TY - RPRT TI - Thrips Infestation Predictor for Cotton: An Online Tool for Informed Thrips Management AU - Kennedy, G. A3 - Scientific Societies DA - 2017/4/1/ PY - 2017/4/1/ DO - 10.1094/GROW-COT-04-17-103 PB - Scientific Societies UR - http://dx.doi.org/10.1094/GROW-COT-04-17-103 ER - TY - CHAP TI - Commentary Concrete Ethics AU - Herkert, Joseph R. T2 - Engineering Ethics PY - 2017/5/15/ DO - 10.4324/9781315256474-55 SP - 663-665 PB - Routledge UR - http://dx.doi.org/10.4324/9781315256474-55 ER - TY - JOUR TI - Self-Driving Cars: Ethical Responsibilities of Design Engineers AU - Borenstein, Jason AU - Herkert, Joseph AU - Miller, Keith T2 - IEEE Technology and Society Magazine AB - In the wake of the exposure of Volkswagen's diesel engine test-rigging, a Bloomberg Business journalist described the company as "driven by engineering-crazed executives" [2] and The New York Times ran a story noting how with today's complex computer systems in automobiles, there are numerous opportunities for misdeeds both by automakers and hackers [3]. With the advent of so-called autonomous or self-driving cars, such issues may become even more pervasive and problematic. From a legal perspective, a key focal point is who would be at fault if and when an accident occurs [4]. Much also has been written about the ethical complexities posed by self-driving cars [5]-[6]. In accordance with Moore's Law, "[a]s technological revolutions increase their social impact, ethical problems increase" [7]. Yet relatively little has been said about the ethical responsibilities of the designers of self-driving cars. DA - 2017/// PY - 2017/// DO - 10.1109/MTS.2017.2696600 VL - 36 IS - 2 SP - 67-75 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85021124475&partnerID=MN8TOARS ER - TY - CONF TI - Ethics and responsible innovation in biotechnology communities: A pedagogy of engaged scholarship AU - Herkert, J.R. AU - Kuzma, J. AU - Roberts, J.P. AU - Banks, E. AU - Stauffer, S.A. C2 - 2017/// C3 - ASEE Annual Conference and Exposition, Conference Proceedings DA - 2017/// VL - 2017-June UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85030554888&partnerID=MN8TOARS ER - TY - CHAP TI - Future Directions in Engineering Ethics Research: Microethics, Macroethics and the Role of Professional Societies AU - Herkert, Joseph R. T2 - Engineering Ethics PY - 2017/5/15/ DO - 10.4324/9781315256474-45 SP - 551-562 PB - Routledge UR - http://dx.doi.org/10.4324/9781315256474-45 ER - TY - JOUR TI - The Use of Multi-Criteria Decision Analysis in Food Safety Risk-Benefit Assessment AU - Ruzante, J. AU - Grieger, K. AU - Woodward, K. AU - Lambertini, E. AU - Kowalcyk, B. T2 - Food Protection Trends DA - 2017/// PY - 2017/// VL - 37 IS - 2 SP - 132–139 ER - TY - RPRT TI - Develop and Validate Risk Ranking Model v3 to Inform RRM-PT List AU - Grieger, K.D. AU - Aceituno, A. AU - Andrews, L. AU - Womack, D. AU - Li, M. AU - Havellar, A. A3 - United States Food and Drug Administration DA - 2017/// PY - 2017/// PB - United States Food and Drug Administration ER - TY - RPRT TI - Comprehensive analysis of available tools and methodologies for Horizon Scanning AU - Jovanovic, A. AU - Ahmad, M. AU - Quintero, F.A. AU - Porcari, A. AU - Borsella, E. AU - Hristozov, D. AU - Grieger, K.D. AU - Jensen, K. A3 - caLIBRAte research project DA - 2017/// PY - 2017/// M3 - Deliverable PB - caLIBRAte research project ER - TY - JOUR TI - A framework for One Health research AU - Lebov, J. AU - Grieger, K. AU - Womack, D. AU - Zaccaro, D. AU - Whitehead, N. AU - Kowalcyk, B. AU - MacDonald, P.D.M. T2 - One Health AB - The need for multidisciplinary research to address today's complex health and environmental challenges has never been greater. The One Health (OH) approach to research ensures that human, animal, and environmental health questions are evaluated in an integrated and holistic manner to provide a more comprehensive understanding of the problem and potential solutions than would be possible with siloed approaches. However, the OH approach is complex, and there is limited guidance available for investigators regarding the practical design and implementation of OH research. In this paper we provide a framework to guide researchers through conceptualizing and planning an OH study. We discuss key steps in designing an OH study, including conceptualization of hypotheses and study aims, identification of collaborators for a multi-disciplinary research team, study design options, data sources and collection methods, and analytical methods. We illustrate these concepts through the presentation of a case study of health impacts associated with land application of biosolids. Finally, we discuss opportunities for applying an OH approach to identify solutions to current global health issues, and the need for cross-disciplinary funding sources to foster an OH approach to research. DA - 2017/6// PY - 2017/6// DO - 10.1016/j.onehlt.2017.03.004 VL - 3 SP - 44-50 J2 - One Health LA - en OP - SN - 2352-7714 UR - http://dx.doi.org/10.1016/j.onehlt.2017.03.004 DB - Crossref ER - TY - JOUR TI - The role of alternative testing strategies in environmental risk assessment of engineered nanomaterials AU - Hjorth, Rune AU - Holden, Patricia A. AU - Hansen, Steffen Foss AU - Colman, Benjamin P. AU - Grieger, Khara AU - Hendren, Christine Ogilvie T2 - Environmental Science: Nano AB - Within toxicology there is a pressure to find new test systems to replace, reduce and refine animal testing. In nanoecotoxicology this raises a number of questions. DA - 2017/// PY - 2017/// DO - 10.1039/c6en00443a VL - 4 IS - 2 SP - 292-301 J2 - Environ. Sci.: Nano LA - en OP - SN - 2051-8153 2051-8161 UR - http://dx.doi.org/10.1039/c6en00443a DB - Crossref ER - TY - CHAP TI - Looking over, looking out, and moving forward: The review of contingency theory in public relations AU - Cheng, Y. AU - Cameron, G. T2 - Public Relations Theories for contemporary China. A2 - Chen, Xianhong PY - 2017/// PB - Communication University of China Publishing House ER - TY - CHAP TI - The status of social-mediated crisis communication (SMCC) research: An analysis of published articles in 2002-2014 AU - Cheng, Y. AU - Cameron, G. T2 - Social Media and Crisis Communication A2 - Austin, L. A2 - Jin, Y. AB - In order to present a comprehensive overview of the social-mediated crisis communication (SMCC) research, ten Social Sciences Citation Index (SSCI) academic journals, mainly in relevant academic disciplines such as public relations or communication, were selected for full screening, ranging from 2002 to 2014. Public perception and media use became the most dominant area in SMCC research. Discussions emphasized public motivation for online media use, public strategies, emotions, engagement, identification, and generated online content in crises. In both Western and Eastern contexts, SMCC research has realized the empowering function of social media. Among several measurements for Crisis Communication Effectiveness (CCE), it was found that reputation was most frequently used, followed by media publicity, revenue reputation, cost reduction, and organizational-public relationship. Organizations, social media, and stakeholders, as three major research perspectives were clearly identified in SMCC research. For the types of organizations, it was found that governments or corporations were mostly discussed, whereas only 4 out of 69 articles discussed nonprofit organizations. PY - 2017/// DO - 10.4324/9781315749068-2 SP - 9–20 PB - Routledge ER - TY - JOUR TI - Oxidative Depolymerization of Lignin Using Supported Niobium Catalysts AU - Das, Lalitendu AU - Kolar, Praveen AU - Sharma-Shivappa, Ratna AU - Classen, John AU - Osborne, Jason T2 - ChemEngineering AB - Valorization of lignin into aromatics has driven researchers for decades. In this research, niobium was deposited on oyster shells (OSNC) and carbon rods (CRNC) and tested as a catalyst for depolymerization of lignin. Catalysts (2%, 5%, and 8% loading) were synthesized via wet impregnation. Batch experiments were performed at 95 °C, using 8 g of lignin, and 1 g of catalyst. Our research indicates that niobium supported catalysts are effective in partial oxidation of lignin. Maximum vanillin concentration for OSNC was found to be 86.25 mg L−1 (0.1 wt%) at 5% niobium whereas, as for CRNC, maximum vanillin concentration was found to be 139.40 mg L−1 (0.17 wt%) at 2% niobium loading. Addition of hydrogen peroxide into the batch reactor decreased the concentration of vanillin production. DA - 2017/11/29/ PY - 2017/11/29/ DO - 10.3390/chemengineering1020017 VL - 1 IS - 2 SP - 17 J2 - ChemEngineering LA - en OP - SN - 2305-7084 UR - http://dx.doi.org/10.3390/chemengineering1020017 DB - Crossref ER - TY - BOOK TI - TOGETHER WITH TECHNOLOGY: Writing Review, Enculturation, and Technological Mediation AU - Swarts, J. DA - 2017/// PY - 2017/// DO - 10.4324/9781315223452 SE - 1-179 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85088624177&partnerID=MN8TOARS ER - TY - CONF TI - Emerging Technologies, New Governance Arrangements, and the Time-Honored Challenges: Searching for Novelty in Anticipatory Governance AU - Delborne, J. T2 - Advancing Science for Policy through Interdisciplinary Research in Regulation C2 - 2017/11/17/ C3 - Advancing Science for Policy through Interdisciplinary Research in Regulation CY - University of California, Berkeley DA - 2017/11/17/ PY - 2017/11/17/ ER - TY - CONF TI - NASPAA Accreditation Site Visitor Training AU - Berry-James, R.M. T2 - 2017 COMPA 46th Annual Conference on Emerging Strategies Leading to a More Inclusive and Diverse Society C2 - 2017/3/17/ CY - Atlanta, GA DA - 2017/3/17/ PY - 2017/3/17/ ER - TY - CONF TI - Teaching Cultural Competence in Public Administration: Lessons Learned from Problem Based Approaches AU - Berry-James, R.M. T2 - Program Evaluation: Enhancing Credibility and Building Ownership of Lessons Learned, 2017 Annual Conference Saluting the Public Service: a Bold & Noble Profession C2 - 2017/3/17/ CY - Atlanta, GA DA - 2017/3/17/ PY - 2017/3/17/ ER - TY - SOUND TI - Luncheon Plenary on Perspectives on Social Equity in a Mythical Post Racial Society training AU - Berry-James, R.M. DA - 2017/3/16/ PY - 2017/3/16/ ER - TY - CONF TI - Responsible Innovation: New Directions in Public Service on track Human Resources, Leadership and Public Management AU - Berry-James, R.M. T2 - 2017 Annual Conference Saluting the Public Service: a Bold & Noble Profession C2 - 2017/3/17/ CY - Atlanta, GA DA - 2017/3/17/ PY - 2017/3/17/ ER - TY - SOUND TI - NASPAA Accreditation Site Visitor Training AU - Berry-James, R.M. DA - 2017/3/17/ PY - 2017/3/17/ ER - TY - CONF TI - Evaluating the Complexity of Food Systems for Vulnerable Citizens: Sustainable Policy Practices AU - Berry-James, R.M. AU - Chojnacki, K. AU - Decker, W. T2 - Policy, Planning and Program Evaluation Track, 2017 SECoPA Conference Defending Public Administration in a Time of Uncertainty C2 - 2017/10/4/ CY - Hollywood, FL DA - 2017/10/4/ PY - 2017/10/4/ ER - TY - SOUND TI - Fortune Favors the Brave! AU - Berry-James, R.M. DA - 2017/10/11/ PY - 2017/10/11/ M3 - Judge at the Voinovich Public Innovation Challenge ER - TY - CONF TI - The Skills and Resources Needed to be Effective MPA and PhD Directors AU - Berry-James, R.M. T2 - 2017 NASPAA Annual Conference C2 - 2017/10/11/ CY - Washington, DC DA - 2017/10/11/ PY - 2017/10/11/ ER - TY - CONF TI - Responsible Innovation in Food Biotechnology: Exploring Cultural Attitudes and Public Trust AU - Berry-James, R.M. T2 - 2017 NASPAA Annual Conference C2 - 2017/10/11/ CY - Washington, DC DA - 2017/10/11/ PY - 2017/10/11/ ER - TY - SOUND TI - Diversity and Inclusion. 2017-2018 The State of Diversity in Government and Public Service, Public Administration and Policy AU - Berry-James, R.M. DA - 2017/11/2/ PY - 2017/11/2/ ER - TY - CHAP TI - Effectiveness of mediation in the state agency grievance process AU - Katz Jameson, Jessica AU - Berry-James, RaJade M. AU - Daley, Dennis M. AU - Coggburn, Jerrell D. T2 - The Mediation Handbook PY - 2017/9/19/ DO - 10.4324/9781315648330-18 SP - 164-169 PB - Routledge SN - 9781315648330 UR - http://dx.doi.org/10.4324/9781315648330-18 ER - TY - CONF TI - Emerging Technologies and Public Engagement AU - Delbourne, Jason T2 - US-China Agricultural Biotechnology Safety Administration Collaboration Workshop: Communication, Engagement, and Biotechnology. C2 - 2017/10/2/ CY - James B. Hunt Jr. Library, North Carolina State University, Raleigh, NC DA - 2017/10/2/ PY - 2017/10/2/ ER - TY - CONF TI - Strategies of engagement in synthetic biology AU - Delbourne, Jason T2 - Engineering Resilience Workshop. C2 - 2017/9/12/ CY - Heron Island, Australia DA - 2017/9/12/ PY - 2017/9/12/ ER - TY - SOUND TI - Emerging biotechnologies and public engagement: Reflections on the NASEM report on gene drives AU - Delborne, Jason DA - 2017/3/8/ PY - 2017/3/8/ ER - TY - CONF TI - Engineering: responsible innovation AU - Delborne, Jason T2 - Genetic Engineering and Society Center C2 - 2017/2/27/ CY - Arizona State University, Tempe, AZ DA - 2017/2/27/ PY - 2017/2/27/ ER - TY - CONF TI - Incorporating public engagement in research and governance AU - Delborne, Jason T2 - American Association for the Advancement of Science Annual Meeting C2 - 2017/2/17/ CY - Boston, MA DA - 2017/2/17/ PY - 2017/2/17/ ER - TY - BLOG TI - The Ring of Engagement AU - Delborne, J.A. T2 - Prometheus: The Science Policy Blog DA - 2017/3/3/ PY - 2017/3/3/ PB - Center for Science and Technology Policy Research, University of Colorado at Boulder UR - http://ciresblogs.colorado.edu/prometheus/2017/03/03/the-ring-of-engagement/ ER - TY - CONF TI - Municipal Wastewater Application to Forests: Using Participatory Science to Understand Human Exposure and Risks to Chemical Contaminants of Concern AU - Hedgespeth, M.L. AU - McEachran, A.D. AU - Rashash, D. AU - Shea, D. AU - Strynar, M. AU - Delborne, J.A. AU - Nichols, E.G. T2 - Society of Environmental Toxicology and Chemistry, North America, 38th Annual Meeting C2 - 2017/11/12/ CY - Minneapolis, MN DA - 2017/11/12/ PY - 2017/11/12/ ER - TY - CONF TI - The Role of Phospholipid Metabolism in Maize Adaptation to Low Phosphorus and Cold Conditions AU - Rellan-Alvarez, R T2 - Gordon Research Conference Plant Lipids: Structure, Metabolism & Function C2 - 2017/// CY - Galveston, TX DA - 2017/// PY - 2017/// ER - TY - SOUND TI - Identification of phospholipid metabolic patterns involved in maize adaptation to highland conditions AU - Rellan-Alvarez, R. DA - 2017/// PY - 2017/// M3 - seminar ER - TY - SOUND TI - Identification of phospholipid metabolic patterns involved in maize adaptation to low phosphorus and cold conditions AU - Rellan-Alvarez, R. DA - 2017/// PY - 2017/// M3 - seminar ER - TY - SOUND TI - Convergent phospholipid metabolism in highland adapted maize? AU - Rellan-Alvarez, R DA - 2017/// PY - 2017/// M3 - seminar ER - TY - SOUND TI - Towards and understanding of maize adaptation to highlands using a combination of lipidomics and quantitative and population genetics AU - Rellan-Alvarez, R DA - 2017/// PY - 2017/// ER - TY - RPRT TI - Translation regulation of uORFs-containing genes in Arabidopsis AU - Merchante, C. AU - Yun, J. AU - Valpuesta-Fernandez, V. AU - Stepanova, A. AU - Alonso, J. DA - 2017/// PY - 2017/// ER - TY - RPRT TI - Sequestration of CO2 with H2 into useful products AU - Adams, M.W.W. AU - Kelly, R.M. AU - Hawkins, A.S. AU - Menon, A.L. AU - Lipscomb, G.P. AU - Schut, G.J. DA - 2017/3// PY - 2017/3// M1 - 9,587,256 M3 - US Patent SN - 9,587,256 ER - TY - JOUR TI - In situ validation of fungal N translocation to cereal rye mulches under no-till soybean production AU - Wells, M. Scott AU - Reberg-Horton, S. Chris AU - Mirsky, Steven B. AU - Maul, Jude E. AU - Hu, Shuijin T2 - Plant and Soil AB - The ability of grass mulches to inhibit weed performance has been linked to their limitations on nitrogen availability to the weeds. Fungal translocation of N from the soil to the surface mulch has been confirmed in laboratories, but this mechanism has not been documented under field conditions. Experiments used 15N (NH4)2SO4 , 99.7 at.%, which was uniformly injected below the soil surface at a rate of 1 mg 15 N kg−1 soil. Some plots were treated with a fungicide (Captan) every 2 weeks after injection, while others were not treated. Nitrogen transfer was monitored by measuring levels in surface residue, soybean tissue, and extractable soil inorganic N pools. Despite the N release from the cereal rye (Secale cereale L.) tissues ranging from 15 to 50 kg N ha−1, there was a detectable increase in 15N enrichment of 10–15 % in the cereal rye tissue. Six weeks after injection, tissue from the plots not treated with fungicide contained 36 % more 15 N. The increased 15N enrichment in the cereal rye mulch supports laboratory observations that soil inorganic N is translocated into surface mulch via fungal mechanisms. These findings illustrate microbial-mediated sinks for nitrogen in cereal rye mulches in no-till soybean production systems. DA - 2017/// PY - 2017/// DO - 10.1007/S11104-016-2989-8 VL - 410 IS - 1-2 SP - 153–165 SN - 0032-079X 1573-5036 UR - http://dx.doi.org/10.1007/S11104-016-2989-8 KW - Secale cereale L. KW - Cover crop mulch KW - Plant-microbial N competition KW - Fungal N translocation KW - Weed suppression KW - N-15 stable isotope KW - N immobilization ER - TY - SOUND TI - CRISPR and the Ethics of Editing Genes AU - Delbourne, Jason AU - Godwin, John DA - 2017/9/28/ PY - 2017/9/28/ ER - TY - CONF TI - Public engagement: Rationales, methods, and intended outcomes AU - Delbourne, Jason T2 - International Workshop Assessing the Security Implications of Genome Editing Technology C2 - 2017/10/13/ CY - Hanover, Germany DA - 2017/10/13/ PY - 2017/10/13/ ER - TY - JOUR TI - Diversity of bacteria and archaea from two shallow marine hydrothermal vents from Vulcano Island AU - Antranikian, Garabed AU - Suleiman, Marcel AU - Schäfers, Christian AU - Adams, Michael W. W. AU - Bartolucci, Simonetta AU - Blamey, Jenny M. AU - Birkeland, Nils-Kåre AU - Bonch-Osmolovskaya, Elizaveta AU - da Costa, Milton S. AU - Cowan, Don AU - Danson, Michael AU - Forterre, Patrick AU - Kelly, Robert AU - Ishino, Yoshizumi AU - Littlechild, Jennifer AU - Moracci, Marco AU - Noll, Kenneth AU - Oshima, Tairo AU - Robb, Frank AU - Rossi, Mosè AU - Santos, Helena AU - Schönheit, Peter AU - Sterner, Reinhard AU - Thauer, Rudolf AU - Thomm, Michael AU - Wiegel, Jürgen AU - Stetter, Karl Otto T2 - Extremophiles DA - 2017/5/10/ PY - 2017/5/10/ DO - 10.1007/s00792-017-0938-y VL - 21 IS - 4 SP - 733-742 J2 - Extremophiles LA - en OP - SN - 1431-0651 1433-4909 UR - http://dx.doi.org/10.1007/s00792-017-0938-y DB - Crossref KW - Hyperthermophiles KW - Archaea KW - Diversity KW - Hydrothermal marine shallow vents ER - TY - JOUR TI - Elevating the conversation about GE crops AU - Gould, Fred AU - Amasino, Richard M AU - Brossard, Dominique AU - Buell, C Robin AU - Dixon, Richard A AU - Falck-Zepeda, Jose B AU - Gallo, Michael A AU - Giller, Ken E AU - Glenna, Leland L AU - Griffin, Timothy AU - Hamaker, Bruce R AU - Kareiva, Peter M AU - Magraw, Daniel AU - Mallory-Smith, Carol AU - Pixley, Kevin V AU - Ransom, Elizabeth P AU - Rodemeyer, Michael AU - Stelly, David M AU - Stewart, C Neal AU - Whitaker, Robert J T2 - Nature Biotechnology DA - 2017/4// PY - 2017/4// DO - 10.1038/NBT.3841 VL - 35 IS - 4 SP - 302-304 SN - 1087-0156 1546-1696 UR - http://dx.doi.org/10.1038/NBT.3841 ER - TY - JOUR TI - C aldicellulosiruptor saccharolyticus transcriptomes reveal consequences of chemical pretreatment and genetic modification of lignocellulose AU - Blumer‐Schuette, Sara E. AU - Zurawski, Jeffrey V. AU - Conway, Jonathan M. AU - Khatibi, Piyum AU - Lewis, Derrick L. AU - Li, Quanzi AU - Chiang, Vincent L. AU - Kelly, Robert M. T2 - Microbial Biotechnology AB - Summary Recalcitrance of plant biomass is a major barrier for commercially feasible cellulosic biofuel production. Chemical and enzymatic assays have been developed to measure recalcitrance and carbohydrate composition; however, none of these assays can directly report which polysaccharides a candidate microbe will sense during growth on these substrates. Here, we propose using the transcriptomic response of the plant biomass‐deconstructing microbe, Caldicellulosiruptor saccharolyticus , as a direct measure of how suitable a sample of plant biomass may be for fermentation based on the bioavailability of polysaccharides. Key genes were identified using the global gene response of the microbe to model plant polysaccharides and various types of unpretreated, chemically pretreated and genetically modified plant biomass. While the majority of C. saccharolyticus genes responding were similar between plant biomasses; subtle differences were discernable, most importantly between chemically pretreated or genetically modified biomass that both exhibit similar levels of solubilization by the microbe. Furthermore, the results here present a new paradigm for assessing plant–microbe interactions that can be deployed as a biological assay to report on the complexity and recalcitrance of plant biomass. DA - 2017/3/20/ PY - 2017/3/20/ DO - 10.1111/1751-7915.12494 VL - 10 IS - 6 SP - 1546-1557 J2 - Microb. Biotechnol. LA - en OP - SN - 1751-7915 1751-7915 UR - http://dx.doi.org/10.1111/1751-7915.12494 DB - Crossref ER - TY - JOUR TI - Ethanol production by the hyperthermophilic archaeon Pyrococcus furiosus by expression of bacterial bifunctional alcohol dehydrogenases AU - Keller, Matthew W. AU - Lipscomb, Gina L. AU - Nguyen, Diep M. AU - Crowley, Alexander T. AU - Schut, Gerrit J. AU - Scott, Israel AU - Kelly, Robert M. AU - Adams, Michael W. W. T2 - Microbial Biotechnology AB - Summary Ethanol is an important target for the renewable production of liquid transportation fuels. It can be produced biologically from pyruvate, via pyruvate decarboxylase, or from acetyl‐CoA, by alcohol dehydrogenase E (AdhE). Thermophilic bacteria utilize AdhE, which is a bifunctional enzyme that contains both acetaldehyde dehydrogenase and alcohol dehydrogenase activities. Many of these organisms also contain a separate alcohol dehydrogenase (AdhA) that generates ethanol from acetaldehyde, although the role of AdhA in ethanol production is typically not clear. As acetyl‐CoA is a key central metabolite that can be generated from a wide range of substrates, AdhE can serve as a single gene fuel module to produce ethanol through primary metabolic pathways. The focus here is on the hyperthermophilic archaeon Pyrococcus furiosus, which grows by fermenting sugar to acetate, CO 2 and H 2 . Previously, by the heterologous expression of adhA from a thermophilic bacterium, P. furiosus was shown to produce ethanol by a novel mechanism from acetate, mediated by AdhA and the native enzyme aldehyde oxidoreductase ( AOR ). In this study, the AOR gene was deleted from P. furiosus to evaluate ethanol production directly from acetyl‐CoA by heterologous expression of the adhE gene from eight thermophilic bacteria. Only AdhEs from two Thermoanaerobacter strains showed significant activity in cell‐free extracts of recombinant P. furiosus and supported ethanol production in vivo . In the AOR deletion background, the highest amount of ethanol (estimated 61% theoretical yield) was produced when adhE and adhA from Thermoanaerobacter were co‐expressed. DA - 2017/2/14/ PY - 2017/2/14/ DO - 10.1111/1751-7915.12486 VL - 10 IS - 6 SP - 1535-1545 J2 - Microb. Biotechnol. LA - en OP - SN - 1751-7915 1751-7915 UR - http://dx.doi.org/10.1111/1751-7915.12486 DB - Crossref ER - TY - SOUND TI - A Decade of Synthetic Biology AU - Delborne, J. DA - 2017/12/14/ PY - 2017/12/14/ ER - TY - CONF TI - Municipal Wastewater Application to Forests: Using Participatory Science to Understand Human Exposure and Risks to Chemical Contaminants of Concern AU - Hedgespeth, M.L. AU - McEachran, A.D. AU - Rashash, D. AU - Shea, D. AU - Strynar, M. AU - Delborne, J.A. AU - Nichols, E.G. T2 - Carolinas Society of Environmental Toxicology and Chemistry Regional Meeting C2 - 2017/5/17/ CY - Charleston, SC DA - 2017/5/17/ PY - 2017/5/17/ ER - TY - CONF TI - Gene Drives over the Horizon: A Model, for Anticipatory Governance AU - Backus, G.A. AU - Delborne, J.A. T2 - Annual Meeting of the Society for Social Studies of Science C2 - 2017/8/31/ CY - Boston, MA DA - 2017/8/31/ PY - 2017/8/31/ ER - TY - CONF TI - Envisioning Responsible Innovation in Biotechnology for Conservation: Engagement, GM Chestnut Trees, and Gene Drive Mice AU - Delborne, J.A. T2 - Annual Meeting of the Society for Social Studies of Science C2 - 2017/8/31/ CY - Boston, MA DA - 2017/8/31/ PY - 2017/8/31/ ER - TY - JOUR TI - Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences AU - Bucksch, Alexander AU - Atta-Boateng, Acheampong AU - Azihou, Akomian F. AU - Battogtokh, Dorjsuren AU - Baumgartner, Aly AU - Binder, Brad M. AU - Braybrook, Siobhan A. AU - Chang, Cynthia AU - Coneva, Viktoirya AU - DeWitt, Thomas J. AU - Fletcher, Alexander G. AU - Gehan, Malia A. AU - Diaz-Martinez, Diego Hernan AU - Hong, Lilan AU - Iyer-Pascuzzi, Anjali S. AU - Klein, Laura L. AU - Leiboff, Samuel AU - Li, Mao AU - Lynch, Jonathan P. AU - Maizel, Alexis AU - Maloof, Julin N. AU - Markelz, R. J. Cody AU - Martinez, Ciera C. AU - Miller, Laura A. AU - Mio, Washington AU - Palubicki, Wojtek AU - Poorter, Hendrik AU - Pradal, Christophe AU - Price, Charles A. AU - Puttonen, Eetu AU - Reese, John B. AU - Rellán-Álvarez, Rubén AU - Spalding, Edgar P. AU - Sparks, Erin E. AU - Topp, Christopher N. AU - Williams, Joseph H. AU - Chitwood, Daniel H. T2 - Frontiers in Plant Science AB - The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics. DA - 2017/6/9/ PY - 2017/6/9/ DO - 10.3389/fpls.2017.00900 VL - 8 J2 - Front. Plant Sci. OP - SN - 1664-462X UR - http://dx.doi.org/10.3389/fpls.2017.00900 DB - Crossref KW - plant biology KW - plant science KW - morphology KW - mathematics KW - topology KW - modeling ER - TY - JOUR TI - Co-ordinated Changes in the Accumulation of Metal Ions in Maize (Zea mays ssp. mays L.) in Response to Inoculation with the Arbuscular Mycorrhizal Fungus Funneliformis mosseae AU - Ramírez-Flores, M Rosario AU - Rellán-Álvarez, Rubén AU - Wozniak, Barbara AU - Gebreselassie, Mesfin-Nigussie AU - Jakobsen, Iver AU - Olalde-Portugal, Víctor AU - Baxter, Ivan AU - Paszkowski, Uta AU - Sawers, Ruairidh J H T2 - Plant and Cell Physiology AB - Arbuscular mycorrhizal symbiosis is an ancient interaction between plants and fungi of the phylum Glomeromycota. In exchange for photosynthetically fixed carbon, the fungus provides the plant host with greater access to soil nutrients via an extensive network of root-external hyphae. Here, to determine the impact of the symbiosis on the host ionome, the concentration of 19 elements was determined in the roots and leaves of a panel of 30 maize varieties, grown under phosphorus-limiting conditions, with or without inoculation with the fungus Funneliformis mosseae. Although the most recognized benefit of the symbiosis to the host plant is greater access to soil phosphorus, the concentration of a number of other elements responded significantly to inoculation across the panel as a whole. In addition, variety-specific effects indicated the importance of plant genotype to the response. Clusters of elements were identified that varied in a co-ordinated manner across genotypes, and that were maintained between non-inoculated and inoculated plants. DA - 2017/8/2/ PY - 2017/8/2/ DO - 10.1093/pcp/pcx100 VL - 58 IS - 10 SP - 1689–1699 SN - 0032-0781 1471-9053 UR - http://dx.doi.org/10.1093/pcp/pcx100 KW - Arbuscular mycorrhiza KW - Ionome KW - Maize KW - Plant nutrition ER - TY - BOOK TI - Preparing for the Future Products of Biotechnology AU - Murray, R. AU - Amasino, R. AU - Bradbury, S. AU - Evans, B. AU - Evans, S. AU - Isaacs, Farren AU - Krebs, M. AU - Kuzma, J. AU - Maxon, M AU - Medina, R AU - Rejeski, D AU - Wolt, J AB - Between 1973 and 2016, the ways to manipulate DNA to endow new characteristics in an organism (that is, biotechnology) have advanced, enabling the development of products that were not previously possible. What will the likely future products of biotechnology be over the next 5–10 years? What scientific capabilities, tools, and/or expertise may be needed by the regulatory agencies to ensure they make efficient and sound evaluations of the likely future products of biotechnology? Preparing for Future Products of Biotechnology analyzes the future landscape of biotechnology products and seeks to inform forthcoming policy making. This report identifies potential new risks and frameworks for risk assessment and areas in which the risks or lack of risks relating to the products of biotechnology are well understood. DA - 2017/// PY - 2017/// DO - 10.17226/24605 M3 - National Academies of Science, Engineering and Medicine Committee Report PB - National Academies Press SN - 9780309452052 ER - TY - JOUR TI - Global questioners: examining journalists’ aggressiveness at Chinese premiers’ press conferences (1993–2015) AU - Wu, Feng AU - Cheng, Yang AU - Chao, Duo T2 - Asian Journal of Communication AB - This paper explores the different levels of aggressiveness in five dimensions exhibited by journalists with diverse global backgrounds at the press conferences of four Chinese premiers. Four attributes of the journalists’ home countries are examined: (1) power distance, (2) press freedom, (3) stage of development, and (4) frequency of questioning opportunities. The results show that journalists from countries with lower power distances tend to be more direct in their question designs than those with higher power distances; journalists with higher levels of press freedom tend to show more initiative, directness, assertiveness, and adversarialness than those with lower levels; journalists from developed countries are more direct, assertive, adversarial, and accountable than their counterparts; frequent questioners are more assertive, adversarial, and accountable than those infrequent. The theoretical and practical implications of journalists’ aggressive behaviors are discussed. DA - 2017/1/26/ PY - 2017/1/26/ DO - 10.1080/01292986.2017.1281322 VL - 27 IS - 4 SP - 357-377 J2 - Asian Journal of Communication LA - en OP - SN - 0129-2986 1742-0911 UR - http://dx.doi.org/10.1080/01292986.2017.1281322 DB - Crossref KW - Global journalism KW - journalism professionalism KW - journalists' aggressiveness KW - politician-journalist relations KW - Chinese premiers' press conferences ER - TY - JOUR TI - Public relations, media coverage, and public opinion in contemporary China: Testing agenda building theory in a social mediated crisis AU - Cheng, Yang AU - Huang, Yi-Hui Christine AU - Chan, Ching Man T2 - Telematics and Informatics AB - This study investigates a social mediated crisis triggered by the Guo Meimei incident that negatively affected the Red Cross Society of China (RCSC). RCSC’s public relations efforts, media coverage, and public opinion on micro-blogs are examined through the theoretical grounding of agenda building. Evidence shows that organizational public relations activities strongly influence media coverage at the first level, but exert no influence upon online public opinion. RCSC’s agenda neither forms issue salience of online public opinion, nor effectively influences public’s attitude on the issue. This study extends the theorization of the effects of agenda building by adding contextual factors about social media, political, and cultural characteristics in China. DA - 2017/6// PY - 2017/6// DO - 10.1016/J.TELE.2016.05.012 VL - 34 IS - 3 SP - 765-773 J2 - Telematics and Informatics LA - en OP - SN - 0736-5853 UR - http://dx.doi.org/10.1016/J.TELE.2016.05.012 DB - Crossref KW - Public relations KW - Time series KW - Social media KW - Agenda building KW - Crisis KW - China ER - TY - JOUR TI - Responses of rice paddy micro-food webs to elevated CO2 are modulated by nitrogen fertilization and crop cultivars AU - Hu, Zhengkun AU - Zhu, Chunwu AU - Chen, Xiaoyun AU - Bonkowski, Michael AU - Griffiths, Bryan AU - Chen, Fajun AU - Zhu, Jianguo AU - Hu, Shuijin AU - Hu, Feng AU - Liu, Manqiang T2 - Soil Biology and Biochemistry AB - Elevated atmospheric CO2 concentrations (eCO2) often increase plant growth but simultaneously lead to the nitrogen (N) limitation in soil. The corresponding mitigation strategy such as supplementing N fertilizer and growing high-yielding cultivars at eCO2 would further modify soil ecosystem structure and function. Little attention has, however, been directed toward assessing the responses of soil food web. We report results from a long-term free air CO2 enrichment (FACE) experiment in a rice paddy agroecosystem that examined the responses of soil micro-food webs to eCO2 and exogenous nitrogen fertilization (eN) in the rhizosphere of two rice cultivars with distinctly weak and strong responses to eCO2. Soil micro-food web parameters, including microfauna (protists and nematodes) and soil microbes (bacteria and fungi from phospholipid fatty acid (PLFA) analysis), as well as soil C and N variables, were determined at the heading and ripening stages of rice. Results showed that eCO2 effects on soil micro-food webs depended strongly on N fertilization, rice cultivar and growth stage. eCO2 stimulated the fungal energy channel at the ripening stage, as evidenced by increases in fungal biomass (32%), fungi:bacteria ratio (18%) and the abundance of fungivorous nematodes (64%), mainly due to an enhanced carbon input. The eN fueled the bacterial energy channel by increasing the abundance of flagellates and bacterivorous nematodes, likely through alleviating the N-limitation of plants and rhizosphere under eCO2. While eCO2 decreased the abundance of herbivorous nematodes under the weak-responsive cultivar by 59% and 47% with eN at the heading and ripening stage, respectively, the numbers of herbivorous nematodes almost tripled (×2.9; heading) and doubled (×1.6; ripening) under the strong-responsive cultivar with eCO2 at eN due to higher root quantity and quality. Structural equation model (SEM) showed that lower trophic-level organisms were affected by bottom-up forces of altered soil resources induced by eCO2 and eN, and effects on higher trophic level organisms were driven by bottom-up cascades with 69% of the variation being explained. Taken together, strategies to adapt climate change by growing high-yielding crop cultivars under eCO2 may face a trade-off by negative soil feedbacks through the accumulation of root-feeding crop pest species. DA - 2017/11// PY - 2017/11// DO - 10.1016/J.SOILBIO.2017.07.008 VL - 114 SP - 104-113 J2 - Soil Biology and Biochemistry LA - en OP - SN - 0038-0717 UR - http://dx.doi.org/10.1016/J.SOILBIO.2017.07.008 DB - Crossref KW - Global change KW - Crop cultivar KW - Rhizosphere KW - Soil food webs KW - Root microbiome KW - Soil fauna ER - TY - CHAP TI - Egg Freezing and the Feminist Quest for Equality in the Workplace AU - Harwood, Karey T2 - Reproductive Ethics A2 - Campo-Engelstein, L. A2 - Burcher, P. PY - 2017/// DO - 10.1007/978-3-319-52630-0_5 SP - 63–75 PB - Springer International Publishing SN - 9783319526294 9783319526300 UR - http://dx.doi.org/10.1007/978-3-319-52630-0_5 ER - TY - BOOK TI - Genetic Data Analysis for Plant and Animal Breeding DA - 2017/// PY - 2017/// DO - 10.1007/978-3-319-55177-7 UR - http://dx.doi.org/10.1007/978-3-319-55177-7 ER - TY - JOUR TI - Population extremes for assessing trait value and correlated response of genetically complex traits AU - Rebetzke, G.J. AU - Richards, R.A. AU - Holland, J.B. T2 - Field Crops Research AB - Physiological studies have led to the identification of many traits hypothesized to be useful for breeding improved crop performance. The effect of selection for these traits on yield across breeding populations and across target environments is generally unknown, such that crop breeders may have difficulty in prioritizing evaluation resources among potentially many traits. A simple method to estimate the effect on crop performance from selection on a proposed trait would facilitate trait adoption toward implementation and delivery in improved varieties. The response to indirect selection for different traits can be accurately predicted with nearly-isogenic lines differing for only small regions of the genome and those traits under investigation. An alternative approach better suited to complex, polygenic traits is the assessment of direct and indirect response in ‘tails’ representing phenotypic extremes from a distribution for a target trait. The smaller set of lines representing the two tail groups can then be evaluated more extensively for yield or other expensive and difficult to phenotype traits. Assuming an infinitesimal model appropriate for polygenic traits, we used simulations to understand the influence of population size, proportion of lines sampled in each tail group, trait heritability, and the genotypic correlation between the selection and evaluation trait on the resulting difference between tail means. The power of the tail comparison test was closely related to the heritability of the selection trait and its genotypic correlation with the evaluation trait, demonstrating that the tail comparison test can appropriately evaluate and rank the potential utility of different selection traits. Increasing the entry-mean heritability through multiple environment testing can be coupled with larger population and tail group sizes to increase power and confidence in assessment of both selection and response trait values. We assessed the selection of phenotypic distribution tails for water productivity traits in wheat. Reduced-tillering tails were associated with an average 14% reduction in tiller number and significantly reduced yields (−5%), particularly at wider row-spacings. High vigour tails were associated with a 49% increase in early ground cover, 40% increase in NDVI score, and greater yields (+18%) across all sampled environments. Assessment of population tails across multiple genetic backgrounds will guide selection in commercial breeding programs and facilitate trait delivery in improved cultivars. DA - 2017/// PY - 2017/// DO - 10.1016/j.fcr.2016.10.019 VL - 201 SP - 122-132 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84996607156&partnerID=MN8TOARS KW - Heritability KW - Selection KW - Managed environments KW - Drought KW - QTL KW - Quantitative trait loci KW - Genetic correlation KW - Indirect selection KW - NIL ER - TY - JOUR TI - Modifications to a LATE MERISTEM IDENTITY gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.) AU - Andres, R.J. AU - Coneva, V. AU - Frank, M.H. AU - Tuttle, J.R. AU - Samayoa, L.F. AU - Han, S.-W. AU - Kaur, B. AU - Zhu, L. AU - Fang, H. AU - Bowman, D.T. AU - Rojas-Pierce, M. AU - Haigler, C.H. AU - Jones, D.C. AU - Holland, J.B. AU - Chitwood, D.H. AU - Kuraparthy, V. T2 - Proceedings of the National Academy of Sciences of the United States of America AB - Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D1), which is responsible for the major leaf shapes in cotton. The l-D1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype. DA - 2017/// PY - 2017/// DO - 10.1073/pnas.1613593114 VL - 114 IS - 1 SP - E57-E66 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85007524047&partnerID=MN8TOARS KW - cotton KW - leaf shape KW - okra KW - gene cloning ER - TY - BLOG TI - Politics “Trumps” Science in the Regulation of Genetically Engineered Crops AU - Kuzma, J. T2 - GES Center Blog DA - 2017/11/7/ PY - 2017/11/7/ PB - Genetic Engineering and Society Center/North Carolina State University UR - https://research.ncsu.edu/ges/2017/11/politics-trumps-science-regulation-genetically-engineered-crops/ ER - TY - CONF TI - Indoor arthropod communities and distributions in U.S. homes AU - Bertone, M.A. AU - Leong, M. AU - Bayless, K.M. AU - Trautwein, M.D. T2 - 9th International Conference on Urban Pests A2 - Davies, M. P. A2 - Pfeiffer, C. A2 - Robinson, W. H. C2 - 2017/// C3 - 9th International conference on urban pests CY - Birmingham, England, United Kingdom DA - 2017/// PY - 2017/7/9/ SP - 17–23 ER - TY - BOOK TI - Never out of season: How having the food we want when we want it threatens our food supply and our future AU - Dunn, Rob R. DA - 2017/// PY - 2017/// PB - Little Brown Books ER - TY - CHAP TI - Behavioral and brain-based research on free moral agency: Threatening or empowering? AU - Racine, E. AU - Dubljević, V. T2 - Neuroethics: Anticipating the Future A2 - Illes, J. AB - The belief that people are free human beings is central to much explanation of human behavior as well as to a broad set of social practices such as law, ethics, and politics. Neuroscience has been heralded as a game-changer that will radically alter how people perceive human freedom and potentially lead to the denial of its very existence. This chapter first examines some of the claims made by neuroscience research that challenge beliefs in free moral agency. It posits that a commonly held but unfounded objectivist and essential stance toward free moral agency and an equally common dichotomist fact–value/is–ought tension are at the center of these problematic interpretations. A resolution can be found in pragmatist theory and recent research in social psychology, both of which suggest that knowledge can also empower moral agency. PY - 2017/// DO - 10.1093/oso/9780198786832.003.0020 SP - 388–410 PB - Oxford University Press SN - 9780198786832 ER - TY - JOUR TI - Forum: Biosecurity Governance for a Realistic New World AU - Kuzma, J. T2 - Issues in Science and Technology DA - 2017/// PY - 2017/// VL - 33 IS - 2 ER - TY - CHAP TI - Risk, Environmental Governance, and Emerging Biotechnology AU - Kuzma, J. T2 - Environmental Governance Reconsidered: Challenges, Choices, and Opportunities A2 - Durant, R. A2 - Fiorino, D.J. A2 - O'Leary, R. PY - 2017/// ET - 2nd PB - MIT Press UR - https://mitpress.mit.edu/books/environmental-governance-reconsidered-0 ER - TY - JOUR TI - Teacher Education: Modes of Communication within Asynchronous and Synchronous Communication Platforms AU - Madden, L. AU - Jones, M.G. AU - Childers, G. T2 - Journal of Classroom Interactions DA - 2017/// PY - 2017/// VL - 52 IS - 2 SP - 16–30 ER - TY - JOUR TI - Exploring multimedia principles for supporting conceptual learning of electricity and magnetism with visuohaptic simulations AU - Magana, A. AU - Sanchez, K. AU - Shaikh, U. AU - Jones, M.G. AU - Tan, H. AU - Guyaquil, A. AU - Benes, B. T2 - Computers in Education DA - 2017/// PY - 2017/// VL - 8 IS - 2 SP - 8–23 ER - TY - JOUR TI - The potential for the use of gene drives for pest control in New Zealand: a perspective AU - Dearden, Peter K. AU - Gemmell, Neil J. AU - Mercier, Ocean R. AU - Lester, Philip J. AU - Scott, Maxwell J. AU - Newcomb, Richard D. AU - Buckley, Thomas R. AU - Jacobs, Jeanne M. E. AU - Goldson, Stephen G. AU - Penman, David R. T2 - Journal of the Royal Society of New Zealand AB - Genetic technologies such as gene editing and gene drive systems have recently emerged as potential tools for pest control. Gene drives, in particular, have been described as potential solutions to the pest problems that beset New Zealand. Here we describe the current state of gene drive technologies and present a series of examples to examine the potential benefits and problems arising from gene drive approaches for pest control in New Zealand. We consider the risks and barriers, both biological and social, that would need to be addressed to deploy such systems against our key pests with particular reference to the unique characteristics of New Zealand’s biota, environment and peoples. Gene drives are a potentially useful technology for the eradication of pests in New Zealand but a great deal of research and understanding, as well as public acceptance, is required before they can be implemented. DA - 2017/10/25/ PY - 2017/10/25/ DO - 10.1080/03036758.2017.1385030 VL - 48 IS - 4 SP - 225-244 J2 - Journal of the Royal Society of New Zealand LA - en OP - SN - 0303-6758 1175-8899 UR - http://dx.doi.org/10.1080/03036758.2017.1385030 DB - Crossref KW - Bioheritage KW - bioprotection KW - CRISPR KW - gene drives KW - pest control KW - social licence ER - TY - BLOG TI - Insight into molecular basis of plant-infecting arbovirus persistence in the vector: Conserved responses to viruses in insects AU - Rotenberg, D. AU - Martin, K. AU - Whitfield, A. T2 - Virology Highlights Blog DA - 2017/// PY - 2017/// PB - Elsevier UR - http://www.elsevierblogs.com/virology/insight-into-molecular-basis-of-plant-infecting-arbovirus-persistence-in-the-vector/ ER - TY - JOUR TI - Wildlife species preferences differ among children in continental and island locations AU - Shapiro, Hannah G. AU - Peterson, M. Nils AU - Stevenson, Kathryn T. AU - Frew, Kristin N. AU - Langerhans, R. Brian T2 - Environmental Conservation AB - SUMMARY Efforts to prioritize wildlife for conservation benefit from an understanding of public preferences for particular species, yet no studies have integrated species preferences with key attributes of the conservation landscape such as whether species occur on islands (where invasive exotics are the primary extinction threat) or continents (where land use change is the primary extinction threat). In this paper, we compare wildlife species preferences among children from a continental location (North Carolina, USA, n = 433) and an island location (Andros Island, The Bahamas, n = 197). Children on the island preferred feral domesticated species and different types of taxa than mainland children, perhaps due to the strongly divergent species richness between the regions (e.g. island children showed greater preferences for invertebrates, lizards and aquatic species). Boys preferred fish, birds and lizards more than girls, whereas girls preferred mammals. The fact that island children showed strong preferences for invasive species suggests challenges for conservation efforts on islands, where controlling invasive exotic species is often of paramount importance, but can conflict with cultural preferences for these same species. DA - 2017/3/29/ PY - 2017/3/29/ DO - 10.1017/S0376892917000133 VL - 44 IS - 4 SP - 389-396 J2 - Envir. Conserv. LA - en OP - SN - 0376-8929 1469-4387 UR - http://dx.doi.org/10.1017/S0376892917000133 DB - Crossref KW - wildlife preferences KW - cross-cultural KW - human dimensions KW - children KW - environmental education KW - conservation ER - TY - CHAP TI - Is It Time to Abandon the Strong Interpretation of the Dual-Process Model in Neuroethics? AU - Dubljević, Veljko T2 - Debates About Neuroethics PY - 2017/// DO - 10.1007/978-3-319-54651-3_9 SP - 129-140 OP - PB - Springer International Publishing SN - 9783319546506 9783319546513 UR - http://dx.doi.org/10.1007/978-3-319-54651-3_9 DB - Crossref ER - TY - JOUR TI - What's in Your School Yard? Using Citizen Science Wildlife Cameras to Conduct Authentic Scientific Investigations AU - Schuttler, Stephanie AU - Glenn, David AU - Belair, Catherine AU - Hohm, Jordan AU - Humphries, Denise AU - Pasion, Dayson AU - Dunn, Robert AU - Kays, Roland T2 - Science Scope DA - 2017/// PY - 2017/// DO - 10.2505/4/ss17_041_01_63 VL - 041 IS - 01 J2 - Sci. Scope LA - en OP - SN - 0887-2376 UR - http://dx.doi.org/10.2505/4/ss17_041_01_63 DB - Crossref ER - TY - JOUR TI - The Basic Reproductive Number for Disease Systems with Multiple Coupled Heterogeneities AU - Lloyd, Alun AU - Kitron, Uriel AU - Perkins, Alex AU - Prokopec, Gonzalo Vazquez AU - Waller, Lance T2 - bioRxiv AB - In mathematical epidemiology, a well-known formula describes the impact of heterogeneity on the basic reproductive number, R0, for situations in which transmission is separable and for which there is one source of variation in susceptibility and one source of variation in infectiousness. This formula is written in terms of the magnitudes of the heterogeneities, as quantified by their coefficients of variation, and the correlation between them. A natural question to ask is whether analogous results apply when there are multiple sources of variation in susceptibility and/or infectiousness. In this paper we demonstrate that with three or more coupled heterogeneities, R0 under separable transmission depends on details of the distribution of the heterogeneities in a way that is not seen in the well-known simpler situation. We provide explicit formulae for the cases of multivariate normal and multivariate log-normal distributions, showing that R0 can again be expressed in terms of the magnitudes of the heterogeneities and the pairwise correlations between them. The formulae, however, differ between the two