU - Chiang, Vincent L T2 - Current Opinion in Biotechnology AB - The pathway of monolignol biosynthesis involves many components interacting in a metabolic grid to regulate the supply and ratios of monolignols for lignification. The complexity of the pathway challenges any intuitive prediction of the output without mathematical modeling. Several models have been presented to quantify the metabolic flux for monolignol biosynthesis and the regulation of lignin content, composition, and structure in plant cell walls. Constraint-based models using data from transgenic plants were formulated to describe steady-state flux distribution in the pathway. Kinetic-based models using enzyme reaction and inhibition constants were developed to predict flux dynamics for monolignol biosynthesis in wood-forming cells. This review summarizes the recent progress in flux modeling and its application to lignin engineering for improved plant development and utilization. DA - 2019/4// PY - 2019/4// DO - 10.1016/J.COPBIO.2018.12.003 VL - 56 SP - 187-192 J2 - Current Opinion in Biotechnology LA - en OP - SN - 0958-1669 UR - http://dx.doi.org/10.1016/J.COPBIO.2018.12.003 DB - Crossref ER - TY - JOUR TI - Directions for research and training in plant omics: Big Questions and Big Data AU - Argueso, Cristiana T. AU - Assmann, Sarah M. AU - Birnbaum, Kenneth D. AU - Chen, Sixue AU - Dinneny, José R. AU - Doherty, Colleen J. AU - Eveland, Andrea L. AU - Friesner, Joanna AU - Greenlee, Vanessa R. AU - Law, Julie A. AU - Marshall-Colón, Amy AU - Mason, Grace Alex AU - O'Lexy, Ruby AU - Peck, Scott C. AU - Schmitz, Robert J. AU - Song, Liang AU - Stern, David AU - Varagona, Marguerite J. AU - Walley, Justin W. AU - Williams, Cranos M. T2 - Plant Direct AB - Abstract A key remit of the NSF ‐funded “Arabidopsis Research and Training for the 21 st Century” ( ART ‐21) Research Coordination Network has been to convene a series of workshops with community members to explore issues concerning research and training in plant biology, including the role that research using Arabidopsis thaliana can play in addressing those issues. A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al., Plant Physiology , 175, 2017, 1499). In this white paper, we provide a summary of the discussions and insights arising from the second ART ‐21 workshop. The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through post‐doctorates, early career and established investigators. Our hope is that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems. DA - 2019/4// PY - 2019/4// DO - 10.1002/PLD3.133 VL - 3 IS - 4 SP - e00133 J2 - Plant Direct LA - en OP - SN - 2475-4455 UR - http://dx.doi.org/10.1002/PLD3.133 DB - Crossref KW - genomics KW - metabolomics KW - proteomics KW - training KW - transcriptomics ER - TY - BLOG TI - Biotechnology Oversight Gets an Early Make-Over by Trump’s White House and USDA: Part 1—The Executive Order AU - Kuzma, J. T2 - GES Blog DA - 2019/// PY - 2019/// PB - Genetic Engineering and Society Center/North Carolina State University UR - https://research.ncsu.edu/ges/2019/06/ag-biotech-oversight-makeover-part-1-eo/ ER - TY - BLOG TI - Biotechnology Oversight Gets an Early Make-Over by Trump’s White House and USDA: Part 2 – The USDA-APHIS Rule AU - Kuzma, J. T2 - GES Blog DA - 2019/7/2/ PY - 2019/7/2/ PB - Genetic Engineering and Society Center/North Carolina State University UR - https://research.ncsu.edu/ges/2019/07/ag-biotech-oversight-makeover-part-2-usda-aphis-rule/ ER - TY - JOUR TI - Public Reason and Reasonable Conceptions of Justice AU - Dubljević, V. T2 - Sofia Philosophical Review DA - 2019/// PY - 2019/// VL - 12 IS - 1 SP - 24–46 ER - TY - CHAP TI - Review of Virtual Reality Hardware Employed in K-20 Science Education AU - Hite, R. AU - Childers, G. AU - Jones, M.G. T2 - Handbook of Mobile Teaching and Learning A2 - Zhang, A. A2 - Cristol, D. PY - 2019/// DO - 10.1007/978-3-642-41981-2_123-1 ET - 2nd SP - 1–12 PB - Springer Nature UR - https://doi.org/10.1007/978-3-642-41981-2_123-1 ER - TY - BOOK TI - Discovery engineering in physical science: Case studies for grades 6–12 AU - Jones, M.G. AU - Corin, E. AU - Ennes, M. AU - Cayton, E. AU - Childers, G. DA - 2019/// PY - 2019/// PB - National Science Teachers Association Press ER - TY - JOUR TI - Pre-Service and In-Service Science Teachers’ Technological Acceptance of 3D, Haptic-Enabled Virtual Reality Instructional Technology AU - Hite, R. AU - Jones, M.G. AU - Childers, G. AU - Chesnutt, K. AU - Corin, E.N. AU - Pereyra, M. T2 - Electronic Journal of Science Education DA - 2019/// PY - 2019/// VL - 23 IS - 1 UR - https://ejse.southwestern.edu/article/view/18732 ER - TY - CHAP TI - Chapter 9. Radically reframing the climate debate AU - Goodwin, Jean T2 - Argumentation in Context PY - 2019/9/23/ DO - 10.1075/aic.17.09goo SP - 157-172 OP - PB - John Benjamins Publishing Company SN - 9789027204028 9789027262134 UR - http://dx.doi.org/10.1075/aic.17.09goo DB - Crossref ER - TY - BOOK TI - Science Breakthroughs to Advance Food and Agricultural Research by 2030 DA - 2019/// PY - 2019/// DO - 10.17226/25059 SE - 1-228 ER - TY - JOUR TI - Automated Imaging, Tracking, and Analytics Pipeline for Differentiating Environmental Effects on Root Meristematic Cell Division AU - Buckner, Eli AU - Madison, Imani AU - Chou, Hsuan AU - Matthiadis, Anna AU - Melvin, Charles E. AU - Sozzani, Rosangela AU - Williams, Cranos AU - Long, Terri A. T2 - Frontiers in Plant Science AB - Exposure of plants to abiotic stresses, whether individually or in combination, triggers dynamic changes to gene regulation. These responses induce distinct changes in phenotypic characteristics, enabling the plant to adapt to changing environments. For example, iron deficiency and heat stress have been shown to alter root development by reducing primary root growth and reducing cell proliferation, respectively. Currently, identifying the dynamic temporal coordination of genetic responses to combined abiotic stresses remains a bottleneck. This is, in part, due to an inability to isolate specific intervals in developmental time where differential activity in plant stress responses plays a critical role. Here, we observed that iron deficiency, in combination with temporary heat stress, suppresses the expression of iron deficiency-responsive pPYE::LUC (POPEYE::luciferase) and pBTS::LUC (BRUTUS::luciferase) reporter genes. Moreover, root growth was suppressed less under combined iron deficiency and heat stress than under either single stress condition. To further explore the interaction between pathways, we also created a computer vision pipeline to extract, analyze, and compare high-dimensional dynamic spatial and temporal cellular data in response to heat and iron deficiency stress conditions at high temporal resolution. Specifically, we used fluorescence light sheet microscopy to image Arabidopsis thaliana roots expressing CYCB1;1:GFP, a marker for cell entry into mitosis, every 20 min for 24 h exposed to either iron sufficiency, iron deficiency, heat stress, or combined iron deficiency and heat stress. Our pipeline extracted spatiotemporal metrics from these time-course data. These metrics showed that the persistency and timing of CYCB1;1:GFP signal were uniquely different under combined iron deficiency and heat stress conditions versus the single stress conditions. These metrics also indicated that the spatiotemporal characteristics of the CYCB1;1:GFP signal under combined stress were more dissimilar to the control response than the response seen under iron deficiency for the majority of the 24-h experiment. Moreover, the combined stress response was less dissimilar to the control than the response seen under heat stress. This indicated that pathways activated when the plant is exposed to both iron deficiency and heat stress affected CYCB1;1:GFP spatiotemporal function antagonistically. DA - 2019/11/19/ PY - 2019/11/19/ DO - 10.3389/fpls.2019.01487 VL - 10 J2 - Front. Plant Sci. OP - SN - 1664-462X UR - http://dx.doi.org/10.3389/fpls.2019.01487 DB - Crossref KW - light sheet imaging KW - image analysis KW - cell cycle progression KW - heat stress and iron deficiency stresses KW - combined stresses ER - TY - CHAP TI - Pediatric Neuro-enhancement, Best Interest, and Autonomy: A Case of Normative Reversal AU - Dubljević, Veljko AU - Racine, Eric T2 - Advances in Neuroethics AB - The debate on “cognitive enhancement” has moved from discussions about enhancement in adults to enhancement in children and adolescents. Similar to positions expressed in the adult context, some have argued that pediatric cognitive enhancement is acceptable and even laudable. However, the implications differ between the adult and the pediatric contexts. For example, in the debate over cognitive enhancement in adults, i.e., those who have legal majority, respect for autonomy demands that personal preferences not be overridden in absence of strong arguments because competent adults are in the best position to recognize and protect their own interests. However, the concepts of best interest and autonomy provide a different picture in the case of pediatric enhancement. In the context of decision-making involving minors, it is assumed that the parents are in the best position to promote and protect the interests of their children and this is chiefly why they are granted the authority to make decisions on their behalf. However, we argue in favor of guarding the physical integrity of children from intrusive medical interventions without medical need and with clear and detrimental effects (e.g., suppressing growth). We also support leaving open other legitimate life trajectory and career choices, as this is in the best interest of the child, even if they are less in line with the expectations of parents or success in educational settings. In addition, parental decision-making in favor of cognitive enhancement suffers from a lack of information about cognitive enhancers (e.g., safety and efficacy) and potential biases. Thus, bearing in mind these issues and the development of volitional capacities of children, we argue that pediatric enhancement is not a morally acceptable practice and “inevitability” can be curbed with clear and fair rules that establish duties of state representatives, physicians, and public institutions. We conclude by canvassing evidence-based policy options that could protect the open future of minors and define the parameters of parental decision-making analogous to the cases of nicotine and alcohol. PY - 2019/// DO - 10.1007/978-3-030-10677-5_13 SP - 199-212 OP - PB - Springer International Publishing SN - 9783030106768 9783030106775 UR - http://dx.doi.org/10.1007/978-3-030-10677-5_13 DB - Crossref ER - TY - JOUR TI - A nonparametric spatial test to identify factors that shape a microbiome AU - Singh, Susheela P. AU - Staicu, Ana-Maria AU - Dunn, Robert R. AU - Fierer, Noah AU - Reich, Brian J. T2 - The Annals of Applied Statistics AB - The advent of high-throughput sequencing technologies has made data from DNA material readily available, leading to a surge of microbiome-related research establishing links between markers of microbiome health and specific outcomes. However, to harness the power of microbial communities we must understand not only how they affect us, but also how they can be influenced to improve outcomes. This area has been dominated by methods that reduce community composition to summary metrics, which can fail to fully exploit the complexity of community data. Recently, methods have been developed to model the abundance of taxa in a community, but they can be computationally intensive and do not account for spatial effects underlying microbial settlement. These spatial effects are particularly relevant in the microbiome setting because we expect communities that are close together to be more similar than those that are far apart. In this paper, we propose a flexible Bayesian spike-and-slab variable selection model for presence-absence indicators that accounts for spatial dependence and cross-dependence between taxa while reducing dimensionality in both directions. We show by simulation that in the presence of spatial dependence, popular distance-based hypothesis testing methods fail to preserve their advertised size, and the proposed method improves variable selection. Finally, we present an application of our method to an indoor fungal community found within homes across the contiguous United States. DA - 2019/12// PY - 2019/12// DO - 10.1214/19-aoas1262 VL - 13 IS - 4 SP - 2341-2362 J2 - Ann. Appl. Stat. LA - en OP - SN - 1932-6157 UR - http://dx.doi.org/10.1214/19-aoas1262 DB - Crossref KW - Bayesian nonparametrics KW - Dirichlet process KW - high dimensional data KW - spatial modeling KW - spike-and-slab prior KW - variable selection ER - TY - JOUR TI - Tissue-specific changes in size and shape of the ligaments and tendons of the porcine knee during post-natal growth AU - Cone, Stephanie G. AU - Piercy, Hope E. AU - Lambeth, Emily P. AU - Ru, Hongyu AU - Piedrahita, Jorge A. AU - Spang, Jeffrey T. AU - Fordham, Lynn A. AU - Fisher, Matthew B. T2 - PLOS ONE AB - Prior studies have analyzed growth of musculoskeletal tissues between species or across body segments; however, little research has assessed the differences in similar tissues within a single joint. Here we studied changes in the length and cross-sectional area of four ligaments and tendons, (anterior cruciate ligament, patellar tendon, medial collateral ligament, lateral collateral ligament) in the tibiofemoral joint of female Yorkshire pigs through high-field magnetic resonance imaging throughout growth. Tissue lengths increased by 4- to 5-fold from birth to late adolescence across the tissues while tissue cross-sectional area increased by 10–20-fold. The anterior cruciate ligament and lateral collateral ligament showed allometric growth favoring change in length over change in cross-sectional area while the patellar tendon and medial collateral ligament grow in an isometric manner. Additionally, changes in the length and cross-sectional area of the anterior cruciate ligament did not increase as much as in the other ligaments and tendon of interest. Overall, these findings suggest that musculoskeletal soft tissue morphometry can vary within tissues of similar structure and within a single joint during post-natal growth. DA - 2019/10/23/ PY - 2019/10/23/ DO - 10.1371/journal.pone.0219637 VL - 14 IS - 10 SP - SN - 1932-6203 ER - TY - JOUR TI - Amending marginal sandy soils with biochar and lignocellulosic fermentation residual sustains fertility in elephantgrass bioenergy cropping systems AU - Reyes-Cabrera, Joel AU - Erickson, John E. AU - Leon, Ramon G. AU - Silveira, Maria L. AU - Sollenberger, Lynn E. T2 - NUTRIENT CYCLING IN AGROECOSYSTEMS DA - 2019/9// PY - 2019/9// DO - 10.1007/s10705-019-10011-6 VL - 115 IS - 1 SP - 69-83 SN - 1573-0867 KW - Soil fertility KW - Nutrient management KW - Bioenergy KW - Elephantgrass KW - Residuals KW - Biochar KW - Nutrient cycling ER - TY - JOUR TI - A Genome Wide Association Study Reveals Markers and Genes Associated with Resistance to Fusarium verticillioides Infection of Seedlings in a Maize Diversity Panel AU - Stagnati, Lorenzo AU - Lanubile, Alessandra AU - Samayoa, Luis F. AU - Bragalanti, Mario AU - Giorni, Paola AU - Busconi, Matteo AU - Holland, James B. AU - Marocco, Adriano T2 - G3-GENES GENOMES GENETICS AB - Fusarium verticillioides infects maize, causing ear rot, yield loss and contamination by fumonisin mycotoxins. The fungus can be transmitted via kernels and cause systemic infection in maize. Maize resistance to the fungus may occur at different developmental stages, from seedling to maturity. Resistance during kernel germination is part of the plant-pathogen interaction and so far this aspect has not been investigated. In the present study, a genome wide association study (GWAS) of resistance to Fusarium during the seedling developmental stage was conducted in a maize diversity panel using 226,446 SNP markers. Seedling germination and disease phenotypes were scored on artificially inoculated kernels using the rolled towel assay. GWAS identified 164 SNPs significantly associated with the traits examined. Four SNPs were associated with disease severity score after inoculation, 153 were associated with severity in asymptomatic kernels and 7 with the difference between the severity ratings in inoculated and non-inoculated seeds. A set of genes containing or physically near the significant SNPs were identified as candidates for Fusarium resistance at the seedling stage. Functional analysis revealed that many of these genes are directly involved in plant defense against pathogens and stress responses, including transcription factors, chitinase, cytochrome P450, and ubiquitination proteins. In addition, 25 genes were found in high linkage disequilibrium with the associated SNPs identified by GWAS and four of them directly involved in disease resistance. These findings contribute to understanding the complex system of maize-F. verticillioides and may improve genomic selection for Fusarium resistance at the seedling stage. DA - 2019/2// PY - 2019/2// DO - 10.1534/g3.118.200916 VL - 9 IS - 2 SP - 571-579 SN - 2160-1836 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85061232004&partnerID=MN8TOARS KW - Fusarium verticillioides KW - resistance to seedling disease KW - Genome Wide Association Studies KW - Maize KW - Rolled Towel Assay KW - SNPs ER - TY - JOUR TI - Effects on white-tailed deer following eastern coyote colonization AU - Bragina, Eugenia V. AU - Kays, Roland AU - Hody, Allison AU - Moorman, Christopher E. AU - Deperno, Christopher S. AU - Mills, L. Scott T2 - JOURNAL OF WILDLIFE MANAGEMENT AB - ABSTRACT The expansion or recovery of predators can affect local prey populations. Since the 1940s, coyotes ( Canis latrans ) have expanded into eastern North America where they are now the largest predator and prey on white‐tailed deer ( Odocoileus virginianus ). However, their effect on deer populations remains controversial. We tested the hypothesis that coyotes, as a novel predator, would affect deer population dynamics across large spatial scales, and the strongest effects would occur after a time lag following initial coyote colonization that allows for the predator populations to grow. We evaluated deer population trends from 1981 to 2014 in 384 counties of 6 eastern states in the United States with linear mixed models. We included deer harvest data as a proxy for deer relative abundance, years since coyote arrival in a county as a proxy of coyote abundance, and landscape and climate covariates to account for environmental effects. Overall, deer populations in all states experienced positive population growth following coyote arrival. Time since coyote arrival was not a significant predictor in any deer population models and our results indicate that coyotes are not controlling deer populations at a large spatial scale in eastern North America. © 2019 The Wildlife Society. DA - 2019/5// PY - 2019/5// DO - 10.1002/jwmg.21651 VL - 83 IS - 4 SP - 916-924 SN - 1937-2817 KW - eastern coyote KW - novel predator KW - population growth rate KW - predator-prey dynamics KW - spatial compensation ER - TY - JOUR TI - Brassica carinata Seeding Rate and Row Spacing Effects on Morphology, Yield, and Oil AU - Mulvaney, Michael J. AU - Leon, Ramon G. AU - Seepaul, Ramdeo AU - Wright, David L. AU - Hoffman, Travis L. T2 - AGRONOMY JOURNAL AB - Core Ideas Carinata growth and yield was influenced more by row spacing than seeding rate. Rows spaced at 36 cm maximized carinata yield. Carinata branching was favored by wider row spacing. Carinata ( Brassica carinata A. Braun) is an oilseed crop with potential as a winter crop in the southeastern United States to diversify crop rotations and provide biofuel production and livestock feed. The objective was to evaluate the effects of row spacing and seeding rate on carinata yield and oil composition. Field experiments were conducted in Jay and Quincy, FL, from 2013 to 2016 evaluating carinata growth, seed and oil yield, and oil composition grown in a factorial arrangement of four seeding rates (3, 6, 9, and 12 kg ha −1 ) and four row spacings (18, 36, 53, and 89 cm). No interactions between seeding rate and row spacing were detected. Seeding rate did not influence any of the variables studied. In contrast, row spacing affected seed and oil yield, branch production, and pods per plant. Seed yield (ranked from highest to lowest) was 2761, 2286, 1851, and 1572 kg ha −1 for rows spaced at 36, 18, 53, and 89 cm, respectively. Branching and pods per plant increased with row spacing. Neither seeding rate nor row spacing affected oil concentration and quality. Oil concentration averaged 40%, of which more than a third was erucic acid (C22:1). Protein concentration was 31%, and glucosinolate concentration was 93 μmol g −1 . The results of the present study demonstrated that carinata can be successfully grown in the southeastern United States, reaching yields and oil quality similar to those reported at other latitudes, and can be a source of biofuel, protein for animal feed, and cropping system diversification for growers. DA - 2019/// PY - 2019/// DO - 10.2134/agronj2018.05.0316 VL - 111 IS - 2 SP - 528-535 SN - 1435-0645 ER - TY - JOUR TI - Application Timing Affects Tolerance of Zoysiagrass to Fluazifop-P-butyl and Safening Effect of Triclopyr AU - Liu, Wenwen AU - Unruh, J. Bryan AU - Kenworthy, Kevin E. AU - MacDonald, Gregory E. AU - Trenholm, Laurie E. AU - Leon, Ramon G. T2 - CROP SCIENCE AB - ABSTRACT Aryloxyphenoxypropionate (AOPP) herbicides, such as fluazifop‐P‐butyl, can be used for postemergence control of grassy weeds in zoysiagrass ( Zoysia spp.), although the turf might suffer transient injury. This injury can be reduced by tank mixing fluazifop‐P‐butyl with triclopyr, an herbicide that behaves as a safener for AOPP herbicides. To characterize seasonal variation in zoysiagrass injury caused by fluazifop‐P‐butyl and triclopyr applications, we conducted a 2‐yr study on three Zoysia spp. cultivars (‘Empire’, ‘Geo’, and ‘Zeon’) at Jay, FL, from August 2015 to April 2017, evaluating how injury and turf quality were affected after spring, summer, and fall applications. The level of injury and changes in turf quality were influenced by fluazifop‐P‐butyl application timing, but the most sensitive season varied with the cultivar. The seasons with the greatest injury were also the ones in which the safening activity of triclopyr was most effective. In addition, when triclopyr was applied with fluazifop‐P‐butyl, the quality of all evaluated cultivars recovered to the level of nontreated controls by 2 wk after treatment. Nonstructural carbohydrate content was not affected by herbicide applications, but there were major differences in glucose and starch content between above‐ and belowground tissue depending on cultivar and season. Overall, our study confirmed that tank mixing triclopyr can reduce fluazifop‐P‐butyl phytotoxicity in zoysiagrass, and in the case of relatively tolerant cultivars, it might allow the use of rates higher than the current labeled rate with little negative impact on turf quality while providing better control of both broadleaf and grassy weeds. DA - 2019/// PY - 2019/// DO - 10.2135/cropsci2018.12.0724 VL - 59 IS - 4 SP - 1789-1798 SN - 1435-0653 ER - TY - JOUR TI - High-throughput genotyping in onion reveals structure of genetic diversity and informative SNPs useful for molecular breeding AU - Villano, Clizia AU - Esposito, Salvatore AU - Carucci, Francesca AU - Iorizzo, Massimo AU - Frusciante, Luigi AU - Carputo, Domenico AU - Aversano, Riccardo T2 - Molecular Breeding DA - 2019/1// PY - 2019/1// DO - 10.1007/s11032-018-0912-0 VL - 39 IS - 1 SP - SN - 1380-3743 1572-9788 UR - http://dx.doi.org/10.1007/S11032-018-0912-0 KW - Allium sp KW - KASP KW - SNPs KW - Population structure ER - TY - JOUR TI - Optimizing the deployment of ultra-low volume and 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 AB - Abstract 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 not well understood, however. 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] over the 11-year study period, 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. Author Summary Over half of the world’s population is at risk of infection by dengue virus (DENV) from Aedes a egypti mosquitoes . While most infected people experience mild or asymptomatic infections, dengue can cause severe symptoms, such as hemorrhage, shock, and death. A vaccine against dengue exists, but it can increase the risk of severe disease in people who have not been previously infected by one of the four DENV serotypes. In many places, therefore, the best currently available way to prevent outbreaks is by controlling the mosquito population. Our study used a simulation model to explore alternative strategies for deploying insecticide in the city of Iquitos in the Peruvian Amazon. Our simulations closely matched empirical patterns from studies of dengue’s ecology and epidemiology in Iquitos, such as mosquito population dynamics, human household structure, demography, human and mosquito movement, and virus transmission. Our results indicate that an insecticide that has a long-lasting, residual effect will have the biggest impact on reducing DENV transmission. For non-residual insecticides, we find that it is best to begin spraying close to the start of the dengue transmission season, as mosquito populations can rebound quickly and resume previous levels of transmission. DA - 2019/10/2/ PY - 2019/10/2/ DO - 10.1101/19007971 UR - https://doi.org/10.1101/19007971 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 AB - Abstract The lack of effective vaccines for many endemic diseases often forces policymakers to enact control programs that rely on non-immunizing controls, such as vector control, in order to reduce the massive burden of these diseases. It is well known that controls can have counterintuitive effects, such as the honeymoon effect, in which partially effective controls cause not only a greater initial reduction in infection than expected for an infection near its endemic equilibrium, but also large outbreaks during control as a result of accumulation of susceptibles. Unfortunately, many control measures cannot be maintained indefinitely, and the results of cessation are not well 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 the control measures, 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 model results from a number of settings when non-immunizing controls are used against an infection that confers immunity. Finally, we also 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. Author Summary Many common endemic infections lack effective, inexpensive vaccinations, and control relies instead on transmission reduction, e.g. mosquito population reduction for dengue. Often, these controls are used with the immediate goal of decreasing the current incidence with little importance placed on what will happen at later points in time, and much less what will happen once the control is stopped. Here, by looking at the cumulative incidence since the beginning of the control period, instead of the instantaneous incidence, we show that when controls are stopped, or fail, the resulting outbreaks can be large enough to completely eliminate any benefit of the control. We call this result the divorce effect . Further, we show that this result is not limited to specific transmission pathways or epidemiological parameters, but is instead tied directly to the reduction of herd immunity inherent in non-immunizing controls. Lastly, by evaluating programs to minimize the magnitude of the divorce effect, we show that without maintaining herd immunity, or successfully continuing control for decades, it is impossible to keep the costs of post-control outbreaks from outweighing the benefits of the control program. DA - 2019/4/19/ PY - 2019/4/19/ DO - 10.1101/608653 VL - 4 UR - https://doi.org/10.1101/608653 ER - TY - JOUR TI - AI Assistants and the Paradox of Internal Automaticity AU - Bauer, William A. AU - Dubljević, Veljko T2 - Neuroethics DA - 2019/11/1/ PY - 2019/11/1/ DO - 10.1007/s12152-019-09423-6 VL - 11 J2 - Neuroethics LA - en OP - SN - 1874-5490 1874-5504 UR - http://dx.doi.org/10.1007/s12152-019-09423-6 DB - Crossref KW - AI assistants KW - AI ethics KW - Autonomy KW - Internal automaticity KW - External automaticity KW - Cognition ER - TY - JOUR TI - Neuroconsumerism and Comprehensive Neuroethics AU - Scheper, Abigail AU - Dubljević, Veljko T2 - AJOB Neuroscience AB - In her article “Dimensions of Ethical Direct-to-Consumer Neurotechnologies,” Kreitmair (2019) presents a strong case for the seven ethical dimensions she outlines pertaining to direct-to-consumer (... DA - 2019/10/2/ PY - 2019/10/2/ DO - 10.1080/21507740.2019.1665125 VL - 10 IS - 4 SP - 185-187 UR - https://doi.org/10.1080/21507740.2019.1665125 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 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 - 2019/// PY - 2019/// DO - 10.1111/een.12787 KW - Arthropod-plant interactions KW - necrophagy KW - phylloplane resource KW - plant-provided food KW - scavenging KW - trichomes ER - TY - JOUR TI - Diversity and structure of the bacterial microbiome of the American dog tick, Dermacentor variabilis, is dominated by the endosymbiont Francisella AU - Travanty, Nicholas V. AU - Ponnusamy, Loganathan AU - Kakumanu, Madhavi L. AU - Nicholson, William L. AU - Apperson, Charles S. T2 - SYMBIOSIS DA - 2019/11// PY - 2019/11// DO - 10.1007/s13199-019-00642-2 VL - 79 IS - 3 SP - 239-250 SN - 1878-7665 KW - Dermacentor variabilis KW - American dog tick KW - Microbiome KW - 16S rDNA KW - QIIME 2 analysis KW - Francisella endosymbiont ER - TY - JOUR TI - Evaluating climate change behaviors and concern in the family context AU - Lawson, Danielle F. AU - Stevenson, Kathryn T. AU - Peterson, M. Nils AU - Carrier, Sarah J. AU - Seekamp, Erin AU - Strnad, Renee T2 - Environmental Education Research AB - Although research suggests that family dynamics likely play a role in shaping children’s behaviors, few studies focus on environmental behaviors, and none to our knowledge investigate how parents shape climate change mitigation behaviors among their children. We begin to fill this gap through a quantitative case study using matched household-level survey data from 182 coastal North Carolina families (n = 241 parents aged 29–77; n = 182 students aged 11–14) associated with 15 middle school science teachers. Family climate change discussions, parent behaviors, and children’s climate change concern levels predicted the degree to which children will participate in individual-level climate mitigation behaviors. These results provide evidence that promoting climate-related conversations within households may promote climate action even when parents are apathetic about climate change. Similarly, parental behaviors, but not their concern levels, were important predictors of adolescent behaviors. This study highlights novel ways that family dynamics may promote climate change mitigating behaviors and a new pathway to promoting climate mitigation at familial, and ultimately, societal levels. DA - 2019/1/21/ PY - 2019/1/21/ DO - 10.1080/13504622.2018.1564248 VL - 25 IS - 5 SP - 678-690 J2 - Environmental Education Research LA - en OP - SN - 1350-4622 1469-5871 UR - http://dx.doi.org/10.1080/13504622.2018.1564248 DB - Crossref KW - Climate change KW - families KW - environmental behaviors KW - intergenerational KW - children KW - quantitative research ER - TY - JOUR TI - Interactions among Locus of Control, Environmental Attitudes and Pro-Environmental Behaviour in China AU - Giefer, Madeline M AU - Peterson, M Nils AU - Chen, Xiaodong T2 - Environmental Conservation AB - Summary Promoting environmentally conscious behaviour requires an understanding of the complex cognitive mechanisms by which people decide to act environmentally. Research suggests that locus of control (LOC), or the extent to which a person feels his or her own actions can produce broader change, is an important predictor of environmental behaviour; however, little is known about how LOC interacts with other cognitive motivators. This study uses a nationwide survey from China to test whether LOC moderates the effect of environmental attitudes on behaviour. Respondents with external LOC (i.e., those who believe personal actions cannot produce change) reported lower pro-environmental behaviour than those with internal LOC (i.e., those who believe personal actions can produce change). In addition, the influence of environmental attitudes on pro-environmental behaviour was stronger among respondents with external LOC than those with internal LOC. These results support efforts to promote conservation in China by promoting internal LOC and add a novel suggestion that attitude-based messaging is more efficacious among audiences with external LOC. DA - 2019/4/14/ PY - 2019/4/14/ DO - 10.1017/S0376892919000043 VL - 46 IS - 03 SP - 234-240 J2 - Envir. Conserv. LA - en OP - SN - 0376-8929 1469-4387 UR - http://dx.doi.org/10.1017/S0376892919000043 DB - Crossref KW - environmental messaging KW - household consumption KW - natural resources KW - new environmental paradigm ER - TY - JOUR TI - Using qualitative methods to support recovery of endangered species: The case of red-cockaded woodpecker foraging habitat AU - Garabedian, James E. AU - Peterson, M. Nils AU - Moorman, Christopher E. AU - Kilgo, John C. T2 - Global Ecology and Conservation AB - Meta-analyses are powerful tools for synthesizing wildlife-habitat relationships, but small sample sizes and complex species-habitat relationships often preclude correlative meta-analyses on endangered species. In this study, we demonstrate qualitative comparative analysis (QCA) as a tool that can reliably synthesize habitat-fitness relationships from small sample sizes for species with narrow habitat requirements. We apply QCA to results from a habitat threshold regression tree model and identify habitat thresholds with consistent positive effects on fitness of the federally endangered red-cockaded woodpecker (Dryobates borealis; RCW) on the Savannah River Site, USA. We reformulated regression tree results in a QCA framework to examine the consistency of threshold effects on RCW fledgling production at the individual group level (n = 47). Synthesizing regression tree results with QCA revealed alternative combinations of habitat thresholds that in conjunction with group size consistently led to above-average fledgling production for 41 of 47 (88%) individual RCW groups. Importantly, QCA identified unique combinations of habitat thresholds and group size related to above-average fledgling production that were not retained in the regression tree model due to small sample sizes. Synthesizing a small habitat-fitness dataset using QCA provided a tractable method to identify unique combinations of habitat and group size conditions that are consistently important to individual fitness, but may not be detected by meta-analyses that can be biased by small sample sizes. QCA offers a viable approach for synthesis of habitat-fitness relationships and can be extended to address many complex issues in endangered species recovery when correlative meta-analyses are not possible. DA - 2019/1// PY - 2019/1// DO - 10.1016/J.GECCO.2019.E00553 VL - 17 SP - e00553 J2 - Global Ecology and Conservation LA - en OP - SN - 2351-9894 UR - http://dx.doi.org/10.1016/J.GECCO.2019.E00553 DB - Crossref KW - Endangered species KW - Habitat threshold KW - Pine forest KW - Meta-analysis KW - Population fitness KW - Recovery plan ER - TY - JOUR TI - Evaluating natural resource planning for longleaf pine ecosystems in the Southeast United States AU - Foster, Michaela AU - Peterson, M. Nils AU - Cubbage, Frederick AU - McMahon, Gerard T2 - Forest Policy and Economics AB - Natural resource plans play a critical role in guiding the sustainable management of forest ecosystems. However, little is known about the quality of management plans. In this study, we evaluated and compared the quality of 35 management plans from federal, state, and nongovernment groups managing longleaf pine ecosystems in the Southeast United States. We developed a plan evaluation tool consisted of five components: (1) Problem and Objective Statement, (2) Fact Base, (3) Actions and Implementation, (4) Integration with Other Plans, and (5) Stakeholder Participation, to examine to what extent plans incorporated planning best practices. We tested a hypothetical model for understanding the relationship among plan components, and our results suggested stakeholder participation predicted clear problem statements, better integration with other plans, and better actions and implementation protocols. The Fact Base component scored highest across most plans while the Actions and Implementation component scored lowest. Newer plans scored modestly higher than older plans, suggesting agencies may be learning to develop better plans over time and indicating older plans should be prioritized for revision. Plans from federal and state agencies scored higher than plans from nongovernmental organizations. Our findings suggest planners should consider incorporating more stakeholder participation, which was positively related to better actions and implementation and improved problem and objective statements. DA - 2019/3// PY - 2019/3// DO - 10.1016/J.FORPOL.2018.11.008 VL - 100 SP - 142-153 J2 - Forest Policy and Economics LA - en OP - SN - 1389-9341 UR - http://dx.doi.org/10.1016/J.FORPOL.2018.11.008 DB - Crossref KW - Plan evaluation KW - Plan quality KW - Longleaf pine ER - TY - JOUR TI - Drivers of Elevational Richness Peaks, Evaluated for Trees in the East Himalaya AU - Rana, Suresh K. AU - Gross, Kevin AU - Price, Trevor D. T2 - The Bulletin of the Ecological Society of America AB - A mid-elevation peak in species richness is common in many clades. Here, we studied trees of the east Himalaya and found a richness peak at 500–1,000 m. We argue that this results from a correlation of climate with both the numbers and kinds of species, coupled with a geometric constraint in which range expansions from the plains introduce few new species at the base, whereas just above the base, novel species have ranges extending from both above and below. We develop a mathematical model to derive conditions for this to happen. A prediction is that species’ elevational ranges should be smaller at lower elevations, as we find. These photographs illustrate the article “Drivers of elevational richness peaks, evaluated for trees in the east Himalaya” by Suresh K. Rana, Kevin Gross, and Trevor D. Price published in Ecology. https://doi.org/10.1002/ecy.2548 DA - 2019/1// PY - 2019/1// DO - 10.1002/BES2.1499 VL - 100 IS - 1 SP - e01499 J2 - Bull Ecol Soc Am LA - en OP - SN - 0012-9623 UR - http://dx.doi.org/10.1002/BES2.1499 DB - Crossref ER - TY - JOUR TI - Do substitute species help or hinder endangered species management? AU - Henry, Erica AU - Brammer-Robbins, Elizabeth AU - Aschehoug, Erik AU - Haddad, Nick T2 - Biological Conservation AB - Substitute species (common species used to represent endangered species) are used to evaluate a range of conservation strategies globally. However, the effectiveness of this approach has not been empirically evaluated. We leveraged a large-scale habitat restoration experiment to test the validity of the substitute species concept. We selected a common butterfly, Satyrodes appalachia, that is on first inspection as near a substitute as possible - it is closely related to, overlaps in distribution, habitat requirements, host use, and life history with Neonympha mitchellii francisci, an endangered butterfly. We integrated small-scale measures of behavior, habitat preference, and demography of both species in our test, demonstrating that subtle differences between two species cause the substitute relationship to fail. Despite nearly identical habitat requirements, we found the endangered butterfly used different host plants, had higher larval survival in restored sites, and was found in more open habitat than the common butterfly. These differences added up to differences in abundances; the endangered species was more abundant than the common species in restored sites, the opposite was true in un-restored sites. Management decisions based on unvalidated substitute species run the risk of doing more harm than good for endangered species conservation. Instead, using experiments to evaluate a target species' response to management will result in effective recovery strategies. DA - 2019/4// PY - 2019/4// DO - 10.1016/J.BIOCON.2019.01.031 VL - 232 SP - 127-130 J2 - Biological Conservation LA - en OP - SN - 0006-3207 UR - http://dx.doi.org/10.1016/J.BIOCON.2019.01.031 DB - Crossref KW - Butterfly KW - Restoration KW - Demography KW - Movement KW - Surrogates KW - N. m. francisci ER - TY - JOUR TI - Landscape heterogeneity is key to forecasting outcomes of plant reintroduction AU - Caughlin, T. Trevor AU - Damschen, Ellen I. AU - Haddad, Nick M. AU - Levey, Douglas J. AU - Warneke, Christopher AU - Brudvig, Lars A. T2 - Ecological Applications AB - Conservation and restoration projects often involve starting new populations by introducing individuals into portions of their native or projected range. Such efforts can help meet many related goals, including habitat creation, ecosystem service provisioning, assisted migration, and the reintroduction of imperiled species following local extirpation. The outcomes of reintroduction efforts, however, are highly variable, with results ranging from local extinction to dramatic population growth; reasons for this variation remain unclear. Here, we ask whether population growth following plant reintroductions is governed by variation at two scales: the scale of individual habitat patches to which individuals are reintroduced, and larger among-landscape scales in which similar patches may be situated in landscapes that differ in matrix type, soil conditions, and other factors. Quantifying demographic variation at these two scales will help prioritize locations for introduction and, once introductions take place, forecast population growth. This work took place within a large-scale habitat fragmentation experiment, where individuals of two perennial forb species were reintroduced into eight replicate ~50-ha landscapes, each containing a set of five ~1-ha patches that varied in their degree of isolation (connected by habitat corridors or unconnected) and edge-to-area ratio. Using data on individual growth, survival, reproductive output, and recruitment collected one to two years after reintroduction, we developed models to forecast population growth, then compared forecasts to observed population sizes, three and six years later. Both the type of patch (connected and unconnected) and identity of the landscape to which individuals were reintroduced had effects on forecasted population growth rates, but only variation associated with landscape identity was an accurate predictor of subsequently observed population growth rates. Models that did not include landscape identity had minimal forecasting ability, revealing the key importance of variation at this scale for accurate prediction. Of the five demographic rates used to model population dynamics, seed production was the most important source of forecast error in population growth rates. Our results point to the importance of accounting for landscape-scale variation in demographic models and demonstrate how such models might assist with prioritizing particular landscapes for species reintroduction projects. DA - 2019/3// PY - 2019/3// DO - 10.1002/EAP.1850 VL - 29 IS - 2 J2 - Ecol Appl LA - en OP - SN - 1051-0761 1939-5582 UR - http://dx.doi.org/10.1002/EAP.1850 DB - Crossref KW - Carphephorus KW - conservation biology KW - demography KW - ecological forecasting KW - habitat fragmentation KW - integral projection model KW - landscape corridor KW - Liatris KW - longleaf pine savanna KW - prediction KW - restoration ecology ER - TY - RPRT TI - Genetic frontiers for conservation: an assessment of synthetic biology and biodiversity conservation: technical assessment AB - In recent years synthetic biology has emerged as a suite of techniques and technologies that enable humans to read, interpret, modify, design and manufacture DNA in order to rapidly influence the forms and functions of cells and organisms, with the potential to reach whole species and ecosystems. As synthetic biology continues to evolve, new tools emerge, novel applications are proposed, and basic research is applied. This assessment is one part of IUCN’s effort to provide recommendations and guidance regarding the potential positive and negative impacts of synthetic biology on biodiversity conservation; it comprises a full assessment and a short synthesis report. DA - 2019/5/6/ PY - 2019/5/6/ DO - 10.2305/iucn.ch.2019.05.en UR - http://dx.doi.org/10.2305/iucn.ch.2019.05.en ER - TY - JOUR TI - 200 Developing exosomes as a mediator for CRISPR/Cas-9 delivery AU - Gupta, N. AU - Polkoff, K. AU - Qiao, L. AU - Cheng, K. AU - Piedrahita, J. T2 - Reproduction, Fertility and Development AB - CRISPR/Cas systems present a powerful gene-editing tool with the potential for widespread therapeutic use; however, current methods of in vivo delivery such as adeno-associated viruses (AAV) may stimulate an immune response, creating the need for an alternative for delivery of CRISPR/Cas9. Exosomes are small vesicles that are released by cells and serve as a delivery system for RNA, proteins, and various molecules to other cells. The focus of this project was to use exosomes as a delivery system for Cas9, exploiting their high uptake by target cells and their ability to avoid the immune system in vivo. Porcine fetal fibroblasts (PFF) were grown to 80% confluency; after 48h, exosomes were isolated and concentrated from conditioned media by filtration with a 0.22-μm filter followed by 100-kDa molecular weight cutoff filter. Transmission electron microscopy, Western blotting for presence of CD81, and an uptake assay for exosomes stained with the lipophilic dye DiI (Invitrogen/Thermo Fisher Scientific, Waltham, MA, USA) were used to characterise isolated exosomes, and average particle size was evaluated by NanoSight (Salisbury, United Kingdom). After characterisation, exosomes were loaded with Cas9 (PNA Bio, Newbury Park, CA, USA) using sonication, incubation with saponin, or extrusion. For each method of loading, 1.0×1011 exosomes and 500ng of Cas9 were used. For sonication, exosomes and Cas9 were sonicated 4 times: 4s on/2s off, left on ice for 2min, and then repeated for 4 more cycles. Loaded exosomes were then incubated at 37°C for 20min. For incubation with saponin, 100μL of 0.6% saponin solution was made in PBS, mixed with exosomes and Cas9, and then incubated on a shaker at 800 rpm for 20min. For extrusion, exosomes and Cas9 were extruded (Avanti Polar Lipids, Alabaster, AL, USA) 10, 15, or 20 times through a 0.22-μm filter. To evaluate efficiency of Cas9 loading into exosomes, loaded exosome samples were split in half, with one-half receiving a proteinase K digest (100μg mL−1) to remove free Cas9 and the other receiving no treatment. Proteinase K-treated and untreated samples were then compared side by side on Western blot staining for Cas9. ImageJ software (National Institutes for Health, Bethesda, MD, USA) was used to quantify band intensity and loading efficiency. With optimal conditions, our preliminary results show loading efficiency for sonication and saponin to be 16.7 and 19.2%, respectively, whereas loading by extrusion was undetectable. For CRISPR/Cas targeting, transgenic PFF carrying one copy of H2B-GFP were used to test delivery of ribonucleotide protein complex (RNP). To verify efficiency of the guide (g)RNA targeting green fluorescent protein (GFP), cells were nucleofected with Cas9 and gRNA. The DNA was extracted, PCR amplified, and sequenced (Eton Bioscience, San Diego, CA, USA) and then evaluated for indels with TIDE, resulting in a 53.2% cleavage efficiency. Next, exosomes will be loaded with RNP to knockout GFP in H2B-GFP cells, and targeting efficiency will be evaluated by flow cytometry and TIDE. We hypothesise that based on loading efficiency and target cell uptake, exosomes will present a safe and efficient method for in vitro and in vivo delivery of Cas9. The financial support of the Comparative Medicine Institute is gratefully acknowledged. DA - 2019/// PY - 2019/// DO - 10.1071/RDV31N1AB200 VL - 31 IS - 1 SP - 225 J2 - Reprod. Fertil. Dev. LA - en OP - SN - 1031-3613 UR - http://dx.doi.org/10.1071/RDV31N1AB200 DB - Crossref ER - TY - JOUR TI - Investigating Potential Relationships Between Adolescents’ Cognitive Development and Perceptions of Presence in 3-D, Haptic-Enabled, Virtual Reality Science Instruction AU - Hite, R. L. AU - Jones, M. G. AU - Childers, G. M. AU - Ennes, M. AU - Chesnutt, K. AU - Pereyra, M. AU - Cayton, E. T2 - Journal of Science Education and Technology DA - 2019/1/19/ PY - 2019/1/19/ DO - 10.1007/S10956-018-9764-Y VL - 28 IS - 3 SP - 265-284 J2 - J Sci Educ Technol LA - en OP - SN - 1059-0145 1573-1839 UR - http://dx.doi.org/10.1007/S10956-018-9764-Y DB - Crossref KW - Cognitive development KW - Instructional technology KW - Science education KW - Virtual presence KW - Virtual reality ER - TY - JOUR TI - Biomechanical Function and Size of the Anteromedial and Posterolateral Bundles of the ACL Change Differently with Skeletal Growth in the Pig Model AU - Cone, Stephanie G. AU - Lambeth, Emily P. AU - Ru, Hongyu AU - Fordham, Lynn A. AU - Piedrahita, Jorge A. AU - Spang, Jeffrey T. AU - Fisher, Matthew B. T2 - CLINICAL ORTHOPAEDICS AND RELATED RESEARCH DA - 2019/9// PY - 2019/9// DO - 10.1097/CORR.0000000000000884 VL - 477 IS - 9 SP - 2161-2174 SN - 1528-1132 ER - TY - JOUR TI - Exogenous and endogenous microbiomes of wild-caught Phormia regina (Diptera: Calliphoridae) flies from a suburban farm by 16S rRNA gene sequencing AU - Deguenon, Jean M. AU - Travanty, Nicholas AU - Zhu, Jiwei AU - Carr, Ann AU - Denning, Steven AU - Reiskind, Michael H. AU - Watson, David W. AU - Roe, R. Michael AU - Ponnusamy, Loganathan T2 - SCIENTIFIC REPORTS AB - Abstract The black blow fly, Phormia regina (Meigen) (Diptera: Calliphoridae) is one of the most abundant carrion flies in North America. Calliphorids are important in agriculture and animal production, veterinary sciences, forensics and medical entomology. While the role of flies in the epidemiology of human and animal diseases is an active area of research, little is known about the microorganisms associated with these insects. We examined the diversity of wild-caught black blow fly endogenous (internal body) and exogenous (external body) microbial communities using 16S rRNA gene sequencing. Overall, 27 phyla, 171 families and 533 genera were detected, and diversity was significantly higher ( P < 0.05) on external body surfaces. At the genus level, Dysgonomonas , Ignatzschineria , Acinetobacter , Vagococcus , Myroides , and Wohlfahrtiimonas were predominant. Cloning and sequencing of nearly full-length fragments of the 16S rRNA gene showed that some of the species identified are known to be pathogenic to humans, animals, and plants. Myroides odoratimimus and Acinetobacter radioresistens are well-known, multi-drug resistant bacteria. These results provide a snapshot of the microbial communities harbored by adult black blow flies and call for more comprehensive studies to better characterize the role these flies may play in the transmission of pathogenic microorganisms. DA - 2019/12/30/ PY - 2019/12/30/ DO - 10.1038/s41598-019-56733-z VL - 9 SP - SN - 2045-2322 ER - TY - JOUR TI - The distribution and spread of naturally occurring Medea selfish genetic elements in the United States AU - Cash, Sarah A. AU - Lorenzen, Marce D. AU - Gould, Fred T2 - Ecology and Evolution AB - Selfish genetic elements (SGEs) are DNA sequences that are transmitted to viable offspring in greater than Mendelian frequencies. Medea SGEs occur naturally in some populations of red flour beetle (Tribolium castaneum) and are expected to increase in frequency within populations and spread among populations. The large-scale U.S. distributions of Medea-4 (M4) had been mapped based on samples from 1993 to 1995. We sampled beetles in 2011-2014 and show that the distribution of M4 in the United States is dynamic and has shifted southward. By using a genetic marker of Medea-1 (M1), we found five unique geographic clusters with high and low M1 frequencies in a pattern not predicted by microsatellite-based analysis of population structure. Our results indicate the absence of rigid barriers to Medea spread in the United States, so assessment of what factors have limited its current distribution requires further investigation. There is great interest in using synthetic SGEs, including synthetic Medea, to alter or suppress pest populations, but there is concern about unpredicted spread of these SGEs and potential for populations to become resistant to them. The finding of patchy distributions of Medea elements suggests that released synthetic SGEs cannot always be expected to spread uniformly, especially in target species with limited dispersal. DA - 2019/11/27/ PY - 2019/11/27/ DO - 10.1002/ece3.5876 VL - 9 IS - 24 SP - 14407-14416 J2 - Ecology and Evolution LA - en OP - SN - 2045-7758 2045-7758 UR - http://dx.doi.org/10.1002/ece3.5876 DB - Crossref KW - maternal effect KW - Medea KW - red flour beetle KW - selfish genetic element ER - TY - JOUR TI - Nitrogen Gas Fixation and Conversion to Ammonium Using Microbial Electrolysis Cells AU - Ortiz-Medina, Juan F. AU - Grunden, Amy M. AU - Hyman, Michael R. AU - Call, Douglas F. T2 - ACS Sustainable Chemistry & Engineering AB - Ammonia (NH3) is an important industrial chemical that is produced using the energy- and carbon-intensive Haber-Bosch process. Recovering NH3 from microorganisms that fix nitrogen gas (N2) may provide a sustainable alternative because their specialized nitrogenase enzymes can reduce N2 to ammonium (NH4+) without the need for high temperature and pressure. This study explored the possibility of converting N2 into NH4+ using anaerobic, single-chamber microbial electrolysis cells (MECs). N2 fixation rates [based on an acetylene gas (C2H2) to ethylene gas (C2H4) conversion assay] of a microbial consortium increased significantly when the applied voltage between the anode and cathode increased from 0.7 to 1.0 V and reached a maximum of ∼40 nmol of C2H4 min–1 mg protein–1, which is comparable to model aerobic N2-fixing bacteria. The presence of NH4+, which can inhibit the activity of the nitrogenase enzyme, did not significantly reduce N2 fixation rates. Upon addition of methionine sulfoximine, an NH4+ uptake inhibitor, NH4+ was recovered at rates approaching 5.2 × 10–12 mol of NH4+ s–1 cm–2 (normalized to the anode surface area). Relative to the electrical energy consumed, the normalized energy demand [MJ mol–1 (NH4+)] was negative because of the energy-rich methane gas recovered in the MEC. Including the substrate energy resulted in total energy demands as low as 24 MJ mol–1. Community analysis results of the anode biofilms revealed that Geobacter species predominated in both the presence and absence of NH4+, suggesting that they played a key role in current generation and N2 fixation. This study shows that MECs may provide a new route for generating NH4+. DA - 2019/1// PY - 2019/1// DO - 10.1021/ACSSUSCHEMENG.8B05763 VL - 7 IS - 3 SP - 3511-3519 J2 - ACS Sustainable Chem. Eng. LA - en OP - SN - 2168-0485 2168-0485 UR - http://dx.doi.org/10.1021/ACSSUSCHEMENG.8B05763 DB - Crossref KW - Nitrogen fixation KW - Ammonium production KW - Haber-Bosch KW - Microbial electrochemical technology KW - Geobacter ER - TY - JOUR TI - Laboratory and Field Evaluation of Host-Related Foraging Odor-Cue Combinations to Attract Drosophila suzukii (Diptera: Drosophilidae) AU - Cloonan, Kevin R. AU - Hernandez-Cumplido, Johnattan AU - De Sousa, Ana Luiza Viana AU - Ramalho, Dagmara Gomes AU - Burrack, Hannah J. AU - Della Rosa, Linda AU - Diepenbrock, Lauren M. AU - Ballman, Elissa AU - Drummond, Francis A. AU - Gut, Larry J. AU - Hesler, Stephen AU - Isaacs, Rufus AU - Leach, Heather AU - Loeb, Gregory M. AU - Nielsen, Anne L. AU - Nitzsche, Peter AU - Park, Kyoo R. AU - Syed, Zainulabeuddin AU - Van Timmeren, Steven AU - Wallingford, Anna K. AU - Walton, Vaughn M. AU - Rodriguez-Saona, Cesar T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - Abstract The invasive spotted-wing drosophila, Drosophila suzukii (Matsumura), is a major pest of soft-skinned fruits. Since its introduction into North America and Europe, significant progress has been made in understanding the volatile cues used by this fly during food, oviposition site, and mate finding. Despite this progress, commercially available lures are non-selective. Here, we tested two Hanseniaspora uvarum (Niehaus) yeast compounds (isoamyl acetate and isobutyl acetate) and a leaf compound β-cyclocitral alone and in combination with a blend of four fermentation compounds (‘Fermentation lure’: acetic acid, ethanol, methionol, and acetoin) to improve D. suzukii attraction and selectivity. In laboratory assays, males and females were attracted to all seven individual compounds, although in electrophysiological assays, their antennae exhibited a dose-dependent response to only four of these compounds. In two-choice cage studies, the Fermentation lure was more attractive to D. suzukii than water controls, whereas β-cyclocitral and the mixture of isoamyl acetate and isobutyl acetate were not attractive in this larger-cage study. Moreover, adding the two-component H. uvarum compound blend to the Fermentation lure reduced D. suzukii attraction to the Fermentation blend. When these experiments were repeated in blueberry, raspberry, blackberry, and cherry orchards across several states in the United States over 2 yr, similar outcomes were observed: β-cyclocitral or the mixture of the H. uvarum blend did not improve the attractiveness of the Fermentation lure or its selectivity. This study demonstrates that cues from different sources may interfere with each other and reduce D. suzukii attraction to otherwise attractive odor combinations. DA - 2019/12// PY - 2019/12// DO - 10.1093/jee/toz224 VL - 112 IS - 6 SP - 2850-2860 SN - 1938-291X KW - spotted-wing drosophila KW - invasive pest KW - attractant KW - yeast KW - behavior-based strategy ER - TY - JOUR TI - The Corn–Cotton Agroecosystem in the Mid-Southern United States: What Insecticidal Event Pyramids Should be Used in Each Crop to Extend Vip3A Durability AU - Caprio, Michael A AU - Kurtz, Ryan AU - Catchot, Angus AU - Kerns, David AU - Reisig, Dominic AU - Gore, Jeff AU - Reay-Jones, Francis P F T2 - Journal of Economic Entomology AB - Recent studies suggest that resistance in Helicoverpa zea (Boddie) (Lepidoptera, Noctuidae) to Cry1A(b/c) and Cry2Ab2 toxins from the bacterium Bacillus thuringiensis Berliner (Bacillales: Bacillaceae) has increased and field efficacy is impacted in transgenic corn and cotton expressing these toxins. A third toxin, Vip3A, is available in pyramids expressing two or more Bt toxins in corn hybrids and cotton varieties, but uncertainty exists regarding deployment strategies. During a growing season, H. zea infests corn and cotton, and debate arises over use of Vip3A toxin in corn where H. zea is not an economic pest. We used a three-locus, spatially explicit simulation model to evaluate when using Vip3A in corn might hasten evolution of resistance to Vip3A, with implications in cotton where H. zea is a key pest. When using a conventional refuge in corn and initial resistance allele frequencies of Cry1A and Cry2A were 10%, transforming corn with Vip3A slowed resistance to these toxins and delayed resistance evolution to the three-toxin pyramid as a whole. When Cry resistance allele frequencies exceeded 30%, transforming corn with Vip3A hastened the evolution of resistance to the three-toxin pyramid in cotton. When using a seed blend refuge strategy, resistance was delayed longest when Vip3A was not incorporated into corn and used only in cotton. Simulations of conventional refuges were generally more durable than seed blends, even when 75% of the required refuge was not planted. Extended durability of conventional refuges compared to other models of resistance evolution are discussed as well as causes for unusual survivorship in seed blends. DA - 2019/8/3/ PY - 2019/8/3/ DO - 10.1093/jee/toz208 VL - 112 IS - 6 SP - 2894-2906 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/toz208 DB - Crossref KW - resistance management KW - genetics KW - crop protection KW - Bt corn KW - Helicoverpa ER - TY - JOUR TI - In Situ Joint Stiffness Increases During Skeletal Growth but Decreases Following Partial and Complete Anterior Cruciate Ligament Injury AU - Cone, Stephanie G. AU - Piedrahita, Jorge A. AU - Spang, Jeffrey T. AU - Fisher, Matthew B. T2 - JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME AB - Partial and complete anterior cruciate ligament (ACL) injuries occur in both pediatric and adult populations and can result in loss of joint stability and function. The sigmoidal shape of knee joint function (load-translation curve) under applied loads includes a low-load region (described by slack length) followed by a high-load region (described by stiffness). However, the impact of age and injury on these parameters is not fully understood. The current objective was to measure the effects of age and injury on the shape of joint function in a porcine model. In response to an applied anterior-posterior tibial load, in situ slack did not change (p > 0.05), despite sevenfold increases in joint size with increasing age. Joint stiffness increased from an average of 10 N/mm in early youth to 47 N/mm in late adolescence (p < 0.05). In situ ACL stiffness increased similarly, and changes in in situ joint stiffness and ACL stiffness were highly correlated across ages. With complete ACL injury, in situ slack length increased by twofold to fourfold and in situ stiffness decreased threefold to fourfold across ages (p < 0.05). Partial ACL injury resulted in less dramatic, but statistically significant, increases in joint slack and significant decreases in in situ joint stiffness in the adolescent age groups (p < 0.05). This work furthers our understanding of the interaction between joint biomechanics and ACL function throughout growth and the impact of ACL injury in the skeletally immature joint. DA - 2019/12// PY - 2019/12// DO - 10.1115/1.4044582 VL - 141 IS - 12 SP - SN - 1528-8951 ER - TY - JOUR TI - PBDEs Concentrate in the Fetal Portion of the Placenta: Implications for Thyroid Hormone Dysregulation AU - Ruis, Matthew T. AU - Rock, Kylie D. AU - Hall, Samantha M. AU - Horman, Brian AU - Patisaul, Heather B. AU - Stapleton, Heather M. T2 - ENDOCRINOLOGY AB - Abstract During pregnancy, the supply of thyroid hormone (TH) to the fetus is critically important for fetal growth, neural development, metabolism, and maintenance of pregnancy. Additionally, in cases where maternal and placental TH regulation is significantly altered, there is an increased risk of several adverse pregnancy outcomes. It is unclear what may be disrupting placental TH regulation; however, studies suggest that environmental contaminants, such as polybrominated diphenyl ethers (PBDEs), could be playing a role. In this study, Wistar rats were gestationally exposed to a mixture of PBDEs for 10 days. THs and PBDEs were quantified in paired maternal serum, dissected placenta, and fetuses, and mRNA expression of transporters in the placenta was assessed. Significantly higher concentrations of PBDEs were observed in the fetal portion of the placenta compared with the maternal side, suggesting that PBDEs are actively transported across the interface. PBDEs were also quantified in 10 recently collected human maternal and fetal placental tissues; trends paralleled observations in the rat model. We also observed an effect of PBDEs on T3 levels in dam serum, as well as suggestive changes in the T3 levels of the placenta and fetus that varied by fetal sex. mRNA expression in the placenta also significantly varied by fetal sex and dose. These observations suggest the placenta is a significant modifier of fetal exposures, and that PBDEs are impacting TH regulation in a sex-specific manner during this critical window of development. DA - 2019/11// PY - 2019/11// DO - 10.1210/en.2019-00463 VL - 160 IS - 11 SP - 2748-2758 SN - 1945-7170 ER - TY - JOUR TI - Inoculation with the mycorrhizal fungus Rhizophagus irregularis modulates the relationship between root growth and nutrient content in maize (Zea mays ssp. mays L.) AU - Rosario Ramirez-Flores, M. AU - Bello-Bello, Elohim AU - Rellan-Alvarez, Ruben AU - Sawers, Ruairidh J. H. AU - Olalde-Portugal, Victor T2 - PLANT DIRECT AB - Plant root systems play a fundamental role in nutrient and water acquisition. In resource-limited soils, modification of root system architecture is an important strategy to optimize plant performance. Most terrestrial plants also form symbiotic associations with arbuscular mycorrhizal fungi to maximize nutrient uptake. In addition to direct delivery of nutrients, arbuscular mycorrhizal fungi benefit the plant host by promoting root growth. Here, we aimed to quantify the impact of arbuscular mycorrhizal symbiosis on root growth and nutrient uptake in maize. Inoculated plants showed an increase in both biomass and the total content of twenty quantified elements. In addition, image analysis showed mycorrhizal plants to have denser, more branched root systems. For most of the quantified elements, the increase in content in mycorrhizal plants was proportional to root and overall plant growth. However, the increase in boron, calcium, magnesium, phosphorus, sulfur, and strontium was greater than predicted by root system size alone, indicating fungal delivery to be supplementing root uptake. DA - 2019/12// PY - 2019/12// DO - 10.1002/pld3.192 VL - 3 IS - 12 SP - SN - 2475-4455 KW - image analysis KW - ionomics KW - maize KW - maize/Zea mays KW - mycorrhizae/mycorrhizal symbiosis KW - nutrient uptake and metabolism KW - root development 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 - Luis Balaguer, Maria A. 