multivariate distributions, demonstrating that no formula of this type applies generally when there are three or more coupled heterogeneities. We see that the results of the formulae are approximately equal when heterogeneities are relatively small and show that an earlier result in the literature (Koella, 1991) should be viewed in this light. We provide numerical illustrations of our results and discuss a setting in which coupled heterogeneities are likely to have a major impact on the value of R0. We also describe a rather surprising result: in a system with three heterogeneities, R0 can exhibit non-monotonic behavior with increasing levels of heterogeneity, in marked contrast to the familiar two heterogeneity setting in which R0 either increases or decreases with increasing heterogeneity. DA - 2017/// PY - 2017/// DO - 10.1016/j.mbs.2019.108294 SP - 220004 KW - Disease transmission model KW - Heterogeneity KW - Basic reproductive number KW - Coupled heterogeneities ER - TY - JOUR TI - Adaptive filtering for hidden node detection and tracking in networks AU - Hamilton, Franz AU - Setzer, Beverly AU - Chavez, Sergio AU - Tran, Hien AU - Lloyd, Alun L T2 - Chaos: An Interdisciplinary Journal of Nonlinear Science DA - 2017/// PY - 2017/// VL - 27 IS - 7 SP - 073106 ER - TY - JOUR TI - Evaluating strategies for reversing CRISPR-Cas9 gene drives AU - Vella, Michael R. AU - Gunning, Christian E. AU - Lloyd, Alun L. AU - Gould, Fred T2 - Scientific Reports AB - Abstract A gene drive biases inheritance of a gene so that it increases in frequency within a population even when the gene confers no fitness benefit. There has been renewed interest in environmental releases of engineered gene drives due to recent proof of principle experiments with the CRISPR-Cas9 system as a drive mechanism. Release of modified organisms, however, is controversial, especially when the drive mechanism could theoretically alter all individuals of a species. Thus, it is desirable to have countermeasures to reverse a drive if a problem arises. Several genetic mechanisms for limiting or eliminating gene drives have been proposed and/or developed, including synthetic resistance, reversal drives, and immunizing reversal drives. While predictions about efficacy of these mechanisms have been optimistic, we lack detailed analyses of their expected dynamics. We develop a discrete time model for population genetics of a drive and proposed genetic countermeasures. Efficacy of drive reversal varies between countermeasures. For some parameter values, the model predicts unexpected behavior including polymorphic equilibria and oscillatory dynamics. The timing and number of released individuals containing a genetic countermeasure can substantially impact outcomes. The choice among countermeasures by researchers and regulators will depend on specific goals and population parameters of target populations. DA - 2017/5/30/ PY - 2017/5/30/ DO - 10.1101/144097 VL - 5 SP - 11038 UR - https://doi.org/10.1101/144097 ER - TY - JOUR TI - Taxonomy of the order Mononegavirales: update 2017 AU - Amarasinghe, Gaya K. AU - Bào, Yīmíng AU - Basler, Christopher F. AU - Bavari, Sina AU - Beer, Martin AU - Bejerman, Nicolás AU - Blasdell, Kim R. AU - Bochnowski, Alisa AU - Briese, Thomas AU - Bukreyev, Alexander AU - Calisher, Charles H. AU - Chandran, Kartik AU - Collins, Peter L. AU - Dietzgen, Ralf G. AU - Dolnik, Olga AU - Dürrwald, Ralf AU - Dye, John M. AU - Easton, Andrew J. AU - Ebihara, Hideki AU - Fang, Qi AU - Formenty, Pierre AU - Fouchier, Ron A. M. AU - Ghedin, Elodie AU - Harding, Robert M. AU - Hewson, Roger AU - Higgins, Colleen M. AU - Hong, Jian AU - Horie, Masayuki AU - James, Anthony P. AU - Jiāng, Dàohóng AU - Kobinger, Gary P. AU - Kondo, Hideki AU - Kurath, Gael AU - Lamb, Robert A. AU - Lee, Benhur AU - Leroy, Eric M. AU - Li, Ming AU - Maisner, Andrea AU - Mühlberger, Elke AU - Netesov, Sergey V. AU - Nowotny, Norbert AU - Patterson, Jean L. AU - Payne, Susan L. AU - Paweska, Janusz T. AU - Pearson, Michael N. AU - Randall, Rick E. AU - Revill, Peter A. AU - Rima, Bertus K. AU - Rota, Paul AU - Rubbenstroth, Dennis AU - Schwemmle, Martin AU - Smither, Sophie J. AU - Song, Qisheng AU - Stone, David M. AU - Takada, Ayato AU - Terregino, Calogero AU - Tesh, Robert B. AU - Tomonaga, Keizo AU - Tordo, Noël AU - Towner, Jonathan S. AU - Vasilakis, Nikos AU - Volchkov, Viktor E. AU - Wahl-Jensen, Victoria AU - Walker, Peter J. AU - Wang, Beibei AU - Wang, David AU - Wang, Fei AU - Wang, Lin-Fa AU - Werren, John H. AU - Whitfield, Anna E. AU - Yan, Zhichao AU - Ye, Gongyin AU - Kuhn, Jens H. T2 - Archives of Virology AB - In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). DA - 2017/4/7/ PY - 2017/4/7/ DO - 10.1007/S00705-017-3311-7 VL - 162 IS - 8 SP - 2493-2504 J2 - Arch Virol LA - en OP - SN - 0304-8608 1432-8798 UR - http://dx.doi.org/10.1007/S00705-017-3311-7 DB - Crossref ER - TY - JOUR TI - Household Dynamics of Wildlife Value Orientations AU - Clark, Kalysha E. AU - Cupp, Katie AU - Phelps, Crystal L. AU - Peterson, M. Nils AU - Stevenson, Kathryn T. AU - Serenari, Christopher T2 - Human Dimensions of Wildlife AB - Wildlife value orientations (WVOs) shape attitudes and behavior toward wildlife. Although demographic correlates of WVOs are well established, these relationships are largely unknown among children and within family units. The only previous study addressing these topics used fathers’ perceptions as proxies for family member WVOs. We surveyed North Carolina households (n = 136) to test hypotheses regarding whether individuals can assess household WVOs and what variables shape WVOs within households. Fathers and mothers accurately assessed WVOs of their children. Membership in a household was the most important predictor of an individual’s WVOs (accounting for 37% [ρ = .37] of the variance predicted by the model). Younger age, being female, and lack of participation in hunting were associated with more protectionist WVOs. These results provide the first household level support for divergence between generations from utilitarian toward protectionist WVOs. Our results suggest that household unit may be a critical element to consider in WVO research. DA - 2017/8// PY - 2017/8// DO - 10.1080/10871209.2017.1345022 VL - 22 IS - 5 SP - 483-491 J2 - Human Dimensions of Wildlife LA - en OP - SN - 1087-1209 1533-158X UR - http://dx.doi.org/10.1080/10871209.2017.1345022 DB - Crossref KW - Children KW - education KW - families KW - household KW - protectionist KW - utilitarian KW - wildlife value orientation ER - TY - JOUR TI - Evaluating relationships between hunting and biodiversity knowledge among children AU - Peterson, M. Nils AU - Chesonis, Tessa AU - Stevenson, Kathryn T. AU - Bondell, Howard D. T2 - Wildlife Society Bulletin AB - ABSTRACT We investigated how hunting participation and associated demographic variables relate to biodiversity knowledge among children. Past participation in hunting among elementary age children in North Carolina, USA, surveyed during 2014 was high (29%) and a positive predictor of student's ability to name native wildlife species after controlling for gender, ethnicity, and grade level. Minorities and girls had lower biodiversity knowledge scores and were less supportive of hunting. Our findings suggest children may view hunting differently than adults and that youth hunting programs, particularly those targeting very young children, may be fruitful ways to promote biodiversity knowledge. Such efforts, however, may be most valuable among minorities because Hispanic children had the lowest participation in hunting and Black children had both low participation rates and lowest biodiversity knowledge scores. © 2017 The Wildlife Society. DA - 2017/8/14/ PY - 2017/8/14/ DO - 10.1002/WSB.792 VL - 41 IS - 3 SP - 530-536 J2 - Wildl. Soc. Bull. LA - en OP - SN - 1938-5463 UR - http://dx.doi.org/10.1002/WSB.792 DB - Crossref KW - biodiversity KW - children KW - education KW - ethnicity KW - gender KW - hunting KW - knowledge ER - TY - JOUR TI - Production Risk, Farmer Welfare, and Bt Corn in the Philippines AU - Sanglestsawai, Santi AU - Rodriguez, Divina Gracia P. AU - Rejesus, Roderick M. AU - Yorobe, Jose M., Jr. T2 - Agricultural and Resource Economics Review AB - We determine the production risk effects and welfare implications of single-trait Bt corn adoption in the Philippines. We use a stochastic production function estimation approach that allows for examining the skewness effects of Bt within a damage abatement specification. Our results indicate that Bt corn has a statistically significant yield increasing, risk-increasing (i.e., variance-increasing) and downside risk-reducing (i.e., skewness-increasing) effects. Based on risk premium, certainty equivalent, and loss probability welfare measures, Bt corn farmers in the Philippines are better-off (in absolute terms) relative to non-Bt farmers given Bt corn's dominant yield increasing effect and downside risk-reducing effect. DA - 2017/10/2/ PY - 2017/10/2/ DO - 10.1017/AGE.2017.1 VL - 46 IS - 3 SP - 507-528 J2 - Agric. Resour. Econom. Rev. LA - en OP - SN - 1068-2805 2372-2614 UR - http://dx.doi.org/10.1017/AGE.2017.1 DB - Crossref KW - Bt corn KW - damage abatement KW - downside risk KW - GM crop KW - production risk KW - skewness KW - stochastic production function ER - TY - JOUR TI - The neglected geography of human pathogens and diseases AU - Stensgaard, Anna-Sofie AU - Dunn, Robert R. AU - Vennervald, Birgitte J. AU - Rahbek, Carsten T2 - Nature Ecology & Evolution DA - 2017/6/22/ PY - 2017/6/22/ DO - 10.1038/S41559-017-0190 VL - 1 IS - 7 J2 - Nat Ecol Evol LA - en OP - SN - 2397-334X UR - http://dx.doi.org/10.1038/S41559-017-0190 DB - Crossref ER - TY - JOUR TI - Regulation of Drosophila Lifespan by bellwether Promoter Alleles AU - Garcia, Júlia Frankenberg AU - Carbone, Mary Anna AU - Mackay, Trudy F. C. AU - Anholt, Robert R. H. T2 - Scientific Reports AB - Longevity varies among individuals, but how natural genetic variation contributes to variation in lifespan is poorly understood. Drosophila melanogaster presents an advantageous model system to explore the genetic underpinnings of longevity, since its generation time is brief and both the genetic background and rearing environment can be precisely controlled. The bellwether (blw) gene encodes the α subunit of mitochondrial ATP synthase. Since metabolic rate may influence lifespan, we investigated whether alternative haplotypes in the blw promoter affect lifespan when expressed in a co-isogenic background. We amplified 521 bp upstream promoter sequences containing alternative haplotypes and assessed promoter activity both in vitro and in vivo using a luciferase reporter system. The AG haplotype showed significantly greater expression of luciferase than the GT haplotype. We then overexpressed a blw cDNA construct driven by either the AG or GT haplotype promoter in transgenic flies and showed that the AG haplotype also results in greater blw cDNA expression and a significant decrease in lifespan relative to the GT promoter haplotype, in male flies only. Thus, our results show that naturally occurring regulatory variants of blw affect lifespan in a sex-specific manner. DA - 2017/6/23/ PY - 2017/6/23/ DO - 10.1038/S41598-017-04530-X VL - 7 IS - 1 J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/S41598-017-04530-X DB - Crossref ER - TY - JOUR TI - Inquiry Into Action: Ecosystems and Animals AU - Ennes, Megan AU - Kubasko, Dennis AU - Jones, M. Gail T2 - Science Scope DA - 2017/// PY - 2017/// DO - 10.2505/4/ss17_041_03_28 VL - 041 IS - 03 J2 - Sci. Scope LA - en OP - SN - 0887-2376 UR - http://dx.doi.org/10.2505/4/ss17_041_03_28 DB - Crossref ER - TY - JOUR TI - Learning from a distance: high school students’ perceptions of virtual presence, motivation, and science identity during a remote microscopy investigation AU - Childers, Gina AU - Jones, M. Gail T2 - International Journal of Science Education AB - Through partnerships with scientists, students can now conduct research in science laboratories from a distance through remote access technologies. The purpose of this study was to explore factors that contribute to a remote learning environment by documenting high school students’ perceptions of science motivation, science identity, and virtual presence during a remote microscopy investigation. Exploratory factor analysis identified 3 factors accounting for 63% of the variance, which suggests that Science Learning Drive (students’ perception of their competence and performance in science and intrinsic motivation to do science), Environmental Presence (students’ perception of control of the remote technology, sensory, and distraction factors in the learning environment, and relatedness to scientists), and Inner Realism Presence (students’ perceptions of how real is the remote programme and being recognised as a science-oriented individual) were factors that contribute to a student’s experience during a remote investigation. Motivation, science identity, and virtual presence in remote investigations are explored. DA - 2017/2/11/ PY - 2017/2/11/ DO - 10.1080/09500693.2016.1278483 VL - 39 IS - 3 SP - 257-273 J2 - International Journal of Science Education LA - en OP - SN - 0950-0693 1464-5289 UR - http://dx.doi.org/10.1080/09500693.2016.1278483 DB - Crossref KW - Motivation KW - learning technologies ER - TY - JOUR TI - Teaching Systems Thinking in the Context of the Water Cycle AU - Lee, Tammy D. AU - Gail Jones, M. AU - Chesnutt, Katherine T2 - Research in Science Education DA - 2017/6/23/ PY - 2017/6/23/ DO - 10.1007/s11165-017-9613-7 VL - 49 IS - 1 SP - 137-172 J2 - Res Sci Educ LA - en OP - SN - 0157-244X 1573-1898 UR - http://dx.doi.org/10.1007/s11165-017-9613-7 DB - Crossref KW - Systems thinking KW - Elementary teachers KW - Water cycle KW - Teacher education ER - TY - JOUR TI - Elementary Teachers’ Selection and Use of Visual Models AU - Lee, Tammy D. AU - Gail Jones, M. T2 - Journal of Science Education and Technology DA - 2017/7/29/ PY - 2017/7/29/ DO - 10.1007/s10956-017-9705-1 VL - 27 IS - 1 SP - 1-29 J2 - J Sci Educ Technol LA - en OP - SN - 1059-0145 1573-1839 UR - http://dx.doi.org/10.1007/s10956-017-9705-1 DB - Crossref KW - Visual models KW - Modeling KW - Systems thinking KW - In-service elementary KW - Preservice elementary ER - TY - JOUR TI - Erratum: Corrigendum: Effects of Nitrogen and Shading on Root Morphologies, Nutrient Accumulation, and Photosynthetic Parameters in Different Rice Genotypes AU - Pan, Shenggang AU - Liu, Haidong AU - Mo, Zhaowen AU - Patterson, Bob AU - Duan, Meiyang AU - Tian, Hua AU - Hu, Shuijin AU - Tang, Xiangru T2 - Scientific Reports AB - Scientific Reports 6: Article number: 32148; published online: 25 August 2016; updated: 30 March 2017 The original version of this Article contained a typographical error in the spelling of the author Shuijin Hu, which was incorrectly given as Shuijing Hu. This has now been corrected in the PDF and HTML versions of the Article. DA - 2017/3/30/ PY - 2017/3/30/ DO - 10.1038/SREP45611 VL - 7 IS - 1 J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/SREP45611 DB - Crossref ER - TY - JOUR TI - Climate-induced migration: using mental models to explore aggregate and individual decision-making AU - Whitley, Cameron Thomas AU - Rivers III, Louie AU - Mattes, Seven AU - Marquart-Pyatt, Sandra T. AU - Ligmann-Zielinska, Arika AU - Olabisi, Laura Schmitt AU - Du, Jing T2 - Journal of Risk Research AB - The US Dust Bowl of the 1930s (a prolong period of drought experienced in the United States accompanied by severe sand storms) is often described as an abnormal event. However, climate change is likely to increase the frequency and impact of similar occurrences. Because of this, a growing number of scholars have begun to examine multiple facets of climate-induced migration from various disciplinary traditions. Specifically, scholars have called for continued research into individual decision-making processes. Responding to this call, we construct a mental model from historical interviews of those who migrated to California during the US Dust Bowl. Our model provides insight into the migration process with a unique focus on individual decision-making processes of migrants. DA - 2017/1/31/ PY - 2017/1/31/ DO - 10.1080/13669877.2017.1281331 VL - 21 IS - 8 SP - 1019-1035 J2 - Journal of Risk Research LA - en OP - SN - 1366-9877 1466-4461 UR - http://dx.doi.org/10.1080/13669877.2017.1281331 DB - Crossref KW - climate change KW - climate migration KW - drought KW - dust bowl KW - mental models ER - TY - JOUR TI - Mental models of food security in rural Mali AU - Rivers III, Louie AU - Sanga, Udita AU - Sidibe, Amadou AU - Wood, Alexa AU - Paudel, Rajiv AU - Marquart-Pyatt, Sandra T. AU - Ligmann-Zielinska, Arika AU - Olabisi, Laura Schmitt AU - Du, Eric Jing AU - Liverpool-Tasie, Saweda T2 - Environment Systems and Decisions DA - 2017/12/8/ PY - 2017/12/8/ DO - 10.1007/S10669-017-9669-Y VL - 38 IS - 1 SP - 33-51 J2 - Environ Syst Decis LA - en OP - SN - 2194-5403 2194-5411 UR - http://dx.doi.org/10.1007/S10669-017-9669-Y DB - Crossref ER - TY - JOUR TI - Using participatory modeling processes to identify sources of climate risk in West Africa AU - Schmitt Olabisi, Laura AU - Liverpool-Tasie, Saweda AU - Rivers, Louie AU - Ligmann-Zielinska, Arika AU - Du, Jing AU - Denny, Riva AU - Marquart-Pyatt, Sandra AU - Sidibé, Amadou T2 - Environment Systems and Decisions AB - Participatory modeling has been widely recognized in recent years as a powerful tool for dealing with risk and uncertainty. By incorporating multiple perspectives into the structure of a model, we hypothesize that sources of risk can be identified and analyzed more comprehensively compared to traditional ‘expert-driven’ models. However, one of the weaknesses of a participatory modeling process is that it is typically not feasible to involve more than a few dozen people in model creation, and valuable perspectives on sources of risk may therefore be absent. We sought to address this weakness by conducting parallel participatory modeling processes in three countries in West Africa with similar climates and smallholder agricultural systems, but widely differing political and cultural contexts. Stakeholders involved in the agricultural sector in Ghana, Mali, and Nigeria participated in either a scenario planning process or a causal loop diagramming process, in which they were asked about drivers of agricultural productivity and food security, and sources of risk, including climate risk, between the present and mid-century (2035–2050). Participants in all three workshops identified both direct and indirect sources of climate risk, as they interact with other critical drivers of agricultural systems change, such as water availability, political investment in agriculture, and land availability. We conclude that participatory systems methods are a valuable addition to the suite of methodologies for analyzing climate risk and that scientists and policy-makers would do well to consider dynamic interactions between drivers of risk when assessing the resilience of agricultural systems to climate change. DA - 2017/10/4/ PY - 2017/10/4/ DO - 10.1007/S10669-017-9653-6 VL - 38 IS - 1 SP - 23-32 J2 - Environ Syst Decis LA - en OP - SN - 2194-5403 2194-5411 UR - http://dx.doi.org/10.1007/S10669-017-9653-6 DB - Crossref ER - TY - JOUR TI - Food security in Africa: a cross-scale, empirical investigation using structural equation modeling AU - Denny, Riva C. H. AU - Marquart-Pyatt, Sandra T. AU - Ligmann-Zielinska, Arika AU - Olabisi, Laura Schmitt AU - Rivers, Louie AU - Du, Jing AU - Liverpool-Tasie, Lenis Saweda O. T2 - Environment Systems and Decisions DA - 2017/9/20/ PY - 2017/9/20/ DO - 10.1007/S10669-017-9652-7 VL - 38 IS - 1 SP - 6-22 J2 - Environ Syst Decis LA - en OP - SN - 2194-5403 2194-5411 UR - http://dx.doi.org/10.1007/S10669-017-9652-7 DB - Crossref ER - TY - JOUR TI - Les systèmes CRISPR-Cas comme arme contre les bactéries pathogènes AU - Bikard, David AU - Barrangou, Rodolphe T2 - Biologie Aujourd'hui AB - CRISPR-Cas systems (Clustered Regularly Interspaced Short Palindromic Repeats) are the adaptive immune system of bacteria and archaea. They target foreign genetic elements thanks to small RNAs able to guide Cas nucleases to destroy them. These nucleases can be reprogrammed to target chromosomal sequences rather than invasive genetic elements. Whereas targeting the genome of eukaryotic cells enables the efficient genesis of mutations, DNA breaks induced by Cas nucleases are lethal in bacteria. This property can be used in the development of novel antimicrobial strategies. CRISPR-Cas systems can be delivered to target bacteria using bacteriophage capsids in order to specifically eliminate bacteria carrying antibiotic resistance genes or virulence factors. These technologies enable the development of novel tools based on CRISPR-Cas systems to specifically eliminate pathogenic bacteria and precisely modify the composition of various microbiomes. DA - 2017/// PY - 2017/// DO - 10.1051/JBIO/2018004 VL - 211 IS - 4 SP - 265-270 J2 - Biologie Aujourd'hui OP - SN - 2105-0678 2105-0686 UR - http://dx.doi.org/10.1051/JBIO/2018004 DB - Crossref ER - TY - JOUR TI - GIS-based allocation of herbaceous biomass in biorefineries and depots AU - Gonzales, Daniela S. AU - Searcy, Stephen W. T2 - Biomass and Bioenergy AB - While sufficient biomass has been identified to meet the Renewable Fuel Standard (RFS2)1 targets by previous studies, availability does not equal access. Our objective was to quantify the potential accessible and stranded herbaceous biomass from different scenarios of predicted available biomass in both Texas and the US. The location and size of potential biorefineries and depots was determined using the geographic location of suitable lands for biomass, the transportation infrastructure and published economic constraints for minimum biomass supplied to a facility within a specified neighborhood. Our GIS-based heuristic addresses the capacitated facility location problem by distributing potential biomass along a county's suitable lands. Road and rail proximity optionally was included in the algorithm. The total stranded biomass in Texas was 28% of the total available biomass. Including the constraint of the transportation network accessibility (rail and appropriate roads) when determining facility location increased the total stranded biomass to 33%. Using county centroids as supply points and potential facilities led to an increase of 7% in total biomass captured by all facilities in Texas when compared to our raster-based heuristic. The nationwide accessible biomass is 90% of the available biomass, 78% of which is captured by biorefineries. In total, 77 biorefineries and 171 depots were identified in the US, which projects to 184 million Mg year−1 delivered to biorefineries and depots, or 65.3 billion liters of advanced biofuels, more than the targeted 60 billion liters of advanced cellulosic biofuel in the RFS2. DA - 2017/2// PY - 2017/2// DO - 10.1016/j.biombioe.2016.12.009 VL - 97 SP - 1-10 J2 - Biomass and Bioenergy LA - en OP - SN - 0961-9534 UR - http://dx.doi.org/10.1016/j.biombioe.2016.12.009 DB - Crossref KW - Billion-ton study KW - Biomass KW - Perennial grasses KW - Switchgrass KW - Precipitation ER - TY - JOUR TI - Tracking 19th Century Late Blight from Archival Documents using Text Analytics and Geoparsing AU - Tateosian, L. AU - Guenter, R. AU - Yang, Y.P. AU - Ristaino, J. T2 - Free and Open Source Software for Geospatial (FOSS4G) Conference Proceedings DA - 2017/// PY - 2017/// DO - 10.7275/R5J964K5 VL - 17 IS - 1 SP - 17 UR - http://scholarworks.umass.edu/foss4g/vol17/iss1/17/ ER - TY - JOUR TI - Thrips developmental stage-specific transcriptome response to tomato spotted wilt virus during the virus infection cycle in Frankliniella occidentalis, the primary vector AU - Schneweis, Derek J. AU - Whitfield, Anna E. AU - Rotenberg, Dorith T2 - Virology AB - Tomato spotted wilt virus (TSWV) is transmitted by Frankliniella occidentalis in a circulative-propagative manner. Little is known about thrips vector response to TSWV during the infection process from larval acquisition to adult inoculation of plants. Whole-body transcriptome response to virus infection was determined for first-instar larval, pre-pupal and adult thrips using RNA-Seq. TSWV responsive genes were identified using preliminary sequence of a draft genome of F. occidentalis as a reference and three developmental-stage transcriptomes were assembled. Processes and functions associated with host defense, insect cuticle structure and development, metabolism and transport were perturbed by TSWV infection as inferred by ontologies of responsive genes. The repertoire of genes responsive to TSWV varied between developmental stages, possibly reflecting the link between thrips development and the virus dissemination route in the vector. This study provides the foundation for exploration of tissue-specific expression in response to TSWV and functional analysis of thrips gene function. DA - 2017/1// PY - 2017/1// DO - 10.1016/J.VIROL.2016.10.009 VL - 500 SP - 226-237 J2 - Virology LA - en OP - SN - 0042-6822 UR - http://dx.doi.org/10.1016/J.VIROL.2016.10.009 DB - Crossref KW - Western flower thrips KW - Thysanoptera KW - Virus-vector interactions KW - Tospovirus KW - Bunyaviridae KW - transcriptome ER - TY - JOUR TI - Transcriptome changes associated with Tomato spotted wilt virus infection in various life stages of its thrips vector, Frankliniella fusca (Hinds) AU - Shrestha, Anita AU - Champagne, Donald E. AU - Culbreath, Albert K. AU - Rotenberg, Dorith AU - Whitfield, Anna E. AU - Srinivasan, Rajagopalbabu T2 - Journal of General Virology AB - Persistent propagative viruses maintain intricate interactions with their arthropod vectors. In this study, we investigated the transcriptome-level responses associated with a persistent propagative phytovirus infection in various life stages of its vector using an Illumina HiSeq sequencing platform. The pathosystem components included a Tospovirus, Tomato spotted wilt virus (TSWV), its insect vector, Frankliniella fusca (Hinds), and a plant host, Arachis hypogaea (L.). We assembled (de novo) reads from three developmental stage groups of virus-exposed and non-virus-exposed F. fusca into one transcriptome consisting of 72 366 contigs and identified 1161 differentially expressed (DE) contigs. The number of DE contigs was greatest in adults (female) (562) when compared with larvae (first and second instars) (395) and pupae (pre- and pupae) (204). Upregulated contigs in virus-exposed thrips had blastx annotations associated with intracellular transport and virus replication. Upregulated contigs were also assigned blastx annotations associated with immune responses, including apoptosis and phagocytosis. In virus-exposed larvae, Blast2GO analysis identified functional groups, such as multicellular development with downregulated contigs, while reproduction, embryo development and growth were identified with upregulated contigs in virus-exposed adults. This study provides insights into differences in transcriptome-level responses modulated by TSWV in various life stages of an important vector, F. fusca. DA - 2017/8/1/ PY - 2017/8/1/ DO - 10.1099/jgv.0.000874 VL - 98 IS - 8 SP - 2156-2170 LA - en OP - SN - 0022-1317 1465-2099 UR - http://dx.doi.org/10.1099/jgv.0.000874 DB - Crossref KW - Frankliniella fusca KW - transcriptomes KW - de novo assembly KW - differentially expressed contigs KW - TSWV ER - TY - JOUR TI - Development and use of a piggyBac -based jumpstarter system in Drosophila suzukii AU - Chu, Fu-Chyun AU - Klobasa, William AU - Grubbs, Nathaniel AU - Lorenzen, Marcé D. T2 - Archives of Insect Biochemistry and Physiology AB - Spotted wing drosophila, Drosophila suzukii, is an invasive pest that primarily attacks fresh, soft-skinned fruit. Although others have reported successful integration of marked piggyBac elements into the D. suzukii genome, with a very respectable transgenesis rate of ∼16%, here we take this work a step further by creating D. suzukii jumpstarter strains. These were generated through integration of a fluorescent-marked Minos element carrying a heat shock protein 70-driven piggyBac transposase gene. We demonstrate that there is a dramatic increase in transformation rates when germline transformation is performed in a transposase-expressing background. For example, we achieved transformation rates as high as 80% when microinjecting piggyBac-based plasmids into embryos derived from one of these D. suzukii jumpstarter strains. We also investigate the effect of insert size on transformation efficiency by testing the ability of the most efficient jumpstarter strain to catalyze integration of differently-sized piggyBac elements. Finally, we demonstrate the ability of a jumpstarter strain to remobilize an already-integrated piggyBac element to a new location, demonstrating that our jumpstarter strains could be used in conjunction with a piggyBac-based donor strain for genome-wide mutagenesis of D. suzukii. DA - 2017/12/1/ PY - 2017/12/1/ DO - 10.1002/arch.21439 VL - 97 IS - 3 SP - e21439 J2 - Arch. Insect Biochem. Physiol. LA - en OP - SN - 0739-4462 UR - http://dx.doi.org/10.1002/arch.21439 DB - Crossref KW - germline transformation KW - Minos KW - mutagenesis KW - piggyBac KW - transgenesis ER - TY - JOUR TI - Agricultural production: assessment of the potential use of Cas9-mediated gene drive systems for agricultural pest control AU - Scott, Maxwell J. AU - Gould, Fred AU - Lorenzen, Marcé AU - Grubbs, Nathaniel AU - Edwards, Owain AU - O’Brochta, David T2 - Journal of Responsible Innovation AB - To highlight how gene drives could be useful for control of agricultural insect pests, we selected species that are pests of animals (New World screwworm), plants (spotted wing Drosophila, diamondback moth, Bemisia tabaci whitefly), or stored grains (red flour beetle). With the exception of whitefly, routine methods for delivering DNA to the germline and selecting for genetically modified insects have been developed. The traditional approach in agriculture has been to suppress insect pest populations using insecticides and other farming practices. Similarly, we suggest the main use of gene drives in agriculture will be for population suppression through targeting essential genes. We provide examples of gene drives that target specific genes including female-essential genes. Further, we discuss issues related to containment in the laboratory and eventual field testing of strains harboring a Cas9-mediated gene drive system. DA - 2017/12/11/ PY - 2017/12/11/ DO - 10.1080/23299460.2017.1410343 VL - 5 IS - sup1 SP - S98-S120 J2 - Journal of Responsible Innovation LA - en OP - SN - 2329-9460 2329-9037 UR - http://dx.doi.org/10.1080/23299460.2017.1410343 DB - Crossref KW - Gene drive KW - Cas9 KW - sterile insect technique KW - agricultural pest insect ER - TY - JOUR TI - Applicability of Benford's Law to Compliance Assessment of Self-Reported Wastewater Treatment Plant Discharge Data AU - Beiglou, P.H.B. AU - Gibbs, C. AU - Rivers, L. AU - Adhikari, U. AU - Mitchell, J. T2 - Journal of Environmental Assessment Policy and Management AB - The United States (U.S.) environmental regulatory system relies heavily on self-reports to assess compliance among regulated facilities. However, the regulatory agencies have expressed concerns regarding the potential for fraud in self-reports and suggested that the likelihood of detection in the federal and state enforcement processes is low. In this paper, we apply Benford’s Law to three years of self-reported discharge parameters from wastewater treatment plant facilities in one U.S. state. We conclude that Benford’s Law alone may not be a reliable method for detecting potential data mishandling for individual facility–parameter combinations, but may provide information about the types of parameters most likely to be fraudulently reported and types of facilities most likely to do so. From a regulatory perspective, this information may help to prioritise potential fraud risks in self reporting and better direct limited resources. DA - 2017/// PY - 2017/// DO - 10.1142/S146433321750017X VL - 19 IS - 4 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85032199422&partnerID=MN8TOARS ER - TY - CHAP TI - Conservation criminology and the global trade in electronic waste: Applying a multi-disciplinary research framework AU - Gibbs, C. AU - McGarrell, E.F. AU - Axelrod, M. AU - Rivers, L. T2 - Transnational Environmental Crime AB - Contents: Introduction Part I Thinking about Transnational Environmental Crime: Transnational environmental crime: exploring (un)charted territory, Liselotte Bisschop Conceptualising and combating transnational environmental crime, Glen Wright The global transference of toxic harms, Diane Heckenberg Causes for speciesism: difference, distance and denial, Ragnhild Sollund Dire forecast: a theoretical model of the impact of climate change on crime, Robert Agnew Where might we be headed? Some of the possible consequences of climate change for the criminological research agenda, Stephen Farrall. Part II Conflicts, Victimisation and the Environment: Cross-national environmental injustice and human rights issues: a review of evidence in the developing world, Francis O. Adeola Environmental disputes and human rights violations: a role for criminologists, Richard D. Clark When social movements bypass the poor: asbestos pollution, international litigation and Griqua cultural identity, Linda Waldman Deforestation crimes and conflicts in the Amazon, Tim Boekhout van Solinge Toward defining the concept of environmental crime on the basis of sustainability, Ali Mohamed Al-Damkhi, Ali Mohamed Khuraibet, Sabah Ahmed Abdul-Wahab and Faten Abdul-Hameed Al-Attar. Part III Pollution and Waste: Green criminology and dirty collar crime, Vincenzo Ruggiero and Nigel South Is it all going to waste? Illegal transports of e-waste in a European trade hub, Liselot Bisschop International waste trafficking: preliminary explorations, Ana KlenovA!ek and Goradz MeA!ko Conservation criminology and the global trade in electronic waste: applying a multi-disciplinary research framework, Carole Gibbs, Edmund F. McGarrell, Mark Axelrod and Louie Rivers III Toxic atmospheres: air pollution, trade and the politics of regulation, Reece Walters. Part IV Biodiversity and Wildlife Crime: The a corporate colonisation of naturea (TM): bio-prospecting, bio-piracy and the development of green criminology, Nigel South Crime, bio-agriculture and the exploitation of hunger, Reece Walters The transnational illegal wildlife trade, Greg L. Warchol The international ban on ivory sales and its effect on elephant poaching in Africa, Andrew M. Lemieux and Ronald V. Clarke Preventing wildlife crimes: solutions that can overcome the a tragedy of the commonsa (TM), Stephen F. Pires and William D. Moreto. Part V Combating Transnational Environmental Crimes: Police, law enforcement and the environment, Kevin Tomkins Strengthening the weakest links: strategies for improving the enforcement of environmental laws globally, Anita Sundari Akella and James B. Cannon Usage of special investigation measures in detecting environmental crime: international and Macedonian perspective, Marina Malis Sazdovska Cross-border police cooperation in tackling environmental crime, Toine Spapens NGO engagement in environmental law enforcement: critical reflections, Rob White Name index. PY - 2017/// DO - 10.4324/9781315084589 SP - 297-320 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85061752331&partnerID=MN8TOARS ER - TY - JOUR TI - Racial Disparities in Context: Student-, School-, and County-Level Effects on the Likelihood of Obesity among Elementary School Students AU - Piontak, Joy Rayanne AU - Schulman, Michael D. T2 - Sociology of Race and Ethnicity AB - Childhood obesity rates in the United States have risen since the 1980s and are especially high among racial minorities. Researchers document differentials in obesity rates by race, socioeconomic status, school characteristics, and place. In this study, the authors examine the impact of race on the likelihood of obesity at the student, school, and county levels and the interactions between student race and school racial composition. The data are from 74,661 third to fifth grade students in 317 schools in 38 North Carolina counties. Multilevel logistic regression models showed that racial differences in the likelihood of obesity persisted even when racial composition and socioeconomic disadvantage at the school level were controlled. The differences between white and nonwhite students slightly decreased once school-level measures were added. The magnitude of the effects of student-level race on the relative odds of obesity varied according to the racial composition of the school. These student- and school-level results held even when county-level race and socioeconomic variables were controlled. The results show that contextual factors at the school and county levels are important social determinants of racial disparities in the likelihood of childhood obesity. DA - 2017/8/11/ PY - 2017/8/11/ DO - 10.1177/2332649217722026 VL - 4 IS - 2 SP - 245-260 J2 - Sociology of Race and Ethnicity LA - en OP - SN - 2332-6492 2332-6506 UR - http://dx.doi.org/10.1177/2332649217722026 DB - Crossref KW - racial segregation KW - public health KW - health disparities KW - children ER - TY - JOUR TI - Genome Editing of Food-Grade Lactobacilli To Develop Therapeutic Probiotics AU - Pijkeren, Jan-Peter AU - Barrangou, Rodolphe T2 - Microbiology Spectrum AB - Lactic acid bacteria have been used historically for food manufacturing mainly to ensure preservation via fermentation. More recently, lactic acid bacteria have been exploited to promote human health, and many strains serve as industrial workhorses. Recent advances in microbiology and molecular biology have contributed to understanding the genetic basis of many of their functional attributes. These include dissection of biochemical processes that drive food fermentation, and identification and characterization of health-promoting features that positively impact the composition and roles of microbiomes in human health. Recently, the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-based technologies has revolutionized our ability to manipulate genomes, and we are on the cusp of a broad-scale genome editing revolution. Here, we discuss recent advances in genetic alteration of food-grade bacteria, with a focus on CRISPR-associated enzyme genome editing, single-stranded DNA recombineering, and the modification of bacteriophages. These tools open new avenues for the genesis of next-generation biotherapeutic agents with improved genotypes and enhanced health-promoting functional features. DA - 2017/10/3/ PY - 2017/10/3/ DO - 10.1128/microbiolspec.bad-0013-2016 VL - 5 IS - 5 ER - TY - JOUR TI - Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum AU - Hidalgo-Cantabrana, Claudio AU - Crawley, Alexandra B. AU - Sanchez, Borja AU - Barrangou, Rodolphe T2 - Frontiers in Microbiology AB - Diverse CRISPR-Cas systems provide adaptive immunity in many bacteria and most archaea, via a DNA-encoded, RNA-mediated, nucleic-acid targeting mechanism. Over time, CRISPR loci expand via iterative uptake of invasive DNA sequences into the CRISPR array during the adaptation process. These genetic vaccination cards thus provide insights into the exposure of strains to phages and plasmids in space and time, revealing the historical predatory exposure of a strain. These genetic loci thus constitute a unique basis for genotyping of strains, with potential of resolution at the strain-level. Here, we investigate the occurrence and diversity of CRISPR-Cas systems in the genomes of various Bifidobacterium longum strains across three sub-species. Specifically, we analysed the genomic content of 66 genomes belonging to B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis, and identified 25 strains that carry 29 total CRISPR-Cas systems. We identify various Type I and Type II CRISPR-Cas systems that are widespread in this species, notably I-C, I-E and II-C. Noteworthy, Type I-C systems showed extended CRISPR arrays, with extensive spacer diversity. We show how these hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates. By investigating CRISPR spacer sequences, we reveal their origin and implicate phages and prophages as drivers of CRISPR immunity expansion in this species, with redundant targeting of select prophages. Analysis of CRISPR spacer origin also revealed novel PAM sequences. Our results suggest that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in Bifidobacterium longum, and show that these sequences are useful for typing across three subspecies. DA - 2017/9// PY - 2017/9// DO - 10.3389/fmicb.2017.01851 VL - 8 KW - CRISPR-Cas systems KW - genotyping KW - probiotics KW - Bifidobacterium longum ER - TY - JOUR TI - Repurposing CRISPR-Cas systems as DNA-based smart antimicrobials AU - Barrangou, Rodolphe AU - Ousterout, David G T2 - Cell and Gene Therapy Insights DA - 2017/2/8/ PY - 2017/2/8/ DO - 10.18609/cgti.2017.008 VL - 3 IS - 1 SP - 63-72 ER - TY - JOUR TI - Immune Loss as a Driver of Coexistence During Host-Phage Coevolution AU - Weissman, Jake L AU - Holmes, Rayshawn AU - Barrangou, Rodolphe AU - Moineau, Sylvain AU - Fagan, William F AU - Levin, Bruce AU - Johnson, Philip L F AB - Abstract Bacteria and their viral pathogens face constant pressure for augmented immune and infective capabilities, respectively. Under this reciprocally imposed selective regime, we expect to see a runaway evolutionary arms race, ultimately leading to the extinction of one species. Despite this prediction, in many systems host and pathogen coexist with minimal coevolution even when well-mixed. Previous work explained this puzzling phenomenon by invoking fitness tradeoffs, which can diminish an arms race dynamic. Here we propose that the regular loss of immunity by the bacterial host can also produce host-phage coexistence. We pair a general model of immunity with an experimental and theoretical case study of the CRISPR-Cas immune system to contrast the behavior of tradeoff and loss mechanisms in well-mixed systems. We find that, while both mechanisms can produce stable coexistence, only immune loss does so robustly within realistic parameter ranges. DA - 2017/2/3/ PY - 2017/2/3/ DO - 10.1101/105908 VL - 2 UR - https://doi.org/10.1101/105908 ER - TY - JOUR TI - QnAs with Rodolphe Barrangou AU - Nair, Prashant T2 - Proceedings of the National Academy of Sciences AB - The past decade in biological research might well be christened the age of CRISPR, a once-curious feature of bacterial genomes that spawned a handy tool for editing genes. Using CRISPR-based tools, researchers are making leaps in basic clinical research, and biotechnology companies are racing to launch trials of gene therapies for an array of diseases. Yet the immediate gains from this game-changing technique might spring from its application to agriculture. Hornless dairy cattle, drought-resistant wheat, and nonbrowning mushrooms are merely the harbingers of an approaching agricultural revolution, says Rodolphe Barrangou, a molecular biologist and food scientist at North Carolina State University. Barrangou’s foresight stems from his long familiarity with CRISPR. More than a decade ago, while working at the Danish food ingredient manufacturer Danisco (now DuPont), Barrangou furnished experimental proof for the notion that CRISPR confers a form of adaptive immunity that helps bacteria fend off invading viruses. For this crucial insight into the fundamental biology of CRISPR, Barrangou was honored with 2017 National Academy of Sciences Award in molecular biology. PNAS spoke to Barrangou about his wide-ranging work on CRISPR. Rodolphe Barrangou. Image courtesy of North Carolina State University (Raleigh, NC). > PNAS:CRISPR entered the spotlight when its potential as a genome editor became apparent, but your tryst with it began more than a decade ago while working with Philippe Horvath in the food industry. Those efforts led to a milestone 2007 article in Science , in which you demonstrated that bacteria use CRISPR-Cas systems as a form of adaptive immunity against viruses (1). Could you take our readers down memory lane? > Barrangou:For a long time, people didn’t really have a clue what these repeated DNA sequences—the CRISPR arrays—in … DA - 2017/7/3/ PY - 2017/7/3/ DO - 10.1073/pnas.1710348114 VL - 114 IS - 28 SP - 7183-7184 ER - TY - JOUR TI - On the global CRISPR array behavior in class I systems AU - Toms, Alice AU - Barrangou, Rodolphe T2 - Biology Direct AB - Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthed, much emphasis has been placed on details of individual strains and model systems within the CRISPR-Cas classification, and that collection of information as a whole affords the opportunity to analyze CRISPR-Cas systems from a quantitative perspective to gain insight into distribution of CRISPR array sizes across the different classes, types and subtypes. CRISPR diversity, nomenclature, occurrence, and biological functions have generated a plethora of data that created a need to understand the size and distribution of these various systems to appreciate their features and complexity.By utilizing a statistical framework and visual analytic techniques, we have been able to test several hypotheses about CRISPR loci in bacterial class I systems. Quantitatively, though CRISPR loci can expand to hundreds of spacers, the mean and median sizes are 40 and 25, respectively, reflecting rather modest acquisition and/or retention overall. Histograms uncovered that CRISPR array size displayed a parametric distribution, which was confirmed by a goodness-of fit test. Mapping the frequency of CRISPR loci on a standardized chromosome plot revealed that CRISPRs have a higher probability of occurring at clustered locations along the positive or negative strand. Lastly, when multiple arrays occur in a particular system, the size of a particular CRISPR array varies with its distance from the cas operon, reflecting acquisition and expansion biases.This study establishes that bacterial Class I CRISPR array size tends to follow a geometric distribution; these CRISPRs are not randomly distributed along the chromosome; and the CRISPR array closest to the cas genes is typically larger than loci in trans. Overall, we provide an analytical framework to understand the features and behavior of CRISPR-Cas systems through a quantitative lens.This article was reviewed by Eugene Koonin (NIH-NCBI) and Uri Gophna (Tel Aviv University). DA - 2017/12// PY - 2017/12// DO - 10.1186/s13062-017-0193-2 ER - TY - JOUR TI - Advances in Industrial Biotechnology Using CRISPR-Cas Systems AU - Donohoue, Paul D. AU - Barrangou, Rodolphe AU - May, Andrew P. T2 - Trends in Biotechnology AB - The term 'clustered regularly interspaced short palindromic repeats' (CRISPR) has recently become synonymous with the genome-editing revolution. The RNA-guided endonuclease CRISPR-associated protein 9 (Cas9), in particular, has attracted attention for its promise in basic research and gene editing-based therapeutics. CRISPR-Cas systems are efficient and easily programmable nucleic acid-targeting tools, with uses reaching beyond research and therapeutic development into the precision breeding of plants and animals and the engineering of industrial microbes. CRISPR-Cas systems have potential for many microbial engineering applications, including bacterial strain typing, immunization of cultures, autoimmunity or self-targeted cell killing, and the engineering or control of metabolic pathways for improved biochemical synthesis. In this review, we explore the fundamental characteristics of CRISPR-Cas systems and highlight how these features can be used in industrial settings. DA - 2017/8// PY - 2017/8// DO - 10.1016/j.tibtech.2017.07.007 VL - 8 IS - 2 SP - 134–146 ER - TY - CONF TI - Tracking 19th century late blight from archival documents using text analytics and geoparsing AU - Tateosian, Laura AU - Guenter, Rachael AU - Yang, Yi-Peng AU - Ristaino, Jean C2 - 2017/// C3 - Free and Open Source Software for Geospatial (FOSS4G) Conference Proceedings DA - 2017/// VL - 17 SP - 17 M1 - 1 ER - TY - RPRT TI - A Risk Analysis of precision farming for tomato production AU - Liu, Yangxuan AU - Langemeier, Michael AU - Small, Ian AU - Joseph, Laura AU - Fry, William AU - Ristaino, Jean AU - Saville, Amanda DA - 2017/// PY - 2017/// ER - TY - CONF TI - Evolutionary relatedness and sources of US lineages of Phytophthora infestans (Mont.) de Bary. AU - Saville, Amanda C AU - Ristaino, Jean T2 - APSNET C2 - 2017/// C3 - 2017 APS Annual Meeting DA - 2017/// ER - TY - CONF TI - Charles Darwin and the Irish Potato Famine:“A Painfully Interesting Subject” AU - Ristaino, Jean B AU - Pfister, Donald T2 - APSNET C2 - 2017/// C3 - 2017 APS Annual Meeting DA - 2017/// ER - TY - CONF TI - A species of Pestalotiopsis identified infecting red mangrove in The Bahamas AU - Rossi, Ryann E AU - Layman, Craig A AU - Ristaino, Jean B T2 - APSNET C2 - 2017/// C3 - 2017 APS Annual Meeting DA - 2017/// ER - TY - CHAP TI - The triple response assay and its use to characterize ethylene mutants in arabidopsis AU - Merchante, C. AU - Stepanova, A.N. T2 - Methods in Molecular Biology AB - Exposure of plants to ethylene results in drastic morphological changes. Seedlings germinated in the dark in the presence of saturating concentrations of ethylene display a characteristic phenotype known as the triple response. This phenotype is robust and easy to score. In Arabidopsis the triple response is usually evaluated at 3 days post germination in seedlings grown in the dark in rich media supplemented with 10 μM of the ethylene precursor ACC in air or in unsupplemented media in the presence of 10 ppm ethylene. The triple response in Arabidopsis consists of shortening and thickening of hypocotyls and roots and exaggeration of the curvature of apical hooks. The search for Arabidopsis mutants that fail to show this phenotype in ethylene or, vice versa, display the triple response in the absence of exogenously supplied hormone has allowed the identification of the key components of the ethylene biosynthesis and signaling pathways. Herein, we describe a simple protocol for assaying the triple response in Arabidopsis. The method can also be employed in many other dicot species, with minor modifications to account for species-specific differences in germination. We also compiled a comprehensive table of ethylene-related mutants of Arabidopsis, including many lines with auxin-related defects, as wild-type levels of auxin biosynthesis, transport, signaling, and response are necessary for the normal response of plants to ethylene. PY - 2017/// DO - 10.1007/978-1-4939-6854-1_13 VL - 1573 SP - 163-209 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85015705453&partnerID=MN8TOARS KW - Phytohormone KW - Ethylene KW - ACC KW - Triple response KW - Arabidopsis KW - Seedlings KW - Germination KW - Hypocotyl KW - Root KW - Apical hook KW - Mutants ER - TY - JOUR TI - Editorial: Relevance of translational regulation on plant growth and environmental responses AU - Ferrando, A. AU - Castellano, M.M. AU - Lisón, P. AU - Leister, D. AU - Stepanova, A.N. AU - Hanson, J. T2 - Frontiers in Plant Science AB - EDITORIAL article Front. Plant Sci., 19 December 2017Sec. Plant Physiology Volume 8 - 2017 | https://doi.org/10.3389/fpls.2017.02170 DA - 2017/// PY - 2017/// DO - 10.3389/fpls.2017.02170 VL - 8 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85040509996&partnerID=MN8TOARS KW - mRNA translation KW - translation factors KW - post-transcriptional regulation KW - translatome KW - organellar gene expression ER - TY - JOUR TI - Malate-dependent Fe accumulation is a critical checkpoint in the root developmental response to low phosphate AU - Mora-Macías, Javier AU - Ojeda-Rivera, Jonathan Odilón AU - Gutiérrez-Alanís, Dolores AU - Yong-Villalobos, Lenin AU - Oropeza-Aburto, Araceli AU - Raya-González, Javier AU - Jiménez-Domínguez, Gabriel AU - Chávez-Calvillo, Gabriela AU - Rellán-Álvarez, Rubén AU - Herrera-Estrella, Luis AU - al., T2 - Proceedings of the National Academy of Sciences AB - Low phosphate (Pi) availability constrains plant development and seed production in both natural and agricultural ecosystems. When Pi is scarce, modifications of root system architecture (RSA) enhance the soil exploration ability of the plant and lead to an increase in Pi uptake. In Arabidopsis, an iron-dependent mechanism reprograms primary root growth in response to low Pi availability. This program is activated upon contact of the root tip with low-Pi media and induces premature cell differentiation and the arrest of mitotic activity in the root apical meristem, resulting in a short-root phenotype. However, the mechanisms that regulate the primary root response to Pi-limiting conditions remain largely unknown. Here we report on the isolation and characterization of two low-Pi insensitive mutants (lpi5 and lpi6), which have a long-root phenotype when grown in low-Pi media. Cellular, genomic, and transcriptomic analysis of low-Pi insensitive mutants revealed that the genes previously shown to underlie Arabidopsis Al tolerance via root malate exudation, known as SENSITIVE TO PROTON RHIZOTOXICITY (STOP1) and ALUMINUM ACTIVATED MALATE TRANSPORTER 1 (ALMT1), represent a critical checkpoint in the root developmental response to Pi starvation in Arabidopsis thaliana Our results also show that exogenous malate can rescue the long-root phenotype of lpi5 and lpi6 Malate exudation is required for the accumulation of Fe in the apoplast of meristematic cells, triggering the differentiation of meristematic cells in response to Pi deprivation. DA - 2017/4/11/ PY - 2017/4/11/ DO - 10.1073/pnas.1701952114 VL - 114 IS - 17 SP - E3563-E3572 J2 - Proc Natl Acad Sci USA LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.1701952114 DB - Crossref KW - phosphate KW - root response KW - iron KW - cell differentiation KW - gene regulation ER - TY - JOUR TI - Insecticide Susceptibility Screening Against Culex and Aedes (Diptera: Culicidae) Mosquitoes From the United States AU - Richards, Stephanie L AU - Balanay, Jo Anne G AU - White, Avian V AU - Hope, Joe AU - Vandock, Kurt AU - Byrd, Brian D AU - Reiskind, Michael H T2 - Journal of Medical Entomology AB - Mosquitoes exposed to sublethal doses of insecticides may be selected for resistance to insecticide active ingredients (AIs). Mosquitoes are exposed to AIs through agricultural, public/private mosquito control programs, homeowners, and other sources. Hence, mosquito control programs should routinely measure the resistance/susceptibility status of mosquito populations of public health concern. The objectives here were to determine resistance status for six AIs used in adult mosquito control in the United States to assess how resistance/susceptibility differs between AI, mosquito species (states where > 1 species collected), and between years (some populations sampled for 2 yr). Field-collected eggs from 21 mosquito populations of six different species or hybrid species (Aedes albopictus Skuse [Diptera: Culicidae], Aedes aegypti L. [Diptera: Culicidae], Culex nigripalpus Theobald, Culex pipiens L. [Diptera: Culicidae], Culex quinquefasciatus Say [Diptera: Culicidae], Cx. pipiens/quinquefasciatus) were obtained. Centers for Disease Control and Prevention bottle bioassays were used to assess the resistance/susceptibility status for six AIs (bifenthrin, deltamethrin, etofenprox, malathion, permethrin, and phenothrin). World Health Organization guidelines were used to classify mosquitoes as susceptible (98–100% mortality at diagnostic time [DT]), possibly resistant (80–97% mortality at DT), or resistant (<80% mortality at DT). Significant differences were observed in mosquito susceptibility/resistance between species and AIs. In states where both Aedes and Culex were collected, the odds of exhibiting resistance in Culex were 68–69 times higher than Aedes (Texas odds ratio: 69.30; 95% confidence interval: 5.86, 819.44; P = 0.001; North Carolina odds ratio: 67.99; 95% confidence interval: 15.21, 303.94; P < 0.0001). Some level of resistance was detected against all tested AIs in several mosquito populations and some varied between 2015 and 2016. DA - 2017/11/23/ PY - 2017/11/23/ DO - 10.1093/jme/tjx198 VL - 55 IS - 2 SP - 398-407 LA - en OP - SN - 0022-2585 1938-2928 UR - http://dx.doi.org/10.1093/jme/tjx198 DB - Crossref KW - Chemical control KW - insecticide resistance KW - insecticide testing KW - mosquito control ER - TY - JOUR TI - Female Mimicry by Sneaker Males Has a Transcriptomic Signature in Both the Brain and the Gonad in a Sex-Changing Fish AU - Todd, Erica V AU - Liu, Hui AU - Lamm, Melissa S AU - Thomas, Jodi T AU - Rutherford, Kim AU - Thompson, Kelly C AU - Godwin, John R AU - Gemmell, Neil J T2 - Molecular Biology and Evolution AB - Phenotypic plasticity represents an elegant adaptive response of individuals to a change in their environment. Bluehead wrasses (Thalassoma bifasciatum) exhibit astonishing sexual plasticity, including female-to-male sex change and discrete male morphs that differ strikingly in behavior, morphology, and gonadal investment. Using RNA-seq transcriptome profiling, we examined the genes and physiological pathways underlying flexible behavioral and gonadal differences among female, dominant (bourgeois) male, and female-mimic (sneaker) male blueheads. For the first time in any organism, we find that female mimicry by sneaker males has a transcriptional signature in both the brain and the gonad. Sneaker males shared striking similarity in neural gene expression with females, supporting the idea that males with alternative reproductive phenotypes have "female-like brains." Sneaker males also overexpressed neuroplasticity genes, suggesting that their opportunistic reproductive strategy requires a heightened capacity for neuroplasticity. Bourgeois males overexpressed genes associated with socio-sexual behaviors (e.g., isotocin), but also neuroprotective genes and biomarkers of oxidative stress and aging, indicating a hitherto unexplored cost to these males of attaining the reproductively privileged position at the top of the social hierarchy. Our novel comparison of testicular transcriptomes in a fish with male sexual polymorphism associates greater gonadal investment by sneaker males with overexpression of genes involved in cell proliferation and sperm quality control. We propose that morphological female-mimicry by sneaker male teleosts entails pervasive downregulation of androgenesis genes, consistent with low androgen production in males lacking well-developed secondary sexual characters. DA - 2017/11/8/ PY - 2017/11/8/ DO - 10.1093/molbev/msx293 VL - 35 IS - 1 SP - 225-241 LA - en OP - SN - 0737-4038 1537-1719 UR - http://dx.doi.org/10.1093/molbev/msx293 DB - Crossref KW - developmental plasticity KW - alternative male reproductive strategies KW - transcriptomics KW - phenotypic plasticity ER - TY - JOUR TI - Developing gene drive technologies to eradicate invasive rodents from islands AU - Leitschuh, Caroline M. AU - Kanavy, Dona AU - Backus, Gregory A. AU - Valdez, Rene X. AU - Serr, Megan AU - Pitts, Elizabeth A. AU - Threadgill, David AU - Godwin, John T2 - Journal of Responsible Innovation AB - Island ecosystems are highly threatened by invasive rats and mice. Currently, the only effective technology for eradicating rodents from islands is toxicants. Though effective, they are expensive and have high failure rates. They are not species-specific and are potentially dangerous to humans. Gene drive technology is one alternative to toxicants for rodent eradication. Gene drive methods of rodent eradication offer an alternative to killing that has the potential to be more species-specific, more humane, and more biologically safe for use around humans. Technologies in development aim to apply either natural meiotic drive or clustered regularly interspersed short palindromic repeats to influence offspring development so that all offspring are phenotypically male, eventually creating a population that is not reproductively viable. Implementing this technology would involve releasing laboratory-developed engineered mice into wild populations. Some areas for further research include assessing the ecological effects of releasing engineered mice, the potential risks for the accidental or deliberate release of genetically modified organisms into mainland mouse populations, and the social, ethical, and regulatory acceptability of the technology. DA - 2017/12/19/ PY - 2017/12/19/ DO - 10.1080/23299460.2017.1365232 VL - 5 IS - sup1 SP - S121-S138 J2 - Journal of Responsible Innovation LA - en OP - SN - 2329-9460 2329-9037 UR - http://dx.doi.org/10.1080/23299460.2017.1365232 DB - Crossref KW - Invasive rodents KW - eradication KW - biodiversity KW - gene drive KW - CRISPR ER - TY - JOUR TI - Organic solvent exposure and depressive symptoms among licensed pesticide applicators in the Agricultural Health Study AU - Siegel, Miriam AU - Starks, Sarah E. AU - Sanderson, Wayne T. AU - Kamel, Freya AU - Hoppin, Jane A. AU - Gerr, Fred T2 - International Archives of Occupational and Environmental Health AB - Although organic solvents are often used in agricultural operations, neurotoxic effects of solvent exposure have not been extensively studied among farmers. The current analysis examined associations between questionnaire-based metrics of organic solvent exposure and depressive symptoms among farmers. Results from 692 male Agricultural Health Study participants were analyzed. Solvent type and exposure duration were assessed by questionnaire. An “ever-use” variable and years of use categories were constructed for exposure to gasoline, paint/lacquer thinner, petroleum distillates, and any solvent. Depressive symptoms were ascertained with the Center for Epidemiologic Studies Depression Scale (CES-D); scores were analyzed separately as continuous (0–60) and dichotomous (<16 versus ≥16) variables. Multivariate linear and logistic regression models were used to estimate crude and adjusted associations between measures of solvent exposure and CES-D score. Forty-one percent of the sample reported some solvent exposure. The mean CES-D score was 6.5 (SD 6.4; median 5; range 0–44); 92% of the sample had a score below 16. After adjusting for covariates, statistically significant associations were observed between ever-use of any solvent, long duration of any solvent exposure, ever-use of gasoline, ever-use of petroleum distillates, and short duration of petroleum distillate exposure and continuous CES-D score (p < 0.05). Although nearly all associations were positive, fewer statistically significant associations were observed between metrics of solvent exposure and the dichotomized CES-D variable. Solvent exposures were associated with depressive symptoms among farmers. Efforts to limit exposure to organic solvents may reduce the risk of depressive symptoms among farmers. DA - 2017/7/12/ PY - 2017/7/12/ DO - 10.1007/s00420-017-1245-8 VL - 90 IS - 8 SP - 849-857 J2 - Int Arch Occup Environ Health LA - en OP - SN - 0340-0131 1432-1246 UR - http://dx.doi.org/10.1007/s00420-017-1245-8 DB - Crossref KW - Farmers KW - Organic solvent exposure KW - Depressive symptoms KW - CES-D KW - Epidemiology ER - TY - JOUR TI - Raw milk consumption and other early-life farm exposures and adult pulmonary function in the Agricultural Lung Health Study AU - Wyss, Annah B AU - House, John S AU - Hoppin, Jane A AU - Richards, Marie AU - Hankinson, John L AU - Long, Stuart AU - Henneberger, Paul K AU - Beane Freeman, Laura E AU - Sandler, Dale P AU - O’Connell, Elizabeth Long AU - Cummings, Christie Barker AU - Umbach, David M AU - London, Stephanie J T2 - Thorax AB - Literature suggests that early exposure to the farming environment protects against atopy and asthma; few studies have examined pulmonary function. We evaluated associations between early-life farming exposures and pulmonary function in 3061 adults (mean age=63) from a US farming population using linear regression. Childhood raw milk consumption was associated with higher FEV 1 (β=49.5 mL, 95% CI 2.8 to 96.1 mL, p=0.04) and FVC (β=66.2 mL, 95% CI 13.2 to 119.1 mL, p=0.01). We did not find appreciable associations with other early-life farming exposures. We report a novel association between raw milk consumption and higher pulmonary function that lasts into older adulthood. DA - 2017/7/8/ PY - 2017/7/8/ DO - 10.1136/thoraxjnl-2017-210031 VL - 73 IS - 3 SP - 279-282 J2 - Thorax LA - en OP - SN - 0040-6376 1468-3296 UR - http://dx.doi.org/10.1136/thoraxjnl-2017-210031 DB - Crossref KW - COPD epidemiology KW - Asthma Epidemiology KW - Allergic lung disease KW - Occupational Lung Disease KW - Respiratory Measurement ER - TY - JOUR TI - Endocrine Disruption of Vasopressin Systems and Related Behaviors AU - Patisaul, Heather B. T2 - Frontiers in Endocrinology AB - Endocrine disrupting chemicals (EDCs) are chemicals that interfere with the organizational or activational effects of hormones. Although the vast majority of the EDC literature focuses on steroid hormone signaling related impacts, growing evidence from a myriad of species reveals that the nonapeptide hormones vasopressin (AVP) and oxytocin (OT) may also be EDC targets. EDCs shown to alter pathways and behaviors coordinated by AVP and/or OT include the plastics component bisphenol a (BPA), the soy phytoestrogen genistein (GEN), and various flame retardants. Many effects are sex specific and likely involve action at nuclear estrogen receptors. Effects include the elimination or reversal of well-characterized sexually dimorphic aspects of the AVP system, including innervation of the lateral septum and other brain regions critical for social and other non-reproductive behaviors. Disruption of magnocellular AVP function has also been reported in rats, suggesting possible effects on hemodynamics and cardiovascular function. DA - 2017/6/19/ PY - 2017/6/19/ DO - 10.3389/fendo.2017.00134 VL - 8 J2 - Front. Endocrinol. OP - SN - 1664-2392 UR - http://dx.doi.org/10.3389/fendo.2017.00134 DB - Crossref KW - bisphenol KW - oxytocin KW - sex differences KW - EDC KW - genistein KW - soy KW - social KW - anxiety KW - estrogens ER - TY - JOUR TI - Chemical Contributions to Neurodevelopmental Disorders AU - Patisaul, Heather B. T2 - Policy Insights from the Behavioral and Brain Sciences AB - Children increasingly receive diagnoses of neurodevelopmental disorders (NDDs). Causes are multifactorial, but growing consensus identifies environmental factors, especially chemical exposures, as primary drivers, with some individuals more genetically susceptible to these external pressures than others. Our current system of chemical management prioritizes rapid commercialization over disease prevention. This strategy privatizes economic benefits but socializes health costs. The evidence linking chemical exposure to neurodevelopmental risk merits greater attention by regulators. Public health concerns, particularly for children and other vulnerable groups, should be elevated in chemical risk assessment. The financial and emotional burden of preventable NDDs on U.S. children and their families calls for comprehensive policy attention. DA - 2017/8/24/ PY - 2017/8/24/ DO - 10.1177/2372732217719909 VL - 4 IS - 2 SP - 123-130 J2 - Policy Insights from the Behavioral and Brain Sciences LA - en OP - SN - 2372-7322 2372-7330 UR - http://dx.doi.org/10.1177/2372732217719909 DB - Crossref ER - TY - CHAP TI - Society and policy maker’s responsibilities AU - Kuzma, J. T2 - Consumer Perception of Product Risks and Benefits PY - 2017/// DO - 10.1007/978-3-319-50530-5_29 SP - 547-566 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85034015085&partnerID=MN8TOARS ER - TY - CONF TI - Ethics and Responsible Innovation in Biotechnology Communities: A Pedagogy of Engaged Scholarship AU - Herkert, Joseph AU - Kuzma, Jennifer AU - Roberts, Pat AU - Banks, Erin AU - Stauffer, Sharon AB - Abstract Issues surrounding genetic engineering, biotechnology, and synthetic biology are contentious, especially when applied to food, the environment, and industrial applications for which direct human consent and medical benefits are not present. How researchers, developers, and policy-makers communicate about and reflect upon their work is of utmost importance to these fields. Increased understanding about how participants within and across various professional contexts conceive of and frame the ethical dimensions of their work can assist with future cross-sector dialogue, and potentially conflict resolution. In this paper we present the results to date of a two year NSF-funded project which employs a novel approach for comparative analyses of meanings of responsible innovation (RI) and ethics in genetic engineering, biotechnology and synthetic biology, while cultivating socially-responsible cultures of R&D among graduate students, faculty, and outside practitioners. The project innovates in four key respects: 1) it focuses on bioengineering, specifically in areas in which engineering ethics programs have not routinely been applied--genetic engineering, biotechnology and synthetic biology; 2) it evaluates an example pedagogy of engaged scholarship, student facilitation of focus groups, for learning and cultivating ethical cultures; 3) it uses framings of RI as key parts of the dialogue about ethical cultures in biotechnology; and 4) it compares meanings of RI across five sectors—government, academe, industry, trade organizations, and non-profit organizations with advocacy roles. The project has two major components: 1) two four-day interdisciplinary workshops for graduate students (some from a program to maximize student diversity and some from an NSF-IGERT on Genetic Pest Management) in which the students consider meanings of RI, examine micro- and macro-ethical issues associated with biotechnology, and learn about focus groups as a research method and how to facilitate them; and 2) fifteen focus groups (three from each biotechnology sector) moderated by the students who were enrolled in the workshop. In the paper we report on the first year of the project (one student workshop and one focus group for each sector) including the workshop design and focus group protocol, as well as preliminary analysis of project results. Data collected include pre- and post-surveys from the workshop and stakeholder focus groups designed to test participants’ attitudes towards RI and measure core values from cultural theory in relation to policy values regarding RI, as well as qualitative analysis of the focus group transcripts. Workshop outcomes are based on a student workshop evaluation and analysis of student learning in the workshop, including pre- and post-tests on study-specific questions and moral reasoning using the DIT-2 instrument. Preliminary results indicate that the workshop was successful in achieving goals of increasing student learning about ethics and RI, and confidence in moderating focus groups and in conversations with stakeholders. Some interesting differences between stakeholder groups in policy values related to RI are emerging in the focus groups. Industry, and to a lesser extent academic and trade groups, seem less in favor of elements of RI after the focus groups. There are also some observable differences in core values among stakeholder groups. C2 - 2017/// C3 - 2017 ASEE Annual Conference & Exposition Proceedings DA - 2017/// DO - 10.18260/1-2--28299 VL - 2017-June PB - ASEE Conferences UR - http://dx.doi.org/10.18260/1-2--28299 ER - TY - JOUR TI - Plasmodium knowlesi invasion following spread by infected mosquitoes, macaques and humans AU - Yakob, Laith AU - Lloyd, Alun L. AU - Kao, Rowland R. AU - Ferguson, Heather M. AU - Brock, Patrick M. AU - Drakeley, Chris AU - Bonsall, Michael B. T2 - Parasitology AB - SUMMARY Plasmodium knowlesi is increasingly recognized as a major cause of malaria in Southeast Asia. Anopheles leucosphyrous group mosquitoes transmit the parasite and natural hosts include long-tailed and pig-tailed macaques. Despite early laboratory experiments demonstrating successful passage of infection between humans, the true role that humans play in P. knowlesi epidemiology remains unclear. The threat posed by its introduction into immunologically naïve populations is unknown despite being a public health priority for this region. A two-host species mathematical model was constructed to analyse this threat. Global sensitivity analysis using Monte Carlo methods highlighted the biological processes of greatest influence to transmission. These included parameters known to be influential in classic mosquito-borne disease models (e.g. vector longevity); however, interesting ecological components that are specific to this system were also highlighted: while local vectors likely have intrinsic preferences for certain host species, how plastic these preferences are, and how this is shaped by local conditions, are key determinants of parasite transmission potential. Invasion analysis demonstrates that this behavioural plasticity can qualitatively impact the probability of an epidemic sparked by imported infection. Identifying key vector sub/species and studying their biting behaviours constitute important next steps before models can better assist in strategizing disease control. DA - 2017/3/27/ PY - 2017/3/27/ DO - 10.1017/S0031182016002456 VL - 145 IS - 1 SP - 101-110 J2 - Parasitology LA - en OP - SN - 0031-1820 1469-8161 UR - http://dx.doi.org/10.1017/S0031182016002456 DB - Crossref KW - invasion analysis KW - Plasmodium knowlesi KW - vector-borne disease KW - mathematical model KW - vector behaviour ER - TY - JOUR TI - Orientation changes in the cruciate ligaments of the knee during skeletal growth: A porcine model AU - Cone, Stephanie G. AU - Simpson, Sean G. AU - Piedrahita, Jorge A. AU - Fordham, Lynn A. AU - Spang, Jeffrey T. AU - Fisher, Matthew B. T2 - Journal of Orthopaedic Research AB - ABSTRACT Musculoskeletal injuries in pediatric patients are on the rise, including significant increases in anterior cruciate ligament (ACL) injuries. Previous studies have found major anatomical changes during skeletal growth in the soft tissues of the knee. Specifically, the ACL and the posterior cruciate ligament (PCL) change in their relative orientation to the tibial plateau throughout growth. In order to develop age‐specific treatments for ACL injuries, the purpose of this study was to characterize orientation changes in the cruciate ligaments of the Yorkshire pig, a common pre‐clinical model, during skeletal growth in order to verify the applicability of this model for pediatric musculoskeletal studies. Hind limbs were isolated from female Yorkshire pigs ranging in age from newborn to late adolescence and were then imaged using high field strength magnetic resonance imaging. Orientation changes were quantified from the magnetic resonance images using image segmentation software. Statistically significant increases were found in the coronal and sagittal angles of the ACL relative to the tibial plateau during pre‐adolescent growth. Additional changes were observed in the PCL angle, Blumensaat angle, intercondylar roof angle, and the aspect ratio of the intercondylar notch. Only the sagittal angle of the ACL relative to the tibial plateau experienced statistically significant changes through late adolescence. The age‐dependent properties of the ACL and PCL in the female pig mirrored results found in female human patients, suggesting that the porcine model may provide a pre‐clinical platform to study the cruciate ligaments during skeletal growth. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2725–2732, 2017. DA - 2017/5/23/ PY - 2017/5/23/ DO - 10.1002/jor.23594 VL - 35 IS - 12 SP - 2725-2732 J2 - J. Orthop. Res. LA - en OP - SN - 0736-0266 UR - http://dx.doi.org/10.1002/jor.23594 DB - Crossref KW - anterior cruciate ligament KW - posterior cruciate ligament KW - adolescent KW - porcine KW - MRI ER - TY - JOUR TI - Animal Models in Tissue Engineering. Part II AU - Piedrahita, Jorge A. AU - Williams, J. Koudy T2 - Tissue Engineering Part C: Methods AB - Tissue Engineering Part C: MethodsVol. 23, No. 12 IntroductionAnimal Models in Tissue Engineering. Part IIJorge A. Piedrahita and J. Koudy WilliamsJorge A. PiedrahitaComparative Medicine Institute, North Carolina State University, Raleigh, North Carolina.Search for more papers by this author and J. Koudy WilliamsWake Forest Institute for Regenerative Medicine, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina.Search for more papers by this authorPublished Online:1 Dec 2017https://doi.org/10.1089/ten.tec.2017.0458AboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View article"*Animal Models in Tissue Engineering. Part II." Tissue Engineering Part C: Methods, 23(12), pp. 827–828FiguresReferencesRelatedDetailsCited byPerformance of marrow stromal cell-seeded small-caliber multilayered vascular graft in a senescent sheep model14 June 2018 | Biomedical Materials, Vol. 13, No. 5 Volume 23Issue 12Dec 2017 InformationCopyright 2017, Mary Ann Liebert, Inc.To cite this article:Jorge A. Piedrahita and J. Koudy Williams.Animal Models in Tissue Engineering. Part II.Tissue Engineering Part C: Methods.Dec 2017.827-828.http://doi.org/10.1089/ten.tec.2017.0458Published in Volume: 23 Issue 12: December 1, 2017Online Ahead of Editing: November 1, 2017PDF download DA - 2017/12// PY - 2017/12// DO - 10.1089/ten.TEC.2017.0458 VL - 23 IS - 12 SP - 827-828 J2 - Tissue Engineering Part C: Methods LA - en OP - SN - 1937-3384 1937-3392 UR - http://dx.doi.org/10.1089/ten.TEC.2017.0458 DB - Crossref ER - TY - JOUR TI - Improved Chondrogenic Potential and Proteomic Phenotype of Porcine Chondrocytes Grown in Optimized Culture Conditions AU - Koh, Sehwon AU - Purser, Molly AU - Wysk, Richard AU - Piedrahita, Jorge A. T2 - Cellular Reprogramming AB - For successful cartilage tissue engineering, the ability to generate a high number of chondrocytes in vitro while avoiding terminal differentiation or de-differentiation is critical. The ability to accomplish this by using the abundant and easily sampled costal cartilage could provide a practical alternative to the use of articular cartilage and mesenchymal stem cells. Chondrocytes isolated from pig costal cartilage were expanded in either serum-free medium with FGF2 (SFM) or fetal bovine serum-containing medium (SCM), under either high (21%) or low (5%) oxygen conditions. Overall, chondrocytes cultured in SFM and low oxygen (Low-SFM) demonstrated the highest cell growth rate (p < 0.05). The effect of passage number on the differentiation status of the chondrocytes was analyzed by alkaline phosphatase (AP) staining and real-time PCR for known chondrocyte quality markers. AP staining indicated that chondrocytes grown in SCM had a higher proportion of terminally differentiated (hypertrophic) chondrocytes (p < 0.05). At the mRNA level, expression ratios of ACAN/VCAN and COL2/COL1 were significantly higher (p < 0.05) in cells expanded in Low-SFM, indicating reduced de-differentiation. In vitro re-differentiation capacity was assessed after a 6-week induction, and chondrocytes grown in Low-SFM showed similar expression ratios of COL2/COL1 and ACAN/VCAN to native cartilage. Proteomic analysis of in vitro produced cartilage indicated that the Low-SFM condition most closely matched the proteomic profile of native costal and articular cartilage. In conclusion, Low-SFM culture conditions resulted in improved cell growth rates, reduced levels of de-differentiation during expansion, greater ability to re-differentiate into cartilage on induction, and an improved proteomic profile that resembles that of in vivo cartilage. DA - 2017/8// PY - 2017/8// DO - 10.1089/cell.2017.0005 VL - 19 IS - 4 SP - 232-244 J2 - Cellular Reprogramming LA - en OP - SN - 2152-4971 2152-4998 UR - http://dx.doi.org/10.1089/cell.2017.0005 DB - Crossref KW - chondrocytes KW - serum-free culture KW - low oxygen KW - pig KW - proteomics ER - TY - JOUR TI - Generation of a Stable Transgenic Swine Model Expressing a Porcine Histone 2B-eGFP Fusion Protein for Cell Tracking and Chromosome Dynamics Studies AU - Sper, Renan B. AU - Koh, Sehwon AU - Zhang, Xia AU - Simpson, Sean AU - Collins, Bruce AU - Sommer, Jeff AU - Petters, Robert M. AU - Caballero, Ignacio AU - Platt, Jeff L. AU - Piedrahita, Jorge A. T2 - PLOS ONE AB - Transgenic pigs have become an attractive research model in the field of translational research, regenerative medicine, and stem cell therapy due to their anatomic, genetic and physiological similarities with humans. The development of fluorescent proteins as molecular tags has allowed investigators to track cell migration and engraftment levels after transplantation. Here we describe the development of two transgenic pig models via SCNT expressing a fusion protein composed of eGFP and porcine Histone 2B (pH2B). This fusion protein is targeted to the nucleosomes resulting a nuclear/chromatin eGFP signal. The first model (I) was generated via random insertion of pH2B-eGFP driven by the CAG promoter (chicken beta actin promoter and rabbit Globin poly A; pCAG-pH2B-eGFP) and protected by human interferon-β matrix attachment regions (MARs). Despite the consistent, high, and ubiquitous expression of the fusion protein pH2B-eGFP in all tissues analyzed, two independently generated Model I transgenic lines developed neurodegenerative symptoms including Wallerian degeneration between 3-5 months of age, requiring euthanasia. A second transgenic model (II) was developed via CRISPR-Cas9 mediated homology-directed repair (HDR) of IRES-pH2B-eGFP into the endogenous β-actin (ACTB) locus. Model II transgenic animals showed ubiquitous expression of pH2B-eGFP on all tissues analyzed. Unlike the pCAG-pH2B-eGFP/MAR line, all Model II animals were healthy and multiple pregnancies have been established with progeny showing the expected Mendelian ratio for the transmission of the pH2B-eGFP. Expression of pH2B-eGFP was used to examine the timing of the maternal to zygotic transition after IVF, and to examine chromosome segregation of SCNT embryos. To our knowledge this is the first viable transgenic pig model with chromatin-associated eGFP allowing both cell tracking and the study of chromatin dynamics in a large animal model. DA - 2017/1/12/ PY - 2017/1/12/ DO - 10.1371/journal.pone.0169242 VL - 12 IS - 1 SP - e0169242 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.doi.org/10.1371/journal.pone.0169242 DB - Crossref ER - TY - JOUR TI - Chemical Constituents of Sweetpotato Genotypes in Relation to Textural Characteristics of Processed French Fries AU - Sato, Ai AU - Truong, Van-Den AU - Johanningsmeier, Suzanne D. AU - Reynolds, Rong AU - Pecota, Kenneth V. AU - Yencho, G. Craig T2 - Journal of Food Science AB - Abstract Sweetpotato French fries (SPFF) are growing in popularity, however limited information is available on SPFF textural properties in relation to chemical composition. This study investigated the relationship between chemical components of different sweetpotato varieties and textural characteristics of SPFF. Sixteen sweetpotato genotypes were evaluated for (1) chemical constituents; (2) instrumental and sensory textural properties of SPFF; and (3) the relationship between chemical components, instrumental measurements, and sensory attributes. Dry matter (DM), alcohol‐insoluble solids (AIS), starch, sugar, and oil content, and also α‐ and β‐amylase activities were quantified in raw sweetpotatoes and SPFF. Peak force and overall hardness describing instrumental textural properties of SPFF were measured using a texture analyzer. Descriptive sensory analysis was conducted and 10 attributes were evaluated by a trained panel. Results showed that DM, AIS, and starch content in raw sweetpotatoes were significantly correlated ( P < 0.05) with instrumental peak force and overall hardness ( r = 0.41 to 0.68), and with sensory surface roughness, hardness, fracturability, and crispness ( r = 0.63 to 0.90). Total sugar content in raw sweetpotatoes was positively correlated with sensory smoothness and moistness ( r = 0.77), and negatively correlated with instrumental peak force and overall hardness ( r = –0.62 to –0.69). Instrumental measurements were positively correlated with sensory attributes of hardness, fracturability, and crispness ( r = 0.68 to 0.96) and negatively correlated with oiliness, smoothness, moistness, and cohesiveness ( r = –0.61 to –0.91). Therefore, DM, AIS, starch, and total sugar contents and instrumental measurements could be used as indicators to evaluate sweetpotato genotypes for SPFF processing. Practical Application In recent years, sweetpotato French fries (SPFF) have grown in popularity, but limited information is available on SPFF textural properties in relation to the differences in chemical constituents among sweetpotato varieties. This study demonstrated that sensory texture attributes of SPFF varied widely and were significantly correlated with chemical components such as dry matter, starch, and total sugar contents of raw sweetpotatoes and instrumental texture measurements of SPFF. The knowledge generated from this study will benefit the food industry and breeding programs with the selection of sweetpotato varieties for improved SPFF quality. DA - 2017/11/27/ PY - 2017/11/27/ DO - 10.1111/1750-3841.13978 VL - 83 IS - 1 SP - 60-73 J2 - Journal of Food Science LA - en OP - SN - 0022-1147 UR - http://dx.doi.org/10.1111/1750-3841.13978 DB - Crossref KW - descriptive sensory analysis KW - French fries texture KW - instrumental measurement KW - Ipomoea batatas KW - sweetpotato French fries ER - TY - JOUR TI - Sweetpotato (Ipomoea batatas L.) AU - Mwanga, Robert O. M. AU - Andrade, Maria I. AU - Carey, Edward E. AU - Low, Jan W. AU - Yencho, G. Craig AU - Grüneberg, Wolfgang J. T2 - Genetic Improvement of Tropical Crops DA - 2017/// PY - 2017/// DO - 10.1007/978-3-319-59819-2_6 SP - 181-218 ER - TY - JOUR TI - Effect of Atmospheric Pressure Plasma on Handsheets and Pulps AU - Cornelius, C. AU - Saquing, C. AU - Venditti, R. AU - McCord, M.G. AU - Bourham, M.A. T2 - BioResources DA - 2017/// PY - 2017/// VL - 12 IS - 4 SP - 8199–8216 UR - https://bioresources.cnr.ncsu.edu/resources/the-effect-of-atmospheric-pressure-plasma-on-paper-and-pulps/ ER - TY - JOUR TI - Desizing of PVA sized pet/cotton fabrics with atmospheric pressure plasma AU - Cornelius, Carrie AU - McCord, Marian AU - Bourham, Mohamed AU - Hauser, Peter T2 - Cellulose DA - 2017/11/21/ PY - 2017/11/21/ DO - 10.1007/s10570-017-1586-1 VL - 25 IS - 1 SP - 869-881 J2 - Cellulose LA - en OP - SN - 0969-0239 1572-882X UR - http://dx.doi.org/10.1007/s10570-017-1586-1 DB - Crossref KW - Plasma KW - Grafting KW - Textile KW - Size KW - Polyester KW - Cotton KW - Polyvinyl alcohol KW - Desizing ER - TY - JOUR TI - Evolutionary Adaptations of Palmer Amaranth (Amaranthus palmeri) to Nitrogen Fertilization and Crop Rotation History Affect Morphology and Nutrient-Use Efficiency AU - Bravo, Washington AU - Leon, Ramon G. AU - Ferrell, Jason A. AU - Mulvaney, Michael J. AU - Wood, C. Wesley T2 - Weed Science AB - Palmer amaranth control has become a major challenge for multiple cropping systems across the southeastern and midwestern United States. Despite extensive research on herbicide-resistance evolution, little research has been done exploring how Palmer amaranth might also be evolving other adaptive traits in response to different selection forces present in agricultural fields and the enrichment of soils with nutrients such as nitrogen. The objective of the present study was to determine whether Palmer amaranth populations have evolved different morphology and growth patterns in response to glyphosate use and fertilization history. Ten Palmer amaranth populations, including glyphosate-resistant (GR) and glyphosate-susceptible (GS) populations, were collected from different cropping systems with histories of high and low nitrogen fertilization in the states of Florida and Georgia. All populations were grown in pots filled with soil fertilized with either 0 or 40 kgNha −1 , and their response to nitrogen was compared for morphological, growth, and nutrient-use traits. Populations differed in how they modified their morphology and growth in response to N, with major differences in traits such as foliar area, branch production, leaf shape, and canopy architecture. Populations with high nitrogen-fertilization histories had higher (>43%) nutrient-use efficiency (NUE) than populations with low nitrogen-fertilization histories. Similarly, GR populations have evolved higher NUE (>47%) and changed canopy architecture more than GS populations in response to nitrogen fertilization. The results of the present study highlight the importance of paying more attention to adaptations to cultural practices that might increase weediness and how genetic changes in traits involved in morphology and metabolism might favor compensatory mechanisms increasing the fitness of the population carrying herbicide-resistant traits. DA - 2017/// PY - 2017/// DO - 10.1017/wsc.2017.73 VL - 66 IS - 02 SP - 180-189 KW - Crop rotation KW - evolution KW - fitness KW - integrated weed management KW - nutrient content KW - resistance ER - TY - JOUR TI - Potassium and Nitrogen Fertilization Effects on Jiggs Bermudagrass Herbage Accumulation, Root–Rhizome Mass, and Tissue Nutrient Concentration AU - Yarborough, J.K. AU - Vendramini, J.M.B. AU - Silveira, M.L.A. AU - Sollenberger, L.E. AU - Leon, R.G. AU - Sellers, B. AU - Sanchez, JMD AU - Leite de Oliveira, F. AU - Kuhawara, F. AU - Gomes, V. AU - Cecato., U. AU - Soares Filho, C.V. T2 - Crop, Forage and Turfgrass Management AB - Core Ideas Bermudagrass K fertilization affects forage characteristics. Bermudagrass K fertilization effects are influenced by N fertilization. K fertilization is crucial to increase belowground reserves of bermudagrass. Adequate supply of potassium (K) is an important factor that can affect bermudagrass [ Cynodon dactylon (L.) Pers.] production and persistence, particularly in soils with limited nutrient holding capacity. The objectives of this study were to (i) evaluate the effects of different nitrogen (N) and K fertilization strategies on Jiggs bermudagrass herbage accumulation (HA), root–rhizome mass, and K concentration and accumulation in above‐ and belowground tissue; and (ii) identify the critical minimum tissue K concentration below which bermudagrass HA is reduced. The experiment was conducted in a greenhouse at Ona, FL, from August to December, 2014 and 2015. Treatments were a factorial combination of three N (0, 45, and 90 lb/acre) and four K 2 O fertilization levels (0, 18, 36, and 72 lb K 2 O/acre, the equivalent of 0, 15, 30, and 60 lb K/acre) after every harvest, distributed in a completely randomized design with four replicates. Herbage was harvested every 6 weeks, and root and rhizome mass determined at the end of each year. There were no effects of K fertilization on HA and root–rhizome mass when no N was applied; however, Jiggs HA and root–rhizome biomass increased linearly with increasing K fertilization levels at 45 and 90 lb N/acre. For these N levels, HA increased with tissue K concentration up to 1.4%. Root and rhizome K concentrations decreased linearly with increasing levels of N. Conversely, root–rhizome K content increased with increasing levels of N fertilization. Potassium fertilization increased HA and root–rhizome mass of Jiggs bermudagrass; however, the responses were influenced by N fertilization levels. DA - 2017/// PY - 2017/// DO - 10.2134/cftm2017.04.0029 VL - 3 IS - 1 SP - 0 LA - en SN - 2374-3832 UR - https://dl.sciencesocieties.org/publications/cftm/abstracts/3/1/cftm2017.04.0029 DB - Crossref Y2 - 2019/2/8/ ER - TY - JOUR TI - Sesame tolerance to preplant applications of 2,4-D and dicamba AU - Sperry, B.P. AU - Ferrell, J.A. AU - Leon, R.G. AU - Rowland, D.L. AU - Mulvaney, M.J. AU - Dias, J.L.C.S. T2 - Weed Technology AB - Two separate experiments were conducted in 2015 and 2016 in Citra, FL to investigate the effects of preplant application timing of 2,4-D and dicamba on sesame stand and yield. Nonlinear regression analysis was performed to determine the application timing that caused 10% stand or yield reduction (GR 10 ) compared to the nontreated control (NTC) and expressed as d before planting (DBP; longer intervals indicate more injury). Likewise, regression analysis was used to determine sesame stand that resulted in 10% yield reduction (YR 10 ) expressed as plants m −1 row. Stand measured 3 wk after planting (WAP) revealed 2,4-D applied at 0.53 kg ae ha −1 to be the least injurious treatment to sesame stand (GR 10 =6.4 DBP). Conversely, dicamba at 1.12 kg ha −1 produced a GR 10 of 15.7 DBP for sesame stand at 3 WAP. 2,4-D applied at 0.53 and 1.06 kg ha −1 and dicamba applied at 0.56 kg ha −1 had the lowest GR 10 for yield of 2, 3.7, and 3 DBP, respectively. Dicamba applied at 1.12 kg ha −1 proved to be the most injurious treatment to yield, which produced a GR 10 value of 10.3 DBP. To simulate possible stand losses associated with dicamba or 2,4-D and the subsequent effect on yield, a separate experiment was conducted in which sesame was thinned to various plant densities and yield was recorded to determine the relationship between plant stand and seed yield. The regression analysis of these data was then compared to that of the experiment treated with 2,4-D and dicamba to separate any physiological effects of the herbicides that would lead to yield reduction from yield effects due to stand loss only. Rate constants were compared and no statistical differences were detected between herbicide and non-herbicide treatments, suggesting that yield reductions that occur from preplant applications of 2,4-D and dicamba were purely due to stand reductions. DA - 2017/// PY - 2017/// DO - 10.1017/wet.2017.37 VL - 31 IS - 04 SP - 590–598 KW - Crop injury KW - burndown KW - preplant ER - TY - JOUR TI - Impact of potassium and nitrogen fertilization on bahiagrass herbage accumulation and nutrient concentration AU - Yarborough, J.K. AU - Vendramini, J.M.B. AU - Silveira, M.L. AU - Sollenberger, L.E. AU - Leon, R.G. AU - Sanchez, J.M.D. AU - Oliveira, F. AU - Kuhawara, F. AU - Gomes, V. AU - Cecato, U. AU - Soares Filho, V. T2 - Agronomy Journal AB - Core Ideas Bahiagrass pastures on soils with low K concentration may not respond to K fertilization. Tissue K concentration in bahiagrass is variable and dependent on fertilization levels. Bahiagrass tissue K concentration of 17 g kg −1 was related to the greatest herbage accumulation in plants receiving greater levels of fertilization. Bahiagrass ( Paspalum notatum Flügge) is the most utilized forage for beef cattle ( Bos spp.) in Florida, but there is concern that bahiagrass pastures are declining due to insufficient K fertilization. Two studies determined the effects of K and N fertilization on bahiagrass herbage mass (HM) and nutritive value in field plots (Exp. 1), and greenhouse (Exp. 2). At two locations from May to December 2014 and 2015, Exp. 1 evaluated the combinations of three N fertilization levels (0, 50 kg N ha −1 in May, or 50 kg N ha −1 in May and August) and two levels of K fertilization (0 or 42 kg K ha −1 ). Potassium fertilization did not affect HM, crude protein (CP), or in vitro digestible organic matter (IVDOM); however, tissue K concentration increased from 10.6 to 11.2 g kg −1 with increasing K fertilization. Plots fertilized with N had greater HM than the control, but there was no difference between plots fertilized in May only vs. those fertilized in May and August. Experiment 2 was conducted in a greenhouse in 2014 and 2015 with a factorial combination of three levels of N fertilization (0, 50, and 100 kg N ha −1 ) and four levels of K fertilization (0, 16, 33, and 66 kg K ha −1 ). There was a quadratic relationship between tissue K concentration and herbage accumulation (HA) and maximum HA occurred with tissue K concentration of 17 g kg −1 . Bahiagrass tissue K concentration and response to K fertilization are variable and can be related to fertilization levels. DA - 2017/// PY - 2017/// DO - 10.2134/agronj2016.10.0589 VL - 109 IS - 3 SP - 1099–1105 ER - TY - JOUR TI - Efficacy of aquatic herbicides on rotala (Rotala rotundifolia) AU - Della Torre, C.J. AU - Gettys, L.A. AU - Haller, W.T. AU - Ferrell, J.A. AU - Leon, R. T2 - Journal of Aquatic Plant Management DA - 2017/// PY - 2017/// VL - 55 SP - 13–18 ER - TY - JOUR TI - Effect of sequential applications of protoporphyrinogen oxidase (PPO) inhibiting herbicides on Palmer amaranth (Amaranthus palmeri) in peanut (Arachis hypogaea) AU - Sperry, B.P. AU - Ferrell, J.A. AU - Smith, H.C. AU - Fernandez, V.J. AU - Leon, R.G. AU - Smith, C.A. T2 - Weed Technology AB - Two experiments were conducted in 2013 and 2014 in Florida to evaluate the effects of protoporphyrinogen oxidase (PPO)-inhibiting herbicides and single versus sequential applications on Palmer amaranth control and peanut injury. Protoporphyrinogen oxidase-inhibiting herbicides are among the last available herbicides for the POST control of acetolactate synthase (ALS)-resistant Palmer amaranth in peanut. Lactofen (219 g ai ha –1 ) applied 5 d after the initial application provided the highest level of Palmer amaranth control 7 and 14 d after initial application (DAIT). Delaying sequential applications of lactofen to 15 d resulted in the highest level of Palmer amaranth control 21 and 28 DAIT. Similar to Palmer amaranth control, foliar injury to peanut was often highest from lactofen applications, and by 28 DAIT lactofen treatments were the only treatments that caused foliar injury. Although no statistical difference was observed between yields of plots treated with acifluorfen (280 g ai ha –1 ), bentazon (560 g ai ha –1 ), 2,4-DB (280 g ae ha –1 ) alone or in combination with each other, plots treated with sequential applications of lactofen 5 or 15 DAIT produced the lowest yields. Sequential applications of lactofen applied 15 DAIT controlled Palmer amaranth more effectively than any other treatment but also caused the highest level of peanut injury. The use of sequential applications of lactofen was the most effective method for control of Palmer amaranth in this study, but did reduce peanut yield. DA - 2017/// PY - 2017/// DO - 10.1017/wet.2016.3 VL - 31 IS - 01 SP - 46–52 KW - ALS-resistant Palmer amaranth KW - sequential applications KW - crop injury ER - TY - JOUR TI - Diversity and spatial heterogeneity of weed communities in a sugarcane cropping system in the dry tropics of Costa Rica AU - Leon, R.G. AU - Agüero, R. AU - Calderón, D. T2 - Weed Science AB - Weed diversity, structure, and distribution within and outside agricultural fields affect not only ecological processes but also weed management strategies. We studied how areas managed differently within and outside the field determine weed communities in a sugarcane cropping system in the dry tropics of Costa Rica. A total of 120 weed species were detected, which was similar to surveys conducted in subtropical and temperate conditions. Weed species richness was highest in undisturbed field borders and lowest in rows and furrows. The area where tractors turn within the field (turn area) had similar richness compared with the borders, despite being one of the most disturbed management areas studied. The most predominant weed species were divided between generalists and species that exhibited clear preferences for management area or soil texture. Soil texture was more important for determining weed community structure than management area when considering weed species affecting weed control decisions. The results indicated that disturbance in the management area and, especially, weed control practices are critical factors affecting weed diversity, but availability of resources for weed growth such as nutrients, soil moisture, and light can mitigate some of the limitations imposed by weed control on weed diversity, especially in the turn area. Differences in weed communities between management areas within fields indicated the existence of conditions that favor key weed species, and this information can be used to anticipate their population growth and help determine when and where more intensive control should be implemented. DA - 2017/// PY - 2017/// DO - 10.1614/ws-d-16-00066.1 VL - 65 IS - 01 SP - 128–140 KW - control KW - disturbance KW - diversity KW - habitat KW - soil KW - texture KW - tropicsweed ER - TY - JOUR TI - Converting bahiagrass pasture land to elephantgrass bioenergy production enhances biomass yield and water quality AU - Reyes-Cabrera, J. AU - Erickson, JE AU - Leon, RG AU - Silveira, ML AU - Rowland, DL AU - Sollenberger, LE AU - Morgan, KT T2 - Agriculture Ecosystems and Environment AB - Changing pasture land to the production of bioenergy crops will affect regional water dynamics. Returning by-products of industrial conversion of bioenergy crops like fermentation residual or biochar back to the field could be used to improve sustainable nutrient management, but could also impact water quantity and quality in ways that are poorly understood. The objective of this study was to assess the effects of land-use conversion from low-input bahiagrass (Paspalum notatum Flüggé) pastures to elephantgrass [Pennisetum purpureum (L.) Schum.] for bioenergy production under different nutrient management practices on biomass yield, crop water dynamics and nitrate-nitrogen (NO3-N) leaching during growing and dormant seasons. Treatments evaluated were 1) bahiagrass + 50 kg N ha−1; 2) elephantgrass + 50 kg N ha−1; 3) elephantgrass + 50 kg N ha−1 + fermentation residual; 4) elephantgrass + 50 kg N ha−1 + biochar; and 5) elephantgrass + 250 kg N ha−1. Data were collected on crop evapotranspiration (ET), water use efficiency, drainage, NO3-N leaching, and aboveground dry matter accumulation. Dry matter yield of elephantgrass was 4- to 7-fold greater than bahiagrass after the first growing season, but was similar among elephantgrass treatments. Elephantgrass produced with no residual amendments reduced drainage (approx. 