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 - 2019/// PY - 2019/// DO - 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 - BOOK TI - Gendered Paths into STEM. Disparities Between Females and Males in STEM Over the Life-Span AU - Ertl, Bernhard AU - Luttenberger, Silke AU - Lazarides, Rebecca AU - Jones, M. Gail AU - Paechter, Manuela A3 - Ertl, B. A3 - Luttenberger, S. A3 - Lazarides, Rebecca A3 - Jones, M.G. A3 - Paechter, M. AB - EDITORIAL article Front. Psychol., 17 December 2019 | https://doi.org/10.3389/fpsyg.2019.02758 DA - 2019/// PY - 2019/// DO - 10.3389/fpsyg.2019.02758 VL - 10 PB - Frontiers in Psychology SE - KW - attributions KW - self-concept KW - motivation KW - gender-sensitive didactics KW - occupational choices ER - TY - JOUR TI - Examining climate change and food security in Ghana through an intersectional framework AU - Wood, A.L. AU - Ansah, P. AU - Rivers, L. AU - Ligmann-Zielinska, A. T2 - Journal of Peasant Studies AB - As the effects of climate change intensify, subsistence farmers in Ghana are expected to face increased food insecurity, due to their reliance on rainfed agriculture. Within households, young women are expected to support all aspects of household food security, and will experience a more burdensome load of labor, as a dwindling stock of natural resources will make daily tasks more time consuming. The intersection of age, gender, and location inhibits young women's decision-making responsibilities and wage-earning potential. Climate change exacerbates this dynamic, which restricts opportunities to acquire sufficient food and places increased stress on household food systems. DA - 2019/// PY - 2019/// DO - 10.1080/03066150.2019.1655639 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85073950754&partnerID=MN8TOARS KW - Climate change KW - food security KW - intersectionality KW - Ghana KW - farming 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, Marcé 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 - 2019/12/19/ PY - 2019/12/19/ DO - 10.1002/ece3.5946 VL - 10 IS - 2 SP - 863-874 J2 - Ecology and Evolution LA - en OP - SN - 2045-7758 2045-7758 UR - http://dx.doi.org/10.1002/ece3.5946 DB - Crossref KW - gene drive KW - maternal effect KW - Medea KW - selfish genetic element ER - TY - JOUR TI - Noninvasive measures of physiological stress are confounded by exposure AU - Lafferty, Diana J. R. AU - Zimova, Marketa AU - Clontz, Lindsay AU - Hacklander, Klaus AU - Mills, L. Scott T2 - SCIENTIFIC REPORTS AB - Abstract Glucocorticoids and glucocorticoid metabolites are increasingly used to index physiological stress in wildlife. Although feces is often abundant and can be collected noninvasively, exposure to biotic and abiotic elements may influence fecal glucocorticoid metabolite (FGM) concentrations, leading to inaccurate conclusions regarding wildlife physiological stress. Using captive snowshoe hares ( Lepus americanus ) and simulated environmental conditions, we evaluated how different realistic field conditions and temporal sampling constraints might influence FGM concentrations using an 11-oxoetiocholanolone-enzyme immunoassay. We quantified how fecal pellet age (i.e., 0–6 days), variable summer temperatures, and precipitation affected FGM concentrations. Fecal pellet age had a strong effect on FGM concentrations (β Age = 0.395, s.d. = 0.085; β 2 Age = −0.061, s.d. = 0.012), which were lowest at the beginning and end of our exposure period (e.g., mean day6 = 37.7 ng/mg) and typically highest in the middle (mean day3 = 51.8 ng/mg). The effect of fecal pellet age on FGM concentrations varied across treatments with warm-dry and cool-wet conditions resulting in more variable FGM concentrations relative to control samples. Given the confounding effects of exposure and environmental conditions, if fresh fecal pellet collection is not an option, we encourage researchers to develop a temporally consistent sampling protocol to ensure all samples are exposed to similar environmental conditions. DA - 2019/// PY - 2019/// DO - 10.1038/s41598-019-55715-5 VL - 9 ER - TY - JOUR TI - Biological interactions between nanomaterials and placental development and function following oral exposure AU - Mortensen, Ninell P. AU - Johnson, Leah M. AU - Grieger, Khara D. AU - Ambroso, Jeffrey L. AU - Fennell, Timothy R. T2 - REPRODUCTIVE TOXICOLOGY AB - We summarize the literature involving the deposition of nanomaterials within the placenta following oral exposure and the biological interactions between nanomaterials and placental development and function. The review focuses on the oral exposure of metal and metal oxide engineered nanomaterials (ENMs), carbon-based ENMs, and nanoplastics in animal models, with a minor discussion of intravenous injections. Although the literature suggests that the placenta is an efficient barrier in preventing nanomaterials from reaching the fetus, nanomaterials that accumulate in the placenta may interfere with its development and function. Furthermore, some studies have demonstrated a decrease in placental weight and association with adverse fetal health outcomes following oral exposure to nanomaterials. Since nanomaterials are increasingly used in food, food packaging, and have been discovered in drinking water, the risk for adverse impacts on placental development and functions, with secondary effects on embryo-fetal development, following unintentional maternal ingestion of nanomaterials requires further investigation. DA - 2019/12// PY - 2019/12// DO - 10.1016/j.reprotox.2019.08.016 VL - 90 SP - 150-165 SN - 0890-6238 KW - Nanomaterials KW - Engineered nanomaterials KW - Nanoplastics KW - In utero KW - Exposure KW - Placenta development KW - Placental functions KW - Fetal health outcome ER - TY - ER - TY - CONF TI - Towards a genetic approach to invasive rodent eradications: Assessing reproductive competitiveness between wild and laboratory mice AU - Campbell, K.J. AU - Saah, J.R. AU - Brown, P.R. AU - Godwin, J. AU - Gould, F. AU - Howald, G.R. AU - Piaggio, A. AU - Thomas, P. AU - Tompkins, D.M. AU - Threadgill, D. AU - Delborne, J. AU - Kanavy, D.M. AU - Kuikin, T. AU - Packard, H. AU - Serr, M. AU - Shiels, A. A2 - Veitch, C.R A2 - Clout, MN A2 - Martin, AR A2 - Russell, JC A2 - West, CJ C2 - 2019/// C3 - Island invasives: scaling up to meet the challenge DA - 2019/// DO - 10.2305/IUCN.CH.2019.SSC-OP.62.en SP - 64–70 M1 - 62 PB - IUCN UR - http://www.issg.org/pdf/publications/2019_Island_Invasives/PrintFiles/Serr.pdf ER - TY - JOUR TI - Partnering with bioRxiv AU - Barrangou, Rodolphe T2 - The CRISPR Journal AB - The CRISPR JournalVol. 2, No. 6 EditorialsPartnering with bioRxivRodolphe BarrangouRodolphe BarrangouSearch for more papers by this authorPublished Online:16 Dec 2019https://doi.org/10.1089/crispr.2019.29076.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Partnering with bioRxiv." The CRISPR Journal, 2(6), p. 342FiguresReferencesRelatedDetails Volume 2Issue 6Dec 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Partnering with bioRxiv.The CRISPR Journal.Dec 2019.342-342.http://doi.org/10.1089/crispr.2019.29076.rbaPublished in Volume: 2 Issue 6: December 16, 2019PDF download DA - 2019/// PY - 2019/// DO - 10.1089/crispr.2019.29076.rba VL - 2 IS - 6 SP - 342-342 ER - TY - JOUR TI - Foresight is 2020: Ten Bold Predictions for the New CRISPR Year AU - Barrangou, Rodolphe T2 - The CRISPR Journal AB - The CRISPR JournalVol. 2, No. 6 EditorialsFree AccessForesight is 2020: Ten Bold Predictions for the New CRISPR YearRodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR JournalSearch for more papers by this authorPublished Online:16 Dec 2019https://doi.org/10.1089/crispr.2019.29075.rbaAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Whereas most people use the last few days of the year to reflect on the events that shaped the previous 12 months, I have decided to embrace the disruptiveness of CRISPR and pre-emptively offer 10 bold predictions to set the stage for what promises to be yet another eventful, perhaps pivotal, year for genome editing.Rather than offer a linear progression of incremental insights into what is likely to come, I will channel the ability of our field to leap ahead and offer colorful, perhaps contrarian, predictions of what may (hopefully will) happen for CRISPR in the next 12 months.1.Notwithstanding lingering technical issues (e.g., off-target effects and immunogenicity concerns) and public apprehension, there will be several genome editing clinical successes. This year closes with promising early clinical news from Victoria Gray, the first U.S.–based sickle-cell patient treated with a CRISPR therapy. In 2020, investigational new drug filings will trend up and U.S. FDA regulators will support active recruiting for several clinical trials. I hope they will quickly generate positive results for several indications by various groups of investigators and clinicians. Both safety and efficacy for multiple indications may well be in the cards for 2020.2.In an era of scientific skepticism, the public will embrace CRISPR and increasingly appreciate the real-world benefits of genome editing. Despite widespread misinformation, distrust in the scientific enterprise, and low confidence in scientists dedicating their lives to solving real challenges, team science will step up and share more wonderful stories. In place of sensational media headlines and overdramatized fearmongering, I am looking for the real stories of the scientists leading the revolution and of the people benefiting from it.3.Europe catches up with the world. The good thing about science is that (sometimes) it is immune to politics—just sound thinking, creative minds, and the scientific method. European pundits and regulators will eventually open their eyes to see the light and objectively assess the upside of CRISPR for diverse applications for their health, food, environmental, and commercial benefits. #crispEUr4.Rather than continue with toolbox expansion, current CRISPR tools will be put to good use. After years of next-generation Cas mining and optimization of the Cas, dCas, nCas and fused-effector domains, we will appreciate that the current tools are polished enough for most users and uses. With a useful Cas (Cas-9, 12, 13, et al.) toolbox, diverse applications (editing the genome, transcriptome, and epigenome) and optimized technologies (such as prime editing), currently available tools will be harnessed and implemented with greater urgency and less concerns about technology enhancement.5.Beyond therapeutics. With increasingly promising signs of clinical success, the potential of genome editing will be unleashed for livestock, crops, and even trees for a more sustainable agriculture and healthier planet. Organisms spanning most branches of the tree of life will be enhanced for broad societal benefits.6.Cooler heads prevail. Despite the continuation of intellectual property disputes and interference proceedings, progress toward commercialization of actual products and the need to split large pies that cannot be eaten whole will compel dominant parties to partner and split the proceeds. After all, science is a team sport hinging on scientific collaborations, and the community spirit will behoove key players and leaders to play nice.7.Business dealmakers join the fray. Investors and strategists will be intrigued by deflated stock prices given the extraordinary potential. Underperforming CRISPR stocks and underwhelming financial performance—symptoms that have affected the biotech sector as a whole—have not dampened the upside of CRISPR. The recent report of sickle-cell clinical data pushed valuations significantly higher. It would not be a surprise to see pharma competitively bid for early-stage CRISPR companies and undervalued tickers. Will we see our first CRISPR start-up acquisition in 2020? #CRISPRM&A8.CRISPR responsibility. Two major reports on germline editing, from the National Academies/Royal Society and the World Health Organization, will be released in 2020. We hope the reports will coordinate, with all the voices of CRISPR being heard, so we can build consensual and broadly acceptable frameworks to ensure we use CRISPR responsibly, especially regarding usage in human embryos for germline editing. The public has asked for it, and the community has been working on it. The science versus society gap will be bridged.9.CRISPR fatigue. Despite all the fanfare, I suspect there will be some CRISPR fatigue in 2020: after years of Addgene-fueled democratization, Odin-fed biohacking, and inexorable publication and citation growth, the rate at which CRISPR is expanding will start to slow down and plateau. This is not necessarily a bad thing, as most users in need have already adopted this technology.10.CRISPR goes global. Beyond academic scientists blazing new trails and investors hunting for new technologies, nations will define visions and strategies to expand and build national CRISPR portfolios to harness the bio-economy and keep up with the competition. Leading nations have claimed a stake in the scientific literature and intellectual property arenas, but as business appetite broadens and commercialization success advances, it will be perilous not to seize editing opportunities.So get some rest to prepare for an exciting and eventful year ahead!FiguresReferencesRelatedDetails Volume 2Issue 6Dec 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Foresight is 2020: Ten Bold Predictions for the New CRISPR Year.The CRISPR Journal.Dec 2019.341-342.http://doi.org/10.1089/crispr.2019.29075.rbaPublished in Volume: 2 Issue 6: December 16, 2019PDF download DA - 2019/// PY - 2019/// DO - 10.1089/crispr.2019.29075.rba VL - 2 IS - 6 SP - 341-342 ER - TY - JOUR TI - Time To Let CRISPR B.E.? AU - Barrangou, Rodolphe T2 - The CRISPR Journal AB - The CRISPR JournalVol. 2, No. 2 EditorialTime To Let CRISPR B.E.?Rodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR JournalSearch for more papers by this authorPublished Online:18 Apr 2019https://doi.org/10.1089/crispr.2019.29055.rdbAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Time To Let CRISPR B.E.?." The CRISPR Journal, 2(2), p. 67FiguresReferencesRelatedDetails Volume 2Issue 2Apr 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Time To Let CRISPR B.E.?.The CRISPR Journal.Apr 2019.67-67.http://doi.org/10.1089/crispr.2019.29055.rdbPublished in Volume: 2 Issue 2: April 18, 2019PDF download DA - 2019/4// PY - 2019/4// DO - 10.1089/crispr.2019.29055.rdb VL - 2 IS - 2 SP - 67-67 ER - TY - JOUR TI - Taking CRISPR to New Heights AU - Barrangou, Rodolphe T2 - The CRISPR Journal AB - The CRISPR JournalVol. 2, No. 3 EditorialTaking CRISPR to New HeightsRodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR Journal.Search for more papers by this authorPublished Online:21 Jun 2019https://doi.org/10.1089/crispr.2019.29064.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Taking CRISPR to New Heights." The CRISPR Journal, 2(3), p. 133FiguresReferencesRelatedDetails Volume 2Issue 3Jun 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Taking CRISPR to New Heights.The CRISPR Journal.Jun 2019.133-133.http://doi.org/10.1089/crispr.2019.29064.rbaPublished in Volume: 2 Issue 3: June 21, 2019PDF download DA - 2019/6// PY - 2019/6// DO - 10.1089/crispr.2019.29064.rba VL - 2 IS - 3 SP - 133-133 ER - TY - JOUR TI - CRISPR on the Move in 2019 AU - Barrangou, Rodolphe T2 - The CRISPR Journal AB - The CRISPR JournalVol. 2, No. 1 EditorialCRISPR on the Move in 2019Rodolphe BarrangouRodolphe BarrangouDr. Barrangou is a co-founder of Intellia Therapeutics and Locus Biosciences.Editor-in-Chief, The CRISPR JournalSearch for more papers by this authorPublished Online:21 Feb 2019https://doi.org/10.1089/crispr.2019.29043.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"CRISPR on the Move in 2019." The CRISPR Journal, 2(1), pp. 1–2FiguresReferencesRelatedDetails Volume 2Issue 1Feb 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.CRISPR on the Move in 2019.The CRISPR Journal.Feb 2019.1-2.http://doi.org/10.1089/crispr.2019.29043.rbaPublished in Volume: 2 Issue 1: February 21, 2019PDF download DA - 2019/2// PY - 2019/2// DO - 10.1089/crispr.2019.29043.rba VL - 2 IS - 1 SP - 1-2 ER - TY - JOUR TI - Bringing CRISPR to the Cinema AU - Barrangou, Rodolphe T2 - The CRISPR Journal AB - The CRISPR JournalVol. 2, No. 4 EditorialBringing CRISPR to the CinemaRodolphe BarrangouRodolphe BarrangouEditor in Chief, The CRISPR Journal.Search for more papers by this authorPublished Online:16 Aug 2019https://doi.org/10.1089/crispr.2019.29070.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Bringing CRISPR to the Cinema." The CRISPR Journal, 2(4), p. 187FiguresReferencesRelatedDetails Volume 2Issue 4Aug 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Bringing CRISPR to the Cinema.The CRISPR Journal.Aug 2019.187-187.http://doi.org/10.1089/crispr.2019.29070.rbaPublished in Volume: 2 Issue 4: August 16, 2019PDF download DA - 2019/8/1/ PY - 2019/8/1/ DO - 10.1089/crispr.2019.29070.rba VL - 2 IS - 4 SP - 187-187 ER - TY - JOUR TI - Thinking About CRISPR: The Ethics of Human Genome Editing AU - Barrangou, Rodolphe T2 - The CRISPR Journal AB - The CRISPR JournalVol. 2, No. 5 EditorialThinking About CRISPR: The Ethics of Human Genome EditingRodolphe BarrangouRodolphe BarrangouEditor-in-Chief, The CRISPR Journal.Search for more papers by this authorPublished Online:9 Oct 2019https://doi.org/10.1089/crispr.2019.29072.rbaAboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"Thinking About CRISPR: The Ethics of Human Genome Editing." The CRISPR Journal, 2(5), pp. 247–248FiguresReferencesRelatedDetailsCited byDemocratizing CRISPR? Stories, practices, and politics of science and governance on the agricultural gene editing frontier25 February 2020 | Elementa: Science of the Anthropocene, Vol. 8 Volume 2Issue 5Oct 2019 InformationCopyright 2019, Mary Ann Liebert, Inc., publishersTo cite this article:Rodolphe Barrangou.Thinking About CRISPR: The Ethics of Human Genome Editing.The CRISPR Journal.Oct 2019.247-248.http://doi.org/10.1089/crispr.2019.29072.rbaPublished in Volume: 2 Issue 5: October 9, 2019PDF download DA - 2019/10/1/ PY - 2019/10/1/ DO - 10.1089/crispr.2019.29072.rba VL - 2 IS - 5 SP - 247-248 ER - TY - JOUR TI - Profile of Rodolphe Barrangou AU - Davis, Tinsley H. T2 - Proceedings of the National Academy of Sciences AB - CRISPR, the Instapot of genome editing tools, has its origins in a bacterial immune system that recognizes and slices the genetic material of invading phages. Rodolphe Barrangou, a professor of food science at North Carolina State University, demonstrated the original function of the characteristic repeating genetic sequences long before it became a household word. Barrangou is now turning CRISPR inward, using bacterial cells’ own machinery to edit bacteria. “Unfortunately, bacteria do not typically have good DNA repair mechanisms, so self-targeting usually turns out to be lethal,” explains Barrangou, who was elected to the National Academy of Sciences in 2018. In his Inaugural Article, Barrangou outlines how repurposing the existing type I-E CRISPR-Cas3 system of Lactobacillus crispatus and inserting repair templates can enable targeted editing of this common member of the human microbiome (1). Photograph of Rodolphe Barrangou. Image courtesy of North Carolina State University/Marc Hall. Probiotic bacterium L. acidophilus NCFM. Image courtesy of North Carolina State University/Courtney Klotz, Valerie Lapham, and Charles Mooney. Born in France in 1975, Barrangou found his appetite for science relatively late, when he decided to major in chemistry at the Universite Rene Descartes in Paris. After earning a bachelor’s degree in 1996, he pursued a master’s degree in biological engineering at the Universite de Technologie Compiegne. Barrangou could not envision spending “10 to 20 years working on 1 molecule, 1 project,” as an organic chemist, and engineering was not quite the right fit either. A microbiology class on fermentation propelled him toward a second master’s degree in food science and the field he has helped shape for the past 2 decades. “The living part of microbes was a whole different dimensionality.” Barrangou found the shorter life cycle of projects in the food industry compelling and thinks some of the appeal is a nod to … DA - 2019/7// PY - 2019/7// DO - 10.1073/pnas.1911079116 VL - 116 IS - 32 SP - 15754-15756 ER - TY - JOUR TI - The repurposing of type I-E CRISPR-Cascade for gene activation in plants AU - Young, Joshua K. AU - Gasior, Stephen L. AU - Jones, Spencer AU - Wang, Lijuan AU - Navarro, Pedro AU - Vickroy, Becca AU - Barrangou, Rodolphe T2 - Communications Biology AB - CRISPR-Cas systems are robust and facile tools for manipulating the genome, epigenome and transcriptome of eukaryotic organisms. Most groups use class 2 effectors, such as Cas9 and Cas12a, however, other CRISPR-Cas systems may provide unique opportunities for genome engineering. Indeed, the multi-subunit composition of class 1 systems offers to expand the number of domains and functionalities that may be recruited to a genomic target. Here we report DNA targeting in Zea mays using a class 1 type I-E CRISPR-Cas system from S. thermophilus. First, we engineer its Cascade complex to modulate gene expression by tethering a plant transcriptional activation domain to 3 different subunits. Next, using an immunofluorescent assay, we confirm Cascade cellular complex formation and observe enhanced gene activation when multiple subunits tagged with the transcriptional activator are combined. Finally, we examine Cascade mediated gene activation at chromosomal DNA targets by reprogramming Zea mays cells to change color. DA - 2019/10/18/ PY - 2019/10/18/ DO - 10.1038/s42003-019-0637-6 UR - https://doi.org/10.1038/s42003-019-0637-6 ER - TY - JOUR TI - Genome editing using the endogenous type I CRISPR-Cas system in Lactobacillus crispatus AU - Hidalgo-Cantabrana, Claudio AU - Goh, Yong Jun AU - Pan, Meichen AU - Sanozky-Dawes, Rosemary AU - Barrangou, Rodolphe T2 - Proceedings of the National Academy of Sciences AB - CRISPR-Cas systems are now widely used for genome editing and transcriptional regulation in diverse organisms. The compact and portable nature of class 2 single effector nucleases, such as Cas9 or Cas12, has facilitated directed genome modifications in plants, animals, and microbes. However, most CRISPR-Cas systems belong to the more prevalent class 1 category, which hinges on multiprotein effector complexes. In the present study, we detail how the native type I-E CRISPR-Cas system, with a 5'-AAA-3' protospacer adjacent motif (PAM) and a 61-nucleotide guide CRISPR RNA (crRNA) can be repurposed for efficient chromosomal targeting and genome editing in Lactobacillus crispatus, an important commensal and beneficial microbe in the vaginal and intestinal tracts. Specifically, we generated diverse mutations encompassing a 643-base pair (bp) deletion (100% efficiency), a stop codon insertion (36%), and a single nucleotide substitution (19%) in the exopolysaccharide priming-glycosyl transferase (p-gtf). Additional genetic targets included a 308-bp deletion (20%) in the prophage DNA packaging Nu1 and a 730-bp insertion of the green fluorescent protein gene downstream of enolase (23%). This approach enables flexible alteration of the formerly genetically recalcitrant species L. crispatus, with potential for probiotic enhancement, biotherapeutic engineering, and mucosal vaccine delivery. These results also provide a framework for repurposing endogenous CRISPR-Cas systems for flexible genome targeting and editing, while expanding the toolbox to include one of the most abundant and diverse systems found in nature. DA - 2019/8/6/ PY - 2019/8/6/ DO - 10.1073/pnas.1905421116 UR - https://doi.org/10.1073/pnas.1905421116 KW - CRISPR KW - Cas3 KW - type I-E KW - genome editing KW - probiotic ER - TY - JOUR TI - The Genomic Basis for Short-Term Evolution of Environmental Adaptation in Maize AU - Wisser, Randall J. AU - Fang, Zhou AU - Holland, James B. AU - Teixeira, Juliana E. C. AU - Dougherty, John AU - Weldekidan, Teclemariam AU - Leon, Natalia AU - Flint-Garcia, Sherry AU - Lauter, Nick AU - Murray, Seth C. AU - Xu, Wenwei AU - Hallauer, Arnel T2 - GENETICS AB - Understanding the evolutionary capacity of populations to adapt to novel environments is one of the major pursuits in genetics. Moreover, for plant breeding, maladaptation is the foremost barrier to capitalizing on intraspecific variation in order to develop new breeds for future climate scenarios in agriculture. Using a unique study design, we simultaneously dissected the population and quantitative genomic basis of short-term evolution in a tropical landrace of maize that was translocated to a temperate environment and phenotypically selected for adaptation in flowering time phenology. Underlying 10 generations of directional selection, which resulted in a 26-day mean decrease in female-flowering time, [Formula: see text] of the heritable variation mapped to [Formula: see text] of the genome, where, overall, alleles shifted in frequency beyond the boundaries of genetic drift in the expected direction given their flowering time effects. However, clustering these non-neutral alleles based on their profiles of frequency change revealed transient shifts underpinning a transition in genotype-phenotype relationships across generations. This was distinguished by initial reductions in the frequencies of few relatively large positive effect alleles and subsequent enrichment of many rare negative effect alleles, some of which appear to represent allelic series. With these genomic shifts, the population reached an adapted state while retaining [Formula: see text] of the standing molecular marker variation in the founding population. Robust selection and association mapping tests highlighted several key genes driving the phenotypic response to selection. Our results reveal the evolutionary dynamics of a finite polygenic architecture conditioning a capacity for rapid environmental adaptation in maize. DA - 2019/12// PY - 2019/12// DO - 10.1534/genetics.119.302780 VL - 213 IS - 4 SP - 1479-1494 SN - 1943-2631 UR - https://doi.org/10.1534/genetics.119.302780 KW - recurrent selection KW - flowering time KW - genetic diversity KW - plant breeding KW - agriculture KW - climate change ER - TY - JOUR TI - Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks AU - Clark, Natalie M. AU - Buckner, Eli AU - Fisher, Adam P. AU - Nelson, Emily C. AU - Nguyen, Thomas T. AU - Simmons, Abigail R. AU - Balaguer, Maria A. de Luis AU - Butler-Smith, Tiara AU - Sheldon, Parnell J. AU - Bergmann, Dominique C. AU - Williams, Cranos M. AU - Sozzani, Rossangela T2 - NATURE COMMUNICATIONS AB - Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play a crucial role in cell renewal, regeneration, and organization. A number of stem cell type-specific genes have a known role in stem cell maintenance, identity, and/or division. Yet, how genes expressed across different stem cell types, referred to here as stem-cell-ubiquitous genes, contribute to stem cell regulation is less understood. Here, we find that, in the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks. Development of a mathematical model of TCX2 expression allows us to show that TCX2 orchestrates the coordinated division of different stem cell types. Our results highlight that genes expressed across different stem cell types ensure cross-communication among cells, allowing them to divide and develop harmonically together. DA - 2019/12/6/ PY - 2019/12/6/ DO - 10.1038/s41467-019-13132-2 VL - 10 SP - SN - 2041-1723 ER - TY - JOUR TI - Female and minority experiences in an astronomy-based science hobby AU - Hite, Rebecca AU - Jones, M. Gail AU - Andre, Tom AU - Childers, Gina AU - Corin, Elysa T2 - Cultural Studies of Science Education DA - 2019/2/6/ PY - 2019/2/6/ DO - 10.1007/s11422-018-9884-y VL - 14 IS - 4 SP - 937-962 J2 - Cult Stud of Sci Educ LA - en OP - SN - 1871-1502 1871-1510 UR - http://dx.doi.org/10.1007/S11422-018-9884-Y DB - Crossref KW - Hobbies KW - Astronomy KW - STEM underrepresentation KW - Motivation KW - Self-determination ER - TY - JOUR TI - Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells AU - Pickar-Oliver, Adrian AU - Black, Joshua B. AU - Lewis, Mae M. AU - Mutchnick, Kevin J. AU - Klann, Tyler S. AU - Gilcrest, Kylie A. AU - Sitton, Madeleine J. AU - Nelson, Christopher E. AU - Barrera, Alejandro AU - Bartelt, Luke C. AU - Reddy, Timothy E. AU - Beisel, Chase L. AU - Barrangou, Rodolphe AU - Gersbach, Charles A. T2 - NATURE BIOTECHNOLOGY AB - Class 2 CRISPR–Cas systems, such as Cas9 and Cas12, have been widely used to target DNA sequences in eukaryotic genomes. However, class 1 CRISPR–Cas systems, which represent about 90% of all CRISPR systems in nature, remain largely unexplored for genome engineering applications. Here, we show that class 1 CRISPR–Cas systems can be expressed in mammalian cells and used for DNA targeting and transcriptional control. We repurpose type I variants of class 1 CRISPR–Cas systems from Escherichia coli and Listeria monocytogenes, which target DNA via a multi-component RNA-guided complex termed Cascade. We validate Cascade expression, complex formation and nuclear localization in human cells, and demonstrate programmable CRISPR RNA (crRNA)-mediated targeting of specific loci in the human genome. By tethering activation and repression domains to Cascade, we modulate the expression of targeted endogenous genes in human cells. This study demonstrates the use of Cascade as a CRISPR-based technology for targeted eukaryotic gene regulation, highlighting class 1 CRISPR–Cas systems for further exploration. Type I CRISPR–Cas systems, the largest group of CRISPR systems in nature, can be repurposed for DNA targeting and gene regulation in human cells DA - 2019/12// PY - 2019/12// DO - 10.1038/s41587-019-0235-7 VL - 37 IS - 12 SP - 1493-+ SN - 1546-1696 ER - TY - JOUR TI - FIRST RECORD OF MANSONIA DYARI FROM SAINT CROIX, UNITED STATES VIRGIN ISLANDS AU - Seger, Krystal R. AU - Drummond, Aubrey, II AU - Delgado, David AU - Day, Corey A. AU - Sither, Charles B. AU - Soghigian, John AU - Wiegmann, Brian M. AU - Reiskind, Michael H. AU - Ellis, Brett R. AU - Byrd, Brian D. T2 - JOURNAL OF THE AMERICAN MOSQUITO CONTROL ASSOCIATION AB - The first report of Mansonia dyari on Saint Croix, United States Virgin Islands (USVI), is confirmed. Adult and larval specimens were collected in 2018 and 2019 through adult surveillance and larval collections. Specimens were identified by microscopic methods, and a representative specimen was confirmed by DNA sequencing (mitochondrial cytochrome c oxidase subunit I). Morphological features are reviewed and compared with Mansonia flaveola, a species previously reported in the USVI. Notes are provided on the locations, collection methods, and mosquito associates found with Ma. dyari in the USVI. DA - 2019/9// PY - 2019/9// DO - 10.2987/19-6859.1 VL - 35 IS - 3 SP - 214-216 SN - 1943-6270 KW - Caribbean KW - distribution KW - Mansonia dyari KW - surveillance ER - TY - JOUR TI - Predicting and visualizing features of CRISPR-Cas systems AU - Nethery, Matthew A. AU - Barrangou, Rodolphe T2 - CRISPR-CAS ENZYMES AB - Pervasive application of CRISPR–Cas systems in genome editing has prompted an increase in both interest and necessity to further elucidate existing systems as well as discover putative novel systems. The ubiquity and power of current computational platforms have made in silico approaches to CRISPR–Cas identification and characterization accessible to a wider audience and increasingly amenable for processing extensive data sets. Here, we describe in silico methods for predicting and visualizing notable features of CRISPR–Cas systems, including Cas domain determination, CRISPR array visualization, and inference of the protospacer-adjacent motif. The efficiency of these tools enables rapid exploration of CRISPR–Cas diversity across prokaryotic genomes and supports scalable analysis of large genomic data sets. DA - 2019/// PY - 2019/// DO - 10.1016/bs.mie.2018.10.016 VL - 616 SP - 1-25 SN - 0076-6879 ER - TY - JOUR TI - Spread of the famine lineage of Phytophthora infestans into the African and Asian continents AU - Saville, Amanda C AU - Ristaino, Jean T2 - Plant Health 2019 DA - 2019/// PY - 2019/// ER - TY - CONF TI - Noninvasive diagnosis of tomato late blight via smartphone fingerprinting of leaf volatiles AU - Li, Zheng AU - Paul, Rajesh AU - Tis, Taleb Ba AU - Saville, Amanda AU - Hansel, Jeana AU - Ristaino, Jean AU - Wei, Qingshan T2 - AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA C2 - 2019/// C3 - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY DA - 2019/// VL - 257 ER - TY - JOUR TI - Non-invasive plant disease diagnostics enabled by smartphone-based fingerprinting of leaf volatiles AU - Li, Zheng AU - Paul, Rajesh AU - Tis, Taleb Ba AU - Saville, Amanda C AU - Hansel, Jeana C AU - Yu, Tao AU - Ristaino, Jean B AU - Wei, Qingshan T2 - Nature plants DA - 2019/// PY - 2019/// VL - 5 IS - 8 SP - 856-866 ER - TY - JOUR TI - Phytophthora acaciae sp. nov., a new species causing gummosis of black wattle in Brazil AU - Alves, Tatiane C Albuquerque AU - Tessmann, Dauri J AU - Ivors, Kelly L AU - Ristaino, Jean B AU - Santos, Álvaro F T2 - Mycologia DA - 2019/// PY - 2019/// SP - 1-11 ER - TY - JOUR TI - Genomic microsatellites evidence species diversity and origin of Peronospora tabacina, an important pathogen of tobacco AU - Nowicki, Marcin AU - Hadziabdic, Denita AU - Boggess, Sarah L AU - Runge, Fabian AU - Thines, Marco AU - Ristaino, Jean AU - Spring, Otmar AU - Trigiano, Robert N T2 - Plant Health 2019 DA - 2019/// PY - 2019/// ER - TY - JOUR TI - Evaluation of a strain of Bacillus subtilis for management of Phytophthora blight of bell pepper AU - Hansel, Jeana AU - Ristaino, Jean T2 - Plant Health 2019 DA - 2019/// PY - 2019/// ER - TY - JOUR TI - Detection of Phytophthora infestans by LAMP, real-time LAMP and droplet digital PCR AU - Ristaino, Jean Beagle AU - Saville, Amanda AU - Paul, Rajesh AU - Cooper, Donald AU - Wei, Qingshan T2 - Plant Disease DA - 2019/// PY - 2019/// IS - ja ER - TY - JOUR TI - A Smartphone-Based Volatile Sensor Platform for Noninvasive Detection of Plant Pathogens AU - Li, Zheng AU - Paul, Rajesh AU - Tis, Taleb Ba AU - Saville, Amanda C AU - Hansel, Jeana AU - Ristaino, Jean AU - Wei, Qingshan T2 - Plant Health 2019 DA - 2019/// PY - 2019/// ER - TY - CONF TI - Minimally Invasive Extraction of Plant DNA Via a Polymeric Microneedle Patch for on-Site Detection of Plant Pathogens AU - Paul, Rajesh AU - Saville, Amanda AU - Hansel, Jeana AU - Ye, Yanqi AU - Ball, Carmin AU - Williams, Alyssa AU - Chang, Xinyuan AU - Chen, Guojun AU - Gu, Zhen AU - Ristaino, Jean AU - others T2 - AIChE C2 - 2019/// C3 - 2019 AIChE Annual Meeting DA - 2019/// ER - TY - JOUR TI - Microneedle-based Rapid Plant DNA Extraction: Towards In-Field Detection of Plant Pathogens AU - Paul, Rajesh AU - Saville, Amanda C AU - Hansel, Jeana AU - Ye, Yanqi AU - Ball, Carmin AU - Williams, Alyssa AU - Xinyuan, Xinyuan AU - Chen, Guojun AU - Gu, Zhen AU - Ristaino, Jean AU - others T2 - Plant Health 2019 DA - 2019/// PY - 2019/// ER - TY - JOUR TI - An improved plant toolset for high-throughput recombineering AU - Brumos, J. AU - Zhao, C. AU - Gong, Y. AU - Soriano, D. AU - Patel, A.P. AU - Perez-Amador, M.A. AU - Stepanova, A.N. AU - Alonso, J.M 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 make it possible to directly modify the target genes in their native chromosomal location, 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 obtained results provided by the direct chromosomal tagging achievable by genome editing strategies. These simple and customizable recombineering toolsets and protocols allow for high-throughput generation of a variety of genetic modifications. In addition, a highly efficient recombinase-mediated cassette exchange system has been developed to facilitate the transfer of the desired sequences from a BAC clone to a transformation-compatible binary vector, expanding the use of the recombineering approaches beyond Arabidopsis . The utility of this system is demonstrated by the generation of over 250 whole-gene translational fusions and 123 Arabidopsis transgenic lines corresponding to 62 auxin-related genes, and the characterization of the translational reporter expression patterns for 14 auxin biosynthesis genes. DA - 2019/6/3/ PY - 2019/6/3/ DO - 10.1101/659276 VL - 6 UR - https://doi.org/10.1101/659276 ER - TY - JOUR TI - Single-gene resolution of locally adaptive genetic variation in Mexican maize AU - Gates, Daniel J AU - Runcie, Dan AU - Janzen, Garrett M. AU - Navarro, Alberto Romero AU - Willcox, Martha AU - Sonder, Kai AU - Snodgrass, Samantha J. AU - Rodríguez-Zapata, Fausto AU - Sawers, Ruairidh J. H. AU - Rellán-Álvarez, Rubén AU - Buckler, Edward S. AU - Hearne, Sarah AU - Hufford, Matthew B. AU - Ross-Ibarra, Jeffrey T2 - [Biorxiv] AB - Abstract Threats to crop production due to climate change are one of the greatest challenges facing plant breeders today. While considerable adaptive variation exists in traditional landraces, natural populations of crop wild relatives, and ex situ germplasm collections, separating adaptive alleles from linked deleterious variants that impact agronomic traits is challenging and has limited the utility of these diverse germplasm resources. Modern genome editing techniques such as CRISPR offer a potential solution by targeting specific alleles for transfer to new backgrounds, but such methods require a higher degree of precision than traditional mapping approaches can achieve. Here we present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association. DA - 2019/7/18/ PY - 2019/7/18/ DO - 10.1101/706739 VL - 7 M3 - bioRxiv preprint UR - http://dx.doi.org/10.1101/706739 ER - TY - JOUR TI - Maintaining historic disturbance regimes increases species' resilience to catastrophic hurricanes T2 - Global Change Biology AB - Abstract As habitat loss and fragmentation, urbanization, and global climate change accelerate, conservation of rare ecosystems increasingly relies on human intervention. However, any conservation strategy is vulnerable to unpredictable, catastrophic events. Whether active management increases or decreases a system's resilience to these events remains unknown. Following Hurricane Irma's landfall in our habitat restoration study sites, we found that rare ecosystems with active, human‐imposed management suffered less damage in a hurricane's path than unmanaged systems. At the center of Irma's landfall, we found Croton linearis ' (a locally rare plant that is the sole host for two endangered butterfly species) survival and population growth rates in the year of the hurricane were higher in previously managed plots than in un‐managed controls. In the periphery of Irma's circulation, the effect of prior management was stronger than that of the hurricane. Maintaining the historical disturbance regime thus increased the resilience of the population to major hurricane disturbance. As climate change increases the probability and intensity of severe hurricanes, human management of disturbance‐adapted landscapes will become increasingly important for maintaining populations of threatened species in a storm's path. Doing nothing will accelerate extinction. DA - 2019/12/18/ PY - 2019/12/18/ DO - 10.1111/gcb.14932 UR - http://dx.doi.org/10.1111/gcb.14932 KW - butterfly KW - conservation KW - endangered species KW - habit restoration KW - hurricane KW - population dynamics ER - TY - JOUR TI - Articulating ‘free, prior and informed consent’ (FPIC) for engineered gene drives AU - George, Dalton R. AU - Kuiken, Todd AU - Delborne, Jason A. T2 - Proceedings of the Royal Society B: Biological Sciences AB - Recent statements by United Nations bodies point to free, prior and informed consent (FPIC) as a potential requirement in the development of engineered gene drive applications. As a concept developed in the context of protecting Indigenous rights to self-determination in land development scenarios, FPIC would need to be extended to apply to the context of ecological editing. Without an explicit framework of application, FPIC could be interpreted as a narrowly framed process of community consultation focused on the social implications of technology, and award little formal or advisory power in decision-making to Indigenous peoples and local communities. In this paper, we argue for an articulation of FPIC that attends to issues of transparency, iterative community-scale consent, and shared power through co-development among Indigenous peoples, local communities, researchers and technology developers. In realizing a comprehensive FPIC process, researchers and developers have an opportunity to incorporate enhanced participation and social guidance mechanisms into the design, development and implementation of engineered gene drive applications. DA - 2019/12/18/ PY - 2019/12/18/ DO - 10.1098/rspb.2019.1484 VL - 286 IS - 1917 SP - 20191484 J2 - Proc. R. Soc. B. LA - en OP - SN - 0962-8452 1471-2954 UR - http://dx.doi.org/10.1098/rspb.2019.1484 DB - Crossref KW - responsible research and innovation KW - public engagement KW - indigenous peoples KW - synthetic biology KW - Convention on Biological Diversity KW - community engagement ER - TY - JOUR TI - Interplay between Developmental Flexibility and Determinism in the Evolution of Mimetic Heliconius Wing Patterns AU - Concha, Carolina AU - Wallbank, Richard W.R. AU - Hanly, Joseph J. AU - Fenner, Jennifer AU - Livraghi, Luca AU - Rivera, Edgardo Santiago AU - Paulo, Daniel F. AU - Arias, Carlos AU - Vargas, Marta AU - Sanjeev, Manu AU - Morrison, Colin AU - Tian, David AU - Aguirre, Paola AU - Ferrara, Sabrina AU - Foley, Jessica AU - Pardo-Diaz, Carolina AU - Salazar, Camilo AU - Linares, Mauricio AU - Massardo, Darli AU - Counterman, Brian A. AU - Scott, Maxwell J. AU - Jiggins, Chris D. AU - Papa, Riccardo AU - Martin, Arnaud AU - McMillan, W. Owen T2 - Current Biology AB - To what extent can we predict how evolution occurs? Do genetic architectures and developmental processes canalize the evolution of similar outcomes in a predictable manner? Or do historical contingencies impose alternative pathways to answer the same challenge? Examples of Müllerian mimicry between distantly related butterfly species provide natural replicates of evolution, allowing us to test whether identical wing patterns followed parallel or novel trajectories. Here, we explore the role that the signaling ligand WntA plays in generating mimetic wing patterns in Heliconius butterflies, a group with extraordinary mimicry-related wing pattern diversity. The radiation is relatively young, and numerous cases of wing pattern mimicry have evolved within the last 2.5-4.5 Ma. WntA is an important target of natural selection and is one of four major effect loci that underlie much of the pattern variation in the group. We used CRISPR/Cas9 targeted mutagenesis to generate WntA-deficient wings in 12 species and a further 10 intraspecific variants, including three co-mimetic pairs. In all tested butterflies, WntA knockouts affect pattern broadly and cause a shift among every possible scale cell type. Interestingly, the co-mimics lacking WntA were very different, suggesting that the gene networks that pattern a wing have diverged considerably among different lineages. Thus, although natural selection channeled phenotypic convergence, divergent developmental contexts between the two major Heliconius lineages opened different developmental routes to evolve resemblance. Consequently, even under very deterministic evolutionary scenarios, our results underscore a surprising unpredictability in the developmental paths underlying convergence in a recent radiation. DA - 2019/12// PY - 2019/12// DO - 10.1016/j.cub.2019.10.010 VL - 29 IS - 23 SP - 3996-4009.e4 J2 - Current Biology LA - en OP - SN - 0960-9822 UR - http://dx.doi.org/10.1016/j.cub.2019.10.010 DB - Crossref ER - TY - JOUR TI - Stand age and species traits alter the effects of understory removal on litter decomposition and nutrient dynamics in subtropical Eucalyptus plantations AU - Chen, Yuanqi AU - Zhang, Yanju AU - Cao, Jianbo AU - Fu, Shenglei AU - Hu, Shuijin AU - Wu, Jianping AU - Zhao, Jie AU - Liu, Zhanfeng T2 - GLOBAL ECOLOGY AND CONSERVATION AB - Litter decomposition is a crucial ecological process that regulates nutrient cycling. However, the effects of understory plants and overstory trees on litter decomposition and nutrient dynamics are still poorly understood. We conducted understory plants removal and/or overstory trees removal to examine the resulting effects on litter decomposition and nutrient mineralization in two Eucalyptus plantations with contrasting ages (8-yr-old, 29-yr-old) in subtropical China. Litter bags containing naturally senesced leaves of either overstory Eucalyptus urophylla or understory Dicranopteris dichotoma were placed in field and periodically collected for analyses of carbon (C), nitrogen (N), phosphorus (P) and calculation of mass loss. Our results showed that understory plants removal significantly reduced litter decomposition of E. urophylla in both plantations, but N and P mineralization were reduced only in the 8-yr-old plantation. In contrast, it reduced litter decomposition of D. dichotoma only in the 29-yr-old plantation, but had no effects on N and P mineralization in either plantation. In comparison, overstory tree removal did not have any effects on decomposition or mineralization of N and P of E. urophylla and D. dichotoma litters. These results indicate that the role of understory plants in mediating litter decomposition and nutrient mineralization is more important than overstory trees, and it can be altered by stand age and plant species. Our findings could facilitate the understanding of ecological processes of litter decomposition and nutrient mineralization in subtropical forest ecosystems. DA - 2019/10// PY - 2019/10// DO - 10.1016/j.gecco.2019.e00693 VL - 20 ER - TY - JOUR TI - From risk perception to risk governance in nanotechnology: a multi-stakeholder study AU - Porcari, Andrea AU - Borsella, Elisabetta AU - Benighaus, Christina AU - Grieger, Khara AU - Isigonis, Panagiotis AU - Chakravarty, Somik AU - Kines, Pete AU - Jensen, Keld Alstrup T2 - JOURNAL OF NANOPARTICLE RESEARCH AB - Abstract Nanotechnology is widely used in several industrial and consumer sectors and has the potential to grow further and expand globally. An exploration of stakeholder (SH)’s perceptions is essential to ensuring that robust risk governance processes are in place for nanotechnology and nano-related products. In response, numerous studies have been conducted to investigate SH’s perceptions of nanotechnology and nano-related products over the past 15 years. To build on this work and to capture current perceptions across a wide panel of SHs, we conducted a multi-national and cross-sectoral SH study of awareness, perceptions and opinions regarding the use and potential impact on society and the environment of nanomaterials (NMs) and nano-related products, and SH’s expectations about risk governance. The study was conducted using both quantitative and qualitative inquiries and targeted more than 3000 SHs across different sectors in a total of 15 countries. Results showed a tendency towards more convergence of opinions amongst all the relevant SHs and the public respondents than in past studies. There was consensus on the crucial importance of having unbiased, scientific and trustable information regarding the potential impacts of NMs and nano-related products on the environment, health and safety. SHs were interested in having more internationally harmonised and robust regulation for NMs and nano-related products; improved scientific evidence on nanomaterial hazards, exposures and effects; as well as specific guidance on the safe use of NMs. Overall, this work provides an updated scenario of SHs’ perceptions regarding nanotechnology and nano-related products, underscoring the importance of including SH needs in effective risk governance strategies. DA - 2019/11// PY - 2019/11// DO - 10.1007/s11051-019-4689-9 VL - 21 IS - 11 SP - SN - 1572-896X UR - https://doi.org/10.1007/s11051-019-4689-9 KW - Nanomaterials KW - Nano-related products KW - Risk assessment KW - Risk management KW - Risk communication KW - Decision analysis KW - Risk-benefit of nanomaterials KW - Societal implications ER - TY - JOUR TI - Sex-specific behavioral effects following developmental exposure to tetrabromobisphenol A (TBBPA) in Wistar rats AU - Rock, Kylie D. AU - Gillera, Sagi Enicole A. AU - Devarasetty, Pratyush AU - Horman, Brian AU - Knudsen, Gabriel AU - Birnbaum, Linda S. AU - Fenton, Suzanne E. AU - Heather, Patisaul B. T2 - NEUROTOXICOLOGY AB - Tetrabromobisphenol A (TBBPA) has become a ubiquitous indoor contaminant due to its widespread use as an additive flame retardant in consumer products. Reported evidence of endocrine disruption and accumulation of TBBPA in brain tissue has raised concerns regarding its potential effects on neurodevelopment and behavior. The goal of the present study was to examine the impact of developmental TBBPA exposure, across a wide range of doses, on sexually dimorphic non-reproductive behaviors in male and female Wistar rats. We first ran a pilot study using a single TBBPA dose hypothesized to produce behavioral effects. Wistar rat dams were orally exposed using cookie treats to 0 or 0.1 mg TBBPA/kg bw daily from gestational day (GD) 9 to postnatal day (PND) 21 to assess offspring (both sexes) activity and anxiety-related behaviors. Significant effects were evident in females, with exposure increasing activity levels. Thus, this dose was used as the lowest TBBPA dose in a subsequent, larger study conducted as part of a comprehensive assessment of TBBPA toxicity. Animals were exposed to 0, 0.1, 25, or 250 mg TBBPA/kg bw daily by oral gavage starting on GD 6 through PND 90 (dosed dams GD 6 - PND 21, dosed offspring PND 22 - PND 90). Significant behavioral findings were observed for male offspring, with increased anxiety-like behavior as the primary phenotype. These findings demonstrate that exposure to environmental contaminants, like TBBPA, can have sex-specific effects on behavior highlighting the vulnerability of the developing brain. DA - 2019/12// PY - 2019/12// DO - 10.1016/j.neuro.2019.09.003 VL - 75 SP - 136-147 SN - 1872-9711 KW - brain KW - anxiety KW - endocrine disruptions KW - sex differences KW - hyperactivity KW - neural KW - sexually dimorphic KW - neurotoxic KW - flame retardants KW - elevated plus maze KW - neurodevelopment ER - TY - JOUR TI - Examining six modes of relationships in a social-mediated crisis in China: an exploratory study of contingent organization–public relationships (COPR) AU - Cheng, Yang AU - Cameron, Glen T. T2 - Journal of Applied Communication Research AB - The relationship management theory and contingency theory of conflict management, as two dominant approaches in the field of public relations, bolstered by a tapestry of literature from cross-disciplinary fields, were brought together to conceptualize the concept of contingent organization–public relationships (COPR). To generate the theoretical robustness of COPR and test its practical applicability, we selected a social-mediated crisis occurring in China and collected data through mixed-methods, including both content analysis and in-depth interviews. Quantitatively, content analysis of 338 Red Cross’s press releases and 4003 media coverage and 136,754 public posts during a 3-year time range provided a natural history of the application of COPR in crises. Qualitative interviews also offered in-depth information on the perceptions of stances and relationships from each party in this incident. Findings concluded that COPR addressed the dynamic and contingent multi-party relationships in contemporary China. DA - 2019/11/2/ PY - 2019/11/2/ DO - 10.1080/00909882.2019.1695874 VL - 47 IS - 6 SP - 689-705 J2 - Journal of Applied Communication Research LA - en OP - SN - 0090-9882 1479-5752 UR - http://dx.doi.org/10.1080/00909882.2019.1695874 DB - Crossref KW - Contingency theory KW - contingent relationship KW - conflict KW - dynamism KW - China KW - social-mediated crisis ER - TY - JOUR TI - Structural and functional insights into the Diabrotica virgifera virgifera ATP-binding cassette transporter gene family AU - Adedipe, Folukemi AU - Grubbs, Nathaniel AU - Coates, Brad AU - Wiegmman, Brian AU - Lorenzen, Marcé T2 - BMC Genomics AB - Abstract Background The western corn rootworm, Diabrotica virgifera virgifera , is a pervasive pest of maize in North America and Europe, which has adapted to current pest management strategies. In advance of an assembled and annotated D. v. virgifera genome, we developed transcriptomic resources to use in identifying candidate genes likely to be involved in the evolution of resistance, starting with members of the ATP-binding cassette (ABC) transporter family. Results In this study, 65 putative D. v. virgifera ABC ( Dvv ABC) transporters were identified within a combined transcriptome assembly generated from embryonic, larval, adult male, and adult female RNA-sequence libraries. Phylogenetic analysis placed the deduced amino-acid sequences of the Dvv ABC transporters into eight subfamilies (A to H). To supplement our sequence data with functional analysis, we identified orthologs of Tribolium castaneum ABC genes which had previously been shown to exhibit overt RNA interference (RNAi) phenotypes. We identified eight such D. v. virgifera genes, and found that they were functionally similar to their T. castaneum counterparts. Interestingly, depletion of DvvABCB_39715 and DvvABCG_3712 transcripts in adult females produced detrimental reproductive and developmental phenotypes, demonstrating the potential of these genes as targets for RNAi-mediated insect control tactics. Conclusions By combining sequence data from four libraries covering three distinct life stages, we have produced a relatively comprehensive de novo transcriptome assembly for D. v. virgifera . Moreover, we have identified 65 members of the ABC transporter family and provided the first insights into the developmental and physiological roles of ABC transporters in this pest species. DA - 2019/11/27/ PY - 2019/11/27/ DO - 10.1186/s12864-019-6218-8 VL - 20 IS - 1 SP - J2 - BMC Genomics LA - en OP - SN - 1471-2164 UR - http://dx.doi.org/10.1186/s12864-019-6218-8 DB - Crossref KW - ATP-binding cassette (ABC) transporter KW - Phylogenetic KW - Transcriptome KW - RNA interference (RNAi) KW - Corn rootworm ER - TY - JOUR TI - Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage AU - Nethery, Matthew A. AU - Henriksen, Emily DeCrescenzo AU - Daughtry, Katheryne V AU - Johanningsmeier, Suzanne D. AU - Barrangou, Rodolphe T2 - BMC GENOMICS AB - Abstract Background Lactobacillus buchneri is a lactic acid bacterium frequently associated with food bioprocessing and fermentation and has been found to be either beneficial or detrimental to industrial food processes depending on the application. The ability to metabolize lactic acid into acetic acid and 1,2-propandiol makes L. buchneri invaluable to the ensiling process, however, this metabolic activity leads to spoilage in other applications, and is especially damaging to the cucumber fermentation industry. This study aims to augment our genomic understanding of L. buchneri in order to make better use of the species in a wide range of applicable industrial settings. Results Whole-genome sequencing (WGS) was performed on seven phenotypically diverse strains isolated from spoiled, fermented cucumber and the ATCC type strain for L. buchneri , ATCC 4005. Here, we present our findings from the comparison of eight newly-sequenced and assembled genomes against two publicly available closed reference genomes, L. buchneri CD034 and NRRL B-30929. Overall, we see ~ 50% of all coding sequences are conserved across these ten strains. When these coding sequences are clustered by functional description, the strains appear to be enriched in mobile genetic elements, namely transposons. All isolates harbor at least one CRISPR-Cas system, and many contain putative prophage regions, some of which are targeted by the host’s own DNA-encoded spacer sequences. Conclusions Our findings provide new insights into the genomics of L. buchneri through whole genome sequencing and subsequent characterization of genomic features, building a platform for future studies and identifying elements for potential strain manipulation or engineering. DA - 2019/11/27/ PY - 2019/11/27/ DO - 10.1186/s12864-019-6274-0 VL - 20 IS - 1 SP - SN - 1471-2164 UR - https://doi.org/10.1186/s12864-019-6274-0 KW - Lactobacillus buchneri KW - Comparative genomics KW - Lactic acid bacteria KW - CRISPR-Cas systems KW - Fermentation KW - Spoilage KW - Food microbiology ER - TY - JOUR TI - Cognitive Enhancement and the Problem of the Pressure to Enhance: Rational Choice Modeling and Normative Justification AU - Dubljevic, Veljko AU - Dubljevic, V T2 - NEUROETHICS, JUSTICE AND AUTONOMY: PUBLIC REASON IN THE COGNITIVE ENHANCEMENT DEBATE AB - The problem of regulating cognitive neuroenhancement for healthy adults has generated considerable interest. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-13643-7_2 VL - 19 SP - 13-25 SN - 1875-0036 ER - TY - BOOK TI - Neuroethics, Justice and Autonomy: Public Reason in the Cognitive Enhancement Debate AU - Dubljevic, V AB - This book explicitly addresses the policy options in a democratic society regarding cognitive enhancement drugs and devices. The book offers an in-depth case by case analysis of existing and emerging cognitive neuroenhancement technologies and canvasses a distinct approach DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-13643-7 VL - 19 SE - 1-138 SN - 978-3-030-13642-0 ER - TY - JOUR TI - Neuropharmacology, Addiction and Autonomy: A Proposal for Public Policy on Adderall and Ritalin as Pharmacological Enhancements AU - Dubljevic, Veljko AU - Dubljevic, V T2 - NEUROETHICS, JUSTICE AND AUTONOMY: PUBLIC REASON IN THE COGNITIVE ENHANCEMENT DEBATE AB - The use of medical drugs such as Adderall (mixed amphetamine salts) and Ritalin (methylphenidate) by healthy adults for enhancement of cognitive function is a social trend that has gained in momentum (see, e.g., DeSantis et al. in J Am Coll Health 57(3):315–324, 2008; Maher in Nature 452(7188):674–675, 2008; Ragan et al. in Neuropharmacology 64:588–595, 2012), and accordingly has generated a lot of attention in academia (for an overview see Racine in Pragmatic neuroethics: improving treatment and understanding of the mind-brain. MIT Press, Cambridge, 2010, Chap. 6). DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-13643-7_4 VL - 19 SP - 45-63 SN - 1875-0036 ER - TY - JOUR TI - The Application of Rawlsian Principles of Justice on Cognition-Enhancement Drugs: A Policy Proposal AU - Dubljevic, Veljko AU - Dubljevic, V T2 - NEUROETHICS, JUSTICE AND AUTONOMY: PUBLIC REASON IN THE COGNITIVE ENHANCEMENT DEBATE AB - StimulantStimulants medication, which has been dubbed “smart drugs”, offers the potential for enhancement of cognitionCognition , which by itself is seen as a “promise” or a “threat” due to the drastic changes of the lives of all citizens in society. The current lack of adequate regulation could potentially lead to widespread violation of rights and justice, especially since directEthics debate coercion, direct and indirectEthics debate coercion, indirect coercionCoercion may be brought to bear on many individuals, as a result from utility calculations of employers and other corporate actors. The pressure to enhance is likely to become very high in the military and education contexts, but the most far-reaching influence would come from the sphere of business. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-13643-7_1 VL - 19 SP - 3-12 SN - 1875-0036 ER - TY - JOUR TI - Is the Proposal of the Political Notion of Autonomy Problematic? AU - Dubljevic, Veljko AU - Dubljevic, V T2 - NEUROETHICS, JUSTICE AND AUTONOMY: PUBLIC REASON IN THE COGNITIVE ENHANCEMENT DEBATE AB - My prior work on autonomyAutonomy (see Dubljević in Am J Bioeth Neurosci 4(4):44–51, 2013 and Chap. 3 ) took up the challenge posed by FelsenFelsen, Gidon and ReinerReiner, Peter B (Am J Bioeth Neurosci 2(3):3–14, 2011) to substantially address how autonomy should be viewed in light of new evidence fromNeuroscience (cognitive) neuroscience. I argued that it is premature to propose that the empirical data renders autonomy ‘Quixotic’, posited that the moral–political notion of autonomy was mistakenly associated with the metaphysical concept of “free will”, and offered ideal-typical degrees of coercionCoercion and compulsion which qualify instances in which autonomy might be diminished or entirely lacking. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-13643-7_6 VL - 19 SP - 87-108 SN - 1875-0036 ER - TY - JOUR TI - Are There Problems with the Economic Disincentives Model of Regulation? AU - Dubljevic, Veljko AU - Dubljevic, V T2 - NEUROETHICS, JUSTICE AND AUTONOMY: PUBLIC REASON IN THE COGNITIVE ENHANCEMENT DEBATE AB - In the chapter on empirical constraints of psychopharmacological cognitiveCognitive enhancement pharmacological enhancersPsychopharmaceutical enhancers (Chap. 4 ), I analyzed available information and policy options for the two of the most commonly used cognitiveRegulation, regulations enhancement enhancementRegulation, regulations cognitive enhancement (CE) drugs: Adderall and Ritalin. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-13643-7_7 VL - 19 SP - 109-122 SN - 1875-0036 ER - TY - JOUR TI - Legitimate Public Policies on Electro-magnetic Cognitive Enhancements AU - Dubljevic, Veljko AU - Dubljevic, V T2 - NEUROETHICS, JUSTICE AND AUTONOMY: PUBLIC REASON IN THE COGNITIVE ENHANCEMENT DEBATE AB - Drugs are not the only means of brain modulation. Indeed, medical devices have long since known to be able to modulate, and perhaps even improve, cognitionCognition . However, there has been a considerable amount of speculationCognitive enhancement speculation about regarding what kinds of medical devices might offer cognitiveRegulation, regulations enhancement enhancementRegulation, regulations cognitive enhancement (CE) and what would be the accompanying ethical and regulatory challenges. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-13643-7_5 VL - 19 SP - 65-83 SN - 1875-0036 ER - TY - JOUR TI - A Proposal for a Reconstruction of the Concept of Autonomy AU - Dubljevic, Veljko AU - Dubljevic, V T2 - NEUROETHICS, JUSTICE AND AUTONOMY: PUBLIC REASON IN THE COGNITIVE ENHANCEMENT DEBATE AB - In many spheres of scholarship, including bioethics andPolitical (approach) to neuroethics neuroethicsNeuroethics , there seems to be a significant misunderstanding involving the conflation of the metaphysical concept of free will with the moral–political concept of autonomyAutonomy . Ever since Benjamin LibetLibet, Benjamin published the results of his experiments measuring the timing of a decisionEthics debate free decision-making to move by using electro-encephalography (Libet 1985), neuroscientific findings have been given a new impetus for metaphysical debates, which have mistakenly spilled over in practical philosophyPhilosophy . DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-13643-7_3 VL - 19 SP - 27-41 SN - 1875-0036 ER - TY - JOUR TI - A thrips vector of tomato spotted wilt virus responds to tomato acylsugar chemical diversity with reduced oviposition and virus inoculation AU - Ben-Mahmoud, Sulley AU - Anderson, Taylor AU - Chappell, Thomas M. AU - Smeda, John R. AU - Mutschler, Martha A. AU - Kennedy, George G. AU - De Jong, Darlene M. AU - Ullman, Diane E. T2 - Scientific Reports AB - Abstract There is increasing evidence that acylsugars deter insect pests and plant virus vectors, including the western flower thrips (WFT), Frankliniella occidentalis (Pergande), vector of tomato spotted wilt virus (TSWV). Acylsugars are sugar-polyesters composed of saturated, un-saturated, and variously branched short and long chain fatty acids (FAs) esterified to a glucose (acylglucose) or sucrose (acylsucrose) moiety. We sought to understand how acylsucrose amount and composition of associated FA profiles interacted to mediate resistance to WFT oviposition and TSWV inoculation on tomato leaves. Towards this goal, we examined WFT oviposition and TSWV inoculation behavior on tomato lines bred to exude varying amounts of acylsucrose in association with diverse FA profiles. Our data show that as acylsucrose amounts increased, WFT egg-laying (oviposition) decreased and TSWV inoculation was suppressed. Western flower thrips also responded to FA profiles that included iC4, iC11, nC12 and nC10 FA. These findings support improving acylsugar-mediated resistance against WFT by breeding tomatoes exuding greater amounts of acylsucrose associated with specific FA profiles. We show that increasing acylsucrose amount output by type IV trichomes and selecting for particular FA profiles through advanced breeding profoundly affects WFT behavior in ways that benefit management of WFT as direct pests and as TSWV vectors. DA - 2019/11/20/ PY - 2019/11/20/ DO - 10.1038/s41598-019-53473-y VL - 9 IS - 1 SP - J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-019-53473-y DB - Crossref ER - TY - JOUR TI - Electropermeabilization-based fluorescence in situ hybridization of whole-mount plant parasitic nematode specimens AU - Ruark-Seward, Casey L. AU - Davis, Eric L. AU - Sit, Tim L. T2 - METHODSX AB - A fluorescence in situ hybridization (FISH) protocol was developed for nematodes in which nucleic acid probes are introduced within the organism via electroporation. This modification of existing FISH protocols removes numerous chemical wash steps, and thus, reduces protocol time and specimen loss while improving hybridization sensitivity. The presented work is optimized for juveniles of soybean cyst nematode (SCN; Heterodera glycines) and has been used to identify both host and associated-microbial (viral) targets. Moreover, through the use of two different long wavelength fluorophores, two probes can be colocalized within one individual. This protocol may be adapted to identify targets-of-interest within other life stages and nematode species.This protocol improves:•Hands-on protocol time (by approximately 1.5 h).•Specimen loss (fewer aspiration steps).•Hybridization (allows colocalization with two nucleic acid probes and increases sensitivity). DA - 2019/// PY - 2019/// DO - 10.1016/j.mex.2019.11.009 VL - 6 SP - 2720-2728 SN - 2215-0161 KW - Nematode KW - RNA KW - FISH KW - Localization KW - Fluorescence KW - Gene expression KW - Virus ER - TY - CHAP TI - Economic principles and concepts in area-wide genetic pest management. AU - Brown, Z. S. AU - Jones, M. S. AU - Mumford, J. T2 - The economics of integrated pest management of insects AB - The objective of the article was to explore the key economic principles for the inclusion of genetically engineered insects within integrated pest management (IPM) programmes, discussing proposed examples with agriculture and health applications. PY - 2019/// DO - 10.1079/9781786393678.0096 SP - 96-121 OP - PB - CABI SN - 9781786393678 UR - http://dx.doi.org/10.1079/9781786393678.0096 DB - Crossref ER - TY - JOUR TI - Effects of global change factors and living roots on root litter decomposition in a Qinghai-Tibet alpine meadow AU - Shu, Meng AU - Zhao, Qingzhou AU - Li, Zhen AU - Zhang, Lin AU - Wang, Peng AU - Hu, Shuijin T2 - SCIENTIFIC REPORTS AB - Roots account for a major part of plant biomass in Tibetan alpine meadows. Understanding root decomposition with global change is key to predict carbon (C) and nutrient dynamics on the Qinghai-Tibet Plateau. Yet, few experiments have carefully examined root decomposition as influenced by global change. We conducted a field study to investigate the effects of nitrogen (N) addition, air warming, precipitation change, and the presence/absence of living roots on root decomposition in a Tibetan alpine meadow. Our results showed that N addition increased the mass and C remaining, and induced N accumulation in the litter. Increased precipitation significantly amplified the positive effect of N addition on litter mass remaining. The presence of alive roots in the litterbags decreased root litter C remaining but significantly increased N and phosphorus remaining of the litter. However, we did not find any significant effects of air warming on the litter decomposition. In the Qinghai-Tibet Plateau, N deposition is predicted to increase and precipitation regime is predicted to change. Our results suggest that the interaction between increased N and precipitation may reduce root decomposition in the Qinghai-Tibet Plateau in the future, and that the large stock of living roots exert a dominant impact on nutrient dynamics of root decomposition in the Tibetan alpine systems. DA - 2019/11/15/ PY - 2019/11/15/ DO - 10.1038/s41598-019-53450-5 VL - 9 SP - SN - 2045-2322 ER - TY - JOUR TI - The Pragmatic Force of Making an Argument AU - Goodwin, Jean AU - Innocenti, Beth T2 - Topoi DA - 2019/5/11/ PY - 2019/5/11/ DO - 10.1007/s11245-019-09643-8 VL - 38 IS - 4 SP - 669-680 J2 - Topoi LA - en OP - SN - 0167-7411 1572-8749 UR - http://dx.doi.org/10.1007/s11245-019-09643-8 DB - Crossref KW - Argumentation KW - Argument KW - Pragmatic theories of argumentation KW - Function of argumentation KW - Force of argumentation KW - Normative pragmatics ER - TY - JOUR TI - Best practices from nano-risk analysis relevant for other emerging technologies AU - Grieger, Khara AU - Jones, Jacob L. AU - Hansen, Steffen Foss AU - Hendren, Christine Ogilvie AU - Jensen, Keld Alstrup AU - Kuzma, Jennifer AU - Baun, Anders T2 - Nature Nanotechnology AB - The experiences gained from the past 15 years of nanomaterial risk analysis may be useful for the risk analysis efforts of other emerging technologies. DA - 2019/11// PY - 2019/11// DO - 10.1038/s41565-019-0572-1 VL - 14 IS - 11 SP - 998-1001 J2 - Nat. Nanotechnol. LA - en OP - SN - 1748-3387 1748-3395 UR - http://dx.doi.org/10.1038/s41565-019-0572-1 DB - Crossref ER - TY - JOUR TI - Extreme thermophiles as emerging metabolic engineering platforms AU - Crosby, James R AU - Laemthong, Tunyaboon AU - Lewis, April M AU - Straub, Christopher T AU - Adams, Michael WW AU - Kelly, Robert M T2 - Current Opinion in Biotechnology AB - Going forward, industrial biotechnology must consider non-model metabolic engineering platforms if it is to have maximal impact. This will include microorganisms that natively possess strategic physiological and metabolic features but lack either molecular genetic tools or such tools are rudimentary, requiring further development. If non-model platforms are successfully deployed, new avenues for production of fuels and chemicals from renewable feedstocks or waste materials will emerge. Here, the challenges and opportunities for extreme thermophiles as metabolic engineering platforms are discussed. DA - 2019/10// PY - 2019/10// DO - 10.1016/j.copbio.2019.02.006 VL - 59 SP - 55-64 J2 - Current Opinion in Biotechnology LA - en OP - SN - 0958-1669 UR - http://dx.doi.org/10.1016/j.copbio.2019.02.006 DB - Crossref ER - TY - JOUR TI - "Yes, and ... ": continuing the scholarly conversation about teacher labor in PK-12 education* AU - Rudick, C. Kyle AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - Prior to my (Dannels’) daughter starting elementary school, I took on the challenge of finding a school as almost a full-blown research project. I toured multiple schools (we live in a school distr... DA - 2019/11/14/ PY - 2019/11/14/ DO - 10.1080/03634523.2020.1684690 VL - 11 SP - SN - 1479-5795 ER - TY - JOUR TI - Physicochemical data of p-cresol, butyric acid, and ammonia AU - Kolar, Praveen AU - Classen, John AU - Hall, Steven G. T2 - Data in Brief AB - There is a renewed interest in treating odorous contaminants such as butyric acid, p-cresol, and ammonia that are emitted from animal farming operations. However, developing newer treatment technologies require quantitative information regarding the properties of the target pollutants. Therefore, in this communication, baseline data related to physicochemical and thermodynamic properties of butyric acid, p-cresol, and ammonia were predicted using computational chemistry. Density functional theory was employed via B3LYP functional coupled with polarized 6-31G (d) basis set without any solvent effects using Gaussian 16W and GaussView6. The predicted baseline properties collected here are expected to be useful to scientists and engineers working in environmental mitigation technologies in developing treatment processes and make the animal agricultural industry environmental friendly and sustainable. DA - 2019/10// PY - 2019/10// DO - 10.1016/j.dib.2019.104356 VL - 26 SP - 104356 J2 - Data in Brief LA - en OP - SN - 2352-3409 UR - http://dx.doi.org/10.1016/j.dib.2019.104356 DB - Crossref KW - Butyric acid KW - p-cresol KW - Ammonia KW - Indole KW - Density functional theory ER - TY - JOUR TI - Online crisis communication in a post-truth Chinese society: Evidence from interdisciplinary literature AU - Cheng, Yang AU - Lee, Chia-Jui T2 - Public Relations Review AB - Through a thematic content analysis of 118 journal articles from interdisciplinary fields, this study reviews the research trends of online crisis communication literature in a Chinese post-truth society, where objective facts play a diminishing role, and Chinese people are losing their trust, despite the best efforts of organizations to deal with fake news in crises. Results of this study disclose some unique crisis communication strategies (e.g., strategic distraction, rumor-rebuttal, fabrication, acting cute, and content censorship) in crises of China. Influential contextual factors such as the political system, cultural values, and media features are identified as well. Theoretical and practical implications of this study are discussed, and a greater picture of online crisis communication in contexts is posited for future research. DA - 2019/11// PY - 2019/11// DO - 10.1016/j.pubrev.2019.101826 VL - 45 IS - 4 SP - 101826 J2 - Public Relations Review LA - en OP - SN - 0363-8111 UR - http://dx.doi.org/10.1016/j.pubrev.2019.101826 DB - Crossref KW - Social media KW - Post-truth KW - Misinformation KW - Context KW - Crisis communication strategies KW - Trust KW - China ER - TY - JOUR TI - One thousand plant transcriptomes and the phylogenomics of green plants AU - Leebens-Mack, James H. AU - Barker, Michael S. AU - Carpenter, Eric J. AU - Deyholos, Michael K. AU - Gitzendanner, Matthew A. AU - Graham, Sean W. AU - Grosse, Ivo AU - Li, Zheng AU - Melkonian, Michael AU - Mirarab, Siavash AU - Porsch, Martin AU - Quint, Marcel AU - Rensing, Stefan A. AU - Soltis, Douglas E. AU - Soltis, Pamela S. AU - Stevenson, Dennis W. AU - Ullrich, Kristian K. AU - Wickett, Norman J. AU - DeGironimo, Lisa AU - Edger, Patrick P. AU - Jordon-Thaden, Ingrid E. AU - Joya, Steve AU - Liu, Tao AU - Melkonian, Barbara AU - Miles, Nicholas W. AU - Pokorny, Lisa AU - Quigley, Charlotte AU - Thomas, Philip AU - Villarreal, Juan Carlos AU - Augustin, Megan M. AU - Barrett, Matthew D. AU - Baucom, Regina S. AU - Beerling, David J. AU - Benstein, Ruben Maximilian AU - Biffin, Ed AU - Brockington, Samuel F. AU - Burge, Dylan O. AU - Burris, Jason N. AU - Burris, Kellie P. AU - Burtet-Sarramegna, Valerie AU - Caicedo, Ana L. AU - Cannon, Steven B. AU - Cebi, Zehra AU - Chang, Ying AU - Chater, Caspar AU - Cheeseman, John M. AU - Chen, Tao AU - Clarke, Neil D. AU - Clayton, Harmony AU - Covshoff, Sarah AU - Crandall-Stotler, Barbara J. AU - Cross, Hugh AU - dePamphilis, Claude W. AU - Der, Joshua P. AU - Determann, Ron AU - Dickson, Rowan C. AU - Di Stilio, Veronica S. AU - Ellis, Shona AU - Fast, Eva AU - Feja, Nicole AU - Field, Katie J. AU - Filatov, Dmitry A. AU - Finnegan, Patrick M. AU - Floyd, Sandra K. AU - Fogliani, Bruno AU - Garcia, Nicolas AU - Gateble, Gildas AU - Godden, Grant T. AU - Goh, Falicia AU - Greiner, Stephan AU - Harkess, Alex AU - Heaney, James Mike AU - Helliwell, Katherine E. AU - Heyduk, Karolina AU - Hibberd, Julian M. AU - Hodel, Richard G. J. AU - Hollingsworth, Peter M. AU - Johnson, Marc T. J. AU - Jost, Ricarda AU - Joyce, Blake AU - Kapralov, Maxim V. AU - Kazamia, Elena AU - Kellogg, Elizabeth A. AU - Koch, Marcus A. AU - Von Konrat, Matt AU - Konyves, Kalman AU - Kutchan, Toni M. AU - Lam, Vivienne AU - Larsson, Anders AU - Leitch, Andrew R. AU - Lentz, Roswitha AU - Li, Fay-Wei AU - Lowe, Andrew J. AU - Ludwig, Martha AU - Manos, Paul S. AU - Mavrodiev, Evgeny AU - McCormick, Melissa K. AU - McKain, Michael AU - McLellan, Tracy AU - McNeal, Joel R. AU - Miller, Richard E. AU - Nelson, Matthew N. AU - Peng, Yanhui AU - Ralph, Paula AU - Real, Daniel AU - Riggins, Chance W. AU - Ruhsam, Markus AU - Sage, Rowan F. AU - Sakai, Ann K. AU - Scascitella, Moira AU - Schilling, Edward E. AU - Schlosser, Eva-Marie AU - Sederoff, Heike AU - Servick, Stein AU - Sessa, Emily B. AU - Shaw, A. Jonathan AU - Shaw, Shane W. AU - Sigel, Erin M. AU - Skema, Cynthia AU - Smith, Alison G. AU - Smithson, Ann AU - Stewart, C. Neal, Jr. AU - Stinchcombe, John R. AU - Szovenyi, Peter AU - Tate, Jennifer A. AU - Tiebel, Helga AU - Trapnell, Dorset AU - Villegente, Matthieu AU - Wang, Chun-Neng AU - Weller, Stephen G. AU - Wenzel, Michael AU - Weststrand, Stina AU - Westwood, James H. AU - Whigham, Dennis F. AU - Wu, Shuangxiu AU - Wulff, Adrien S. AU - Yang, Yu AU - Zhu, Dan AU - Zhuang, Cuili AU - Zuidof, Jennifer AU - Chase, Mark W. AU - Pires, J. Chris AU - Rothfels, Carl J. AU - Yu, Jun AU - Chen, Cui AU - Chen, Li AU - Cheng, Shifeng AU - Li, Juanjuan AU - Li, Ran AU - Li, Xia AU - Lu, Haorong AU - Ou, Yanxiang AU - Sun, Xiao AU - Tan, Xuemei AU - Tang, Jingbo AU - Tian, Zhijian AU - Wang, Feng AU - Wang, Jun AU - Wei, Xiaofeng AU - Xu, Xun AU - Yan, Zhixiang AU - Yang, Fan AU - Zhong, Xiaoni AU - Zhou, Feiyu AU - Zhu, Ying AU - Zhang, Yong AU - Ayyampalayam, Saravanaraj AU - Barkman, Todd J. AU - Nguyen, Nam-Phuong AU - Matasci, Naim AU - Nelson, David R. AU - Sayyari, Erfan AU - Wafula, Eric K. AU - Walls, Ramona L. AU - Warnow, Tandy AU - An, Hong AU - Arrigo, Nils AU - Baniaga, Anthony E. AU - Galuska, Sally AU - Jorgensen, Stacy A. AU - Kidder, Thomas I. AU - Kong, Hanghui AU - Lu-Irving, Patricia AU - Marx, Hannah E. AU - Qi, Xinshuai AU - Reardon, Chris R. AU - Sutherland, Brittany L. AU - Tiley, George P. AU - Welles, Shana R. AU - Yu, Rongpei AU - Zhan, Shing AU - Gramzow, Lydia AU - Theissen, Gunter AU - Wong, Gane Ka-Shu T2 - NATURE AB - Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life. DA - 2019/10/31/ PY - 2019/10/31/ DO - 10.1038/s41586-019-1693-2 VL - 574 IS - 7780 SP - 679-+ SN - 1476-4687 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85074238403&partnerID=MN8TOARS ER - TY - JOUR TI - Locally Fixed Alleles: A method to localize gene drive to island populations AU - Sudweeks, Jaye AU - Hollingsworth, Brandon AU - Blondel, Dimitri V AU - Campbell, Karl J. AU - Dhole, Sumit AU - Eisemann, John D. AU - Edwards, Owain AU - Godwin, John AU - Howald, Gregg R. AU - Oh, Kevin P. AU - Piaggio, Antoinette J. AU - Prowse, Thomas A. A. AU - Ross, Joshua V AU - Saah, J. Royden AU - Shiels, Aaron B. AU - Thomas, Paul Q. AU - Threadgill, David W. AU - Vella, Michael R. AU - Gould, Fred AU - Lloyd, Alun L. T2 - SCIENTIFIC REPORTS AB - Abstract Invasive species pose a major threat to biodiversity on islands. While successes have been achieved using traditional removal methods, such as toxicants aimed at rodents, these approaches have limitations and various off-target effects on island ecosystems. Gene drive technologies designed to eliminate a population provide an alternative approach, but the potential for drive-bearing individuals to escape from the target release area and impact populations elsewhere is a major concern. Here we propose the “Locally Fixed Alleles” approach as a novel means for localizing elimination by a drive to an island population that exhibits significant genetic isolation from neighboring populations. Our approach is based on the assumption that in small island populations of rodents, genetic drift will lead to alleles at multiple genomic loci becoming fixed. In contrast, multiple alleles are likely to be maintained in larger populations on mainlands. Utilizing the high degree of genetic specificity achievable using homing drives, for example based on the CRISPR/Cas9 system, our approach aims at employing one or more locally fixed alleles as the target for a gene drive on a particular island. Using mathematical modeling, we explore the feasibility of this approach and the degree of localization that can be achieved. We show that across a wide range of parameter values, escape of the drive to a neighboring population in which the target allele is not fixed will at most lead to modest transient suppression of the non-target population. While the main focus of this paper is on elimination of a rodent pest from an island, we also discuss the utility of the locally fixed allele approach for the goals of population suppression or population replacement. Our analysis also provides a threshold condition for the ability of a gene drive to invade a partially resistant population. DA - 2019/11/1/ PY - 2019/11/1/ DO - 10.1038/s41598-019-51994-0 VL - 9 SP - SN - 2045-2322 ER - TY - JOUR TI - Collaborative networks in gene editing AU - Huang, Ying AU - Porter, Alan AU - Zhang, Yi AU - Barrangou, Rodolphe T2 - NATURE BIOTECHNOLOGY DA - 2019/10// PY - 2019/10// DO - 10.1038/s41587-019-0275-z VL - 37 IS - 10 SP - 1107-1109 SN - 1546-1696 ER - TY - JOUR TI - Control of Filth Flies, Cochliomyia macellaria (Diptera: Calliphoridae), Musca domestica (Diptera: Muscidae), and Sarcophaga bullata (Diptera: Sarcophagidae), Using Novel Plant-Derived Methyl Ketones AU - Deguenon, Jean M AU - Zhu, Jiwei AU - Denning, Steven AU - Reiskind, Michael H AU - Watson, David W AU - Roe, R Michael T2 - Journal of Medical Entomology AB - Abstract Filth flies live in close proximity to humans and livestock and transmit pathogens. Current control relies on chemical insecticides, and flies can develop resistance to these insecticides. The public is also interested in natural and safer insecticides. Therefore, alternative pesticides compatible with the synanthropic nature of flies are needed. Four plant aliphatic methyl ketones were evaluated for control of adult house flies, Musca domestica L., blow flies, Cochliomyia macellaria (F.), and gray flesh flies, Sarcophaga bullata (Parker). In sealed petri dish assays, 2-heptanone, 2-octanone, 2-nonanone, and 2-undecanone exhibited fumigant activity against house flies with 24-h LC50s of 6.9, 7.5, 8.0, and 9.2 µg/cm3, respectively. Further research focused on undecanone (a U.S. EPA-registered biopesticide). When tested in larger enclosures at 1.7, 2.3, and 2.8 µg/cm3, undecanone provided 60.4, 82.2, and 94.4% house fly mortality; 56.9, 75.6, and 92.5% flesh fly mortality; and 62.1, 84.5, and 97.9% blow fly mortality, respectively, after a 2-h exposure. In a two-choice behavioral assay with 194.6 µg/cm2 of the test compound on the treatment versus an untreated surface of the same area, the overall mean repellencies for blow flies were 84.7% for undecanone versus 87.6% for N,N-diethyl-meta-toluamide (DEET). For house flies, mean repellencies were 80.7% for undecanone and 84.9% for DEET. The house fly topical LD50 for undecanone was 58.1 µg per fly. Undecanone was far less expensive for filth fly control than the gold standard for insect fumigation, methyl bromide. DA - 2019/6/26/ PY - 2019/6/26/ DO - 10.1093/jme/tjz107 VL - 56 IS - 6 SP - 1704-1714 LA - en OP - SN - 0022-2585 1938-2928 UR - http://dx.doi.org/10.1093/jme/tjz107 DB - Crossref KW - fumigant KW - repellent KW - methyl ketone KW - 2-undecanone KW - methyl bromide ER - TY - JOUR TI - Comparative Vector Efficiency of Two Prevalent Mosquito Species for Dog Heartworm in North Carolina AU - Spence Beaulieu, Meredith R AU - Reiskind, Michael H T2 - Journal of Medical Entomology AB - Abstract The dog heartworm, Dirofilaria immitis (Leidy) (Spirurida: Onchocercidae), is a devastating parasite of domestic and wild canines vectored by a multitude of mosquito species. Although many species are implicated as vectors, not all contribute equally to disease transmission, with demonstrated variation in vector efficiency between and within species. We investigated the vector efficiency of mosquitoes derived from wild-caught North Carolina populations of two known heartworm vectors: a native species, Aedes triseriatus (Say) (Diptera: Culicidae), and an invasive species, Aedes albopictus (Skuse). We compared the parasite developmental times within the mosquito, mosquito longevity and fecundity, and the vector efficiency index between the two species. We found that the tested composite North Carolina population of Ae. triseriatus was an efficient vector of D. immitis under laboratory conditions, whereas the local composite population of Ae. albopictus was a competent but relatively poor vector. Compared with Ae. triseriatus, Ae. albopictus showed a longer time for parasite development, lower infection rates, and lower vector efficiency. Additionally, Ae. albopictus was the sole species to exhibit significant parasite-induced mortality. These results are in contrast to prior studies of populations of Ae. albopictus from locations outside of North Carolina, which have implicated the species as a highly competent heartworm vector. The variation seen for different strains of the same species emphasizes the heritable nature of D. immitis vector competence and highlights the need for local infection studies for accurate transmission risk assessment in a particular locale. DA - 2019/11/5/ PY - 2019/11/5/ DO - 10.1093/jme/tjz190 VL - 11 LA - en OP - SN - 0022-2585 1938-2928 UR - http://dx.doi.org/10.1093/jme/tjz190 DB - Crossref KW - Aedes albopictus KW - Aedes triseriatus KW - parasite-induced mortality KW - vector competence KW - Dirofilaria immitis ER - TY - JOUR TI - Governing evolution: A socioecological comparison of resistance management for insecticidal transgenic Bt crops among four countries AU - Carrière, Yves AU - Brown, Zachary S. AU - Downes, Sharon J. AU - Gujar, Govind AU - Epstein, Graham AU - Omoto, Celso AU - Storer, Nicholas P. AU - Mota-Sanchez, David AU - Søgaard Jørgensen, Peter AU - Carroll, Scott P. T2 - Ambio AB - Cooperative management of pest susceptibility to transgenic Bacillus thuringiensis (Bt) crops is pursued worldwide in a variety of forms and to varying degrees of success depending on context. We examine this context using a comparative socioecological analysis of resistance management in Australia, Brazil, India, and the United States. We find that a shared understanding of resistance risks among government regulators, growers, and other actors is critical for effective governance. Furthermore, monitoring of grower compliance with resistance management requirements, surveillance of resistance, and mechanisms to support rapid implementation of remedial actions are essential to achieve desirable outcomes. Mandated resistance management measures, strong coordination between actors, and direct linkages between the group that appraises resistance risks and growers also appear to enhance prospects for effective governance. Our analysis highlights factors that could improve current governance systems and inform other initiatives to conserve susceptibility as a contribution to the cause of public good. DA - 2019/3/21/ PY - 2019/3/21/ DO - 10.1007/s13280-019-01167-0 VL - 3 J2 - Ambio LA - en OP - SN - 0044-7447 1654-7209 UR - http://dx.doi.org/10.1007/s13280-019-01167-0 DB - Crossref KW - Bacillus thuringiensis crops KW - Conservation and monitoring KW - Institutional analysis and development KW - Sustainability KW - Transgenic crops 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 - 2019/// PY - 2019/// DO - 10.1177/0040517519877468 KW - negative Poisson's ratio KW - auxetic structure KW - knitted fabric KW - finite element analysis KW - curling ER - TY - JOUR TI - Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development AU - Vallarino, José G. AU - Merchante, Catharina AU - Sánchez‐Sevilla, José F. AU - Luis Balaguer, María Angels AU - Pott, Delphine M. AU - Ariza, María T. AU - Casañal, Ana AU - Posé, David AU - Vioque, Amalia AU - Amaya, Iraida AU - Willmitzer, Lothar AU - Solano, Roberto AU - Sozzani, Rosangela AU - Fernie, Alisdair R. AU - Botella, Miguel A. AU - Giovannoni, James J. AU - Valpuesta, Victoriano AU - Osorio, Sonia T2 - Plant Biotechnology Journal AB - Abstract FaMADS9 is the strawberry ( Fragaria x ananassa ) gene that exhibits the highest homology to the tomato ( Solanum lycopersicum ) RIN gene. Transgenic lines were obtained in which FaMADS9 was silenced. The fruits of these lines did not show differences in basic parameters, such as fruit firmness or colour, but exhibited lower Brix values in three of the four independent lines. The gene ontology MapMan category that was most enriched among the differentially expressed genes in the receptacles at the white stage corresponded to the regulation of transcription, including a high percentage of transcription factors and regulatory proteins associated with auxin action. In contrast, the most enriched categories at the red stage were transport, lipid metabolism and cell wall. Metabolomic analysis of the receptacles of the transformed fruits identified significant changes in the content of maltose, galactonic acid‐1,4‐lactone, proanthocyanidins and flavonols at the green/white stage, while isomaltose, anthocyanins and cuticular wax metabolism were the most affected at the red stage. Among the regulatory genes that were differentially expressed in the transgenic receptacles were several genes previously linked to flavonoid metabolism, such as MYB10 , DIV , ZFN1 , ZFN2 , GT2 , and GT5 , or associated with the action of hormones, such as abscisic acid, SHP , ASR , GTE7 and SnRK2.7 . The inference of a gene regulatory network, based on a dynamic Bayesian approach, among the genes differentially expressed in the transgenic receptacles at the white and red stages, identified the genes KAN1 , DIV , ZFN2 and GTE7 as putative targets of FaMADS9. A MADS9 ‐specific CArG box was identified in the promoters of these genes. DA - 2019/10/11/ PY - 2019/10/11/ DO - 10.1111/pbi.13257 VL - 18 IS - 4 SP - 929-943 J2 - Plant Biotechnol J LA - en OP - SN - 1467-7644 1467-7652 UR - http://dx.doi.org/10.1111/pbi.13257 DB - Crossref ER - TY - JOUR TI - Patterns of genetic divergence among populations of Aedes aegypti L. (Diptera: Culicidae) in the southeastern USA T2 - Parasites & Vectors AB - Abstract Background The yellow fever mosquito, Aedes aegypti is a public health concern in the USA, especially in the wake of emergent diseases such as Zika and chikungunya. Aedes aegypti populations dwindled after the invasion of Aedes albopictus in the 1980s and many populations were extirpated. However, in some areas Ae. aegypti persisted in small populations and there are reports of recent resurgences of Ae. aegypti in Florida, Louisiana, Nevada and California. We assessed the population genetic structure of Ae. aegypti in Florida and Georgia, which has concomitant consequences related to mosquito dispersal, pesticide resistance and vectorial capacity. Methods We collected Ae. aegypti across Florida and in Georgia using ovitraps. We hatched the eggs and reared them to adults, and after sacrifice we extracted their DNA. We then probed each individual for variation in 6 microsatellite markers, which we used to address population genetic characteristics. Results We collected Ae. aegypti and genotyped seven Florida populations and one Georgia population using microsatellite markers. We found evidence of isolation by distance model of gene flow supported by driving distance among cities within Florida and two theoretic genetic clusters. Conclusions Significant genetic structure between some populations with substantial gene flow between geographically distant cities suggests regional genetic structuring of Ae. aegypti in Florida. This study provides information on the genetic exchange between populations of Ae. aegypti in the southeastern USA and suggests potential routes of spread of this species. DA - 2019/12// PY - 2019/12// DO - 10.1186/s13071-019-3769-0 UR - http://dx.doi.org/10.1186/s13071-019-3769-0 KW - Aedes aegypti KW - Genetic structure KW - Competitive exclusion KW - Satyrization ER - TY - JOUR TI - Rodent gene drives for conservation: opportunities and data needs AU - Godwin, John AU - Serr, Megan AU - Barnhill-Dilling, S. Kathleen AU - Blondel, Dimitri V. AU - Brown, Peter R. AU - Campbell, Karl AU - Delborne, Jason AU - Lloyd, Alun L. AU - Oh, Kevin P. AU - Prowse, Thomas A. A. AU - Saah, Royden AU - Thomas, Paul T2 - Proceedings of the Royal Society B: Biological Sciences AB - Invasive rodents impact biodiversity, human health and food security worldwide. The biodiversity impacts are particularly significant on islands, which are the primary sites of vertebrate extinctions and where we are reaching the limits of current control technologies. Gene drives may represent an effective approach to this challenge, but knowledge gaps remain in a number of areas. This paper is focused on what is currently known about natural and developing synthetic gene drive systems in mice, some key areas where key knowledge gaps exist, findings in a variety of disciplines relevant to those gaps and a brief consideration of how engagement at the regulatory, stakeholder and community levels can accompany and contribute to this effort. Our primary species focus is the house mouse, Mus musculus , as a genetic model system that is also an important invasive pest. Our primary application focus is the development of gene drive systems intended to reduce reproduction and potentially eliminate invasive rodents from islands. Gene drive technologies in rodents have the potential to produce significant benefits for biodiversity conservation, human health and food security. A broad-based, multidisciplinary approach is necessary to assess this potential in a transparent, effective and responsible manner. DA - 2019/11/6/ PY - 2019/11/6/ DO - 10.1098/rspb.2019.1606 VL - 286 IS - 1914 SP - 20191606 J2 - Proc. R. Soc. B LA - en OP - SN - 0962-8452 1471-2954 UR - http://dx.doi.org/10.1098/rspb.2019.1606 DB - Crossref KW - rodent KW - mice KW - rat KW - biodiversity KW - gene drive KW - island 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 AB - Abstract 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. 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 biotic stresses like sweetpotato virus disease on genetic variation management. These results will inform future deployment of genomic selection in sweetpotato. Key Message A 36-SNP diagnostic marker set has been developed for quality assurance and control to support global sweetpotato breeding optimization efforts. Breeding population structure is shaped by sweetpotato virus disease prevalence. DA - 2019/10/31/ PY - 2019/10/31/ DO - 10.1101/826792 VL - 10 UR - https://doi.org/10.1101/826792 ER - TY - JOUR TI - Relating nitrogen concentration and light intensity to the growth and lipid accumulation of Dunaliella viridis in a photobioreactor AU - Lai, Yi-Chun AU - Karam, Amanda L. AU - Sederoff, Heike W. AU - Ducoste, Joel J. AU - Reyes, , III T2 - Journal of Applied Phycology DA - 2019/12/28/ PY - 2019/12/28/ DO - 10.1007/s10811-019-01897-4 VL - 31 IS - 6 SP - 3397-3409 UR - https://doi.org/10.1007/s10811-019-01897-4 KW - Dunaliella viridis KW - Chlorophyta KW - Lipid KW - Light KW - Nitrogen KW - Photobioreactor ER - TY - JOUR TI - The Carrot Nuclear Genome and Comparative Analysis AU - Iorizzo, Massimo AU - Macko-Podgorni, Alicja AU - Senalik, Douglas AU - Van Deynze, Allen AU - Simon, Philipp W. T2 - CARROT GENOME AB - The first draft of the carrot genome of an orange inbred line, “DC-27,” was published in 2014. However, the genome assembly was fragmented and not assembled to the chromosome level, which limited its application for comprehensive genetic and genomic analyses. In 2016, a high-quality chromosome level, genome assembly of a doubled-haploid orange carrot DH1 was published, which rapidly advanced carrot genetic and genomic studies. The sequenced genome enabled the ability to identify candidate genes underlying important agronomic and nutrition-related traits such as root development, the accumulation of terpenoids, β-carotenes, and anthocyanins. Genome-level contributions include the clarification of phylogenetic relationships within carrot germplasm and the elucidation of the evolutionary history within the Euasterid II and Euasterid I clades. In this chapter, a description of the history of efforts made to characterize the carrot genome in the pre- and post-genomic era and the partners involved in the development of the high-quality carrot genome assembly are also described. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-03389-7_11 SP - 187-204 SN - 2199-479X ER - TY - JOUR TI - Carrot Molecular Genetics and Mapping AU - Iorizzo, Massimo AU - Ellison, Shelby AU - Pottorff, Marti AU - Cavagnaro, Pablo F. T2 - CARROT GENOME AB - Carrot (Daucus carota L.) is an important root vegetable crop that is consumed worldwide and is appreciated for its taste and nutritional content (e.g., provitamin A carotenoids, anthocyanins, vitamins, and other minerals). Carrot genetic research has improved vastly over the past few decades due to advancements in molecular genomic resources developed for carrot. The increasing availability of DNA sequences such as expressed sequence tags (ESTs), creation of a physical map, sequencing of the carrot genome, and the numerous advancements in DNA genotyping has enabled the study of phenotypic variation of crop traits through the development of genetic linkage maps, which enable the ability to identify QTLs and their underlying genetic basis. In addition, the creation of genetic and genomic tools for carrot has enabled the study of diversity within carrot populations and germplasm collections, enabled genome-wide association studies (GWASs), characterization of populations at the species level, and comparative genomics with other crops and model species. Combined, these tools will advance the breeding process for carrot by enabling a targeted approach to improving traits by utilizing marker-assisted selection (MAS) strategies. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-03389-7_7 SP - 101-117 SN - 2199-479X ER - TY - PCOMM TI - White-tailed deer and coyote colonization: a response to kilgo et al. (2019) AU - Bragina, Eugenia V. AU - Kays, Roland AU - Hody, Allison AU - Moorman, Christopher E. AU - DePerno, Christopher S. AU - Mills, L. Scott AB - We stand by our conclusion that there have not been large‐scale declines in white‐tailed deer populations following coyote colonization of the eastern United States. However, we agree that coyote predation can affect deer populations locally and therefore and should be considered in deer harvest planning in the region. DA - 2019/11// PY - 2019/11// DO - 10.1002/jwmg.21766 SP - 1641-1643 ER - TY - JOUR TI - Carrot Carotenoid Genetics and Genomics AU - Simon, Philipp W. AU - Geoffriau, Emmanuel AU - Ellison, Shelby AU - Iorizzo, Massimo T2 - CARROT GENOME AB - Carotenoids are essential for photosynthesis, and they are the ultimate source of all dietary vitamin A. They account for the striking diversity of orange, yellow, and red carrot storage root color, and this likely contributes to the fact that carotenoids are the most extensively studied class of compounds in carrot, where their biosynthesis and accumulation have been evaluated across diverse genetic backgrounds and environments. Many genes in the 2-C-methyl-D-erythritol-4-phosphate pathway (MEP) and carotenoid biosynthetic pathways have been identified and characterized in carrot, and genes in those pathways are expressed in carrot roots of all colors, including white carrots which contain at most trace amounts of carotenoids. The active functioning of genes in the carotenoid pathway in carrot roots of all colors should be expected since pathway products serve as precursors for hormones important in plant development. 1-Deoxy-d-xylulose-5-phosphate synthase (DXS) in the MEP pathway and the phytoene synthase and lycopene β-cyclase (PSY, LCYB) genes in the carotenoid pathway provide some level of overall regulation or modulation of these respective pathways, and these genes are incrementally upregulated in carrots with higher carotenoid content but variation in their expression does not account for the diverse content and composition of carotenoids in different colors of carrots. In contrast, genetic polymorphism in the Y and Y2 genes accounts for much for the variation in carotenoids accumulated in white, yellow, and orange carrots, and with the sequencing of the carrot genome, the genetic basis for these genes is becoming revealed. A candidate for the Y gene, DCAR_032551, is not a member of either the MEP or carotenoid biosynthesis pathway but rather a regulator of photosystem development and carotenoid storage. A clear candidate for the Y2 gene has not been identified, but no carotenoid biosynthetic gene was found in the genomic region defined by fine mapping of Y2. The Or gene, which regulates chromoplast development in other crops, was also recently associated with the presence of carotenoids in carrot. The discovery of genes outside the carotenoid biosynthetic pathway that contributes to carotenoid colors of carrots is but one exciting consequence of sequencing the carrot genome. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-03389-7_14 SP - 247-260 SN - 2199-479X ER - TY - JOUR TI - Discovery of Novel Thrips Vector Proteins That Bind to the Viral Attachment Protein of the Plant Bunyavirus Tomato Spotted Wilt Virus AU - Badillo-Vargas, I.E. AU - Chen, Y. AU - Martin, K.M. AU - Rotenberg, D. AU - Whitfield, A.E. T2 - Journal of Virology AB - The plant-pathogenic virus tomato spotted wilt virus (TSWV) encodes a structural glycoprotein (GN) that, like with other bunyavirus/vector interactions, serves a role in viral attachment and possibly in entry into arthropod vector host cells. It is well documented that Frankliniella occidentalis is one of nine competent thrips vectors of TSWV transmission to plant hosts. However, the insect molecules that interact with viral proteins, such as GN, during infection and dissemination in thrips vector tissues are unknown. The goals of this project were to identify TSWV-interacting proteins (TIPs) that interact directly with TSWV GN and to localize the expression of these proteins in relation to virus in thrips tissues of principal importance along the route of dissemination. We report here the identification of six TIPs from first-instar larvae (L1), the most acquisition-efficient developmental stage of the thrips vector. Sequence analyses of these TIPs revealed homology to proteins associated with the infection cycle of other vector-borne viruses. Immunolocalization of the TIPs in L1 revealed robust expression in the midgut and salivary glands of F. occidentalis, the tissues most important during virus infection, replication, and plant inoculation. The TIPs and GN interactions were validated using protein-protein interaction assays. Two of the thrips proteins, endocuticle structural glycoprotein and cyclophilin, were found to be consistent interactors with GN These newly discovered thrips protein-GN interactions are important for a better understanding of the transmission mechanism of persistent propagative plant viruses by their vectors, as well as for developing new strategies of insect pest management and virus resistance in plants.IMPORTANCE Thrips-transmitted viruses cause devastating losses to numerous food crops worldwide. For negative-sense RNA viruses that infect plants, the arthropod serves as a host as well by supporting virus replication in specific tissues and organs of the vector. The goal of this work was to identify thrips proteins that bind directly to the viral attachment protein and thus may play a role in the infection cycle in the insect. Using the model plant bunyavirus tomato spotted wilt virus (TSWV), and the most efficient thrips vector, we identified and validated six TSWV-interacting proteins from Frankliniella occidentalis first-instar larvae. Two proteins, an endocuticle structural glycoprotein and cyclophilin, were able to interact directly with the TSWV attachment protein, GN, in insect cells. The TSWV GN-interacting proteins provide new targets for disrupting the viral disease cycle in the arthropod vector and could be putative determinants of vector competence. DA - 2019/// PY - 2019/// DO - 10.1128/JVI.00699-19 VL - 93 IS - 21 SP - e00699-19 SN - 1098-5514 UR - https://doi.org/10.1101/416560 KW - Bunyavirales KW - insect vector KW - orthotospovirus KW - plant virology KW - thrips KW - vector biology KW - virus-vector interactions ER - TY - JOUR TI - Carrot Organelle Genomes: Organization, Diversity, and Inheritance AU - Spooner, David M. AU - Simon, Philipp W. AU - Senalik, Douglas AU - Iorizzo, Massimo T2 - CARROT GENOME AB - Cultivated carrot (Daucus carota subsp. sativus) is one of about 25–40 related wild species in the genus Daucus depending on the classification. It is part of a widely distributed and taxonomically complex family Apiaceae (Umbelliferae) containing 466 genera and 3820 species that is one of the largest families of seed plants. Members of the Apiaceae, particularly the genus Daucus, have been the subject of intensive recent molecular studies on the structure and genetics of plastids and mitochondria. This chapter summarizes organellar (plastids and mitochondria) structure, function, mutational rates, and inter-organelle DNA transfer in the Apiaceae and inheritance in the genus Daucus, with a wider focus on the Apiaceae and the sister family Araliaceae, and places these data in the context of other studies in the angiosperms. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-03389-7_12 SP - 205-223 SN - 2199-479X ER - TY - JOUR TI - Private Land Conservation and Public Policy: Land Trusts, Land Owners, and Conservation Easements AU - Parker, Dominic P. AU - Thurman, Walter N. T2 - ANNUAL REVIEW OF RESOURCE ECONOMICS, VOL 11 AB - We highlight the extraordinary growth in private conservation via land trusts and conservation easements and describe the problems arising from the interplay of public finance and private decisions. We offer a framework for understanding the popularity of easements and land trusts and for evaluating policy reforms aimed at improving their performance. The framework, grounded in institutional and organizational economics in the tradition of Ronald Coase, Oliver Williamson, and Yoram Barzel, focuses on the measurement and monitoring costs faced by public and private stakeholders under current and prospective policy arrangements. We illustrate how the framework can be applied to contemporary debates about the appropriate tax treatment of donated easements, requirements that they be held in perpetuity, and the extent to which government should regulate private land trusts. DA - 2019/// PY - 2019/// DO - 10.1146/annurev-resource-100518-094121 VL - 11 SP - 337-354 SN - 1941-1359 KW - land trusts KW - conservation easements KW - tax incentives KW - land conservation ER - TY - JOUR TI - Carrot Genetics, Omics and Breeding Toolboxes AU - Bostan, Hamed AU - Senalik, Douglas AU - Simon, Philipp W. AU - Iorizzo, Massimo T2 - CARROT GENOME AB - Today, researchers routinely generate and analyze large and complex omics, genetics and breeding datasets for both model and nonmodel crop species including carrot. This has resulted in the massive production and availability of omics data, which opened multiple challenges to store, organize and make those data available to the research and breeding communities. The value of these resources increases significantly when it is organized, annotated, effectively integrated with other data and made available to browse, query and analyze. In this chapter, we summarize the available omics, genetics and breeding resources for carrot and other Daucus species in different public and private databases. We also discuss the challenges for collecting, integrating and interpreting this data with a focus on the lack of dedicated, centralized and user-friendly bioinformatics platforms, breeding toolboxes and infrastructures for the carrot genome. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-03389-7_13 SP - 225-245 SN - 2199-479X ER - TY - JOUR TI - Carrot Anthocyanin Diversity, Genetics, and Genomics AU - Cavagnaro, Pablo F. AU - Iorizzo, Massimo T2 - CARROT GENOME AB - Purple carrots (Daucus carota ssp. sativus var. atrorubens Alef.) accumulate anthocyanins in their roots, petioles, and other plant parts. These flavonoid pigments represent an excellent dietary source of antioxidant and anti-inflammatory agents. In addition, carrot anthocyanins are also used as food dyes. Compositional variation in carrot root, mainly with regard to the content of acylated (AA) and non-acylated anthocyanins (NAA), strongly influences the bioavailability and chemical stability of these pigments, therefore conditioning their potential use as nutraceutical agents or as food colorants. In this context, genetic diversity analysis for root anthocyanin composition is relevant for selecting materials for either purpose. Also, knowledge on the genetic basis underlying anthocyanin biosynthesis and modification is expected to aid in the development of new varieties with high nutraceutical or for extracting food dyes. In the last decades, germplasm collections have been characterized for anthocyanin content and composition. Various simply inherited traits for root and petiole anthocyanin pigmentation and acylation, including P1, P3 and Raa1, and QTL for root anthocyanins, have been described and mapped to two regions of chromosome 3, in different genetic backgrounds. Recent advances in high-throughput sequencing and bioinformatic analyses have facilitated the discovery of candidate regulatory genes for root and petiole pigmentation associated with the P3 region in chromosome 3, as well as structural genes involved in anthocyanin glycosylation and acylation. In this chapter, we reviewed recent advances in diversity, genetic, and genomic studies related to carrot anthocyanin pigmentation. DA - 2019/// PY - 2019/// DO - 10.1007/978-3-030-03389-7_15 SP - 261-277 SN - 2199-479X ER - TY - JOUR TI - "Yes, and ...": continuing the scholarly conversation about Hispanic Serving Institutions AU - Rudick, C. Kyle AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION DA - 2019/10/2/ PY - 2019/10/2/ DO - 10.1080/03634523.2019.1646979 VL - 68 IS - 4 SP - 528-533 SN - 1479-5795 ER - TY - JOUR TI - Evaluating Optimal Spray Timing, Planting Date, and Current Thresholds for Lygus lineolaris (Hemiptera: Miridae) in Virginia and North Carolina Cotton AU - Aghaee, Mohammad-Amir AU - Dorman, Seth J AU - Taylor, Sally V AU - Reisig, Dominic D T2 - Journal of Economic Entomology AB - Economically damaging infestations of Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae), the tarnished plant bug, have been increasing in North Carolina and Virginia cotton since 2009. We conducted experiments to compare prophylactically timed sprays based on cotton phenology and current action thresholds based on sweep net and drop cloth sampling. In the second year of the study, we included planting date as a factor, with early and late-planted cotton. We found L. lineolaris nymph densities were reduced by at least 60% in North Carolina and 74% in Virginia in threshold plots when compared with the untreated control. Protecting the crop from first square through the fourth week of bloom afforded at least 30% control across planting dates in Virginia and at least 40% control in North Carolina. Economic returns were two to three times greater in early-planted cotton than in late-planted cotton. Treating cotton at action threshold or using prophylactic sprays from first square until the sixth week of bloom in early-planted cotton yielded over $500/ha in net returns in both North Carolina and Virginia. This study supports previous research that shows controlling L. lineolaris infestations during squaring and early weeks of flowering is critical for maximizing yield potential. Our findings also suggest that prebloom and bloom thresholds based on adult and nymphal density devised in the Mid-South may need revision in North Carolina and Virginia. DA - 2019/1/5/ PY - 2019/1/5/ DO - 10.1093/jee/toy407 VL - 112 IS - 3 SP - 1207-1216 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/toy407 DB - Crossref KW - plant bug KW - cotton KW - planting date KW - integrated pest management KW - sampling method ER - TY - JOUR TI - Helicoverpa zea (Lepidoptera: Noctuidae) Oviposition and Larval Vertical Distribution in Bt Cotton Under Different Levels of Nitrogen and Irrigation AU - Braswell, Lewis R AU - Reisig, Dominic D AU - Sorenson, Clyde E AU - Collins, Guy D T2 - Journal of Economic Entomology AB - In some Bt cotton (Gossypium hirsutum L.) varieties, bollworm (Helicoverpa zea Boddie) larval behavior differs from non-Bt varieties. Laboratory assays indicate bollworm larvae can detect Bt proteins, which may cause behavioral differences. Plant stress from factors including fertility and water availability causes changes in plant physiology and Bt expression. Our objective was to determine whether nitrogen and irrigation influenced bollworm behavior in Bt cotton by recording the vertical distribution of eggs and larvae over time. We conducted small plot experiments with Cry1Ac + Cry1F cotton in 2016 and 2017 with three nitrogen rates, along with irrigated and nonirrigated treatments during 2017. Bollworm locations were determined by in-field examination of 10-20 cotton plants per plot over 6-8 wk. The location of each egg and larva was recorded by node, with instar estimation of each larva. Oviposition was higher in in plots receiving nitrogen; first and second instars were also more common in plots receiving nitrogen or irrigation, whereas older instars had similar numbers among treatments. Oviposition was more evenly distributed throughout the canopy earlier in the sampling period than during later weeks, with more eggs in the top third of the canopy in only three of 14-wk. Early instars were also evenly distributed throughout the canopy. Later, instars moved to the middle portions of the canopy, away from bottom nodes, and did not move toward the terminal. Understanding bollworm behavior can inform both crop scouting and resistance management decisions. DA - 2019/2/15/ PY - 2019/2/15/ DO - 10.1093/jee/toz023 VL - 112 IS - 3 SP - 1237-1250 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/toz023 DB - Crossref KW - insect behavior KW - behavioral resistance KW - Bacillus thuringiensis KW - sampling KW - bollworm ER - TY - JOUR TI - Genetic Structure and Subclonal Variation of Extant and Recent U.S. Lineages of Phytophthora infestans AU - Saville, Amanda AU - Ristaino, Jean Beagle T2 - Phytopathology AB - The oomycete Phytophthora infestans is an important plant pathogen on potato and tomato crops. We examined the genetic structure of extant 20th and 21st century U.S. lineages of P. infestans and compared them with populations from South America and Mexico to examine genetic relationships and potential sources of lineages. US-23, currently the most prevalent lineage detected in the United States, shared genetic similarity primarily with the BR-1 lineage identified in the 1990s from Bolivia and Brazil. Lineages US-8, US-14, and US-24, predominantly virulent on potato, formed a cluster distinct from other U.S. lineages. Many of the other U.S. lineages shared significant genetic similarity with Mexican populations. The US-1 lineage, dominant in the mid-20th century, clustered with US-1 lineages from Peru. A survey of the presence of RXLR effector PiAVR2 revealed that some lineages carried PiAVR2, its resistance-breaking variant PiAVR2-like, or both. Minimum spanning networks developed from simple sequence repeat genotype datasets from USABlight outbreaks clearly showed the expansion of US-23 over a 6-year time period and geographic substructuring of some lineages in the western United States. Many clonal lineages of P. infestans in the United States have come from introductions from Mexico, but the US-23 and US-1 lineages were most likely introduced from other sources. DA - 2019/9// PY - 2019/9// DO - 10.1094/PHYTO-09-18-0357-R VL - 109 IS - 9 SP - 1614-1627 J2 - Phytopathology LA - en OP - SN - 0031-949X 1943-7684 UR - http://dx.doi.org/10.1094/PHYTO-09-18-0357-R DB - Crossref KW - ecology KW - epidemiology ER - TY - JOUR TI - Valorization of Swine Manure into Hydrochars AU - Lentz, Zac AU - Kolar, Praveen AU - Classen, John J. T2 - Processes AB - There is a significant interest in valorizing swine manure that is produced in enormous quantities. Therefore, considering the high moisture content in swine manure, the objective of this research was to convert manure slurry into hydrochars via hydrothermal carbonization and analyze the yields, pH, energy contents, and thermal and oxidation kinetic parameters. Experiments were performed in triplicate in 250 mL kettle reactors lined with polypropylene at 180 °C, 200 °C, 240 °C, 220 °C, and 260 °C for 24 h. Analyses of the results indicated that the process temperature affected the hydrochar yields, with yield generally decreasing with increasing temperature, but it had little effect on the composition of the hydrochar. The hydrochars were found to have higher volatile contents and H/C and O/C ratios and about 85% of the energy compared to coal. However, the presence of high fraction (35–38%) of ash in hydrochars is a serious concern and needs to be addressed before the complete utilization of hydrochars as fuels. The surface characterization of hydrochars coupled with wet chemistry experiments indicated that hydrochars were equipped with nitrogen functional groups with points of zero charges between 6.76 and 7.85, making them suitable as adsorbents and soil remediation agents and energy storage devices. DA - 2019/8/23/ PY - 2019/8/23/ DO - 10.3390/pr7090560 VL - 7 IS - 9 SP - 560 J2 - Processes LA - en OP - SN - 2227-9717 UR - http://dx.doi.org/10.3390/pr7090560 DB - Crossref KW - swine manure KW - valorization KW - char KW - hydrothermal carbonization KW - characterization ER - TY - JOUR TI - Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana AU - Powers, Samantha K. AU - Holehouse, Alex S. AU - Korasick, David A. AU - Schreiber, Katherine H. AU - Clark, Natalie M. AU - Jing, Hongwei AU - Emenecker, Ryan AU - Han, Soeun AU - Tycksen, Eric AU - Hwang, Ildoo AU - Sozzani, Rosangela AU - Jez, Joseph M. AU - Pappu, Rohit V. AU - Strader, Lucia C. T2 - MOLECULAR CELL AB - The phytohormone auxin plays crucial roles in nearly every aspect of plant growth and development. The auxin response factor (ARF) transcription factor family regulates auxin-responsive gene expression and exhibits nuclear localization in regions of high auxin responsiveness. Here we show that the ARF7 and ARF19 proteins accumulate in micron-sized assemblies within the cytoplasm of tissues with attenuated auxin responsiveness. We found that the intrinsically disordered middle region and the folded PB1 interaction domain of ARFs drive protein assembly formation. Mutation of a single lysine within the PB1 domain abrogates cytoplasmic assemblies, promotes ARF nuclear localization, and results in an altered transcriptome and morphological defects. Our data suggest a model in which ARF nucleo-cytoplasmic partitioning regulates auxin responsiveness, providing a mechanism for cellular competence for auxin signaling. DA - 2019/10/3/ PY - 2019/10/3/ DO - 10.1016/j.molcel.2019.06.044 VL - 76 IS - 1 SP - 177-+ SN - 1097-4164 ER - TY - JOUR TI - Susceptibility of Corn Earworm (Lepidoptera: Noctuidae) to Cry1A.105 and Cry2Ab2 in North and South Carolina AU - Bilbo, Tom R AU - Reay-Jones, Francis P F AU - Reisig, Dominic D AU - Greene, Jeremy K T2 - Journal of Economic Entomology AB - Abstract The corn earworm, Helicoverpa zea (Boddie), is managed in corn and cotton in the United States primarily using transgenic cultivars that produce insecticidal proteins from the bacterium Bacillus thuringiensis (Bt). However, increasing reports of resistance to one or more Bt proteins threaten the continued efficacy of Bt traits. To better understand the development of resistance of H. zea to Bt corn and cotton in the southeastern United States, we monitored for resistance to Cry1A.105 and Cry2Ab2 among 22 field populations of H. zea collected in non-Bt and Bt corn expressing Cry1A.105 + Cry2Ab2 during 2017 and 2018. Colonies were established in the laboratory and progeny were screened in diet-overlay bioassays to purified Cry1A.105 and Cry2Ab2 proteins. Compared with two susceptible laboratory colonies, all 14 field colonies tested with Cry1A.105 were highly resistant, with resistance ratios (RRs) ranging from 13.5 to >4,000. For Cry2Ab2, 19 colonies were tested and RRs ranged from 0.26 to 33.7. Field populations were significantly more susceptible to Cry2Ab2 than Cry1A.105. We documented variability in F0 and F1 pupal weight and developmental rates of natural populations of H. zea, but observed no significant correlation with susceptibility to either Cry1A.105 or Cry2Ab2. Our results expand on the recent reports of H. zea resistance to Cry1A and Cry2A proteins and will aid in the design and deployment of future pyramided crops in the United States. DA - 2019/3/29/ PY - 2019/3/29/ DO - 10.1093/jee/toz062 VL - 112 IS - 4 SP - 1845-1857 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/toz062 DB - Crossref KW - Helicoverpa zea KW - corn KW - cotton KW - resistance ER - TY - JOUR TI - Entry of bunyaviruses into plants and vectors AU - Chen, Yuting AU - Dessau, Moshe AU - Rotenberg, Dorith AU - Rasmussen, David A. AU - Whitfield, Anna E. T2 - VIRUS ENTRY AB - The majority of plant-infecting viruses are transmitted by arthropod vectors that deliver them directly into a living plant cell. There are diverse mechanisms of transmission ranging from direct binding to the insect stylet (non-persistent transmission) to persistent-propagative transmission in which the virus replicates in the insect vector. Despite this diversity in interactions, most arthropods that serve as efficient vectors have feeding strategies that enable them to deliver the virus into the plant cell without extensive damage to the plant and thus effectively inoculate the plant. As such, the primary virus entry mechanism for plant viruses is mediated by the biological vector. Remarkably, viruses that are transmitted in a propagative manner (bunyaviruses, rhabdoviruses, and reoviruses) have developed an ability to replicate in hosts from two kingdoms. Viruses in the order Bunyavirales are of emerging importance and with the advent of new sequencing technologies, we are getting unprecedented glimpses into the diversity of these viruses. Plant-infecting bunyaviruses are transmitted in a persistent, propagative manner must enter two unique types of host cells, plant and insect. In the insect phase of the virus life cycle, the propagative viruses likely use typical cellular entry strategies to traverse cell membranes. In this review, we highlight the transmission and entry strategies of three genera of plant-infecting bunyaviruses: orthotospoviruses, tenuiviruses, and emaraviruses. DA - 2019/// PY - 2019/// DO - 10.1016/bs.aivir.2019.07.001 VL - 104 SP - 65-96 SN - 1557-8399 ER - TY - JOUR TI - Perceptions of Resilience in Fishery-Dependent Bahamian Communities Following a Category 4 Hurricane AU - Valdez, Rene Xavier AU - Peterson, Nils AU - Chen, Alyssa AU - Steward, Michael AU - Hannameyer, Katrina AU - Seebaluck, Hans AU - Hulthen, Kaj AU - Langerhans, R. Brian T2 - FISHERIES AB - Fishery‐dependent communities in coastal environments are often vulnerable to hurricanes, but diverse and accessible fisheries may buffer the effects of extreme storms and promote community resilience. We began evaluating this possibility with a qualitative study in the Lowe Sound and Red Bays communities in The Bahamas immediately after the impact of a category 4 hurricane. We interviewed 68 households, asking about the relationships between the storm's impacts and fisheries resources. Lowe Sound respondents described fisheries as natural insurance that provided food and income. Both communities indicated that retaining access to boats was critically important. Respondents most often blamed impacts on low‐elevation geography, followed by religious interpretations. Fishers linked damages with climate change more often than other community members, suggesting that fishers have an experiential knowledge of climate change. We discuss the importance of fisheries as natural insurance, how recovery efforts can strengthen resilience, and potential outreach strategies that incorporate local knowledge. DA - 2019/11// PY - 2019/11// DO - 10.1002/fsh.10310 VL - 44 IS - 11 SP - 515-523 SN - 1548-8446 ER - TY - JOUR TI - Helicoverpa zea (Lepidoptera: Noctuidae) Preference for Plant Structures, and Their Location, Within Bt Cotton Under Different Nitrogen and Irrigation Regimes AU - Braswell, Lewis R AU - Reisig, Dominic D AU - Sorenson, Clyde E AU - Collins, Guy D T2 - Journal of Economic Entomology AB - Helicoverpa zea Boddie is a common economic pest of cotton (Gossypium hirsutum L.), including transgenic cotton varieties that express Bacillus thuringiensis (Bt). Helicoverpa zea oviposition is similar in Bt and non-Bt cotton, but behavior of H. zea larvae can be different in the presence of Bt, with neonates moving away from terminals faster in single-toxin Bt than non-Bt cotton or avoiding Bt-treated diet in the lab. We quantified H. zea oviposition and larval distribution on structures within cotton plants in small plot experiments of Cry1Ac + Cry1F cotton for 2 yr under different irrigation and nitrogen treatments. More eggs were oviposited on plants receiving nitrogen application during 2016 and on leaves in the top section of irrigated plants during 2017, but other treatment effects on eggs or larvae were minimal. Helicoverpa zea eggs were most common on leaves in the top third of plants at position zero and middle section of cotton plants throughout the season, but some oviposition occurred on fruiting structures as well. First and second instars were more common on squares in the top section of plants during 2016 and bolls in the middle and lower sections during 2017 due to oviposition lower in the canopy during 2017. During both years, third through fifth instars were more common on bolls in the middle and lower section of plants closer to the main stem. These findings have resistance management implications as extended larval feeding on bolls could optimize nutrition, decrease Bt susceptibility, and potentially influence behavioral resistance. DA - 2019/4/26/ PY - 2019/4/26/ DO - 10.1093/jee/toz105 VL - 112 IS - 4 SP - 1741-1751 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/toz105 DB - Crossref KW - insect behavior KW - behavioral resistance KW - Bacillus thuringiensis KW - sampling KW - bollworm ER - TY - JOUR TI - Perinatal bisphenol A (BPA) exposure alters brain oxytocin receptor (OTR) expression in a sex- and region- specific manner: A CLARITY-BPA consortium follow-up study AU - Witchey, Shannah K. AU - Fuchs, Joelle AU - Patisaul, Heather B. T2 - NEUROTOXICOLOGY AB - Bisphenol A (BPA) is a well-characterized endocrine disrupting chemical (EDC) used in plastics, epoxy resins and other products. Neurodevelopmental effects of BPA exposure are a major concern with multiple rodent and human studies showing that early life BPA exposure may impact the developing brain and sexually dimorphic behaviors. The CLARITY-BPA (Consortium Linking Academic and Regulatory Insights on BPA Toxicity) program was established to assess multiple endpoints, including neural, across a wide dose range. Studies from our lab as part of (and prior to) CLARITY-BPA have shown that BPA disrupts estrogen receptor expression in the developing brain, and some evidence of oxytocin (OT) and oxytocin receptor (OTR) disruption in the hypothalamus and amygdala. While BPA disruption of steroid hormone function is well documented, less is known about its capacity to alter nonapeptide signals. In this CLARITY-BPA follow up study, we used remaining juvenile rat tissues to test the hypothesis that developmental BPA exposure affects OTR expression across the brain. Perinatal BPA exposure (2.5, 25, or 2500 μg/kg body weight (bw)/day) spanned gestation and lactation with dams gavaged from gestational day 6 until birth and then the offspring gavaged directly through weaning. Ethinyl estradiol (0.5 μg/kg bw/day) was used as a reference estrogen. Animals of both sexes were sacrificed as juveniles and OTR expression assessed by receptor binding. Our results demonstrate prenatal exposure to BPA can eliminate sex differences in OTR expression in three hypothalamic regions, and that male OTR expression may be more susceptible. Our data also identify a sub-region of the BNST with sexually dimorphic OTR expression not previously reported in juvenile rats that is also susceptible to BPA. DA - 2019/9// PY - 2019/9// DO - 10.1016/j.neuro.2019.06.007 VL - 74 SP - 139-148 SN - 1872-9711 KW - Behavior KW - Estrogen KW - Endocrine disruption KW - Sexual differentiation KW - Neuroendocrine KW - Oxytocin ER - TY - JOUR TI - Tethered homing gene drives: A new design for spatially restricted population replacement and suppression AU - Dhole, Sumit AU - Lloyd, Alun L. AU - Gould, Fred T2 - EVOLUTIONARY APPLICATIONS AB - Optimism regarding potential epidemiological and conservation applications of modern gene drives is tempered by concern about the possibility of unintended spread of engineered organisms beyond the target population. In response, several novel gene drive approaches have been proposed that can, under certain conditions, locally alter characteristics of a population. One challenge for these gene drives is the difficulty of achieving high levels of localized population suppression without very large releases in the face of gene flow. We present a new gene drive system, tethered homing (TH), with improved capacity for both localization and population suppression. The TH drive is based on driving a payload gene using a homing construct that is anchored to a spatially restricted gene drive. We use a proof-of-concept mathematical model to show the dynamics of a TH drive that uses engineered underdominance as an anchor. This system is composed of a split homing drive and a two-locus engineered underdominance drive linked to one part of the split drive (the Cas endonuclease). We use simple population genetic simulations to show that the tethered homing technique can offer improved localized spread of costly transgenic payload genes. Additionally, the TH system offers the ability to gradually adjust the genetic load in a population after the initial alteration, with minimal additional release effort. We discuss potential solutions for improving localization and the feasibility of creating TH drive systems. Further research with models that include additional biological details will be needed to better understand how TH drives would behave in natural populations, but the preliminary results shown here suggest that tethered homing drives can be a useful addition to the repertoire of localized gene drives. DA - 2019/9// PY - 2019/9// DO - 10.1111/eva.12827 VL - 12 IS - 8 SP - 1688-1702 SN - 1752-4571 UR - http://dx.doi.org/10.1111/eva.12827 KW - Cas KW - CRISPR KW - gene drive KW - genetic engineering KW - population alteration KW - underdominance ER - TY - JOUR TI - Engaging International Publics via Mobile-Enhanced CSR (mCSR): A Cross-National Study on Stakeholder Reactions to Corporate Disaster Relief Efforts AU - Chen, Yi-Ru Regina AU - Cheng, Yang AU - Hung-Baesecke, Chun-Ju Flora AU - Jin, Yan T2 - American Behavioral Scientist AB - With globalization, corporations increasingly have to consider both domestic stakeholders and overseas stakeholders (i.e., international publics) in their corporate social responsibility (CSR) practice. Digitalization empowers international publics to scrutinize and react to a (multinational) corporation’s CSR strategy, further affecting corporate outcomes of CSR practice. Drawing on the social media context and attribution theory, this study investigated international publics’ reactions to corporate disaster relief, an emerging type of mobile-enhanced CSR (i.e., mCSR) practice, in the United States and China by looking at individuals’ engagement with mobile social media during disasters, attribution of CSR motives, and level of CSR skepticism. Using structural equation modeling analysis, the survey data of randomly recruited Americans ( n = 816) and mainland Chinese ( n = 430) suggested that mobile social media engagement reinforces the values-, strategic-, and stakeholder-driven motives of mCSR in the United States and China. Egoistic-driven CSR motives elicited publics’ skepticism toward mCSR, while values- and stakeholder-driven motives inhibited skepticism in both countries. However, the effect of strategic-driven motives on skepticism was inconsistent internationally. Last, CSR skepticism triggered negative relational outcomes between the mCSR-performing corporation and various stakeholders in both countries. This study advances CSR and attribution theory and contributes to the practice of CSR, public relations, and international business in the social media and disaster response context. DA - 2019/3/7/ PY - 2019/3/7/ DO - 10.1177/0002764219835258 VL - 63 IS - 12 SP - 1603-1623 J2 - American Behavioral Scientist LA - en OP - SN - 0002-7642 1552-3381 UR - http://dx.doi.org/10.1177/0002764219835258 DB - Crossref KW - public relations KW - corporate social responsibility KW - mobile phones KW - social media KW - international publics ER - TY - JOUR TI - Psychiatric Neuroethics-Studies in Research and Practice AU - Dubljevic, Veljko T2 - BIOETHICS AB - BioethicsVolume 33, Issue 8 p. 974-975 BOOK REVIEW Psychiatric Neuroethics—Studies in Research and Practice Walter Glannon Oxford University Press, 2019. 408 pp. ISBN 978-0-19-875885-3, $44.95. Veljko Dubljevic, Corresponding Author Veljko Dubljevic veljko.dubljevic@yahoo.com orcid.org/0000-0003-3606-587X Department of Philosophy and Religious studies, North Carolina State University, Raleigh, North Carolina, USASearch for more papers by this author Veljko Dubljevic, Corresponding Author Veljko Dubljevic veljko.dubljevic@yahoo.com orcid.org/0000-0003-3606-587X Department of Philosophy and Religious studies, North Carolina State University, Raleigh, North Carolina, USASearch for more papers by this author First published: 06 August 2019 https://doi.org/10.1111/bioe.12643Read 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. Volume33, Issue8Special Issue: Bioethics and ActivismOctober 2019Pages 974-975 RelatedInformation DA - 2019/10// PY - 2019/10// DO - 10.1111/bioe.12643 VL - 33 IS - 8 SP - 974-975 SN - 1467-8519 UR - https://doi.org/10.1111/bioe.12643 ER - TY - JOUR TI - “Lies build trust”: Social capital, masculinity, and community-based resource management in a Mexican fishery AU - Siegelman, Ben AU - Haenn, Nora AU - Basurto, Xavier T2 - World Development AB - This paper relates how fishermen in San Evaristo on Mexico’s Baja peninsula employ fabrications to strengthen bonds of trust and navigate the complexities of common pool resource extraction. We argue this trickery complicates notions of social capital in community-based natural resource management, which emphasize communitarianism in the form of trust. Trust, defined as a mutual dependability often rooted in honesty, reliable information, or shared expectations, has long been recognized as essential to common pool resource management. Despite this, research that takes a critical approach to social capital places attention on the activities that foster social networks and their norms by arguing that social capital is a process. A critical approach illuminates San Evaristeño practices of lying and joking across social settings and contextualizes these practices within cultural values of harmony. As San Evaristeños assert somewhat paradoxically, for them “lies build trust.” Importantly, a critical approach to this case study forces consideration of gender, an overlooked topic in social capital research. San Evaristeña women are excluded from the verbal jousting through which men maintain ties supporting their primacy in fishery management. Both men’s joke-telling and San Evaristeños’ aversion to conflict have implications for conservation outcomes. As a result, we use these findings to help explain local resistance to outsiders and external management strategies including land trusts, fishing cooperatives, and marine protected areas. DA - 2019/11// PY - 2019/11// DO - 10.1016/j.worlddev.2019.05.031 VL - 123 SP - 104601 J2 - World Development LA - en OP - SN - 0305-750X UR - http://dx.doi.org/10.1016/j.worlddev.2019.05.031 DB - Crossref KW - Community-based natural resource management KW - Small-scale fisheries KW - Social capital KW - Common pool resources KW - Feminist political ecology KW - Latin America ER - TY - JOUR TI - Transgressive segregation and maternal genetic effects of non–target site fluazifop-P-butyl tolerance in Zoysia spp. AU - Liu, Wenwen AU - Kenworthy, Kevin E. AU - MacDonald, Gregory E. AU - Unruh, J. Bryan AU - Trenholm, Laurie E. AU - Leon, Ramon G. T2 - Weed Science AB - Abstract Zoysia germplasm exhibit different levels of sensitivity to fluazifop-P-butyl, but the genetic factors responsible for such differences are unknown. Segregation patterns of the fluazifop-P-butyl tolerance trait were studied under greenhouse conditions. In total, 244 F 1 lines were generated from multiple crosses between the tolerant line 5337-2 (non–target site tolerance) and three more-sensitive lines (123, 252, and 5330-23). Progeny segregation showed that fluazifop-P-butyl tolerance within zoysiagrass ( Zoysia spp.) is expressed as a quantitative trait with a wide range of intermediate phenotypes between parental phenotypes. Transgressive segregation was extensive and largely favored susceptibility in most families, but was especially evident for 5337-2 × 123 and 5337-2 × 5330-23. The segregation patterns for biomass reduction and percent injury were different within reciprocal crosses and among three different family crosses. Reciprocal effects were observed in growth reduction for 5337-2 × 5330-23, in percent injury at 3 wk after the treatment (WAT), and for 5337-2 × 252 at 6 WAT. This indicated that fluazifop-P-butyl tolerance was not completely controlled by nuclear genetic factors in 5337-2 and maternal/cytoplasmic inheritance was also partially responsible. These results suggested that fluazifop-P-butyl tolerance may be attributed to multiple genetic mechanisms, which could present a challenge for future breeding efforts because of the difficulty of fixing multiple traits within a breeding population. DA - 2019/9// PY - 2019/9// DO - 10.1017/wsc.2019.26 VL - 67 IS - 05 SP - 504-509 UR - https://doi.org/10.1017/wsc.2019.26 KW - Te-Ming Paul Tseng KW - Mississippi State University KW - Acetyl-coenzyme A carboxylase KW - ACCase KW - herbicide resistance KW - genetic diversity KW - graminicide KW - inheritance KW - heritability KW - quantitative trait ER - TY - JOUR TI - Influence of multiple herbicide resistance on growth in Amaranthus tuberculatus AU - Jones, E A L AU - Owen, M D K AU - Leon, R G T2 - Weed Research AB - Summary Plant defence traits, such as herbicide resistance mutations, may incur a fitness cost to plants that become evident when the trait is not needed. However, individuals with multiple herbicide resistance traits may decrease fitness beyond that of plants with a single herbicide resistance mutation. Multiple herbicide‐resistant ( MHR ) Amaranthus tuberculatus populations are becoming more prevalent in Midwest United States agroecosystems. The objective was to determine whether selected MHR A. tuberculatus populations express differential development when grown in a herbicide‐free environment. The hypothesis was that MHR A. tuberculatus populations become increasingly less fit when additional herbicide resistances evolve. Multiple herbicide‐resistant and herbicide‐susceptible A. tuberculatus populations were grown in a herbicide‐free field for 20 weeks for two seasons. Differences ( P < 0.001) in apical growth were detected 5 and 7 weeks after transplanting for all populations in 2016 and 2017 respectively. Gender and population influenced ( P < 0.001) flowering date, with males flowering up to 1.5 weeks earlier than females, but did not cause pollination asynchrony. Shoot biomass was not different ( P = 0.84) across A. tuberculatus populations, but there were differences ( P < 0.001) for gender and year. Seed production was different amongst A. tuberculatus populations ( P = 0.001), but was not influenced by the number of MHR traits. Conversely, a negative quadratic relationship between seed mass and the number of MHR traits was observed ( r 2 = 0.32; P < 0.001). The experiment results demonstrate that MHR in A. tuberculatus populations is not incurring a fitness penalty that will remove the populations in the immediate future. DA - 2019/6// PY - 2019/6// DO - 10.1111/wre.12361 VL - 59 IS - 3 SP - 235-244 UR - https://doi.org/10.1111/wre.12361 KW - tall waterhemp KW - evolution KW - fitness penalty KW - herbicide resistance KW - weed management ER - TY - JOUR TI - Neonicotinoid seed treatments of soybean provide negligible benefits to US farmers AU - Mourtzinis, Spyridon AU - Krupke, Christian H. AU - Esker, Paul D. AU - Varenhorst, Adam AU - Arneson, Nicholas J. AU - Bradley, Carl A. AU - Byrne, Adam M. AU - Chilvers, Martin I. AU - Giesler, Loren J. AU - Herbert, Ames AU - Kandel, Yuba R. AU - Kazula, Maciej J. AU - Hunt, Catherine AU - Lindsey, Laura E. AU - Malone, Sean AU - Mueller, Daren S. AU - Naeve, Seth AU - Nafziger, Emerson AU - Reisig, Dominic D. AU - Ross, William J. AU - Rossman, Devon R. AU - Taylor, Sally AU - Conley, Shawn P. T2 - Scientific Reports AB - Abstract Neonicotinoids are the most widely used insecticides worldwide and are typically deployed as seed treatments (hereafter NST) in many grain and oilseed crops, including soybeans. However, there is a surprising dearth of information regarding NST effectiveness in increasing soybean seed yield, and most published data suggest weak, or inconsistent yield benefit. The US is the key soybean-producing nation worldwide and this work includes soybean yield data from 194 randomized and replicated field studies conducted specifically to evaluate the effect of NSTs on soybean seed yield at sites within 14 states from 2006 through 2017. Here we show that across the principal soybean-growing region of the country, there are negligible and management-specific yield benefits attributed to NSTs. Across the entire region, the maximum observed yield benefits due to fungicide (FST = fungicide seed treatment) + neonicotinoid use (FST + NST) reached 0.13 Mg/ha. Across the entire region, combinations of management practices affected the effectiveness of FST + NST to increase yield but benefits were minimal ranging between 0.01 to 0.22 Mg/ha. Despite widespread use, this practice appears to have little benefit for most of soybean producers; across the entire region, a partial economic analysis further showed inconsistent evidence of a break-even cost of FST or FST + NST. These results demonstrate that the current widespread prophylactic use of NST in the key soybean-producing areas of the US should be re-evaluated by producers and regulators alike. DA - 2019/9/9/ PY - 2019/9/9/ DO - 10.1038/s41598-019-47442-8 VL - 9 IS - 1 SP - 11207 SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-019-47442-8 ER - TY - JOUR TI - Epigenetic silencing of a multifunctional plant stress regulator AU - Zander, Mark AU - Willige, Bjorn C. AU - He, Yupeng AU - Nguyen, Thu A. AU - Langford, Amber E. AU - Nehring, Ramlah AU - Howell, Elizabeth AU - McGrath, Robert AU - Bartlett, Anna AU - Castanon, Rosa AU - Nery, Joseph R. AU - Chen, Huaming AU - Zhang, Zhuzhu AU - Jupe, Florian AU - Stepanova, Anna AU - Schmitz, Robert J. AU - Lewsey, Mathew G. AU - Chory, Joanne AU - Ecker, Joseph R. T2 - ELIFE AB - The central regulator of the ethylene (ET) signaling pathway, which controls a plethora of developmental programs and responses to environmental cues in plants, is ETHYLENE-INSENSITIVE2 (EIN2). Here we identify a chromatin-dependent regulatory mechanism at EIN2 requiring two genes: ETHYLENE-INSENSITIVE6 (EIN6), which is a H3K27me3 demethylase also known as RELATIVE OF EARLY FLOWERING6 (REF6), and EIN6 ENHANCER (EEN), the Arabidopsis homolog of the yeast INO80 chromatin remodeling complex subunit IES6 (INO EIGHTY SUBUNIT). Strikingly, EIN6 (REF6) and the INO80 complex redundantly control the level and the localization of the repressive histone modification H3K27me3 and the histone variant H2A.Z at the 5’ untranslated region (5’UTR) intron of EIN2. Concomitant loss of EIN6 (REF6) and the INO80 complex shifts the chromatin landscape at EIN2 to a repressive state causing a dramatic reduction of EIN2 expression. These results uncover a unique type of chromatin regulation which safeguards the expression of an essential multifunctional plant stress regulator. DA - 2019/8/16/ PY - 2019/8/16/ DO - 10.7554/eLife.47835 VL - 8 SP - SN - 2050-084X ER - TY - JOUR TI - Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.) AU - Bannoud, Florencia AU - Ellison, Shelby AU - Paolinelli, Marcos AU - Horejsi, Thomas AU - Senalik, Douglas AU - Fanzone, Martin AU - Iorizzo, Massimo AU - Simon, Philipp W. AU - Cavagnaro, Pablo F. T2 - THEORETICAL AND APPLIED GENETICS DA - 2019/9// PY - 2019/9// DO - 10.1007/s00122-019-03366-5 VL - 132 IS - 9 SP - 2485-2507 SN - 1432-2242 ER - TY - JOUR TI - Genomic-Wide Association Study of Popping Expansion in Tropical Popcorn and Field Corn Germplasm AU - Camargo Senhorinho, Henrique Jose AU - Dacal Coan, Marlon Matias AU - Marino, Thiago Pablo AU - Kuki, Mauricio Carlos AU - Barth Pinto, Ronald Jose AU - Scapim, Carlos Alberto AU - Holland, James Brendan T2 - CROP SCIENCE AB - Popcorn is a popular snack food with higher grain value compared with “field corn” maize ( Zea mays L.). In general, popcorn germplasm is less improved than common maize cultivars, with less favorable agronomic performance and greater susceptibility to pests, diseases, and lodging, especially in tropical environments. One approach to expanding and improving popcorn germplasm is to introduce favorable alleles for agronomic performance from field corn. If markers tagging quantitative trait loci (QTLs) associated with popping expansion were identified, they could be selected with markers to maintain popping expansion in breeding populations derived from crosses between field and popcorn germplasm. The objectives of this study were to identify single nucleotide polymorphism (SNP) markers and putative candidate genes associated with higher popping expansion in a diverse sample of popcorn and field corns relevant to Brazilian breeding programs. We applied a comprehensive genome‐wide association study (GWAS) for popping expansion, using 165,089 SNP markers in 183 inbred lines with 2 yr of trial data. Four SNPs were significantly associated with popping expansion, three of which were colocalized to previously reported meta‐QTLs, and one that was novel. Annotated genes closely linked to the associated SNPs were identified with functions related with starch content, which plays an important role in popping expansion quality. If these associations can be validated independently, they can be useful for breeders to select agronomically superior genotypes with greater popping expansion. DA - 2019/// PY - 2019/// DO - 10.2135/cropsci2019.02.0101 VL - 59 IS - 5 SP - 2007-2019 SN - 1435-0653 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85073380607&partnerID=MN8TOARS ER - TY - JOUR TI - Development, survival, and feeding behavior of Helicoverpa zea (Lepidoptera: Noctuidae) relative to Bt protein concentrations in corn ear tissues AU - Bilbo, Tom R. AU - Reay-Jones, Francis P. F. AU - Reisig, Dominic D. AU - Greene, Jeremy K. AU - Turnbull, Matthew W. T2 - PLOS ONE AB - The corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), preferentially oviposits and feeds on ears of corn (Zea mays L.) and can be managed using transgenic hybrids that produce insecticidal proteins from the bacterium Bacillus thuringiensis (Bt). Concentrations of Bt proteins can vary spatially and temporally in plant tissues, creating a heterogeneous environment that can increase the risk of resistance development. We planted small-plot trials of nine Bt and non-Bt corn hybrids in South Carolina in 2016 and 2017 and investigated the development, survival, feeding injury, and feeding behavior in corn ear tissues. ELISA was used to quantify the concentrations of Cry1F and Cry2Ab2 in young silk, old silk, maternal tip tissue, kernels, and husk. Cry1F and Cry2Ab2 significantly varied with silk age and both proteins were generally highest in the silk and tip tissue. Hybrids with pyramided proteins significantly reduced feeding injury to the silk, tip, and kernel ear tissues, which was less apparent with single Bt protein hybrids. The pyramided hybrid expressing Vip3A incurred no injury to either the ear tip or kernels, and only eight 1st instar larvae were collected in the silk of 520 sampled ears. Age of larvae significantly varied among ear tissues but not between hybrids. Depending on hybrid family, mean larval instar in the silk, tip, and kernels was 1st or 2nd, 3rd, and 5th, respectively. Instar-specific feeding penetrance into corn ears increased with age but did not differ between hybrids. We characterized the instar- and tissue-specific feeding behavior of H. zea larvae but did not detect differences in feeding behavior between Bt and non-Bt hybrids. Implications for resistance management strategies such as seed mixtures are discussed. DA - 2019/8/19/ PY - 2019/8/19/ DO - 10.1371/journal.pone.0221343 VL - 14 IS - 8 SP - e0221343 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0221343 DB - Crossref ER - TY - JOUR TI - Genome Editing, Gene Drives, and Synthetic Biology: Will They Contribute to Disease-Resistant Crops, and Who Will Benefit? AU - Pixley, Kevin V. AU - Falck-Zepeda, Jose B. AU - Giller, Ken E. AU - Glenna, Leland L. AU - Gould, Fred AU - Mallory-Smith, Carol A. AU - Stelly, David M. AU - Stewart, C. Neal, Jr. T2 - ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 57, 2019 AB - Genetically engineered crops have been grown for more than 20 years, resulting in widespread albeit variable benefits for farmers and consumers. We review current, likely, and potential genetic engineering (GE) applications for the development of disease-resistant crop cultivars. Gene editing, gene drives, and synthetic biology offer novel opportunities to control viral, bacterial, and fungal pathogens, parasitic weeds, and insect vectors of plant pathogens. We conclude that there will be no shortage of GE applications to tackle disease resistance and other farmer and consumer priorities for agricultural crops. Beyond reviewing scientific prospects for genetically engineered crops, we address the social institutional forces that are commonly overlooked by biological scientists. Intellectual property regimes, technology regulatory frameworks, the balance of funding between public- and private-sector research, and advocacy by concerned civil society groups interact to define who uses which GE technologies, on which crops, and for the benefit of whom. Ensuring equitable access to the benefits of genetically engineered crops requires affirmative policies, targeted investments, and excellent science. DA - 2019/// PY - 2019/// DO - 10.1146/annurev-phyto-080417-045954 VL - 57 SP - 165-188 SN - 1545-2107 KW - gene drives KW - gene editing KW - genetically engineered crops KW - science and society KW - social equity KW - synthetic biology ER - TY - JOUR TI - Specific Gene Disruption in the Major Livestock PestsCochliomyia hominivoraxandLucilia cuprinaUsing CRISPR/Cas9 AU - Paulo, Daniel F AU - Williamson, Megan E AU - Arp, Alex P AU - Li, Fang AU - Sagel, Agustin AU - Skoda, Steven R AU - Sanchez-Gallego, Joel AU - Vasquez, Mario AU - Quintero, Gladys AU - Pérez de León, Adalberto A AU - Belikoff, Esther J AU - Azeredo-Espin, Ana M L AU - McMillan, W Owen AU - Concha, Carolina AU - Scott, Maxwell J T2 - G3 Genes|Genomes|Genetics AB - Abstract Cochliomyia hominivorax and Lucilia cuprina are major pests of livestock. Their larvae infest warm-blooded vertebrates and feed on host’s tissues, resulting in severe industry losses. As they are serious pests, considerable effort has been made to develop genomic resources and functional tools aiming to improve their management and control. Here, we report a significant addition to the pool of genome manipulation tools through the establishment of efficient CRISPR/Cas9 protocols for the generation of directed and inheritable modifications in the genome of these flies. Site-directed mutations were introduced in the C. hominivorax and L. cuprina yellow genes (ChY and LcY) producing lightly pigmented adults. High rates of somatic mosaicism were induced when embryos were injected with Cas9 ribonucleoprotein complexes (RNPs) pre-assembled with guide RNAs (sgRNAs) at high concentrations. Adult flies carrying disrupted yellow alleles lacked normal pigmentation (brown body phenotype) and efficiently transmitted the mutated alleles to the subsequent generation, allowing the rapid creation of homozygous strains for reverse genetics of candidate loci. We next used our established CRISPR protocol to disrupt the C. hominivorax transformer gene (Chtra). Surviving females carrying mutations in the Chtra locus developed mosaic phenotypes of transformed ovipositors with characteristics of male genitalia while exhibiting abnormal reproductive tissues. The CRISPR protocol described here is a significant improvement on the existing toolkit of molecular methods in calliphorids. Our results also suggest that Cas9-based systems targeting Chtra and Lctra could be an effective means for controlling natural populations of these important pests. DA - 2019/9/1/ PY - 2019/9/1/ DO - 10.1534/g3.119.400544 VL - 9 IS - 9 SP - 3045-3055 LA - en OP - SN - 2160-1836 UR - http://dx.doi.org/10.1534/g3.119.400544 DB - Crossref KW - Functional genomics KW - reverse genetics KW - myiasis KW - New World Screwworm fly KW - Australian Sheep Blowfly KW - gene drive KW - CRISPR KW - Cas9 KW - brown body KW - yellow KW - transformer ER - TY - JOUR TI - Validation and Characterization of Maize Multiple Disease Resistance QTL AU - Martins, Lais B. AU - Rucker, Elizabeth AU - Thomason, Wade AU - Wisser, Randall J. AU - Holland, James B. AU - Balint-Kurti, Peter T2 - G3-GENES GENOMES GENETICS AB - Abstract Southern Leaf Blight, Northern Leaf Blight, and Gray Leaf Spot, caused by ascomycete fungi, are among the most important foliar diseases of maize worldwide. Previously, disease resistance quantitative trait loci (QTL) for all three diseases were identified in a connected set of chromosome segment substitution line (CSSL) populations designed for the identification of disease resistance QTL. Some QTL for different diseases co-localized, indicating the presence of multiple disease resistance (MDR) QTL. The goal of this study was to perform an independent test of several of the MDR QTL identified to confirm their existence and derive a more precise estimate of allele additive and dominance effects. Twelve F2:3 family populations were produced, in which selected QTL were segregating in an otherwise uniform genetic background. The populations were assessed for each of the three diseases in replicated trials and genotyped with markers previously associated with disease resistance. Pairwise phenotypic correlations across all the populations for resistance to the three diseases ranged from 0.2 to 0.3 and were all significant at the alpha level of 0.01. Of the 44 QTL tested, 16 were validated (identified at the same genomic location for the same disease or diseases) and several novel QTL/disease associations were found. Two MDR QTL were associated with resistance to all three diseases. This study identifies several potentially important MDR QTL and demonstrates the importance of independently evaluating QTL effects following their initial identification. DA - 2019/9// PY - 2019/9// DO - 10.1534/g3.119.400195 VL - 9 IS - 9 SP - 2905-2912 SN - 2160-1836 UR - https://doi.org/10.1534/g3.119.400195 KW - Disease KW - Maize KW - QTL KW - Resistance KW - Genetics of Immunity ER - TY - JOUR TI - Variation in anthocyanin profiles of 27 genotypes of red cabbage over two growing seasons AU - Strauch, Renee C. AU - Mengist, Molla F. AU - Pan, Kevin AU - Yousef, Gad G. AU - Iorizzo, Massimo AU - Brown, Allan F. AU - Lila, Mary Ann T2 - FOOD CHEMISTRY AB - Acylated anthocyanins, such as those found in red cabbage, are more heat-, light-, and alkaline pH-stable than non-acylated anthocyanins, making them attractive for a variety of commercial applications. A UPLC-DAD-MSE method with an optimized chromatographic strategy was used to identify 29 red cabbage anthocyanins, predominantly acylated and glucosylated cyanidin derivatives. Anthocyanin profiles of 27 red cabbage genotypes harvested in consecutive growing seasons were measured and assessed for variation. Three unique anthocyanin profile fingerprints were identified through hierarchical clustering analysis. PCA analysis identified anthocyanin accumulation traits and genotypes with high diversity which can be utilized in future investigations into the genetic and molecular basis for anthocyanin production, acylation, and diversity. DA - 2019/12/15/ PY - 2019/12/15/ DO - 10.1016/j.foodchem.2019.125289 VL - 301 SP - SN - 1873-7072 KW - Red cabbage KW - Acylated anthocyanin KW - Breeding population KW - HPLC-DAD-MSE ER - TY - JOUR TI - Threshold-Dependent Gene Drives in the Wild: Spread, Controllability, and Ecological Uncertainty AU - Backus, Gregory A AU - Delborne, Jason A T2 - BioScience AB - Abstract Gene drive technology could allow the intentional spread of a desired gene throughout an entire wild population in relatively few generations. However, there are major concerns that gene drives could either fail to spread or spread without restraint beyond the targeted population. One potential solution is to use more localized threshold-dependent drives, which only spread when they are released in a population above a critical frequency. However, under certain conditions, small changes in gene drive fitness could lead to divergent outcomes in spreading behavior. In the face of ecological uncertainty, the inability to estimate gene drive fitness in a real-world context could prove problematic because gene drives designed to be localized could spread to fixation in neighboring populations if ecological conditions unexpectedly favor the gene drive. This perspective offers guidance to developers and managers because navigating gene drive spread and controllability could be risky without detailed knowledge of ecological contexts. DA - 2019/9/18/ PY - 2019/9/18/ DO - 10.1093/biosci/biz098 VL - 69 IS - 11 SP - 900-907 LA - en OP - SN - 0006-3568 1525-3244 UR - http://dx.doi.org/10.1093/biosci/biz098 DB - Crossref KW - gene drives KW - conservation KW - uncertainty KW - modeling KW - biotechnology ER - TY - JOUR TI - Networks of Networks? Toward an External Perspective on Whole Networks T2 - Perspectives on Public Management and Governance AB - Abstract In light of the burgeoning literature in whole, goal-directed networks for managing wicked problems in public management, it is timely to examine the theoretical evolution that has both shaped and constrained our understanding of these networks. In this article, we argue that contemporary study of whole networks has been dominated by an internal theoretical lens aimed at understanding how internal characteristics influence network functioning and effectiveness. This perspective assumes networks operate in differentiated environments rather than emphasizing interdependence as part of a broader ecology—networks of networks. In this article, we draw from population ecology to introduce the concept of network domains and offer evidence drawn from a population of 60 health-oriented networks in three counties to illustrate domain level characteristics. Using an inductive mode of theorizing, we leverage insights from these domains to consider population dynamics and pose propositions for advancing a program of study into domain level characteristics that may shape and constrain whole networks and their members. DA - 2019/8/31/ PY - 2019/8/31/ DO - 10.1093/ppmgov/gvz005 UR - http://dx.doi.org/10.1093/ppmgov/gvz005 ER - TY - JOUR TI - Purpose-Oriented Networks: The Architecture of Complexity T2 - Perspectives on Public Management and Governance DA - 2019/8/31/ PY - 2019/8/31/ DO - 10.1093/ppmgov/gvz012 UR - http://dx.doi.org/10.1093/ppmgov/gvz012 ER - TY - JOUR TI - Methodological considerations in pre- and post-emergency network identification and data collection for disaster risk reduction: Lessons from wildfire response networks in the American Northwest T2 - International Journal of Disaster Risk Reduction AB - While social network analysis continues to enjoy considerable attention, literature on social network data collection often lacks explicit attention to methods. This presents special challenges to approaching the problems of undertaking social network analysis and of studying disaster preparedness, planning, and, ultimately, risk reduction. In this paper, we address this issue by presenting our synthesis of several strategies for network analyses from our processes for network identification and data collection in a longitudinal study of multi-jurisdictional, inter-agency wildfire response networks in the American Northwest. In the course of this ongoing project, the process of detecting and collecting data on pre-existing and emergent networks in the real world was not a matter of one theoretical or empirical judgement, but rather several. We alternated between: (1) spatio-ecological detection of jurisdictions adjacent to areas at-risk for large wildfires; (2) a hybrid approach to selecting actors and agencies identified as common participants in wildfire response networks; and (3) event-based detections of parties to specific wildfire response networks. We conclude with steps for thinking through network identification and bounding, integrating networks, conceptualizing rosters and ties in initial and events-based phases, and how to manage longitudinal network data collection. DA - 2019/11// PY - 2019/11// DO - 10.1016/j.ijdrr.2019.101260 UR - http://dx.doi.org/10.1016/j.ijdrr.2019.101260 ER - TY - JOUR TI - Evaluation of Insecticide Resistance in Aedes albopictus (Diptera: Culicidae) in North Carolina, 2017 AU - Richards, Stephanie L. AU - White, Avian V. AU - Byrd, Brian D. AU - Reiskind, Michael H. AU - Doyle, Michael S. T2 - JOURNAL OF MEDICAL ENTOMOLOGY AB - Mosquitoes may develop resistance to insecticide active ingredients (AIs) found in formulated products (FPs) due to environmental exposure from insecticides in mosquito control and/or unrelated to mosquito control, e.g., agricultural, household pest control. Mosquito control programs should implement resistance management strategies by assessing resistance in targeted populations, rotating different classes of insecticides based on resistance testing, and/or increasing insecticide concentration (i.e., saturation, using maximum labeled rate) to overcome emerging resistance. Resistance testing is often done solely on AIs, but should, in some cases, include both AIs and FPs at the concentrations mosquitoes may encounter in the field. The resistance/susceptibility status was determined for adulticides used in mosquito control. Centers for Disease Control and Prevention (CDC) bottle bioassays were used to assess resistance/susceptibility status for eight AIs (i.e., bifenthrin, permethrin, sumethrin/prallethrin, deltamethrin, tau-fluvalinate, chlorpyrifos, malathion, and naled) and eight FPs (TalStar, Biomist 3 + 15, Duet, Suspend Polyzone, Mavrik, MosquitoMist, Fyfanon, and Dibrom) that respectively contain the AIs. Current CDC guidelines were utilized: susceptible (97-100% mortality at diagnostic time [DT]), developing resistance (90-96% mortality at DT), or resistant (<90% mortality at DT). Significant differences were observed in mosquito susceptibility/resistance among and between AIs and FPs. DA - 2019/5// PY - 2019/5// DO - 10.1093/jme/tjy216 VL - 56 IS - 3 SP - 761-773 SN - 1938-2928 KW - CDC bottle bioassay KW - pyrethroid KW - organophosphate KW - active ingredient KW - formulated product ER - TY - JOUR TI - Different microbial responses in top- and sub-soils to elevated temperature and substrate addition in a semiarid grassland on the Loess Plateau AU - Bai, Tongshuo AU - Tao, Jinjin AU - Li, Zhen AU - Shu, Meng AU - Yan, Xuebin AU - Wang, Peng AU - Ye, Chenglong AU - Guo, Hui AU - Wang, Yi AU - Hu, Shuijin T2 - EUROPEAN JOURNAL OF SOIL SCIENCE AB - The Loess Plateau soil in northwest China originated from wind sediments and is characterized by deep soil profiles and large organic carbon (C) content. Severe soil erosion constantly exposes deep soils to the surface, making the organic C vulnerable to microbial decomposition. Few, however, have so far examined how soil microbial activity and community composition in the deep loess soil respond to perturbations. We examined microbial responses in three layers of a clay‐loam loess (topsoil, 0–20 cm; midsoil, 40–60 cm; subsoil, 80–100 cm) to substrate additions (0.8 g glucose‐C kg −1 soil) under two temperature regimes (25 and 35°C). Soil C:N ratio was significantly larger in the subsoil (20.3) than topsoil (7.4). Glucose addition significantly increased CO 2 efflux during a 30‐day incubation period and the relative magnitude of the increase was four times larger in the subsoil than topsoil. The temperature sensitivity ( Q 10 ) of soil CO 2 efflux increased significantly with soil depth in the absence of glucose addition (i.e., ambient soil), but it decreased under glucose addition. Also, glucose addition significantly increased phenol oxidase and peroxidase activities in the subsoil, which might contribute to the stimulation of microbial CO 2 efflux. Composition of the microbial community was more affected by temperature increase in the topsoil, but more responsive to labile C addition in the subsoil. Together, these results indicated that the composition of soil communities and microbial activities in the topsoil and deep soil responded differently to warming and labile C input. Our findings suggest that organic C in deep loess soils can be highly sensitive to environmental changes, emphasizing the need for more long‐term monitoring and quantitative assessment of organic C release from this important C pool. Highlights Microbial responses to labile C and warming were examined along a Loess Plateau soil profile. Microbial respiration was more responsive to C addition and warming in deep soil than topsoil. Microbial composition and activity were sensitive to temperature in the topsoil but to labile C in the subsoil. Climate change may facilitate CO 2 efflux from deep Loess Plateau soils. DA - 2019/9// PY - 2019/9// DO - 10.1111/ejss.12800 VL - 70 IS - 5 SP - 1025-1036 SN - 1365-2389 KW - carbon mineralization KW - deep soil exposure KW - labile C addition KW - Loess Plateau KW - microbial community composition KW - temperature sensitivity ER - TY - JOUR TI - A Diverse Microbial Community Supports Larval Development and Survivorship of the Asian Tiger Mosquito (Diptera: Culicidae) AU - Travanty, Nicholas V. AU - Apperson, Charles S. AU - Ponnusamy, Loganathan T2 - JOURNAL OF MEDICAL ENTOMOLOGY AB - Laboratory microcosm experiments were conducted to evaluate effects of bacteria isolated from senescent white oak leaves on the growth and survivorship of larval Aedes albopictus (Skuse). Larvae hatched from surface-sterilized eggs were reared in microcosms containing individual bacterial isolates, combined isolates (Porphyrobacter sp., Enterobacter asburiae, Acidiphilium rubrum, Pseudomonas syringae, and Azorhizobium caulinodans), a positive control containing a microbial community from an infusion of white oak leaves, and a negative control consisting of sterile culture media. Experiments were conducted for 21 d after which microcosms were deconstructed, larval survivorship was calculated, and bacteria contained in pupae, and adults that developed were quantified to determine rates of transstadial transmission. Positive control microcosms containing diverse microbial communities had an average (±SE) pupation rate of 89.3 (±5.8)% and average larval survivorship of 96.0 (± 2.3)%. Pupation in microcosms with bacterial isolates only occurred twice among all experimental replications; average larval survivorship ranged from 19 to 56%, depending on treatment. Larval growth was not found to be dependent on bacterial isolate density or isolate species, and larval survivorship was dependent on bacterial isolate density, not on isolate species. Potential mechanisms for failed development of larvae in microcosms with bacterial isolates are discussed. Bacterial isolates alone did not support larval development. High larval survivorship in positive control microcosms suggests that a diverse microbial community is required to complete larval development. Additional studies are needed to evaluate larval growth and survivorship on nonbacterial microbes, such as fungi and protozoa. DA - 2019/5// PY - 2019/5// DO - 10.1093/jme/tjz003 VL - 56 IS - 3 SP - 632-640 SN - 1938-2928 KW - Quercus alba KW - mosquito KW - microcosms KW - transstadial transmission KW - microbial communities ER - TY - JOUR TI - Does the U.S. public support using gene drives in agriculture? And what do they want to know? AU - Jones, Michael S. AU - Delborne, Jason A. AU - Elsensohn, Johanna AU - Mitchell, Paul D. AU - Brown, Zachary S. T2 - Science Advances AB - With gene drives for agricultural pest control on the horizon, a survey suggests the public is receptive but concerned about risk. DA - 2019/9// PY - 2019/9// DO - 10.1126/sciadv.aau8462 VL - 5 IS - 9 SP - eaau8462 J2 - Sci. Adv. LA - en OP - SN - 2375-2548 UR - http://dx.doi.org/10.1126/sciadv.aau8462 DB - Crossref ER - TY - JOUR TI - Azteca ants maintain unique microbiomes across functionally distinct nest chambers AU - Lucas, Jane M. AU - Madden, Anne A. AU - Penick, Clint A. AU - Epps, Mary Jane AU - Marting, Peter R. AU - Stevens, Julia L. AU - Fergus, Daniel J. AU - Dunn, Robert R. AU - Meineke, Emily K. T2 - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES AB - The microbiome of built structures has considerable influence over an inhabitant's well-being, yet the vast majority of research has focused on human-built structures. Ants are well-known architects, capable of constructing elaborate dwellings, the microbiome of which is underexplored. Here, we explore the bacterial and fungal microbiomes in functionally distinct chambers within and outside the nests of Azteca alfari ants in Cecropia peltata trees. We predicted that A. alfari colonies (1) maintain distinct microbiomes within their nests compared to the surrounding environment, (2) maintain distinct microbiomes among nest chambers used for different functions, and (3) limit both ant and plant pathogens inside their nests. In support of these predictions, we found that internal and external nest sampling locations had distinct microbial communities, and A. alfari maintained lower bacterial richness in their ‘nurseries’. While putative animal pathogens were suppressed in chambers that ants actively inhabited, putative plant pathogens were not, which does not support our hypothesis that A. alfari defends its host trees against microbial antagonists. Our results show that ants influence microbial communities inside their nests similar to studies of human homes. Unlike humans, ants limit the bacteria in their nurseries and potentially prevent the build-up of insect-infecting pathogens. These results highlight the importance of documenting how indoor microbiomes differ among species, which might improve our understanding of how to promote indoor health in human dwellings. DA - 2019/7/31/ PY - 2019/7/31/ DO - 10.1098/rspb.2019.1026 VL - 286 IS - 1908 SP - SN - 1471-2954 KW - Azteca KW - Cecropia KW - microbiome KW - microbe KW - myrmecophyte ER - TY - JOUR TI - Controlling invasive rodents via synthetic gene drive and the role of polyandry AU - Manser, Andri AU - Cornell, Stephen J. AU - Sutter, Andreas AU - Blondel, Dimitri V. AU - Serr, Megan AU - Godwin, John AU - Price, Tom A. R. T2 - Proceedings of the Royal Society B: Biological Sciences AB - House mice are a major ecosystem pest, particularly threatening island ecosystems as a non-native invasive species. Rapid advances in synthetic biology offer new avenues to control pest species for biodiversity conservation. Recently, a synthetic sperm-killing gene drive construct called t-Sry has been proposed as a means to eradicate target mouse populations owing to a lack of females. A factor that has received little attention in the discussion surrounding such drive applications is polyandry. Previous research has demonstrated that sperm-killing drivers are extremely damaging to a male’s sperm competitive ability. Here, we examine the importance of this effect on the t-Sry system using a theoretical model. We find that polyandry substantially hampers the spread of t-Sry such that release efforts have to be increased three- to sixfold for successful eradication. We discuss the implications of our finding for potential pest control programmes, the risk of drive spread beyond the target population, and the emergence of drive resistance. Our work highlights that a solid understanding of the forces that determine drive dynamics in a natural setting is key for successful drive application, and that exploring the natural diversity of gene drives may inform effective gene drive design. DA - 2019/8/21/ PY - 2019/8/21/ DO - 10.1098/rspb.2019.0852 VL - 286 IS - 1909 SP - 20190852 J2 - Proc. R. Soc. B LA - en OP - SN - 0962-8452 1471-2954 UR - http://dx.doi.org/10.1098/rspb.2019.0852 DB - Crossref KW - gene drive KW - polyandry KW - invasive species KW - pest control KW - house mouse ER - TY - JOUR TI - Effects of Five Growing Media and Two Fertilizer Levels on Polybag-Raised Camden Whitegum (Eucalyptus benthamii Maiden & Cambage) Seedling Morphology and Drought Hardiness AU - Shalizi, Mohammad Nasir AU - Goldfarb, Barry AU - Burney, Owen Thomas AU - Shear, Theodore Henry T2 - FORESTS AB - In developing countries, tree seedlings are often produced in polybags filled with mixtures of locally available materials. Seedling growth and quality can be affected by the type and amount of these substrates used in the mixture. Differences in seedling growth and quality can also be significantly affected when fertilization is employed during the nursery growing period. In this study, we assessed the effects of five different growing media and two fertilization regimes on nursery growth, seedling morphology and early post-planting response to drought of Eucalyptus benthamii (Maiden & Cambage) seedlings. First, we evaluated the effects of each media by fertilizer treatment combination on morphological attributes during a nursery growing period. Seedlings raised in fertilized media without rice hulls yielded higher growth, root dry mass, shoot dry mass, total dry mass, Dickson quality index (DQI) scores, and number of first order lateral roots (FOLRs). Root to shoot ratio (R:S ratio) was, however, greater in non-fertilized media that contained rice hulls. We then conducted a simulated outplanting and drought hardiness experiment, in which seedlings were planted in 13.2 L containers and irrigated for one month, followed by the imposition of drought stress. Seedlings in fertilized media composed of sand, topsoil and compost showed greater growth than those in rice hull-containing media, during the irrigation phase. With the discontinuation of irrigation and prevention of precipitation reaching the seedlings, seedlings grown in non-fertilized media containing rice hulls survived longer than those in other media. There were no large differences in survival among other media or between fertilized and other non-fertilized seedlings. Seedling total size and shoot height at the time of planting played a major role in survival. Smaller seedlings with smaller shoot sizes and greater R:S ratios survived longer. This study demonstrates that growing media and fertilization can be manipulated to affect seedling morphology in the nursery and, ultimately, seedling performance and survival under water stressed conditions. DA - 2019/7// PY - 2019/7// DO - 10.3390/f10070543 VL - 10 IS - 7 SP - SN - 1999-4907 KW - seedling growth KW - nutrition KW - seedling quality KW - survival KW - xylem water potential KW - reforestation ER - TY - JOUR TI - Developing a Comprehensive, Adaptive, and International Biosafety and Biosecurity Program for Advanced Biotechnology: The iGEM Experience T2 - Applied Biosafety AB - The international synthetic biology competition iGEM (formally known as the international Genetically Engineered Machines competition) has a dedicated biosafety and biosecurity program.A review of specific elements of the program and a series of concrete examples illustrate how experiences in implementing the program have helped improved policy, including an increasing diversity of sources for genetic parts and organisms, keeping pace with technical developments, considering pathways toward future environmental release, addressing antimicrobial resistance, and testing the efficacy of current biosecurity arrangements.iGEM's program is forward-leaning, in that it addresses both traditional (pathogen-based) and emerging risks both in terms of new technologies and new risks. It is integrated into the technical work of the competition-with clearly described roles and responsibilities for all members of the community. It operates throughout the life cycle of projects-from project design to future application. It makes use of specific tools to gather and review biosafety and biosecurity information, making it easier for those planning and conducting science and engineering to recognize potential risks and match them with appropriate risk management approaches, as well as for specialists to review this information to identify gaps and strengthen plans.Integrating an increasingly adaptive risk management approach has allowed iGEM's biosafety and biosecurity program to become comprehensive, be cross-cutting, and cover the competition's life cycle. DA - 2019/6// PY - 2019/6// DO - 10.1177/1535676019838075 UR - http://dx.doi.org/10.1177/1535676019838075 KW - synthetic biology KW - biological engineering KW - biotechnology KW - adaptive biosafety KW - iGEM KW - genetic engineering ER - TY - JOUR TI - Enclothed cognition: putting lab coats to the test AU - Jones, M. Gail AU - Lee, Tammy AU - Chesnutt, Katherine AU - Carrier, Sarah AU - Ennes, Megan AU - Cayton, Emily AU - Madden, Lauren AU - Huff, Pamela T2 - International Journal of Science Education AB - Although there has been some success with programmes that aim to increase STEM involvement by women and underserved minorities, science educators continue to seek ways to promote students’ interest in STEM. This study builds on social cognitive career theory (SCCT) and the theory of enclothed cognition to assess the impact of wearing lab coats on 5th-grade students. Students were assigned to a treatment group (that wore lab coats, n = 106) or a control group (that did not wear lab coats, n = 110) for 10 science classes taught by their classroom science teacher. Students were assessed pre and post to the intervention with a survey designed to measure science interest, recognition from others as a science person, science self-efficacy, and STEM career goals. Results showed students’ interest in science was not significantly changed due to wearing the lab coat, but the lab coats did have significant effects on students’ perceived recognition by others as being a science learner. Furthermore, those treatment students with low self-efficacy (compared to those with high self-efficacy) and those with who did not report having access to a parent with a STEM career had significant increases in perceptions of self-efficacy in science. DA - 2019/8/12/ PY - 2019/8/12/ DO - 10.1080/09500693.2019.1649504 VL - 41 IS - 14 SP - 1962-1976 J2 - International Journal of Science Education LA - en OP - SN - 0950-0693 1464-5289 UR - http://dx.doi.org/10.1080/09500693.2019.1649504 DB - Crossref KW - Attitudes KW - career KW - enclothed cognition KW - self-efficacy KW - self-concept ER - TY - JOUR TI - Arthropod entrapment increases specialist predators on a sticky crop and reduces damage AU - Nelson, Peter N. AU - Burrack, Hannah J. AU - Sorenson, Clyde E. T2 - BIOLOGICAL CONTROL AB - Maximizing plant defensive strategies is integral to effective integrated pest management. Direct defenses, in the form of chemical and morphological components that inhibit pest damage, underlie host plant resistance, while indirect defenses including food provisioning and semiochemical production, improve biological control. Interactions between the two defensive strategies may be disruptive, complementary, or synergistic and are an important consideration for effective pest management programs. Glandular trichomes are plant structures that inhibit or entrap arthropods, protecting plants against herbivores, potentially at the cost of reducing natural enemy efficacy. Glandular trichomes may also contribute to indirect defense, as predatory arthropods adapted to “sticky” surfaces scavenge on entrapped arthropods. Scavenging increases predator abundance and reduces plant damage; this protective mutualism has been demonstrated with multiple sticky wild flowers but has not been assessed in an economically important plant, such as tobacco. We augmented dead arthropods (carrion) on tobacco plants grown under conditions similar to commercial production and assessed tri-trophic interactions. Carrion augmentation increased predator abundance, reduced damage to reproductive structures, and increased leaf yield, but did not reduce pest densities. We determined that systemic insecticide use did not affect carrion entrapment on tobacco plants. Review of the literature revealed that a variety of economically important plants entrap arthropods on their surfaces, indicating this mutualism has potential for development into a conservation biological control tactic. DA - 2019/10// PY - 2019/10// DO - 10.1016/j.biocontrol.2019.104021 VL - 137 SP - SN - 1090-2112 KW - Trichomes KW - Mutualism KW - Plant-provided food KW - Scavenging KW - Conservation biological control KW - Numerical response ER - TY - JOUR TI - Measuring the effect of non-crop flowering plants on natural enemies in organic tobacco AU - Aurora Toennisson, T. AU - Klein, Johanna Tartan AU - Burrack, Hannah T2 - BIOLOGICAL CONTROL AB - The use of “insectary strips” of sunflowers and buckwheat is widely promoted by organic certifiers to promote control of the green peach aphid (Myzus persicae) and other pests in organic tobacco. However, no published research supports this recommendation in tobacco, and results from other crops are mixed. We performed a series of experiments to test the effects of non-crop plantings of sunflowers and buckwheat on key pest and beneficial insects adjacent to organic tobacco fields in North Carolina. Although some reduction in M. persicae infestations and increases in numbers of beneficial insects were observed on tobacco plants near field-edge insectary treatments, these effects were small and were observed only over a short distance into the crop. Planting additional insectary strips in the field interior did not reduce aphid numbers in comparison to control treatments and led to increases in some pest insects. These conservation biological control techniques are unlikely to be a reliable method of controlling M. persicae and other pest insects in organic tobacco. DA - 2019/10// PY - 2019/10// DO - 10.1016/j.biocontrol.2019.104023 VL - 137 SP - SN - 1090-2112 KW - Myzus persicae KW - Sunflower KW - Buckwheat KW - Insectary plantings KW - Conservation biological control ER - TY - JOUR TI - Outcomes and characterization of chromosomal self-targeting by native CRISPR-Cas systems in Streptococcus thermophilus AU - Canez, Cassandra AU - Selle, Kurt AU - Goh, Yong Jun AU - Barrangou, Rodolphe T2 - FEMS MICROBIOLOGY LETTERS AB - ABSTRACT CRISPR-Cas systems provide adaptive immunity against phages in prokaryotes via DNA-encoded, RNA-mediated, nuclease-dependent targeting and cleavage. Due to inefficient and relatively limited DNA repair pathways in bacteria, CRISPR-Cas systems can be repurposed for lethal DNA targeting that selects for sequence variants. In this study, the relative killing efficiencies of endogenous Type I and Type II CRISPR-Cas systems in the model organism Streptococcus thermophilus DGCC7710 were assessed. Additionally, the genetic and phenotypic outcomes of chromosomal targeting by plasmid-programmed Type I-E or Type II-A systems were analyzed. Efficient killing was observed using both systems, in a dose-dependent manner when delivering 0.4–400 ng of plasmid DNA. Targeted PCR screening and genome sequencing were used to determine the genetic basis enabling survival, showing that evasion of Type I-E self-targeting was primarily the result of low-frequency defective plasmids that excised the targeting spacer. The most notable genotype recovered from Type II-A targeting of genomic locus, lacZ, was a 34 kb-deletion derived from homologous recombination (HR) between identical conserved sequences in two separate galE coding regions, resulting in 2% loss of the genome. Collectively, these results suggest that HR contributes to the plasticity and remodeling of bacterial genomes, leading to evasion of genome targeting by CRISPR-Cas systems. DA - 2019/5// PY - 2019/5// DO - 10.1093/femsle/fnz105 VL - 366 IS - 9 SP - SN - 1574-6968 UR - https://doi.org/10.1093/femsle/fnz105 KW - CRISPR KW - lactic acid bacteria KW - Cas9 KW - Streptococcus KW - genome editing ER - TY - JOUR TI - Effects of aridity on soil microbial communities and functions across soil depths on the Mongolian Plateau AU - Chen, Dima AU - Saleem, Muhammad AU - Cheng, Junhui AU - Mi, Jia AU - Chu, Pengfei AU - Tuvshintogtokh, Indree AU - Hu, Shuijin AU - Bai, Yongfei T2 - FUNCTIONAL ECOLOGY AB - Abstract Arid and semi‐arid grassland ecosystems cover about 15% of the global land surface and provide vital soil carbon (C) and nitrogen (N) sequestration. Although half of the soil C and N is stored in deep soils (below 30 cm), no regional‐scale study of microbial properties and their functions through the soil profile has been conducted in these drylands. To explore the distribution and determinants of microbial properties and C and N mineralization rates through soil profile along aridity gradient at a regional scale, we investigated these variables for four soil layers (0–20, 20–40, 40–60 and 60–100 cm) in 132 plots on the Mongolia Plateau. Soil microbial properties (biomass and bacteria:fungi ratio) and C and N mineralization rates decreased with increasing soil depth and aridity at the regional scale. Aridity‐induced declines in soil microbial properties mainly resulted from the negative effects of aridity on ANPP/root biomass and soil organic C (SOC) in the surface soil layers (0–20 and 20–40 cm) but from the direct and indirect (via SOC and soil C/N) negative effects of aridity in the deep soil layers (40–60 and 60–100 cm). Aridity‐induced declines in soil C mineralization rates mainly resulted from the negative indirect effect of aridity on SOC and microbial properties in each soil layer, with weaker effects of SOC and stronger effects of soil microbes in the deep soil layers. Aridity‐induced declines in soil N mineralization rates mainly resulted from the negative indirect effect of aridity on SOC in the three soil layers above 60 cm and mainly resulted from the negative direct effect of aridity in the 60–100 cm soil layer. Aridity via direct or indirect effects strongly determined the patterns of soil microbial properties and C and N mineralization throughout soil profiles on the Mongolian Plateau. These findings suggest that the increases in aridity are likely to induce changes in soil micro‐organisms and their associated functions across soil depths of semi‐arid grasslands, and future models should consider the dynamic interactions between substrates and microbial properties across soil depths in global drylands. A plain language summary is available for this article. DA - 2019/8// PY - 2019/8// DO - 10.1111/1365-2435.13359 VL - 33 IS - 8 SP - 1561-1571 SN - 1365-2435 KW - biogeographical patterns KW - depth profile KW - microbial community structure KW - semi-arid grasslands KW - soil carbon mineralization KW - soil nitrogen mineralization ER - TY - JOUR TI - Quantitative fermentation of unpretreated transgenic poplar by Caldicellulosiruptor bescii AU - Straub, Christopher T. AU - Khatibi, Piyum A. AU - Wang, Jack P. AU - Conway, Jonathan M. AU - Williams-Rhaesa, Amanda M. AU - Peszlen, Ilona M. AU - Chiang, Vincent L. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - NATURE COMMUNICATIONS AB - Abstract Microbial fermentation of lignocellulosic biomass to produce industrial chemicals is exacerbated by the recalcitrant network of lignin, cellulose and hemicelluloses comprising the plant secondary cell wall. In this study, we show that transgenic poplar ( Populus trichocarpa ) lines can be solubilized without any pretreatment by the extreme thermophile Caldicellulosiruptor bescii that has been metabolically engineered to shift its fermentation products away from inhibitory organic acids to ethanol. Carbohydrate solubilization and conversion of unpretreated milled biomass is nearly 90% for two transgenic lines, compared to only 25% for wild-type poplar. Unexpectedly, unpretreated intact poplar stems achieved nearly 70% of the fermentation production observed with milled poplar as the substrate. The nearly quantitative microbial conversion of the carbohydrate content of unpretreated transgenic lignocellulosic biomass bodes well for full utilization of renewable biomass feedstocks. DA - 2019/8/7/ PY - 2019/8/7/ DO - 10.1038/s41467-019-11376-6 VL - 10 SP - SN - 2041-1723 ER - TY - JOUR TI - Short communication: Transcriptional response to a large genomic island deletion in the dairy starter culture Streptococcus thermophilus AU - Selle, Kurt AU - Andersen, Joakim M. AU - Barrangou, Rodolphe T2 - JOURNAL OF DAIRY SCIENCE AB - Streptococcus thermophilus is a lactic acid bacterium widely used in the syntrophic fermentation of milk into yogurt and cheese. Streptococcus thermophilus has adapted to ferment milk primarily through reductive genome evolution but also through acquisition of genes conferring proto-cooperation with Lactobacillus bulgaricus and efficient metabolism of milk macronutrients. Genomic analysis of Strep. thermophilus strains suggests that mobile genetic elements have contributed to genomic evolution through horizontal gene transfer and genomic plasticity. We previously used the endogenous type II CRISPR-Cas [clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR-associated sequences (Cas)] system in Strep. thermophilus to isolate derivatives lacking the chromosomal mobile genetic element and expandable island that display decreased fitness under routine culturing conditions. Of note, the Lac operon and Leloir pathway genes were deleted in the largest expendable genomic island (102 kbp), rendering the strain incapable of acidifying milk. However, the removal of other open reading frames in the same island had unclear effects on the fitness and regulatory networks of Strep. thermophilus. To uncover the physiological basis for the observed phenotypic changes and underlying regulatory networks affected by deletion of the 102-kbp genomic island in Strep. thermophilus, we analyzed the transcriptome of the mutant that lacked ∼5% of its genome. In addition to the loss of transcripts encoded by the deleted material, we detected a total of 56 genes that were differentially expressed, primarily encompassing 10 select operons. Several predicted metabolic pathways were affected, including amino acid and purine metabolism, oligopeptide transport, and iron transport. Collectively, these results suggest that deletion of a 102-kb genomic island in Strep. thermophilus influences compensatory transcription of starvation stress response genes and metabolic pathways involved in important niche-related adaptation. DA - 2019/9// PY - 2019/9// DO - 10.3168/jds.2019-16397 VL - 102 IS - 9 SP - 7800-7806 SN - 1525-3198 KW - fermentation KW - Streptococcus thermophilus KW - transcriptome KW - CRISPR ER - TY - JOUR TI - Risk Governance of Nanomaterials: Review of Criteria and Tools for Risk Communication, Evaluation, and Mitigation AU - Isigonis, Panagiotis AU - Hristozov, Danail AU - Benighaus, Christina AU - Giubilato, Elisa AU - Grieger, Khara AU - Pizzol, Lisa AU - Semenzin, Elena AU - Linkov, Igor AU - Zabeo, Alex AU - Marcomini, Antonio T2 - Nanomaterials AB - Nanotechnologies have been increasingly used in industrial applications and consumer products across several sectors, including construction, transportation, energy, and healthcare. The widespread application of these technologies has raised concerns regarding their environmental, health, societal, and economic impacts. This has led to the investment of enormous resources in Europe and beyond into the development of tools to facilitate the risk assessment and management of nanomaterials, and to inform more robust risk governance process. In this context, several risk governance frameworks have been developed. In our study, we present and review those, and identify a set of criteria and tools for risk evaluation, mitigation, and communication, the implementation of which can inform better risk management decision-making by various stakeholders from e.g., industry, regulators, and the civil society. Based on our analysis, we recommend specific methods from decision science and information technologies that can improve the existing risk governance tools so that they can communicate, evaluate, and mitigate risks more transparently, taking stakeholder perspectives and expert opinion into account, and considering all relevant criteria in establishing the risk-benefit balance of these emerging technologies to enable more robust decisions about the governance of their risks. DA - 2019/5/4/ PY - 2019/5/4/ DO - 10.3390/nano9050696 VL - 9 IS - 5 SP - 696 J2 - Nanomaterials LA - en OP - SN - 2079-4991 UR - http://dx.doi.org/10.3390/nano9050696 DB - Crossref KW - manufactured nanomaterials KW - risk governance KW - decision analysis KW - risk communication KW - risk perception KW - risk assessment KW - risk management ER - TY - JOUR TI - Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change AU - Todd, Erica V. AU - Ortega-Recalde, Oscar AU - Liu, Hui AU - Lamm, Melissa S. AU - Rutherford, Kim M. AU - Cross, Hugh AU - Black, Michael A. AU - Kardailsky, Olga AU - Marshall Graves, Jennifer A. AU - Hore, Timothy A. AU - Godwin, John R. AU - Gemmell, Neil J. T2 - Science Advances AB - Ovary-to-testis transformation in a sex-changing fish involves transcriptomic and epigenomic reprogramming. DA - 2019/7// PY - 2019/7// DO - 10.1126/sciadv.aaw7006 VL - 5 IS - 7 SP - eaaw7006 J2 - Sci. Adv. LA - en OP - SN - 2375-2548 UR - http://dx.doi.org/10.1126/sciadv.aaw7006 DB - Crossref ER - TY - JOUR TI - Wheat Straw Return Influences Nitrogen-Cycling and Pathogen Associated Soil Microbiota in a Wheat-Soybean Rotation System AU - Yang, Hongjun AU - Ma, Jiaxin AU - Rong, Zhenyang AU - Zeng, Dandan AU - Wang, Yuanchao AU - Hu, Shuijin AU - Ye, Wenwu AU - Zheng, Xiaobo T2 - FRONTIERS IN MICROBIOLOGY AB - Returning straw to soil is an effective way to sustain or improve soil quality and crop yields. However, a robust understanding of the impact of straw return on the composition of the soil microbial communities under field conditions has remained elusive. In this study, we characterized the effects of wheat straw return on soil bacterial and fungal communities in a wheat–soybean rotation system over a 3-yr period, using Illumina-based 16S rRNA and internal transcribed region (ITS) amplicon sequencing. Wheat straw return significantly affected the -diversity of the soil bacterial, but not fungal, community. It enhanced the relative abundance of the bacterial phylum Proteobacteria and the fungal phylum Zygomycota, but reduced that of the bacterial phylum Acidobacteria and the fungal phylum Ascomycota. Notably, it enriched the relative abundance of nitrogen-cycling bacterial genera such as Bradyrhizobium and Rhizobium. Analysis of soil chemical properties indicated that straw return soils had significantly higher total nitrogen contents than no straw return soils. In addition, the relative abundance of fungal genera containing pathogens was significantly lower in straw return soils relative to control soils, such as Fusarium, Alternaria, and Myrothecium. These results suggested a selection effect from the three-year continuous straw return treatment and the soil bacterial and fungal communities were moderately changed. DA - 2019/8/8/ PY - 2019/8/8/ DO - 10.3389/fmicb.2019.01811 VL - 10 SP - SN - 1664-302X KW - wheat straw return KW - wheat-soybean rotation KW - soil bacterial and fungal community KW - 16S rRNA and ITS amplicon sequencing KW - nitrogen-cycling microbe KW - plant pathogen ER - TY - JOUR TI - Lignocellulose solubilization and conversion by extremely thermophilic Caldicellulosiruptor bescii improves by maintaining metabolic activity AU - Straub, Christopher T. AU - Khatibi, Piyum A. AU - Otten, Jonathan K. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - BIOTECHNOLOGY AND BIOENGINEERING AB - The extreme thermophile Caldicellulosiruptor bescii solubilizes and metabolizes the carbohydrate content of lignocellulose, a process that ultimately ceases because of biomass recalcitrance, accumulation of fermentation products, inhibition by lignin moieties, and reduction of metabolic activity. Deconstruction of low loadings of lignocellulose (5 g/L), either natural or transgenic, whether unpretreated or subjected to hydrothermal processing, by C. bescii typically results in less than 40% carbohydrate solubilization. Mild alkali pretreatment (up to 0.09 g NaOH/g biomass) improved switchgrass carbohydrate solubilization by C. bescii to over 70% compared to less than 30% for no pretreatment, with two-thirds of the carbohydrate content in the treated switchgrass converted to acetate and lactate. C. bescii grown on high loadings of unpretreated switchgrass (50 g/L) retained in a pH-controlled bioreactor slowly purged (τ = 80 hr) with growth media without a carbon source improved carbohydrate solubilization to over 40% compared to batch culture at 29%. But more significant was the doubling of solubilized carbohydrate conversion to fermentation products, which increased from 40% in batch to over 80% in the purged system, an improvement attributed to maintaining the bioreactor culture in a metabolically active state. This strategy should be considered for optimizing solubilization and conversion of lignocellulose by C. bescii and other lignocellulolytic microorganisms. DA - 2019/8// PY - 2019/8// DO - 10.1002/bit.26993 VL - 116 IS - 8 SP - 1901-1908 SN - 1097-0290 KW - biofuels KW - bioreactor KW - Caldicellulosiruptor bescii KW - lignocellulose KW - switchgrass ER - TY - JOUR TI - Determinants of sulphur chemolithoautotrophy in the extremely thermoacidophilic Sulfolobales AU - Zeldes, Benjamin M. AU - Loder, Andrew J. AU - Counts, James A. AU - Haque, Mashkurul AU - Widney, Karl A. AU - Keller, Lisa M. AU - Albers, Sonja-Verena AU - Kelly, Robert M. T2 - ENVIRONMENTAL MICROBIOLOGY AB - Summary Species in the archaeal order Sulfolobales thrive in hot acid and exhibit remarkable metabolic diversity. Some species are chemolithoautotrophic, obtaining energy through the oxidation of inorganic substrates, sulphur in particular, and acquiring carbon through the 3‐hydroxypropionate/4‐hydroxybutyrate (3‐HP/4‐HB) CO 2 ‐fixation cycle. The current model for sulphur oxidation in the Sulfolobales is based on the biochemical analysis of specific proteins from Acidianus ambivalens , including sulphur oxygenase reductase (SOR) that disproportionates S° into H 2 S and sulphite (SO 3 2− ). Initial studies indicated SOR catalyses the essential first step in oxidation of elemental sulphur, but an ancillary role for SOR as a ‘recycle’ enzyme has also been proposed. Here, heterologous expression of both SOR and membrane‐bound thiosulphate‐quinone oxidoreductase (TQO) from Sulfolobus tokodaii ‘restored’ sulphur oxidation capacity in Sulfolobus acidocaldarius DSM639, but not autotrophy, although earlier reports indicate this strain was once capable of chemolithoautotrophy. Comparative transcriptomic analyses of Acidianus brierleyi , a chemolithoautotrophic sulphur oxidizer, and S. acidocaldarius DSM639 showed that while both share a strong transcriptional response to elemental sulphur, S. acidocaldarius DSM639 failed to upregulate key 3‐HP/4‐HB cycle genes used by A. brierleyi to drive chemolithoautotrophy. Thus, the inability for S. acidocaldarius DSM639 to grow chemolithoautotrophically may be rooted more in gene regulation than the biochemical capacity. DA - 2019/10// PY - 2019/10// DO - 10.1111/1462-2920.14712 VL - 21 IS - 10 SP - 3696-3710 SN - 1462-2920 ER - TY - JOUR TI - Synthetic Biology and the United Nations T2 - Trends in Biotechnology AB - Synthetic biology is a rapidly emerging interdisciplinary field of science and engineering that aims to redesign living systems through reprogramming genetic information. The field has catalysed global debate among policymakers and publics. Here we describe how synthetic biology relates to these international deliberations, particularly the Convention on Biological Diversity (CBD). DA - 2019/6// PY - 2019/6// DO - 10.1016/j.tibtech.2019.05.011 UR - http://dx.doi.org/10.1016/j.tibtech.2019.05.011 ER - TY - JOUR TI - Sensitivity of plant species to warming and altered precipitation dominates the community productivity in a semiarid grassland on the Loess Plateau AU - Su, Fanglong AU - Wei, Yanan AU - Wang, Fuwei AU - Guo, Jiuxin AU - Zhang, Juanjuan AU - Wang, Yi AU - Guo, Hui AU - Hu, Shuijin T2 - ECOLOGY AND EVOLUTION AB - Abstract Global warming and changes in precipitation patterns can critically influence the structure and productivity of terrestrial ecosystems. However, the underlying mechanisms are not fully understood. We conducted two independent but complementary experiments (one with warming and precipitation manipulation (+ or – 30%) and another with selective plant removal) in a semiarid grassland on the Loess Plateau, northwestern China, to assess how warming and altered precipitation affect plant community. Our results showed that warming and altered precipitation affected community aboveground net primary productivity (ANPP) through impacting soil moisture. Results of the removal experiment showed competitive relationships among dominant grasses, the dominant subshrub and nondominant species, which played a more important role than soil moisture in the response of plant community to warming and altered precipitation. Precipitation addition intensified the competition but primarily benefited the dominant subshrub. Warming and precipitation reduction enhanced water stresses but increased ANPP of the dominant subshrub and grasses, indicating that plant tolerance to drought critically meditated the community responses. These findings suggest that specie competitivity for water resources as well as tolerance to environmental stresses may dominate the responses of plant communities on the Loess Plateaus to future climate change factors. DA - 2019/7// PY - 2019/7// DO - 10.1002/ece3.5312 VL - 9 IS - 13 SP - 7628-7638 SN - 2045-7758 KW - aboveground net primary productivity KW - plant community KW - plant interspecific relationship KW - soil moisture KW - tolerance to drought ER - TY - JOUR TI - Complete Genome Sequence of Maize Mosaic Nucleorhabdovirus AU - Martin, Kathleen M. AU - Whitfield, Anna E. T2 - MICROBIOLOGY RESOURCE ANNOUNCEMENTS AB - The complete genome sequence of maize mosaic virus (MMV) was obtained using next-generation sequencing from infected Peregrinus maidis and rapid amplification of cDNA ends from infected Zea mays . The genome of MMV is 12,170 bases, and this project completed the 5′ and 3′ ends and amended the polymerase sequence. DA - 2019/7// PY - 2019/7// DO - 10.1128/MRA.00637-19 VL - 8 IS - 29 SP - SN - 2576-098X ER - TY - JOUR TI - Anticipating risks, governance needs, and public perceptions of de-extinction AU - Valdez, R.X. AU - Kuzma, J. AU - Cummings, C.L. AU - Nils Peterson, M. T2 - Journal of Responsible Innovation AB - Advances in biotechnology may allow for de-extinction. Potential impacts of de-extinct species remain uncertain; they may improve ecosystem function, or hinder conservation efforts and damage socio-ecological systems. To better anticipate de-extinction's outcomes, ethical dilemmas, and governance needs, we surveyed experts from multiple disciplinary backgrounds. We applied a mixed-method approach to our analysis, integrating quantitative responses of perceived outcomes with qualitative responses, to clarify and provide context. Overall, respondents indicated de-extinction was more likely to induce hazards, not benefits. Reasons for this viewpoint included a ‘moral hazard’ argument, suggesting conservation policies could be undermined if society perceives that species need less protection because they can be revived later. Pessimistic views of de-extinction were linked to concerns about unclear development paths. Experts believed the public might be skeptical about de-extinction. Our results suggest future de-extinction efforts may benefit from collaborative efforts to clarify hazards and explore salient concerns among the engaged public. DA - 2019/// PY - 2019/// DO - 10.1080/23299460.2019.1591145 VL - 6 IS - 2 SP - 211-231 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85063940651&partnerID=MN8TOARS KW - De-extinction KW - governance KW - environmental risk KW - moral risk KW - technological pessimism ER - TY - JOUR TI - Procedurally Robust Risk Assessment Framework for Novel Genetically Engineered Organisms and Gene Drives AU - Kuzma, Jennifer T2 - Regulation & Governance AB - Abstract In this article, a new framework for improving risk assessments of novel genetically engineered organisms (GEOs) is developed and applied. The Procedurally Robust Risk Assessment Framework (PRRAF) provides a set of principles and criteria for assessing and enhancing risk assessment protocols for GEOs under conditions of high uncertainty. The application of PRRAF is demonstrated using the case of a genetically engineered mosquito designed to kill its wild population and therefore decrease disease transmission. Assessments for regulatory approval of this genetically engineered insect fall short of several PPRAF criteria under the principles of humility, procedural validity, inclusion, anticipation, and reflexivity. With the emergence of GEOs designed to spread in ecosystems, such as those with gene drives, it will become increasingly important for regulatory agencies and technology developers to bolster their risk analysis methods and processes prior to field testing. PRRAF can be used as a flexible guide for doing so within a variety of institutional, regulatory, and governance contexts. DA - 2019/3/8/ PY - 2019/3/8/ DO - 10.1111/rego.12245 VL - 3 J2 - Regulation & Governance LA - en OP - SN - 1748-5983 1748-5991 UR - http://dx.doi.org/10.1111/rego.12245 DB - Crossref KW - gene drive KW - gene editing KW - GMO KW - governance KW - risk analysis ER - TY - JOUR TI - Colony Collapse and the Consequences of Bee Disease: Market Adaptation to Environmental Change AU - Rucker, Randal R. AU - Thurman, Walter N. AU - Burgett, Michael T2 - JOURNAL OF THE ASSOCIATION OF ENVIRONMENTAL AND RESOURCE ECONOMISTS AB - The most extensive markets for pollination services in the world are those for honey bee pollination in the United States. They play important roles in coordinating agricultural producers and migratory beekeepers, who both produce honey and provide pollination for crops. Recent trends in bee disease—including the still poorly understood colony collapse disorder, or CCD—can usefully be viewed in the context of how markets respond to environmental change. We analyze economic indicators of input and output markets related to managed honey bee operations, looking for effects from CCD. We find strong evidence of adaptation in these markets and remarkably little to suggest dramatic and widespread economic effects from CCD. DA - 2019/9/1/ PY - 2019/9/1/ DO - 10.1086/704360 VL - 6 IS - 5 SP - 927-960 SN - 2333-5963 KW - pollinator health KW - pollination markets KW - colony collapse disorder KW - honey bees KW - market adaptation ER - TY - JOUR TI - Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes AU - Conte, Matthew A. AU - Joshi, Rajesh AU - Moore, Emily C. AU - Nandamuri, Sri Pratima AU - Gammerdinger, William J. AU - Roberts, Reade B. AU - Carleton, Karen L. AU - Lien, Sigbjorn AU - Kocher, Thomas D. T2 - GIGASCIENCE AB - African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2–28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation. DA - 2019/4// PY - 2019/4// DO - 10.1093/gigascience/giz030 VL - 8 IS - 4 SP - SN - 2047-217X KW - genome assembly KW - African cichlids KW - comparative genomics KW - genome rearrangements KW - chromosome evolution KW - karyotype KW - inversion KW - recombination KW - transposable elements KW - genetic maps ER - TY - JOUR TI - Using Collaborative Cross Mouse Population to Fill Data Gaps in Risk Assessment: A Case Study of Population-Based Analysis of Toxicokinetics and Kidney Toxicodynamics of Tetrachloroethylene AU - Luo, Yu-Syuan AU - Cichocki, Joseph A. AU - Hsieh, Nan-Hung AU - Lewis, Lauren AU - Wright, Fred A. AU - Threadgill, David W. AU - Chiu, Weihsueh A. AU - Rusyn, Ivan T2 - ENVIRONMENTAL HEALTH PERSPECTIVES AB - Background: Interindividual variability in susceptibility remains poorly characterized for environmental chemicals such as tetrachloroethylene (PERC). Development of population-based experimental models provide a potential approach to fill this critical need in human health risk assessment. Objectives: In this study, we aimed to better characterize the contribution of glutathione (GSH) conjugation to kidney toxicity of PERC and the degree of associated interindividual toxicokinetic (TK) and toxicodynamic (TD) variability by using the Collaborative Cross (CC) mouse population. Methods: Male mice from 45 strains were intragastrically dosed with PERC (1,000mg/kg) or vehicle (5% Alkamuls EL-620 in saline), and time-course samples were collected for up to 24 h. Population variability in TK of S-(1,2,2-trichlorovinyl)GSH (TCVG), S-(1,2,2-trichlorovinyl)-L-cysteine (TCVC), and N-acetyl-S-(1,2,2-trichlorovinyl)-L-cysteine (NAcTCVC) was quantified in serum, liver, and kidney, and analyzed using a toxicokinetic model. Effects of PERC on kidney weight, fatty acid metabolism–associated genes [Acot1 (Acyl-CoA thioesterase 1), Fabp1 (fatty acid-binding protein 1), and Ehhadh (enoyl-coenzyme A, hydratase/3-hydroxyacyl coenzyme A dehydrogenase)], and a marker of proximal tubular injury [KIM-1 (kidney injury molecule-1)/Hepatitis A virus cellular receptor 1 (Havcr1)] were evaluated. Finally, quantitative data on interstrain variability in both formation of GSH conjugation metabolites of PERC and its kidney effects was used to calculate adjustment factors for the interindividual variability in both TK and TD. Results: Mice treated with PERC had significantly lower kidney weight, higher kidney-to-body weight (BW) ratio, and higher expression of fatty acid metabolism–associated genes (Acot1, Fabp1, and Ehhadh) and a marker of proximal tubular injury (KIM-1/Havcr1). Liver levels of TCVG were significantly correlated with KIM-1/Havcr1 in kidney, consistent with kidney injury being associated with GSH conjugation. We found that the default uncertainty factor for human variability may be marginally adequate to protect 95%, but not more, of the population for kidney toxicity mediated by PERC. Discussion: Overall, this study demonstrates the utility of the CC mouse population in characterizing metabolism–toxicity interactions and quantifying interindividual variability. Further refinement of the characterization of interindividual variability can be accomplished by incorporating these data into in silico population models both for TK (such as a physiologically based pharmacokinetic model), as well as for toxicodynamic responses. https://doi.org/10.1289/EHP5105 DA - 2019/6// PY - 2019/6// DO - 10.1289/EHP5105 VL - 127 IS - 6 SP - SN - 1552-9924 ER - TY - JOUR TI - The role of phenotypic plasticity and rapid adaptation in determining invasion success of Plantago virginica AU - Luo, , Xi AU - Xu, Xinyu AU - Zheng, Yi AU - Guo, Hui AU - Hu, Shuijin T2 - BIOLOGICAL INVASIONS DA - 2019/8// PY - 2019/8// DO - 10.1007/s10530-019-02004-x VL - 21 IS - 8 SP - 2679-2692 SN - 1573-1464 KW - Invasion success KW - Plantago virginica KW - Phenotypic plasticity KW - Rapid adaptation KW - Nitrogen addition KW - Invasive plant ER - TY - JOUR TI - From Ethylene-Auxin Interactions to Auxin Biosynthesis and Signal Integration AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - PLANT CELL AB - The field of plant hormone biology, like many other research areas in plant sciences, has benefited tremendously from the adoption of Arabidopsis ( Arabidopsis thaliana ) as a model system. The development of a great genetic toolbox in this species led to the identification of many of the core DA - 2019/7// PY - 2019/7// DO - 10.1105/tpc.19.00339 VL - 31 IS - 7 SP - 1393-1394 SN - 1532-298X UR - https://doi.org/10.1105/tpc.19.00339 ER - TY - JOUR TI - Landscape patterns in top-down control of decomposition: omnivory disrupts a tropical detrital-based trophic cascade AU - Simon, Troy N. AU - Binderup, Andrew J. AU - Flecker, Alex S. AU - Gilliam, James F. AU - Marshall, Michael C. AU - Thomas, Steven A. AU - Travis, Joseph AU - Reznick, David N. AU - Pringle, Catherine M. T2 - ECOLOGY AB - Detrital-based trophic cascades are often considered weak or absent in tropical stream ecosystems because of the prevalence of omnivorous macroconsumers and the dearth of leaf-shredding insects. In this study, we isolate top-down effects of three macroconsumer species on detrital processing in headwater streams draining Trinidad's northern mountains. We separated effects of different macroconsumers by experimentally manipulating their temporal access to isolated benthic habitat over the diel cycle. We found no evidence that omnivorous macroconsumers, including a freshwater crab (Eudaniela garmani) and guppy (Poecilia reticulata), increased leaf decomposition via consumption. By contrast, above a waterfall excluding guppies, the insectivorous killifish, Anablepsoides hartii, reduced the biomass of the leaf-shredding insect Phylloicus hansoni 4-fold, which consequently reduced leaf decomposition rates 1.6-fold. This detrital cascade did not occur below the barrier waterfall, where omnivorous guppies join the assemblage and reduce killifish densities; here killifish had no significant effects on Phylloicus or decomposition rates. These patterns of detrital processing were also observed in upstream–downstream comparisons in a landscape study across paired reaches of six streams. Above waterfalls, where killifish were present, but guppies absent, leaf decomposition rates and Phylloicus biomass were 2.5- and ~35-fold lower, respectively, compared to measurements below waterfalls. Moreover, the strength of top-down control by killifish is reflected by the 20- and 5-fold reductions in variability (±SE) surrounding mean Phylloicus biomass and leaf decomposition rates in upstream relative to downstream reaches where no top-down control was detected. Findings show a clear, detrital-based trophic cascade among killifish, a leaf-shredding insect, and leaf decomposition rates. Results also show how omnivorous guppies disrupt this cascade by depressing killifish densities, thereby releasing invertebrate shredders from predation, and significantly increasing decomposition rates. Moreover, this combination of direct and indirect trophic interactions drives patterns in decomposition rates in stream networks at a landscape scale, resulting in significantly lower rates of decomposition above vs. below barrier waterfalls. Our findings reveal that omnivory can result in significant indirect effects on a key ecosystem process, illustrating the importance of these hidden trophic pathways in detrital-based systems and suggesting that resource control in tropical systems may be even more complex than previously envisioned. DA - 2019/7// PY - 2019/7// DO - 10.1002/ecy.2723 VL - 100 IS - 7 ER - TY - JOUR TI - Do Bee Wings Adapt for Flight in Urban Environments? AU - Beasley, DeAnna E. AU - Fitzgerald, Jacquelyn L. AU - Fowler, Alison AU - Keleher, Kirsten AU - Lopez-Uribe, Margarita M. AU - Dunn, Robert R. T2 - SOUTHEASTERN NATURALIST AB - Understanding how organisms respond to urban-associated environmental changes is key to protecting vulnerable species. Bees, in particular, have gained interest due to their economic and ecological roles. We used a geometric morphometric approach to describe changes in wing shape and size in the solitary bee Andrena barbara (Barbara's Miner) collected across an urban landscape. We found that, although the wing morphology suggests a limited dispersal ability in its short and narrow frame, the urban landscape did not significantly explain how wing shape or size vary. Our findings are consistent with other studies that show little variation in wing morphology in urban solitary bees, and suggests that urban habitats may potentially serve an important role in bee conservation. DA - 2019/5// PY - 2019/5// DO - 10.1656/058.018.0210 VL - 18 IS - 2 SP - 183-191 SN - 1938-5412 ER - TY - JOUR TI - The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde 3-phosphate during glycolysis AU - Scott, Israel M. AU - Rubinstein, Gabriel M. AU - Poole, Farris L., II AU - Lipscomb, Gina L. AU - Schut, Gerrit J. AU - Williams-Rhaesa, Amanda M. AU - Stevenson, David M. AU - Amador-Noguez, Daniel AU - Kelly, Robert M. AU - Adams, Michael W. W. T2 - JOURNAL OF BIOLOGICAL CHEMISTRY AB - Caldicellulosiruptor bescii is an extremely thermophilic, cellulolytic bacterium with a growth optimum at 78 °C and is the most thermophilic cellulose degrader known. It is an attractive target for biotechnological applications, but metabolic engineering will require an in-depth understanding of its primary pathways. A previous analysis of its genome uncovered evidence that C. bescii may have a completely uncharacterized aspect to its redox metabolism, involving a tungsten-containing oxidoreductase of unknown function. Herein, we purified and characterized this new member of the aldehyde ferredoxin oxidoreductase family of tungstoenzymes. We show that it is a heterodimeric glyceraldehyde-3-phosphate (GAP) ferredoxin oxidoreductase (GOR) present not only in all known Caldicellulosiruptor species, but also in 44 mostly anaerobic bacterial genera. GOR is phylogenetically distinct from the monomeric GAP-oxidizing enzyme found previously in several Archaea. We found that its large subunit (GOR-L) contains a single tungstopterin site and one iron-sulfur [4Fe-4S] cluster, that the small subunit (GOR-S) contains four [4Fe-4S] clusters, and that GOR uses ferredoxin as an electron acceptor. Deletion of either subunit resulted in a distinct growth phenotype on both C5 and C6 sugars, with an increased lag phase, but higher cell densities. Using metabolomics and kinetic analyses, we show that GOR functions in parallel with the conventional GAP dehydrogenase, providing an alternative ferredoxin-dependent glycolytic pathway. These two pathways likely facilitate the recycling of reduced redox carriers (NADH and ferredoxin) in response to environmental H2 concentrations. This metabolic flexibility has important implications for the future engineering of this and related species. Caldicellulosiruptor bescii is an extremely thermophilic, cellulolytic bacterium with a growth optimum at 78 °C and is the most thermophilic cellulose degrader known. It is an attractive target for biotechnological applications, but metabolic engineering will require an in-depth understanding of its primary pathways. A previous analysis of its genome uncovered evidence that C. bescii may have a completely uncharacterized aspect to its redox metabolism, involving a tungsten-containing oxidoreductase of unknown function. Herein, we purified and characterized this new member of the aldehyde ferredoxin oxidoreductase family of tungstoenzymes. We show that it is a heterodimeric glyceraldehyde-3-phosphate (GAP) ferredoxin oxidoreductase (GOR) present not only in all known Caldicellulosiruptor species, but also in 44 mostly anaerobic bacterial genera. GOR is phylogenetically distinct from the monomeric GAP-oxidizing enzyme found previously in several Archaea. We found that its large subunit (GOR-L) contains a single tungstopterin site and one iron-sulfur [4Fe-4S] cluster, that the small subunit (GOR-S) contains four [4Fe-4S] clusters, and that GOR uses ferredoxin as an electron acceptor. Deletion of either subunit resulted in a distinct growth phenotype on both C5 and C6 sugars, with an increased lag phase, but higher cell densities. Using metabolomics and kinetic analyses, we show that GOR functions in parallel with the conventional GAP dehydrogenase, providing an alternative ferredoxin-dependent glycolytic pathway. These two pathways likely facilitate the recycling of reduced redox carriers (NADH and ferredoxin) in response to environmental H2 concentrations. This metabolic flexibility has important implications for the future engineering of this and related species. DA - 2019/6/21/ PY - 2019/6/21/ DO - 10.1074/jbc.RA118.007120 VL - 294 IS - 25 SP - 9995-10005 SN - 1083-351X KW - glycolysis KW - cellulose KW - metabolism KW - metabolomics KW - metalloenzyme KW - oxidation-reduction (redox) KW - anaerobic glycolysis KW - iron-sulfur protein KW - pterin KW - tungsten ER - TY - JOUR TI - Transfer Student Success: Exploring Community College, University, and Individual Predictors AU - Umbach, Paul D. AU - Tuchmayer, Jeremy B. AU - Clayton, Ashley B. AU - Smith, Kathleen N. T2 - COMMUNITY COLLEGE JOURNAL OF RESEARCH AND PRACTICE AB - This paper investigates community college transfer success by exploring the relationship between individual and institutional-level characteristics at students’ two- and four-year institutions. Using statewide administrative data from North Carolina, this study employs a cross-classified multilevel model to investigate the impact that a student’s community college and four-year transfer institution have on post-transfer success. Our findings offer important and compelling insights into the relationship between transfer students, the community college they attended, the four-year transfer institution, and educational outcomes. While individual effects were small, we find several institutional factors associated with student success. Attendance at a large community college or having a public university in the same county as their community college is positively associated with student success, whereas size of the university is negatively related to grades during the first year and persistence to the second year. While the four-year institution’s selectivity is negatively related to many of our outcomes, transferring to a Historically Black College or University is positively associated with GPA, college persistence, and degree completion. DA - 2019/// PY - 2019/// DO - 10.1080/10668926.2018.1520658 VL - 43 IS - 9 SP - 599-617 SN - 1521-0413 ER - TY - JOUR TI - Multi-attribute preferences for northern bobwhite habitat restoration among texas landowners AU - Valdez, Rene X. AU - Peterson, Markus J. AU - Peterson, Tarla Rai AU - Peterson, M. Nils AU - Perez, Robert M. T2 - WILDLIFE SOCIETY BULLETIN AB - ABSTRACT Northern bobwhite ( Colinus virginianus ) abundance has declined range‐wide over the long term due to factors such as habitat loss and deterioration. Private land management is critical to bobwhite conservation because most bobwhites occur on private lands, but little research has been conducted regarding how private land managers and landowners make decisions about whether and how to restore northern bobwhite habitat. To begin addressing this deficit, we used a choice‐based conjoint approach to determine how Texas, USA, landowners and land managers (surveyed in November 2017) weigh the importance of northern bobwhite hunting opportunities, costs, and labor when making habitat restoration decisions. We also used a latent class analysis to break respondents into segments based on their valuations of these attributes. The results of our latent class analysis indicate that managers and landowners can be grouped into several segments, and most segments do not place a high value on bobwhite hunting opportunities, but instead are more interested in minimizing out‐of‐pocket costs and labor input. Bobwhite habitat restoration programs yielding cost shares ≥50%, labor inputs at ≤30 days/year, and likely coveys flushed per hunting day >4 broadly appealed to landowners; however, ensuring low labor costs was most important, particularly for pragmatic landowners. This indicates that policies minimizing labor inputs and maximizing cost shares may be preferred over increasing hunting opportunities. Finally, we discuss the management preferences and practices of the segment most interested in maximizing bobwhite hunting opportunities and potential outreach strategies for segments of opportunistic and pragmatic landowners who may be persuaded to manage for bobwhite habitat if they perceived this management as economically viable. © 2019 The Authors. Wildlife Society Bulletin Published by Wiley Periodicals, Inc. DA - 2019/6// PY - 2019/6// DO - 10.1002/wsb.975 VL - 43 IS - 2 SP - 272-281 SN - 2328-5540 KW - choice-based conjoint analysis KW - Colinus virginianus KW - landowner preferences KW - latent class analysis KW - northern bobwhite KW - private lands conservation ER - TY - JOUR TI - Delivery of maize mosaic virus to planthopper vectors by microinjection increases infection efficiency and facilitates functional genomics experiments in the vector AU - Yao, Jianxiu AU - Rotenberg, Dorith AU - Whitfield, Anna E. T2 - JOURNAL OF VIROLOGICAL METHODS AB - The corn planthopper, Peregrinus maidis, not only causes direct damage to plants by feeding, but also transmits maize mosaic virus (MMV) to the plant hosts. The virus is transmitted in a propagative manner but the acquisition of MMV by the vector feeding on infected plants can result in low acquisition and inoculation efficiency. Here, we increased the acquisition efficiency by delivering the virus directly into the hemocoel through microinjection, which resulted in efficient virus infection of the insect and transmission to maize. We found that delivery of virus by injection of 10 ng MMV (50 nl, 200 μg/ml virions) into P. maidis resulted in 93% transmission efficiency. In dose-response experiments, MMV abundance in insects and transmission efficiency decreased as the amount of virus inoculum delivered into the hemocoel was reduced. Examination of virus distribution in the vector using immunolabeling and confocal microscopy revealed similar tissue distributions in the injected insects when compared to those of previous studies using feeding on plants for virus acquisition. The utility of virus inoculation by microinjection for functional analysis in virus-vector interaction was explored. Co-microinjection of MMV virions and the dsRNA of PI3Kδ (a transcript that is less abundant in MMV-infected insects), resulted in a reduction in PI3Kδ expression and higher virus titers in P. maidis. These findings demonstrated that virus microinjection is a robust method for obtaining large numbers of infected planthoppers that are competent in transmitting MMV and, in combination with RNAi, could significantly facilitate the functional analysis of P. maidis-MMV interactions. DA - 2019/8// PY - 2019/8// DO - 10.1016/j.jviromet.2019.05.010 VL - 270 SP - 153-162 ER - TY - JOUR TI - Migratory gauntlets on oceanic islands: Watershed disturbance increases the cost of amphidromy AU - Hain, Ernie F. AU - Moody, Kristine N. AU - Lamphere, Bradley A. AU - Nelson, Stacy A. C. AU - McIntyre, Peter B. AU - Gilliam, James F. AU - Blum, Michael J. T2 - ECOLOGY OF FRESHWATER FISH AB - Abstract Migratory fishes can be threatened by conditions encountered along dispersal pathways that impede access to feeding or breeding grounds. In this study, we tested the hypothesis that amphidromous fishes are equally or more sensitive to conditions along dispersal pathways than conditions in primary residential habitats. We did so by conducting distribution‐wide population surveys of all five amphidromous gobies native to the Hawaiian Islands to assess responses to in‐stream habitat, invasive species and watershed land use. We used Redundancy Analyses to assess whether goby densities varied according to local, downstream or upstream conditions. We found that population densities of the two non‐climbing species ( Eleotris sandwicensis , Stenogobius hawaiiensis ) varied according to local land use and local habitat conditions. Greater densities of E. sandwicensis also were found in watersheds with greater forest cover upstream of survey sites. Lower densities of two species that migrate farther inland ( Awaous stamineus , Sicyopterus stimpsoni ) were observed in watersheds with greater anthropogenic land use downstream or at the stream mouth. Population densities of E. sandwicensis and both Sicydiine species ( Lentipes concolor, S. stimpsoni ) also were lower when non‐native Poeciliids were locally present or present downstream in the watershed. These findings suggest that densities of native Hawaiian amphidromous fishes are equally or more sensitive to conditions along migratory pathways relative to conditions in primary residential habitats. Thus, alleviating pressures by removing invasive species and restoring habitat along dispersal pathways could be effective approaches to increasing densities of amphidromous species, especially those that migrate farther inland to higher elevations. DA - 2019/7// PY - 2019/7// DO - 10.1111/eff.12467 VL - 28 IS - 3 SP - 446-458 SN - 1600-0633 KW - biological invasions KW - diadromy KW - Gobiidae KW - Hawai'i KW - land use KW - Poeciliidae ER - TY - JOUR TI - Extraction of Plant DNA by Microneedle Patch for Rapid Detection of Plant Diseases AU - Paul, Rajesh AU - Saville, Amanda C. AU - Hansel, Jeana C. AU - Ye, Yanqi AU - Ball, Carmin AU - Williams, Alyssa AU - Chang, Xinyuan AU - Chen, Guojun AU - Gu, Zhen AU - Ristaino, Jean B. AU - Wei, Qingshan T2 - ACS Nano AB - In-field molecular diagnosis of plant diseases via nucleic acid amplification is currently limited by cumbersome protocols for extracting and isolating pathogenic DNA from plant tissues. To address this challenge, a rapid plant DNA extraction method was developed using a disposable polymeric microneedle (MN) patch. By applying MN patches on plant leaves, amplification-assay-ready DNA can be extracted within a minute from different plant species. MN-extracted DNA was used for direct polymerase chain reaction amplification of plant plastid DNA without purification. Furthermore, using this patch device, extraction of plant pathogen DNA (Phytophthora infestans) from both laboratory-inoculated and field-infected leaf samples was performed for detection of late blight disease in tomato. MN extraction achieved 100% detection rate of late blight infections for samples after 3 days of inoculation when compared to the conventional gold standard cetyltrimethylammonium bromide (CTAB)-based DNA extraction method and 100% detection rate for all blind field samples tested. This simple, cell-lysis-free, and purification-free DNA extraction method could be a transformative approach to facilitate rapid sample preparation for molecular diagnosis of various plant diseases directly in the field. DA - 2019/6/9/ PY - 2019/6/9/ DO - 10.1021/acsnano.9b00193 VL - 13 IS - 6 SP - 6540-6549 J2 - ACS Nano LA - en OP - SN - 1936-0851 1936-086X UR - http://dx.doi.org/10.1021/acsnano.9b00193 DB - Crossref KW - plant disease KW - DNA extraction KW - microneedle patch KW - Phytophthora infestans KW - nucleic acid amplification KW - point-of-care diagnostics ER - TY - JOUR TI - A Resilience Approach to Community-Scale Climate Adaptation AU - Choko, Onyinye Prince AU - Olabisi, Laura Schmitt AU - Onyeneke, Robert Ugochukwu AU - Chiemela, Stella Nwawulu AU - Liverpool-Tasie, Lenis Saweda O. AU - Rivers, Louie, III T2 - SUSTAINABILITY AB - Climate risk is expected to impact rural communities in West Africa in multiple ways. However, most current research addresses resilience and climate adaptation at either the national or the household scale; very little is known about community-scale interventions. We interviewed 934 community members in six communities in southeastern Nigeria about sources of climate risk and community-based actions for climate change adaptation. We found these communities contained multiple active and engaged groups that have implemented a wide range of interventions to reduce climate risk, most of which are seen as effective by community members. Flooding was the most common form of risk in this region, but drought, windstorms, and irregular rainy seasons are also frequent, implying that effective climate adaptation will have to be sensitive to multiple types of risk. Structural interventions (constructing roads, bridges, etc.) were the most common type of intervention, suggesting that communities are capable of marshalling considerable organizational and human power for adaptation efforts, even in the absence of external assistance. Efforts to boost community resilience and adaptation to climate change would benefit from first understanding what community actions are currently underway, and working with the groups implementing these actions to support and extend them. DA - 2019/6/1/ PY - 2019/6/1/ DO - 10.3390/su11113100 VL - 11 IS - 11 SP - SN - 2071-1050 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85067305236&partnerID=MN8TOARS KW - climate change KW - resilience KW - community adaptation KW - Nigeria KW - flooding ER - TY - JOUR TI - Effects of Co-occurring Species Present in Swine Lagoons on Adsorption of Copper on Eggshell AU - Hess, Brianna J. AU - Kolar, Praveen AU - Classen, John J. AU - Knappe, Detlef AU - Cheng, Jay J. T2 - INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH DA - 2019/8// PY - 2019/8// DO - 10.1007/s41742-019-00203-x VL - 13 IS - 4 SP - 613-622 SN - 2008-2304 KW - Adsorption KW - Eggshell KW - Copper KW - Swine lagoons KW - Acetate KW - Ammonia ER - TY - JOUR TI - Rethinking restoration targets for American chestnut using species distribution modeling AU - Barnes, Jessica Cavin AU - Delborne, Jason A. T2 - Biodiversity and Conservation DA - 2019/7/2/ PY - 2019/7/2/ DO - 10.1007/s10531-019-01814-8 VL - 28 IS - 12 SP - 3199-3220 J2 - Biodivers Conserv LA - en OP - SN - 0960-3115 1572-9710 UR - http://dx.doi.org/10.1007/s10531-019-01814-8 DB - Crossref KW - Assisted evolution KW - Climate change KW - Forest biotechnology KW - Maxent KW - Niche model KW - Range shift 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, Craig AU - Zeng, Zhao-Bang AB - Abstract The hexaploid sweetpotato ( Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and has 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 