43% across all growing seasons) compared to bahiagrass, and this reduction was exacerbated in the residual treatments. Reduced drainage was associated with increased ET. Elephantgrass, regardless of treatment, reduced the amount of NO3-N lost through drainage compared to bahiagrass. Therefore, replacing bahiagrass with elephantgrass will increase cropping system water use and diminish the rate of groundwater replenishment during the growing season, which could have detrimental effects for other ecosystem processes that rely on this water resource. However, elephantgrass increased the efficiency with which water was used to produce biomass and reduced NO3-N leaching to groundwater. DA - 2017/// PY - 2017/// DO - 10.1016/j.agee.2017.07.021 VL - 248 SP - 20–28 KW - Bioenergy crops KW - Evapotranspiration KW - Water use efficiency KW - Water quality KW - Ecosystem services ER - TY - JOUR TI - Carinata (Brassica carinata) tolerance to preemergence and postemergence herbicides AU - Leon, R.G. AU - Ferrell, J.A. AU - Mulvaney, M.J. T2 - Weed Technology AB - Carinata is a new biofuel crop that was recently introduced in the southeastern USA as a winter crop. This crop is competitive after canopy closure, but there is a need for weed control options at earlier growth stages. Field experiments were conducted from 2014 to 2016 to determine the safety of several PRE and POST herbicides in carinata. Pendimethalin at 1080 g ai ha −1 applied preplant incorporated (PPI) and PRE caused no carinata injury, or plant density and yield reductions. S -metolachlor was also safe at 694, 1070, 1390, and 2780 g ai ha −1 applied at PRE, 3 d after planting (DAP) and at the 2- to 6-leaf stage. Flumioxazin at 72 g ai ha −1 applied PRE was highly injurious on carinata preventing its establishment. Among the POST herbicides evaluated, clopyralid at 210 g ae ha 1 and clethodim at 136 g ai ha −1 caused minor injury to carinata but did not reduce yield compared to the nontreated control. Acifluorfen at 420 g ai ha −1 , bentazon at 840 g ai ha −1 , and carfentrazone at 18 g ai ha −1 applied POST to carinata caused 75 to 100% injury. Under stressful conditions (i.e. high summer temperatures) all POST herbicides caused more injury than under more favorable conditions for growth in Florida (i.e. winter). The present study identified pendimethalin, S -metolachlor, clopyralid and clethodim as potential herbicides for weed control in carinata, and flumioxazin, acifluorfen, bentazon, and carfentrazone as herbicides that can be used to control volunteer carinata plants in rotational crops. DA - 2017/// PY - 2017/// DO - 10.1017/wet.2017.62 VL - 31 IS - 06 SP - 877–882 KW - Crop establishment KW - crop rotation KW - integrated weed management KW - volunteer crop control ER - TY - JOUR TI - Biochar changes root growth and root distribution of soybean during early vegetative stages AU - Reyes-Cabrera, J. AU - Leon, R.G. AU - Erickson, J.E. AU - Silveira, M.L. AU - Rowland, D.L. AU - Morgan, K.T. T2 - Crop Science AB - A better understanding of changes in root growth and distribution when soil is treated with biochar is needed. The aim of this study was to assess root distribution responses when biochar is added to the soil. A greenhouse study was conducted to investigate the effects of topdressing or incorporating four biochar rates on soybean [ Glycine max (L.) Merr.] root distribution during early vegetative stages grown in lysimeters (depth: 35 cm). On average, topdressing either 10 or 25 Mg biochar ha −1 increased root length density (RLD) 39% and root surface area (RSA) 36% in the 0‐ to 0.05‐m soil layer compared with the control. In the 0.05‐ to 0.15‐m soil layer, incorporation of 10 Mg ha −1 increased RLD 35%. Similarly, incorporation of either 10 or 25 Mg biochar ha −1 increased RSA 38% compared with the control. Incorporation of 25 and 50 Mg biochar ha −1 in the top 0.15 m of soil increased leaf area 29 and 31% compared with topdressing 50 Mg biochar ha −1 and with the control, respectively. Biochar increased soybean RLD, RSA, and leaf area, especially when incorporated into the soil. Overall, our findings indicate that biochar application and placement within the soil affects plant‐rooting distribution, which represents an important management practice to increase RLD and RSA. Future research should focus on evaluating biochar rates and application methods under field conditions. DA - 2017/// PY - 2017/// DO - 10.2135/cropsci2016.01.0075 VL - 57 IS - 1 SP - 454–461 ER - TY - CHAP TI - Measuring Protein Movement, Oligomerization State, and Protein–Protein Interaction in Arabidopsis Roots Using Scanning Fluorescence Correlation Spectroscopy (Scanning FCS) AU - Clark, Natalie M. AU - Sozzani, Rosangela T2 - Plant Genomics A2 - Busch, Wolfgang T3 - Methods in Molecular Biology AB - Scanning fluorescence correlation spectroscopy (scanning FCS) can be used to determine protein movement, oligomerization state, and protein–protein interaction. Here, we describe how to use the scanning FCS techniques of raster image correlation spectroscopy (RICS) and pair correlation function (pCF) to determine the rate and direction of protein movement. In addition, we detail how number and brightness (N&B) and cross-correlation analyses can be used to determine oligomerization state and binding ratios of protein complexes. We specifically describe how to acquire suitable images for scanning FCS analysis using the model plant Arabidopsis and how to perform the various analyses using the SimFCS software. PY - 2017/// DO - 10.1007/978-1-4939-7003-2_16 VL - 1610 SP - 251-266 PB - Springer New York SN - 978-1-4939-7001-8 978-1-4939-7003-2 UR - http://link.springer.com/10.1007/978-1-4939-7003-2_16 DB - Crossref Y2 - 2019/1/30/ KW - Scanning fluorescence correlation spectroscopy KW - Diffusion coefficient KW - Protein movement KW - Oligomerization state KW - Protein stoichiometry ER - TY - CHAP TI - Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach AU - Luis Balaguer, Maria Angels AU - Sozzani, Rosangela T2 - Plant Gene Regulatory Networks A2 - Kaufmann, Kerstin A2 - Mueller-Roeber, Bernd T3 - Methods in Molecular Biology AB - Gene regulatory network (GRN) models have been shown to predict and represent interactions among sets of genes. Here, we first show the basic steps to implement a simple but computationally efficient algorithm to infer GRNs based on dynamic Bayesian networks (DBNs), and we then explain how to approximate DBN-based GRN models with continuous models. In addition, we show a MATLAB implementation of the key steps of this method, which we use to infer an Arabidopsis root GRN. PY - 2017/// DO - 10.1007/978-1-4939-7125-1_21 VL - 1629 SP - 331-348 PB - Springer New York SN - 978-1-4939-7124-4 978-1-4939-7125-1 UR - http://link.springer.com/10.1007/978-1-4939-7125-1_21 DB - Crossref Y2 - 2019/1/30/ KW - Gene regulatory network KW - Dynamic Bayesian network KW - Ordinary differential equation KW - Arabidopsis root ER - TY - JOUR TI - A Novel, Economical Way to Assess Virulence in Field Populations of Hessian Fly (Diptera: Cecidomyiidae) Utilizing Wheat Resistance Gene H13 as a Model AU - Johnson, Alisha J. AU - Moniem, Hossam E. M. Abdel AU - Flanders, Kathy L. AU - Buntin, G. David AU - Reay-Jones, Francis P. F. AU - Reisig, Dominic AU - Stuart, Jeffery J. AU - Subramanyam, Subhashree AU - Shukle, Richard H. AU - Schemerhorn, Brandon J. T2 - Journal of Economic Entomology AB - Mayetiola destructor (Say) is a serious pest of wheat, Triticum aestivum L., in North America, North Africa, and Central Asia. Singly deployed resistance genes in wheat cultivars have provided effective management of Hessian fly populations for >50 yr. Thirty-five H genes have been documented. Defense mediated by the H gene constitutes strong selection on the Hessian fly population, killing 100% of larvae. A mutation in a matching Hessian fly avirulence gene confers virulence to the H gene, leading to survival on the resistant plant. As the frequency of virulence rises in the population, the H gene loses its effectiveness for pest management. Knowing the frequency of virulence in the population is not only important for monitoring but also for decisions about which H gene should be deployed in regional wheat breeding programs. Here, we present a novel assay for detecting virulence in the field. Hessian fly males were collected in Alabama, Georgia, North Carolina, and South Carolina using sticky traps baited with Hessian fly sex pheromone. Utilizing two PCR reactions, diagnostic molecular markers for the six alleles controlling avirulence and virulence to H13 can be scored based on band size. Throughout the southeast, all three avirulence and three virulence alleles can be identified. In South Carolina, the PCR assay was sensitive enough to detect the spread of virulence into two counties previously documented as 100% susceptible to H13. The new assay also indicates that the previous methods overestimated virulence in the field owing to scoring of the plant instead of the insect. DA - 2017/5// PY - 2017/5// DO - 10.1093/jee/tox129 VL - 110 IS - 4 SP - 1863-1868 KW - Mayetiola destructor KW - Hessian fly KW - vH13 KW - pheromone trap KW - risk assessment ER - TY - JOUR TI - Economic issues to consider for gene drives AU - Mitchell, Paul D. AU - Brown, Zachary AU - McRoberts, Neil T2 - Journal of Responsible Innovation AB - We examine four economic issues regarding gene drive applications made possible by gene editing technologies. First, whether gene drives are self-sustaining or self-limiting will largely determine which types of organizations have incentives to develop and deploy gene drives and greatly influence their governance and regulation. Social factors will also play key roles, particularly public perceptions, with these perceptions co-determined with regulation and governance. Second, gene drive applications will generate unintended negative social impacts that will partially offset benefits. Third, economic surplus, the traditional measure of economic benefits, incompletely captures the welfare impacts of gene drive applications. Fourth, gene drives imply dynamic nonlinearities that make identifying economic equilibria and general policy recommendations challenging. The potentially substantial benefits, coupled with the technical, social, and economic uncertainties surrounding gene drives, suggest that a responsible course of action is to move forward while maintaining regulatory flexibility and conducting research to resolve key uncertainties. DA - 2017/12/22/ PY - 2017/12/22/ DO - 10.1080/23299460.2017.1407914 VL - 5 IS - sup1 SP - S180-S202 J2 - Journal of Responsible Innovation LA - en OP - SN - 2329-9460 2329-9037 UR - http://dx.doi.org/10.1080/23299460.2017.1407914 DB - Crossref KW - Gene editing KW - CRISPR-Cas9 KW - malaria KW - mosquito-vectored diseases KW - invasive species KW - agriculture ER - TY - JOUR TI - Preference Heterogeneity in the Structural Estimation of Efficient Pigovian Incentives for Insecticide Spraying to Reduce Malaria AU - Brown, Zachary S. AU - Kramer, Randall A. T2 - Environmental and Resource Economics DA - 2017/1/18/ PY - 2017/1/18/ DO - 10.1007/s10640-017-0115-x VL - 70 IS - 1 SP - 169-190 J2 - Environ Resource Econ LA - en OP - SN - 0924-6460 1573-1502 UR - http://dx.doi.org/10.1007/s10640-017-0115-x DB - Crossref KW - Discrete choice models KW - Preference heterogeneity KW - Externalities KW - Pigovian incentives KW - Malaria KW - Insecticides KW - Locational sorting models ER - TY - JOUR TI - A roadmap for gene drives: using institutional analysis and development to frame research needs and governance in a systems context AU - Kuzma, J. AU - Gould, F. AU - Brown, Z. AU - Collins, J. AU - Delborne, J. AU - Frow, E. AU - Esvelt, K. AU - Guston, D. AU - Leitschuh, C. AU - Oye, K. AU - Stauffer, S. T2 - Journal of Responsible Innovation AB - The deployment of gene drives is emerging as an alternative for protecting endangered species, controlling agricultural pests, and reducing vector-borne diseases. This paper reports on a workshop held in February 2016 to explore the complex intersection of political, economic, ethical, and ecological risk issues associated with gene drives. Workshop participants were encouraged to use systems thinking and mapping to describe the connections among social, policy, economic, and ecological variables as they intersect within governance systems. In this paper, we analyze the workshop transcripts and maps using the Institutional Analysis and Development (IAD) framework to categorize variables associated with gene drive governance and account for the complexities of socio-ecological systems. We discuss how the IAD framework can be used in the future to test hypotheses about how features of governance systems might lead to certain outcomes and inform the design of research programs, public engagement, and anticipatory governance of gene drives. DA - 2017/// PY - 2017/// DO - 10.1080/23299460.2017.1410344 VL - 5 IS - sup1 SP - S13-S39 KW - Gene drive KW - governance KW - risk KW - systems KW - IAD KW - genetic engineering ER - TY - JOUR TI - The Economics, Regulation and International Implications of Gene Drives in Agriculture AU - Brown, Z.S. T2 - Choices DA - 2017/// PY - 2017/// VL - Quarter 2 UR - http://www.choicesmagazine.org/choices-magazine/submitted-articles/economic-regulatory-and-international-implications-of-gene-drives-in-agriculture ER - TY - JOUR TI - Spatial distribution of Megacopta cribraria (Hemiptera: Plataspidae) adults, eggs and parasitism by Paratelenomus saccharalis (Hymenoptera: Platygastridae) in soybean AU - Knight, I.A. AU - Roberts, P.M. AU - Gardner, W.A. AU - Oliver, K.M. AU - Reay-Jones, F.P.F. AU - Reisig, D.D. AU - Toews, M.D. T2 - Environmental Entomology AB - Since 2014, populations of the kudzu bug, Megacopta cribraria (F.) (Hemiptera: Plataspidae), have declined in the southeastern United States and seldom require treatment. This decline follows the discovery of Paratelenomus saccharalis (Dodd; Hymenoptera: Platygastridae), a non-native egg parasitoid. The objective of this project was to observe the temporal and spatial dynamics of P. saccharalis parasitism of kudzu bug egg masses in commercial soybean fields. Four fields were sampled weekly for kudzu bugs and egg masses at a density of one sample per 0.6 ha. Sampling commenced when soybean reached the R2 maturity stage and continued until no more egg masses were present. Responses including kudzu bugs, egg masses, and parasitism rates were analyzed using ANOVA, Spatial Analysis by Distance Indices (SADIE), and SaTScan spatial analysis software. Egg masses were collected from the field, held in the lab and monitored for emergence of kudzu bug nymphs or P. saccharalis. Kudzu bug populations were generally lower than previously reported in the literature and spatial aggregation was not consistently observed. Egg parasitism was first detected in early July and increased to nearly 40% in mid-August. Significant spatial patterns in parasitism were observed with spatio-temporal clusters being loosely associated with clusters of egg masses. There were no significant differences in parasitism rates between field margins and interiors, suggesting that P. saccharalis is an effective parasitoid of kudzu bug egg masses on a whole-field scale. DA - 2017/// PY - 2017/// DO - 10.1093/ee/nvx150 VL - 46 IS - 6 SP - 1292-1298 KW - Natural enemy KW - biological control KW - invasive species KW - soybean pest management ER - TY - RPRT TI - North Carolina soybean scouting and field guide AU - Drake Stowe, K. AU - Crozier, C. AU - Dunphy, J. AU - Everman, W. AU - Reisig, D. AU - Thiessen, L. A3 - North Carolina Soybean Producers Association DA - 2017/// PY - 2017/// PB - North Carolina Soybean Producers Association ER - TY - JOUR TI - Efficacy of insecticidal seed treatments and bifenthrin in-furrow for annual white grub, 2016 AU - Reisig, D. AU - Goldsworthy, E. T2 - Arthropod Management Tests DA - 2017/// PY - 2017/// DO - 10.1093/amt/tsx137 VL - 43 IS - 1 ER - TY - JOUR TI - Efficacy of a new insecticidal seed treatment, cyantraniliprole for annual white grub, 2016 AU - Reisig, D. AU - Goldsworthy, E. T2 - Arthropod Management Tests DA - 2017/// PY - 2017/// DO - 10.1093/amt/tsx136 VL - 43 IS - 1 ER - TY - JOUR TI - Diel flight activity and intra-plant distribution of Megacopta cribraria (Hemiptera: Plataspidae) adults in soybean AU - Del Pozo-Valdivia, A. AU - Reisig, D. T2 - J. Entomol. Sci AB - Megacopta cribraria (F.) (Hemiptera: Plataspidae), the kudzu bug, is a soybean pest in the southeastern United States. Accidentally introduced into Georgia in 2009 from Asia, kudzu bug can reduce up to 60% of soybean yield when left uncontrolled. There is limited information on the life history of this invasive pest in soybean. The main goals of this research were to investigate the daily flight activity pattern and intra-plant distribution of kudzu bug adults in soybean. This was accomplished through experiments in two locations in North Carolina during 2013 in which dispersing adult kudzu bugs captured on white sticky cards between 0900–1700 h were counted hourly, and adults on plants were visually sampled between 0900–1200 h from soybean maturity group IV to VII plants. Adult captures on sticky cards were higher from 1300 to 1500 h across sampling dates, suggesting that dispersal or flight activity peaks during this interval. When soybean plants were visually inspected, most of the adults formed aggregations on the main stem, with aggregations most common in the middle section of plants. The number of aggregations per plant, the number of adults per plant, and the male-to-female ratio were not influenced by maturity group. Soybean plant height did not affect adult densities per plant. However, densities varied depending on the date of sampling. Implications of this research on kudzu bug biology are discussed. DA - 2017/// PY - 2017/// DO - 10.18474/jes16-06pt.1 VL - 52 IS - 4 SP - 311–322 KW - dispersion KW - soybean maturity group KW - plant height KW - adult aggregation KW - sex ratio ER - TY - JOUR TI - 2016 soybean insect losses in the Southern US AU - Musser, F.R. AU - Catchot, A. L. AU - Davis, J.A. AU - Herbert, D. A. AU - Lorenz, G. M. AU - Reed, T. AU - Reisig, D.D. AU - Stewart, S.D. T2 - Midsouth Entomol DA - 2017/// PY - 2017/// VL - 10 SP - 1–13 ER - TY - BOOK TI - Vigilante environmentalism: Are gene drives changing how we value and govern ecosystems? AU - Kuiken, T. DA - 2017/// PY - 2017/// DO - 10.4324/9781315168418 SE - 95-112 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85050540917&partnerID=MN8TOARS ER - TY - RPRT TI - Potential Implications of New Synthetic Biology and Genomic Research Trajectories on the International Treaty for Plant Genetic Resources for Food and Agriculture DA - 2017/10// PY - 2017/10// UR - http://www.fao.org/fileadmin/user_upload/faoweb/plant-treaty/GB7/gb7_90.pdf ER - TY - CONF TI - What Are Subject Liaisons When “Collections” and “Subjects” Don’t Matter? AU - Orcutt, Darby AU - Waller, Mira AU - Warren, Scott AB - In this interactive lively lunch discussion, participants explored issues around how the traditional subject liaison role is evolving. Users increasingly require functional information support (e.g., for geographic information system (GIS) or data mining) rather than simply domain-specific. At the same time, reports from the Association of Research Libraries (ARL) Pilot Library Liaison Institute and others have noted self-conscious trends toward developing liaison roles that engage and support the full research life cycle, as opposed to traditional service models focused on building and promoting library collections as more or less fixed products. Hosts Darby Orcutt, Mira Waller, and Scott Warren outlined some the major theme surrounding the future of these new roles and with participants explored questions that include: What does it mean to be a collections librarian in this new world? What new skills do we need to develop? What old skills should we not lose? How do we adapt both our institutions and our individual staff without sacrificing our (or their) very identities? C2 - 2017/// C3 - "Roll With the Times, or the Times Roll Over You" DA - 2017/// DO - 10.5703/1288284316478 PB - Purdue University Press ER - TY - CONF TI - Rolling With the Wheels of Commerce: The Challenges of Business and Industry- Based Resources AU - Cooper, Natasha AU - McCracken, Peter AU - Orcutt, Darby AU - Rotenberg, Ellen AB - Collections and liaison librarians receive requests for specialized resources that may require use of passwords or other mediated access, local hosting, or special software. Sometimes, although not always, these resources are used in a business or industry setting, and their subscription and licensing processes do not follow typical academic library acquisitions patterns. Librarians may also receive requests for raw data that is part of a subscribed resource. How do librarians respond to these user needs? How do vendors make decisions about which products to bring to the academic library market? The authors present views on these issues and options to consider. C2 - 2017/// C3 - "Roll With the Times, or the Times Roll Over You" DA - 2017/// DO - 10.5703/1288284316446 PB - Purdue University Press ER - TY - JOUR TI - Reviews-in-Brief AU - Orcutt, Darby T2 - Collection Management DA - 2017/4/3/ PY - 2017/4/3/ DO - 10.1080/01462679.2017.1319241 VL - 42 IS - 2 SP - 120-121 ER - TY - JOUR TI - Ein lohnendes Unterfangen und neue Herausforderungen. Videospiele: Bestände und Services der NCSU Libraries” [A Worthwhile Endeavour and New Challenges. Video Games: Holdings and Services at NCSU Libraries] AU - Orcutt, Darby AU - Jefferies, Jason AU - Wust, Markus T2 - BuB - Forum Bibliothek und Information DA - 2017/// PY - 2017/// VL - 11 SP - 606-610 ER - TY - JOUR TI - Liaisonship, the Law, & Libraries: Supporting Content Mining Research AU - Orcutt, Darby T2 - Against the Grain DA - 2017/9// PY - 2017/9// VL - 29 IS - 4 SP - 26-27 UR - https://against-the-grain.com/2017/10/v29-4-liaisonship-the-law-libraries-supporting-content-mining-research/ ER - TY - JOUR TI - Rules of the road for insect gene drive research and testing AU - Adelman, Z. AU - Akbari, O. AU - Bauer, J. AU - Bier, E. AU - Bloss, C. AU - Carter, S.R. AU - Callender, C. AU - Denis, A.C. AU - Cowhey, P. AU - Dass, B. AU - Delborne, J. AU - Devereaux, M. AU - Ellsworth, P. AU - Friedman, R.M. AU - Gantz, V. AU - Gibson, C. AU - Hay, B.A. AU - Hoddle, M. AU - James, A.A. AU - James, S. AU - Jorgenson, L. AU - Kalichman, M. AU - Marshall, J. AU - McGinnis, W. AU - Newman, J. AU - Pearson, A. AU - Quemada, H. AU - Rudenko, L. AU - Shelton, A. AU - Vinetz, J.M. AU - Weisman, J. AU - Wong, B. AU - Wozniak, C. T2 - Nature Biotechnology DA - 2017/// PY - 2017/// DO - 10.1038/nbt.392620 VL - 35 IS - 8 SP - 716–718 ER - TY - RPRT TI - Prototype to Patient Treatment: Dialogue on Safety, Regulation, Privacy, Security, and Acceptability for Wearable Medical Devices AU - Foley, R.W. AU - Asare, P. AU - Delborne, J. AU - Lach, J. AU - Misra, V. A3 - University of Virginia DA - 2017/// PY - 2017/// DO - 10.18130/V3804XJ4K M3 - Workshop report PB - University of Virginia UR - https://doi.org/10.18130/V3804XJ4K ER - TY - RPRT TI - Genetically Engineered Algae Public Engagement Strategies: A Stakeholder Workshop Report AU - Delborne, J. AU - Farooque, M. AU - Shapiro, J. A3 - ECAST: Expert and Citizen Assessment of Science and Technology DA - 2017/// PY - 2017/// PB - ECAST: Expert and Citizen Assessment of Science and Technology UR - https://ecastnetwork.org/research/genetically-engineered-algae-public-engagement-strategies/ ER - TY - JOUR TI - The effects of mepiquat chloride applied to cotton at early bloom and physiological cutout AU - Collins, G. D. AU - Edmisten, K. L. AU - Wells, R. AU - Whitaker, J. R. T2 - Journal of Cotton Science DA - 2017/// PY - 2017/// VL - 21 IS - 3 SP - 183-189 ER - TY - BOOK TI - Oral communication in the disciplines: A resource for teacher development and training AU - Dannels, D.P. AU - Palmerton, P.R. AU - Gaffney, L.H. DA - 2017/// PY - 2017/// PB - Anderson, South Carolina: Parlor Press ER - TY - BOOK TI - Dr. Eleanor's book of common ants of Chicago AU - Spicer Rice, E. AU - Wild, A.L AU - Dunn, R.R. DA - 2017/// PY - 2017/// PB - Chicago: The University of Chicago Press ER - TY - JOUR TI - Approaches to agricultural innovation and their effectiveness AU - L. Kick, Edward AU - Zering, Kelly AU - Classen, John T2 - AIMS Agriculture and Food AB - Citation: Edward L. Kick, Kelly Zering, John Classen. Approaches to agricultural innovation and their effectiveness[J]. AIMS Agriculture and Food, 2017, 2(4): 370-373. doi: 10.3934/agrfood.2017.4.370 DA - 2017/// PY - 2017/// DO - 10.3934/agrfood.2017.4.370 VL - 2 IS - 4 SP - 370-373 LA - en OP - SN - 2471-2086 UR - http://dx.doi.org/10.3934/agrfood.2017.4.370 DB - Crossref ER - TY - JOUR TI - Socially controlled sex change in fishes AU - Godwin, J. AU - Lamm, M. T2 - Hormones, Brain and Behavior, vol 2: Non-Mammalian Hormone-Behavior Systems, 3rd edition DA - 2017/// PY - 2017/// SP - 31-46 ER - TY - JOUR TI - Revisiting Graduate Student Training to Address Agricultural and Environmental Societal Challenges AU - Duckworth, Owen W. AU - Andrews, Megan Y. AU - Cubeta, Marc A. AU - Grunden, Amy M. AU - Ojiambo, Peter S. T2 - AGRICULTURAL & ENVIRONMENTAL LETTERS AB - Core Ideas Society is faced with daunting environmental and agricultural challenges. There is a pressing need for multidisciplinary teams of collaborative scientists. Novel graduate educational models may be needed to train students to address grand challenges. An example of illustrating the model through microbiome science of plants and soil is presented. Society and the higher education system are faced with daunting challenges associated with supplying food, energy, and water to a growing population while maintaining environmental quality and preserving natural resources. Too often, the higher education system does not facilitate collaborative immersion required to foster concerted multidisciplinary efforts needed to address societal grand challenges. In this commentary, we present an innovative model of cohort education, which equips graduate students with core skills and enables collaborative dissertation research among students. In addition, we provide an example of a program aimed at understanding the plant–soil microbiome, a critical research area that may yield significant advances in plant health and productivity. DA - 2017/12// PY - 2017/12// DO - 10.2134/ael2017.06.0019 VL - 2 IS - 1 SP - SN - 2471-9625 ER - TY - JOUR TI - Dose-Duration Reciprocity for G protein activation: Modulation of kinase to substrate ratio alters cell signaling AU - Liao, Kang-Ling AU - Melvin, Charles E. AU - Sozzani, Rosangela AU - Jones, Roger D. AU - Elston, Timothy C. AU - Jones, Alan M. T2 - PLOS ONE AB - In animal cells, activation of heterotrimeric G protein signaling generally occurs when the system’s cognate signal exceeds a threshold, whereas in plant cells, both the amount and the exposure time of at least one signal, D-glucose, are used toward activation. This unusual signaling property called Dose-Duration Reciprocity, first elucidated in the genetic model Arabidopsis thaliana, is achieved by a complex that is comprised of a 7-transmembrane REGULATOR OF G SIGNALING (RGS) protein (AtRGS1), a Gα subunit that binds and hydrolyzes nucleotide, a Gβγ dimer, and three WITH NO LYSINE (WNK) kinases. D-glucose is one of several signals such as salt and pathogen-derived molecular patterns that operates through this protein complex to activate G protein signaling by WNK kinase transphosphorylation of AtRGS1. Because WNK kinases compete for the same substrate, AtRGS1, we hypothesize that activation is sensitive to the AtRGS1 amount and that modulation of the AtRGS1 pool affects the response to the stimulant. Mathematical simulation revealed that the ratio of AtRGS1 to the kinase affects system sensitivity to D-glucose, and therefore illustrates how modulation of the cellular AtRGS1 level is a means to change signal-induced activation. AtRGS1 levels change under tested conditions that mimic physiological conditions therefore, we propose a previously-unknown mechanism by which plants react to changes in their environment. DA - 2017/12/29/ PY - 2017/12/29/ DO - 10.1371/journal.pone.0190000 VL - 12 IS - 12 SP - SN - 1932-6203 ER - TY - JOUR TI - Surveillance for Immature Mosquitoes in Windshield Wash Basins at Gas Stations AU - Reiskind, M.H. AU - Hopperstad, K.A. T2 - Journal of Medical Entomology AB - Gas stations often provide windshield wash basins (WWBs) that customers may use to clean their windshields. Motivated by casual observations, we conducted a survey of WWBs in and around Raleigh, NC, to determine whether these WWBs also serve as larval habitats for mosquitoes. We found that 27.7% (95% CI: 12.4–43.14%) of the 36 surveyed gas stations had mosquito larvae in their WWBs, and 22.4% (95% CI: 15.07–29.1%) of the 152 WWBs surveyed were positive for mosquito larvae. Two species were identified inhabiting these containers: Aedes albopictus (Skuse) and Culex quinquefasciatus Say. Aedes albopictus was associated with clear, unturbid water, whereas Cx. quinquefasciatus did not have any significant association with water characteristics. Pupae of both species were observed, suggesting these habitats could be sources of pest mosquitoes. Gas stations may be a convenient surveillance target for vector control specialists and may provide insight into human-aided mosquito dispersal. DA - 2017/// PY - 2017/// DO - 10.1093/jme/tjx129 VL - 54 IS - 6 SP - 1775-1777 SN - 1938-2928 UR - https://doi.org/10.1093/jme/tjx129 KW - Aedes albopictus KW - Culex quinquefasciatus KW - Zika KW - dispersal KW - sampling ER - TY - JOUR TI - Environmental endocrine disruption of brain and behavior AU - Patisaul, H. B. AU - Gore, A. C. AU - Crews, D. T2 - Hormones, Brain and Behavior, vol 5: Development of Hormone-Behavior Relationships, 3rd edition DA - 2017/// PY - 2017/// SP - 63-88 ER - TY - JOUR TI - Using CRISPR-Cas systems as antimicrobials AU - Bikard, David AU - Barrangou, Rodolphe T2 - CURRENT OPINION IN MICROBIOLOGY AB - Although CRISPR-Cas systems naturally evolved to provide adaptive immunity in bacteria and archaea, Cas nucleases can be co-opted to target chromosomal sequences rather than invasive genetic elements. Although genome editing is the primary outcome of self-targeting using CRISPR-based technologies in eukaryotes, self-targeting by CRISPR is typically lethal in bacteria. Here, we discuss how DNA damage introduced by Cas nucleases in bacteria can efficiently and specifically lead to plasmid curing or drive cell death. Specifically, we discuss how various CRISPR-Cas systems can be engineered and delivered using phages or phagemids as vectors. These principles establish CRISPR-Cas systems as potent and programmable antimicrobials, and open new avenues for the development of CRISPR-based tools for selective removal of bacterial pathogens and precise microbiome composition alteration. DA - 2017/6// PY - 2017/6// DO - 10.1016/j.mib.2017.08.005 VL - 37 SP - 155-160 SN - 1879-0364 ER - TY - JOUR TI - The effect of artificial selection on phenotypic plasticity in maize AU - Gage, Joseph L. AU - Jarquin, Diego AU - Romay, Cinta AU - Lorenz, Aaron AU - Buckler, Edward S. AU - Kaeppler, Shawn AU - Alkhalifah, Naser AU - Bohn, Martin AU - Campbell, Darwin A. AU - Edwards, Jode AU - Ertl, David AU - Flint-Garcia, Sherry AU - Gardiner, Jack AU - Good, Byron AU - Hirsch, Candice N. AU - Holland, Jim AU - Hooker, David C. AU - Knoll, Joseph AU - Kolkman, Judith AU - Kruger, Greg AU - Lauter, Nick AU - Lawrence-Dill, Carolyn J. AU - Lee, Elizabeth AU - Lynch, Jonathan AU - Murray, Seth C. AU - Nelson, Rebecca AU - Petzoldt, Jane AU - Rocheford, Torbert AU - Schnable, James AU - Schnable, Patrick S. AU - Scully, Brian AU - Smith, Margaret AU - Springer, Nathan M. AU - Srinivasan, Srikant AU - Walton, Renee AU - Weldekidan, Teclemariam AU - Wisser, Randall J. AU - Xu, Wenwei AU - Yu, Jianming AU - Leon, Natalia T2 - NATURE COMMUNICATIONS AB - Abstract Remarkable productivity has been achieved in crop species through artificial selection and adaptation to modern agronomic practices. Whether intensive selection has changed the ability of improved cultivars to maintain high productivity across variable environments is unknown. Understanding the genetic control of phenotypic plasticity and genotype by environment (G × E) interaction will enhance crop performance predictions across diverse environments. Here we use data generated from the Genomes to Fields (G2F) Maize G × E project to assess the effect of selection on G × E variation and characterize polymorphisms associated with plasticity. Genomic regions putatively selected during modern temperate maize breeding explain less variability for yield G × E than unselected regions, indicating that improvement by breeding may have reduced G × E of modern temperate cultivars. Trends in genomic position of variants associated with stability reveal fewer genic associations and enrichment of variants 0–5000 base pairs upstream of genes, hypothetically due to control of plasticity by short-range regulatory elements. DA - 2017/11/7/ PY - 2017/11/7/ DO - 10.1038/s41467-017-01450-2 VL - 8 IS - 1 SP - SN - 2041-1723 UR - https://doi.org/10.1038/s41467-017-01450-2 ER - TY - JOUR TI - The Gender Dynamics of Conditional Cash Transfers and Smallholder Farming in Calakmul, Mexico AU - Radel, C. AU - Schmook, B. AU - Haenn, N. AU - Green, L. T2 - Women’s Studies International Forum AB - We explore how Oportunidades, Mexico's anti-poverty conditional cash transfer (CCT) program, impacts production and gender dynamics in the smallholder agricultural sector. A 2010 household survey in one southeastern municipality (Calakmul) captured data on Oportunidades receipt, land use and yields, as well as gendered patterns of asset control, decision-making, labor, and income receipt. Our analysis suggests that households with Oportunidades are more likely to engage in semi-subsistence maize cultivation and on average harvest more maize. Thus Oportunidades appears to support semi-subsistence production. We also document persistent gender gaps in land control, decision-making, labor, and income receipt. Nonetheless, we find that households with Oportunidades have on average smaller gaps of particular kinds: women receiving Oportunidades are more likely to hold de jure land rights and to share in income receipt from four main crops. These effects of Oportunidades on gendered smallholder production dynamics are important ones in smallholder women's lives. DA - 2017/// PY - 2017/// DO - 10.1016/j.wsif.2016.06.004 VL - 65 IS - Special issue: Latin American women’s farm land and communal forests SP - 17–27 J2 - Women's Studies International Forum LA - en OP - SN - 0277-5395 UR - http://dx.doi.org/10.1016/j.wsif.2016.06.004 DB - Crossref KW - Gender KW - Intra-household resource management KW - Maize KW - Oportunidades KW - Women's empowerment ER - TY - JOUR TI - Regional Survey of Mosquito Control Knowledge and Usage In North Carolina AU - Richards, Stephanie L. AU - Balanay, Jo Anne G. AU - Byrd, Brian D. AU - Reiskind, Michael H. AU - Styers, Diane M. T2 - Journal of the American Mosquito Control Association AB - Mosquitoes are a nuisance and can transmit pathogens to humans and other animals, resulting in notable morbidity and mortality. Organized mosquito control programs conduct surveillance, source reduction, treatment of mosquito oviposition sites, and adulticiding to protect public health. However, in some regions, there has been a decline in county and municipal mosquito control programs, and homeowners increasingly contract with private mosquito control companies or address mosquito-related issues themselves at the household level. The extent to which these services are being used, the potential for mosquito and/or insecticide exposure around the home, and the access to these services by individuals of different socioeconomic categories are not known. We conducted regional (western, central, eastern) assessments of public perception and knowledge of mosquito control services in a variety of communities of different socioeconomic categories (low, moderate, high) and types (urban, suburban, rural) in 3 North Carolina counties. We also assessed the respondents' basic knowledge of mosquito-borne diseases. Most respondents thought mosquito control was important to protect against both nuisance mosquitoes and mosquito-borne disease. The majority of people would pay ≤$50/year for mosquito control and most thought this should be covered by municipal/county taxes. Many respondents (31%, 95% confidence interval [CI] 26–35%) personally undertake mosquito control on their properties, but only 5.3% (95% CI 3.1–7.5%) contract with professional mosquito control services, with no significant differences between region, community type, or socioeconomic category in the proportion using private mosquito control services. While there were significant differences between factor levels (3 regions, 3 community types, 3 socioeconomic categories) in some responses, there were no significant differences observed between respondents, regardless of factor level, in the willingness to contribute funds to a community-based mosquito control program. DA - 2017/12// PY - 2017/12// DO - 10.2987/17-6669.1 VL - 33 IS - 4 SP - 331-339 J2 - Journal of the American Mosquito Control Association LA - en OP - SN - 8756-971X 1943-6270 UR - http://dx.doi.org/10.2987/17-6669.1 DB - Crossref KW - Knowledge KW - mosquito-borne disease KW - practices ER - TY - JOUR TI - Quantifying pteridines in the heads of blow flies (Diptera: Calliphoridae): Application for forensic entomology AU - Cammack, J. A. AU - Reiskind, M. H. AU - Guisewite, L. M. AU - Denning, S. S. AU - Watson, D. W. T2 - FORENSIC SCIENCE INTERNATIONAL AB - In forensic cases involving entomological evidence, establishing the postcolonization interval (post-CI) is a critical component of the investigation. Traditional methods of estimating the post-CI rely on estimating the age of immature blow flies (Diptera: Calliphoridae) collected from remains. However, in cases of delayed discovery (e.g., when remains are located indoors), these insects may have completed their development and be present in the environment as adults. Adult fly collections are often ignored in cases of advanced decomposition because of a presumed little relevance to the investigation; herein we present information on how these insects can be of value. In this study we applied an age-grading technique to estimate the age of adults of Chrysomya megacephala (Fabricius), Cochliomyia macellaria (Fabricius), and Phormia regina (Meigen), based on the temperature-dependent accumulation of pteridines in the compound eyes, when reared at temperatures ranging from 5 to 35 °C. Age could be estimated for all species*sex*rearing temperature combinations (mean r2 ± SE: 0.90 ± 0.01) for all but P. regina reared at 5.4 °C. These models can be used to increase the precision of post-CI estimates for remains found indoors, and the high r2 values of 22 of the 24 regression equations indicates that this is a valid method for estimating the age of adult blow flies at temperatures ≥15 °C. DA - 2017/11// PY - 2017/11// DO - 10.1016/j.forsciint.2017.09.006 VL - 280 SP - 44-48 SN - 1872-6283 KW - Chrysomya megacephala KW - Cochliomyia macellaria KW - Phormia regina KW - Spectrofluorometry KW - Indoor remains ER - TY - JOUR TI - Hows, whats, and (don't forget) whos: the future of inquiry in communication, teaching, and learning AU - Dannels, Deanna P. T2 - COMMUNICATION EDUCATION AB - When our daughter was young, we would take her camping in the mountains of North Carolina, and one of the “must do’s” was always gem mining. I remember one of the first times we took her gem mining... DA - 2017/// PY - 2017/// DO - 10.1080/03634523.2017.1349918 VL - 66 IS - 4 SP - 496-499 SN - 1479-5795 ER - TY - JOUR TI - Guest editorial: CRISPRcas9: CRISPR-Cas systems: at the cutting edge of microbiology AU - Barrangou, Rodolphe AU - Bikard, David T2 - Current Opinion in Microbiology DA - 2017/6// PY - 2017/6// DO - 10.1016/j.mib.2017.09.015 VL - 37 SP - vii-viii ER - TY - JOUR TI - Functional Analysis of the Glucan Degradation Locus in Caldicellulosiruptor bescii Reveals Essential Roles of Component Glycoside Hydrolases in Plant Biomass Deconstruction AU - Conway, Jonathan M. AU - McKinley, Bennett S. AU - Seals, Nathaniel L. AU - Hernandez, Diana AU - Khatibi, Piyum A. AU - Poudel, Suresh AU - Giannone, Richard J. AU - Hettich, Robert L. AU - Williams-Rhaesa, Amanda M. AU - Lipscomb, Gina L. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT The ability to hydrolyze microcrystalline cellulose is an uncommon feature in the microbial world, but it can be exploited for conversion of lignocellulosic feedstocks into biobased fuels and chemicals. Understanding the physiological and biochemical mechanisms by which microorganisms deconstruct cellulosic material is key to achieving this objective. The glucan degradation locus (GDL) in the genomes of extremely thermophilic Caldicellulosiruptor species encodes polysaccharide lyases (PLs), unique cellulose binding proteins (tāpirins), and putative posttranslational modifying enzymes, in addition to multidomain, multifunctional glycoside hydrolases (GHs), thereby representing an alternative paradigm for plant biomass degradation compared to fungal or cellulosomal systems. To examine the individual and collective in vivo roles of the glycolytic enzymes, the six GH genes in the GDL of Caldicellulosiruptor bescii were systematically deleted, and the extents to which the resulting mutant strains could solubilize microcrystalline cellulose (Avicel) and plant biomass (switchgrass or poplar) were examined. Three of the GDL enzymes, Athe_1867 (CelA) (GH9-CBM3-CBM3-CBM3-GH48), Athe_1859 (GH5-CBM3-CBM3-GH44), and Athe_1857 (GH10-CBM3-CBM3-GH48), acted synergistically in vivo and accounted for 92% of naked microcrystalline cellulose (Avicel) degradation. However, the relative importance of the GDL GHs varied for the plant biomass substrates tested. Furthermore, mixed cultures of mutant strains showed that switchgrass solubilization depended on the secretome-bound enzymes collectively produced by the culture, not on the specific strain from which they came. These results demonstrate that certain GDL GHs are primarily responsible for the degradation of microcrystalline cellulose-containing substrates by C. bescii and provide new insights into the workings of a novel microbial mechanism for lignocellulose utilization. IMPORTANCE The efficient and extensive degradation of complex polysaccharides in lignocellulosic biomass, particularly microcrystalline cellulose, remains a major barrier to its use as a renewable feedstock for the production of fuels and chemicals. Extremely thermophilic bacteria from the genus Caldicellulosiruptor rapidly degrade plant biomass to fermentable sugars at temperatures of 70 to 78°C, although the specific mechanism by which this occurs is not clear. Previous comparative genomic studies identified a genomic locus found only in certain Caldicellulosiruptor species that was hypothesized to be mainly responsible for microcrystalline cellulose degradation. By systematically deleting genes in this locus in Caldicellulosiruptor bescii , the nuanced, substrate-specific in vivo roles of glycolytic enzymes in deconstructing crystalline cellulose and plant biomasses could be discerned. The results here point to synergism of three multidomain cellulases in C. bescii , working in conjunction with the aggregate secreted enzyme inventory, as the key to the plant biomass degradation ability of this extreme thermophile. DA - 2017/12// PY - 2017/12// DO - 10.1128/aem.01828-17 VL - 83 IS - 24 SP - SN - 1098-5336 KW - Caldicellulosiruptor KW - extreme thermophile KW - cellulose degradation KW - lignocellulose KW - glycoside hydrolase KW - cellulase ER - TY - JOUR TI - Endocrine disrupting chemicals and behavior: Re-evaluating the science at a critical turning point AU - Barrett, Emily S. AU - Patisaul, Heather B. T2 - HORMONES AND BEHAVIOR DA - 2017/11// PY - 2017/11// DO - 10.1016/j.yhbeh.2017.09.010 VL - 96 SP - A1-A6 SN - 1095-6867 ER - TY - JOUR TI - Differences in biomass and water dynamics between a cotton-peanut rotation and a sweet sorghum bioenergy crop with and without biochar and vinasse as soil amendments AU - Reyes-Cabrera, Joel AU - Leon, Ramon G. AU - Erickson, John E. AU - Rowland, Diane L. AU - Silveira, Maria L. AU - Morgan, Kelly T. T2 - FIELD CROPS RESEARCH AB - Land use conversion of row crops to bioenergy cropping systems in the southeastern United States (U.S.) creates concerns associated with water use and NO3-N leaching. Production of energy from biomass is associated with large amounts of byproducts generated during biofuel processing. Biochar and vinasse are two nutrient rich byproducts that could be land-applied to bioenergy crops to reduce reliance on synthetic fertilizer. However, effects on water dynamics of applying these byproducts to support biomass production is poorly understood, particularly when bioenergy crops replace traditional row crops. Thus, this study aimed to compare a cotton (Gossypium hirsutum L.)