implemented 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 - 2019/7/2/ PY - 2019/7/2/ DO - 10.1101/689638 VL - 7 UR - https://doi.org/10.1101/689638 ER - TY - JOUR TI - Conservation and diversity in expression of candidate genes regulating socially-induced female-male sex change in wrasses AU - Thomas, Jodi T. AU - Todd, Erica V AU - Muncaster, Simon AU - Lokman, P. Mark AU - Damsteegt, Erin L. AU - Liu, Hui AU - Soyano, Kiyoshi AU - Gleonnec, Florence AU - Lamm, Melissa S. AU - Godwin, John R. AU - Gemmell, Neil J. T2 - PEERJ AB - Fishes exhibit remarkably diverse, and plastic, patterns of sexual development, most striking of which is sequential hermaphroditism, where individuals readily reverse sex in adulthood. How this stunning example of phenotypic plasticity is controlled at a genetic level remains poorly understood. Several genes have been implicated in regulating sex change, yet the degree to which a conserved genetic machinery orchestrates this process has not yet been addressed. Using captive and in-the-field social manipulations to initiate sex change, combined with a comparative qPCR approach, we compared expression patterns of four candidate regulatory genes among three species of wrasses (Labridae)-a large and diverse teleost family where female-to-male sex change is pervasive, socially-cued, and likely ancestral. Expression in brain and gonadal tissues were compared among the iconic tropical bluehead wrasse (Thalassoma bifasciatum) and the temperate spotty (Notolabrus celidotus) and kyusen (Parajulus poecilepterus) wrasses. In all three species, gonadal sex change was preceded by downregulation of cyp19a1a (encoding gonadal aromatase that converts androgens to oestrogens) and accompanied by upregulation of amh (encoding anti-müllerian hormone that primarily regulates male germ cell development), and these genes may act concurrently to orchestrate ovary-testis transformation. In the brain, our data argue against a role for brain aromatase (cyp19a1b) in initiating behavioural sex change, as its expression trailed behavioural changes. However, we find that isotocin (it, that regulates teleost socio-sexual behaviours) expression correlated with dominant male-specific behaviours in the bluehead wrasse, suggesting it upregulation mediates the rapid behavioural sex change characteristic of blueheads and other tropical wrasses. However, it expression was not sex-biased in temperate spotty and kyusen wrasses, where sex change is more protracted and social groups may be less tightly-structured. Together, these findings suggest that while key components of the molecular machinery controlling gonadal sex change are phylogenetically conserved among wrasses, neural pathways governing behavioural sex change may be more variable. DA - 2019/6/11/ PY - 2019/6/11/ DO - 10.7717/peerj.7032 VL - 7 SP - SN - 2167-8359 KW - Protogynous sex change KW - Bluehead wrasse KW - Spotty wrasse KW - Kyusen wrasse KW - Quantitative real-time PCR KW - Sex-biased gene expression KW - cyp19a1a KW - cyp19a1b KW - amh KW - Isotocin ER - TY - JOUR TI - Divergent responses of leaf N:P:K stoichiometry to nitrogen fertilization in rice and weeds AU - Sun, Xiao AU - Guo, Jiuxin AU - Guo, Shiwei AU - Guo, Hui AU - Hu, Shuijin T2 - WEED SCIENCE AB - Abstract Nitrogen (N) inputs have been found to exert strong influence on leaf stoichiometry in natural ecosystems, but there are few studies investigating the effects of N in agroecosystems. Using a 5-yr fertilization experiment in rice fields, we examined the effects of N inputs on leaf stoichiometry of one crop, rice ( Oryza sativa L.), and its four common weeds, barnyardgrass [ Echinochloa crus-galli (L.) P. Beauv.], Monochoria korsakowii Regel and Mack, alligatorweed [ Alternanthera philoxeroides (Mart.) Griseb.], and Japanese mazus [ Mazus pumilus (Burm. f.) Steenis], and further evaluated whether and how straw return mediates these effects. We found that rice and weed leaf nitrogen:phosphorus:potassium (N:P:K) stoichiometry exhibited divergent responses to N fertilizer. Weed leaf N:P:K stoichiometry was not sensitive to low (120 kg N ha −1 ) and regular (240 kg N ha −1 ) N inputs, but rice plants were, with significantly increased leaf N concentration and N:P and N:K ratios. The opposite trend was found for high N inputs (360 kg N ha −1 ). Rice leaf N concentration [N] did not increase further, and N:P ratios even decreased, whereas E. crus-galli and M. korsakowii had significantly increased [N] and N-related stoichiometry. We also found that the positive effects of regular N inputs on rice leaf N:P and N:K ratios were significantly dampened by straw return, but the positive effects on N:P ratios in M. pumilus leaves were enhanced by straw return. Compared with weeds, rice leaves contained low elemental concentrations across fertilization levels at grain-filling stages. These results indicate that rice has a lower N requirement than weeds at grain-filling stages, and the N supply should be managed at a relative low level to reduce the nutrient acquisition and competitive abilities of weeds. From a stoichiometric perspective, this study highlights the importance of N management in combination with straw return in controlling weeds and increasing the nutrient-use efficiency of crops. DA - 2019/5// PY - 2019/5// DO - 10.1017/wsc.2019.7 VL - 67 IS - 3 SP - 339-345 SN - 1550-2759 KW - Agroecosystem KW - M KW - pumilus KW - Oryza sativa KW - straw return ER - TY - JOUR TI - Variation in tolerance mechanisms to fluazifop-P-butyl among selected zoysiagrass lines AU - Liu, Wenwen AU - MacDonald, Gregory E. AU - Unruh, J. Bryan AU - Kenworthy, Kevin E. AU - Trenholm, Laurie E. AU - Leon, Ramon G. T2 - WEED SCIENCE AB - Abstract Breeding herbicide tolerance into new cultivars can improve safety and weed control in turfgrass systems. The sensitivity to fluazifop-P-butyl of 27 zoysiagrass ( Zoysia spp.) lines was screened under greenhouse conditions to identify potential tolerant germplasm for breeding programs. The herbicide rate that caused 50% biomass reduction (GR 50 ) and the rate that caused 50% injury (ID 50 ) were calculated to select the three most-tolerant and the five most-susceptible lines for studying the physiological mechanisms responsible for fluazifop-P-butyl tolerance. The differences in GR 50 and ID 50 between susceptible and tolerant lines ranged from 4-fold to more than 10-fold. Cytochrome P450–mediated metabolism was not detected in fluazifop-P-butyl–tolerant lines. Sequencing of the ACCase gene confirmed that none of the seven previously reported mutations conferring resistance to acetyl-CoA carboxylase (ACCase)-inhibiting herbicides in other species were present in any of the tolerant or susceptible zoysiagrass lines studied. An Ala-2073-Thr substitution was identified in two tolerant lines, but this mutation did not completely explain the tolerant phenotype. No clear differences in absorption and translocation rates of 14 C-radiolabeled fluazifop-P-butyl were observed among most lines, with the exception of a susceptible line that exhibited greater translocation than two of the tolerant lines. Metabolite profiles did not differ between tolerant and susceptible lines. Our results suggest that the diversity in tolerance to fluazifop-P-butyl in zoysiagrass germplasm is most likely the result of a combination of different, minor, additive non–target site mechanisms such as translocation rate and compartmentation after absorption. DA - 2019/5// PY - 2019/5// DO - 10.1017/wsc.2019.6 VL - 67 IS - 3 SP - 288-295 SN - 1550-2759 UR - https://doi.org/10.1017/wsc.2019.6 KW - ACCase KW - Acetyl-coenzyme A carboxylase KW - genetic diversity KW - graminicide KW - herbicide resistance ER - TY - JOUR TI - Influences of multiple clay minerals on the phosphorus transport driven by Aspergillus niger AU - Zhang, Lin AU - Hu, Yunxiao AU - Han, Feiyu AU - Wu, Yiling AU - Tian, Da AU - Su, Mu AU - Wang, Shimei AU - Li, Zhen AU - Hu, Shuijin T2 - APPLIED CLAY SCIENCE AB - Phosphorus (P) is a major limiting nutrient for plant growth. Clay minerals are able to work as active centers in soil system due to their high surface area and CEC. Yet, effects of clay minerals on P biogeochemical cycle driven by microorganisms are still unclear. In this study, hydroxylapatite and three typical clay minerals (kaolinite, palygorskite, and montmorillonite) were incubated with Aspergillus niger to investigate microbial influences on P release and adsorption. Due to the mineral particles, hyphae wrapped small montmorillonite particles (<10 μm, confirmed by SEM and TEM), which promoted microbial bioactivities, e.g., respiration and acid production. P consumption by the fungus lowered the available P from 143 to 68 ppm. Meanwhile, ATR-IR spectra and HPLC analysis confirmed the intense adsorption of oxalic acid (the primary microbial secretion) onto montmorillonite. Despite the higher acid production, both the high adsorption capability of the clay and the acid consumed by phosphate dissolution caused that pH values increased from ~2 to ~4 after montmorillonite addition. In contrast, low CEC, dispersibility, and surface area of kaolinite and palygorskite limited their ability to enhance microbial activities and the subsequent interactions with hyphae. Therefore, clay minerals, especially montmorillonite, can drive P transport with the favor from fungi in ecosystem. DA - 2019/9/1/ PY - 2019/9/1/ DO - 10.1016/j.clay.2019.04.026 VL - 177 SP - 12-18 SN - 1872-9053 KW - A. niger KW - Clay minerals KW - Morphology KW - Oxalic acid KW - P KW - Respiration ER - TY - JOUR TI - RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data AU - Perkins, Patrick AU - Mazzoni-Putman, Serina AU - Stepanova, Anna AU - Alonso, Jose AU - Heber, Steffen T2 - BMC GENOMICS AB - Ribo-seq is a popular technique for studying translation and its regulation. A Ribo-seq experiment produces a snap-shot of the location and abundance of actively translating ribosomes within a cell's transcriptome. In practice, Ribo-seq data analysis can be sensitive to quality issues such as read length variation, low read periodicities, and contaminations with ribosomal and transfer RNA. Various software tools for data preprocessing, quality assessment, analysis, and visualization of Ribo-seq data have been developed. However, many of these tools require considerable practical knowledge of software applications, and often multiple different tools have to be used in combination with each other.We present riboStreamR, a comprehensive Ribo-seq quality control (QC) platform in the form of an R Shiny web application. RiboStreamR provides visualization and analysis tools for various Ribo-seq QC metrics, including read length distribution, read periodicity, and translational efficiency. Our platform is focused on providing a user-friendly experience, and includes various options for graphical customization, report generation, and anomaly detection within Ribo-seq datasets.RiboStreamR takes advantage of the vast resources provided by the R and Bioconductor environments, and utilizes the Shiny R package to ensure a high level of usability. Our goal is to develop a tool which facilitates in-depth quality assessment of Ribo-seq data by providing reference datasets and automatically highlighting quality issues and anomalies within datasets. DA - 2019/6/6/ PY - 2019/6/6/ DO - 10.1186/s12864-019-5700-7 VL - 20 SP - SN - 1471-2164 KW - Ribo-seq KW - Next-generation sequencing KW - Data analysis KW - Web application ER - TY - JOUR TI - Taxonomy of the order Bunyavirales: update 2019 AU - Abudurexiti, Abulikemu AU - Adkins, Scott AU - Alioto, Daniela AU - Alkhovsky, Sergey V. AU - Avsic-Zupanc, Tatjana AU - Ballinger, Matthew J. AU - Bente, Dennis A. AU - Beer, Martin AU - Bergeron, Eric AU - Blair, Carol D. AU - Briese, Thomas AU - Buchmeier, Michael J. AU - Burt, Felicity J. AU - Calisher, Charles H. AU - Chang, Chenchen AU - Charrel, Remi N. AU - Choi, Il Ryong AU - Clegg, J. Christopher S. AU - Torre, Juan Carlos AU - Lamballerie, Xavier AU - Deng, Fei AU - Di Serio, Francesco AU - Digiaro, Michele AU - Drebot, Michael A. AU - Duan, Xiaomei AU - Ebihara, Hideki AU - Elbeaino, Toufic AU - Ergunay, Koray AU - Fulhorst, Charles F. AU - Garrison, Aura R. AU - Gao, George Fu AU - Gonzalez, Jean-Paul J. AU - Groschup, Martin H. AU - Guenther, Stephan AU - Haenni, Anne-Lise AU - Hall, Roy A. AU - Hepojoki, Jussi AU - Hewson, Roger AU - Hu, Zhihong AU - Hughes, Holly R. AU - Jonson, Miranda Gilda AU - Junglen, Sandra AU - Klempa, Boris AU - Klingstrom, Jonas AU - Kou, Chun AU - Laenen, Lies AU - Lambert, Amy J. AU - Langevin, Stanley A. AU - Liu, Dan AU - Lukashevich, Igor S. AU - Luo, Tao AU - Lu, Chuanwei AU - Maes, Piet AU - Souza, William Marciel AU - Marklewitz, Marco AU - Martelli, Giovanni P. AU - Matsuno, Keita AU - Mielke-Ehret, Nicole AU - Minutolo, Maria AU - Mirazimi, Ali AU - Moming, Abulimiti AU - Muehlbach, Hans-Peter AU - Naidu, Rayapati AU - Navarro, Beatriz AU - Teixeira Nunes, Marcio Roberto AU - Palacios, Gustavo AU - Papa, Anna AU - Pauvolid-Correa, Alex AU - Paweska, Janusz T. AU - Qiao, Jie AU - Radoshitzky, Sheli R. AU - Resende, Renato O. AU - Romanowski, Victor AU - Sall, Amadou Alpha AU - Salvato, Maria S. AU - Sasaya, Takahide AU - Shen, Shu AU - Shi, Xiaohong AU - Shirako, Yukio AU - Simmonds, Peter AU - Sironi, Manuela AU - Song, Jin-Won AU - Spengler, Jessica R. AU - Stenglein, Mark D. AU - Su, Zhengyuan AU - Sun, Surong AU - Tang, Shuang AU - Turina, Massimo AU - Wang, Bo AU - Wang, Cheng AU - Wang, Hualin AU - Wang, Jun AU - Wei, Taiyun AU - Whitfield, Anna E. AU - Zerbini, F. Murilo AU - Zhang, Jingyuan AU - Zhang, Lei AU - Zhang, Yanfang AU - Zhang, Yong-Zhen AU - Zhang, Yujiang AU - Zhou, Xueping AU - Zhu, Liying AU - Kuhn, Jens H. T2 - ARCHIVES OF VIROLOGY AB - In February 2019, following the annual taxon ratification vote, the order Bunyavirales was amended by creation of two new families, four new subfamilies, 11 new genera and 77 new species, merging of two species, and deletion of one species. This article presents the updated taxonomy of the order Bunyavirales now accepted by the International Committee on Taxonomy of Viruses (ICTV). DA - 2019/7// PY - 2019/7// DO - 10.1007/s00705-019-04253-6 VL - 164 IS - 7 SP - 1949-1965 SN - 1432-8798 ER - TY - JOUR TI - Taxonomy of the order Mononegavirales: update 2019 AU - Amarasinghe, Gaya K. AU - Ayllon, Maria A. AU - Bao, Yiming AU - Basler, Christopher F. AU - Bavari, Sina AU - Blasdell, Kim R. AU - Briese, Thomas AU - Brown, Paul A. AU - Bukreyev, Alexander AU - Balkema-Buschmann, Anne AU - Buchholz, Ursula J. AU - Chabi-Jesus, Camila AU - Chandran, Kartik AU - Chiapponi, Chiara AU - Crozier, Ian AU - Swart, Rik L. AU - Dietzgen, Ralf G. AU - Dolnik, Olga AU - Drexler, Jan F. AU - Duerrwald, Ralf AU - Dundon, William G. AU - Duprex, W. Paul AU - Dye, John M. AU - Easton, Andrew J. AU - Fooks, Anthony R. AU - Formenty, Pierre B. H. AU - Fouchier, Ron A. M. AU - Freitas-Astua, Juliana AU - Griffiths, Anthony AU - Hewson, Roger AU - Horie, Masayuki AU - Hyndman, Timothy H. AU - Jiang, Daohong AU - Kitajima, Elliott W. AU - Kobinger, Gary P. AU - Kondo, Hideki AU - Kurath, Gael AU - Kuzmin, Ivan V. AU - Lamb, Robert A. AU - Lavazza, Antonio AU - Lee, Benhur AU - Lelli, Davide AU - Leroy, Eric M. AU - Li, Jianrong AU - Maes, Piet AU - Marzano, Shin-Yi L. AU - Moreno, Ana AU - Muhlberger, Elke AU - Netesov, Sergey V. AU - Nowotny, Norbert AU - Nylund, Are AU - Okland, Arnfinn L. AU - Palacios, Gustavo AU - Palyi, Bernadett AU - Paweska, Janusz T. AU - Payne, Susan L. AU - Prosperi, Alice AU - Ramos-Gonzalez, Pedro Luis AU - Rima, Bertus K. AU - Rota, Paul AU - Rubbenstroth, Dennis AU - Shi, Mang AU - Simmonds, Peter AU - Smither, Sophie J. AU - Sozzi, Enrica AU - Spann, Kirsten AU - Stenglein, Mark D. AU - Stone, David M. AU - Takada, Ayato AU - Tesh, Robert B. AU - Tomonaga, Keizo AU - Tordo, Noel AU - Towner, Jonathan S. AU - Hoogen, Bernadette AU - Vasilakis, Nikos AU - Wahl, Victoria AU - Walker, Peter J. AU - Wang, Lin-Fa AU - Whitfield, Anna E. AU - Williams, John V. AU - Zerbini, F. Murilo AU - Zhang, Tao AU - Zhang, Yong-Zhen AU - Kuhn, Jens H. T2 - ARCHIVES OF VIROLOGY AB - In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). DA - 2019/7// PY - 2019/7// DO - 10.1007/s00705-019-04247-4 VL - 164 IS - 7 SP - 1967-1980 SN - 1432-8798 ER - TY - JOUR TI - Genetics of cocaine and methamphetamine consumption and preference in Drosophila melanogaster AU - Highfill, Chad A. AU - Baker, Brandon M. AU - Stevens, Stephenie D. AU - Anholt, Robert R. H. AU - Mackay, Trudy F. C. T2 - PLOS GENETICS AB - Illicit use of psychostimulants, such as cocaine and methamphetamine, constitutes a significant public health problem. Whereas neural mechanisms that mediate the effects of these drugs are well-characterized, genetic factors that account for individual variation in susceptibility to substance abuse and addiction remain largely unknown. Drosophila melanogaster can serve as a translational model for studies on substance abuse, since flies have a dopamine transporter that can bind cocaine and methamphetamine, and exposure to these compounds elicits effects similar to those observed in people, suggesting conserved evolutionary mechanisms underlying drug responses. Here, we used the D. melanogaster Genetic Reference Panel to investigate the genetic basis for variation in psychostimulant drug consumption, to determine whether similar or distinct genetic networks underlie variation in consumption of cocaine and methamphetamine, and to assess the extent of sexual dimorphism and effect of genetic context on variation in voluntary drug consumption. Quantification of natural genetic variation in voluntary consumption, preference, and change in consumption and preference over time for cocaine and methamphetamine uncovered significant genetic variation for all traits, including sex-, exposure- and drug-specific genetic variation. Genome wide association analyses identified both shared and drug-specific candidate genes, which could be integrated in genetic interaction networks. We assessed the effects of ubiquitous RNA interference (RNAi) on consumption behaviors for 34 candidate genes: all affected at least one behavior. Finally, we utilized RNAi knockdown in the nervous system to implicate dopaminergic neurons and the mushroom bodies as part of the neural circuitry underlying experience-dependent development of drug preference. DA - 2019/5// PY - 2019/5// DO - 10.1371/journal.pgen.1007834 VL - 15 IS - 5 SP - SN - 1553-7404 ER - TY - JOUR TI - "Yes, and ... *" continuing the scholarly conversation about contingent labor in higher education AU - Rudick, C. Kyle AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - In the past month, I (Dannels) was in a discussion with a long-time contingent faculty member in our college about her experiences in that role. She shared with me the following: It is kind of like... DA - 2019/// PY - 2019/// DO - 10.1080/03634523.2019.1572198 VL - 68 IS - 2 SP - 259-263 SN - 1479-5795 ER - TY - JOUR TI - "Yes, and ... *": continuing the scholarly conversation about mentoring in higher education AU - Rudick, C. Kyle AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - I just want to recover. I want a reset button. It is one thing feeling like you do not belong in graduate school. It is another thing being told you do not belong here by the person you moved acros... DA - 2019/// PY - 2019/// DO - 10.1080/03634523.2018.1538523 VL - 68 IS - 1 SP - 128-131 SN - 1479-5795 ER - TY - JOUR TI - "Yes, and ... *": continuing the scholarly conversation about the dark side of social media AU - Rudick, C. Kyle AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - “I don’t want to attend class because the student who wrote those racist comments is in my class, and I do not want to be in class with him.” “Someone posted my address and threatened to burn down ... DA - 2019/// PY - 2019/// DO - 10.1080/03634523.2019.1608663 VL - 68 IS - 3 SP - 393-398 SN - 1479-5795 ER - TY - JOUR TI - Animal production, insecticide use and self-reported symptoms and diagnoses of COPD, including chronic bronchitis, in the Agricultural Health Study AU - Rinsky, Jessica L. AU - Richardson, David B. AU - Kreiss, Kathleen AU - Nylander-French, Leena AU - Freeman, Laura E. Beane AU - London, Stephanie J. AU - Henneberger, Paul K. AU - Hoppin, Jane A. T2 - ENVIRONMENT INTERNATIONAL AB - Occupational exposure to animal production is associated with chronic bronchitis symptoms; however, few studies consider associations with chronic obstructive pulmonary disease (COPD). We estimated associations between animal production activities and prevalence of self-reported COPD among farmers in the Agricultural Health Study.During a 2005-2010 interview, farmers self-reported information about: their operations (i.e., size, type, number of animals, insecticide use), respiratory symptoms, and COPD diagnoses (i.e., COPD, chronic bronchitis, emphysema). Operations were classified as small or medium/large based on regulatory definitions. Farmers were classified as having a COPD diagnosis, chronic bronchitis symptoms (cough and phlegm for ≥3 months during 2 consecutive years), or both. Polytomous logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI).Of 22,491 participating farmers (median age: 59 years), 922 (4%) reported a COPD diagnosis only, 254 (1%) reported a diagnosis and symptoms, and 962 (4%) reported symptoms only. Compared to raising no commercial animals, raising animals on a medium/large operation was positively associated with chronic bronchitis symptoms with (OR: 1.59; 95% CI: 1.16, 2.18) and without a diagnosis (OR: 1.69; 95% CI: 1.42, 2.01). Ever use of multiple organophosphates, carbaryl, lindane, and permethrin were positively associated with chronic bronchitis symptoms.Animal production work, including insecticide use, was positively associated with chronic bronchitis symptoms; but not consistently with COPD diagnosis alone. Our results support the need for further investigation into the role of animal production-related exposures in the etiology of COPD and better respiratory protection for agricultural workers. DA - 2019/6// PY - 2019/6// DO - 10.1016/j.envint.2019.02.049 VL - 127 SP - 764-772 SN - 1873-6750 KW - Epidemiology KW - Occupational health KW - Environmental health KW - Pesticide ER - TY - JOUR TI - Population-Based Analysis of DNA Damage and Epigenetic Effects of 1,3-Butadiene in the Mouse AU - Lewis, Lauren AU - Borowa-Mazgaj, Barbara AU - Conti, Aline AU - Chappell, Grace A. AU - Luo, Yu-Syuan AU - Bodnar, Wanda AU - Konganti, Kranti AU - Wright, Fred A. AU - Threadgill, David W. AU - Chiu, Weihsueh A. AU - Pogribny, Igor P. AU - Rusyn, Ivan T2 - CHEMICAL RESEARCH IN TOXICOLOGY AB - Metabolism of 1,3-butadiene, a known human and rodent carcinogen, results in formation of reactive epoxides, a key event in its carcinogenicity. Although mice exposed to 1,3-butadiene present DNA adducts in all tested tissues, carcinogenicity is limited to liver, lung, and lymphoid tissues. Previous studies demonstrated that strain- and tissue-specific epigenetic effects in response to 1,3-butadiene exposure may influence susceptibly to DNA damage and serve as a potential mechanism of tissue-specific carcinogenicity. This study aimed to investigate interindividual variability in the effects of 1,3-butadiene using a population-based mouse model. Male mice from 20 Collaborative Cross strains were exposed to 0 or 635 ppm 1,3-butadiene by inhalation (6 h/day, 5 days/week) for 2 weeks. We evaluated DNA damage and epigenetic effects in target (lung and liver) and nontarget (kidney) tissues of 1,3-butadiene-induced carcinogenesis. DNA damage was assessed by measuring N-7-(2,3,4-trihydroxybut-1-yl)-guanine (THB-Gua) adducts. To investigate global histone modification alterations, we evaluated the trimethylation and acetylation of histones H3 and H4 across tissues. Changes in global cytosine DNA methylation were evaluated from the levels of methylation of LINE-1 and SINE B1 retrotransposons. We quantified the degree of variation across strains, deriving a chemical-specific human variability factor to address population variability in carcinogenic risk, which is largely ignored in current cancer risk assessment practice. Quantitative trait locus mapping identified four candidate genes related to chromatin remodeling whose variation was associated with interstrain susceptibility. Overall, this study uses 1,3-butadiene to demonstrate how the Collaborative Cross mouse population can be used to identify the mechanisms for and quantify the degree of interindividual variability in tissue-specific effects that are relevant to chemically induced carcinogenesis. DA - 2019/5// PY - 2019/5// DO - 10.1021/acs.chemrestox.9b00035 VL - 32 IS - 5 SP - 887-898 SN - 1520-5010 ER - TY - JOUR TI - Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci AU - Varble, Andrew AU - Meaden, Sean AU - Barrangou, Rodolphe AU - Westra, Edze R. AU - Marraffini, Luciano A. T2 - NATURE MICROBIOLOGY AB - CRISPR (clustered regularly interspaced short palindromic repeats) loci and their associated (cas) genes encode an adaptive immune system that protects prokaryotes from viral1 and plasmid2 invaders. Following viral (phage) infection, a small fraction of the prokaryotic cells are able to integrate a small sequence of the invader’s genome into the CRISPR array1. These sequences, known as spacers, are transcribed and processed into small CRISPR RNA guides3–5 that associate with Cas nucleases to specify a viral target for destruction6–9. Although CRISPR−cas loci are widely distributed throughout microbial genomes and often display hallmarks of horizontal gene transfer10–12, the drivers of CRISPR dissemination remain unclear. Here, we show that spacers can recombine with phage target sequences to mediate a form of specialized transduction of CRISPR elements. Phage targets in phage 85, ΦNM1, ΦNM4 and Φ12 can recombine with spacers in either chromosomal or plasmid-borne CRISPR loci in Staphylococcus, leading to either the transfer of CRISPR-adjacent genes or the propagation of acquired immunity to other bacteria in the population, respectively. Our data demonstrate that spacer sequences not only specify the targets of Cas nucleases but also can promote horizontal gene transfer. CRISPR spacers can recombine with phage target sequences to mediate a form of specialized transduction that can promote transfer of CRISPR elements to other bacteria in the population. DA - 2019/6// PY - 2019/6// DO - 10.1038/s41564-019-0400-2 VL - 4 IS - 6 SP - 956-963 SN - 2058-5276 UR - https://doi.org/10.1038/s41564-019-0400-2 ER - TY - JOUR TI - Effect of processing and oil type on carotene bioaccessibility in traditional foods prepared with flour and puree from orange-fleshed sweetpotatoes AU - Chilungo, Sarah AU - Muzhingi, Tawanda AU - Truong, Van-Den AU - Allen, Jonathan C. T2 - INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY AB - Summary Consumption of Orange‐Fleshed sweetpotato ( OFSP ) and products as source of provitamin A is being promoted to tackle vitamin A deficiency ( VAD ) in sub‐Saharan Africa. However, limited information is available on β‐carotene retention in foods and delivery after digestion. The study assessed carotene retention and bioaccessibility following in vitro digestion on traditional foods having OFSP among the ingredients. Sunflower oil, margarine and beef fat were evaluated on their effect on β‐carotene bioaccessibility. Porridge and chapatis were prepared with either OFSP puree or flours in the formulations. Carotene retention was highest in chapatis (83%) as compared to porridge (65%). Micerallisation efficiency of all‐trans β‐carotene was comparable between similar products but greater in chapatis (62%) than porridge (11%). Sunflower oil had the highest all‐trans β‐carotene bioaccessibility compared to margarine and beef fat. The results support the promotion of consumption of OFSP ‐based products as good source of provitamin A to fight VAD . DA - 2019/6// PY - 2019/6// DO - 10.1111/ijfs.14106 VL - 54 IS - 6 SP - 2055-2063 SN - 1365-2621 KW - Bioaccessibility KW - in vitro digestion KW - oil type KW - provitamin A KW - sweetpotato KW - beta-carotene ER - TY - JOUR TI - Enhanced Pb immobilization via the combination of biochar and phosphate solubilizing bacteria AU - Chen, Haoming AU - Zhang, Jiawen AU - Tang, Lingyi AU - Su, Mu AU - Tian, Da AU - Zhang, Lin AU - Li, Zhen AU - Hu, Shuijin T2 - ENVIRONMENT INTERNATIONAL AB - Application of biochar in heavy metal remediation suffers from lack of long-term stability. Phosphate-solubilizing bacteria (PSB) are able to elevate P release and the subsequent reaction with Pb to form stable pyromorphite. This study investigated the feasibility of applying PSB modified biochar to enhance immobilization of Pb2+. An alkaline biochar produced from rice husk (RB) and a slightly acidic biochar produced from sludge (SB) were selected. It showed that the biochars can effectively remove Pb2+ via adsorption, i.e., aqueous Pb concentrations after RB and SB addition were reduced by 18.61 and 53.89% respectively. The addition of PSB increased the Pb2+ removal for both biochars (to 24.11 and 60.85%, respectively). In particular, PSB significantly enhanced the formation of stable pyromorphite on surface of SB. This is due to that the evenly distributed PSB enhanced P release and regulated pH on the biochar surface. Moreover, small particles (<0.074 mm) showed their higher ability to induce the formation of pyromorphite, for both RB and SB. Nevertheless, SB demonstrated higher capability of sorption, together with its more abundant P content, which provided a more suitable platform to attract PSB to immobilize heavy metals. Therefore, the combination of biochar and PSB is a promising candidate material for heavy metal remediation. However, the types and particle size distribution of biochar should be addressed. DA - 2019/6// PY - 2019/6// DO - 10.1016/j.envint.2019.03.068 VL - 127 SP - 395-401 SN - 1873-6750 KW - Lead KW - Biochar KW - Phosphate-solubilizing bacteria KW - Immobilization KW - Pyromorphite ER - TY - JOUR TI - Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli AU - Goh, Yong Jun AU - Barrangou, Rodolphe T2 - CURRENT OPINION IN BIOTECHNOLOGY AB - Our evolving understanding on the mechanisms underlying the health-promoting attributes of probiotic lactobacilli, together with an expanding genome editing toolbox have made this genus an ideal chassis for the development of living therapeutics. The rising adoption of CRISPR-based technologies for prokaryotic engineering has demonstrated precise, efficient and scalable genome editing and tunable transcriptional regulation that can be translated into next-generation development of probiotic lactobacilli with enhanced robustness and designer functionalities. Here, we discuss how these tools in conjunction with the naturally abundant and diverse native CRISPR-Cas systems can be harnessed for Lactobacillus cell surface engineering and the delivery of biotherapeutics. DA - 2019/4// PY - 2019/4// DO - 10.1016/j.copbio.2018.11.009 VL - 56 SP - 163-171 SN - 1879-0429 UR - https://doi.org/10.1016/j.copbio.2018.11.009 ER - TY - JOUR TI - The genomics of invasion: characterization of red lionfish (Pterois volitans) populations from the native and introduced ranges (vol 21, pg 2471, 2019) AU - Reiskind, M. O. Burford AU - Reed, E. M. X. AU - Elias, A. AU - Giacomini, J. J. AU - McNear, A. F. AU - Nieuwsma, J. AU - Parker, G. A. AU - Roberts, R. B. AU - Rossi, R. E. AU - Stephenson, C. N. AU - Stevens, J. L. AU - Williams, B. E. T2 - BIOLOGICAL INVASIONS AB - In the original publication of this article, Figs. 2 and 3 were published incorrectly. DA - 2019/7// PY - 2019/7// DO - 10.1007/s10530-019-01999-7 VL - 21 IS - 7 SP - 2485-2487 SN - 1573-1464 ER - TY - JOUR TI - The genomics of invasion: characterization of red lionfish (Pterois volitans) populations from the native and introduced ranges AU - Reiskind, M. O. Burford AU - Reed, E. M. X. AU - Elias, A. AU - Giacomini, J. J. AU - McNear, A. F. AU - Nieuwsma, J. AU - Parker, G. A. AU - Roberts, R. B. AU - Rossi, R. E. AU - Stephenson, C. N. AU - Stevens, J. L. AU - Williams, B. E. T2 - BIOLOGICAL INVASIONS DA - 2019/7// PY - 2019/7// DO - 10.1007/s10530-019-01992-0 VL - 21 IS - 7 SP - 2471-2483 SN - 1573-1464 UR - http://dx.doi.org/10.1007/s10530-019-01992-0 KW - Invasion KW - Hybridization KW - Red lionfish KW - Pterois volitans KW - Pterois miles KW - ddRADseq ER - TY - JOUR TI - A potential new tool for the toolbox: assessing gene drives for eradicating invasive rodent populations AU - Campbell, Karl AU - Saah, J.R. AU - Brown, P.R. AU - Godwin, John AU - Howald, G.R. AU - Piaggio, Antoinette AU - Thomas, P AU - Tompkins, D.M. AU - Threadgill, David AU - Delborne, Jason AU - Kanavy, D.M. AU - Kuiken, Todd AU - Packard, H AU - Serr, Megan AU - Shiels, Aaron DA - 2019/1// PY - 2019/1// VL - 1 SP - ER - TY - JOUR TI - Stability of neonicotinoid sensitivity in Frankliniella fusca populations found in agroecosystems of the southeastern USA AU - Chappell, Thomas M AU - Huseth, Anders S AU - Kennedy, George G T2 - Pest Management Science AB - Abstract BACKGROUND Insecticide resistance arises at a given location in response to selection acting on novel genotypes or standing variation, or allelic migration. Fitness costs of resistance may slow resistance evolution or result in reversion to susceptibility, but consistent and geographically widespread use of insecticides may provide sufficient selection to offset the fitness costs of resistance. Understanding this relationship is important to the success of insecticide resistance management. We report the existence of fitness costs of neonicotinoid resistance in field‐collected populations of the tobacco thrips ( Frankliniella fusca ), which increasingly challenge upland cotton production in the southeastern USA. RESULTS Populations (14 of 15 in 2015; 4 of 5 in 2016) investigated showed a loss of resistance to imidacloprid after multiple generations without exposure to the insecticide. Populations studied in 2016 were each split into two colonies, and one of each pair was repeatedly exposed to imidacloprid. In three of the four populations that lost resistance, imidacloprid‐exposed colonies lost resistance significantly more slowly than did corresponding unexposed colonies. CONCLUSION For imidacloprid resistance to be broadly increasing in the landscapes of the southeastern USA despite fitness costs of resistance, selection for resistance must be sufficient to overcome the costs. Findings encourage investigation into why costs are overcome in this system, potentially including geographic extent of neonicotinoid use or prevalence of low‐dose exposure. © 2019 Society of Chemical Industry DA - 2019/2/13/ PY - 2019/2/13/ DO - 10.1002/ps.5319 VL - 75 IS - 6 SP - 1539-1545 J2 - Pest Management Science LA - en OP - SN - 1526-498X 1526-4998 UR - http://dx.doi.org/10.1002/ps.5319 DB - Crossref KW - resistance evolution KW - insecticide resistance management KW - tobacco thrips KW - neonicotinoid KW - agroecosystem ER - TY - JOUR TI - CRISPR-Directed Microbiome Manipulation across the Food Supply Chain AU - Barrangou, Rodolphe AU - Notebaart, Richard A. T2 - TRENDS IN MICROBIOLOGY AB - The advent of CRISPR-based technologies has revolutionized genetics over the past decade, and genome editing is now widely implemented for diverse medical and agricultural applications, such as correcting genetic disorders and improving crop and livestock breeding. CRISPR-based technologies are also of great potential to alter the genetic content of food bacteria in order to control the composition and activity of microbial populations across the food supply chain, from the farm to consumer products. Advancing the food supply chain is of great societal importance as it involves optimizing fermentation processes to enhance taste and sensory properties of food products, as well as improving food quality and safety by controlling spoilage bacteria and pathogens. Here, we discuss the various CRISPR technologies that can alter bacterial functionalities and modulate the composition of microbial communities in foods. We illustrate how these applications can be harnessed along the food supply chain to manipulate microbiomes that encompass spoilage and pathogenic bacteria as well as desirable starter cultures and health-promoting probiotics. DA - 2019/6// PY - 2019/6// DO - 10.1016/j.tim.2019.03.006 VL - 27 IS - 6 SP - 489-496 SN - 1878-4380 UR - https://doi.org/10.1016/j.tim.2019.03.006 ER - TY - JOUR TI - Beyond ICS: How Should We Govern Complex Disasters in the United States? AU - Nowell, Branda AU - Steelman, Toddi T2 - JOURNAL OF HOMELAND SECURITY AND EMERGENCY MANAGEMENT AB - Abstract The complexity of large-scale disasters requires governance structures that can integrate numerous responders quickly under often chaotic conditions. Complex disasters – by definition – span multiple jurisdictions and activate numerous response functions carried out by numerous legally autonomous public, nonprofit, and private actors. The command operating structure of the Incident Command System (ICS) is a hierarchical structure used to manage complex incidents. Increasingly, complex disasters are seen as networks of multiple actors. Improving our capacity to respond to large-scale, complex disasters requires moving beyond the “hierarchy versus networks” debate to understand the conditions under which governance structures can best serve disaster response goals. Understanding the capabilities and limitations of the governance structures embedded in our national policy tools and frameworks can enhance our ability to govern effectively in networked contexts. In this article, we suggest the need to shift focus to build greater capacity for hybrid and network governance approaches, including a more sophisticated understanding of the conditions under which these governance forms are most effective. DA - 2019/5// PY - 2019/5// DO - 10.1515/jhsem-2018-0067 VL - 16 IS - 2 SP - SN - 1547-7355 KW - ICS KW - network governance ER - TY - JOUR TI - Warmer waters masculinize wild populations of a fish with temperature-dependent sex determination AU - Honeycutt, J. L. AU - Deck, C. A. AU - Miller, S. C. AU - Severance, M. E. AU - Atkins, E. B. AU - Luckenbach, J. A. AU - Buckel, J. A. AU - Daniels, H. V. AU - Rice, J. A. AU - Borski, R. J. AU - Godwin, J. T2 - Scientific Reports AB - Abstract Southern flounder ( Paralichthys lethostigma ) exhibit environmental sex determination (ESD), where environmental factors can influence phenotypic sex during early juvenile development but only in the presumed XX female genotype. Warm and cold temperatures masculinize fish with mid-range conditions producing at most 50% females. Due to sexually dimorphic growth, southern flounder fisheries are dependent upon larger females. Wild populations could be at risk of masculinization from ESD due to globally increasing water temperatures. We evaluated the effects of habitat and temperature on wild populations of juvenile southern flounder in North Carolina, USA. While northern habitats averaged temperatures near 23 °C and produced the greatest proportion of females, more southerly habitats exhibited warmer temperatures (>27 °C) and consistently produced male-biased sex ratios (up to 94% male). Rearing flounder in the laboratory under temperature regimes mimicking those of natural habitats recapitulated sex ratio differences observed across the wild populations, providing strong evidence that temperature is a key factor influencing sex ratios in nursery habitats. These studies provide evidence of habitat conditions interacting with ESD to affect a key demographic parameter in an economically important fishery. The temperature ranges that yield male-biased sex ratios are within the scope of predicted increases in ocean temperature under climate change. DA - 2019/4/25/ PY - 2019/4/25/ DO - 10.1038/s41598-019-42944-x VL - 9 IS - 1 SP - J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-019-42944-x DB - Crossref ER - TY - JOUR TI - Simplification of vector communities during suburban succession AU - Spence Beaulieu, Meredith R. AU - Hopperstad, Kristen AU - Dunn, Robert R. AU - Reiskind, Michael H. T2 - PLOS ONE AB - Suburbanization is happening rapidly on a global scale, resulting in changes to the species assemblages present in previously undeveloped areas of land. Community-level changes after anthropogenic land-use change have been studied in a variety of organisms, but the effects on arthropods of medical and veterinary importance remain poorly characterized. Shifts in diversity, abundance, and community composition of such arthropods, like mosquitoes, can significantly impact vector-borne disease dynamics due to varying vectorial capacity between different species. In light of these potential implications for vector-borne diseases, we investigated changes in mosquito species assemblage after suburbanization by sampling mosquitoes in neighborhoods of different ages in Wake County, North Carolina, US. We found that independent of housing density and socioeconomic status, mosquito diversity measures decreased as suburban neighborhoods aged. In the oldest neighborhoods, the mosquito assemblage reached a distinct suburban climax community dominated by the invasive, peridomestic container-breeding Aedes albopictus, the Asian tiger mosquito. Aedes albopictus is a competent vector of many pathogens of human concern, and its dominance in suburban areas places it in close proximity with humans, allowing for heightened potential of host-vector interactions. While further research is necessary to explicitly characterize the effects of mosquito community simplification on vector-borne disease transmission in highly suburbanized areas, the current study demonstrates that suburbanization is disrupting mosquito communities so severely that they do not recover their diversity even 100 years after the initial disturbance. Our understanding of the community-level effects of anthropogenic land-use change on arthropod vectors will become increasingly important as we look to mitigate disease spread in a global landscape that is continually developed and altered by humans. DA - 2019/5/1/ PY - 2019/5/1/ DO - 10.1371/journal.pone.0215485 VL - 14 IS - 5 SP - e0215485 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0215485 DB - Crossref ER - TY - JOUR TI - Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste AU - Mathews, Stephanie L. AU - Epps, Mary Jane AU - Blackburn, R. Kevin AU - Goshe, Michael B. AU - Grunden, Amy M. AU - Dunn, Robert R. T2 - ROYAL SOCIETY OPEN SCIENCE AB - A citizen science project found that the greenhouse camel cricket ( Diestrammena asynamora ) is common in North American homes. Public response was to wonder ‘what good are they anyway?’ and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle ( Dermestes maculatus ) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified that were capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms. DA - 2019/3// PY - 2019/3// DO - 10.1098/rsos.180748 VL - 6 IS - 3 SP - SN - 2054-5703 KW - greenhouse camel cricket KW - hide beetle KW - Cedecea lapagei KW - lignocellulose KW - secretome ER - TY - JOUR TI - Human indoor climate preferences approximate specific geographies AU - Just, Michael G. AU - Nichols, Lauren M. AU - Dunn, Robert R. T2 - ROYAL SOCIETY OPEN SCIENCE AB - Human engineering of the outdoors led to the development of the indoor niche, including home construction. However, it is unlikely that domicile construction mechanics are under direct selection for humans. Nonetheless, our preferences within indoor environments are, or once were, consequential to our fitness. The research of human homes does not usually consider human evolution, and, therefore, we are without previous predictions about indoor climate preference. We worked with citizen scientists to collect indoor climate data from homes ( n = 37) across the USA. We then compared these data to recent global terrestrial climate data (0.5° grid cells, n = 67 420) using a climate dissimilarity index. We also compared some climate-related physiological parameters (e.g. thermoneutral zone (TNZ)) between humans and a selection of non-human primates. On average, our study homes were most similar in climate to the outdoor conditions of west central Kenya. We found that the indoor climates of our study homes largely matched the TNZ of humans and other primates. Overall, we identified the geographical distribution of the global outdoor climate that is most similar to the interiors of our study homes and summarized study home indoor climate preferences. DA - 2019/3// PY - 2019/3// DO - 10.1098/rsos.180695 VL - 6 IS - 3 SP - SN - 2054-5703 KW - climate dissimilarity KW - human niche construction KW - human associates KW - thermal comfort KW - indoor biome ER - TY - JOUR TI - Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems AU - Faure, Guilhem AU - Shmakov, Sergey A. AU - Makarova, Kira S. AU - Wolf, Yuri I. AU - Crawley, Alexandra B. AU - Barrangou, Rodolphe AU - Koonin, Eugene V. T2 - RNA BIOLOGY AB - Trans-activating CRISPR (tracr) RNA is a distinct RNA species that interacts with the CRISPR (cr) RNA to form the dual guide (g) RNA in type II and subtype V-B CRISPR-Cas systems. The tracrRNA-crRNA interaction is essential for pre-crRNA processing as well as target recognition and cleavage. The tracrRNA consists of an antirepeat, which forms an imperfect hybrid with the repeat in the crRNA, and a distal region containing a Rho-independent terminator. Exhaustive comparative analysis of the sequences and predicted structures of the Class 2 CRISPR guide RNAs shows that all these guide RNAs share distinct structural features, in particular, the nexus stem-loop that separates the repeat-antirepeat hybrid from the distal portion of the tracrRNA and the conserved GU pair at that end of the hybrid. These structural constraints might ensure full exposure of the spacer for target recognition. Reconstruction of tracrRNA evolution for 4 tight bacterial groups demonstrates random drift of repeat-antirepeat complementarity within a window of hybrid stability that is, apparently, maintained by selection. An evolutionary scenario is proposed whereby tracrRNAs evolved on multiple occasions, via rearrangement of a CRISPR array to form the antirepeat in different locations with respect to the array. A functional tracrRNA would form if, in the new location, the antirepeat is flanked by sequences that meet the minimal requirements for a promoter and a Rho-independent terminator. Alternatively, or additionally, the antirepeat sequence could be occasionally ‘reset’ by recombination with a repeat, restoring the functionality of tracrRNAs that drift beyond the required minimal hybrid stability. DA - 2019/4/3/ PY - 2019/4/3/ DO - 10.1080/15476286.2018.1493331 VL - 16 IS - 4 SP - 435-448 SN - 1555-8584 UR - https://doi.org/10.1080/15476286.2018.1493331 ER - TY - JOUR TI - The intestinal environment as an evolutionary adaptation to mouthbrooding in the Astatotilapia burtoni cichlid AU - Faber-Hammond, Josh J. AU - Coyle, Kaitlin P. AU - Bacheller, Shannon K. AU - Roberts, Cameron G. AU - Mellies, Jay L. AU - Roberts, Reade B. AU - Renn, Suzy C. P. T2 - FEMS MICROBIOLOGY ECOLOGY AB - ABSTRACT Many of the various parental care strategies displayed by animals are accompanied by a significant reduction in food intake that imposes a substantial energy trade-off. Mouthbrooding, as seen in several species of fish in which the parent holds the developing eggs and fry in the buccal cavity, represents an extreme example of reduced food intake during parental investment and is accompanied by a range of physiological adaptations. In this study we use 16S sequencing to characterize the gut microbiota of female Astatotilapia burtoni cichlid fish throughout the obligatory phase of self-induced starvation during the brooding cycle in comparison to stage-matched females that have been denied food for the same duration. In addition to a reduction of gut epithelial turnover, we find a dramatic reduction in species diversity in brooding stages that recovers upon release of fry and refeeding that is not seen in females that are simply starved. Based on overall species diversity as well as differential abundance of specific bacterial taxa, we suggest that rather than reflecting a simple deprivation of caloric intake, the gut microbiota is more strongly influenced by physiological changes specific to mouthbrooding including the reduced epithelial turnover and possible production of antimicrobial agents. DA - 2019/3// PY - 2019/3// DO - 10.1093/femsec/fiz016 VL - 95 IS - 3 SP - SN - 1574-6941 KW - cichlid fish KW - mouthbrooding KW - social behavior KW - parental care KW - starvation KW - hibernation KW - estivation ER - TY - JOUR TI - Evidence of effectiveness in the Cohesive Strategy: measuring and improving wildfire response AU - Steelman, Toddi AU - Nowell, Branda T2 - INTERNATIONAL JOURNAL OF WILDLAND FIRE AB - The United States’ National Cohesive Wildfire Management Strategy aims to achieve greater social and ecological resilience to wildfire. It also raises the question: cohesive for whom and for what purpose? In this article, we address the wildfire response goal and what a cohesive response means. Namely, we define a cohesive response as the ability to co-manage across scales for a more effective wildfire response. Our approach is grounded in the reality of the growing complexity of wildfire – both biophysically and socio-politically. We suggest that suppression and fire operations are necessary, but insufficient in the face of this growing complexity as we seek safer and effective wildfire response. Using network-based concepts and drawing from the literature on socio-ecological resilience, we consider how scales can be matched, what can and should be communicated across scales, and what this means for creating more adaptable institutions for more effective wildfire response. Survey results from 21 fires during the 2013 wildfire season are presented to illustrate relative areas of strength and weakness related to wildfire response and how these measurements can feed into processes to facilitate social learning, adaptation and ultimately more resilient socio-ecological wildfire response institutions. DA - 2019/// PY - 2019/// DO - 10.1071/WF18136 VL - 28 IS - 4 SP - 267-274 SN - 1448-5516 KW - co-management KW - disasters KW - networks KW - network governance KW - resilience KW - socio-ecological ER - TY - JOUR TI - Fabric infused with a botanical repellent for protection against mosquitoes AU - Halbkat, Lilah AU - Luan, Kun AU - Cave, Grayson AU - McCord, Marian AU - Roe, Michael AU - DenHartog, Emiel AU - Travanty, Nicholas J. AU - Apperson, Charles S. AU - West, Andre J. T2 - JOURNAL OF THE TEXTILE INSTITUTE AB - Mosquito resistant apparel has become increasingly sought-after due to the rise in vector-borne illnesses such as the Zika Virus, Malaria, and Dengue Fever. Botanical insect repellents have been introduced to the market for consumers that desire a natural solution involving no pesticides or added chemicals. Fabric swatches consisting of 80% nylon and 20% elastane were separately treated with an organic repellent using a patented nonwoven vessel. The fabrics were then tested for effectiveness in repelling the mosquito Aedes aegypti using an arm-in-cage assay, the most commonly used method for mosquito repellents. The repellents were also evaluated and rated by study participants according to their preference for the appeal of the scent. The treatment method is user-friendly, enabling consumers to treat their clothing with an organic insect repellent as opposed to applying a synthetic chemical to their clothing and skin. The infused fabrics showed to be effective at repelling mosquitoes for up to 8 h after repellent infusion. DA - 2019/10/3/ PY - 2019/10/3/ DO - 10.1080/00405000.2019.1603576 VL - 110 IS - 10 SP - 1468-1474 SN - 1754-2340 KW - Infused KW - repellent KW - fabric KW - protective KW - garment KW - insect ER - TY - JOUR TI - CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline AU - Nethery, Matthew A. AU - Barrangou, Rodolphe T2 - RNA BIOLOGY AB - A CRISPR locus, defined by an array of repeat and spacer elements, constitutes a genetic record of the ceaseless battle between bacteria and viruses, showcasing the genomic integration of spacers acquired from invasive DNA. In particular, iterative spacer acquisitions represent unique evolutionary histories and are often useful for high-resolution bacterial genotyping, including comparative analysis of closely related organisms, clonal lineages, and clinical isolates. Current spacer visualization methods are typically tedious and can require manual data manipulation and curation, including spacer extraction at each CRISPR locus from genomes of interest. Here, we constructed a high-throughput extraction pipeline coupled with a local web-based visualization tool which enables CRISPR spacer and repeat extraction, rapid visualization, graphical comparison, and progressive multiple sequence alignment. We present the bioinformatic pipeline and investigate the loci of reference CRISPR-Cas systems and model organisms in 4 well-characterized subtypes. We illustrate how this analysis uncovers the evolutionary tracks and homology shared between various organisms through visual comparison of CRISPR spacers and repeats, driven through progressive alignments. Due to the ability to process unannotated genome files with minimal preparation and curation, this pipeline can be implemented promptly. Overall, this efficient high-throughput solution supports accelerated analysis of genomic data sets and enables and expedites genotyping efforts based on CRISPR loci. DA - 2019/4/3/ PY - 2019/4/3/ DO - 10.1080/15476286.2018.1493332 VL - 16 IS - 4 SP - 577-584 SN - 1555-8584 UR - https://doi.org/10.1080/15476286.2018.1493332 KW - CRISPR-Cas KW - repeat detection KW - software KW - CRISPR spacer KW - crRNA ER - TY - JOUR TI - Phytophthora acaciae sp. nov., a new species causing gummosis of black wattle in Brazil AU - Alves, Tatiane C. Albuquerque AU - Tessmann, Dauri J. AU - Ivors, Kelly L. AU - Ristaino, Jean B. AU - dos Santos, Álvaro F. T2 - Mycologia AB - A new Phytophthora species was found associated with gummosis in black wattle plantations in the subtropical, humid, south of Brazil. The new species Phytophthora acaciae is formally named herein based on phylogenetic and morphological analyses. This is the fourth Phytophthora species found from this pathogen complex in black wattle plantations causing gummosis in Brazil. The other three species are P. nicotianae, P. boehmeriae, and P. frigida. Phytophthora acaciae is heterothallic with amphigynous antheridia, noncaducous, papillate sporangia and is placed in the Phytophthora clade 2 based on nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) sequences. Maximum parsimony and maximum likelihood phylogenetic analyses of P. acaciae isolates based on multigene sequences, including partial DNA sequences of three nuclear protein-coding genes (β-tubulin, translation elongation factor-1α, and ras-related protein), two mitochondrial protein-coding genes (cytochrome c oxidase subunits I and II), in addition to ITS sequence data, support the delimitation of this new species on Acacia mearnsii from the other previously described clade 2 Phytophthora species. Pathogenicity trial confirmed that the new species causes necrotic lesions on the plant stem, with either the presence or absence of gum. DA - 2019/4/9/ PY - 2019/4/9/ DO - 10.1080/00275514.2019.1575685 VL - 111 IS - 3 SP - 445-455 J2 - Mycologia LA - en OP - SN - 0027-5514 1557-2536 UR - http://dx.doi.org/10.1080/00275514.2019.1575685 DB - Crossref KW - Forest fungi KW - Oomycetes KW - phylogenetics KW - Straminipila KW - taxonomy KW - 1 new taxon ER - TY - JOUR TI - The Development of the INFEWS-ER: A Virtual Resource Center for Transdisciplinary Graduate Student Training at the Nexus of Food, Energy, and Water AU - Rodríguez, Luis F. AU - Marshall, Anna-Maria AU - Cotton, Dan AU - Koelsch, Richard AU - Koziel, Jacek AU - Meyer, Deanne AU - Steward, Dan AU - Heemstra, Jill AU - Padmanabahn, Anand AU - Classen, John AU - Meyer, Nathan J. AU - Ruddell, Benjamin L. AU - Ryan, Sean M. AU - Cai, Ximing AU - Habib, Emad AU - Saundry, Peter D. T2 - Frontiers in Environmental Science AB - Problems at the nexus of Food, Energy and Water Systems (FEWS) are among the most complex challenges we face. Spanning simple to complex temporal, geographic, social, and political framings, the questions raised at this nexus require multi-disciplinary if not transdisciplinary approaches. Answers to these questions must draw from engineering, the physical and biological sciences, and the social sciences. Practical solutions depend upon a wide community of stakeholders, including industry, policy-makers, and the general public. Yet there are many obstacles to working in a transdisciplinary environment: unfamiliar concepts, specialized terminology, and countless 'blind' spots. Graduate education occurs in disciplinary 'silos', often with little regard for the unintended consequences of our research. Existing pedagogical models do not usually train students to understand neighboring disciplines, thus limiting student learning to narrow areas of expertise, and obstructing their potential for transdisciplinary discourse over their careers. Our goal is a virtual resource center—the INFEWS-ER—that provides educational opportunities to supplement graduate students, especially in their development of transdisciplinary competences. Addressing the grand challenges at the heart of the FEWS nexus will depend upon such competence. Students and scholars from diverse disciplines are working together to develop the INFEWS-ER. To date, we have sponsored both a workshop and a symposium to identify priorities to design the initial curriculum. We have also conducted surveys of the larger community of FEWS researchers. Our work confirms a widespread interest in transdisciplinary training and helps to identify core themes and promising pedagogical approaches. Our curriculum now centers upon several 'Cohort Challenges', supported by various 'Toolbox Modules' organized around key themes (e.g., communicating science). We plan to initiate the first cohort of students in October of 2018. Students who successfully complete their Cohort Challenges will be certified as the FEW Graduate Scholars. In this paper, we describe the development of this curriculum. We begin with the need for training in transdisciplinary research. We then describe the workshop and symposium, as well as our survey results. We conclude with an outline of the curriculum, including the current Cohort Challenges and Toolbox Modules. DA - 2019/4/25/ PY - 2019/4/25/ DO - 10.3389/fenvs.2019.00038 VL - 7 SP - J2 - Front. Environ. Sci. OP - SN - 2296-665X UR - http://dx.doi.org/10.3389/fenvs.2019.00038 DB - Crossref KW - collaborative learning KW - pedagogy KW - convergence research KW - divergent thinking KW - team-based learning KW - online education KW - active learning KW - wicked problems ER - TY - JOUR TI - Interactions Between Biotic and Abiotic Factors Affect Survival in Overwintering Drosophila suzukii (Diptera: Drosophilidae) AU - Stockton, Dara AU - Wallingford, Anna AU - Rendon, Dalila AU - Fanning, Philip AU - Green, Clarence K. AU - Diepenbrock, Lauren AU - Ballman, Elissa AU - Walton, Vaughn M. AU - Isaacs, Rufus AU - Leach, Heather AU - Sial, Ashfaq A. AU - Drummond, Francis AU - Burrack, Hannah AU - Loeb, Gregory M. T2 - ENVIRONMENTAL ENTOMOLOGY AB - Drosophila suzukii Matsumura is an invasive species affecting berry crops and cherries throughout North America, South America, and Europe. Previous research suggests that in temperate climates, the overwintering success of D. suzukii is likely dependent on access to food, shelter, and adequate cold hardening. We performed a multi-state study under field conditions for two winters to determine whether D. suzukii sex, phenotype (summer-morphotype, winter-morphotype), and life stage (adults, pupae) affected survival over time while recording naturally-occurring spatial and temporal variation in temperature. Access to food was provided and the flies were buried under leaf litter. Baited traps were deployed to determine whether local populations of D. suzukii were active throughout the winter season. The duration of exposure, mean daily temperature, and cumulative time below freezing significantly affected survival. Below freezing, D. suzukii survival was significantly reduced, particularly in northern locations. In contrast, we observed sustained survival up to 10 wk in southern locations among adults and pupae. Biotic factors also significantly affected survival outcomes: female survival was greater than male survival, winter-morphotype survival was greater than summer-morphotype survival, and adult survival was greater than pupal survival. In the north, wild D. suzukii were captured only in early winter, while in the south they were found throughout the winter. These data suggest that although adult D. suzukii may overwinter in sheltered microclimates, this ability may be limited in regions where the ground temperature, or site of overwintering, falls below freezing for extended durations. DA - 2019/4// PY - 2019/4// DO - 10.1093/ee/nvy192 VL - 48 IS - 2 SP - 454-464 SN - 1938-2936 KW - SWD KW - cold tolerance KW - habitat KW - survival KW - morphotype ER - TY - JOUR TI - An algorithm for quantitatively estimating non-occupational pesticide exposure intensity for spouses in the Agricultural Health Study AU - Deziel, Nicole C. AU - Freeman, Laura E. Beane AU - Hoppin, Jane A. AU - Thomas, Kent AU - Lerro, Catherine C. AU - Jones, Rena R. AU - Hines, Cynthia J. AU - Blair, Aaron AU - Graubard, Barry I AU - Lubin, Jay H. AU - Sandler, Dale P. AU - Chen, Honglei AU - Andreotti, Gabriella AU - Alavanja, Michael C. AU - Friesen, Melissa C. T2 - JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY AB - Residents of agricultural areas experience pesticide exposures from sources other than direct agricultural work. We developed a quantitative, active ingredient-specific algorithm for cumulative (adult, married lifetime) non-occupational pesticide exposure intensity for spouses of farmers who applied pesticides in the Agricultural Health Study (AHS). The algorithm addressed three exposure pathways: take-home, agricultural drift, and residential pesticide use. Pathway-specific equations combined (i) weights derived from previous meta-analyses of published pesticide exposure data and (ii) information from the questionnaire on frequency and duration of pesticide use by applicators, home proximity to treated fields, residential pesticide usage (e.g., termite treatments), and spouse’s off-farm employment (proxy for time at home). The residential use equation also incorporated a published probability matrix that documented the likelihood active ingredients were used in home pest treatment products. We illustrate use of these equations by calculating exposure intensities for the insecticide chlorpyrifos and herbicide atrazine for 19,959 spouses. Non-zero estimates for ≥1 pathway were found for 78% and 77% of spouses for chlorpyrifos and atrazine, respectively. Variability in exposed spouses’ intensity estimates was observed for both pesticides, with 75th to 25th percentile ratios ranging from 7.1 to 7.3 for take-home, 6.5 to 8.5 for drift, 2.4 to 2.8 for residential use, and 3.8 to 7.0 for the summed pathways. Take-home and drift estimates were highly correlated (≥0.98), but were not correlated with residential use (0.01‒0.02). This algorithm represents an important advancement in quantifying non-occupational pesticide relative exposure differences and will facilitate improved etiologic analyses in the AHS spouses. The algorithm could be adapted to studies with similar information. DA - 2019/4// PY - 2019/4// DO - 10.1038/s41370-018-0088-z VL - 29 IS - 3 SP - 344-357 SN - 1559-064X ER - TY - JOUR TI - Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus AU - Stuckert, Adam M. M. AU - Moore, Emily AU - Coyle, Kaitlin P. AU - Davison, Ian AU - MacManes, Matthew D. AU - Roberts, Reade AU - Summers, Kyle T2 - BMC EVOLUTIONARY BIOLOGY AB - Color and pattern phenotypes have clear implications for survival and reproduction in many species. However, the mechanisms that produce this coloration are still poorly characterized, especially at the genomic level. Here we have taken a transcriptomics-based approach to elucidate the underlying genetic mechanisms affecting color and pattern in a highly polytypic poison frog. We sequenced RNA from the skin from four different color morphs during the final stage of metamorphosis and assembled a de novo transcriptome. We then investigated differential gene expression, with an emphasis on examining candidate color genes from other taxa. Overall, we found differential expression of a suite of genes that control melanogenesis, melanocyte differentiation, and melanocyte proliferation (e.g., tyrp1, lef1, leo1, and mitf) as well as several differentially expressed genes involved in purine synthesis and iridophore development (e.g., arfgap1, arfgap2, airc, and gart). Our results provide evidence that several gene networks known to affect color and pattern in vertebrates play a role in color and pattern variation in this species of poison frog. DA - 2019/4/18/ PY - 2019/4/18/ DO - 10.1186/s12862-019-1410-7 VL - 19 SP - SN - 1471-2148 KW - Aposematism KW - Coloration KW - Color variation KW - Poison frog ER - TY - JOUR TI - Promises and perils of gene drives: Navigating the communication of complex, post-normal science AU - Brossard, Dominique AU - Belluck, Pam AU - Gould, Fred AU - Wirz, Christopher D. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - In November of 2017, an interdisciplinary panel discussed the complexities of gene drive applications as part of the third Sackler Colloquium on "The Science of Science Communication." The panel brought together a social scientist, life scientist, and journalist to discuss the issue from each of their unique perspectives. This paper builds on the ideas and conversations from the session to provide a more nuanced discussion about the context surrounding responsible communication and decision-making for cases of post-normal science. Deciding to use gene drives to control and suppress pests will involve more than a technical assessment of the risks involved, and responsible decision-making regarding their use will require concerted efforts from multiple actors. We provide a review of gene drives and their potential applications, as well as the role of journalists in communicating the extent of uncertainties around specific projects. We also discuss the roles of public opinion and online environments in public engagement with scientific processes. We conclude with specific recommendations about how to address current challenges and foster more effective communication and decision-making for complex, post-normal issues, such as gene drives. DA - 2019/4/16/ PY - 2019/4/16/ DO - 10.1073/pnas.1805874115 VL - 116 IS - 16 SP - 7692-7697 SN - 0027-8424 KW - gene drives KW - science communication KW - public engagement ER - TY - JOUR TI - Influence of Weed Manipulation in Field Borders on Brown Stink Bug (Hemiptera: Pentatomidae) Densities and Damage in Field Corn AU - Babu, Arun AU - Reisig, Dominic D AU - Walgenbach, James F AU - Heiniger, Ronnie W AU - Everman, Wesley T2 - Environmental Entomology AB - Brown stink bug, Euschistus servus (Say), is a damaging pest of corn, Zea mays L. (Cyperales: Poaceae), in the southeastern United States. In North Carolina, during the spring, winter-planted wheat, Triticum aestivum L. (Cyperales: Poaceae), serves as the earliest available crop host, and E. servus seems to prefer this crop over seedling corn. In the absence of wheat in the agroecosystem, weeds serve as a bridge host for a portion of overwintered E. servus populations until they move to corn and other subsequent crops. Our objective was to reduce densities of E. servus in corn by manipulating the weedy field borders with mowing and applications of dicamba herbicide. During the study, multiple species of stink bugs (n =16) were found associated with weed plots. However, E. servus was the predominant (>94%) stink bug species in the corn. In this farmscape, density of E. servus adults in the unmanaged weed plots began declining around the second week of May, followed by an increase in density in adjacent corn plots. This movement coincided with the seedling growth of corn. In 2016, applications of dicamba in the weedy field border resulted in a lower density of E. servus in herbicide-treated weed plots compared with untreated plots. Despite this difference, manipulations of weeds did not lead to any significant changes in density of E. servus adults in corn. Further evidence suggested that a prominent external source of E. servus, other than field-bordering weeds, in the farmscape was likely driving densities in corn. DA - 2019/2/27/ PY - 2019/2/27/ DO - 10.1093/ee/nvz016 VL - 48 IS - 2 SP - 444-453 LA - en OP - SN - 0046-225X 1938-2936 UR - http://dx.doi.org/10.1093/ee/nvz016 DB - Crossref KW - Euschistus servus KW - ecology KW - movement KW - mowing KW - farmscape ER - TY - JOUR TI - A Reviewer's Guide to Qualitative Rigor AU - Nowell, Branda AU - Albrecht, Kate T2 - JOURNAL OF PUBLIC ADMINISTRATION RESEARCH AND THEORY AB - Institutions are useful for advancing methodologies within disciplines. Through required coursework, doctoral students are indoctrinated into basic guidelines and frameworks that provide a common foundation for scholars to interact with one another. Lacking such forums in many of our doctoral granting institutions (Stout 2013), the field of public management continues to struggle with an ambivalence toward qualitative approaches. Lack of shared understanding concerning basic tenets of qualitative methodology abounds. This article is intended for qualitative consumers, those not formally trained in qualitative methods but who serve as peer reviewers, content experts, and advisors in arenas where qualitative methods are encountered. Adopting a postpositivistic stance dominant in the field, we seek to offer a pragmatic perspective on qualitative methods with regards to some basic tenets of rigor appropriate (and inappropriate) for assessing the contribution of qualitative research. We argue that the first step in this effort is to stop conflating data type (qualitative versus quantitative) with inductive versus deductive modes of inquiry. Using deductive modes as the basis for comparison, we discuss both common, as well as, diverging criteria of quality and rigor for inductive modes of inquiry. We conclude with a discussion of rigor in emerging methods which utilize qualitative data but from within a deductive, mixed, or hybrid mode of inquiry. DA - 2019/4// PY - 2019/4// DO - 10.1093/jopart/muy052 VL - 29 IS - 2 SP - 348-363 SN - 1477-9803 ER - TY - JOUR TI - Development and Dispersal of Helicoverpa zea (Lepidoptera: Noctuidae) on Non-Bt and Bt Pyramided Cotton AU - Braswell, Lewis R AU - Reisig, Dominic D AU - Sorenson, Clyde E AU - Collins, Guy D T2 - Environmental Entomology AB - Bollworm (Helicoverpa zea Boddie) (Lepidoptera: Noctuidae) can cause economic losses in both non-Bt and Bt cotton. Larvae modify their behavior in the presence of Bt by moving away from terminals faster in Bt cotton compared to non-Bt cotton and avoiding Bt-treated diets. Our objectives were to understand differences in bollworm egg and larvae populations within, and dispersal away from, non-Bt and Bt pyramided-toxin cotton. We conducted small plot experiments in 2016 and 2017 to monitor on-plant egg and larval numbers, and off-plant dispersal of larvae, from non-Bt and different Bt toxin pyramided cotton. Bollworm adults preferred to oviposit in most Bt toxin pyramids compared to non-Bt; this was likely unrelated to detection of Bt by adults, but rather density-dependent aversion from high larval populations. First instar numbers were similar in all non-Bt/Bt toxin pyramids and dispersed at a similar rate. Second through fifth instar numbers were higher in non-Bt than Bt toxin pyramids but dispersed equally from all non-Bt/Bt toxin pyramids, regardless of Bt pyramid type. Development times of larvae were often slower in Bt toxin pyramids compared to non-Bt. Fifth instars were found in, and dispersing from, Bt toxin pyramids containing Vip3A, raising concerns of resistance development. Furthermore, differences in oviposition rate among non-Bt/Bt toxin pyramids and slowed development rate of larvae on Bt varieties could create inconsistencies in generation times emerging from Bt and non-Bt hosts, which could contribute to resistance development. DA - 2019/1/31/ PY - 2019/1/31/ DO - 10.1093/ee/nvz006 VL - 48 IS - 2 SP - 465-477 LA - en OP - SN - 0046-225X 1938-2936 UR - http://dx.doi.org/10.1093/ee/nvz006 DB - Crossref KW - behavioral resistance KW - density dependence KW - insect behavior ER - TY - JOUR TI - Self-Driving Cars and Engineering Ethics: The Need for a System Level Analysis AU - Borenstein, Jason AU - Herkert, Joseph R. AU - Miller, Keith W. T2 - SCIENCE AND ENGINEERING ETHICS DA - 2019/4// PY - 2019/4// DO - 10.1007/s11948-017-0006-0 VL - 25 IS - 2 SP - 383-398 SN - 1471-5546 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85033584947&partnerID=MN8TOARS KW - Artificial intelligence KW - Automation KW - Engineering ethics KW - Self-driving cars KW - Socio-technical systems ER - TY - JOUR TI - A camouflage conundrum: unexpected differences in winter coat color between sympatric species AU - Davis, Brandon M. AU - Kumar, Alexander V AU - Mills, L. Scott T2 - ECOSPHERE AB - Abstract Across the globe, more than 21 species undergo seasonal changes in coloration, molting white in winter to become camouflaged against snow. Given the adaptive value of seasonal camouflage against local snow duration, one might predict that sympatric coat color changing species would have similar winter coat color. This hypothesis, however, contrasts with anecdotal evidence and modeling results that predict sympatric winter white and winter brown species in some areas with transient snow cover. In one such area, West Virginia, we document coat color phenology between three sympatric species: snowshoe hares ( Lepus americanus ), long‐tailed weasels ( Mustela frenata ), and least weasels ( Mustela nivalis ). Using a combination of field methods, we document and quantify each species’ winter coat color, illustrating an interspecific polymorphic response in winter coloration among sympatric winter white snowshoe hares and winter brown weasels. We then hypothesize what forces drive the interspecific differences between snowshoe hare and weasel winter coloration, highlighting areas of focus for future seasonal coat color research. DA - 2019/3// PY - 2019/3// DO - 10.1002/ecs2.2658 VL - 10 IS - 3 SP - SN - 2150-8925 KW - camouflage KW - coat color change KW - Lepus americanus KW - Mustela frenata KW - Mustela nivalis KW - phenology KW - West Virginia ER - TY - JOUR TI - Diel periodicity and visual cues guide oviposition behavior in Phlebotomus papatasi, vector of old-world cutaneous leishmaniasis AU - Shymanovich, Tatsiana AU - Faw, Lindsey AU - Hajhashemi, Nima AU - Teague, Jimmie AU - Schal, Coby AU - Ponnusamy, Loganathan AU - Apperson, Charles S. AU - Hatano, Eduardo AU - Wasserberg, Gideon T2 - PLOS NEGLECTED TROPICAL DISEASES AB - Background: Phlebotomine sand flies are vectors of human leishmaniases, important neglected tropical diseases. In this study, we investigated diel patterns of oviposition behavior, effects of visual cues on oviposition-site selection, and whether these affect the attraction of gravid Phlebotomus papatasi (Scopoli), the vector of old-world cutaneous leishmaniasis, to olfactory cues from oviposition sites. Methodology/principal findings: To evaluate these questions, we conducted a series of experiments using attraction and oviposition assays within free-flight test chambers containing gravid females entrained under a 14:10 hrs light:dark photoperiod. By replacing sticky-screens or moist filter papers every three hours, we showed that oviposition site search occurs mainly in the latest part of the night whereas peak oviposition occurs during the early part of the night. Behavioral responses to olfactory oviposition cues are regulated by time-of-day and can be disrupted by transient exposure to a constant darkness photoperiod. Gravid females, but not any other stage, age, or sex, were attracted to dark, round oviposition jars, possibly resembling rodent burrow openings. This visual attraction disappeared in the absence of an illumination source. Egg deposition rate was not affected by jar color. Olfactory cues had the strongest effect when the visual cues were minimal. Conclusion and significance: Our study showed, for the first time, that visual cues in the form of oviposition-site color, lighting level, and photoperiod are important in guiding the oviposition behavior of phlebotomine sand flies. Furthermore, such visual cues could modify the flies’ sensitivity to olfactory oviposition cues. Our results suggest that chemosensory and visual cues are complementary, with visual cues used to orient gravid females towards oviposition sites, possibly at long- to medium-ranges during crepuscular periods, while olfactory cues are used to approach the burrow in darkness and assess its suitability at close-range. Implications to sand fly control are discussed. DA - 2019/3// PY - 2019/3// DO - 10.1371/journal.pntd.0007165 VL - 13 IS - 3 SP - SN - 1935-2735 ER - TY - JOUR TI - Sophistical refutations in the climate change debates AU - Goodwin, Jean T2 - Journal of Argumentation in Context AB - Abstract A case study of a short televised debate between a climate scientist and an advocate for climate skepticism provides the basis for developing a contemporary conception of sophistry. The sophist has a high degree of argumentative content knowledge – knowledge of a domain selected and structured in ways that are most germane for its use in making arguments. The sophist also makes the deliberate choice to argue for a disreputable view, one that goes against the views of the majority, or of the experts. Sophistry, drawing as it does on argumentative skill, is difficult to manage. The best approach is likely to refuse debate; but if debate is unavoidable, then the sophist must be met with equal skill. It will be hard to develop such skill, however, as long as the sophist’s view is thought to be disreputable. DA - 2019/// PY - 2019/// DO - 10.1075/jaic.18008.goo VL - 8 IS - 1 SP - 40-64 J2 - JAIC LA - en OP - SN - 2211-4742 2211-4750 UR - http://dx.doi.org/10.1075/jaic.18008.goo DB - Crossref KW - argumentation KW - argument KW - sophistry KW - climate communication KW - science communication KW - climate skepticism KW - fallacies KW - argumentative content knowledge KW - scientific consensus ER - TY - JOUR TI - Training population selection and use of fixed effects to optimize genomic predictions in a historical USA winter wheat panel AU - Sarinelli, J. Martin AU - Murphy, J. Paul AU - Tyagi, Priyanka AU - Holland, James B. AU - Johnson, Jerry W. AU - Mergoum, Mohamed AU - Mason, Richard E. AU - Babar, Ali AU - Harrison, Stephen AU - Sutton, Russell AU - Griffey, Carl A. AU - Brown-Guedira, Gina T2 - THEORETICAL AND APPLIED GENETICS AB - The optimization of training populations and the use of diagnostic markers as fixed effects increase the predictive ability of genomic prediction models in a cooperative wheat breeding panel. Plant breeding programs often have access to a large amount of historical data that is highly unbalanced, particularly across years. This study examined approaches to utilize these data sets as training populations to integrate genomic selection into existing pipelines. We used cross-validation to evaluate predictive ability in an unbalanced data set of 467 winter wheat (Triticum aestivum L.) genotypes evaluated in the Gulf Atlantic Wheat Nursery from 2008 to 2016. We evaluated the impact of different training population sizes and training population selection methods (Random, Clustering, PEVmean and PEVmean1) on predictive ability. We also evaluated inclusion of markers associated with major genes as fixed effects in prediction models for heading date, plant height, and resistance to powdery mildew (caused by Blumeria graminis f. sp. tritici). Increases in predictive ability as the size of the training population increased were more evident for Random and Clustering training population selection methods than for PEVmean and PEVmean1. The selection methods based on minimization of the prediction error variance (PEV) outperformed the Random and Clustering methods across all the population sizes. Major genes added as fixed effects always improved model predictive ability, with the greatest gains coming from combinations of multiple genes. Maximum predictabilities among all prediction methods were 0.64 for grain yield, 0.56 for test weight, 0.71 for heading date, 0.73 for plant height, and 0.60 for powdery mildew resistance. Our results demonstrate the utility of combining unbalanced phenotypic records with genome-wide SNP marker data for predicting the performance of untested genotypes. DA - 2019/4// PY - 2019/4// DO - 10.1007/s00122-019-03276-6 VL - 132 IS - 4 SP - 1247-1261 SN - 1432-2242 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85060724945&partnerID=MN8TOARS ER - TY - JOUR TI - Applications of CRISPR Technologies Across the Food Supply Chain AU - Brandt, Katelyn AU - Barrangou, Rodolphe T2 - ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 10 AB - The food industry faces a 2050 deadline for the advancement and expansion of the food supply chain to support the world's growing population. Improvements are needed across crops, livestock, and microbes to achieve this goal. Since 2005, researchers have been attempting to make the necessary strides to reach this milestone, but attempts have fallen short. With the introduction of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins, the food production field is now able to achieve some of its most exciting advancements since the Green Revolution. This review introduces the concept of applying CRISPR-Cas technology as a genome-editing tool for use in the food supply chain, focusing on its implementation to date in crop, livestock, and microbe production, advancement of products to market, and regulatory and societal hurdles that need to be overcome. DA - 2019/// PY - 2019/// DO - 10.1146/annurev-food-032818-121204 VL - 10 IS - 1 SP - 133-150 SN - 1941-1413 KW - CRISPR-Cas KW - genome editing KW - crop development KW - food supply chain KW - livestock ER - TY - JOUR TI - The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size AU - Di Mambro, Riccardo AU - Svolacchia, Noemi AU - Dello Ioio, Raffaele AU - Pierdonati, Emanuela AU - Salvi, Elena AU - Pedrazzini, Emanuela AU - Vitale, Alessandro AU - Perilli, Serena AU - Sozzani, Rosangela AU - Benfey, Philip N. AU - Busch, Wolfgang AU - Costantino, Paolo AU - Sabatini, Sabrina T2 - CURRENT BIOLOGY AB - Plant developmental plasticity relies on the activities of meristems, regions where stem cells continuously produce new cells [1]. The lateral root cap (LRC) is the outermost tissue of the root meristem [1], and it is known to play an important role during root development [2-6]. In particular, it has been shown that mechanical or genetic ablation of LRC cells affect meristem size [7, 8]; however, the molecular mechanisms involved are unknown. Root meristem size and, consequently, root growth depend on the position of the transition zone (TZ), a boundary that separates dividing from differentiating cells [9, 10]. The interaction of two phytohormones, cytokinin and auxin, is fundamental in controlling the position of the TZ [9, 10]. Cytokinin via the ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) control auxin distribution within the meristem, generating an instructive auxin minimum that positions the TZ [10]. We identify a cytokinin-dependent molecular mechanism that acts in the LRC to control the position of the TZ and meristem size. We show that auxin levels within the LRC cells depends on PIN-FORMED 5 (PIN5), a cytokinin-activated intracellular transporter that pumps auxin from the cytoplasm into the endoplasmic reticulum, and on irreversible auxin conjugation mediated by the IAA-amino synthase GRETCHEN HAGEN 3.17 (GH3.17). By titrating auxin in the LRC, the PIN5 and the GH3.17 genes control auxin levels in the entire root meristem. Overall, our results indicate that the LRC serves as an auxin sink that, under the control of cytokinin, regulates meristem size and root growth. DA - 2019/4/1/ PY - 2019/4/1/ DO - 10.1016/j.cub.2019.02.022 VL - 29 IS - 7 SP - 1199-+ SN - 1879-0445 ER - TY - JOUR TI - Citizen Science in Schools: Students Collect Valuable Mammal Data for Science, Conservation, and Community Engagement AU - Schuttler, Stephanie G. AU - Sears, Rebecca S. AU - Orendain, Isabel AU - Khot, Rahul AU - Rubenstein, Daniel AU - Rubenstein, Nancy AU - Dunn, Robert R. AU - Baird, Elizabeth AU - Kandros, Kimberly AU - O'Brien, Timothy AU - Kays, Roland T2 - BIOSCIENCE AB - Citizen science has been touted as an effective means to collect large-scale data while engaging the public. We demonstrate that children as young as 9 years old can collect valuable mammal monitoring data using camera traps while connecting with nature and learning through their own scientific discoveries. Indian, Kenyan, Mexican, and American students used camera traps near their schools and detected 13–37 species, all of which were verified by professionals. These data describe rich mammal faunas near schools, sometimes surpassing nearby protected areas, and included five endangered species. Ninety-four percent of the camera traps were set in accordance with scientific protocols, and the teachers reported the experience as highly engaging for their students. Furthermore, the generated photos and results had community-wide impacts involving local politicians, community members, and the media. We show that children can run sensors to contribute valid scientific data important for conservation and research. DA - 2019/1// PY - 2019/1// DO - 10.1093/biosci/biy141 VL - 69 IS - 1 SP - 69-79 SN - 1525-3244 KW - citizen science KW - camera traps KW - mammals KW - education KW - community conservation ER - TY - JOUR TI - Peanut skin phenolic extract attenuates hyperglycemic responses in vivo and in vitro AU - Christman, Lindsey M. AU - Dean, Lisa L. AU - Allen, Jonathan C. AU - Godinez, Sofia Feng AU - Toomer, Ondulla T. T2 - PLOS ONE AB - Diabetes affects at least 285 million people globally, and this number continues to increase. Clinical complications include impaired glucose metabolism, hyperglycemia, dyslipidemia, atherosclerosis and non-alcoholic fatty liver disease. Evidence has shown that natural phenolics play a protective effect on both the development and management of type 2 diabetes. This study evaluated effects of the extract from peanut skins containing polyphenols on induced- hyperglycemia using in vivo and in vitro methods. A human hepatocellular liver carcinoma cell line (HepG2) was used to investigate the effect of the peanut skin extract on cell viability after exposure to high glucose concentrations. In vivo, the effect of peanut skin extract on an oral glucose tolerance was investigated in human subjects. Fifteen participants aged 21–32 underwent an oral glucose tolerance test with five treatments: 1) 50-gram glucose solution (reference); 2). 50-gram glucose solution, followed by 12 mg of vegi-capsulated maltodextrin; 3) 50-gram glucose solution, followed by 120 mg of vegi-capsulated maltodextrin-encapsulated peanut skin extract; 4). 50-gram glucose solution, followed by 28 grams of unfortified coated peanuts; 5) 50-gram glucose solution, followed by 28 grams of chili lime coated peanuts fortified with encapsulated peanut skin extract. Glucose levels were measured using a continuous monitor. Peanut skin extract was found to attenuate the decrease in cell viability in high glucose treated HepG2 cells, showing a protective effect against hyperglycemia induced cell death. No difference in the glycemic response area under the curve between any treatments using the tolerance test, but the treatment of the peanut skin extract with the glucose reference resulted in a significantly lower peak blood glucose response at 45 minutes, indicating that it was effective at reducing the glycemic response. The present study shows that the phenolic extract of peanut skins has an antidiabetic effect, further confirming their value as a functional food ingredient. DA - 2019/3/27/ PY - 2019/3/27/ DO - 10.1371/journal.pone.0214591 VL - 14 IS - 3 SP - SN - 1932-6203 ER - TY - JOUR TI - Effects of targeting eye color in Tenebrio molitor through RNA interference of tryptophan 2,3‐dioxygenase ( vermilion ): Implications for insect farming AU - Oppert, Brenda AU - Chu, Fu‐Chyun AU - Reyna, Steven AU - Pinzi, Sofia AU - Adrianos, Sherry AU - Perkin, Lindsey AU - Lorenzen, Marcé T2 - Archives of Insect Biochemistry and Physiology AB - Abstract The gene vermilion encodes tryptophan 2,3‐dioxygenase, part of the ommochrome pathway, and is responsible for the dark pigmented eyes in some insects, including beetles. Using RNA interference, we targeted the vermilion gene ortholog in embryos and pupae of the yellow mealworm, Tenebrio molitor , resulting in larvae and adults, respectively, that lacked eye pigment. RNA‐Seq was used to analyze the impact of vermilion ‐specific RNA interference on gene expression. There was a 425‐fold reduction in vermilion gene expression ( p = 0.0003), as well as significant ( p < 0.05) differential expression of 109 other putative genes, most of which were downregulated. Enrichment analysis of Gene Ontology terms found in the differentially expressed data set included genes known to be involved in the ommochrome pathway. However, enrichment analysis also revealed the influence of vermilion expression on genes involved in protein translocation to the endoplasmic reticulum, signal transduction, G‐protein‐coupled receptor signaling, cell‐cycle arrest, mannose biosynthesis, and vitamin transport. These data demonstrate that knockdown of vermilion in T. molitor results in complete loss of eye color (white‐eyed phenotype) and identify other interrelated genes in the vermilion metabolic pathway. Therefore, a dominant marker system based on eye color can be developed for the genetic manipulation of T. molitor to increase the value of mealworms as an alternative food source by decreasing negative traits, such as disease susceptibility, and increasing desired traits, such as protein content and vitamin production. DA - 2019/3/25/ PY - 2019/3/25/ DO - 10.1002/arch.21546 VL - 101 IS - 1 SP - e21546 J2 - Arch. Insect Biochem. Physiol LA - en OP - SN - 0739-4462 1520-6327 UR - http://dx.doi.org/10.1002/arch.21546 DB - Crossref KW - agriculture KW - entomophagy KW - farming KW - gene expression KW - insect eye color KW - protein KW - RNA-Seq KW - Tenebrio molitor KW - vermilion ER - TY - JOUR TI - Pest management by genetic addiction AU - Gould, Fred AU - Dhole, Sumit AU - Lloyd, Alun L. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - In the PNAS article “Cleave and Rescue, a novel selfish genetic element and general strategy for gene drive,” Oberhofer et al. (1) describe an exciting new mechanism for enabling a transgenic sequence to increase in frequency within a sexually reproducing population, even if the transgenic sequence causes individuals bearing it to have somewhat lower fitness than those without it. The authors liken the mechanism to the “gene addiction” that can maintain a useless plasmid in a bacterium. The work of Oberhofer et al. (1) adds substantially to a growing field within genetic engineering, often termed gene drive research, in which selfish genetic elements overcome the rules of Mendelian inheritance and push transgenes into a population. While no engineered gene drives have been released into wild populations, that is the ultimate goal, and both the technical and cultural roads toward that goal have been tortuous at times. Gene drive projects are categorized based on having one of two aims. The first is to physically link a desirable gene to a gene drive mechanism and engineer both into a viable strain of the target organism. If individuals of the strain are released into a sexually reproducing field population of that species, the DNA sequence of the drive mechanism is predicted to increase in frequency in the population and the linked, desirable gene should “hitchhike” along with it. If the population is a mosquito that transmits dengue virus, the desirable gene could be one that codes for an RNA interference molecule targeted to prevent the virus from replicating in the mosquito—thus interfering with its transmission to a person whom the mosquito subsequently bites. Projects with the second aim are designed to suppress or eliminate a pest species, be it a mosquito, rat, roach, or crop pest. Here, the gene drive mechanism itself or … [↵][1]1To whom correspondence should be addressed. Email: fred_gould{at}ncsu.edu. [1]: #xref-corresp-1-1 DA - 2019/3/26/ PY - 2019/3/26/ DO - 10.1073/pnas.1901886116 VL - 116 IS - 13 SP - 5849-5851 SN - 0027-8424 UR - http://dx.doi.org/10.1073/pnas.1901886116 ER - TY - JOUR TI - Imidacloprid is compatible with control provided by the predator Jalysus wickhami Van Duzee (Hemiptera: Berytidae) in flue-cured tobacco (Nicotiana tabacum L.) AU - Nelson, Peter N. AU - Burrack, Hannah J. AU - Sorenson, Clyde E. T2 - CROP PROTECTION AB - Jalysus wickhami Van Duzee is the most abundant predator in North Carolina flue-cured tobacco production but information on the effect of contemporary pest management practices and interactions with other arthropods is lacking. We measured the effect of systemic imidacloprid on J. wickhami in field experiments during 2015 and 2016 by surveying its abundance, the abundance of its prey; the pests Heliothis virescens (Fabricus), Manduca sexta L., and Manduca quinquemaculata (Haworth, 1803); and other predatory arthropods in the agro-ecosystem. Systemic imidacloprid applications did not reduce J. wickhami abundance nor increase the abundance of H. virescens, M. sexta, and M. quinquemaculata, indicating natural control was not affected. J. wickhami abundance was positively correlated with the abundance of prey and predators from another feeding guild, suggesting species interactions have significant implications for the predators. DA - 2019/4// PY - 2019/4// DO - 10.1016/j.cropro.2018.12.002 VL - 118 SP - 15-20 SN - 1873-6904 KW - Integrated pest management KW - Biological control KW - Neonicotinoid KW - Systemic insecticides KW - Heliothis virescens KW - Manduca sexta ER - TY - JOUR TI - Sustainability as a Framework for Considering Gene Drive Mice for Invasive Rodent Eradication AU - Barnhill-Dilling, S. AU - Serr, Megan AU - Blondel, Dimitri AU - Godwin, John T2 - Sustainability AB - Gene drives represent a dynamic and controversial set of technologies with applications that range from mosquito control to the conservation of biological diversity on islands. Currently, gene drives are being developed in mice that may one day serve as an important tool for reducing invasive rodent pests, a key threat to island biodiversity and economies. Gene drives in mice are still in development in laboratories, and wild release of modified mice is likely a distant reality. However, technological changes outpace the existing capacity of regulatory frameworks, and thus require integrated governance frameworks. We suggest sustainability—which gives equal consideration to the environment, economy, and society—as one framework for addressing complexity and uncertainty in the governance of emerging gene drive technologies for invasive species management. We explore the impacts of rodent gene drives on island environments, including potential conservation and restoration of island biodiversity. We outline considerations for rodent gene drives on island economies, including impacts on agricultural and tourism losses, and reductions in biosecurity costs. Finally, we address the social dimension as an essential space for deliberation that will be integral to evaluating the potential deployment of gene drive rodents on islands. DA - 2019/3/4/ PY - 2019/3/4/ DO - 10.3390/su11051334 VL - 11 IS - 5 SP - 1334 J2 - Sustainability LA - en OP - SN - 2071-1050 UR - http://dx.doi.org/10.3390/su11051334 DB - Crossref KW - gene drives KW - invasive species management KW - sustainability ER - TY - JOUR TI - Determining Frankliniella fusca (Thysanoptera: Thripidae) Egg Distribution in Neonicotinoid Seed-Treated Cotton AU - Damon A. D'Ambrosio, AU - Huseth, Anders S. AU - Kennedy, George G. T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - Frankliniella fusca (Hinds) (Thysanoptera: Thripidae) is an early-season cotton pest. Seedlings are injured by larvae, which hatch from eggs oviposited into seedlings and feed on developing plant tissue. Better understanding F. fusca oviposition in cotton may improve their management and address new challenges such as resistance to neonicotinoid seed treatments (NSTs). Cotton seedlings exposed to F. fusca were either cleared and stained to determine egg density and location, or dissected and washed to determine larval distribution. Experiments were conducted in the greenhouse with a susceptible population and field with a NST-resistant population. Eggs of both populations were recovered predominantly in cotyledons. Larvae were more uniformly distributed on seedlings. On NST seedlings, oviposition by the susceptible population was reduced and preference shifted to true leaves. NSTs did not alter egg placement by the resistant population. These findings suggest that injury to cotton seedlings is primarily caused by F. fusca emerging on the cotyledons, and then moving to developing leaves. The oviposition shift in NST plants correlates with how systemic NSTs have been reported to concentrate in cotyledons. This can better inform management tactics in cotton, such as well-timed foliar sprays, which, given the current resistance issue, are needed to maintain effective thrips management. DA - 2019/4// PY - 2019/4// DO - 10.1093/jee/toy393 VL - 112 IS - 2 SP - 827-834 SN - 1938-291X KW - imidacloprid KW - thiamethoxam KW - resistance management KW - tobacco thrip KW - Gossypium hirsutum ER - TY - JOUR TI - Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract AU - Foley, Matthew H. AU - O'Flaherty, Sarah AU - Barrangou, Rodolphe AU - Theriot, Casey M. T2 - PLOS PATHOGENS AB - Research on bile acids has increased dramatically due to recent studies demonstrating their ability to significantly impact the host, microbiome, and various disease states [1–3]. Although these liver-synthesized molecules assist in the absorption and digestion of dietary fat in the intestine, their reabsorption and recirculation also gives them access to peripheral organs [4] (Fig 1A). Bile acids serve as substrates for bile acid receptors (BARs) found throughout the body that control critical regulatory and metabolic processes and therefore represent an important class of bioactive molecules [5]. Despite the importance of bile acids to host health, there remain gaps in our knowledge about the bacterial enzymes driving their composition and modification. Open in a separate window Fig 1 Bile salt hydrolases act on circulating conjugated bile acids in the gut-liver axis. (A) Bile acids synthesized in the liver and stored in the gall bladder enter the small intestine through the duodenum where they reach millimolar concentrations. The majority of bile acids (95%) are reabsorbed in the ileum and recirculate to the liver through the portal vein. The remaining population transit to the colon as they continue to be reabsorbed, and a small (<5%) amount exit through the feces. Recirculating bile acids access host tissues outside the intestines to impart systemic effects on host physiology. (B) BSHs cleave the amide bond in conjugated bile acids to open up the bile acid pool to increased complexity. The gut microbiota performs additional chemistry on deconjugated bile acids to generate the secondary bile acid pool, which can undergo enterohepatic circulation and be reconjugated in the liver. These transformations are illustrated to the right as conjugated CA is deconjugated, subjected to 7 α-dehydroxylation to become DCA, and subsequently reconjugated. (C) Monomeric BSH overlay from Bifidobacterium longum (PDB ID 2HEZ), Enteroccocus faecalis (PDB ID 4WL3), Lactobacillus salivarius (PDB ID 5HKE), and Clostridium perfringens (PDB ID 2BJF). Hydrolyzed TDCA in the CpBSH active site is coordinated by several loops that contain the most variation in the peptide backbone compared to the other structures. BSH, bile salt hydrolase; CA, cholic acid; CpBSH, C. perfringens BSH; DCA,; TDCA, taurodeoxycholic acid; PDB ID, Protein Data Bank ID. DA - 2019/3// PY - 2019/3// DO - 10.1371/journal.ppat.1007581 VL - 15 IS - 3 SP - SN - 1553-7374 UR - https://doi.org/10.1371/journal.ppat.1007581 ER - TY - JOUR TI - Associations between access to healthcare, environmental quality, and end-stage renal disease survival time: Proportional-hazards models of over 1,000,000 people over 14 years AU - Kosnik, Marissa B. AU - Reif, David M. AU - Lobdell, Danelle T. AU - Astell-Burt, Thomas AU - Feng, Xiaoqi AU - Hader, John D. AU - Hoppin, Jane A. T2 - PLOS ONE AB - Prevalence of end-stage renal disease (ESRD) in the US increased by 74% from 2000 to 2013. To investigate the role of the broader environment on ESRD survival time, we evaluated average distance to the nearest hospital by county (as a surrogate for access to healthcare) and the Environmental Quality Index (EQI), an aggregate measure of ambient environmental quality composed of five domains (air, water, land, built, and sociodemographic), at the county level across the US. Associations between average hospital distance, EQI, and survival time for 1,092,281 people diagnosed with ESRD between 2000 and 2013 (age 18+, without changes in county residence) from the US Renal Data System were evaluated using proportional-hazards models adjusting for gender, race, age at first ESRD service date, BMI, alcohol and tobacco use, and rurality. The models compared the average distance to the nearest hospital (<10, 10–20, >20 miles) and overall EQI percentiles [0–5), [5–20), [20–40), [40–60), [60–80), [80–95), and [95–100], where lower percentiles are interpreted as better EQI. In the full, non-stratified model with both distance and EQI, there was increased survival for patients over 20 miles from a hospital compared to those under 10 miles from a hospital (hazard ratio = 1.14, 95% confidence interval = 1.12–1.15) and no consistent direction of association across EQI strata. In the full model stratified by average hospital distance, under 10 miles from a hospital had increased survival in the worst EQI strata (median survival 3.0 vs. 3.5 years for best vs. worst EQI, respectively), however for people over 20 miles from a hospital, median survival was higher in the best (4.2 years) vs worst (3.4 years) EQI. This association held across different rural/urban categories and age groups. These results demonstrate the importance of considering multiple factors when studying ESRD survival and future efforts should consider additional components of the broader environment. DA - 2019/3/21/ PY - 2019/3/21/ DO - 10.1371/journal.pone.0214094 VL - 14 IS - 3 SP - SN - 1932-6203 UR - https://doi.org/10.1371/journal.pone.0214094 ER - TY - JOUR TI - Drosophila suzukii (Diptera: Drosophilidae) Oviposition and Adult Emergence in Six Wine Grape Varieties Grown in Virginia AU - Shrader, Meredith Edana AU - Burrack, Hannah J. AU - Pfeiffer, Douglas G. T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - Drosophila suzukii (Matsumura) is a pest of small fruits and grapes in the United States and in its home range of Japan. Physiological and morphological laboratory testing was performed on six commonly grown wine grape varieties in Virginia. Skin thickness, penetration force, and ºBrix were analyzed to determine ovipositional preferences. Experiments were performed for three consecutive years from grapes collected at one Virginia vineyard. More eggs were laid in intact Viognier grapes than any other variety. Oviposition into intact grapes was not affected by skin thickness or ºBrix; however, oviposition increased when penetration force decreased. An ovipositional choice test determined no varietal preferences. Survivorship from egg to adulthood using uninjured and injured grapes was also assessed to determine varietal suitability as D. suzukii hosts, with more flies emerging from injured grapes than uninjured. However, D. suzukii adults did emerge from intact grapes and at higher percentages than previously recorded in other wine grape studies. All varieties had eggs oviposited into them when injured. Determining the time at which each grape variety became susceptible to oviposition was determined using a D. suzukii bioassay spanning 12 wk using grapes from the green pea stage until ripe. Susceptibility to D. suzukii oviposition was based upon ripening period and penetration force. Early ripening varieties may be more susceptible to D. suzukii oviposition in the field with later maturing, harder fleshed-varieties which may escape D. suzukii oviposition. DA - 2019/2// PY - 2019/2// DO - 10.1093/jee/toy305 VL - 112 IS - 1 SP - 139-148 SN - 1938-291X KW - wine grape KW - penetration force KW - susceptibility KW - survivorship KW - skin thickness ER - TY - JOUR TI - Taxonomy of the order Mononegavirales: second update 2018 AU - Maes, Piet AU - Amarasinghe, Gaya K. AU - Ayllon, Maria A. AU - Basler, Christopher F. AU - Bavari, Sina AU - Blasdell, Kim R. AU - Briese, Thomas AU - Brown, Paul A. AU - Bukreyev, Alexander AU - Balkema-Buschmann, Anne AU - Buchholz, Ursula J. AU - Chandran, Kartik AU - Crozier, Ian AU - Swart, Rik L. AU - Dietzgen, Ralf G. AU - Dolnik, Olga AU - Domier, Leslie L. AU - Drexler, Jan F. AU - Duerrwald, Ralf AU - Dundon, William G. AU - Duprex, W. Paul AU - Dye, John M. AU - Easton, Andrew J. AU - Fooks, Anthony R. AU - Formenty, Pierre B. H. AU - Fouchier, Ron A. M. AU - Freitas-Astua, Juliana AU - Ghedin, Elodie AU - Griffiths, Anthony AU - Hewson, Roger AU - Horie, Masayuki AU - Hurwitz, Julia L. AU - Hyndman, Timothy H. AU - Jiang, Daohong AU - Kobinger, Gary P. AU - Kondo, Hideki AU - Kurath, Gael AU - Kuzmin, Ivan V. AU - Lamb, Robert A. AU - Lee, Benhur AU - Leroy, Eric M. AU - Li, Jianrong AU - Marzano, Shin-Yi L. AU - Muhlberger, Elke AU - Netesov, Sergey V. AU - Nowotny, Norbert AU - Palacios, Gustavo AU - Palyi, Bernadett AU - Paweska, Janusz T. AU - Payne, Susan L. AU - Rima, Bertus K. AU - Rota, Paul AU - Rubbenstroth, Dennis AU - Simmonds, Peter AU - Smither, Sophie J. AU - Song, Qisheng AU - Song, Timothy AU - Spann, Kirsten AU - Stenglein, Mark D. AU - Stone, David M. AU - Takada, Ayato AU - Tesh, Robert B. AU - Tomonaga, Keizo AU - Tordo, Noel AU - Towner, Jonathan S. AU - Hoogen, Bernadette AU - Vasilakis, Nikos AU - Wahl, Victoria AU - Walker, Peter J. AU - Wang, David AU - Wang, Lin-Fa AU - Whitfield, Anna E. AU - Williams, John V. AU - Ye, Gongyin AU - Murilo Zerbini, F. AU - Zhang, Yong-Zhen AU - Kuhn, Jens H. T2 - ARCHIVES OF VIROLOGY AB - In October 2018, the order Mononegavirales was amended by the establishment of three new families and three new genera, abolishment of two genera, and creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). DA - 2019/4// PY - 2019/4// DO - 10.1007/s00705-018-04126-4 VL - 164 IS - 4 SP - 1233-1244 SN - 1432-8798 ER - TY - JOUR TI - The genetic architecture of teosinte catalyzed and constrained maize domestication AU - Yang, Chin Jian AU - Samayoa, Luis Fernando AU - Bradbury, Peter J. AU - Olukolu, Bode A. AU - Xue, Wei AU - York, Alessandra M. AU - Tuholski, Michael R. AU - Wang, Weidong AU - Daskalska, Lora L. AU - Neumeyer, Michael A. AU - Jesus Sanchez-Gonzalez, Jose AU - Romay, Maria Cinta AU - Glaubitz, Jeffrey C. AU - Sun, Qi AU - Buckler, Edward S. AU - Holland, James B. AU - Doebley, John F. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - The process of evolution under domestication has been studied using phylogenetics, population genetics-genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance-covariance matrices (G-matrices). While the structure of G-matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory. DA - 2019/// PY - 2019/// DO - 10.1073/pnas.1820997116 VL - 116 IS - 12 SP - 5643-5652 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85063274624&partnerID=MN8TOARS ER - TY - JOUR TI - Differential germination strategies of native and introduced populations of the invasive species Plantago virginica AU - Xu, Xinyu AU - Wolfe, Lorne AU - Diez, Jeffrey AU - Zheng, Yi AU - Guo, Hui AU - Hu, Shuijin T2 - NEOBIOTA AB - Germination strategies are critically important for the survival, establishment and spread of plant species. Although many plant traits related to invasiveness have been broadly studied, the earliest part of the life cycle, germination, has received relatively little attention. Here, we compared the germination patterns between native (North America) and introduced (China) populations of Plantagovirginica for four consecutive years to examine whether there has been adaptive differentiation in germination traits and how these traits are related to local climatic conditions. We found that the introduced populations of P.virginica had significantly higher germination percentages and faster and shorter durations of germination than native populations. Critically, the native populations had a significantly larger proportion of seeds that stayed dormant in all four years, with only 60% of seeds germinating in year 1 (compared to &gt;95% in introduced populations). These results demonstrate striking differences in germination strategies between native and introduced populations which may contribute to their successful invasion. Moreover, the germination strategy of P.virginica in their native range exhibited clear geographical variation across populations, with trends towards higher germination percentages at higher latitudes and lower annual mean temperatures and annual precipitation. In the introduced range, however, their germination strategies were more conserved, with less variation amongst populations, suggesting that P.virginica may have experienced strong selection for earlier life history characteristics. Our findings highlight the need to examine the role of rapid evolution of germination traits in facilitating plant invasion. DA - 2019/3/19/ PY - 2019/3/19/ DO - 10.3897/neobiota.43.30392 IS - 43 SP - 101-118 SN - 1314-2488 KW - Adaptation KW - germination strategy KW - native and introduced populations KW - invasive species KW - Plantago virginica ER - TY - JOUR TI - RGL2 controls flower development, ovule number and fertility in Arabidopsis AU - Dolores Gomez, Maria AU - Fuster-Almunia, Clara AU - Ocana-Cuesta, Javier AU - Alonso, Jose M. AU - Perez-Amador, Miguel A. T2 - PLANT SCIENCE AB - DELLA proteins are a group of plant specific GRAS proteins of transcriptional regulators that have a key role in gibberellin (GA) signaling. In Arabidopsis, the DELLA family is formed by five members. The complexity of this gene family raises the question on whether single DELLA proteins have specific or overlapping functions in the control of several GA-dependent developmental processes. To better understand the roles played by RGL2, one of the DELLA proteins in Arabidopsis, two transgenic lines that express fusion proteins of Venus-RGL2 and a dominant version of RGL2, YPet-rgl2Δ17, were generated by recombineering strategy using a genomic clone that contained the RGL2 gene. The dominant YPet-rgl2Δ17 protein is not degraded by GAs, and therefore it blocks the RGL2-dependent GA signaling and hence RGL2-dependent development. The RGL2 role in seed germination was further confirmed using these genetic tools, while new functions of RGL2 in plant development were uncovered. RGL2 has a clear function in the regulation of flower development, particularly stamen growth and anther dehiscence, which has a great impact in fertility. Moreover, the increased ovule number in the YPet-rgl2Δ17 line points out the role of RGL2 in the determination of ovule number. DA - 2019/4// PY - 2019/4// DO - 10.1016/j.plantsci.2019.01.014 VL - 281 SP - 82-92 SN - 0168-9452 KW - Gibberellin KW - DELLA KW - RGL2 KW - Arabidopsis KW - Development KW - Ovule ER - TY - JOUR TI - Inheritance of Resistance to Colletotrichum gloeosporioides and C-acutatum 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 - PHYTOPATHOLOGY AB - Information on the inheritance of resistance to Colletotrichum gloeosporioides and C. acutatum hemibiotrophic infections (HBI) in strawberry leaf tissue and the genetic control of anthracnose crown rot (ACR) in crown tissue are relatively unknown. Six parental genotypes were crossed in a half-diallel mating design to generate 15 full-sib families. HBI and ACR experiments were conducted concurrently. Both seedlings and parental clones were inoculated with 1 × 106 conidia/ml of C. gloeosporioides or C. acutatum. Percent sporulating leaf area, wilt symptoms, and relative area under the disease progress curve were calculated to characterize resistance among genotypes and full-sib families. Low dominance/additive variance ratios for C. acutatum HBI (0.13) and C. gloeosporioides ACR (0.20) were observed, indicating additive genetic control of resistance to these traits. Heritability estimates were low for C. acutatum HBI (0.25) and C. gloeosporioides HBI (0.16) but moderate for C. gloeosporioides ACR (0.61). A high genetic correlation (rA = 0.98) between resistance to C. acutatum HBI and C. gloeosporioides HBI was observed, suggesting that resistance to these two Colletotrichum spp. may be controlled by common genes in strawberry leaf tissue. In contrast, negative genetic correlations between ACR and both HBI traits (rA = -0.85 and -0.61) suggest that resistance in crown tissue is inherited independently of resistance in leaf tissue in the populations tested. Overall, these findings provide valuable insight into the genetic basis of resistance, and the evaluation and deployment of resistance to HBIs and ACR in strawberry breeding programs. DA - 2019/3// PY - 2019/3// DO - 10.1094/PHYTO-08-18-0283-R VL - 109 IS - 3 SP - 428-435 SN - 1943-7684 ER - TY - JOUR TI - Draft Aphaenogaster genomes expand our view of ant genome size variation across climate gradients AU - Lau, Matthew K. AU - Ellison, Aaron M. AU - Nguyen, Andrew AU - Penick, Clint AU - DeMarcos, Bernice AU - Gotelli, Nicholas J. AU - Sanders, Nathan J. AU - Dunn, Robert R. AU - Cahan, Sara Helms T2 - PEERJ AB - Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of >16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster , a genus with important seed dispersers. In total, we sampled seven colonies of six species: Aphaenogaster ashmeadi , Aphaenogaster floridana , Aphaenogaster fulva , Aphaenogaster miamiana , Aphaenogaster picea , and Aphaenogaster rudis . The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The Aphaenogaster genomes displayed high levels of completeness with 96.1% to 97.6% of Hymenoptera BUSCOs completely represented, relative to currently sequenced ant genomes which ranged from 88.2% to 98.5%. Additionally, the mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8–396.0 Mb) and flow cytometry estimates (210.7–690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature, and annual precipitation had the strongest correlations with genome size, with ants from locations with colder minimum temperatures and higher levels of precipitation having larger genomes. These results suggest that climate extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes. DA - 2019/3/11/ PY - 2019/3/11/ DO - 10.7717/peerj.6447 VL - 7 SP - SN - 2167-8359 KW - Ants KW - Genomics KW - Ecology KW - Climate change KW - Evolution KW - Adaptation ER - TY - JOUR TI - A Simple Model to Predict the Potential Abundance of Aedes aegypti Mosquitoes One Month in Advance AU - Monaghan, Andrew J. AU - Schmidt, Christopher A. AU - Hayden, Mary H. AU - Smith, Kirk A. AU - Reiskind, Michael H. AU - Cabell, Ryan AU - Ernst, Kacey C. T2 - AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE AB - The mosquito Aedes (Stegomyia) aegypti (L.) is the primary vector of dengue, chikungunya, and Zika viruses in the United States. Surveillance for adult Ae. aegypti is limited, hindering understanding of the mosquito’s seasonal patterns and predictions of areas at elevated risk for autochthonous virus transmission. We developed a simple, intuitive empirical model that uses readily available temperature and humidity variables to predict environmental suitability for low, medium, or high potential abundance of adult Ae. aegypti in a given city 1 month in advance. Potential abundance was correctly predicted in 73% of months in arid Phoenix, AZ (over a 10-year period), and 63% of months in humid Miami, FL (over a 2-year period). The monthly model predictions can be updated daily, weekly, or monthly and thus may be applied to forecast suitable conditions for Ae. aegypti to inform vector-control activities and guide household-level actions to reduce mosquito habitat and human exposure. DA - 2019/// PY - 2019/// DO - 10.4269/ajtmh.17-0860 VL - 100 IS - 2 SP - 434-437 SN - 1476-1645 ER - TY - JOUR TI - Papers From a Workshop on Mosquito Ecology and Evolution Inspired by the Career of L. Philip Lounibos AU - Juliano, Steven A. AU - Yee, Donald A. AU - Alto, Barry W. AU - Reiskind, Michael H. T2 - JOURNAL OF MEDICAL ENTOMOLOGY DA - 2019/3// PY - 2019/3// DO - 10.1093/jme/tjy146 VL - 56 IS - 2 SP - 299-302 SN - 1938-2928 ER - TY - JOUR TI - A Statewide Survey of Container Aedes Mosquitoes (Diptera: Culicidae) in North Carolina, 2016: A Multiagency Surveillance Response to Zika Using Ovitraps AU - Reed, Emily M. X. AU - Byrd, Brian D. AU - Richards, Stephanie L. AU - Eckardt, Megan AU - Williams, Carl AU - Reiskind, Michael H. T2 - JOURNAL OF MEDICAL ENTOMOLOGY AB - Native and invasive container-inhabiting Aedes mosquitoes (Diptera: Culicidae) play important roles in the transmission of endemic and traveler-introduced arboviruses in the United States. In response to the emergence of Zika virus into the Americas, we surveyed the distribution of container Aedes spp. of public health importance within North Carolina during 2016 using ovitraps. A seasonal survey was conducted in 18 counties from the mountains to the coast to identify species incriminated in the transmission of chikungunya, dengue, La Crosse, yellow fever, and Zika viruses. Multiple local, state, and federal agencies participated in the study and submitted more than 3,600 ovistrips. Aedes albopictus (Skuse) (81.4%, n = 54,458) was the most common and widespread species found in this survey, followed by Aedes triseriatus (Say) (10.7%, n = 7,169) and Aedes japonicus (Theobald) (7.9%, n = 5,262). We did not find Aedes aegypti and rarely found Aedes hendersoni (Cockerell). We assessed broad-scale climatic and other factors and determined that longitude, elevation, rainfall, and temperature had significant effects on explaining the variation in presence, abundance, and phenology of container Aedes in North Carolina. However, much of the variation in these outcomes was not explained at this coarse scale and may benefit from finer-scale analyses. These efforts represent the largest ovitrap survey ever conducted in the state. DA - 2019/3// PY - 2019/3// DO - 10.1093/jme/tjy190 VL - 56 IS - 2 SP - 483-490 SN - 1938-2928 KW - Aedes albopictus KW - Aedes triseriatus KW - Aedes japonicus KW - distribution ER - TY - JOUR TI - Diverse Components of Resistance to Fusarium verticillioides Infection and Fumonisin Contamination in Four Maize Recombinant Inbred Families AU - Morales, Laura AU - Zila, Charles T. AU - Mejia, Danilo E. Moreta AU - Arbelaez, Melissa Montoya AU - Balint-Kurti, Peter J. AU - Holland, James B. AU - Nelson, Rebecca J. T2 - TOXINS AB - The fungus Fusarium verticillioides can infect maize ears, causing Fusarium ear rot (FER) and contaminating the grain with fumonisins (FUM), which are harmful to humans and animals. Breeding for resistance to FER and FUM and post-harvest sorting of grain are two strategies for reducing FUM in the food system. Kernel and cob tissues have been previously associated with differential FER and FUM. Four recombinant inbred line families from the maize nested associated mapping population were grown and inoculated with F. verticillioides across four environments, and we evaluated the kernels for external and internal infection severity as well as FUM contamination. We also employed publicly available phenotypes on innate ear morphology to explore genetic relationships between ear architecture and resistance to FER and