-peanut (Arachis hypogaea L.) rotation to sweet sorghum [Sorghum bicolor (L.) Moench] receiving annual applications of biochar and vinasse, on biomass yield, crop evapotranspiration, water use efficiency (WUE), NO3-N leaching, and soil volumetric water content. A field study was conducted from 2013 to 2015 to assess the following treatments: cotton + 150 kg N ha−1 (COT), peanut + 30 kg N ha−1 (PEA), and sweet sorghum receiving one of the following i) 30 kg N ha−1 (S30); ii) 30 kg N ha−1 + biochar (S30B); iii) 30 kg N ha−1 + vinasse (S30V); and iv) 150 kg N ha−1 (S150). Similar aboveground dry matter yields were obtained in 2013 and 2015 for cotton and all sweet sorghum treatments and were on average 19 Mg ha−1 for both years. S30 and S150 achieved similar yields. Sweet sorghum and COT exhibited the highest WUE (∼5 g kg−1). S30B increased soil moisture retention at 0–0.2 m depth 36, 29, and 24% in 2013, 2014, and 2015, respectively. Biochar incorporated at 0.15 m soil depth increased soil moisture retention down to 0.4 m. Low N rate application combined with biochar in S30B could represent an alternative management practice to minimize N leaching, recycle nutrients, and increase soil water retention if sweet sorghum were to be widely adopted by farmers in the southeastern U.S. DA - 2017/12// PY - 2017/12// DO - 10.1016/j.fcr.2017.09.012 VL - 214 SP - 123-130 SN - 1872-6852 KW - Soil moisture KW - Bioenergy crops KW - Biochar KW - Vinasse KW - Cotton-peanut rotation KW - Nitrogen leaching ER - TY - JOUR TI - Characterization of ferulic acid removal from aqueous solution by H2O2-modified hydrothermal biochar produced from Chrysanthemum morifolium Ramat. cv. Chuju AU - Xie, Y. AU - Zhou, C. AU - Li, F. Y. AU - Hu, S. J. AU - Zhang, Z. L. AU - Zhang, Z. AU - Wang, J. F. AU - Kong, W. F. T2 - Fresenius Environmental Bulletin DA - 2017/// PY - 2017/// VL - 26 IS - 12 SP - 7478-7491 ER - TY - JOUR TI - CRISPR-based engineering of next-generation lactic acid bacteria AU - Hidalgo-Cantabrana, Claudio AU - O'Flaherty, Sarah AU - Barrangou, Rodolphe T2 - CURRENT OPINION IN MICROBIOLOGY AB - The advent of CRISPR-based technologies has opened new avenues for the development of next-generation food microorganisms and probiotics with enhanced functionalities. Building off two decades of functional genomics studies unraveling the genetic basis for food fermentations and host–probiotic interactions, CRISPR technologies offer a wide range of opportunities to engineer commercially-relevant Lactobacillus and Bifidobacteria. Endogenous CRISPR–Cas systems can be repurposed to enhance gene expression or provide new features to improve host colonization and promote human health. Alternatively, engineered CRISPR–Cas systems can be harnessed to genetically modify probiotics and enhance their therapeutic potential to deliver vaccines or modulate the host immune response. DA - 2017/6// PY - 2017/6// DO - 10.1016/j.mib.2017.05.015 VL - 37 SP - 79-87 SN - 1879-0364 ER - TY - JOUR TI - Animal Models in Tissue Engineering. Part I AU - Piedrahita, Jorge A. AU - Williams, J. Koudy T2 - Tissue Engineering Part C: Methods AB - Animal models play a central and pivotal role in tissue engineering. Although advances in areas such as 3D printing and bioreactor technologies now permit the in vitro development and testing of complex scaffold/cell composites, in vivo testing remains critical not only for refining methods being developed but also for the critical efficacy and safety testing required for regulatory approval. Yet, choosing the appropriate model for a particular application remains a challenge, as each model has its own strengths and weaknesses. In some cases, there are size issues to contend with as scale-up of a 3D structure brings with it considerable challenges with regard to diffusion, infiltration, and structural forces. In others, physiological differences between species make selection of the appropriate animal model that best represents the human disease or injury critical. DA - 2017/11// PY - 2017/11// DO - 10.1089/ten.tec.2017.0402 VL - 23 IS - 11 SP - 641-642 J2 - Tissue Engineering Part C: Methods LA - en OP - SN - 1937-3384 1937-3392 UR - http://dx.doi.org/10.1089/ten.TEC.2017.0402 DB - Crossref KW - animal models KW - tissue engineering KW - regenerative medicine ER - TY - JOUR TI - Trails and Trials in Biotechnology Policy AU - Kuzma, Jennifer T2 - WOMEN IN SUSTAINABLE AGRICULTURE AND FOOD BIOTECHNOLOGY: KEY ADVANCES AND PERSPECTIVES ON EMERGING TOPICS AB - In this chapter, I reflect on my transition from natural science work in biochemistry and biotechnology to becoming a professor in the social and policy sciences. I discuss how I’ve viewed biotechnology policy from standpoints of ethics and philosophy, biochemistry and molecular biology, risk analysis, science and technology policy, and the social sciences. The “trails” of each period of this career have informed my recent work on the policy “trials” or controversies surrounding governance of emerging technologies, including agricultural biotechnology. At this critical juncture of enormous advances in biotechnology (e.g. synthetic biology, gene editing, and gene drives), I end the chapter with a plea for each of us to recognize our own biases and respect the viewpoints of others. I hope to see the current biotechnology revolution shaped by many different viewpoints, so it is done in the best interest of all of society. Only then will we be able to move past the inflamed and divisive rhetoric and enable safe, responsible, socially-desirable and appropriate use of genetic engineering. DA - 2017/// PY - 2017/// DO - 10.1007/978-3-319-52201-2_6 SP - 85-96 SN - 2509-6427 ER - TY - JOUR TI - The triple response assay and its use to characterize ethylene mutants in Arabidopsis AU - Merchante, C. AU - Stepanova, A. N. T2 - Ethylene signaling: methods and protocols DA - 2017/// PY - 2017/// VL - 1573 SP - 163-209 ER - TY - JOUR TI - Selection for water-soluble carbohydrate accumulation and investigation of genetic x environment interactions in an elite wheat breeding population AU - Ovenden, Ben AU - Milgate, Andrew AU - Lisle, Chris AU - Wade, Len J. AU - Rebetzke, Greg J. AU - Holland, James B. T2 - THEORETICAL AND APPLIED GENETICS DA - 2017/11// PY - 2017/11// DO - 10.1007/s00122-017-2969-2 VL - 130 IS - 11 SP - 2445-2461 SN - 1432-2242 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85028760357&partnerID=MN8TOARS ER - TY - JOUR TI - Private protected areas, ecotourism development and impacts on local people's well-being: a review from case studies in Southern Chile AU - Serenari, Christopher AU - Peterson, M. Nils AU - Wallace, Tim AU - Stowhas, Paulina T2 - JOURNAL OF SUSTAINABLE TOURISM AB - Private protected areas (PPAs) are expanding rapidly in less-industrialized nations. This paper explores cases in Los Ríos, Chile, to understand how local people living in and near three PPAs viewed impacts of tourism development on human well-being and local governance asking: (1) Why and how do governing PPA actors engage local people in conservation and ecotourism? (2) How do local people perceive the impacts of PPAs? (3) How do perceived impacts differ between PPA ownership types and contexts? We used an Opportunities, Security and Empowerment research framework derived from local definitions of well-being. Results suggest that governing PPA actors (PPA administrations and Chilean government officials) viewed local people as threats to forest conservation goals, embraced exclusion from reserve governance, but encouraged self-governance among local people through educational campaigns promoting environmental stewardship and ecotourism entrepreneurship. PPA administrations avoided emerging participatory democracy approaches to ensure local resistance did not threaten their authority. Despite asymmetrical power relations, PPA–community partnerships were viewed locally as both improving and damaging well-being. Our findings suggest that the social impacts and consequences of PPAs facilitating ecotourism development should be subjected to the same level of scrutiny that has been given to public protected areas. DA - 2017/// PY - 2017/// DO - 10.1080/09669582.2016.1178755 VL - 25 IS - 12 SP - 1792-1810 SN - 1747-7646 KW - Chile KW - ecotourism KW - private protected area KW - sustainable development KW - well-being ER - TY - JOUR TI - Local Adaptation in Trinidadian Guppies Alters Stream Ecosystem Structure at Landscape Scales despite High Environmental Variability AU - Simon, Troy N. AU - Bassar, Ronald D. AU - Binderup, Andrew J. AU - Flecker, Alex S. AU - Freeman, Mary C. AU - Gilliam, James F. AU - Marshall, Michael C. AU - Thomas, Steven A. AU - Travis, Joseph AU - Reznick, David N. AU - Pringle, Catherine M. T2 - COPEIA AB - While previous studies have shown that evolutionary divergence alters ecological processes in small-scale experiments, a major challenge is to assess whether such evolutionary effects are important in natural ecosystems at larger spatial scales. At the landscape scale, across eight streams in the Caroni drainage, we found that the presence of locally adapted populations of guppies (Poecilia reticulata) is associated with reduced algal biomass and increased invertebrate biomass, while the opposite trends were true in streams with experimentally introduced populations of non-locally adapted guppies. Exclusion experiments conducted in two separate reaches of a single stream showed that guppies with locally adapted phenotypes significantly reduced algae with no effect on invertebrates, while non-adapted guppies had no effect on algae but significantly reduced invertebrates. These divergent effects of phenotype on stream ecosystems are comparable in strength to the effects of abiotic factors (e.g., light) known to be important drivers of ecosystem condition. They also corroborate the results of previous experiments conducted in artificial streams. Our results demonstrate that local adaptation can produce phenotypes with significantly different effects in natural ecosystems at a landscape scale, within a tropical watershed, despite high variability in abiotic factors: five of the seven physical and chemical parameters measured across the eight study streams varied by more than one order of magnitude. Our findings suggest that ecosystem structure is, in part, an evolutionary product and not simply an ecological pattern. DA - 2017/9// PY - 2017/9// DO - 10.1643/ce-16-517 VL - 105 IS - 3 SP - 504-513 SN - 1938-5110 ER - TY - JOUR TI - Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals AU - Theilmann, Mia C. AU - Goh, Yong Jun AU - Nielsen, Kristian Fog AU - Klaenhammer, Todd R. AU - Barrangou, Rodolphe AU - Abou Hachem, Maher T2 - MBIO AB - ABSTRACT Therapeutically active glycosylated phytochemicals are ubiquitous in the human diet. The human gut microbiota (HGM) modulates the bioactivities of these compounds, which consequently affect host physiology and microbiota composition. Despite a significant impact on human health, the key players and the underpinning mechanisms of this interplay remain uncharacterized. Here, we demonstrate the growth of Lactobacillus acidophilus on mono- and diglucosyl dietary plant glycosides (PGs) possessing small aromatic aglycones. Transcriptional analysis revealed the upregulation of host interaction genes and identified two loci that encode phosphotransferase system (PTS) transporters and phospho-β-glucosidases, which mediate the uptake and deglucosylation of these compounds, respectively. Inactivating these transport and hydrolysis genes abolished or severely reduced growth on PG, establishing the specificity of the loci to distinct groups of PGs. Following intracellular deglucosylation, the aglycones of PGs are externalized, rendering them available for absorption by the host or for further modification by other microbiota taxa. The PG utilization loci are conserved in L. acidophilus and closely related lactobacilli, in correlation with versatile growth on these compounds. Growth on the tested PG appeared more common among human gut lactobacilli than among counterparts from other ecologic niches. The PGs that supported the growth of L. acidophilus were utilized poorly or not at all by other common HGM strains, underscoring the metabolic specialization of L. acidophilus . These findings highlight the role of human gut L. acidophilus and select lactobacilli in the bioconversion of glycoconjugated phytochemicals, which is likely to have an important impact on the HGM and human host. IMPORTANCE Thousands of therapeutically active plant-derived compounds are widely present in berries, fruits, nuts, and beverages like tea and wine. The bioactivity and bioavailability of these compounds, which are typically glycosylated, are altered by microbial bioconversions in the human gut. Remarkably, little is known about the bioconversion of PGs by the gut microbial community, despite the significance of this metabolic facet to human health. Our work provides the first molecular insights into the metabolic routes of diet relevant and therapeutically active PGs by Lactobacillus acidophilus and related human gut lactobacilli. This taxonomic group is adept at metabolizing the glucoside moieties of select PG and externalizes their aglycones. The study highlights an important role of lactobacilli in the bioconversion of dietary PG and presents a framework from which to derive molecular insights into their metabolism by members of the human gut microbiota. DA - 2017/// PY - 2017/// DO - 10.1128/mbio.01421-17 VL - 8 IS - 6 SP - SN - 2150-7511 UR - https://doi.org/10.1128/mBio.01421-17 KW - Lactobacillus KW - beta-glucoside KW - bioavailability KW - gut microbiota KW - phytochemical KW - polydatin KW - polyphenols KW - resveratrol KW - xenobiotic metabolism ER - TY - JOUR TI - Higher yields and lower methane emissions with new rice cultivars AU - Jiang, Yu AU - Groenigen, Kees Jan AU - Huang, Shan AU - Hungate, Bruce A. AU - Kessel, Chris AU - Hu, Shuijin AU - Zhang, Jun AU - Wu, Lianhai AU - Yan, Xiaojun AU - Wang, Lili AU - Chen, Jin AU - Hang, Xiaoning AU - Zhang, Yi AU - Horwath, William R. AU - Ye, Rongzhong AU - Linquist, Bruce A. AU - Song, Zhenwei AU - Zheng, Chengyan AU - Deng, Aixing AU - Zhang, Weijian T2 - GLOBAL CHANGE BIOLOGY AB - Abstract Breeding high‐yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane ( CH 4 ) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high‐yielding rice cultivars actually reduce CH 4 emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH 4 emissions in a soil with a high carbon (C) content. Compared to a low‐yielding cultivar, a high‐yielding cultivar significantly increased root porosity and the abundance of methane‐consuming microorganisms, suggesting that the larger and more porous root systems of high‐yielding cultivars facilitated CH 4 oxidation by promoting O 2 transport to soils. Our results were further supported by a meta‐analysis, showing that high‐yielding rice cultivars strongly decrease CH 4 emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH 4 emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high‐yielding cultivars can substantially mitigate paddy CH 4 emission in China and other rice growing regions. DA - 2017/11// PY - 2017/11// DO - 10.1111/gcb.13737 VL - 23 IS - 11 SP - 4728-4738 SN - 1365-2486 KW - meta-analysis KW - methanogenesis KW - methanotrophy KW - roots KW - soil carbon ER - TY - JOUR TI - Factors Associated With Willingness to Plant Non-Bt Maize Refuge and Suggestions for Increasing Refuge Compliance AU - Reisig, Dominic D. T2 - JOURNAL OF INTEGRATED PEST MANAGEMENT AB - Southern U.S. growers who plant Bt maize (Zea mays L.) must plant a separate non-Bt refuge to maintain Bt susceptibility to pests. North Carolina maize growers were surveyed for intention to plant non-Bt maize refuge, understanding of the importance of refuge, and for their perceptions on actions that would encourage refuge plantings. Identical surveys were conducted and compared before and after a short verbal presentation during 2014 on the logic and necessity of planting refuge. An identical survey was given during 2016, but without a verbal presentation and growers were not asked about actions to encourage planting of refuge. Survey responses from 2014 and 2016 were compared and 2016 survey responses were investigated for possible correlations to environmental factors, such as planted crop area and demographic factors by county. Only 38.3 to 44.3% growers indicated they were planning to plant refuge, and 22 to 29.4% were uncertain about this. Additionally, the verbal county meeting presentation did not increase grower intention to plant more refuge. Although this medium increased understanding directly following the presentation, understanding did not change two years later. Total cropland and farm size were most consistently correlated with intention to plant refuge and understanding of the importance of planting refuge. Future efforts to increase compliance and maintain Bt susceptibility in southern U.S. states like North Carolina should focus on reaching smaller-sized growers. Furthermore, the seed industry could also focus on improved breeding, seed availability, and marketing efforts toward companion non-Bt refuge hybrids, as this was popular with growers. DA - 2017/1// PY - 2017/1// DO - 10.1093/jipm/pmx002 VL - 8 IS - 1 SP - SN - 2155-7470 KW - blended refuge KW - block refuge KW - resistance management KW - Helicoverpa zea ER - TY - JOUR TI - Effects of perinatal bisphenol A exposure on the volume of sexually-dimorphic nuclei of juvenile rats: A CLARITY-SPA consortium study AU - Arambula, Sheryl E. AU - Fuchs, Joelle AU - Cao, Jinyan AU - Patisaul, Heather B. T2 - NEUROTOXICOLOGY AB - Bisphenol A (BPA) is a high volume endocrine disrupting chemical found in a wide variety of products including plastics and epoxy resins. Human exposure is nearly ubiquitous, and higher in children than adults. Because BPA has been reported to interfere with sex steroid hormone signaling, there is concern that developmental exposure, even at levels below the current FDA No Observed Adverse Effect Level (NOAEL) of 5mg/kg body weight (bw)/day, can disrupt brain sexual differentiation. The current studies were conducted as part of the CLARITY-BPA (Consortium Linking Academic and Regulatory Insights on BPA Toxicity) program and tested the hypothesis that perinatal BPA exposure would induce morphological changes in hormone sensitive, sexually dimorphic brain regions. Sprague-Dawley rats were randomly assigned to 5 groups: BPA (2.5, 25, or 2500μg/kgbw/day), a reference estrogen (0.5μg ethinylestradiol (EE2)/kgbw/day), or vehicle. Exposure occurred by gavage to the dam from gestational day 6 until parturition, and then to the offspring from birth through weaning. Unbiased stereology was used to quantify the volume of the sexually dimorphic nucleus (SDN), the anteroventral periventricular nucleus (AVPV), the posterodorsal portion of the medial amygdala (MePD), and the locus coeruleus (LC) at postnatal day 28. No appreciable effects of BPA were observed on the volume of the SDN or LC. However, AVPV volume was enlarged in both sexes, even at levels below the FDA NOAEL. Collectively, these data suggest the developing brain is vulnerable to endocrine disruption by BPA at exposure levels below previous estimates by regulatory agencies. DA - 2017/12// PY - 2017/12// DO - 10.1016/j.neuro.2017.09.002 VL - 63 SP - 33-42 SN - 1872-9711 KW - Bisphenol A KW - Brain KW - Hypothalamus KW - Amygdala KW - Locus coeruleus KW - Sexually dimorphic ER - TY - JOUR TI - Differential Expression Profile of lncRNAs from Primary Human Hepatocytes Following DEET and Fipronil Exposure AU - Mitchell, Robert D., III AU - Wallace, Andrew D. AU - Hodgson, Ernest AU - Roe, R. Michael T2 - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES AB - While the synthesis and use of new chemical compounds is at an all-time high, the study of their potential impact on human health is quickly falling behind, and new methods are needed to assess their impact. We chose to examine the effects of two common environmental chemicals, the insect repellent N,N-diethyl-m-toluamide (DEET) and the insecticide fluocyanobenpyrazole (fipronil), on transcript levels of long non-protein coding RNAs (lncRNAs) in primary human hepatocytes using a global RNA-Seq approach. While lncRNAs are believed to play a critical role in numerous important biological processes, many still remain uncharacterized, and their functions and modes of action remain largely unclear, especially in relation to environmental chemicals. RNA-Seq showed that 100 µM DEET significantly increased transcript levels for 2 lncRNAs and lowered transcript levels for 18 lncRNAs, while fipronil at 10 µM increased transcript levels for 76 lncRNAs and decreased levels for 193 lncRNAs. A mixture of 100 µM DEET and 10 µM fipronil increased transcript levels for 75 lncRNAs and lowered transcript levels for 258 lncRNAs. This indicates a more-than-additive effect on lncRNA transcript expression when the two chemicals were presented in combination versus each chemical alone. Differentially expressed lncRNA genes were mapped to chromosomes, analyzed by proximity to neighboring protein-coding genes, and functionally characterized via gene ontology and molecular mapping algorithms. While further testing is required to assess the organismal impact of changes in transcript levels, this initial analysis links several of the dysregulated lncRNAs to processes and pathways critical to proper cellular function, such as the innate and adaptive immune response and the p53 signaling pathway. DA - 2017/10// PY - 2017/10// DO - 10.3390/ijms18102104 VL - 18 IS - 10 SP - SN - 1422-0067 KW - DEET KW - fipronil KW - long non-coding RNA KW - lncRNA KW - primary liver cells KW - epigenetics KW - RNA-Seq KW - transcriptomics KW - Zika virus KW - human hepatocytes ER - TY - JOUR TI - An Empirical Agent-Based Model to Simulate the Adoption of Water Reuse Using the Social Amplification of Risk Framework AU - Kandiah, Venu AU - Binder, Andrew R. AU - Berglund, Emily Z. T2 - RISK ANALYSIS AB - Abstract Water reuse can serve as a sustainable alternative water source for urban areas. However, the successful implementation of large‐scale water reuse projects depends on community acceptance. Because of the negative perceptions that are traditionally associated with reclaimed water, water reuse is often not considered in the development of urban water management plans. This study develops a simulation model for understanding community opinion dynamics surrounding the issue of water reuse, and how individual perceptions evolve within that context, which can help in the planning and decision‐making process. Based on the social amplification of risk framework, our agent‐based model simulates consumer perceptions, discussion patterns, and their adoption or rejection of water reuse. The model is based on the “risk publics” model, an empirical approach that uses the concept of belief clusters to explain the adoption of new technology. Each household is represented as an agent, and parameters that define their behavior and attributes are defined from survey data. Community‐level parameters—including social groups, relationships, and communication variables, also from survey data—are encoded to simulate the social processes that influence community opinion. The model demonstrates its capabilities to simulate opinion dynamics and consumer adoption of water reuse. In addition, based on empirical data, the model is applied to investigate water reuse behavior in different regions of the United States. Importantly, our results reveal that public opinion dynamics emerge differently based on membership in opinion clusters, frequency of discussion, and the structure of social networks. DA - 2017/10// PY - 2017/10// DO - 10.1111/risa.12760 VL - 37 IS - 10 SP - 2005-2022 SN - 1539-6924 UR - https://publons.com/publon/21063762/ KW - Acceptance-resistance KW - agent-based model KW - opinion dynamics KW - risk perceptions KW - social amplification of risk KW - water reuse ER - TY - JOUR TI - A Filter Method for Improved Monitoring of Drosophila suzukii (Diptera: Drosophilidae) Larvae in Fruit AU - Van Timmeren, Steven AU - Diepenbrock, Lauren M. AU - Bertone, Matthew A. AU - Burrack, Hannah J. AU - Isaacs, Rufus T2 - JOURNAL OF INTEGRATED PEST MANAGEMENT AB - Drosophila suzukii Matsumura (Diptera: Drosophilidae) has become a major economic pest of soft-skinned fruits since it was detected in North America in 2008. Control of this fly is achieved through insecticide sprays applied when ripening or ripe fruit are present. Monitoring to aid informed management decisions is challenging since trapping for adults is not a reliable indicator of potential or existing infestation in the fruit. Moreover, current larval monitoring techniques using brown sugar or salt solutions allow for visual detection of late-instar larvae, but they are time consuming and tend to miss smaller larvae. Here, we describe a method combining a salt solution, coffee filter, and microscope that can reliably and efficiently detect small and large larvae of D. suzukii in fruit samples. By sifting the sample liquid through an inexpensive coffee filter, larvae of all instars can be counted quickly and accurately. This method is 1.7 times faster than using a visual tray-based method and can detect more larvae because first instar larvae can be detected. Growers can use this information to target insecticide sprays for curative control of small larvae, identify fields where the presence of larger larvae may indicate an unmarketable crop, or verify that no infestation exists and control programs are working. We provide images to support larval identification of this pest, and we expect this method will become an important component of rebuilding IPM programs in fruit crops affected by D. suzukii. DA - 2017/1// PY - 2017/1// DO - 10.1093/jipm/pmx019 VL - 8 IS - 1 SP - SN - 2155-7470 KW - Spotted wing Drosophila KW - SWD KW - monitoring KW - salt flotation KW - larval sampling ER - TY - JOUR TI - Review of research advances in the screwworm eradication program over the past 25 years AU - Scott, Maxwell J. AU - Concha, Carolina AU - Welch, John B. AU - Phillips, Pamela L. AU - Skoda, Steven R. T2 - Entomologia Experimentalis et Applicata AB - Abstract New World screwworms, C ochliomyia hominivorax ( C oquerel) ( D iptera: C alliphoridae: C hrysomyinae), are devastating pests of warm‐blooded animals that cause significant economic damage to livestock. The successful campaign to eradicate screwworms from continental N orth A merica, led by the US Department of Agriculture and using the sterile insect technique, continues to receive research support that has resulted in improved technologies for all aspects of the program. The process and ingredients for mass‐rearing screwworms is more efficient and sustainable, and there is now a standardized protocol for developing new strains used in mass rearing. Cryopreservation of screwworm embryos allows strains to be preserved and recovered if necessary and also reduces rearing requirements for backup and research strains. Sterile fly release procedures and equipment have been updated leading to optimized sterile fly release rates. Surveillance for screwworm infestations and outbreaks have incorporated new trap designs, habitat analysis, and molecular genetic techniques that enhance monitoring the progress of the program as well as early detection and response to outbreaks. Genetic analyses of screwworm populations across their current range have increased the understanding of genetic differentiation, which may aide in developing new strains and determining the geographic origin of screwworms causing outbreaks when they occur. The ability to release only sterile males, which has been a goal of the program for over 60 years, has recently been accomplished through the development of transgenic sexing strains. The strains carry a conditional female lethal gene and are comparable to the wild‐type strain for several biological parameters that are important for mass production and performance in the field. The strains should improve efficiency of population suppression of the current and future eradication and prevention programs against screwworms. These research advances as well as future considerations are presented. DA - 2017/8/30/ PY - 2017/8/30/ DO - 10.1111/eea.12607 VL - 164 IS - 3 SP - 226-236 J2 - Entomologia Exp Applicata LA - en OP - SN - 0013-8703 1570-7458 UR - http://dx.doi.org/10.1111/eea.12607 DB - Crossref KW - New World screwworm KW - Cochliomyia hominivorax KW - Diptera KW - Calliphoridae KW - Chrysomyinae KW - sterile insect technique KW - SIT KW - insect mass rearing KW - obligate myiasis KW - insect genetics KW - male-only strains KW - insect surveillance ER - TY - JOUR TI - Poultry Feather Meal Application in Organic Flue-Cured Tobacco Production AU - Vann, Matthew AU - Bennett, Nathan AU - Fisher, Loren AU - Reberg-Horton, S. C. AU - Burrack, Hannah T2 - AGRONOMY JOURNAL AB - Core Ideas Poultry feather meal is acceptable in organic flue‐cured tobacco production. Application rates of organic N should reflect those in conventional production. Soil moisture is critical for N mineralization and assimilation. Information on N management in organic flue‐cured tobacco production is limited. Research was conducted from 2012–2013 to determine the effects of two certified organic N sources applied at three rates on the yield, quality, and chemical constituents of flue‐cured tobacco. These organic N sources included Nature Safe 13–0–0 (NS) and Nutrimax 12–1–0 (NM), both of which consisted of hydrolyzed poultry feather meal. Application rates for both fertilizer sources were 17 kg N ha −1 above recommendation (B+), at recommendation (B), and 17 kg N ha −1 below recommendation (B–). A conventional control containing urea‐ammonium‐nitrate (UAN) was applied at the B application rate. Tobacco yield and quality were similar among conventional and organic N programs. Leaf N concentration, SPAD measurements at flowering, and total alkaloid concentration of cured leaves responded positively to increased N application rates, regardless of organic fertilizer source. The largest increases in nitrogenous‐based leaf constituents were observed in this study where B+ treatments were applied; however, those increases did not translate into increased leaf yield or quality and could delay the initiation of leaf senescence in growing seasons with low soil moisture. Results from this study demonstrate the acceptability of poultry feather meal sources for organic tobacco production, and confirm that application rates of organic N sources should follow conventional recommendations. DA - 2017/// PY - 2017/// DO - 10.2134/agronj2017.05.0287 VL - 109 IS - 6 SP - 2800-2807 SN - 1435-0645 ER - TY - JOUR TI - Multirate digital signal processing AU - Alexander, W. E. AU - Williams, C. M. T2 - Digital Signal Processing: Principles, Algorithms and System Design DA - 2017/// PY - 2017/// SP - 389-454 ER - TY - JOUR TI - Longitudinal Study of the Effects of Environmental pH on the Mechanical Properties of Aspergillus niger AU - Zeng, Wenjun AU - Yang, Hua AU - Xuan, Guanghui AU - Dai, Letian AU - Hu, Yunxiao AU - Hu, Shuijin AU - Zhong, Shengkui AU - Li, Zhen AU - Gao, Mingyuan AU - Wang, Shimei AU - Feng, Yuan T2 - ACS BIOMATERIALS SCIENCE & ENGINEERING AB - The regulation of environmental pH is key to the health of an ecosystem, influencing the metabolic activity, growth, and development of organisms within it. Although pH values can be measured by a wide range of readily available technologies ranging from fluorescent dyes and nanosensors, these cannot reveal the history of environmental pH from before monitoring begins. This information is sometimes crucial for piecing together what has happened to an ecosystem, and our long-term goal is therefore to develop technologies capable of obtaining it. Here, we propose monitoring environmental pH over time by tracking mechanical properties of a common fungus. As a first step toward obtaining a time history of pH, we evaluate the effect of pH upon the effective indentation modulus of spores and hyphae of Aspergillus niger. We report that the indentation modulus of this phosphorus-solubilizing fungus, obtained through atomic force microscopy and nanoindentation, correlated with environmental acidity. We observed a significant, monotonic increase in moduli over the course of incubation in an acidic environment, but no change in moduli over time for incubation in a neutral environment. Results show promise for using our scheme to detect and track environmental pH over time, and more broadly for using a microorganism’s mechanical properties as a biomarker for environmental detection. DA - 2017/11// PY - 2017/11// DO - 10.1021/acsbiomaterials.6b00294 VL - 3 IS - 11 SP - 2974-2979 SN - 2373-9878 KW - nano indentation KW - Young's modulus KW - environment KW - pH KW - biomarker ER - TY - JOUR TI - Linkage map construction and QTL analysis for internal heat necrosis in autotetraploid potato AU - Schumann, Mitchell J. AU - Zeng, Zhao-Bang AU - Clough, Mark E. AU - Yencho, G. Craig T2 - Theoretical and Applied Genetics DA - 2017/6/26/ PY - 2017/6/26/ DO - 10.1007/s00122-017-2941-1 VL - 130 IS - 10 SP - 2045-2056 J2 - Theor Appl Genet LA - en OP - SN - 0040-5752 1432-2242 UR - http://dx.doi.org/10.1007/s00122-017-2941-1 DB - Crossref ER - TY - JOUR TI - Introduction to digital signal processing AU - Alexander, W. E. AU - Williams, C. M. T2 - Digital Signal Processing: Principles, Algorithms and System Design DA - 2017/// PY - 2017/// SP - 1-17 ER - TY - JOUR TI - Implementation of discrete time systems AU - Alexander, W. E. AU - Williams, C. M. T2 - Digital Signal Processing: Principles, Algorithms and System Design DA - 2017/// PY - 2017/// SP - 277-350 ER - TY - JOUR TI - Hardware implementation AU - Alexander, W. E. AU - Williams, C. M. T2 - Digital Signal Processing: Principles, Algorithms and System Design DA - 2017/// PY - 2017/// SP - 519-561 ER - TY - JOUR TI - Fundamental DSP concepts AU - Alexander, W. E. AU - Williams, C. M. T2 - Digital Signal Processing: Principles, Algorithms and System Design DA - 2017/// PY - 2017/// SP - 19-157 ER - TY - JOUR TI - Frequency domain analysis AU - Alexander, W. E. AU - Williams, C. M. T2 - Digital Signal Processing: Principles, Algorithms and System Design DA - 2017/// PY - 2017/// SP - 159-204 ER - TY - JOUR TI - Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem AU - Wendrich, Jos R. AU - Moller, Barbara K. AU - Li, Song AU - Saiga, Shunsuke AU - Sozzani, Rosangela AU - Benfey, Philip N. AU - De Rybel, Bert AU - Weijers, Dolf T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem, a group of slowly dividing quiescent center cells is thought to limit stem cell activity to directly neighboring cells, thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction to the more gradual changes in cell division potential and differentiation that occur as cells move further away from the quiescent center. To address this paradox and to infer molecular organization of the root meristem, we used a whole-genome approach to determine dominant transcriptional patterns along root ontogeny zones. We found that the prevalent patterns are expressed in two opposing gradients. One is characterized by genes associated with development, the other enriched in differentiation genes. We confirmed these transcript gradients, and demonstrate that these translate to gradients in protein accumulation and gradual changes in cellular properties. We also show that gradients are genetically controlled through multiple pathways. Based on these findings, we propose that cells in the Arabidopsis root meristem gradually transition from stem cell activity toward differentiation. DA - 2017/10/17/ PY - 2017/10/17/ DO - 10.1073/pnas.1707400114 VL - 114 IS - 42 SP - E8922-E8929 SN - 0027-8424 KW - plant development KW - root meristem KW - Arabidopsis KW - transcriptional regulation ER - TY - JOUR TI - Finite Word Length Effects AU - Alexander, Winser E. AU - Williams, Cranos M. AU - Alexander, WE AU - Williams, CM T2 - DIGITAL SIGNAL PROCESSING: PRINCIPLES, ALGORITHMS AND SYSTEM DESIGN AB - Chapter 6 covers methods used to represent numbers and the impact of the use of finite precision arithmetic for the implementation of discrete time systems. It discusses the representation of numbers using the IEEE floating point representation, computational errors due to rounding, and the multiplication of numbers that are represented using floating point. It covers the analytical basis for the two's complement representation of numbers and computational procedures for numbers represented using two's complement numbers. It covers the scaling of the coefficients for discrete time systems for given word sizes and for a restriction to avoid over ow during computations. It also presents a concept for statistical analysis of rounding errors due to word length effects. DA - 2017/// PY - 2017/// DO - 10.1016/b978-0-12-804547-3.00006-1 SP - 351-388 ER - TY - JOUR TI - Digital signal processing: principles, algorithms and system design preface AU - Alexander, W. E. AU - Williams, C. M. T2 - Digital Signal Processing: Principles, Algorithms and System Design DA - 2017/// PY - 2017/// SP - XXVII- ER - TY - JOUR TI - Digital signal processing systems design AU - Alexander, W. E. AU - Williams, C. M. T2 - Digital Signal Processing: Principles, Algorithms and System Design DA - 2017/// PY - 2017/// SP - 455-517 ER - TY - JOUR TI - Design of digital filters AU - Alexander, W. E. AU - Williams, C. M. T2 - Digital Signal Processing: Principles, Algorithms and System Design DA - 2017/// PY - 2017/// SP - 205-275 ER - TY - JOUR TI - A cooperative governance network for crop genome editing AU - Jordan, N.R. AU - Dorn, K.M. AU - Smith, T.M. AU - Wolf, K.E. AU - Ewing, P.M. AU - Fernandez, A.L. AU - Runck, B.C. AU - Williams, A. AU - Lu, Y. AU - Kuzma, Jennifer AU - al. T2 - EMBO REPORTS AB - Science & Society19 September 2017free access A cooperative governance network for crop genome editing The success of governance networks in other areas could help to find common ground for applying genome editing in agriculture Nicholas R Jordan [email protected] orcid.org/0000-0002-9977-051X Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Kevin M Dorn Department of Plant Pathology, Kansas State University, Manhattan, KS, USA Search for more papers by this author Timothy M Smith Department of Bioproducts & Biosystems Engineering and Institute on the Environment, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Katie E Wolf Humphrey School of Public Affairs, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Patrick M Ewing Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Adria L Fernandez Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Bryan C Runck Department of Geography, Environment and Society, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Alwyn Williams Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA Search for more papers by this author You Lu Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Jennifer Kuzma Genetic Engineering and Society Center and School of Public and International Affairs, North Carolina State University, Raleigh, NC, USA Search for more papers by this author Nicholas R Jordan [email protected] orcid.org/0000-0002-9977-051X Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Kevin M Dorn Department of Plant Pathology, Kansas State University, Manhattan, KS, USA Search for more papers by this author Timothy M Smith Department of Bioproducts & Biosystems Engineering and Institute on the Environment, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Katie E Wolf Humphrey School of Public Affairs, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Patrick M Ewing Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Adria L Fernandez Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Bryan C Runck Department of Geography, Environment and Society, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Alwyn Williams Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA Search for more papers by this author You Lu Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA Search for more papers by this author Jennifer Kuzma Genetic Engineering and Society Center and School of Public and International Affairs, North Carolina State University, Raleigh, NC, USA Search for more papers by this author Author Information Nicholas R Jordan1,‡, Kevin M Dorn2,‡, Timothy M Smith3, Katie E Wolf4, Patrick M Ewing1, Adria L Fernandez1, Bryan C Runck5, Alwyn Williams1, You Lu6 and Jennifer Kuzma7 1Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA 2Department of Plant Pathology, Kansas State University, Manhattan, KS, USA 3Department of Bioproducts & Biosystems Engineering and Institute on the Environment, University of Minnesota, St. Paul, MN, USA 4Humphrey School of Public Affairs, University of Minnesota, St. Paul, MN, USA 5Department of Geography, Environment and Society, University of Minnesota, St. Paul, MN, USA 6Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA 7Genetic Engineering and Society Center and School of Public and International Affairs, North Carolina State University, Raleigh, NC, USA ‡These authors contributed equally to this work EMBO Rep (2017)18:1683-1687https://doi.org/10.15252/embr.201744394 PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Emerging biotechnologies, such as genome editing, may revolutionize agricultural development through rapid and precise genetic manipulation of a wide range of crop traits without having to transfer foreign DNA 1. If so, these new genetic-engineering (GE) technologies can help to generate crop varieties to address critical challenges in agricultural development, such as climate resilience or nutrient uptake, or diet-related problems in nutrition and health in poorer countries. However, society must also be protected from potential harmful effects of genetically manipulated crops on the environment, human health, or social welfare. Governance of these crops must therefore balance agricultural developments with risk assessment and prevention of potential harm. …genome editing is being used to improve the characteristics of major crop plants, but the governance of crop genome editing is poorly defined and developed Presently, genome editing is being used to improve the characteristics of major crop plants, but the governance of crop genome editing is poorly defined and developed. Influential groups concerned with the potential hazards of such crops view this situation with growing alarm, which has created tensions with the academic community and regulatory agencies 2. Both the USA and the European Commission are currently reviewing the governance of crops produced by genome editing and other new technologies. On the US side, at least, the review process appears unlikely to result in governance approaches that will satisfy parties that are concerned with either over- or under-regulation of such crops, and tension and conflicts about them are likely to heighten. We propose an alternative approach for governance of these crops that may help to defuse tensions and enable exploration of genome editing technologies’ potential while protecting society from harm: a cooperative governance network. Such networks have performed well in comparable situations by defining broadly acceptable sustainability criteria for commercial products and processes and establishing institutional capacity for adaptive governance and enforcement in situations where government-based regulation is neither established nor sufficient 3. Cooperative governance networks In cooperative governance networks, different societal sectors—private companies, non-profit organizations, researchers, and governmental agencies—cooperate to manage complex issues related to particular products and processes. Such networks devise and enforce rules for members, who voluntarily consent to be governed. A network's legitimacy and authority to govern stems from several factors: participation of reputable key stakeholders; heterogeneity of represented interests; and internal rule-making processes and outcomes that seek to accommodate the different interests of its participants. Importantly, such networks, if they include influential private interests and reputable civil actors, can exert influence even on actors that do not participate 3. Importantly, such networks, if they include influential private interests and reputable civil actors, can exert influence even on actors that do not participate In a number of cases—governance of coffee, fisheries, electronics, or industrial cleaning products—cooperative governance networks have emerged, competing or consolidating over time, and often converging toward a common sustainability standard. Through this dynamic process, accepted norms and practices emerge, evolve, and become codified. For example, several cooperative governance networks, organized by civil-society organizations or the private sector, have defined sustainability standards for producing coffee that address issues such as ecological conservation, community development, and fair prices for farmers. Organic (1978), Fair trade (1988), SAN/Rainforest Alliance (1995), and Bird Friendly (1996) coffee standards have largely been created by social and environmental organizations, whereas UTZ Certified (1997), Nespresso AAA (2003), and Starbucks C.A.F.E. (2004) are examples of company-led initiatives. Over time, these networks have converged around surprisingly similar goals and rhetoric for sustainable coffee. Networks organized by the private sector have typically placed more emphasis on economic and quality dimensions of performance 4, but all networks have maintained strong and visible support from advocacy and academic organizations: for instance, Nestlé-Nespresso AAA Sustainable Quality Program partners with organizations such as the International Union for Conservation of Nature (IUCN), Fair Labor Association (FLA), and Fair-trade International. Within networks, these advocacy and academic organizations have maintained independence, thereby reserving the right to publicly criticize network performance, and their continued affiliation suggests that these organizations view network participation as a means to advance their sustainability goals. In addition, UTZ and Rainforest Alliance recently announced their intentions to merge later this year in an effort to better coordinate innovations, streamline the certification process, and consolidate market power. All core sectors—investors, breeders, and agricultural organizations as noted above —would have strong incentives to participate in such assessments. Assessments of leading sustainability