FUM. The four families revealed wide variation in external symptomatology at the phenotypic level. Kernel bulk density under inoculation was an accurate indicator of FUM levels. Genotypes with lower kernel density-under both inoculated and uninoculated conditions-and larger cobs were more susceptible to infection and FUM contamination. Quantitative trait locus (QTL) intervals could be classified as putatively resistance-specific and putatively shared for ear and resistance traits. Both types of QTL mapped in this study had substantial overlap with previously reported loci for resistance to FER and FUM. Ear morphology may be a component of resistance to F. verticillioides infection and FUM accumulation. DA - 2019/2// PY - 2019/2// DO - 10.3390/toxins11020086 VL - 11 IS - 2 SP - SN - 2072-6651 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85061125912&partnerID=MN8TOARS KW - maize KW - mycotoxins KW - fumonisin KW - disease resistance KW - morphology ER - TY - JOUR TI - Exotic urban trees conserve similar natural enemy communities to native congeners but have fewer pests AU - Frank, Steven D. AU - Backe, Kristi M. AU - McDaniel, Casey AU - Green, Matthew AU - Widney, Sarah AU - Dunn, Robert R. T2 - PEERJ AB - Urban trees serve a critical conservation function by supporting arthropod and vertebrate communities but are often subject to arthropod pest infestations. Native trees are thought to support richer arthropod communities than exotic trees but may also be more susceptible to herbivorous pests. Exotic trees may be less susceptible to herbivores but provide less conservation value as a consequence. We tested the hypotheses that native species in Acer and Quercus would have more herbivorous pests than exotic congeners and different communities of arthropod natural enemies. The density of scale insects, common urban tree pests, was greatest on a native Acer and a native Quercus than exotic congeners in both years of our research (2012 and 2016) and sometimes reached damaging levels. However, differences in predator and parasitoid abundance, diversity, and communities were not consistent between native and exotic species in either genus and were generally similar. For example, in 2012 neither predator nor parasitoid abundance differed among native and exotic Acer congeners but in 2016 a native species, A. saccharum , had the least of both groups. A native, Q. phellos , had significantly more predators and parasitoids in 2012 than its native and exotic congeners but no differences in 2016. Parasitoid communities were significantly different among Acer species and Quercus species due in each case to greater abundance of a single family on one native tree species. These native and exotic tree species could help conserve arthropod natural enemies and achieve pest management goals. DA - 2019/3/7/ PY - 2019/3/7/ DO - 10.7717/peerj.6531 VL - 7 SP - SN - 2167-8359 KW - Urban trees KW - Parasitoids KW - Conservation KW - Pest management KW - Exotic trees KW - Acer spp. (maple) KW - Quercus spp. (oaks) KW - Natural enemies KW - Native trees KW - Scale insects (Coccoidea) ER - TY - JOUR TI - Optimal Designs for Genomic Selection in Hybrid Crops AU - Guo, Tingting AU - Yu, Xiaoqing AU - Li, Xianran AU - Zhang, Haozhe AU - Zhu, Chengsong AU - Flint-Garcia, Sherry AU - McMullen, Michael D. AU - Holland, James B. AU - Szalma, Stephen J. AU - Wisser, Randall J. AU - Yu, Jianming T2 - MOLECULAR PLANT AB - Improved capacity of genomics and biotechnology has greatly enhanced genetic studies in different areas. Genomic selection exploits the genotype-to-phenotype relationship at the whole-genome level and is being implemented in many crops. Here we show that design-thinking and data-mining techniques can be leveraged to optimize genomic prediction of hybrid performance. We phenotyped a set of 276 maize hybrids generated by crossing founder inbreds of nested association mapping populations for flowering time, ear height, and grain yield. With 10 296 310 SNPs available from the parental inbreds, we explored the patterns of genomic relationships and phenotypic variation to establish training samples based on clustering, graphic network analysis, and genetic mating scheme. Our analysis showed that training set designs outperformed random sampling and earlier methods that either minimize the mean of prediction error variance or maximize the mean of generalized coefficient of determination. Additional analyses of 2556 wheat hybrids from an early-stage hybrid breeding system and 1439 rice hybrids from an established hybrid breeding system validated the approaches. Together, we demonstrated that effective genomic prediction models can be established with a training set 2%-13% of the size of the whole set, enabling an efficient exploration of enormous inference space of genetic combinations. DA - 2019/3/4/ PY - 2019/3/4/ DO - 10.1016/j.molp.2018.12.022 VL - 12 IS - 3 SP - 390-401 SN - 1752-9867 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85061008767&partnerID=MN8TOARS KW - data mining KW - molecular breeding KW - genomic relationship KW - genomic selection KW - optimal design ER - TY - JOUR TI - An agent-based modeling approach to project adoption of water reuse and evaluate expansion plans within a sociotechnical water infrastructure system AU - Kandiah, Venu K. AU - Berglund, Emily Z. AU - Binder, Andrew R. T2 - SUSTAINABLE CITIES AND SOCIETY AB - The introduction of water reuse infrastructure into an existing water supply system is a complex sociotechnical process. For a dual reticulation program, infrastructure designs affect adoption, as the expansion of infrastructure defines when a household can adopt and become active in communicating about water reuse. This research develops a coupled framework to capture the dynamics among consumer adoption and infrastructure expansion. An agent-based modeling approach is used to simulate opinion dynamics within a risk publics framework, which is based on the social amplification of risk and captures changes in perceptions about the risks and benefits of water reuse. The model is applied to simulate and project adoption of water reuse for the Town of Cary, North Carolina, using data about new water reclamation accounts and plans for infrastructure expansion. Performance of the agent-based model is compared with a cellular automata model for simulating historic data. Alternative infrastructure expansion schedules are simulated using the agent-based model to evaluate potable water savings and utilization of reclaimed water capacity, based on adoption projections. The framework provides a sociotechnical approach to evaluate development plans for infrastructure systems that rely on adoption of infrastructure-dependent technologies. DA - 2019/4// PY - 2019/4// DO - 10.1016/j.scs.2018.12.040 VL - 46 SP - SN - 2210-6715 UR - https://publons.com/publon/21063760/ KW - Complex adaptive system KW - Diffusion of innovations KW - Dual water system KW - Sociotechnical transition KW - Urban water management KW - Water reuse KW - Eco-innovation ER - TY - JOUR TI - Taxonomy of the order Bunyavirales: second update 2018 AU - Maes, Piet AU - Adkins, Scott AU - Alkhovsky, Sergey V. AU - Avsic-Zupanc, Tatjana AU - Ballinger, Matthew J. AU - Bente, Dennis A. AU - Beer, Martin AU - Bergeron, Eric AU - Blair, Carol D. AU - Briese, Thomas AU - Buchmeier, Michael J. AU - Burt, Felicity J. AU - Calisher, Charles H. AU - Charrel, Remi N. AU - Choi, Il Ryong AU - Clegg, J. Christopher S. AU - Torre, Juan Carlos AU - Lamballerie, Xavier AU - DeRisi, Joseph L. AU - Digiaro, Michele AU - Drebot, Mike AU - Ebihara, Hideki AU - Elbeaino, Toufic AU - Ergunay, Koray AU - Fulhorst, Charles F. AU - Garrison, Aura R. AU - Gao, George Fu AU - Gonzalez, Jean-Paul J. AU - Groschup, Martin H. AU - Guenther, Stephan AU - Haenni, Anne-Lise AU - Hall, Roy A. AU - Hewson, Roger AU - Hughes, Holly R. AU - Jain, Rakesh K. AU - Jonson, Miranda Gilda AU - Junglen, Sandra AU - Klempa, Boris AU - Klingstrom, Jonas AU - Kormelink, Richard AU - Lambert, Amy J. AU - Langevin, Stanley A. AU - Lukashevich, Igor S. AU - Marklewitz, Marco AU - Martelli, Giovanni P. AU - Mielke-Ehret, Nicole AU - Mirazimi, Ali AU - Muehlbach, Hans-Peter AU - Naidu, Rayapati AU - Teixeira Nunes, Marcio Roberto AU - Palacios, Gustavo AU - Papa, Anna AU - Paweska, Janusz T. AU - Peters, Clarence J. AU - Plyusnin, Alexander AU - Radoshitzky, Sheli R. AU - Resende, Renato O. AU - Romanowski, Victor AU - Sall, Amadou Alpha AU - Salvato, Maria S. AU - Sasaya, Takahide AU - Schmaljohn, Connie AU - Shi, Xiaohong AU - Shirako, Yukio AU - Simmonds, Peter AU - Sironi, Manuela AU - Song, Jin-Won AU - Spengler, Jessica R. AU - Stenglein, Mark D. AU - Tesh, Robert B. AU - Turina, Massimo AU - Wei, Taiyun AU - Whitfield, Anna E. AU - Yeh, Shyi-Dong AU - Murilo Zerbini, F. AU - Zhang, Yong-Zhen AU - Zhou, Xueping AU - Kuhn, Jens H. T2 - ARCHIVES OF VIROLOGY AB - In October 2018, the order Bunyavirales was amended by inclusion of the family Arenaviridae, abolishment of three families, creation of three new families, 19 new genera, and 14 new species, and renaming of three genera and 22 species. This article presents the updated taxonomy of the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). DA - 2019/3// PY - 2019/3// DO - 10.1007/s00705-018-04127-3 VL - 164 IS - 3 SP - 927-941 SN - 1432-8798 ER - TY - JOUR TI - Crosscutting concepts and achievement: Is a sense of size and scale related to achievement in science and mathematics? AU - Chesnutt, Katherine AU - Jones, M. Gail AU - Corin, Elysa N. AU - Hite, Rebecca AU - Childers, Gina AU - Perez, Mariana P. AU - Cayton, Emily AU - Ennes, Megan T2 - JOURNAL OF RESEARCH IN SCIENCE TEACHING AB - Abstract This study examined the relationship between students' ( N = 229) concepts of size and scale and students' achievement in science and mathematics over a 3‐year period. Size and scale are considered one of the big ideas in science that permeates disparate science and mathematics content areas, yet little is known about the relationship between students' conceptualization of size and scale and students' achievement in science and mathematics. The study used a modified panel longitudinal design to follow the same class of students over a 3‐year period. The goal was to explore whether understandings of size and scale are related to achievement in mathematics and science. Results indicated a strong positive significant relationship existed between students' understanding of size and scale and students' science achievement in grades 5 and 8. There was a positive significant relationship between students' concepts of size and scale and students' mathematics achievement in grades 5, 6, 7, and 8. An examination of the relationships is included as well as a discussion of the integration of crosscutting concepts into science and mathematics instruction as a way to support deep learning. DA - 2019/3// PY - 2019/3// DO - 10.1002/tea.21511 VL - 56 IS - 3 SP - 302-321 SN - 1098-2736 KW - achievement KW - crosscutting concepts KW - scale ER - TY - JOUR TI - Extremely Thermoacidophilic Metallosphaera Species Mediate Mobilization and Oxidation of Vanadium and Molybdenum Oxides AU - Wheaton, Garrett H. AU - Vitko, Nicholas P. AU - Counts, James A. AU - Dulkis, Jessica A. AU - Podolsky, Igor AU - Mukherjee, Arpan AU - Kelly, Robert M. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Certain species from the extremely thermoacidophilic genus Metallosphaera directly oxidize Fe(II) to Fe(III), which in turn catalyzes abiotic solubilization of copper from chalcopyrite to facilitate recovery of this valuable metal. In this process, the redox status of copper does not change as it is mobilized. Metallosphaera species can also catalyze the release of metals from ores with a change in the metal's redox state. For example, Metallosphaera sedula catalyzes the mobilization of uranium from the solid oxide U3O8, concomitant with the generation of soluble U(VI). Here, the mobilization of metals from solid oxides (V2O3, Cu2O, FeO, MnO, CoO, SnO, MoO2, Cr2O3, Ti2O3, and Rh2O3) was examined for M. sedula and M. prunae at 70°C and pH 2.0. Of these oxides, only V and Mo were solubilized, a process accelerated in the presence of FeCl3 However, it was not clear whether the solubilization and oxidation of these metals could be attributed entirely to an Fe-mediated indirect mechanism. Transcriptomic analysis for growth on molybdenum and vanadium oxides revealed transcriptional patterns not previously observed for growth on other energetic substrates (i.e., iron, chalcopyrite, organic compounds, reduced sulfur compounds, and molecular hydrogen). Of particular interest was the upregulation of Msed_1191, which encodes a Rieske cytochrome b6 fusion protein (Rcbf, referred to here as V/MoxA) that was not transcriptomically responsive during iron biooxidation. These results suggest that direct oxidation of V and Mo occurs, in addition to Fe-mediated oxidation, such that both direct and indirect mechanisms are involved in the mobilization of redox-active metals by Metallosphaera species.IMPORTANCE In order to effectively leverage extremely thermoacidophilic archaea for the microbially based solubilization of solid-phase metal substrates (e.g., sulfides and oxides), understanding the mechanisms by which these archaea solubilize metals is important. Physiological analysis of Metallosphaera species growth in the presence of molybdenum and vanadium oxides revealed an indirect mode of metal mobilization, catalyzed by iron cycling. However, since the mobilized metals exist in more than one oxidation state, they could potentially serve directly as energetic substrates. Transcriptomic response to molybdenum and vanadium oxides provided evidence for new biomolecules participating in direct metal biooxidation. The findings expand the knowledge on the physiological versatility of these extremely thermoacidophilic archaea. DA - 2019/3// PY - 2019/3// DO - 10.1128/AEM.02805-18 VL - 85 IS - 5 SP - SN - 1098-5336 KW - Metallosphaera KW - biomining KW - extreme thermoacidophily KW - metal biooxidation KW - molybdenum KW - vanadium ER - TY - JOUR TI - Contemporary climatic analogs for 540 North American urban areas in the late 21st century AU - Fitzpatrick, Matthew C. AU - Dunn, Robert R. T2 - NATURE COMMUNICATIONS AB - Abstract A major challenge in articulating human dimensions of climate change lies in translating global climate forecasts into impact assessments that are intuitive to the public. Climate-analog mapping involves matching the expected future climate at a location (e.g., a person’s city of residence) with current climate of another, potentially familiar, location - thereby providing a more relatable, place-based assessment of climate change. For 540 North American urban areas, we used climate-analog mapping to identify the location that has a contemporary climate most similar to each urban area’s expected 2080’s climate. We show that climate of most urban areas will shift considerably and become either more akin to contemporary climates hundreds of kilometers away and mainly to the south or will have no modern equivalent. Combined with an interactive web application, we provide an intuitive means of raising public awareness of the implications of climate change for 250 million urban residents. DA - 2019/2/12/ PY - 2019/2/12/ DO - 10.1038/s41467-019-08540-3 VL - 10 SP - SN - 2041-1723 ER - TY - JOUR TI - Reduction of Pb availability during surficial leaching in different types of soils with addition of apatite and oxalic acid AU - Guo, Chenmeng AU - Tian, Weitao AU - Wang, Zhijun AU - Han, Feiyu AU - Su, Mu AU - Wu, Yiling AU - Li, Zhen AU - Hu, Shuijin T2 - JOURNAL OF SOILS AND SEDIMENTS DA - 2019/2// PY - 2019/2// DO - 10.1007/s11368-018-2100-6 VL - 19 IS - 2 SP - 741-749 SN - 1614-7480 KW - Bioapatite KW - Leaching KW - Oxalic acid KW - Pb KW - Remediation ER - TY - JOUR TI - DOF2.1 Controls Cytokinin-Dependent Vascular Cell Proliferation Downstream of TMO5/LHW AU - Smet, Wouter AU - Sevilem, Iris AU - Luis Balaguer, Maria Angels AU - Wybouw, Brecht AU - Mor, Eliana AU - Miyashima, Shunsuke AU - Blob, Bernhard AU - Roszak, Pawel AU - Jacobs, Thomas B. AU - Boekschoten, Mark AU - Hooiveld, Guido AU - Sozzani, Rosangela AU - Helariutta, Yka AU - De Rybel, Bert T2 - CURRENT BIOLOGY AB - To create a three-dimensional structure, plants rely on oriented cell divisions and cell elongation. Oriented cell divisions are specifically important in procambium cells of the root to establish the different vascular cell types [1, 2]. These divisions are in part controlled by the auxin-controlled TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW) transcription factor complex [3-7]. Loss-of-function of tmo5 or lhw clade members results in strongly reduced vascular cell file numbers, whereas ectopic expression of both TMO5 and LHW can ubiquitously induce periclinal and radial cell divisions in all cell types of the root meristem. TMO5 and LHW interact only in young xylem cells, where they promote expression of two direct target genes involved in the final step of cytokinin (CK) biosynthesis, LONELY GUY3 (LOG3) and LOG4 [8, 9] Therefore, CK was hypothesized to act as a mobile signal from the xylem to trigger divisions in the neighboring procambium cells [3, 6]. To unravel how TMO5/LHW-dependent cytokinin regulates cell proliferation, we analyzed the transcriptional responses upon simultaneous induction of both transcription factors. Using inferred network analysis, we identified AT2G28510/DOF2.1 as a cytokinin-dependent downstream target gene. We further showed that DOF2.1 controls specific procambium cell divisions without inducing other cytokinin-dependent effects such as the inhibition of vascular differentiation. In summary, our results suggest that DOF2.1 and its closest homologs control vascular cell proliferation, thus leading to radial expansion of the root. DA - 2019/2/4/ PY - 2019/2/4/ DO - 10.1016/j.cub.2018.12.041 VL - 29 IS - 3 SP - 520-+ SN - 1879-0445 ER - TY - JOUR TI - Predicting development preferences for fishing sites among diverse anglers AU - Valdez, Rene X. AU - Drake, Michael D. AU - Burke, Conner R. AU - Peterson, M. Nils AU - Serenari, Christopher AU - Howell, Andrew T2 - Urban Ecosystems DA - 2019/2// PY - 2019/2// DO - 10.1007/S11252-018-0800-8 VL - 22 IS - 1 SP - 127–135 SN - 1083-8155 1573-1642 UR - http://dx.doi.org/10.1007/S11252-018-0800-8 KW - Site preference KW - Landscape design KW - Recreational fishing KW - Anglers KW - Visual preference survey ER - TY - JOUR TI - Controls on mineral-associated organic matter formation in a degraded Oxisol AU - Ye, Chenglong AU - Hall, Steven J. AU - Hu, Shuijin T2 - GEODERMA AB - Oxisols are the dominant soil type in humid tropical and subtropical regions and are subjected to both drying–rewetting (DRW) cycles and fluctuating oxygen (O2) availability driven by warm temperatures and abundant rainfall in surface layers. Drying-rewetting cycles and O2 fluctuations may critically affect the microbial transformation of plant litter and subsequent stabilization as mineral-associated organic carbon (MAOC), but experimental data are still limited. We examined the impacts of DRW cycles, and variable O2 regimes with constant moisture, on carbon (C) and iron (Fe) dynamics in a degraded Oxisol (under long-term fallow) with added plant residues. In laboratory incubations (>3 months), both DRW cycling and fluctuating O2 availability induced a flush of respiration and a temporary increase in microbial biomass C (MBC) following soil rewetting or O2 exposure, although MBC was consistently suppressed in these treatments relative to the control (60% water holding capacity under constantly aerobic condition). Consequently, DRW cycles significantly increased but O2 fluctuations significantly decreased cumulative C mineralization relative to the control. Concentrations of short-range-ordered Fe oxides peaked immediately after litter addition and decreased five-fold during the remainder of the experiment. Mineral-associated C (defined as the chemically dispersed <53 μm soil fraction) increased 42–64% relative to initial values but was significantly lower under DRW cycling and fluctuating O2 relative to the control. Correspondingly, these treatments had greater fine particulate organic C (53–250 μm), despite increased CO2 production under DRW cycling. Our data indicate the potential for rapid and significant accrual of MAOC in a degraded Oxisol, but environmental factors such as DRW cycling and fluctuating O2 can inhibit the conversion of plant litter to MAOC—possibly by suppressing microbial biomass formation and/or microbial transformations of organic matter. DA - 2019/3/15/ PY - 2019/3/15/ DO - 10.1016/j.geoderma.2018.12.011 VL - 338 SP - 383-392 SN - 1872-6259 KW - Birch effect KW - Drying rewetting KW - Oxygen fluctuations KW - Litter decomposition KW - Iron redox KW - Mineral-organic associations ER - TY - JOUR TI - Contest models highlight inherent inefficiencies of scientific funding competitions AU - Gross, Kevin AU - Bergstrom, Carl T. T2 - PLOS BIOLOGY AB - Scientific research funding is allocated largely through a system of soliciting and ranking competitive grant proposals. In these competitions, the proposals themselves are not the deliverables that the funder seeks, but instead are used by the funder to screen for the most promising research ideas. Consequently, some of the funding program's impact on science is squandered because applying researchers must spend time writing proposals instead of doing science. To what extent does the community's aggregate investment in proposal preparation negate the scientific impact of the funding program? Are there alternative mechanisms for awarding funds that advance science more efficiently? We use the economic theory of contests to analyze how efficiently grant proposal competitions advance science, and compare them with recently proposed, partially randomized alternatives such as lotteries. We find that the effort researchers waste in writing proposals may be comparable to the total scientific value of the research that the funding supports, especially when only a few proposals can be funded. Moreover, when professional pressures motivate investigators to seek funding for reasons that extend beyond the value of the proposed science (e.g., promotion, prestige), the entire program can actually hamper scientific progress when the number of awards is small. We suggest that lost efficiency may be restored either by partial lotteries for funding or by funding researchers based on past scientific success instead of proposals for future work. DA - 2019/1// PY - 2019/1// DO - 10.1371/journal.pbio.3000065 VL - 17 IS - 1 SP - SN - 1545-7885 ER - TY - CHAP TI - Weed Management in Sugarcane AU - Leon, R.G. AU - Odero, D.C. T2 - Weed control: Sustainability, hazards and cropping systems worldwide A2 - Korres, N.E. A2 - Burgos, N.R. A2 - Duke, S.O. PY - 2019/// ET - 1 SP - 455-469 PB - CRC Press/Taylor & Francis Group ER - TY - CHAP TI - Sustainable Weed Management in Peanut. AU - Leon, R.G. AU - Jordan, D.L. AU - Bolfrey-Arku, G. AU - Dzomeku, I. T2 - Weed control: Sustainability, hazards and cropping systems worldwide A2 - Korres, N.E. A2 - Burgos, N.R. A2 - Duke, S.O. PY - 2019/// ET - 1 SP - 345-366 PB - CRC Press/Taylor & Francis Group ER - TY - JOUR TI - Peanut residue distribution gradients and tillage practices determine patterns of nitrogen mineralization AU - Jani, A.D. AU - Mulvaney, M.J. AU - Enloe, H.A. AU - Erickson, J.E. AU - Leon, R.G. AU - Rowland, D.L. AU - Wood, C.W. T2 - Nutrient Cycling in Agroecosystems DA - 2019/// PY - 2019/// DO - 10.1007/s10705-018-9962-2 VL - 113 IS - 1 SP - 63–76 KW - Peanut KW - Carbon KW - Nitrogen KW - Residues KW - Mineralization KW - Tillage ER - TY - JOUR TI - Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tapirins) from Extremely Thermophilic Caldicellulosiruptor Species AU - Lee, Laura L. AU - Hart, William S. AU - Lunin, Vladimir V. AU - Alahuhta, Markus AU - Bomble, Yannick J. AU - Himmel, Michael E. AU - Blumer-Schuette, Sara E. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Genomes of extremely thermophilic Caldicellulosiruptor species encode novel cellulose binding proteins, called tāpirins, located proximate to the type IV pilus locus. The C-terminal domain of Caldicellulosiruptor kronotskyensis tāpirin 0844 (Calkro_0844) is structurally unique and has a cellulose binding affinity akin to that seen with family 3 carbohydrate binding modules (CBM3s). Here, full-length and C-terminal versions of tāpirins from Caldicellulosiruptor bescii (Athe_1870), Caldicellulosiruptor hydrothermalis (Calhy_0908), Caldicellulosiruptor kristjanssonii (Calkr_0826), and Caldicellulosiruptor naganoensis (NA10_0869) were produced recombinantly in Escherichia coli and compared to Calkro_0844. All five tāpirins bound to microcrystalline cellulose, switchgrass, poplar, and filter paper but not to xylan. Densitometry analysis of bound protein fractions visualized by SDS-PAGE revealed that Calhy_0908 and Calkr_0826 (from weakly cellulolytic species) associated with the cellulose substrates to a greater extent than Athe_1870, Calkro_0844, and NA10_0869 (from strongly cellulolytic species). Perhaps this relates to their specific needs to capture glucans released from lignocellulose by cellulases produced in Caldicellulosiruptor communities. Calkro_0844 and NA10_0869 share a higher degree of amino acid sequence identity (>80% identity) with each other than either does with Athe_1870 (∼50%). The levels of amino acid sequence identity of Calhy_0908 and Calkr_0826 to Calkro_0844 were only 16% and 36%, respectively, although the three-dimensional structures of their C-terminal binding regions were closely related. Unlike the parent strain, C. bescii mutants lacking the tāpirin genes did not bind to cellulose following short-term incubation, suggesting a role in cell association with plant biomass. Given the scarcity of carbohydrates in neutral terrestrial hot springs, tāpirins likely help scavenge carbohydrates from lignocellulose to support growth and survival of Caldicellulosiruptor species.IMPORTANCE The mechanisms by which microorganisms attach to and degrade lignocellulose are important to understand if effective approaches for conversion of plant biomass into fuels and chemicals are to be developed. Caldicellulosiruptor species grow on carbohydrates from lignocellulose at elevated temperatures and have biotechnological significance for that reason. Novel cellulose binding proteins, called tāpirins, are involved in the way that Caldicellulosiruptor species interact with microcrystalline cellulose, and additional information about the diversity of these proteins across the genus, including binding affinity and three-dimensional structural comparisons, is provided here. DA - 2019/2// PY - 2019/2// DO - 10.1128/AEM.01983-18 VL - 85 IS - 3 SP - SN - 1098-5336 KW - Caldicellulosiruptor KW - cellulose binding protein KW - lignocellulose KW - tapirin ER - TY - JOUR TI - Direct and indirect effects of nitrogen enrichment on soil organisms and carbon and nitrogen mineralization in a semi-arid grassland AU - Chen, Dima AU - Xing, Wen AU - Lan, Zhichun AU - Saleem, Muhammad AU - Wu, Yunqiqige AU - Hu, Shuijin AU - Bai, Yongfei T2 - FUNCTIONAL ECOLOGY AB - Abstract Semi‐arid grasslands on the Mongolian Plateau are expected to experience high inputs of anthropogenic reactive nitrogen in this century. It remains unclear, however, how soil organisms and nutrient cycling are directly affected by N enrichment (i.e., without mediation by plant input to soil) vs. indirectly affected via changes in plant‐related inputs to soils resulting from N enrichment. To test the direct and indirect effects of N enrichment on soil organisms (bacteria, fungi and nematodes) and their associated C and N mineralization, in 2010, we designated two subplots (with plants and without plants) in every plot of a six‐level N‐enrichment experiment established in 1999 in a semi‐arid grassland. In 2014, 4 years after subplots with and without plant were established, N enrichment had substantially altered the soil bacterial, fungal and nematode community structures due to declines in biomass or abundance whether plants had been removed or not. N enrichment also reduced the diversity of these groups (except for fungi) and the soil C mineralization rate and induced a hump‐shaped response of soil N mineralization. As expected, plant removal decreased the biomass or abundance of soil organisms and C and N mineralization rates due to declines in soil substrates or food resources. Analyses of plant‐removal‐induced changes (ratios of without‐ to with‐plant subplots) showed that micro‐organisms and C and N mineralization rates were not enhanced as N enrichment increased but that nematodes were enhanced as N enrichment increased, indicating that the effects of plant removal on soil organisms and mineralization depended on trophic level and nutrient status. Surprisingly, there was no statistical interaction between N enrichment and plant removal for most variables, indicating that plant‐related inputs did not qualitatively change the effects of N enrichment on soil organisms or mineralization. Structural equation modelling confirmed that changes in soil communities and mineralization rates were more affected by the direct effects of N enrichment (via soil acidification and increased N availability) than by plant‐related indirect effects. Our results provide insight into how future changes in N deposition and vegetation may modify below‐ground communities and processes in grassland ecosystems. A plain language summary is available for this article. DA - 2019/1// PY - 2019/1// DO - 10.1111/1365-2435.13226 VL - 33 IS - 1 SP - 175-187 SN - 1365-2435 KW - below-ground carbon allocation KW - below-ground communities KW - mass ratio hypothesis KW - plant-soil interactions KW - soil acidification KW - soil food web KW - trophic groups ER - TY - JOUR TI - Moral hazard and adverse selection effects of cost-of-production crop insurance: evidence from the Philippines AU - He, Juan AU - Zheng, Xiaoyong AU - Rejesus, Roderick M. AU - Yorobe, Jose M., Jr. T2 - AUSTRALIAN JOURNAL OF AGRICULTURAL AND RESOURCE ECONOMICS AB - This article examines the moral hazard and adverse selection effects of cost‐of‐production (COP) crop insurance products. Building on existing crop insurance models of moral hazard, as well as a survey‐based data set that allows us to separately identify moral hazard from adverse selection, we find evidence that farmers insured under COP contracts spend more on chemical fertilizers and pesticides (i.e. those inputs whose costs determine the indemnity payments). However, since these same COP insured farmers are still likely to use less inputs (like effort) whose costs do not enter the indemnity payment formula, and yield depends on both types of inputs (i.e. the determinants and non‐determinants of the indemnity payments), the final moral hazard effect of COP insurance on yields is ambiguous. Our analysis also suggests that farmers who tend to spend less on chemical fertilizers and pesticides are the ones with private information on soil conditions and pest incidence. These are the types of farmers who adversely select into COP contracts that only cover weather related losses. DA - 2019/1// PY - 2019/1// DO - 10.1111/1467-8489.12290 VL - 63 IS - 1 SP - 166-197 SN - 1467-8489 KW - adverse selection KW - crop insurance KW - moral hazard ER - TY - JOUR TI - Movement and Demography of At-Risk Butterflies: Building Blocks for Conservation AU - Schultz, Cheryl B. AU - Haddad, Nick M. AU - Henry, Erica H. AU - Crone, Elizabeth E. T2 - ANNUAL REVIEW OF ENTOMOLOGY, VOL 64 AB - The number of insect species at risk of population decline and extinction is increasing rapidly. Yet we know almost nothing about the ecology of these species, except for at-risk butterflies. A growing body of literature shows how butterfly vital rates, including demography and movement, are essential for guiding conservation and recovery. History has shown us that without these data, conservation decisions often weaken, rather than enhance, population viability. This is especially true in changing landscapes. We review knowledge of vital rates across all at-risk butterflies. We have information on movement for 17 of 283 butterfly species and information on demography for 19 species. We find that habitat-specific movement behavior is key to understanding how to connect populations, and habitat-specific demography is central to managing habitats. Methods and analyses worked out for butterflies can provide a scaffold around which to build studies for the conservation of other at-risk insects. DA - 2019/// PY - 2019/// DO - 10.1146/annurev-ento-011118-112204 VL - 64 SP - 167-184 SN - 0066-4170 KW - demography KW - behavior KW - dispersal KW - conservation KW - restoration KW - insect KW - butterfly ER - TY - JOUR TI - Characterization and Repurposing of Type I and Type II CRISPR-Cas Systems in Bacteria AU - Hidalgo-Cantabrana, Claudio AU - Goh, Yong Jun AU - Barrangou, Rodolphe T2 - JOURNAL OF MOLECULAR BIOLOGY AB - CRISPR–Cas systems constitute the adaptive immune system of bacteria and archaea, as a sequence-specific nucleic acid targeting defense mechanism. The sequence-specific recognition and cleavage of Cas effector complexes has been harnessed to developed CRISPR-based technologies and drive the genome editing revolution underway, due to their efficacy, efficiency, and ease of implementation in a broad range of organisms. CRISPR-based technologies offer a wide variety of opportunities in genome remodeling and transcriptional regulation, opening new avenues for therapeutic and biotechnological applications. To repurpose CRISPR–Cas systems for these applications, the various elements of the system need to be first identified and functionally characterized in their native host. Bioinformatic tools are first used to identify putative CRISPR arrays and their associated genes, followed by a comprehensive characterization of the CRISPR–Cas system, encompassing predictions for guide and target sequences. Subsequently, interference assays and transcriptomic analyses should be performed to probe the functionality of the CRISPR–Cas system. Once an endogenous CRISPR–Cas system is characterized as functional, they can be readily repurposed by delivering an engineered synthetic CRISPR array or a small RNA guide for targeted gene manipulation. Alternatively, developing a plasmid-based system for heterologous expression of the necessary CRISPR components can enable exploitation in other organisms. Altogether, there is a wide diversity of native CRISPR–Cas systems in many bacteria and most archaea that await functional characterization and repurposing for genome editing applications in prokaryotes. DA - 2019/1/4/ PY - 2019/1/4/ DO - 10.1016/j.jmb.2018.09.013 VL - 431 IS - 1 SP - 21-33 SN - 1089-8638 KW - CRISPR-Cas systems KW - CRISPR characterization KW - endogenous systems KW - genome editing ER - TY - JOUR TI - Mobile PEAR transcription factors integrate hormone and miRNA cues to prime cambial growth AU - Miyashima, Shunsuke AU - Roszak, Pawel AU - Sevilem, Iris AU - Toyokura, Koichi AU - Blob, Bernhard AU - Heo, Jung-ok AU - Mellor, Nathan AU - Help-Rinta-Rahko, Hanna AU - Otero, Sofia AU - Smet, Wouter AU - Boekschoten, Mark AU - Hooiveld, Guido AU - Hashimoto, Kayo AU - Smetana, Ondřej AU - Siligato, Riccardo AU - Wallner, Eva-Sophie AU - Mähönen, Ari Pekka AU - Kondo, Yuki AU - Melnyk, Charles W. AU - Greb, Thomas AU - Nakajima, Keiji AU - Sozzani, Rosangela AU - Bishopp, Anthony AU - De Rybel, Bert AU - Helariutta, Ykä T2 - Nature AB - Apical growth in plants initiates upon seed germination, whereas radial growth is primed only during early ontogenesis in procambium cells and activated later by the vascular cambium1. Although it is not known how radial growth is organized and regulated in plants, this system resembles the developmental competence observed in some animal systems, in which pre-existing patterns of developmental potential are established early on2,3. Here we show that in Arabidopsis the initiation of radial growth occurs around early protophloem-sieve-element cell files of the root procambial tissue. In this domain, cytokinin signalling promotes the expression of a pair of mobile transcription factors—PHLOEM EARLY DOF 1 (PEAR1) and PHLOEM EARLY DOF 2 (PEAR2)—and their four homologues (DOF6, TMO6, OBP2 and HCA2), which we collectively name PEAR proteins. The PEAR proteins form a short-range concentration gradient that peaks at protophloem sieve elements, and activates gene expression that promotes radial growth. The expression and function of PEAR proteins are antagonized by the HD-ZIP III proteins, well-known polarity transcription factors4—the expression of which is concentrated in the more-internal domain of radially non-dividing procambial cells by the function of auxin, and mobile miR165 and miR166 microRNAs. The PEAR proteins locally promote transcription of their inhibitory HD-ZIP III genes, and thereby establish a negative-feedback loop that forms a robust boundary that demarks the zone of cell division. Taken together, our data establish that during root procambial development there exists a network in which a module that links PEAR and HD-ZIP III transcription factors integrates spatial information of the hormonal domains and miRNA gradients to provide adjacent zones of dividing and more-quiescent cells, which forms a foundation for further radial growth. Radial growth in the roots of Arabidopsis, which is mediated by gene expression activated by the mobile PEAR1 and PEAR2 transcription factors, is initiated around protophloem-sieve-element cell files of procambial tissue. DA - 2019/1// PY - 2019/1// DO - 10.1038/s41586-018-0839-y VL - 565 IS - 7740 SP - 490-494 LA - en SN - 0028-0836, 1476-4687 UR - http://www.nature.com/articles/s41586-018-0839-y DB - Crossref Y2 - 2019/1/30/ ER - TY - JOUR TI - Computational prediction of gene regulatory networks in plant growth and development AU - Haque, Samiul AU - Ahmad, Jabeen S. AU - Clark, Natalie M. AU - Williams, Cranos M. AU - Sozzani, Rosangela T2 - Current Opinion in Plant Biology AB - Plants integrate a wide range of cellular, developmental, and environmental signals to regulate complex patterns of gene expression. Recent advances in genomic technologies enable differential gene expression analysis at a systems level, allowing for improved inference of the network of regulatory interactions between genes. These gene regulatory networks, or GRNs, are used to visualize the causal regulatory relationships between regulators and their downstream target genes. Accordingly, these GRNs can represent spatial, temporal, and/or environmental regulations and can identify functional genes. This review summarizes recent computational approaches applied to different types of gene expression data to infer GRNs in the context of plant growth and development. Three stages of GRN inference are described: first, data collection and analysis based on the dataset type; second, network inference application based on data availability and proposed hypotheses; and third, validation based on in silico, in vivo, and in planta methods. In addition, this review relates data collection strategies to biological questions, organizes inference algorithms based on statistical methods and data types, discusses experimental design considerations, and provides guidelines for GRN inference with an emphasis on the benefits of integrative approaches, especially when a priori information is limited. Finally, this review concludes that computational frameworks integrating large-scale heterogeneous datasets are needed for a more accurate (e.g. fewer false interactions), detailed (e.g. discrimination between direct versus indirect interactions), and comprehensive (e.g. genetic regulation under various conditions and spatial locations) inference of GRNs. DA - 2019/2/1/ PY - 2019/2/1/ DO - 10.1016/j.pbi.2018.10.005 VL - 47 SP - 96-105 J2 - Current Opinion in Plant Biology LA - en OP - SN - 1369-5266 UR - http://www.sciencedirect.com/science/article/pii/S1369526618300839 DB - ScienceDirect Y2 - 2019/1/30/ ER - TY - JOUR TI - International news media framing of invasive rodent eradications AU - Valdez, R. X. AU - Peterson, M. N. AU - Pitts, E. A. AU - Delborne, J. A. T2 - Biological Invasions DA - 2019/1/4/ PY - 2019/1/4/ DO - 10.1007/s10530-018-01911-9 VL - 21 IS - 4 SP - 1439-1449 J2 - Biol Invasions LA - en OP - SN - 1387-3547 1573-1464 UR - http://dx.doi.org/10.1007/s10530-018-01911-9 DB - Crossref KW - News media analysis KW - Invasive rodents KW - Framing KW - Conquest framing ER - TY - TI - Can genetic engineering save disappearing forests? AU - Delborne, J.A. DA - 2019/1/18/ PY - 2019/1/18/ UR - http://theconversation.com/can-genetic-engineering-save-disappearing-forests-109793 N1 - Retrieved from RN - Retrieved from ER - TY - JOUR TI - Limited potential of harvest index improvement to reduce methane emissions from rice paddies AU - Jiang, Yu AU - Qian, Haoyu AU - Wang, Ling AU - Feng, Jinfei AU - Huang, Shan AU - Hungate, Bruce A. AU - Kessel, Chris AU - Horwath, William R. AU - Zhang, Xingyue AU - Qin, Xiaobo AU - Li, Yue AU - Feng, Xiaomin AU - Zhang, Jun AU - Deng, Aixing AU - Zheng, Chenyan AU - Song, Zhenwei AU - Hu, Shuijin AU - Groenigen, Kees Jan AU - Zhang, Weijian T2 - GLOBAL CHANGE BIOLOGY AB - Rice is a staple food for nearly half of the world's population, but rice paddies constitute a major source of anthropogenic CH4 emissions. Root exudates from growing rice plants are an important substrate for methane-producing microorganisms. Therefore, breeding efforts optimizing rice plant photosynthate allocation to grains, i.e., increasing harvest index (HI), are widely expected to reduce CH4 emissions with higher yield. Here we show, by combining a series of experiments, meta-analyses and an expert survey, that the potential of CH4 mitigation from rice paddies through HI improvement is in fact small. Whereas HI improvement reduced CH4 emissions under continuously flooded (CF) irrigation, it did not affect CH4 emissions in systems with intermittent irrigation (II). We estimate that future plant breeding efforts aimed at HI improvement to the theoretical maximum value will reduce CH4 emissions in CF systems by 4.4%. However, CF systems currently make up only a small fraction of the total rice growing area (i.e., 27% of the Chinese rice paddy area). Thus, to achieve substantial CH4 mitigation from rice agriculture, alternative plant breeding strategies may be needed, along with alternative management. DA - 2019/2// PY - 2019/2// DO - 10.1111/gcb.14529 VL - 25 IS - 2 SP - 686-698 SN - 1365-2486 KW - climate change KW - food security KW - greenhouse gases KW - meta-analysis KW - water management ER - TY - JOUR TI - A new insight into lead (II) tolerance of environmental fungi based on a study of Aspergillus niger and Penicillium oxalicum AU - Tian, Da AU - Jiang, Zhongquan AU - Jiang, Liu AU - Su, Mu AU - Feng, Zheye AU - Zhang, Lin AU - Wang, Shimei AU - Li, Zhen AU - Hu, Shuijin T2 - ENVIRONMENTAL MICROBIOLOGY AB - Summary Environmental microorganisms have been widely applied in heavy metal remediation. This study explored the mechanisms of lead tolerance of two typical filamentous fungi, Aspergillus niger and Penicillium oxalicum . It is shown that the mechanisms of reducing Pb toxicity by these two fungi have three major pathways. The secreted oxalic acid can react with Pb (II) to form insoluble Pb minerals, primarily lead oxalate. Then, the enhanced biosorption via forming new border of cell wall prevents the transportation of Pb (II) into hypha. In addition, the fungal activity could be maintained even at high Pb concentration due to the intracellular accumulation. It was confirmed that A. niger has the higher Pb tolerance (up to 1500 mg l −1 Pb level) compared with P. oxalicum (up to 1000 mg l −1 ). Meanwhile, Pb levels below 1000 mg l −1 partially stimulate the bioactivity of A. niger , which was confirmed by its elevated respiration (from 53 to 63 mg C l −1 medium h −1 ). This subsequently enhanced microbial functions of A. niger to resist Pb toxicity. A better understanding of Pb tolerance of these two fungi sheds a bright future of applying them to remediate lead‐contaminated environments. DA - 2019/1// PY - 2019/1// DO - 10.1111/1462-2920.14478 VL - 21 IS - 1 SP - 471-479 SN - 1462-2920 ER - TY - JOUR TI - The genetically engineered American chestnut tree as opportunity for reciprocal restoration in Haudenosaunee communities AU - Barnhill-Dilling, S. Kathleen AU - Delborne, Jason A. T2 - Biological Conservation AB - As genetic engineering becomes a part of the toolkit for the conservation and restoration of biodiversity, a broad range of social science frameworks are required to understand how different groups of people perceive these emerging technologies. Reciprocal restoration is one such framework that offers Indigenous-specific perspective on new applications of genetic engineering for conservation and restoration. 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. This paper uses reciprocal restoration as a framework for evaluating if a restoration project that uses a genetically engineered species could support broader cultural restoration efforts in these communities. Results are complex, but suggest that reciprocal restoration may be possible if certain foundational dimensions – such as kincentric relationships and spiritual responsibilities – are attended to. Reciprocal restoration also offers insight for future cases where Indigenous perspectives on the use of genetic engineering for conservation and restoration are important dimensions of broader governance considerations. DA - 2019/4// PY - 2019/4// DO - 10.1016/j.biocon.2019.01.018 VL - 232 SP - 1-7 J2 - Biological Conservation LA - en OP - SN - 0006-3207 UR - http://dx.doi.org/10.1016/j.biocon.2019.01.018 DB - Crossref KW - Biodiversity conservation & restoration KW - Genetic engineering KW - Indigenous participation in governance ER - TY - JOUR TI - Genetic Covariance of Environments in the Potato National Chip Processing Trial AU - Schmitz Carley, Cari A. AU - Coombs, Joseph J. AU - Clough, Mark E. AU - De Jong, Walter S. AU - Douches, David S. AU - Haynes, Kathleen G. AU - Higgins, Charles R. AU - Holm, David G. AU - Miller, J. Creighton AU - Navarro, Felix M. AU - Novy, Richard G. AU - Palta, Jiwan P. AU - Parish, David L. AU - Porter, Gregory A. AU - Sathuvalli, Vidyasagar R. AU - Thompson, Asunta L. AU - Yencho, G. Craig AU - Zotarelli, Lincoln AU - Endelman, Jeffrey B. T2 - Crop Science AB - The National Chip Processing Trial is a collaborative effort between public breeding programs and the potato ( Solanum tuberosum L.) industry to identify new clones with broad adaptation. The objective of this study was to investigate the genetic covariance of trial locations, based on 337 clones evaluated in 10 states from 2011 to 2016. Three models were considered: (I) assuming a uniform genetic correlation between locations within a year, (II) using a factor‐analytic (FA) model of the total genetic covariance of environments (location–year combinations), and (III) using a FA model of the additive genetic covariance based on 5278 single‐nucleotide polymorphism (SNP) markers. With Model I, the genetic correlation between locations was 0.50 for vine maturity, 0.54 for tuber yield, and 0.72 for specific gravity. The Akaike information criterion decreased as model complexity increased, from Models I to II to III, for maturity and yield but not specific gravity. Of the 10 states in the dataset, Florida stood out for having environments with substantial (up to 88%) genetic variance unexplained by the latent factors. Linear discriminants (LD) of the factor loadings were used to visualize the genetic correlation between locations. For vine maturity, LD1 separated Florida from the other locations, and LD2 separated the remaining southern locations from the northern ones. For yield, LD1 separated Texas from the other locations. This study has created a foundation for the design of more efficient trialing and selection programs for the US potato community. DA - 2019/// PY - 2019/// DO - 10.2135/cropsci2018.05.0314 VL - 59 IS - 1 SP - 107 LA - en OP - SN - 0011-183X UR - http://dx.doi.org/10.2135/cropsci2018.05.0314 DB - Crossref ER - TY - JOUR TI - A Cluster of MYB Transcription Factors Regulates Anthocyanin Biosynthesis in Carrot (Daucus carota L.) Root and Petiole AU - Iorizzo, Massimo AU - Cavagnaro, Pablo F. AU - Bostan, Hamed AU - Zhao, Yunyang AU - Zhang, Jianhui AU - Simon, Philipp W. T2 - FRONTIERS IN PLANT SCIENCE AB - Purple carrots can accumulate large quantities of anthocyanins in their roots and –in some genetic backgrounds- petioles, and therefore they represent an excellent dietary source of antioxidant phytonutrients. In a previous study, using linkage analysis in a carrot F2 mapping population segregating for root and petiole anthocyanin pigmentation, we identified a region in chromosome 3 with co-localized QTL for all anthocyanin pigments of the carrot root, whereas petiole pigmentation segregated as a single dominant gene and mapped to one of these “root pigmentation” regions conditioning anthocyanin biosynthesis. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify candidate genes controlling anthocyanin pigmentation in the carrot root and petiole. Fine mapping was performed in four carrot populations with different genetic backgrounds and patterns of pigmentation. The regions controlling root and petiole pigmentation in chromosome 3 were delimited to 541 kb and 535 kb, respectively. Genome wide prediction of transcription factor families known to regulate the anthocyanin biosynthetic pathway coupled with orthologous and phylogenetic analyses enabled the identification of a cluster of six MYB transcription factors, denominated DcMYB6 to DcMYB11, associated with the regulation of anthocyanin biosynthesis. No anthocyanin biosynthetic genes were present in this region. Comparative transcriptome analysis indicated that upregulation of DcMYB7 was always associated with anthocyanin pigmentation in both root and petiole tissues, whereas DcMYB11 was only upregulated with pigmentation in petioles. In the petiole, the level of expression of DcMYB11 was higher than DcMYB7. DcMYB6, a gene previously suggested as a key regulator of carrot anthocyanin biosynthesis, was not consistently associated with pigmentation in either tissue. These results strongly suggest that DcMYB7 is a candidate gene for root anthocyanin pigmentation in all the genetic backgrounds included in this study. DcMYB11 is a candidate gene for petiole pigmentation in all the purple carrot sources in this study. Since DcMYB7 is co-expressed with DcMYB11 in purple petioles, the latter gene may act also as a co-regulator of anthocyanin pigmentation in the petioles. This study provides linkage-mapping and functional evidence for the candidacy of these genes for the regulation of carrot anthocyanin biosynthesis. DA - 2019/1/14/ PY - 2019/1/14/ DO - 10.3389/fpls.2018.01927 VL - 9 SP - SN - 1664-462X KW - Daucus carota L. KW - anthocyanin accumulation KW - root and petiole KW - regulation KW - fine mapping KW - transcriptome KW - candidate genes ER - TY - JOUR TI - Unique thermo-responsivity and tunable optical performance of poly(N-isopropylacrylamide)-cellulose nanocrystal hydrogel films AU - Sun, Xiaohang AU - Tyagi, Preeti AU - Agate, Sachin AU - Lucia, Lucian AU - McCord, Marian AU - Pal, Lokendra T2 - CARBOHYDRATE POLYMERS AB - A hybrid materials system to modulate lower critical solution temperature (LCST) and moisture content for thermo-responsivity and optical tunability was strategically developed by incorporating cellulose nanocrystals (CNCs) into a poly(N-isopropylacrylamide) (PNIPAm) hydrogel matrix. The PNIPAm/CNC hydrogel films exhibit tunable optical properties and wavelength bandpass selectivity as characterized by PROBE Spectroscopy and Dynamic Light Scattering (DLS). Importantly, the micro/nano structures of the PNIPAm/CNC hydrogel films were completely different when dried below and above the LCST. Below the LCST, PNIPAm/CNC hydrogel films exhibit transparency or semi-transparency due to the uniform bonding of hydrophilic PNIPAm and CNC through hydrogen bonds. Above the LCST, the hydrogel films engage in both hydrophobic PNIPAm and hydrophilic CNC interactions due to changes in PNIPAm conformation which lead to light scattering effects and hence opacity. Furthermore, the incorporation of CNC induces a ∼ 15 °C reduction of the LCST relative to pure PNIPAm hydrogel films. DA - 2019/3/15/ PY - 2019/3/15/ DO - 10.1016/j.carbpol.2018.12.067 VL - 208 SP - 495-503 SN - 1879-1344 KW - Poly(N-isopropylacrylamide) KW - Cellulose nanocrystals KW - Hydrogels KW - Thermal responsive KW - Transparency ER - TY - JOUR TI - Drivers of elevational richness peaks, evaluated for trees in the east Himalaya AU - Rana, Suresh K. AU - Gross, Kevin AU - Price, Trevor D. T2 - ECOLOGY AB - Abstract Along elevational gradients, species richness often peaks at intermediate elevations and not the base. Here we refine and test eight hypotheses to evaluate causes of a richness peak in trees of the eastern Himalaya. In the field, we enumerated trees in 50 plots of size 0.1 ha each at eight zones along an elevational gradient and compared richness patterns with interpolation of elevational ranges of species from a thorough review of literature, including floras from the plains of India. The maximum number of species peaks at similar elevations in the two data sets (at 500 m in the field sampling and between 500 m and 1,000 m in range interpolation); concordance between the methods implies that statistical artefacts are unlikely to explain the peak in the data. We reject most hypotheses (e.g., area, speciation rate, mixing of distinct floras). We find support for a model in which climate (actual evapotranspiration [ AET ] or its correlates) sets both the number of species and each species optimum, coupled with a geometric constraint. We consider that AET declines with elevation, but an abrupt change in the association of AET with geographical distance into the plains means that the location of highest AET , at the base of the mountain, receives range overlaps from fewer species than the location just above the base. We formalize this explanation with a mathematical model to show how this can generate the observed low‐elevation richness peak. DA - 2019/1// PY - 2019/1// DO - 10.1002/ecy.2548 VL - 100 IS - 1 SP - SN - 1939-9170 KW - beta diversity KW - diversification rate KW - elevational gradient KW - geometric constraints KW - Himalaya KW - mid-elevational peak KW - species richness KW - trees ER - TY - JOUR TI - Grazing practices affect the soil microbial community composition in a Tibetan alpine meadow AU - Yang, Fei AU - Niu, Kechang AU - Collins, Courtney G. AU - Yan, Xuebin AU - Ji, Yangguang AU - Ling, Ning AU - Zhou, Xianhui AU - Du, Guozhen AU - Guo, Hui AU - Hu, Shuijin T2 - LAND DEGRADATION & DEVELOPMENT AB - Abstract Grazing is the primary land‐use activity on the Tibetan Plateau and can affect soil microbes and their function through aboveground vegetation removal, animal trampling, and manure deposition. Two distinct grazing systems (i.e., winter grazing [WG] and annual grazing [AG]) dominate on the Tibetan Plateau, but their effects on soil microbes have rarely been assessed. Taking advantage of a 5‐year field experiment that controlled timing and density of grazers via fence exclosures, we examined impacts of different grazing practices on the biomass, diversity, and composition of the soil microbial community in a Tibetan alpine meadow. On the basis of high‐throughput sequencing, we found that grazing had no significant effects on bacterial and fungal α‐diversities but altered their community compositions. Although total soil carbon (TC), total soil nitrogen (TN), and carbon/nitrogen (C/N) were related to both bacterial and fungal community compositions, plant shoot biomass only correlated with bacteria, and soil pH and moisture significantly influenced fungi under grazing. Also, grazing altered plant community composition but did not lead to corresponding changes in bacterial or fungal community composition. Moreover, grazing practices affected the relative abundance of specific bacterial and fungal taxa, reducing Actinobacteria but increasing Basidiomycete fungi in WG. Soil TC and TN were higher, and the soil microbial community was more stable in AG than WG, likely due to more stable litter inputs in AG. Together, these results showed that AG was less disruptive to soil microbes, suggesting that AG may provide a viable option for sustainable utilization and conservation of these fragile alpine systems. DA - 2019/1/15/ PY - 2019/1/15/ DO - 10.1002/ldr.3189 VL - 30 IS - 1 SP - 49-59 SN - 1099-145X KW - alpine meadow KW - bacteria KW - fungi KW - grazing practices KW - Tibetan Plateau ER - TY - JOUR TI - Biodiversity-ecosystem function relationships on bodies and in buildings AU - Dunn, Robert R. AU - Reese, Aspen T. AU - Eisenhauer, Nico T2 - NATURE ECOLOGY & EVOLUTION AB - Biodiversity underpins the function of ecosystems. Here we discuss how biodiversity–ecosystem function theory could apply to our bodies and buildings, outline practical applications and call for further research. DA - 2019/1// PY - 2019/1// DO - 10.1038/s41559-018-0750-9 VL - 3 IS - 1 SP - 7-9 SN - 2397-334X ER - TY - JOUR TI - Invasive plants differentially affect soil biota through litter and rhizosphere pathways: a meta-analysis AU - Zhang, Pei AU - Li, Bo AU - Wu, Jihua AU - Hu, Shuijin T2 - ECOLOGY LETTERS AB - Abstract Invasive plants affect soil biota through litter and rhizosphere inputs, but the direction and magnitude of these effects are variable. We conducted a meta‐analysis to examine the different effects of litter and rhizosphere of invasive plants on soil communities and nutrient cycling. Our results showed that invasive plants increased bacterial biomass by 16%, detritivore abundance by 119% and microbivore abundance by 89% through litter pathway. In the rhizosphere, invasive plants reduced bacterial biomass by 12%, herbivore abundance by 55% and predator abundance by 52%, but increased AM fungal biomass by 36%. Moreover, CO 2 efflux, N mineralisation rate and enzyme activities were all higher in invasive than native rhizosphere soils. These findings indicate that invasive plants may support more decomposers that in turn stimulate nutrient release via litter effect, and enhance nutrient uptake by reducing root grazing but forming more symbioses in the rhizosphere. Thus, we hypothesise that litter‐ and root‐based loops are probably linked to generate positive feedback of invaders on soil systems through stimulating nutrient cycling, consequently facilitating plant invasion. Our findings from limited cases with diverse contexts suggest that more studies are needed to differentiate litter and rhizosphere effects within single systems to better understand invasive plant‐soil interactions. DA - 2019/1// PY - 2019/1// DO - 10.1111/ele.13181 VL - 22 IS - 1 SP - 200-210 SN - 1461-0248 KW - Biological invasions KW - trophic groups KW - nutrient cycling KW - effect size KW - above-belowground interactions KW - plant-soil feedback ER - TY - JOUR TI - Open-Source Software in the Sciences: The Challenge of User Support AU - Swarts, Jason T2 - JOURNAL OF BUSINESS AND TECHNICAL COMMUNICATION AB - This study examines user support issues concerning open-source software in computational sciences. The literature suggests that there are three main problem areas: transparency, learnability, and usability. Looking at questions asked in user communities for chemistry software projects, the author found that for software supported by feature-based documentation, problems of transparency and learnability are prominent, leading users to have difficulty reconciling disciplinary practices and values with software operations. For software supported by task-based documentation, usability problems were more prominent. The author considers the implications of this study for user support and the role that technical communication could play in developing and supporting open-source projects. DA - 2019/1// PY - 2019/1// DO - 10.1177/1050651918780202 VL - 33 IS - 1 SP - 60-90 SN - 1552-4574 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85048131385&partnerID=MN8TOARS KW - science writing KW - manual writing/instructions KW - open source KW - empirical qualitative research KW - user support ER -