governance networks for organic farming (IFOAM), fair trade (FLO), sustainable agriculture (RA-SAN), sustainable forestry (FSC & FEFC), sustainable fisheries (MSC) have found evidence of beneficial environmental effects, through higher levels of adoption and implementation rates of management practices consistent with sustainability criteria 4. For social and economic aspects of sustainability, anecdotal and competitive claims of positive impacts are common: enhancements in income, market access, working and living conditions, and relationships with the wider community. However, there is little rigorous assessment of these effects, due to methodological challenges and limited research resources. A cooperative governance network for genome editing Cooperative governance networks have not yet emerged for the application of genetic engineering or synthetic biology in food and agriculture. Several precursor projects have been initiated, but none led to standard or certification schemes. Industry groups, and environmental and consumer NGOs participated in a two-year project on governance of GMOs in the USA in the early 2000s to develop consensus recommendations on regulatory policy and programs. This goal was not achieved, but the participants did agree on general principles, outcomes, and features of a regulatory system for agricultural biotechnology. … cooperative governance networks are not intended to enlist all interested stakeholders, and they cannot address all societal objections to GM technologies. Given that other governance networks have been successful in establishing standards, rules, and procedures, we propose such an experimental network to address the current tensions around genome-edited crops by developing governance structures to explore their potential role in agriculture, and manage associated risks for society. It would be constituted of voluntary representatives from three core sectors: crop-breeding companies and academic institutions, capital investors, and organizations that represent a broad range of interests in agricultural development, including governmental agencies, industry and research organizations, and NGOs concerned with environmental, human health, and social-welfare issues. The network will exert power by guiding the flow of capital to crop breeders, based on assessments of genome-edited crops that cover a wide range of cultural, social, economic and scientific perspectives, and knowledge sources. Given the explosive rate of innovation in biotechnologies, new approaches to governing their exploration and evaluation are urgently needed. Initially, the network could carry out its assessments using methods from so-called responsible innovation 5 and similar techniques. One relevant method here is narrative-based foresight analysis, which constructs scenarios of broad adoption of genome-edited crops to assess and evaluate their social, environmental, economic, ethical and cultural effects. Such analyses have proven useful in addressing a range of complex and polarizing issues 6. For example, a recent application of foresight analysis to crop development showed that expected sustainability benefits of wide adoption of new high-yield oil palm varieties might be largely negated by previously unanticipated market dynamics. Responsible innovation techniques also emphasize anticipatory and pluralistic elucidation of ethical questions about emerging innovations, as applied recently to potential applications of genome editing for de novo domestication of wild plant species. All core sectors—investors, breeders, and agricultural organizations as noted above—would have strong incentives to participate in such assessments. Investors and breeding entrepreneurs will be very interested in the ability of the network to “de-risk” novel applications of genome editing in crop plants. By closely coupling crop development with broad-based social and environmental assessment, the network will reduce the risk for investors and breeders to produce crop varieties only to see these attacked by influential NGOs. In particular, such de-risking is strongly in the interest of a growing number of so-called impact investors that are concerned with sustainability issues, societal impacts, and broad societal acceptance, in addition to financial returns. These include philanthropies such as the Gates and Buffett Foundations, wealthy individuals, and pension funds. The rapidly growing number of breeding companies that use new biotechnologies also have a strong incentive to participate so as to access funding, because most of these entrepreneurs are small firms that are likely to be capital-limited. Other organizations with different perspectives on genome editing and similar technologies would also have strong incentives to participate in a cooperative governance network. As the discourse on GMOs in food/agriculture has been taking away attention from pressing issues, food/agriculture organizations and regulatory agencies would have a shared interest in avoiding an overspill of the ongoing debate to genome editing and other emerging technologies. The network should also be relevant to NGOs that have supported or opposed current GE crops, and firms, such as retailers, that are concerned with sustainability of agricultural production. Participation enables them to address their core concerns about agricultural use of these technologies and to participate in the design, conduct, and oversight of assessments of genome-edited crops. In addition, the network may appeal to regulatory agencies that value the voluntary and market-based nature of this governance approach. In the USA, network participation by federal agencies would also position them to take regulatory action under the US Coordinating Framework, should these agencies perceive safety risks that would mandate such action 7. Initial scope of cooperative governance To increase the likelihood that the network will attract participants, it would help to limit its scope to the least intrusive and controversial application of genome editing: using site-directed nucleases to induce genetic changes that could also be achieved by non-GE crop breeding or chemical mutagenesis 8. Further, we recommend focusing on crops that would add ecological and economic diversity, rather than dominant staple crops such as maize or rice. Winter-hardy crops for temperate zones are one example of such “diversification” crops 9. Such plants grow in fall and spring, produce marketable commodities such as grains and oilseeds, and make way for crops that mainly grow in the summer. They increase productivity and sustainability and may improve resilience to climate change. Another focal point might be legumes for intercropping for smallholder farms in Africa, where opportunities have been identified for improving the food value of locally adapted landraces as well as wider adaptation of regionally marketable crops. An important application of these nitrogen-fixing plants is intercropping with maize production, which can provide major improvements in yield, soil quality and fertility, efficiency of water and fertilizer use, and nutrition for people and livestock. Many annual and perennial legume species have been used in this way, but almost all require breeding to address the trade-off between food value and the production of biomass, which is critical for their beneficial effects. These crops represent opportunities for focused, locally driven breeding projects to improve human welfare if certain contested aspects, including issues of intellectual property around traditional crops, are successfully navigated through cooperative governance. Legumes for African smallholders and winter-hardy crops for temperate zones share a common problem: There are many potential species that need to be adapted to different climates, soils, dietary needs, and production systems. Yet, public funding for such research is limited, and there is little interest by major breeding companies. We believe that focusing on site-directed nucleases and diversification crops would enhance the legitimacy and salience of a governance network for many potential participants and heighten incentives for participation. Many critics of genetic engineering are particularly concerned about the risks of transgenic crops, but may be more willing to participate in governance of genome editing of diversification crops. Entrepreneurial breeders of diversification crops are likely to be particularly interested in access to capital via participation. Impact investors are likely to view such crops as attractive targets for sustainable development. However, cooperative governance networks are not intended to enlist all interested stakeholders, and they cannot address all societal objections to GM technologies. Rather, the network should seek criteria for applying gene-editing technologies that are acceptable for a reasonably heterogeneous network of participants. If such criteria are produced, and if the network has sufficient authority to influence markets or public policy, stakeholders that choose not to participate come under pressure. They can join the network in an attempt to influence its evolution, or form a competing network to battle for the hearts and minds of influential stakeholders. A governance network must also have “teeth”, that is, the power to impose its rules on its participants. Principally, it could mean that its investors deny funding a particular project in face of an unfavorable assessment. The network's legitimacy will therefore depend on its ability and willingness to deliver verdicts based on compromise. That is, if GE skeptics are to be meaningfully involved, breeders and investors will have to accept decisions that incur costs to enhance transparency, alterations in the development process, or abandonment of certain projects. At the same time, the price for GE skeptics might include a willingness to find compromise rather than entering the process with a blanket mandate to block these technologies. A potential application of genome editing We briefly illustrate the network's assessment process as it might be applied to a winter-hardy crop that could be used to diversify temperate-zone agro-ecosystems. As noted above, such crops produce commercially valuable products, protect soil and water resources, and provide a range of other benefits. However, most of these crops have traits that limit their agricultural and commercial viability. Potentially, genome editing could be used to rapidly improve various traits to promote their wide adoption and resultant benefits. A broad-based assessment process would engage a wide range of stakeholders concerned with social, environmental, and economic sustainability in foresight analysis 9. This effort (Fig 1) begins with a framing question that highlights the characteristics of a particular winter-hardy crop itself, prior to any application of genome editing: If the crop were widely integrated into temperate-zone agriculture, what range of social, economic, environmental, and cultural effects might ensue? Figure 1. Example of deliberative scenario-based foresight analysis applied to winter-hardy crops for development via genome editingInitial analysis focuses on assessment of the crops and their effects on a broad range of biophysical, socioeconomic, and cultural dimensions. This provides the context for evaluation of merits and demerits of the use of biotechnologies to develop new crops traits. Download figure Download PowerPoint Crucially, this deliberative foresight assessment sets the stage for judging the merits and demerits of using genome editing to enhance particular traits of these crops. For example, assessment may forecast large benefits, such as improvement of soil and water resources. However, these benefits might be undermined by potential problems, such as intensified use of irrigation and agrochemicals, or damaging effects on soils and the production of other crops, or other effects of large-scale use, such as disruptions of regional hydrology. Moreover, widespread cultivation of the crop may transform agricultural economies and landscapes, with potential for societal, economic and cultural impacts. After the assessment, consideration will turn to the possible use of genome editing to enhance the benefits of extensive cultivation of the crop—or to limit problematic effects—by improving key traits. For example, genome editing might be applied to traits that affect potential weediness or to enhance traits relevant to production or end usage. Therefore, the key questions of foresight assessment are: If there are both beneficial and problematic effects of widespread cultivation of the crop, can genome editing enhance benefits and reduce undesirable effects? Are these benefits sufficient to outweigh any concerns about using genome editing or about the new crop per se? If the answers to these questions are positive and endorsed under the governing rules of the network, it would then certify the new crop for further investment. Conclusion Given the explosive rate of innovation in biotechnologies, new approaches to governing their exploration and evaluation are urgently needed. Given past successes, a cooperative governance network is a promising vehicle for mobilizing exploration of crop genome editing and may avoid further escalation of polarizing conflict about this technology in civil society. We underscore that we do not view the network as a fixed or permanent institution, but rather an intervention to manage the current situation, in which applications of genome editing to crops are rapidly increasing without consensus on how these applications should be governed. This problem was recently emphasized in a report by the US National Academies of Science, Engineering and Medicine 10, which called for tiered approaches to fill the gap left by outdated statutory definitions. A governance network could fill the earliest tier and enable the broader societal assessments suggested in the National Academies report. Of course, this approach is experimental, and it will have significant logistical challenges and costs. Implementation will require resources to convene potential participants and devise a modus operandi. However, experience with current GE crops shows that such costs must be weighed against legal, commercial, and reputational costs, and, perhaps, the suppression of agricultural innovation that would result if tension and conflict about crops produced by new agricultural biotechnologies are allowed to fester under current governance regimes. Moreover, we anticipate that successful operation of a governance network can broaden cooperation and compromise among investors, scientists, NGOs, companies, and retailers. Via network participation, these can begin to act as an “army of the willing”, to identify situations where some types of GM crops may be broadly acceptable. In turn, we believe that this success could open the door to broader consideration of when and how gene editing and other emerging biotechnologies might be acceptable in food and agriculture, generally. Conflict of interest The authors declare that they have no conflict of interest. Box 1: Further reading Droppelmann KJ, Snapp SS, Waddington SR (2017) Sustainable intensification options for smallholder maize-based farming systems in sub-Saharan Africa. Food Secur 9: 1–18 Cullis C, Kunert K (2017) Unlocking the potential of orphan legumes. J Exp Bot 68: 1895–1903 Guston DH, Sarewitz D (2002) Real-time technology assessment. Technol Soc 24: 93–109 Kearney S, Murray F, Nordan M (2014) A new vision for funding science. Available at https://ssir.org/articles/entry/a_new_vision_for_funding_science Kuzma J, Kokotovich A (2011) Renegotiating GM crop regulation. EMBO Rep 12: 883–888 Milder J, Newsom D (2015) SAN/Rainforest Alliance impacts report: evaluating the effects of the San/Rainforest Alliance certification system on farms, people, and the environment. New York, NY: SAN/RA Østerberg J, Xiang W, Olsen L, Edenbrandt A, Vedel S, Christiansen A, Landes X, Andersen M, Pagh P, Sandøe P et al (2017) Accelerating the domestication of new crops: feasibility and approaches. Trends Plant Sci 22: 373–384 Pew Initiative on Food and Biotechnology (2003) The stakeholder forum on agricultural biotechnology: an overview of the process. Available at http://www.pewtrusts.org/~/media/legacy/uploadedfiles/wwwpewtrustsorg/reports/food_and_biotechnology/pifbstakeholderforumprocesspdf.pdf Ray DK, Foley JA (2013) Increasing global crop harvest frequency: recent trends and future directions. Environ Res Lett 8: 044041 Reinecke J, Manning S, Von Hagen, O (2012) The emergence of a standards market: multiplicity of sustainability standards in the global coffee industry. Organ Stud 33: 789–812 Sedbrook J, Phippen, WB, Marks, MD (2014) New approaches to facilitate rapid domestication of a wild plant to an oilseed crop: example pennycress (Thlaspi arvense L.). Plant Sci 227: 122–132 Snir R (2014) Trends in global nanotechnology regulation: the public-private interplay. Vanderbilt J Entertain Technol Law 17: 107 Silva Dias JC (2015) Plant breeding for harmony between modern agriculture production and the environment. Agric Sci 6: 87–116 References 1. Khatodia S, Bhatotia K, Passricha N, Khurana SP, Tuteja N (2016) The CRISPR/Cas genome-editing tool: application in improvement of crops. Front Plant Sci 7: 506CrossrefPubMedWeb of Science®Google Scholar 2. Kuzma J (2016) Policy: reboot the debate on genetic engineering. Nature 531: 165–167CrossrefCASPubMedWeb of Science®Google Scholar 3. Smith TM, Fischlein M (2010) Rival private governance networks: competing to define the rules of sustainability performance. Glob Environ Change 20: 511–522CrossrefPubMedWeb of Science®Google Scholar 4. Steering Committee of the State-of-Knowledge Assessment of Standards and Certification (2012) Toward sustainability: the roles and limitations of certification. Washington, DC: RESOLVE IncGoogle Scholar 5. Schomberg RV (2013) A vision of responsible innovation. In Responsible innovation, R Owen, M Heintz, J Bessant (eds), pp 51–74. New York, NY: WileyWiley Online LibraryGoogle Scholar 6. Quay R (2010) Anticipatory governance. J Am Plann Assoc 76: 496–511CrossrefWeb of Science®Google Scholar 7. Ostp U (1986) Coordinated framework for regulation of biotechnology. Fed Reg 51: 23302–23350PubMedGoogle Scholar 8. Camacho A, Van Deynze A, Chi-Ham C, Bennett AB (2014) Genetically engineered crops that fly under the US regulatory radar. Nat Biotechnol 32: 1087–1091CrossrefCASPubMedWeb of Science®Google Scholar 9. Jordan N, Dorn K, Runck B, Ewing P, Williams A, Anderson K, Felice L, Haralson K, Goplen J, Altendorf K (2016) Sustainable commercialization of new crops for the agricultural bioeconomy. Elementa 4: 000081Google Scholar 10. National Academies of Sciences, Engineering, and Medicine (2016) Genetically engineered crops: experiences and prospects. Washington, DC: The National Academies PressGoogle Scholar Previous ArticleNext Article Read MoreAbout the coverClose modalView large imageVolume 18,Issue 10,October 2017Cover: Mitochondrial proteins are synthesised in the cytosol by soluble and mitochondria‐bound ribosomes. By electron cryo‐tomography, the clustered organisation of translating ribosomes is revealed on the mitochondrial outer membrane, depicting the spatial distribution of protein import sites. From Vicki AM Gold, Piotr Chroscicki, Piotr Bragoszewski and Agnieszka Chacinska: Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryo‐tomography. For detail, see Article on page 1786. Cover design by Dr Vicki AM Gold, University of Exeter Volume 18Issue 101 October 2017In this issue FiguresReferencesRelatedDetailsLoading ... DA - 2017/10// PY - 2017/10// DO - 10.15252/embr.201744394 VL - 18 IS - 10 SP - 1683-1687 SN - 1469-3178 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85030029022&partnerID=MN8TOARS ER - TY - JOUR TI - The Habitats Humans Provide: Factors affecting the diversity and composition of arthropods in houses AU - Leong, Misha AU - Bertone, Matthew A. AU - Savage, Amy M. AU - Bayless, Keith M. AU - Dunn, Robert R. AU - Trautwein, Michelle D. T2 - SCIENTIFIC REPORTS AB - Abstract The indoor biome is a novel habitat which recent studies have shown exhibit not only high microbial diversity, but also high arthropod diversity. Here, we analyze findings from a survey of 50 houses (southeastern USA) within the context of additional survey data concerning house and room features, along with resident behavior, to explore how arthropod diversity and community composition are influenced by physical aspects of rooms and their usage, as well as the lifestyles of human residents. We found that indoor arthropod diversity is strongly influenced by access to the outdoors and carpeted rooms hosted more types of arthropods than non-carpeted rooms. Arthropod communities were similar across most room types, but basements exhibited more unique community compositions. Resident behavior such as house tidiness, pesticide usage, and pet ownership showed no significant influence on arthropod community composition. Arthropod communities across all rooms in houses exhibit trophic structure—with both generalized predators and scavengers included in the most frequently found groups. These findings suggest that indoor arthropods serve as a connection to the outdoors, and that there is still much yet to be discovered about their impact on indoor health and the unique ecological dynamics within our homes. DA - 2017/11/10/ PY - 2017/11/10/ DO - 10.1038/s41598-017-15584-2 VL - 7 IS - 1 SP - SN - 2045-2322 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85033553350&partnerID=MN8TOARS ER - TY - JOUR TI - The Global Ant Genomics Alliance (GAGA) AU - Boomsma, J.J. AU - Brady, S.G. AU - Dunn, R.R. AU - Gadau, J. AU - Heinze, J. AU - Keller, L. AU - Moreau, C.S. AU - Sanders, N.J. AU - Schrader, L. AU - Schultz, T.R. AU - Sundström, L. AU - Ward, P.S. AU - Wcislo, W.T. AU - Zhang, G. T2 - Myrmecological News DA - 2017/// PY - 2017/// VL - 25 SP - 61-66 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85039766464&partnerID=MN8TOARS ER - TY - JOUR TI - Radiocarbon analysis reveals expanded diet breadth associates with the invasion of a predatory ant AU - Suehiro, Wataru AU - Hyodo, Fujio AU - Tanaka, Hiroshi O. AU - Himuro, Chihiro AU - Yokoi, Tomoyuki AU - Dobata, Shigeto AU - Guenard, Benoit AU - Dunn, Robert R. AU - Vargo, Edward L. AU - Tsuji, Kazuki AU - Matsuura, Kenji T2 - SCIENTIFIC REPORTS AB - Abstract Invasions are ecologically destructive and can threaten biodiversity. Trophic flexibility has been proposed as a mechanism facilitating invasion, with more flexible species better able to invade. The termite hunting needle ant Brachyponera chinensis was introduced from East Asia to the United States where it disrupts native ecosystems. We show that B. chinensis has expanded dietary breadth without shifting trophic position in its introduced range. Transect sampling of ants and termites revealed a negative correlation between the abundance of B. chinensis and the abundance of other ants in introduced populations, but this pattern was not as strong in the native range. Both termite and B. chinensis abundance were higher in the introduced range than in native range. Radiocarbon ( 14 C) analysis revealed that B. chinensis has significantly younger ‘diet age’, the time lag between carbon fixation by photosynthesis and its use by the consumer, in the introduced range than in the native range, while stable isotope analyses showed no change. These results suggest that in the introduced range B. chinensis remains a termite predator but also feeds on other consumer invertebrates with younger diet ages such as herbivorous insects. Radiocarbon analysis allowed us to elucidate cryptic dietary change associated with invasion success. DA - 2017/11/3/ PY - 2017/11/3/ DO - 10.1038/s41598-017-15105-1 VL - 7 IS - 1 SP - SN - 2045-2322 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85032802285&partnerID=MN8TOARS ER - TY - JOUR TI - Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations AU - Saville, Amanda AU - Charles, Melodi AU - Chavan, Suchitra AU - Muñoz, Miguel AU - Gómez-Alpizar, Luis AU - Ristaino, Jean Beagle T2 - Phytopathology AB - Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas. DA - 2017/12// PY - 2017/12// DO - 10.1094/phyto-02-17-0045-r VL - 107 IS - 12 SP - 1541–1548 SN - 0031-949X UR - http://dx.doi.org/10.1094/PHYTO-02-17-0045-R ER - TY - JOUR TI - Point of View: A transatlantic perspective on 20 emerging issues in biological engineering AU - Wintle, Bonnie C. AU - Boehm, Christian R. AU - Rhodes, Catherine AU - Molloy, Jennifer C. AU - Millett, Piers AU - Adam, Laura AU - Breitling, Rainer AU - Carlson, Rob AU - Casagrande, Rocco AU - Dando, Malcolm AU - Doubleday, Robert AU - Drexler, Eric AU - Edwards, Brett AU - Ellis, Tom AU - Evans, Nicholas G. AU - Hammond, Richard AU - Haseloff, Jim AU - Kahl, Linda AU - Kuiken, Todd AU - Lichman, Benjamin R. AU - Matthewman, Colette A. AU - Napier, Johnathan A. AU - Oheigeartaigh, Sean S. AU - Patron, Nicola J. AU - Perello, Edward AU - Shapira, Philip AU - Tait, Joyce AU - Takano, Eriko AU - Sutherland, William J. T2 - ELIFE AB - Advances in biological engineering are likely to have substantial impacts on global society. To explore these potential impacts we ran a horizon scanning exercise to capture a range of perspectives on the opportunities and risks presented by biological engineering. We first identified 70 potential issues, and then used an iterative process to prioritise 20 issues that we considered to be emerging, to have potential global impact, and to be relatively unknown outside the field of biological engineering. The issues identified may be of interest to researchers, businesses and policy makers in sectors such as health, energy, agriculture and the environment. DA - 2017/11/14/ PY - 2017/11/14/ DO - 10.7554/elife.30247 VL - 6 SP - SN - 2050-084X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85036477487&partnerID=MN8TOARS ER - TY - JOUR TI - Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community AU - Wang, Yi AU - Li, Chunyue AU - Tu, Cong AU - Hoyt, Greg D. AU - DeForest, Jared L. AU - Hu, Shuijin T2 - SCIENCE OF THE TOTAL ENVIRONMENT AB - Intensive tillage and high inputs of chemicals are frequently used in conventional agriculture management, which critically depresses soil properties and causes soil erosion and nonpoint source pollution. Conservation practices, such as no-tillage and organic farming, have potential to enhance soil health. However, the long-term impact of no-tillage and organic practices on soil microbial diversity and community structure has not been fully understood, particularly in humid, warm climate regions such as the southeast USA. We hypothesized that organic inputs will lead to greater microbial diversity and a more stable microbial community, and that the combination of no-tillage and organic inputs will maximize soil microbial diversity. We conducted a long-term experiment in the southern Appalachian mountains of North Carolina, USA to test these hypotheses. The results showed that soil microbial diversity and community structure diverged under different management regimes after long term continuous treatments. Organic input dominated the effect of management practices on soil microbial properties, although no-tillage practice also exerted significant impacts. Both no-tillage and organic inputs significantly promoted soil microbial diversity and community stability. The combination of no-tillage and organic management increased soil microbial diversity over the conventional tillage and led to a microbial community structure more similar to the one in an adjacent grassland. These results indicate that effective management through reducing tillage and increasing organic C inputs can enhance soil microbial diversity and community stability. DA - 2017/12/31/ PY - 2017/12/31/ DO - 10.1016/j.scitotenv.2017.07.053 VL - 609 SP - 341-347 SN - 1879-1026 KW - Microbial diversity KW - Microbial community KW - Organic farming KW - Conventional farming KW - Tillage KW - Sustainable agriculture ER - TY - JOUR TI - Investigating the Effect of Growth Phase on the Surface-Layer Associated Proteome of Lactobacillus acidophilus Using Quantitative Proteomics AU - Klotz, Courtney AU - O'Flaherty, Sarah AU - Goh, Yong Jun AU - Barrangou, Rodolphe T2 - FRONTIERS IN MICROBIOLOGY AB - Bacterial surface-layers (S-layers) are semi-porous crystalline arrays that self-assemble to form the outermost layer of some cell envelopes. S-layers have been shown to act as scaffolding structures for the display of auxiliary proteins externally. These S-layer associated proteins have recently gained attention in probiotics due to their direct physical contact with the intestinal mucosa and potential role in cell proliferation, adhesion, and immunomodulation. A number of studies have attempted to catalog the S-layer associated proteome of Lactobacillus acidophilus NCFM under a single condition. However, due to the versatility of the cell surface, we chose to employ a multiplexing-based approach with the intention of accurately contrasting multiple conditions. In this study, a previously described lithium chloride isolation protocol was used to release proteins bound to the L. acidophilus S-layer during logarithmic and early stationary growth phases. Protein quantification values were obtained via TMT (tandem mass tag) labeling combined with a triple-stage mass spectrometry (MS3) method. Results showed significant growth stage-dependent alterations to the surface-associated proteome while simultaneously highlighting the sensitivity and reproducibility of the technology. Thus, this study establishes a framework for quantifying condition-dependent changes to cell surface proteins that can easily be applied to other S-layer forming bacteria. DA - 2017/11/8/ PY - 2017/11/8/ DO - 10.3389/fmicb.2017.02174 VL - 8 SP - SN - 1664-302X KW - Lactobacillus KW - probiotic KW - cell surface KW - S-layer KW - quantitative proteomics ER - TY - JOUR TI - Insecticide Use and Breast Cancer Riskamong Farmers' Wives in the Agricultural Health Study AU - Engel, L. S. AU - Werder, E. AU - Satagopan, J. AU - Blair, A. AU - Hoppin, Jane AU - Koutros, S. AU - Lerro, C. C. AU - Sandler, D. P. AU - Alavanja, M. C. AU - Freeman, L. E. B. AU - al. T2 - ENVIRONMENTAL HEALTH PERSPECTIVES AB - Some epidemiologic and laboratory studies suggest that insecticides are related to increased breast cancer risk, but the evidence is inconsistent. Women engaged in agricultural work or who reside in agricultural areas may experience appreciable exposures to a wide range of insecticides.We examined associations between insecticide use and breast cancer incidence among wives of pesticide applicators (farmers) in the prospective Agricultural Health Study.Farmers and their wives provided information on insecticide use, demographics, and reproductive history at enrollment in 1993-1997 and in 5-y follow-up interviews. Cancer incidence was determined via cancer registries. Among 30,594 wives with no history of breast cancer before enrollment, we examined breast cancer risk in relation to the women's and their husbands' insecticide use using Cox proportional hazards regression to estimate adjusted hazard ratios (HRs) and 95% confidence intervals (CIs).During an average 14.7-y follow-up, 39% of the women reported ever using insecticides, and 1,081 were diagnosed with breast cancer. Although ever use of insecticides overall was not associated with breast cancer risk, risk was elevated among women who had ever used the organophosphates chlorpyrifos [HR=1.4 (95% CI: 1.0, 2.0)] or terbufos [HR=1.5 (95% CI: 1.0, 2.1)], with nonsignificantly increased risks for coumaphos [HR=1.5 (95% CI: 0.9, 2.5)] and heptachlor [HR=1.5 (95% CI: 0.7, 2.9)]. Risk in relation to the wives' use was associated primarily with premenopausal breast cancer. We found little evidence of differential risk by tumor estrogen receptor status. Among women who did not apply pesticides, the husband's use of fonofos was associated with elevated risk, although no exposure-response trend was observed.Use of several organophosphate insecticides was associated with elevated breast cancer risk. However, associations for the women's and husbands' use of these insecticides showed limited concordance. Ongoing cohort follow-up may help clarify the relationship, if any, between individual insecticide exposures and breast cancer risk. https://doi.org/10.1289/EHP1295. DA - 2017/9// PY - 2017/9// DO - 10.1289/ehp1295 VL - 125 IS - 9 SP - SN - 1552-9924 ER - TY - JOUR TI - Impact of growth mode, phase, and rate on the metabolic state of the extremely thermophilic archaeon Pyrococcus furiosus AU - Khatibi, Piyum A. AU - Chou, Chung-jung AU - Loder, Andrew J. AU - Zurawski, Jeffrey V. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - BIOTECHNOLOGY AND BIOENGINEERING AB - Abstract The archaeon Pyrococcus furiosus is emerging as a metabolic engineering platform for production of fuels and chemicals, such that more must be known about this organism's characteristics in bioprocessing contexts. Its ability to grow at temperatures from 70 to greater than 100°C and thereby avoid contamination, offers the opportunity for long duration, continuous bioprocesses as an alternative to batch systems. Toward that end, we analyzed the transcriptome of P. furiosus to reveal its metabolic state during different growth modes that are relevant to bioprocessing. As cells progressed from exponential to stationary phase in batch cultures, genes involved in biosynthetic pathways important to replacing diminishing supplies of key nutrients and genes responsible for the onset of stress responses were up‐regulated. In contrast, during continuous culture, the progression to higher dilution rates down‐regulated many biosynthetic processes as nutrient supplies were increased. Most interesting was the contrast between batch exponential phase and continuous culture at comparable growth rates (∼0.4 hr −1 ), where over 200 genes were differentially transcribed, indicating among other things, N‐limitation in the chemostat and the onset of oxidative stress. The results here suggest that cellular processes involved in carbon and electron flux in P. furiosus were significantly impacted by growth mode, phase and rate, factors that need to be taken into account when developing successful metabolic engineering strategies. DA - 2017/12// PY - 2017/12// DO - 10.1002/bit.26408 VL - 114 IS - 12 SP - 2947-2954 SN - 1097-0290 KW - continuous culture KW - growth phase KW - growth rate KW - hyperthermophiles KW - Pyrococcus furiosus KW - transcriptome ER - TY - JOUR TI - House Dust Endotoxin and Periphera lLeukocyte Counts: Results from Two Large Epidemiologic Studies AU - Fessler, Michael B. AU - Carnes, Megan U. AU - Salo, Paivi M. AU - Wilkerson, Jesse AU - Cohn, Richard D. AU - King, Debra AU - Hoppin, Jane A. AU - Sandler, Dale P. AU - Travlos, Greg AU - London, Stephanie J. AU - Thorne, Peter S. AU - Zeldin, Darryl C. T2 - ENVIRONMENTAL HEALTH PERSPECTIVES AB - Background: The peripheral leukocyte count is a biomarker of inflammation and is associated with human all-cause mortality. Although causes of acute leukocytosis are well-described, chronic environmental determinants of leukocyte number are less well understood. Objectives: We investigated the relationship between house dust endotoxin concentration and peripheral leukocyte counts in human subjects. Methods: The endotoxin–leukocyte relationship was evaluated by linear regression in the National Health and Nutrition Examination Survey (NHANES) 2005–2006 (n=6,254) and the Agricultural Lung Health Study (ALHS; n=1,708). In the ALHS, we tested for a gene [Toll-like Receptor 4 (TLR4), encoding the endotoxin receptor]-by-environment interaction in the endotoxin–leukocyte relationship using regression models with an interaction term. Results: There is a statistically significant, positive association between endotoxin concentration and total leukocyte number [estimated change, 0.186×103/μL (95% CI: 0.070, 0.301×103/μL) per 10-fold change in endotoxin; p=0.004) in the NHANES. Similar positive associations were found for monocytes, lymphocytes, and neutrophils. Stratified analyses revealed possible effect modification by asthma and chronic obstructive pulmonary disease. We observed similar associations in the ALHS. For total leukocytes, there was suggestive evidence in the ALHS of a gene-by-environment interaction for minor allele carrier status at the TLR4 haplotype defined by rs4986790 and rs4986791 (interaction p=0.15). Conclusions: This is, to our knowledge, the first report of an association between house dust endotoxin and leukocyte count in a national survey. The finding was replicated in a farming population. Peripheral leukocyte count may be influenced by residential endotoxin exposure in diverse settings. https://doi.org/10.1289/EHP661 DA - 2017/5// PY - 2017/5// DO - 10.1289/ehp661 VL - 125 IS - 5 SP - SN - 1552-9924 ER - TY - JOUR TI - Desizing of starch sized cotton fabrics with atmospheric pressure plasma AU - Cornelius, Carrie AU - McCord, Marian AU - Bourham, Mohamed AU - Hauser, Peter T2 - CELLULOSE DA - 2017/12// PY - 2017/12// DO - 10.1007/s10570-017-1509-1 VL - 24 IS - 12 SP - 5685-5695 SN - 1572-882X KW - Cotton KW - Starch KW - Desizing KW - Plasma ER - TY - JOUR TI - Catalytic Valorization of Lignin Using Niobium Oxide AU - Das, Lalitendu AU - Kolar, Praveen AU - Sharma-Shivappa, Ratna AU - Classen, John J. AU - Osborne, Jason A. T2 - WASTE AND BIOMASS VALORIZATION DA - 2017/12// PY - 2017/12// DO - 10.1007/s12649-016-9717-8 VL - 8 IS - 8 SP - 2673-2680 SN - 1877-265X KW - Lignin KW - Catalytic oxidation KW - Niobium oxide KW - Vanillin KW - Lattice oxygen ER - TY - JOUR TI - Using bioassays with the green peach aphid (Myzus persicae) to determine residual activity of two systemically soil-applied neonicotinoid insecticides in field-grown tobacco AU - Merchan, H. Alejandro AU - Burrack, Hannah J. T2 - INTERNATIONAL JOURNAL OF PEST MANAGEMENT AB - Duration of systemic pesticide activity under field conditions has wide implications for pest management. Our aim was to determine the duration of activity of systemic insecticides commonly used in cultivated tobacco (Nicotiana tabacum) by measuring the levels of insect infestations on field plots and effects on reproduction and survival of the green peach aphid (Myzus persicae) in controlled bioassays using field grown leaves. Plants were treated with different concentrations of two systemic neonicotinoid pesticides, imidacloprid and thiamethoxam, and grown in small field plots. Our results show that these materials are effective under field conditions against aphids for at least 13 weeks after transplant. Pesticides also affected aphid reproduction and nymph survival in bioassays, although some aphids survived on pesticide-treated leaves. We also observed that leaf age affected aphid survival. We showed that neonicotinoids were very effective against M. persicae, aphids are a useful organism to assess pesticide efficacy early in the growing season, but plant characteristics are more important than pesticide concentration in the second half of the growing season. DA - 2017/// PY - 2017/// DO - 10.1080/09670874.2016.1261202 VL - 63 IS - 4 SP - 322-330 SN - 1366-5863 KW - Green peach aphid KW - tobacco KW - neonicotinoids KW - longevity KW - bioassays ER - TY - JOUR TI - Transcriptomic response of the insect vector, Peregrinus maidis, to Maize mosaic rhabdovirus and identification of conserved responses to propagative viruses in hopper vectors AU - Martin, Kathleen M. AU - Barandoc-Alviar, Karen AU - Schneweis, Derek J. AU - Stewart, Catherine L. AU - Rotenberg, Dorith AU - Whitfield, Anna E. T2 - Virology AB - Maize mosaic virus (MMV) is a plant-pathogenic rhabdovirus that is transmitted by the corn planthopper, Peregrinus maidis, in a propagative manner. P. maidis supports long-term MMV infections with no negative effects on insect performance. To elucidate whole-body transcriptome responses to virus infection, RNA-Seq was used to examine differential gene expression of virus-infected adult insects, and libraries were prepared from replicated groups of virus-exposed insects and non-exposed insects. From the 68,003 de novo-assembled transcripts, 144 were differentially-expressed (DE) during viral infection with comparable numbers up- and down-regulated. DE transcripts with similarity to genes associated with transposable elements (i.e., RNA-directed DNA polymerases) were enriched and may represent a mechanisim for modulating virus infection. Comparison of the P. maidis DE transcripts to published propagative virus-responsive transcript databases for two other hopper vectors revealed that 16% of the DE transcripts were shared across the three systems and may represent conserved responses to propagative viruses. DA - 2017/9// PY - 2017/9// DO - 10.1016/j.virol.2017.05.019 VL - 509 SP - 71-81 J2 - Virology LA - en OP - SN - 0042-6822 UR - http://dx.doi.org/10.1016/j.virol.2017.05.019 DB - Crossref KW - Rhabdoviridae KW - Nucleorhabdovirus KW - Virus-vector interactions KW - Hemipteran KW - Planthopper KW - Transcriptomics ER - TY - JOUR TI - Tolerance in St. Augustinegrass Germplasm against Blissus insularis Barber (Hemiptera: Blissidae) AU - Milla-Lewis, Susana R. AU - Youngs, Katharine M. AU - Arrellano, Consuelo AU - Cardoza, Yasmin J. T2 - CROP SCIENCE AB - St. Augustinegrass [ Stenotaphrum secundatum (Walt.) Kuntze] is a widely used lawn grass in the southern United States due to its stoloniferous growth habit and shade tolerance. However, St. Augustinegrass is prone to thatch accumulation, which is conducive to pest problems, with the southern chinch bug ( Blissus insularis Barber, SCB) being the most economically important one. Previous work to identify additional sources of SCB resistance reported genotypes with comparatively high numbers of recovered insects but low damage ratings. This study was conducted (i) to evaluate the performance of these materials in response to varying SCB feeding densities, and (ii) to determine feeding and oviposition under no‐choice scenarios. Genotypes exposed to 0, 10, or 30 adult SCBs were evaluated after 4 wk for damage and insect survival. Significant differences were observed among genotypes. Across infestation levels, while recovered insect numbers for susceptible check ‘Seville’ and plant introductions 509038 and 509039 were not significantly different, damage ratings were significantly lower for the latter, indicating that these materials were tolerant to SCB feeding. In the no‐choice experiments, survival levels of both males and females on week 4 were significantly lower for resistant check ‘Fx10’, PI 365031, and PI 289729. These genotypes, along with PIs 291594, 300129, and 647924, showed significantly lower SCB oviposition and feeding compared with Seville. Our study was able to confirm that two PIs display tolerance to SCB feeding, and five additional PIs have antibiosis activity against adult SCB (likely antibiosis), representing sources of SCB resistance for future St. Augustinegrass breeding efforts. DA - 2017/// PY - 2017/// DO - 10.2135/cropsci2016.05.0361 VL - 57 SP - S26-S36 SN - 1435-0653 ER - TY - JOUR TI - Sex Specific Placental Accumulation and Behavioral Effects of Developmental Firemaster 550 Exposure in Wistar Rats AU - Baldwin, Kylie R. AU - Phillips, Allison L. AU - Horman, Brian AU - Arambula, Sheryl E. AU - Rebuli, Meghan E. AU - Stapleton, Heather M. AU - Patisaul, Heather B. T2 - SCIENTIFIC REPORTS AB - Firemaster® 550 (FM 550) is a commercial flame retardant mixture of brominated and organophosphate compounds applied to polyurethane foam used in furniture and baby products. Due to widespread human exposure, and structural similarities with known endocrine disruptors, concerns have been raised regarding possible toxicity. We previously reported evidence of sex specific behavioral effects in rats resulting from developmental exposure. The present study expands upon this prior finding by testing for a greater range of behavioral effects, and measuring the accumulation of FM 550 compounds in placental tissue. Wistar rat dams were orally exposed to FM 550 during gestation (0, 300 or 1000 µg/day; GD 9 - 18) for placental measurements or perinatally (0, 100, 300 or 1000 µg/day; GD 9 - PND 21) to assess activity and anxiety-like behaviors. Placental accumulation was dose dependent, and in some cases sex specific, with the brominated components reaching the highest levels. Behavioral changes were predominantly associated with a loss or reversal of sex differences in activity and anxiety-like behaviors. These findings demonstrate that environmental chemicals may sex-dependently accumulate in the placenta. That sex-biased exposure might translate to sex-specific adverse outcomes such as behavioral deficits is a possibility that merits further investigation. DA - 2017/8/2/ PY - 2017/8/2/ DO - 10.1038/s41598-017-07216-6 VL - 7 SP - SN - 2045-2322 ER - TY - JOUR TI - SPATIAL PATTERNS OF MARKET PARTICIPATION AND RESOURCE EXTRACTION: FUELWOOD COLLECTION IN NORTHERN UGANDA AU - Miteva, Daniela A. AU - Kramer, Randall A. AU - Brown, Zachary S. AU - Smith, Martin D. T2 - AMERICAN JOURNAL OF AGRICULTURAL ECONOMICS AB - Abstract While distance to markets is a key determinant of market participation for households that are dependent on natural resources, the distance to the resource stock is also essential. Thus, a household's location with respect to markets and the resource stock determines household market participation and associated resource degradation. Applying a discrete‐choice framework for fuelwood collection in a developing country, we characterize the spatial pattern of market participation regimes and forest use. All else being equal, autarkic households are closest to the forest and furthest from the market, buyer households are closest to the market and furthest from the forest, and seller households are at intermediate distances. Empirical tests based on survey data from northern Uganda support the predictions from our theoretical model. Our findings have important implications for understanding the spatial patterns of forest degradation and determining the control group when designing impact evaluations of the effectiveness of development and conservation interventions. DA - 2017/7// PY - 2017/7// DO - 10.1093/ajae/aax027 VL - 99 IS - 4 SP - 1008-1026 SN - 1467-8276 KW - Spatial model KW - household sorting KW - household production KW - transaction costs KW - fuelwood extraction KW - deforestation KW - forest degradation KW - sub-Saharan Africa KW - quasi-experimental research designs ER - TY - JOUR TI - Rules of the road for insect gene drive research and testing AU - Adelman, Zach AU - Akbari, Omar AU - Bauer, John AU - Bier, Ethan AU - Bloss, Cinnamon AU - Carter, Sarah R AU - Callender, Craig AU - Denis, Adriana Costero-Saint AU - Cowhey, Peter AU - Dass, Brinda AU - Delborne, Jason AU - Devereaux, Mary AU - Ellsworth, Peter AU - Friedman, Robert M AU - Gantz, Valentino AU - Gibson, Clark AU - Hay, Bruce A AU - Hoddle, Mark AU - James, Anthony A AU - James, Stephanie AU - Jorgenson, Lyric AU - Kalichman, Michael AU - Marshall, John AU - McGinnis, William AU - Newman, Jack AU - Pearson, Alan AU - Quemada, Hector AU - Rudenko, Larisa AU - Shelton, Anthony AU - Vinetz, Joseph M AU - Weisman, Jennifer AU - Wong, Brenda AU - Wozniak, Chris T2 - Nature Biotechnology AB - Approximately two years ago, two of us (E.B. and V.G.) demonstrated the first experimental application of CRISPR–Cas9 to 'drive' a desired trait throughout a population of fruit flies. In November 2015, this same team at the University of California, San Diego, joined with A.A.J. and others at the University of California, Irvine, to develop a CRISPR-based gene drive for population modification of the malaria vector mosquito Anopheles stephensi. A month later, a group in the United Kingdom applied a CRISPR-based gene drive to another malaria vector, Anopheles gambiae. DA - 2017/8// PY - 2017/8// DO - 10.1038/nbt.3926 VL - 35 IS - 8 SP - 716-718 J2 - Nat Biotechnol LA - en OP - SN - 1087-0156 1546-1696 UR - http://dx.doi.org/10.1038/nbt.3926 DB - Crossref ER - TY - JOUR TI - Physical access for residue-mineral interactions controls organic carbon retention in an Oxisol soil AU - Ye, Chenglong AU - Bai, Tongshuo AU - Yang, Yi AU - Zhang, Hao AU - Guo, Hui AU - Li, Zhen AU - Li, Huixin AU - Hu, Shuijin T2 - SCIENTIFIC REPORTS AB - Oxisol soils are widely distributed in the humid tropical and subtropical regions and are generally characterized with high contents of metal oxides. High metal oxides are believed to facilitate organic carbon (C) accumulation via mineral-organic C interactions but Oxisols often have low organic C. Yet, the causes that constrain organic C accumulation in Oxisol soil are not exactly clear. Here we report results from a microcosm experiment that evaluated how the quantity and size of crop residue fragments affect soil C retention in a typical Oxisol soil in southeast China. We found that there were significantly higher levels of dissolved organic C (DOC), microbial biomass C (MBC) and C accumulation in the heavy soil fraction in soil amended with fine-sized (<0.2 mm) compared with coarse-sized (5.0 mm) fragments. Attenuated total reflectance-Fourier transform infrared spectroscopy analysis further showed that fine-sized residues promoted stabilization of aliphatic C-H and carboxylic C=O compounds associated with mineral phases. In addition, correlation analysis revealed that the increased content of organic C in the heavy soil fraction was positively correlated with increased DOC and MBC. Together, these results suggest that enhancement of contact between organic materials and soil minerals may promote C stabilization in Oxisols. DA - 2017/7/24/ PY - 2017/7/24/ DO - 10.1038/s41598-017-06654-6 VL - 7 SP - SN - 2045-2322 ER - TY - JOUR TI - Infrared light detection by the hailer's organ of adult american dog ticks, Dermacentor variabilis (Ixodida: Ixodidae) AU - Mitchell, Robert D., III AU - Zhu, Jiwei AU - Carr, Ann L. AU - Dhammi, Anirudh AU - Cave, Grayson AU - Sonenshine, Daniel E. AU - Roe, R. Michael T2 - TICKS AND TICK-BORNE DISEASES AB - The Haller's organ (HO), unique to ticks and mites, is found only on the first tarsus of the front pair of legs. The organ has an unusual morphology consisting of an anterior pit (AP) with protruding sensilla and a posterior capsule (Cp). The current thinking is that the HO's main function is chemosensation analogous to the insect antennae, but the functionality of its atypical structure (exclusive to the Acari) is unexplained. We provide the first evidence that the HO allows the American dog tick, Dermacentor variabilis, to respond to infrared (IR) light. Unfed D. variabilis adults with their HOs present were positively phototactic to IR. However, when the HOs were removed, no IR response was detected. Ticks in these experiments were also attracted to white light with and without the HOs, but were only positively phototactic to white light when the ocelli (primitive eyes) were unobstructed. Covering the eyes did not prevent IR attraction. A putative TRPA1 receptor was characterized from a D. variabilis-specific HO transcriptome we constructed. This receptor was homologous to transient receptor potential cation channel, subfamily A, member 1 (TRPA1) from the pit organ of the pit viper, python, and boa families of snakes, the only receptor identified so far for IR detection. HO scanning electron microscopy (SEM) studies in the American dog tick showed the AP and Cp but also novel structures not previously described; the potential role of these structures in IR detection is discussed. The ability of ticks to use IR for host finding is consistent with their obligatory hematophagy and has practical applications in tick trapping and the development of new repellents. DA - 2017/// PY - 2017/// DO - 10.1016/j.ttbdis.2017.06.001 VL - 8 IS - 5 SP - 764-771 SN - 1877-9603 KW - American dog tick KW - Dermacentor variabilis KW - Haller's organ KW - Infrared KW - TRPA1 KW - Light ER - TY - JOUR TI - Heat tolerance predicts the importance of species interaction effects as the climate changes AU - Diamond, Sarah E. AU - Chick, Lacy AU - Penick, Clint A. AU - Nichols, Lauren M. AU - Cahan, Sara Helms AU - Dunn, Robert R. AU - Ellison, Aaron M. AU - Sandersk, Nathan J. AU - Gotelli, Nicholas J. T2 - INTEGRATIVE AND COMPARATIVE BIOLOGY AB - Few studies have quantified the relative importance of direct effects of climate change on communities versus indirect effects that are mediated thorough species interactions, and the limited evidence is conflicting. Trait-based approaches have been popular in studies of climate change, but can they be used to estimate direct versus indirect effects? At the species level, thermal tolerance is a trait that is often used to predict winners and losers under scenarios of climate change. But thermal tolerance might also inform when species interactions are likely to be important because only subsets of species will be able to exploit the available warmer climatic niche space, and competition may intensify in the remaining, compressed cooler climatic niche space. Here, we explore the relative roles of the direct effects of temperature change and indirect effects of species interactions on forest ant communities that were heated as part of a large-scale climate manipulation at high- and low-latitude sites in eastern North America. Overall, we found mixed support for the importance of negative species interactions (competition), but found that the magnitude of these interaction effects was predictable based on the heat tolerance of the focal species. Forager abundance and nest site occupancy of heat-intolerant species were more often influenced by negative interactions with other species than by direct effects of temperature. Our findings suggest that measures of species-specific heat tolerance may roughly predict when species interactions will influence responses to global climate change. DA - 2017/7// PY - 2017/7// DO - 10.1093/icb/icx008 VL - 57 IS - 1 SP - 112-120 SN - 1557-7023 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85029143849&partnerID=MN8TOARS ER - TY - JOUR TI - Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America AU - Swarts, Kelly AU - Gutaker, Rafal M. AU - Benz, Bruce AU - Blake, Michael AU - Bukowski, Robert AU - Holland, James AU - Kruse-Peeples, Melissa AU - Lepak, Nicholas AU - Prim, Lynda AU - Romay, M. Cinta AU - Ross-Ibarra, Jeffrey AU - Jesus Sanchez-Gonzalez, Jose AU - Schmidt, Chris AU - Schuenemann, Verena J. AU - Krause, Johannes AU - Matson, R. G. AU - Weigel, Detlef AU - Buckler, Edward S. AU - Burbano, Hernan A. T2 - SCIENCE AB - By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaptation. DA - 2017/8/4/ PY - 2017/8/4/ DO - 10.1126/science.aam9425 VL - 357 IS - 6350 SP - 512-515 SN - 1095-9203 UR - https://doi.org/10.1126/science.aam9425 ER - TY - JOUR TI - Factors Influencing Postsecondary STEM Students' Views of the Public Communication of an Emergent Technology: a Cross-National Study from Five Universities AU - Gardner, Grant E. AU - Jones, M. Gail AU - Albe, Virginie AU - Blonder, Ron AU - Laherto, Antti AU - Macher, Daniel AU - Paechter, Manuela T2 - RESEARCH IN SCIENCE EDUCATION AB - Recent efforts in the science education community have highlighted the need to integrate research and theory from science communication research into more general science education scholarship. These synthesized research perspectives are relatively novel but serve an important need to better understand the impacts that the advent of rapidly emerging technologies will have on a new generation of scientists and engineers including their formal communication with engaged citizenry. This cross-national study examined postsecondary science and engineering students’ (n = 254 from five countries: Austria, Finland, France, Israel, and USA) perspectives on the role of science communication in their own formal science and engineering education. More broadly, we examined participants’ understanding of their perceived responsibilities of communicating science and engineering to the general public when an issue contains complex social and ethical implications (SEI). The study is contextualized in the emergent technology of nanotechnology for which SEI are of particular concern and for which the general public often perceives conflicting risks and benefits. Findings indicate that student participants’ hold similar views on the need for their own training in communication as future scientists and engineers. When asked about the role that ethics and risk perception plays in research, development, and public communication of nanotechnology, participants demonstrate similar trajectories of perspectives that are, however, often anchored in very different levels of beginning concern. Results are discussed in the context of considerations for science communication training within formal science education curricula globally. DA - 2017/10// PY - 2017/10// DO - 10.1007/s11165-016-9537-7 VL - 47 IS - 5 SP - 1011-1029 SN - 1573-1898 KW - Science communication KW - Cross-national study KW - Postsecondary KW - Emergent technology KW - Nanotechnology ER - TY - JOUR TI - Evaluating strategies for reversing CRISPR-Cas9 gene drives AU - Vella, Michael R. AU - Gunning, Christian E. AU - Lloyd, Alun L. AU - Gould, Fred T2 - Scientific Reports AB - A gene drive biases inheritance of a gene so that it increases in frequency within a population even when the gene confers no fitness benefit. There has been renewed interest in environmental releases of engineered gene drives due to recent proof of principle experiments with the CRISPR-Cas9 system as a drive mechanism. Release of modified organisms, however, is controversial, especially when the drive mechanism could theoretically alter all individuals of a species. Thus, it is desirable to have countermeasures to reverse a drive if a problem arises. Several genetic mechanisms for limiting or eliminating gene drives have been proposed and/or developed, including synthetic resistance, reversal drives, and immunizing reversal drives. While predictions about efficacy of these mechanisms have been optimistic, we lack detailed analyses of their expected dynamics. We develop a discrete time model for population genetics of a drive and proposed genetic countermeasures. Efficacy of drive reversal varies between countermeasures. For some parameter values, the model predicts unexpected behavior including polymorphic equilibria and oscillatory dynamics. The timing and number of released individuals containing a genetic countermeasure can substantially impact outcomes. The choice among countermeasures by researchers and regulators will depend on specific goals and population parameters of target populations. DA - 2017/9/8/ PY - 2017/9/8/ DO - 10.1038/s41598-017-10633-2 VL - 7 IS - 1 SP - J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-017-10633-2 DB - Crossref ER - TY - JOUR TI - Escherichia coli O157:H7 Acid Sensitivity Correlates with Flocculation Phenotype during Nutrient Limitation AU - Kay, Kathryn L. AU - Breidt, Frederick AU - Fratamico, Pina M. AU - Baranzoni, Gian M. AU - Kim, Gwang-Hee AU - Grunden, Amy M. AU - Oh, Deog-Hwan T2 - FRONTIERS IN MICROBIOLOGY AB - Shiga toxin producing Escherichia coli (STEC) strains vary in acid resistance; however, little is known about the underlying mechanisms that result in strain specific differences. Among 25 STEC O157:H7 strains tested, 7 strains flocculated when grown statically for 18 h in minimal salts medium at 37°C, while 18 strains did not. Interestingly, the flocculation phenotype (cells came out of suspension) was found to correlate with degree of acid sensitivity in an assay with 400 mM acetic acid solution at pH 3.3 targeting acidified foods. Strains exhibiting flocculation were more acid sensitive and were designated FAS, for flocculation acid sensitive, while the acid resistant strain designated PAR for planktonic acid resistant. Flocculation was not observed for any strains during growth in complex medium (Luria Bertani broth). STEC strains B201 and B241 were chosen as representative FAS (2.4 log reduction) and PAR (0.15 log reduction) strains, respectively, due to differences in acid resistance and flocculation phenotype. Results from electron microscopy showed evidence of fimbriae production in B201, whereas fimbriae were not observed in B241.Curli fimbriae production was identified through plating on Congo red differential medium, and all FAS strains showed curli fimbriae production. Surprisingly, 5 PAR strains also had evidence of curli production. Transcriptomic and targeted gene expression data for B201 and B241indicated that csg and hde (curli and acid induced chaperone genes, respectively) expression positively correlated with the phenotypic differences observed for these strains. These data suggest that FAS strains grown in minimal medium express curli, resulting in a flocculation phenotype. This may be regulated by GcvB, which positively regulates curli fimbriae production and represses acid chaperone proteins. RpoS and other regulatory mechanisms may impact curli fimbriae production, as well. These findings may help elucidate mechanisms underlying differences among STEC strains in relating acid resistance and biofilm formation. DA - 2017/7/26/ PY - 2017/7/26/ DO - 10.3389/fmicb.2017.01404 VL - 8 SP - SN - 1664-302X KW - STEC KW - acid resistance KW - nutrient limitation KW - curli KW - GcvB ER - TY - JOUR TI - Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii AU - Zurawski, Jeffrey V. AU - Khatibi, Piyum A. AU - Akinosho, Hannah O. AU - Straub, Christopher T. AU - Compton, Scott H. AU - Conway, Jonathan M. AU - Lee, Laura L. AU - Ragauskas, Arthur J. AU - Davison, Brian H. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT Improving access to the carbohydrate content of lignocellulose is key to reducing recalcitrance for microbial deconstruction and conversion to fuels and chemicals. Caldicellulosiruptor bescii completely solubilizes naked microcrystalline cellulose, yet this transformation is impeded within the context of the plant cell wall by a network of lignin and hemicellulose. Here, the bioavailability of carbohydrates to C. bescii at 70°C was examined for reduced lignin transgenic switchgrass lines COMT3(+) and MYB Trans, their corresponding parental lines (cultivar Alamo) COMT3(−) and MYB wild type (WT), and the natural variant cultivar Cave-in-Rock (CR). Transgenic modification improved carbohydrate solubilization by C. bescii to 15% (2.3-fold) for MYB and to 36% (1.5-fold) for COMT, comparable to the levels achieved for the natural variant, CR (36%). Carbohydrate solubilization was nearly doubled after two consecutive microbial fermentations compared to one microbial step, but it never exceeded 50% overall. Hydrothermal treatment (180°C) prior to microbial steps improved solubilization 3.7-fold for the most recalcitrant line (MYB WT) and increased carbohydrate recovery to nearly 50% for the least recalcitrant lines [COMT3(+) and CR]. Alternating microbial and hydrothermal steps (T→M→T→M) further increased bioavailability, achieving carbohydrate solubilization ranging from 50% for MYB WT to above 70% for COMT3(+) and CR. Incomplete carbohydrate solubilization suggests that cellulose in the highly lignified residue was inaccessible; indeed, residue from the T→M→T→M treatment was primarily glucan and inert materials (lignin and ash). While C. bescii could significantly solubilize the transgenic switchgrass lines and natural variant tested here, additional or alternative strategies (physical, chemical, enzymatic, and/or genetic) are needed to eliminate recalcitrance. IMPORTANCE Key to a microbial process for solubilization of plant biomass is the organism's access to the carbohydrate content of lignocellulose. Economically viable routes will characteristically minimize physical, chemical, and biological pretreatment such that microbial steps contribute to the greatest extent possible. Recently, transgenic versions of plants and trees have been developed with the intention of lowering the barrier to lignocellulose conversion, with particular focus on lignin content and composition. Here, the extremely thermophilic bacterium Caldicellulosiruptor bescii was used to solubilize natural and genetically modified switchgrass lines, with and without the aid of hydrothermal treatment. For lignocellulose conversion, it is clear that the microorganism, plant biomass substrate, and processing steps must all be considered simultaneously to achieve optimal results. Whether switchgrass lines engineered for low lignin or natural variants with desirable properties are used, conversion will depend on microbial access to crystalline cellulose in the plant cell wall. DA - 2017/9// PY - 2017/9// DO - 10.1128/aem.00969-17 VL - 83 IS - 17 SP - SN - 1098-5336 KW - Caldicellulosiruptor KW - switchgrass KW - lignocellulose deconstruction and conversion KW - extreme thermophiles KW - lignocellulose ER - TY - JOUR TI - Within-Plant Distribution and Dynamics of Thrips Species (Thysanoptera: Thripidae) in Cotton AU - Reay-Jones, Francis P. F. AU - Greene, Jeremy K. AU - Herbert, D. Ames AU - Jacobson, Alana L. AU - Kennedy, George G. AU - Reisig, Dominic D. AU - Roberts, Phillip M. T2 - Journal of Economic Entomology AB - A 2-yr study in cotton (Gossypium hirsutum L.) was conducted to determine the abundance and species composition of thrips (Thysanoptera: Thripidae) on different plant parts throughout the season in Alabama, Georgia, North Carolina, South Carolina, and Virginia. Plant parts sampled included seedlings, terminals with two expanded leaves, leaves from the upper, middle, and lower sections of the canopy, white flowers, and medium-sized bolls. Adult thrips were significantly more abundant on seedlings and flowers in 2014, and on flowers followed by seedlings and leaves from the middle canopy in 2015. Immature thrips were significantly more abundant on seedlings, followed by flowers in 2014, and on seedlings followed by leaves from the lower canopy and flowers in 2015. Across locations and plant parts, thrips consisted of Frankliniella tritici (Fitch) (46.8%), Frankliniella fusca Hinds (23.5%), Frankliniella occidentalis (Pergande) (17.1%), Neohydatothrips variabilis (Beach) (7.4%), Thrips tabaci (Lindeman) (1.8%), and other species (3.4%). Frankliniella fusca represented 86.7% of all thrips on seedlings, while F. tritici was more abundant on terminals (51.6%), squares (57.5%), and flowers (75.1%). Across all leaf positions, F. fusca was the most abundant species (28.8%), followed by F. tritici (19.2%), N. variabilis (18.8%), F. occidentalis (12.9%), and T. tabaci (5.2%), as well as other species (15.0%). As neonicotinoid insecticides remain a primary tool to manage seedling infestations of F. fusca, our data indicate that mid- to late-season applications of neonicotinoid insecticides targeting other insect pests will intensify selection pressure for resistance on F. fusca, the primary pest of seedling cotton. DA - 2017/5/5/ PY - 2017/5/5/ DO - 10.1093/jee/tox131 VL - 110 IS - 4 SP - 1563-1575 LA - en OP - SN - 0022-0493 1938-291X UR - http://dx.doi.org/10.1093/jee/tox131 DB - Crossref KW - Gossypium hirsutum KW - Frankliniella fusca KW - Frankliniella occidentalis KW - Frankliniella tritici KW - sampling ER - TY - JOUR TI - VapC toxins drive cellular dormancy under uranium stress for the extreme thermoacidophile Metallosphaera prunae AU - Mukherjee, Arpan AU - Wheaton, Garrett H. AU - Counts, James A. AU - Ijeomah, Brenda AU - Desai, Jigar AU - Kelly, Robert M. T2 - ENVIRONMENTAL MICROBIOLOGY AB - Summary When abruptly exposed to toxic levels of hexavalent uranium, the extremely thermoacidophilic archaeon Metallosphaera prunae , originally isolated from an abandoned uranium mine, ceased to grow, and concomitantly exhibited heightened levels of cytosolic ribonuclease activity that corresponded to substantial degradation of cellular RNA. The M. prunae transcriptome during ‘uranium‐shock’ implicated VapC toxins as possible causative agents of the observed RNA degradation. Identifiable VapC toxins and PIN‐domain proteins encoded in the M. prunae genome were produced and characterized, three of which (VapC4, VapC7, VapC8) substantially degraded M. prunae rRNA in vitro . RNA cleavage specificity for these VapCs mapped to motifs within M. prunae rRNA. Furthermore, based on frequency of cleavage sequences, putative target mRNAs for these VapCs were identified; these were closely associated with translation, transcription, and replication. It is interesting to note that Metallosphaera sedula , a member of the same genus and which has a nearly identical genome sequence but not isolated from a uranium‐rich biotope, showed no evidence of dormancy when exposed to this metal. M. prunae utilizes VapC toxins for post‐transcriptional regulation under uranium stress to enter a cellular dormant state, thereby providing an adaptive response to what would otherwise be a deleterious environmental perturbation. DA - 2017/7// PY - 2017/7// DO - 10.1111/1462-2920.13808 VL - 19 IS - 7 SP - 2831-2842 SN - 1462-2920 ER - TY - JOUR TI - Transcriptomic Analysis in Strawberry Fruits Reveals Active Auxin Biosynthesis and Signaling in the Ripe Receptacle (vol 8, pg 889, 2017) AU - Estrada-Johnson, Elizabeth AU - Csukasi, Fabiana AU - Pizarro, Carmen M. AU - Vallarino, Jose G. AU - Kiryakova, Yulia AU - Vioque, Amalia AU - Merchante, Catharina AU - Brumos, Javier AU - Medina-Escobar, Nieves AU - Botella, Miguel A. AU - Alonso, Jose M. AU - Fernie, Alisdair R. AU - Sanchez-Sevilla, Jose F. AU - Osorio, Sonia AU - Valpuesta, Victoriano T2 - FRONTIERS IN PLANT SCIENCE AB - [This corrects the article on p. 889 in vol. 8, PMID: 28611805.]. DA - 2017/7/24/ PY - 2017/7/24/ DO - 10.3389/fpls.2017.01305 VL - 8 SP - SN - 1664-462X KW - auxin KW - fruit KW - strawberry KW - transcriptome regulation KW - ripening ER - TY - JOUR TI - Tomato spotted wilt virus Can Infect Resistant Tomato when Western Flower Thrips Inoculate Blossoms AU - Houle, J. L. AU - Kennedy, G. G. T2 - PLANT DISEASE AB - Tomato spotted wilt is a major disease of crops worldwide. Resistant cultivars carrying the Sw-5 allele for resistance to tomato spotted wilt disease (TSW) provide the most effective control method in tomato (Solanum lycopersicum). However, infections of fruit on Sw-5+ tomato plants suggest the virus resistance may not be fully expressed in blossoms or developing fruit. The objective of this study was to determine if the thrips vector, the western flower thrips (Frankliniella occidentalis), can transmit non-resistance breaking Tomato spotted wilt virus (TSWV) isolates when confined to blossoms on plants with and without the Sw-5 resistance allele. Twenty-one percent of 33 Sw-5+ plants inoculated by adult thrips feeding on blossom clusters or small fruit developed infections in the reproductive tissue, whereas 68% of 25 Sw-5– plants developed infections. Systemic infections also occurred following inoculation of blossoms in host genotypes with and without Sw-5. These results were further supported by field experiments that showed high proportions of infected fruit as well as a limited infection of foliage on the same stem as the infected fruit in Sw-5+ plants when F. occidentalis were abundant in blossoms. These findings help to explain observations of abundant late season infections of Sw-5 cultivars in commercial plantings and suggest that management of F. occidentalis infestations during the bloom period may be important for effective management of TSWV in susceptible tomato cultivars as well as cultivars expressing the Sw-5 allele for TSW resistance. DA - 2017/9// PY - 2017/9// DO - 10.1094/pdis-12-16-1716-re VL - 101 IS - 9 SP - 1666-1670 SN - 1943-7692 ER - TY - JOUR TI - Reproductive Status of Drosophila suzukii (Diptera: Drosophilidae) Females Influences Attraction to Fermentation-Based Baits and Ripe Fruits AU - Swoboda-Bhattarai, Katharine A. AU - McPhie, Douglas R. AU - Burrack, Hannah J. T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - Drosophila suzukii (Matsumura) is an invasive species that is a devastating pest of soft-skinned fruit crops. Although much effort has been directed toward developing traps and attractants to monitor for D. suzukii, current monitoring tools do not reliably predict fruit infestation. The objective of this study was to determine if D. suzukii females at different developmental stages are differentially attracted to monitoring traps with fermentation-based baits and ripe fruits. Females were collected on the surface of traps, within traps, and on ripe fruits during three experiments at field locations in North Carolina, USA, and were dissected to determine their reproductive status. In general, females collected on ripe fruits were more likely to have mature eggs present in their ovaries and had higher numbers of mature eggs than females collected on the surface of or within monitoring traps. The results of this study have implications for D. suzukii monitoring and the development of effective baits for use in integrated pest management programs. DA - 2017/8// PY - 2017/8// DO - 10.1093/jee/tox150 VL - 110 IS - 4 SP - 1648-1652 SN - 1938-291X KW - monitoring KW - raspberry KW - blackberry KW - invasive species ER - TY - JOUR TI - Organic Food in the Diet: Exposure and Health Implications AU - Brantsæter, Anne Lise AU - Ydersbond, Trond A. AU - Hoppin, Jane A. AU - Haugen, Margaretha AU - Meltzer, Helle Margrete T2 - Annual Review of Public Health AB - The market for organic food products is growing rapidly worldwide. Such foods meet certified organic standards for production, handling, processing, and marketing. Most notably, the use of synthetic fertilizers, pesticides, and genetic modification is not allowed. One major reason for the increased demand is the perception that organic food is more environmentally friendly and healthier than conventionally produced food. This review provides an update on market data and consumer preferences for organic food and summarizes the scientific evidence for compositional differences and health benefits of organic compared with conventionally produced food. Studies indicate some differences in favor of organic food, including indications of beneficial health effects. Organic foods convey lower pesticide residue exposure than do conventionally produced foods, but the impact of this on human health is not clear. Comparisons are complicated by organic food consumption being strongly correlated with several indicators of a healthy lifestyle and by conventional agriculture "best practices" often being quite close to those of organic. DA - 2017/3/20/ PY - 2017/3/20/ DO - 10.1146/annurev-publhealth-031816-044437 VL - 38 IS - 1 SP - 295-313 J2 - Annu. Rev. Public Health LA - en OP - SN - 0163-7525 1545-2093 UR - http://dx.doi.org/10.1146/annurev-publhealth-031816-044437 DB - Crossref KW - organic food KW - organic vegetables KW - naturalness KW - compositional differences KW - health effects ER - TY - JOUR TI - NEUROETHICS: NEUROSCIENCE'S CONTRIBUTIONS TO BIOETHICS AU - Dubljevic, Veljko AU - Jox, Ralf J. AU - Racine, Eric T2 - BIOETHICS AB - BioethicsVolume 31, Issue 5 p. 326-327 Editorial Neuroethics: Neuroscience's Contributions to Bioethics Veljko Dubljević, Veljko DubljevićSearch for more papers by this authorRalf J. Jox, Ralf J. JoxSearch for more papers by this authorEric Racine, Eric RacineSearch for more papers by this author Veljko Dubljević, Veljko DubljevićSearch for more papers by this authorRalf J. Jox, Ralf J. JoxSearch for more papers by this authorEric Racine, Eric RacineSearch for more papers by this author First published: 15 May 2017 https://doi.org/10.1111/bioe.12360Read 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. Volume31, Issue5Special Issue: Neuroethics: Neuroscience's Contributions to BioethicsJune 2017Pages 326-327 RelatedInformation DA - 2017/6// PY - 2017/6// DO - 10.1111/bioe.12360 VL - 31 IS - 5 SP - 326-327 SN - 1467-8519 ER - TY - JOUR TI - Moral enhancement meets normative and empirical reality: Assessing the practical feasibility of moral enhancement neurotechnologies AU - Dubljevic, Veljko AU - Racine, E. T2 - Bioethics AB - Abstract Moral enhancement refers to the possibility of making individuals and societies better from a moral standpoint. A fierce debate has emerged about the ethical aspects of moral enhancement, notably because steering moral enhancement in a particular direction involves choosing amongst a wide array of competing options, and these options entail deciding which moral theory or attributes of the moral agent would benefit from enhancement. Furthermore, the ability and effectiveness of different neurotechnologies to enhance morality have not been carefully examined. In this paper, we assess the practical feasibility of moral enhancement neurotechnologies. We reviewed the literature on neuroscience and cognitive science models of moral judgment and analyzed their implications for the specific target of intervention (cognition, volition or affect) in moral enhancement. We also reviewed and compared evidence on available neurotechnologies that could serve as tools of moral enhancement. We conclude that the predictions of rationalist, emotivist, and dual process models are at odds with evidence, while different intuitionist models of moral judgment are more likely to be aligned with it. Furthermore, the project of moral enhancement is not feasible in the near future as it rests on the use of neurointerventions, which have no moral enhancement effects or, worse, negative effects. DA - 2017/// PY - 2017/// DO - 10.1111/bioe.12355 VL - 31 IS - 5 SP - 338–348 ER - TY - JOUR TI - Long-term nitrogen & phosphorus additions reduce soil microbial respiration but increase its temperature sensitivity in a Tibetan alpine meadow AU - Guo, Hui AU - Ye, Chenglong AU - Zhang, Hao AU - Pan, Shang AU - Ji, Yangguang AU - Li, Zhen AU - Liu, Manqiang AU - Zhou, Xianhui AU - Du, Guozhen AU - Hu, Feng AU - Hu, Shuijin T2 - SOIL BIOLOGY & BIOCHEMISTRY AB - Nutrient availability may exert major controls over soil microbial respiration, especially in carbon (C)-rich, nitrogen (N)-limited ecosystems in high elevation regions, but how soil organic matter (SOM) decomposition and its temperature sensitivity respond to long-term N & P additions in alpine ecosystems remains unclear. We examined the impact of long-term (15 yr) N & P additions on soil microbial respiration and its temperature sensitivity (Q10), and assessed the relative importance of nutrient-induced alterations in substrate quality and the microbial community composition in explaining the variation in soil respiration and temperature sensitivity. We found that N & P additions significantly reduced microbial respiration rates and cumulative C efflux, but increased the Q10 (15/5 °C). Also, N & P additions reduced the biomass of the whole microbial community, gram negative bacteria and fungi, but increased the aromaticity and aliphaticity of soil organic C substrate. Across the treatments, averaged Q10 was positively correlated with the complexity of SOM as characterized by 13C-NMR, supporting the prediction based on kinetic theory that SOM with recalcitrant molecular structure is with high temperature sensitivity. Together, our results showed that changes in both substrate quality and soil microbial community induced by long-term nutrient inputs may alter the response of soil microbial respiration to elevated temperature. Because the positive effects of increasing temperature sensitivity for use of lower quality substrates on C emission may be offset by lower absolute rates at any one temperature, long-term N & P additions increase the uncertainty in predicting the net soil C losses in the scenario of warming on Tibetan Plateau. DA - 2017/10// PY - 2017/10// DO - 10.1016/j.soilbio.2017.05.024 VL - 113 SP - 26-34 SN - 0038-0717 KW - Soil microbial respiration KW - Temperature sensitivity KW - Nitrogen and phosphorus additions KW - Substrate quality KW - Microbial community KW - Tibetan Plateau ER - TY - JOUR TI - Genome-Wide Associations for Water-Soluble Carbohydrate Concentration and Relative Maturity in Wheat Using SNP and DArT Marker Arrays AU - Ovenden, Ben AU - Milgate, Andrew AU - Wade, Len J. AU - Rebetzke, Greg J. AU - Holland, James B. T2 - G3-GENES GENOMES GENETICS AB - Improving water-use efficiency by incorporating drought avoidance traits into new wheat varieties is an important objective for wheat breeding in water-limited environments. This study uses genome wide association studies (GWAS) to identify candidate loci for water-soluble carbohydrate accumulation-an important drought-avoidance characteristic in wheat. Phenotypes from a multi-environment trial with experiments differing in water availability and separate single nucleotide polymorphism (SNP) and diversity arrays technology (DArT) marker sets were used to perform the analyses. Significant associations for water-soluble carbohydrate accumulation were identified on chromosomes 1A, 1B, 1D, 2D, and 4A. Notably, these loci did not collocate with the major loci identified for relative maturity. Loci on chromosome 1D collocated with markers previously associated with the high molecular weight glutenin Glu-D1 locus. Genetic × environmental interactions impacted the results strongly, with significant associations for carbohydrate accumulation identified only in the water-deficit experiments. The markers associated with carbohydrate accumulation may be useful for marker-assisted selection of drought tolerance in wheat. DA - 2017/8// PY - 2017/8// DO - 10.1534/g3.117.039842 VL - 7 IS - 8 SP - 2821-2830 SN - 2160-1836 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85027256280&partnerID=MN8TOARS KW - water-soluble carbohydrates KW - nonstructural carbohydrates KW - association analysis KW - genotype-by-environment interaction KW - molecular marker ER - TY - JOUR TI - Fine Mapping, Transcriptome Analysis, and Marker Development for Y-2, the Gene That Conditions beta-Carotene Accumulation in Carrot (Daucus carota L.) AU - Ellison, Shelby AU - Senalik, Douglas AU - Bostan, Hamed AU - Iorizzo, Massimo AU - Simon, Philipp T2 - G3-GENES GENOMES GENETICS AB - Abstract Domesticated carrots, Daucus carota subsp. sativus, are the richest source of β-carotene in the US diet, which, when consumed, is converted into vitamin A, an essential component of eye health and immunity. The Y2 locus plays a significant role in beta-carotene accumulation in carrot roots, but a candidate gene has not been identified. To advance our understanding of this locus, the genetic basis of β-carotene accumulation was explored by utilizing an advanced mapping population, transcriptome analysis, and nucleotide diversity in diverse carrot accessions with varying levels of β-carotene. A single large effect Quantitative Trait Locus (QTL) on the distal arm of chromosome 7 overlapped with the previously identified β-carotene accumulation QTL, Y2. Fine mapping efforts reduced the genomic region of interest to 650 kb including 72 genes. Transcriptome analysis within this fine mapped region identified four genes differentially expressed at two developmental time points, and 13 genes differentially expressed at one time point. These differentially expressed genes included transcription factors and genes involved in light signaling and carotenoid flux, including a member of the Di19 gene family involved in Arabidopsis photomorphogenesis, and a homolog of the bHLH36 transcription factor involved in maize carotenoid metabolism. Analysis of nucleotide diversity in 25 resequenced carrot accessions revealed a drastic decrease in diversity of this fine-mapped region in orange cultivated accessions as compared to white and yellow cultivated and to white wild samples. The results presented in this study provide a foundation to identify and characterize the gene underlying β-carotene accumulation in carrot. DA - 2017/8// PY - 2017/8// DO - 10.1534/g3.117.043067 VL - 7 IS - 8 SP - 2665-2675 SN - 2160-1836 KW - carotenoids KW - Daucus carota L. KW - genotyping-by-sequencing KW - RNA-sequencing KW - QTL ER - TY - JOUR TI - Construction and setup of a bench-scale algal photosynthetic bioreactor with temperature, light, and pH monitoring for kinetic growth tests AU - Karam, A.L. AU - McMillan, C.C. AU - Lai, Y.-C. AU - De Los Reyes, F.L. AU - Sederoff, H.W. AU - Grunden, A.M. AU - Ranjithan, R.S. AU - Levis, J.W. AU - Ducoste, J.J. T2 - Journal of Visualized Experiments AB - The optimal design and operation of photosynthetic bioreactors (PBRs) for microalgal cultivation is essential for improving the environmental and economic performance of microalgae-based biofuel production. Models that estimate microalgal growth under different conditions can help to optimize PBR design and operation. To be effective, the growth parameters used in these models must be accurately determined. Algal growth experiments are often constrained by the dynamic nature of the culture environment, and control systems are needed to accurately determine the kinetic parameters. The first step in setting up a controlled batch experiment is live data acquisition and monitoring. This protocol outlines a process for the assembly and operation of a bench-scale photosynthetic bioreactor that can be used to conduct microalgal growth experiments. This protocol describes how to size and assemble a flat-plate, bench-scale PBR from acrylic. It also details how to configure a PBR with continuous pH, light, and temperature monitoring using a data acquisition and control unit, analog sensors, and open-source data acquisition software. DA - 2017/// PY - 2017/// DO - 10.3791/55545 VL - 2017 IS - 124 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85021241433&partnerID=MN8TOARS KW - Bioengineering KW - Issue 124 KW - Photosynthetic bioreactors KW - microalgae KW - growth kinetics KW - biofuel KW - temperature KW - light KW - pH KW - automated monitoring ER - TY - JOUR TI - Characterizing the Mechanisms of Lead Immobilization via Bioapatite and Various Clay Minerals AU - Li, Zhen AU - Tang, Lingyi AU - Zheng, Yangfan AU - Tian, Da AU - Su, Mu AU - Zhang, Fan AU - Ma, Shuojia AU - Hu, Shuijin T2 - ACS EARTH AND SPACE CHEMISTRY AB - Immobilizing lead (Pb) in contaminated water and soils via mineralization is an emerging field of interest in environmental remediation. This study investigated the feasibility of applying bioapatite and typical clay minerals (kaolinite, palygorskite, and montmorillonite) to immobilize Pb2+ cations in water. The mechanisms of lead immobilization were studied by inductively coupled plasma optical emission spectrometry (ICP–OES), X-ray diffraction (XRD), and high-resolution transmission electron microscopy (HRTEM). Montmorillonite shows the highest efficiency in Pb remediation (reduced from ∼2000 to 30 ppm) with the addition of bioapatite. The XRD and HRTEM results demonstrated that aqueous Pb removal efficiency is facilitated by bioapatite via reacting with Pb to form pyromorphite mineral [Pb5(PO4)3(F,Cl,OH)]. The high surface area and cation-exchange capability of montmorillonite allow its abundant absorption of Pb2+ and, hence, cause the enriched formation of pyromorphite on its surface. In contrast, the low surface area of kaolinite does not allow substantial absorption of Pb, and pyromorphite was primarily formed in the solution rather than on its surface. In addition, some Pb2+ cations were trapped within the mineral fibrous aggregates of palygorskite, which limits the lead immobilization via the formation of pyromorphite on its surface or within the fibrous aggregates. This study sheds light on the bright future of the application of bioapatite and montmorillonite in Pb-contaminated water and soils. DA - 2017/5// PY - 2017/5// DO - 10.1021/acsearthspacechem.7b00016 VL - 1 IS - 3 SP - 152-157 SN - 2472-3452 KW - lead immobilization KW - bioapatite KW - pyromorphite KW - clay KW - montmorillonite ER - TY - JOUR TI - CAN NEUROSCIENCE CONTRIBUTE TO PRACTICAL ETHICS? A CRITICAL REVIEW AND DISCUSSION OF THE METHODOLOGICAL AND TRANSLATIONAL CHALLENGES OF THE NEUROSCIENCE OF ETHICS AU - Racine, Eric AU - Dubljevic, Veljko AU - Jox, Ralf J. AU - Baertschi, Bernard AU - Christensen, Julia F. AU - Farisco, Michele AU - Jotterand, Fabrice AU - Kahane, Guy AU - Muller, Sabine T2 - BIOETHICS AB - Neuroethics is an interdisciplinary field that arose in response to novel ethical challenges posed by advances in neuroscience. Historically, neuroethics has provided an opportunity to synergize different disciplines, notably proposing a two-way dialogue between an 'ethics of neuroscience' and a 'neuroscience of ethics'. However, questions surface as to whether a 'neuroscience of ethics' is a useful and unified branch of research and whether it can actually inform or lead to theoretical insights and transferable practical knowledge to help resolve ethical questions. In this article, we examine why the neuroscience of ethics is a promising area of research and summarize what we have learned so far regarding its most promising goals and contributions. We then review some of the key methodological challenges which may have hindered the use of results generated thus far by the neuroscience of ethics. Strategies are suggested to address these challenges and improve the quality of research and increase neuroscience's usefulness for applied ethics and society at large. Finally, we reflect on potential outcomes of a neuroscience of ethics and discuss the different strategies that could be used to support knowledge transfer to help different stakeholders integrate knowledge from the neuroscience of ethics. DA - 2017/6// PY - 2017/6// DO - 10.1111/bioe.12357 VL - 31 IS - 5 SP - 328-337 SN - 1467-8519 KW - neuroscience ethics KW - methodology KW - translation KW - practical ethics ER - TY - JOUR TI - Benefits of the development and dissemination of climate-smart rice: ex ante impact assessment of drought-tolerant rice in South Asia AU - Mottaleb, Khondoker A. AU - Rejesus, Roderick M. AU - Murty, M. V. R. AU - Mohanty, Samarendu AU - Li, Tao T2 - MITIGATION AND ADAPTATION STRATEGIES FOR GLOBAL CHANGE DA - 2017/8// PY - 2017/8// DO - 10.1007/s11027-016-9705-0 VL - 22 IS - 6 SP - 879-901 SN - 1573-1596 KW - Climate change KW - Drought tolerance KW - Exante economic impact KW - Rice varieties KW - South Asia ER - TY - JOUR TI - Assessing the Potential for Bias From Nonresponse to a Study Follow-up Interview: An Example From the Agricultural Health Study AU - Rinsky, Jessica L. AU - Richardson, David B. AU - Wing, Steve AU - Beard, John D. AU - Alavanja, Michael AU - Beane Freeman, Laura E. AU - Chen, Honglei AU - Henneberger, Paul K. AU - Kamel, Freya AU - Sandler, Dale P. AU - Hoppin, Jane A. T2 - American Journal of Epidemiology AB - Prospective cohort studies are important tools for identifying causes of disease. However, these studies are susceptible to attrition. When information collected after enrollment is through interview or exam, attrition leads to missing information for nonrespondents. The Agricultural Health Study enrolled 52,394 farmers in 1993–1997 and collected additional information during subsequent interviews. Forty-six percent of enrolled farmers responded to the 2005–2010 interview; 7% of farmers died prior to the interview. We examined whether response was related to attributes measured at enrollment. To characterize potential bias from attrition, we evaluated differences in associations between smoking and incidence of 3 cancer types between the enrolled cohort and the subcohort of 2005–2010 respondents, using cancer registry information. In the subcohort we evaluated the ability of inverse probability weighting (IPW) to reduce bias. Response was related to age, state, race/ethnicity, education, marital status, smoking, and alcohol consumption. When exposure and outcome were associated and case response was differential by exposure, some bias was observed; IPW conditional on exposure and covariates failed to correct estimates. When response was nondifferential, subcohort and full-cohort estimates were similar, making IPW unnecessary. This example provides a demonstration of investigating the influence of attrition in cohort studies using information that has been self-reported after enrollment. DA - 2017/7/7/ PY - 2017/7/7/ DO - 10.1093/aje/kwx098 VL - 186 IS - 4 SP - 395-404 LA - en OP - SN - 0002-9262 1476-6256 UR - http://dx.doi.org/10.1093/aje/kwx098 DB - Crossref KW - attrition KW - epidemiologic methods KW - inverse probability weights KW - loss to follow-up KW - occupational/environmental epidemiology KW - prospective studies KW - selection bias ER - TY - JOUR TI - Assessing the Exposome with External Measures: Commentary on the State of the Science and Research Recommendations AU - Turner, Michelle C. AU - Nieuwenhuijsen, Mark AU - Anderson, Kim AU - Balshaw, David AU - Cui, Yuxia AU - Dunton, Genevieve AU - Hoppin, Jane A. AU - Koutrakis, Petros AU - Jerrett, Michael T2 - Annual Review of Public Health AB - The exposome comprises all environmental exposures that a person experiences from conception throughout the life course. Here we review the state of the science for assessing external exposures within the exposome. This article reviews (a) categories of exposures that can be assessed externally, (b) the current state of the science in external exposure assessment, (c) current tools available for external exposure assessment, and (d) priority research needs. We describe major scientific and technological advances that inform external assessment of the exposome, including geographic information systems; remote sensing; global positioning system and geolocation technologies; portable and personal sensing, including smartphone-based sensors and assessments; and self-reported questionnaire assessments, which increasingly rely on Internet-based platforms. We also discuss priority research needs related to methodological and technological improvement, data analysis and interpretation, data sharing, and other practical considerations, including improved assessment of exposure variability as well as exposure in multiple, critical life stages. DA - 2017/3/20/ PY - 2017/3/20/ DO - 10.1146/annurev-publhealth-082516-012802 VL - 38 IS - 1 SP - 215-239 J2 - Annu. Rev. Public Health LA - en OP - SN - 0163-7525 1545-2093 UR - http://dx.doi.org/10.1146/annurev-publhealth-082516-012802 DB - Crossref KW - exposome KW - external exposures KW - geographic information systems KW - remote sensing KW - global positioning systems KW - smartphones ER - TY - JOUR TI - Tick Haller's Organ, a New Paradigm for Arthropod Olfaction: How Ticks Differ from Insects AU - Carr, Ann L. AU - Mitchell, Robert D., III AU - Dhammi, Anirudh AU - Bissinger, Brooke W. AU - Sonenshine, Daniel E. AU - Roe, R. Michael T2 - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES AB - Ticks are the vector of many human and animal diseases; and host detection is critical to this process. Ticks have a unique sensory structure located exclusively on the 1st pairs of legs; the fore-tarsal Haller's organ, not found in any other animals, presumed to function like the insect antennae in chemosensation but morphologically very different. The mechanism of tick chemoreception is unknown. Utilizing next-generation sequencing and comparative transcriptomics between the 1st and 4th legs (the latter without the Haller's organ), we characterized 1st leg specific and putative Haller's organ specific transcripts from adult American dog ticks, Dermacentor variabilis. The analysis suggested that the Haller's organ is involved in olfaction, not gustation. No known odorant binding proteins like those found in insects, chemosensory lipocalins or typical insect olfactory mechanisms were identified; with the transcriptomic data only supporting a possible olfactory G-protein coupled receptor (GPCR) signal cascade unique to the Haller's organ. Each component of the olfactory GPCR signal cascade was identified and characterized. The expression of GPCR, Gαo and β-arrestin transcripts identified exclusively in the 1st leg transcriptome, and putatively Haller's organ specific, were examined in unfed and blood-fed adult female and male D. variabilis. Blood feeding to repletion in adult females down-regulated the expression of all three chemosensory transcripts in females but not in males; consistent with differences in post-feeding tick behavior between sexes and an expected reduced chemosensory function in females as they leave the host. Data are presented for the first time of the potential hormonal regulation of tick chemosensation; behavioral assays confirmed the role of the Haller's organ in N,N-diethyl-meta-toluamide (DEET) repellency but showed no role for the Haller's organ in host attachment. Further research is needed to understand the potential role of the GPCR cascade in olfaction. DA - 2017/7// PY - 2017/7// DO - 10.3390/ijms18071563 VL - 18 IS - 7 SP - SN - 1422-0067 KW - American dog tick KW - Dermacentor variabilis KW - tick KW - Haller's organ KW - olfaction KW - gustation KW - chemoreception KW - odorant binding proteins KW - GPCR KW - DEET KW - transcriptome ER - TY - JOUR TI - The transcriptional landscape of seasonal coat colour moult in the snowshoe hare AU - Ferreira, Mafalda S. AU - Alves, Paulo C. AU - Callahan, Colin M. AU - Marques, Joao P. AU - Mills, L. Scott AU - Good, Jeffrey M. AU - Melo-Ferreira, Jose T2 - MOLECULAR ECOLOGY AB - Abstract Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study, we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares ( Lepus americanus ). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to brown summer pelage. Using RNA sequencing, we tested whether patterns of expression were consistent with predictions based on the established phases of the hair growth cycle. We found functionally consistent clustering across skin types, with 766 genes differentially expressed between moult stages. “White” pelage showed more differentially expressed genes that were upregulated relative to other skin types, involved in the transition between late telogen (quiescent stage) and the onset of anagen (proliferative stage). Skin samples from transitional “intermediate” and “brown” pelage were transcriptionally similar and resembled the regressive transition to catagen (regressive stage). We also detected differential expression of several key circadian clock and pigmentation genes, providing important means to dissect the bases of alternate seasonal colour morphs. Our results reveal that pelage colour is a useful biomarker for seasonal change but that there is a consistent lag between the main gene expression waves and change in visible coat colour. These experiments establish that developmental sampling from natural populations of nonmodel organisms can provide a crucial resource to dissect the genetic basis and evolution of complex seasonally changing traits. DA - 2017/8// PY - 2017/8// DO - 10.1111/mec.14177 VL - 26 IS - 16 SP - 4173-4185 SN - 1365-294X KW - climate change KW - gene expression KW - Lepus americanus KW - RNA sequencing KW - seasonal coat colour change ER - TY - JOUR TI - The S-layer Associated Serine Protease Homolog PrtX Impacts Cell Surface-Mediated Microbe-Host Interactions of Lactobacillus acidophilus NCFM AU - Johnson, Brant R. AU - O'Flaherty, Sarah AU - Goh, Yong Jun AU - Carroll, Ian AU - Barrangou, Rodolphe AU - Klaenhammer, Todd R. T2 - FRONTIERS IN MICROBIOLOGY AB - Health-promoting aspects attributed to probiotic microorganisms, including adhesion to intestinal epithelia and modulation of the host mucosal immune system, are mediated by proteins found on the bacterial cell surface. Notably, certain probiotic and commensal bacteria contain a surface (S-) layer as the outermost stratum of the cell wall. S-layers are non-covalently bound semi-porous, crystalline arrays of self-assembling, proteinaceous subunits called S-layer proteins (SLPs). Recent evidence has shown that multiple proteins are non-covalently co-localized within the S-layer, designated S-layer associated proteins (SLAPs). In Lactobacillus acidophilus NCFM, SLP and SLAPs have been implicated in both mucosal immunomodulation and adhesion to the host intestinal epithelium. In this study, a S-layer associated serine protease, PrtX (prtX, lba1578), was deleted from the chromosome of L. acidophilus NCFM. Compared to the parent strain, the PrtX-deficient strain (∆prtX) demonstrated increased autoaggregation, an altered cellular morphology, and pleiotropic increases in adhesion to mucin and fibronectin, in vitro. Furthermore, ∆prtX demonstrated increased in vitro immune stimulation of IL-6, IL-12, and IL-10 compared to wild-type, when exposed to mouse dendritic cells. Finally, in vivo colonization of germ-free mice with ∆prtX led to an increase in epithelial barrier integrity. The absence of PrtX within the exoproteome of a ∆prtX strain caused morphological changes, resulting in a pleiotropic increase of the organisms' immunomodulatory properties and interactions with some intestinal epithelial cell components. DA - 2017/6/30/ PY - 2017/6/30/ DO - 10.3389/fmicb.2017.01185 VL - 8 SP - SN - 1664-302X KW - serine protease KW - S-layer KW - S-layer associated proteins KW - Lactobacillus KW - probiotic KW - intestinal barrier integrity KW - mucin KW - fibronectin ER - TY - JOUR TI - Stable Transmission of Borrelia burgdorferi Sensu Stricto on the Outer Banks of North Carolina AU - Levine, J. F. AU - Apperson, C. S. AU - Levin, M. AU - Kelly, T. R. AU - Kakumanu, M. L. AU - Ponnusamy, L. AU - Sutton, H. AU - Salger, S. A. AU - Caldwell, J. M. AU - Szempruch, A. J. T2 - ZOONOSES AND PUBLIC HEALTH AB - The spirochaete (Borrelia burgdorferi) associated with Lyme disease was detected in questing ticks and rodents during a period of 18 years, 1991-2009, at five locations on the Outer Banks of North Carolina. The black-legged tick (Ixodes scapularis) was collected at varied intervals between 1991 and 2009 and examined for B. burgdorferi. The white-footed mouse (Peromyscus leucopus), house mouse (Mus musculus) marsh rice rat (Oryzomys palustris), marsh rabbit (Sylvilagus palustris), eastern cottontail (Sylvilagus floridanus) and six-lined racerunner (Cnemidophorus sexlineatus) were live-trapped, and their tissues cultured to isolate spirochaetes. Borrelia burgdorferi isolates were obtained from questing adult I. scapularis and engorged I. scapularis removed from P. leucopus, O. palustris and S. floridanus. The prevalence of B. burgdorferi infection was variable at different times and sites ranging from 7 to 14% of examined questing I. scapularis. Mitochondrial (16S) rRNA gene phylogenetic analysis from 65 adult I. scapularis identified 12 haplotypes in two major clades. Nine haplotypes were associated with northern/Midwestern I. scapularis populations and three with southern I. scapularis populations. Sixteen isolates obtained from tick hosts in 2005 were confirmed to be B. burgdorferi by amplifying and sequencing of 16S rRNA and 5S-23S intergenic spacer fragments. The sequences had 98-99% identity to B. burgdorferi sensu stricto strains B31, JD1 and M11p. Taken together, these studies indicate that B. burgdorferi sensu stricto is endemic in questing I. scapularis and mammalian tick hosts on the Outer Banks of North Carolina. DA - 2017/8// PY - 2017/8// DO - 10.1111/zph.12302 VL - 64 IS - 5 SP - 337-354 SN - 1863-2378 KW - Borrelia burgdorferi KW - Ixodes scapularis KW - Peromyscus leucopus KW - Oryzomys palustris KW - Sylvilagus palustris KW - Outer Banks KW - North Carolina ER - TY - JOUR TI - Segregation of Hydroxycinnamic Acid Esters Mediating Sweetpotato Weevil Resistance in Storage Roots of Sweetpotato AU - Anyanga, M. O. AU - Yada, B. AU - Yencho, G. C. AU - Ssemakula, G. N. AU - Alajo, A. AU - Farman, D. I. AU - Mwanga, R. O. M. AU - Stevenson, P. C. T2 - Frontiers in Plant Science AB - Resistance to sweetpotato weevils, (Cylas spp.) has been identified in several sweetpotato (Ipomoea batatas) landraces from East Africa and shown to be conferred by hydroxycinnamic acids that occur on the surface of storage roots. The segregation of resistance in this crop is unknown and could be monitored using these chemical traits as markers for resistance in F1 offspring from breeding programmes. For the first time in a segregating population, we quantified the plant chemicals that confer resistance and evaluated levels of insect colonisation of the same progeny in field and laboratory studies. We used a bi-parental mapping population of 287 progenies from a cross between I. batatas ‘New Kawogo’, a weevil resistant Ugandan landrace and I. batatas ‘Beauregard’ a North American orange-fleshed and weevil susceptible cultivar. The progenies were evaluated for resistance to sweetpotato weevil, Cylas puncticollis at three field locations that varied climatically and across two seasons to determine how environment and location influenced resistance. To augment our field open-choice resistance screening, each clone was also evaluated in a no choice experiment with weevils reared in the laboratory. Chemical analysis was used to determine whether differences in resistance to weevils were associated with plant compounds previously identified as conferring resistance. We established linkage between field and laboratory resistance to Cylas spp. and sweetpotato root chemistry. The data also showed that resistance in sweetpotato was mediated by root chemicals in most but not all cases. Multi-location trials especially from Serere data provided evidence that the hydroxycinnamic acid esters are produced constitutively within the plants in different clonal genotypes and that the ecological interaction of these chemicals in sweetpotato with weevils confers resistance. Our data suggest that these chemical traits are controlled quantitatively and that ultimately a knowledge of the genetics of resistance will facilitate management of these traits, enhance our understanding of the mechanistic basis of resistance and speed the development of new sweetpotato varieties with resistance to sweetpotato weevil. DA - 2017/// PY - 2017/// DO - 10.3389/fpls.2017.01011 VL - 8 SP - 1011 KW - sweetpotato weevil KW - insect resistance KW - storage root chemistry KW - segregating population KW - Cylas ER - TY - JOUR TI - Scale and the evolutionarily based approximate number system: an exploratory study AU - Delgado, Cesar AU - Jones, M. Gail AU - You, Hye Sun AU - Robertson, Laura AU - Chesnutt, Katherine AU - Halberda, Justin T2 - INTERNATIONAL JOURNAL OF SCIENCE EDUCATION AB - Crosscutting concepts such as scale, proportion, and quantity are recognised by U.S. science standards as a potential vehicle for students to integrate their scientific and mathematical knowledge; yet, U.S. students and adults trail their international peers in scale and measurement estimation. Culturally based knowledge of scale such as measurement units may be built on evolutionarily-based systems of number such as the approximate number system (ANS), which processes approximate representations of numerical magnitude. ANS is related to mathematical achievement in pre-school and early elementary students, but there is little research on ANS among older students or in science-related areas such as scale. Here, we investigate the relationship between ANS precision in public school U.S. seventh graders and their accuracy estimating the length of standard units of measurement in SI and U.S. customary units. We also explored the relationship between ANS and science and mathematics achievement. Accuracy estimating the metre was positively and significantly related to ANS precision. Mathematics achievement, science achievement, and accuracy estimating other units were not significantly related to ANS. We thus suggest that ANS precision may be related to mathematics understanding beyond arithmetic, beyond the early school years, and to the crosscutting concepts of scale, proportion, and quantity. DA - 2017/// PY - 2017/// DO - 10.1080/09500693.2017.1312626 VL - 39 IS - 8 SP - 1008-1024 SN - 1464-5289 KW - Developmental research KW - cognition KW - evolutionarily based abilities ER - TY - JOUR TI - Responses of neonicotinoid resistant and susceptible Frankliniella fusca life stages to multiple insecticide groups in cotton AU - Huseth, Anders S AU - D'Ambrosio, Damon A AU - Kennedy, George G T2 - Pest Management Science AB - Detection of neonicotinoid resistance in populations of tobacco thrips, Frankliniella fusca Hinds, throughout the southeastern USA has motivated an examination of alternative insecticides to control problematic infestations on seedling cotton. The objective of this study was to refine understanding of stage-specific mortality and reduced oviposition of several common insecticides (acephate, abamectin, cyantraniliprole, spinetoram, imidacloprid, imidacloprid+thiodicarb, thiamethoxam) on neonicotinoid resistant and susceptible F. fusca populations under laboratory and field conditions.Laboratory studies revealed that the average number of eggs per female and larval or adult survivorship responses differed by insecticide and were dependent on the resistance status of the population. In the presence of neonicotinoids, the resistant F. fusca populations exhibited lower mortality and higher egg counts than the susceptible population. In the field study, similar patterns of oviposition suppression were observed, indicating that some insecticides may impact reproductive rate.This study shows that insecticides have different effects on F. fusca oviposition events, larval and adult mortality that are dependent on neonicotinoid resistance status. Because insecticides tested in this study have varied activity on specific F. fusca life stages (e.g. oviposition suppression, larvicidal activity, adulticidal activity), knowledge of stage-specific activity can be used to improve control and enhance long-term product stewardship. © 2017 Society of Chemical Industry. DA - 2017/7/7/ PY - 2017/7/7/ DO - 10.1002/ps.4590 VL - 73 IS - 10 SP - 2118-2130 J2 - Pest Management Science LA - en OP - SN - 1526-498X 1526-4998 UR - http://dx.doi.org/10.1002/ps.4590 DB - Crossref KW - imidacloprid KW - thiamethoxam KW - seed treatment KW - insecticide resistance management KW - Gossypium hirsutum ER - TY - JOUR TI - Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells AU - Balaguer, M. A. D. AU - Fisher, A. P. AU - Clark, N. M. AU - Fernandez-Espinosa, M. G. AU - Moller, B. K. AU - Weijers, D. AU - Lohmann, J. U. AU - Williams, C. AU - Lorenzo, O. AU - Sozzani, Rosangela AU - al. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. To accomplish this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference. We leveraged the topology of our networks to infer potential major regulators. Specifically, through mathematical modeling and experimental validation, we identified PERIANTHIA (PAN) as an important molecular regulator of quiescent center function. The results presented in this work show that our combination of molecular biology, computational biology, and mathematical modeling is an efficient approach to identify candidate factors that function in the stem cells. DA - 2017/9/5/ PY - 2017/9/5/ DO - 10.1073/pnas.1707566114 VL - 114 IS - 36 SP - E7632-E7640 SN - 0027-8424 KW - root stem cell KW - root development KW - cell-type expression profile KW - gene regulatory network KW - modeling ER - TY - JOUR TI - Patterns of preference and practice: bridging actors in wildfire response networks in the American Northwest AU - Faas, A. J. AU - Velez, Anne-Lise K. AU - FitzGerald, Clare AU - Nowell, Branda L. AU - Steelman, Toddi A. T2 - DISASTERS AB - The roles of bridging actors in emergency response networks can be important to disaster response outcomes. This paper is based on an evaluation of wildfire preparedness and response networks in 21 large‐scale wildfire events in the wildland—urban interface near national forests in the American Northwest. The study investigated how key individuals in responder networks anticipated seeking out specific people in perceived bridging roles prior to the occurrence of wildfires, and then captured who in fact assumed these roles during actual large‐scale events. It examines two plausible, but contradictory, bodies of theory—similarity and dissimilarity—that suggest who people might seek out as bridgers and who they would really go to during a disaster. Roughly one‐half of all pre‐fire nominations were consistent with similarity. Yet, while similarity is a reliable indicator of how people expect to organise, it does not hold up for how they organise during the real incident. DA - 2017/7// PY - 2017/7// DO - 10.1111/disa.12211 VL - 41 IS - 3 SP - 527-548 SN - 1467-7717 KW - bridging KW - disaster response KW - networks KW - wildfire ER - TY - JOUR TI - Hybrid modeling and prediction of dynamical systems AU - Hamilton, Franz AU - Lloyd, Alun L. AU - Flores, Kevin B. T2 - PLOS Computational Biology AB - Scientific analysis often relies on the ability to make accurate predictions of a system’s dynamics. Mechanistic models, parameterized by a number of unknown parameters, are often used for this purpose. Accurate estimation of the model state and parameters prior to prediction is necessary, but may be complicated by issues such as noisy data and uncertainty in parameters and initial conditions. At the other end of the spectrum exist nonparametric methods, which rely solely on data to build their predictions. While these nonparametric methods do not require a model of the system, their performance is strongly influenced by the amount and noisiness of the data. In this article, we consider a hybrid approach to modeling and prediction which merges recent advancements in nonparametric analysis with standard parametric methods. The general idea is to replace a subset of a mechanistic model’s equations with their corresponding nonparametric representations, resulting in a hybrid modeling and prediction scheme. Overall, we find that this hybrid approach allows for more robust parameter estimation and improved short-term prediction in situations where there is a large uncertainty in model parameters. We demonstrate these advantages in the classical Lorenz-63 chaotic system and in networks of Hindmarsh-Rose neurons before application to experimentally collected structured population data. DA - 2017/7/10/ PY - 2017/7/10/ DO - 10.1371/journal.pcbi.1005655 VL - 13 IS - 7 SP - e1005655 J2 - PLoS Comput Biol LA - en OP - SN - 1553-7358 UR - http://dx.doi.org/10.1371/journal.pcbi.1005655 DB - Crossref ER - TY - JOUR TI - Greater Coronary Heart Disease Risk With Lower Intensity and Longer Duration Smoking Compared With Higher Intensity and Shorter Duration Smoking: Congruent Results Across Diverse Cohorts AU - Lubin, Jay H. AU - Albanes, Demetrius AU - Hoppin, Jane A. AU - Chen, Honglei AU - Lerro, Catherine C. AU - Weinstein, Stephanie J. AU - Sandler, Dale P. AU - Freeman, Laura E. Beane T2 - NICOTINE & TOBACCO RESEARCH AB - Relative risks (RRs) for coronary heart disease (CHD) by cigarettes/day exhibit a concave pattern, implying the RR increase with each additional cigarette/day consumed decreases with greater intensity. Interpreting this pattern faces limitations, since cigarettes/day alone does not fully characterize smoking-related exposure. A more complete understanding of smoking and CHD risk requires a more comprehensive representation of smoking. Using Poisson regression, we applied a RR model in pack-years and cigarettes/day to analyze two diverse cohorts, the US Agricultural Health Study, with 4396 CHD events and 1 425 976 person-years of follow-up, and the Finnish Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study, with 5979 CHD events and 486 643 person-years. In both cohorts, the concave RR pattern with cigarettes/day was consistent with cigarettes/day modifying a linear RR association for CHD by pack-years within categories of cigarettes/day, indicating that strength of the pack-years association depended on cigarettes/day (p < .01). For example, at 50 pack-years (365 000 total cigarettes), estimated RRs of CHD were 2.1 for accrual at 20 cigarettes/day and 1.5 for accrual at 50 cigarettes/day. RRs for CHD increased with pack-years with smoking intensities affecting the strength of association. For equal pack-years, smoking fewer cigarettes/day for longer duration was more deleterious than smoking more cigarettes/day for shorter duration. We have now observed inverse smoking intensity effects in multiple cohorts with differing smoking patterns and other characteristics, suggesting a common underlying phenomenon. Risk of CHD increases with pack-years of smoking, but accrual intensity strongly influences the strength of the association, such that smoking fewer cigarettes/day for longer duration is more deleterious than smoking more cigarettes/day for shorter duration. This observation offers clues to better understanding biological mechanisms, and reinforces the importance of cessation rather than smoking less to reduce CHD risk. DA - 2017/7// PY - 2017/7// DO - 10.1093/ntr/ntw290 VL - 19 IS - 7 SP - 817-825 SN - 1469-994X ER - TY - JOUR TI - Germline transformation of the western corn rootworm, Diabrotica virgifera virgifera AU - Chu, F. AU - Klobasa, W. AU - Wu, P. AU - Pinzi, S. AU - Grubbs, N. AU - Gorski, S. AU - Cardoza, Y. AU - Lorenzen, M. D. T2 - Insect Molecular Biology AB - Abstract The western corn rootworm (WCR), a major pest of maize, is notorious for rapidly adapting biochemically, behaviourally and developmentally to a variety of control methods. Despite much effort, the genetic basis of WCR adaptation remains a mystery. Since transformation‐based applications such as transposon tagging and enhancer trapping have facilitated genetic dissection of model species such as Drosophila melanogaster , we developed a germline‐transformation system for WCR in an effort to gain a greater understanding of the basic biology of this economically important insect. Here we report the use of a fluorescent‐marked Minos element to create transgenic WCR. We demonstrate that the transgenic strains express both an eye‐specific fluorescent marker and piggyBac transposase . We identified insertion‐site junction sequences via inverse PCR and assessed insertion copy number using digital droplet PCR (ddPCR). Interestingly, most WCR identified as transgenic via visual screening for DsRed fluorescence proved to carry multiple Minos insertions when tested via ddPCR. A total of eight unique insertion strains were created by outcrossing the initial transgenic strains to nontransgenic WCR mates. Establishing transgenic technologies for this beetle is the first step towards bringing a wide range of transformation‐based tools to bear on understanding WCR biology. DA - 2017/4/11/ PY - 2017/4/11/ DO - 10.1111/imb.12305 VL - 26 IS - 4 SP - 440-452 J2 - Insect Mol Biol LA - en OP - SN - 0962-1075 UR - http://dx.doi.org/10.1111/imb.12305 DB - Crossref KW - Minos KW - piggyBac KW - small-scale rearing KW - embryonic microinjection ER - TY - JOUR TI - Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii AU - Coneva, Viktoriya AU - Frank, Margaret H. AU - Balaguer, Maria A. de Luis AU - Li, Mao AU - Sozzani, Rosangela AU - Chitwood, Daniel H. T2 - PLANT PHYSIOLOGY AB - Thicker leaves allow plants to grow in water-limited conditions. However, our understanding of the genetic underpinnings of this highly functional leaf shape trait is poor. We used a custom-built confocal profilometer to directly measure leaf thickness in a set of introgression lines (ILs) derived from the desert tomato Solanum pennellii and identified quantitative trait loci. We report evidence of a complex genetic architecture of this trait and roles for both genetic and environmental factors. Several ILs with thick leaves have dramatically elongated palisade mesophyll cells and, in some cases, increased leaf ploidy. We characterized the thick IL2-5 and IL4-3 in detail and found increased mesophyll cell size and leaf ploidy levels, suggesting that endoreduplication underpins leaf thickness in tomato. Next, we queried the transcriptomes and inferred dynamic Bayesian networks of gene expression across early leaf ontogeny in these lines to compare the molecular networks that pattern leaf thickness. We show that thick ILs share S. pennellii-like expression profiles for putative regulators of cell shape and meristem determinacy as well as a general signature of cell cycle-related gene expression. However, our network data suggest that leaf thickness in these two lines is patterned at least partially by distinct mechanisms. Consistent with this hypothesis, double homozygote lines combining introgression segments from these two ILs show additive phenotypes, including thick leaves, higher ploidy levels, and larger palisade mesophyll cells. Collectively, these data establish a framework of genetic, anatomical, and molecular mechanisms that pattern leaf thickness in desert-adapted tomato. DA - 2017/9// PY - 2017/9// DO - 10.1104/pp.17.00790 VL - 175 IS - 1 SP - 376-391 SN - 1532-2548 ER - TY - JOUR TI - Experimental winter warming modifies thermal performance and primes acorn ants for warm weather AU - MacLean, Heidi J. AU - Penick, Clint A. AU - Dunn, Robert R. AU - Diamond, Sarah E. T2 - Journal of Insect Physiology AB - The frequency of warm winter days is increasing under global climate change, but how organisms respond to warmer winters is not well understood. Most studies focus on growing season responses to warming. Locomotor performance is often highly sensitive to temperature, and can determine fitness outcomes through a variety of mechanisms including resource acquisition and predator escape. As a consequence, locomotor performance, and its impacts on fitness, may be strongly affected by winter warming in winter-active species. Here we use the acorn ant, Temnothorax curvispinosus, to explore how thermal performance (temperature-driven plasticity) in running speed is influenced by experimental winter warming of 3–5 °C above ambient in a field setting. We used running speed as a measure of performance as it is a common locomotor trait that influences acquisition of nest sites and food in acorn ants. Experimental winter warming significantly altered thermal performance for running speed at high (26 and 36 °C) but not low test temperatures (6 and 16 °C). Although we saw little differentiation in thermal performance at cooler test temperatures, we saw a marked increase in running speed at the hotter test temperatures for ants that experienced warmer winters compared with those that experienced cooler winters. Our results provide evidence that overwintering temperatures can substantially influence organismal performance, and suggest that we cannot ignore overwintering effects when forecasting organismal responses to environmental changes in temperature. DA - 2017/7// PY - 2017/7// DO - 10.1016/j.jinsphys.2017.05.010 VL - 100 SP - 77-81 J2 - Journal of Insect Physiology LA - en OP - SN - 0022-1910 UR - http://dx.doi.org/10.1016/j.jinsphys.2017.05.010 DB - Crossref KW - Climate change KW - Experimental climate warming KW - Running speed KW - Ants KW - Phenotypic plasticity ER - TY - JOUR TI - Effects of elevated atmospheric CO2 on dissolution of geological fluorapatite in water and soil AU - Li, Zhen AU - Su, Mu AU - Tian, Da AU - Tang, Lingyi AU - Zhang, Lin AU - Zheng, Yangfan AU - Hu, Shuijin T2 - SCIENCE OF THE TOTAL ENVIRONMENT AB - Most of phosphorus (P) is present as insoluble phosphorus-bearing minerals or organic forms in soil. Geological fluorapatite (FAp) is the dominant mineral-weathering source of P. In this study, FAp was added into water and soil under elevated CO2 to investigate the pathway of P release. Two types of soils (an acidic soil from subtropical China and a saline-alkali soil from Tibet Plateau, China) with similar total P content were studied. In the solution, increased CO2 in air enhanced the dissolution of FAp, i.e., from 0.04 to 1.18 ppm for P and from 2.48 to 13.61 ppm for Ca. In addition, release of Ca and P from FAp reached the maximum (2.14 ppm for P and 13.84 ppm for Ca) under the combination of elevated CO2 and NaCl due to the increasing ion exchange. Consistent with the results from the solution, CO2 elevation promoted P release more significantly (triple) in the saline-alkali soil than in the acidic soil. Therefore, saline-alkali soils in Tibet Plateau would be an important reservoir of available P under the global CO2 rise. This study sheds the light on understanding the geological cycle of phosphorus. DA - 2017/12/1/ PY - 2017/12/1/ DO - 10.1016/j.scitotenv.2017.05.100 VL - 599 SP - 1382-1387 SN - 1879-1026 KW - CO2 KW - Phosphorus KW - Geological fluorapatite KW - Soil KW - Dissolution ER - TY - JOUR TI - Early-life farm exposures and adult asthma and atopy in the Agricultural Lung Health Study AU - House, John S. AU - Wyss, Annah B. AU - Hoppin, Jane A. AU - Richards, Marie AU - Long, Stuart AU - Umbach, David M. AU - Henneberger, Paul K. AU - Beane Freeman, Laura E. AU - Sandler, Dale P. AU - Long O'Connell, Elizabeth AU - Barker-Cummings, Christie AU - London, Stephanie J. T2 - Journal of Allergy and Clinical Immunology AB - BackgroundPrevious studies, mostly from Europe, suggest that early-life farming exposures protect against childhood asthma and allergy; few data exist on asthma and allergy in adults.ObjectiveWe sought to examine associations between early-life farming exposures and current asthma and atopy in an older adult US farming population.MethodsWe analyzed data from 1746 farmers and 1555 spouses (mean age, 63) from a case-control study nested within the Agricultural Health Study. Current asthma and early-life farming exposures were assessed via questionnaires. We defined atopy based on specific IgE > 0.70 IU/mL to at least 1 of 10 allergens measured in blood. We used logistic regression, adjusted for age, sex, race, state (Iowa or North Carolina), and smoking (pack years), to estimate associations between early-life exposures and asthma (1198 cases and 2031 noncases) or atopy (578 cases and 2526 noncases).ResultsExposure to the farming environment in utero and in early childhood had little or no association with asthma but was associated with reduced odds of atopy. The strongest association was seen for having a mother who performed farm activities while pregnant (odds ratio, 0.60; 95% CI, 0.48-0.74) and remained significant in models with correlated early-life exposures including early childhood farm animal contact and raw milk consumption.ConclusionsIn a large US farming population, early-life farm exposures, particularly maternal farming activities while pregnant, were strongly associated with reduced risk of atopy in adults. These results extend previous work done primarily on childhood outcomes and suggest that protective associations of early-life farming exposures on atopy endure across the life course. Previous studies, mostly from Europe, suggest that early-life farming exposures protect against childhood asthma and allergy; few data exist on asthma and allergy in adults. We sought to examine associations between early-life farming exposures and current asthma and atopy in an older adult US farming population. We analyzed data from 1746 farmers and 1555 spouses (mean age, 63) from a case-control study nested within the Agricultural Health Study. Current asthma and early-life farming exposures were assessed via questionnaires. We defined atopy based on specific IgE > 0.70 IU/mL to at least 1 of 10 allergens measured in blood. We used logistic regression, adjusted for age, sex, race, state (Iowa or North Carolina), and smoking (pack years), to estimate associations between early-life exposures and asthma (1198 cases and 2031 noncases) or atopy (578 cases and 2526 noncases). Exposure to the farming environment in utero and in early childhood had little or no association with asthma but was associated with reduced odds of atopy. The strongest association was seen for having a mother who performed farm activities while pregnant (odds ratio, 0.60; 95% CI, 0.48-0.74) and remained significant in models with correlated early-life exposures including early childhood farm animal contact and raw milk consumption. In a large US farming population, early-life farm exposures, particularly maternal farming activities while pregnant, were strongly associated with reduced risk of atopy in adults. These results extend previous work done primarily on childhood outcomes and suggest that protective associations of early-life farming exposures on atopy endure across the life course. DA - 2017/7// PY - 2017/7// DO - 10.1016/j.jaci.2016.09.036 VL - 140 IS - 1 SP - 249-256.e14 J2 - Journal of Allergy and Clinical Immunology LA - en OP - SN - 0091-6749 UR - http://dx.doi.org/10.1016/j.jaci.2016.09.036 DB - Crossref KW - Agriculture KW - agricultural workers' diseases KW - allergy and immunology KW - asthma KW - hygiene hypothesis KW - IgE KW - prenatal exposure delayed effects ER - TY - JOUR TI - Do Tick Attachment Times Vary between Different Tick-Pathogen Systems? AU - Richards, Stephanie L. AU - Langley, Ricky AU - Apperson, Charles S. AU - Watson, Elizabeth T2 - ENVIRONMENTS AB - Improvements to risk assessments are needed to enhance our understanding of tick-borne disease epidemiology. We review tick vectors and duration of tick attachment required for pathogen transmission for the following pathogens/toxins and diseases: (1) Anaplasma phagocytophilum (anaplasmosis); (2) Babesia microti (babesiosis); (3) Borrelia burgdorferi (Lyme disease); (4) Southern tick-associated rash illness; (5) Borrelia hermsii (tick-borne relapsing fever); (6) Borrelia parkeri (tick-borne relapsing fever); (7) Borrelia turicatae (tick-borne relapsing fever); (8) Borrelia mayonii; (9) Borrelia miyamotoi; (10) Coxiella burnetii (Query fever); (11) Ehrlichia chaffeensis (ehrlichiosis); (12) Ehrlichia ewingii (ehrlichiosis); (13) Ehrlichia muris; (14) Francisella tularensis (tularemia); (15) Rickettsia 364D; (16) Rickettsia montanensis; (17) Rickettsia parkeri (American boutonneuse fever, American tick bite fever); (18) Rickettsia ricketsii (Rocky Mountain spotted fever); (19) Colorado tick fever virus (Colorado tick fever); (20) Heartland virus; (21) Powassan virus (Powassan disease); (22) tick paralysis neurotoxin; and (23) Galactose-α-1,3-galactose (Mammalian Meat Allergy-alpha-gal syndrome). Published studies for 12 of the 23 pathogens/diseases showed tick attachment times. Reported tick attachment times varied (<1 h to seven days) between pathogen/toxin type and tick vector. Not all studies were designed to detect the duration of attachment required for transmission. Knowledge of this important aspect of vector competence is lacking and impairs risk assessment for some tick-borne pathogens. DA - 2017/6// PY - 2017/6// DO - 10.3390/environments4020037 VL - 4 IS - 2 SP - SN - 2076-3298 KW - duration of tick attachment KW - tick-borne disease KW - tick KW - transmission dynamics ER - TY - JOUR TI - Differentiation of Life-History Traits among Palmer Amaranth Populations (Amaranthus palmeri) and Its Relation to Cropping Systems and Glyphosate Sensitivity AU - Bravo, Washington AU - Leon, Ramon G. AU - Ferrell, Jason A. AU - Mulvaney, Michael J. AU - Wood, C. Wesley T2 - WEED SCIENCE AB - Palmer amaranth’s ability to evolve resistance to different herbicides has been studied extensively, but there is little information about how this weed species might be evolving other life-history traits that could potentially make it more aggressive and difficult to control. We characterized growth and morphological variation among 10 Palmer amaranth populations collected in Florida and Georgia from fields with different cropping histories, ranging from continuous short-statured crops (vegetables and peanut) to tall crops (corn and cotton) and from intensive herbicide use history to organic production. Palmer amaranth populations differed in multiple traits such as fresh and dry weight, days to flowering, plant height, and leaf and canopy shape. Differences between populations for these traits ranged from 36% up to 87%. Although glyphosate-resistant (GR) populations collected from cropping systems including GR crops exhibited higher values of the aforementioned variables than glyphosate-susceptible (GS) populations, variation in traits was not explained by glyphosate resistance or distance between populations. Cropping system components such as crop rotation and crop canopy structure better explained the differences among populations. The higher growth of GR populations compared with GS populations was likely the result of multiple selection forces present in the cropping systems in which they grow rather than a pleiotropic effect of the glyphosate resistance trait. Results suggest that Palmer amaranth can evolve life-history traits increasing its growth and reproduction potential in cropping systems, which explains its rapid spread throughout the United States. Furthermore, our findings highlight the need to consider the evolutionary consequences of crop rotation structure and the use of more competitive crops, which might promote the selection of more aggressive biotypes in weed species with high genetic variability. DA - 2017/// PY - 2017/// DO - 10.1017/wsc.2017.14 VL - 65 IS - 3 SP - 339-349 SN - 1550-2759 KW - Crop rotation KW - evolution KW - integrated weed management KW - resistance KW - variability ER - TY - JOUR TI - Building Practical Authority for Community Forestry in and through Networks: The role of community-based organisations in the US West AU - Abrams, Jesse AU - Davis, Emily Jane AU - Moseley, Cassandra AU - Nowell, Branda T2 - ENVIRONMENTAL POLICY AND GOVERNANCE AB - Policy and economic changes in the late 20th century fundamentally reorganized the governance of public forestlands in the US West, throwing longstanding rural development trajectories into disarray. Place-based NGOs emerged across the West in the wake of this transformation to help rural communities gain access to the benefits of new restoration-oriented management paradigms. Here we analyse the practical efforts of two of these community-based organizations, Wallowa Resources and the Watershed Research and Training Center, as they attempt to implement community forestry practices in highly complex institutional environments. We focus on the ways in which these organizations access and utilize social networks at multiple scales in order to build the ‘practical authority’ necessary to lead institutional change efforts in and on behalf of rural communities. We consider both the strategic advantages and the practical challenges of working in multiple forums at multiple scales in pursuit of linked community and environmental benefits. Copyright © 2017 John Wiley & Sons, Ltd and ERP Environment DA - 2017/// PY - 2017/// DO - 10.1002/eet.1765 VL - 27 IS - 4 SP - 285-297 SN - 1756-9338 KW - non-governmental organizations KW - rural development KW - community-based natural resource management KW - implementation KW - public lands KW - institutional change ER - TY - JOUR TI - Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root AU - Di Mambro, Riccardo AU - De Ruvo, Micol AU - Pacifici, Elena AU - Salvi, Elena AU - Sozzani, Rosangela AU - Benfey, Philip N. AU - Busch, Wolfgang AU - Novak, Ondrej AU - Ljung, Karin AU - Di Paola, Luisa AU - Maree, Athanasius F. M. AU - Costantino, Paolo AU - Grieneisen, Veronica A. AU - Sabatini, Sabrina T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the Arabidopsis root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin's control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size. DA - 2017/9/5/ PY - 2017/9/5/ DO - 10.1073/pnas.1705833114 VL - 114 IS - 36 SP - E7641-E7649 SN - 0027-8424 KW - plant hormones KW - cell differentiation KW - root meristem KW - computational modeling ER - TY - JOUR TI - Adaptive filtering for hidden node detection and tracking in networks AU - Hamilton, Franz AU - Setzer, Beverly AU - Chavez, Sergio AU - Tran, Hien AU - Lloyd, Alun L. T2 - Chaos: An Interdisciplinary Journal of Nonlinear Science AB - The identification of network connectivity from noisy time series is of great interest in the study of network dynamics. This connectivity estimation problem becomes more complicated when we consider the possibility of hidden nodes within the network. These hidden nodes act as unknown drivers on our network and their presence can lead to the identification of false connections, resulting in incorrect network inference. Detecting the parts of the network they are acting on is thus critical. Here, we propose a novel method for hidden node detection based on an adaptive filtering framework with specific application to neuronal networks. We consider the hidden node as a problem of missing variables when model fitting and show that the estimated system noise covariance provided by the adaptive filter can be used to localize the influence of the hidden nodes and distinguish the effects of different hidden nodes. Additionally, we show that the sequential nature of our algorithm allows for tracking changes in the hidden node influence over time. DA - 2017/7// PY - 2017/7// DO - 10.1063/1.4990985 VL - 27 IS - 7 SP - 073106 J2 - Chaos LA - en OP - SN - 1054-1500 1089-7682 UR - http://dx.doi.org/10.1063/1.4990985 DB - Crossref ER - TY - JOUR TI - A decade of discovery: CRISPR functions and applications AU - Barrangou, Rodolphe AU - Horvath, Philippe T2 - NATURE MICROBIOLOGY AB - This year marks the tenth anniversary of the identification of the biological function of CRISPR–Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR–Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology. Lastly, we provide a perspective on the impacts the field has had on science and beyond. In this Review Article, Horvath and Barrangou describe the discovery of CRISPR–Cas systems as mechanisms of adaptive immunity in prokaryotes and explore the technological applications that have emerged from studying these molecular machines. DA - 2017/7// PY - 2017/7// DO - 10.1038/nmicrobiol.2017.92 VL - 2 IS - 7 SP - SN - 2058-5276 ER - TY - JOUR TI - Testing the relative importance of local resources and landscape connectivity on Bombus impatiens (Hymenoptera, Apidae) colonies AU - Herrmann, John D. AU - Haddad, Nick M. AU - Levey, Douglas J. T2 - APIDOLOGIE AB - Bee populations are decreasing worldwide. The underlying causes are likely determined by factors at different scales. We tested the relative importance of local resources and landscape connectivity on 64 bumblebee (Bombus impatiens) colonies in experimentally isolated and connected habitat fragments. We used colony mass, no. of workers, and no. of gynes to estimate colony performance. Landscape connectivity did not significantly affect colony performance, but local floral resources had a significantly positive effect, especially in isolated fragments. These results suggest that bumblebee colonies encountered sufficient floral resources within the local 1.4 ha habitat fragments to support colony growth, making long-distance foraging trips to neighboring fragments unnecessary. From a conservation perspective, we suggest that efforts to improve colony performance should prioritize boosting local floral resources over manipulation of large-scale landscape features. DA - 2017/7// PY - 2017/7// DO - 10.1007/s13592-017-0499-1 VL - 48 IS - 4 SP - 545-555 SN - 1297-9678 KW - agri-environment scheme KW - foraging distance KW - landscape connectivity KW - habitat fragmentation KW - floral resources ER - TY - JOUR TI - THERMOCHEMICAL CONVERSION: A PROSPECTIVE SWINE MANURE SOLUTION FOR NORTH CAROLINA AU - Lentz, Z. AU - Classen, J. AU - Kolar, P. T2 - TRANSACTIONS OF THE ASABE AB - Abstract. The growth of North Carolina’s swine industry in recent decades has led to a subsequent increase in the production of swine manure. This manure represents a potential threat to environmental and human health, as well as an opportunity to add value to pork production. Technologies for treating swine manure safely while generating products to offset costs are part of an expanding field of research centered on sustainable food production for our growing population. Thermochemical conversion processes use heat to degrade organic feedstocks and drive chemical reactions, which generate valuable products. The high moisture content of swine manure is prohibitive for most thermochemical processes, but gasification and hydrothermal carbonization may be more accommodating. Gasification, a time-tested thermochemical conversion process, yields a combustible gas through a series of endothermic reactions, and hydrothermal carbonization yields a solid, coal-like char that can be used as a fuel or chemical precursor. Advances in thermochemical conversion processes have indicated the potential for yielding valuable products from swine manure, but viable scalable processes are still under development, requiring further research to apply these processes to swine manure management and evaluate the usefulness of their products. This review (1) describes, generally, thermochemical conversion via both hydrothermal gasification (HTG) and hydrothermal carbonization (HTC), (2) shows the usefulness of each conversion process for biomass, and (3) discusses the potential of HTG and HTC of swine manure to enhance the value of pork production. Keywords: Energy, Gases, Hydrothermal carbonization, Hydrothermal gasification, Pig manure, Pigs, Sustainable. DA - 2017/// PY - 2017/// DO - 10.13031/trans.12074 VL - 60 IS - 3 SP - 591-600 SN - 2151-0040 KW - Energy KW - Gases KW - Hydrothermal carbonization KW - Hydrothermal gasification KW - Pig manure KW - Pigs KW - Sustainable ER - TY - JOUR TI - Soil and Foliar Arthropod Abundance and Diversity in Five Cropping Systems in the Coastal Plains of North Carolina AU - Adams, Paul R., III AU - Orr, David B. AU - Arellano, Consuelo AU - Cardoza, Yasmin J. T2 - ENVIRONMENTAL ENTOMOLOGY AB - Soil and foliar arthropod populations in agricultural settings respond to environmental disturbance and degradation, impacting functional biodiversity in agroecosystems. The objective of this study was to evaluate system level management effects on soil and foliar arthropod abundance and diversity in corn and soybean. Our field experiment was a completely randomized block design with three replicates for five farming systems which included: Conventional clean till, conventional long rotation, conventional no-till, organic clean till, and organic reduced till. Soil arthropod sampling was accomplished by pitfall trapping. Foliar arthropod sampling was accomplished by scouting corn and sweep netting soybean. Overall soil arthropod abundance was significantly impacted by cropping in corn and for foliar arthropods in soybeans. Conventional long rotation and organic clean till systems were highest in overall soil arthropod abundance for corn while organic reduced till systems exceeded all other systems for overall foliar arthropod abundance in soybeans. Foliar arthropod abundance over sampling weeks was significantly impacted by cropping system and is suspected to be the result of in-field weed and cover crop cultivation practices. This suggests that the sum of management practices within production systems impact soil and foliar arthropod abundance and diversity and that the effects of these systems are dynamic over the cropping season. Changes in diversity may be explained by weed management practices as sources of disturbance and reduced arthropod refuges via weed reduction. Furthermore, our results suggest agricultural systems lower in management intensity, whether due to organic practices or reduced levels of disturbance, foster greater arthropod diversity. DA - 2017/8// PY - 2017/8// DO - 10.1093/ee/nvx081 VL - 46 IS - 4 SP - 771-783 SN - 1938-2936 KW - organic farming KW - conventional farming KW - clean tillage KW - reduced tillage KW - arthropod abundance and diversity ER - TY - JOUR TI - Selection of simple sequence repeat markers associated with inheritance of sweetpotato virus disease resistance in sweetpotato AU - Yada, B. AU - Alajo, A. AU - Ssemakula, G. N. AU - Mwanga, R. O. M. AU - Brown-Guedira, G. AU - Yencho, G. C. T2 - Crop Science AB - Sweetpotato virus disease (SPVD), a complex of Sweet potato chlorotic stunt virus (SPCSV; Crinivirus ) and Sweet potato feathery mottle virus (SPFMV; Potyvirus ) causes high yield losses in sub‐Saharan Africa (SSA). The development of resistant cultivars to SPVD has been limited by the complex sweetpotato [ Ipomoea batatas (L.) Lam. var. batatas ] genetics and high levels of mutations in the causal viruses. The objectives of this study were to understand the inheritance of SPVD resistance and identify simple‐sequence repeat (SSR) markers associated with its resistance in a biparental sweetpotato mapping population. A total of 287 progeny and parents of the ‘New Kawogo’ × ‘Beauregard’ population were genotyped with 250 SSR markers and phenotyped for SPVD resistance at three sites and two seasons in Uganda. The broad‐sense heritability for SPVD resistance was 0.51. Two progeny showed positive transgressive segregation for overall genotype mean SPVD severity across sites and seasons. A total of seven SSR markers were significantly associated with SPVD resistance in this population. These markers and other SSRs need to be used to fine map the quantitative trait loci (QTL) of SPVD resistance for future implementation of marker‐assisted selection (MAS) for SPVD resistance in sweetpotato. DA - 2017/// PY - 2017/// DO - 10.2135/cropsci2016.08.0695 VL - 57 IS - 3 SP - 1421-1430 ER - TY - JOUR TI - Redundancy as a strategy in disaster response systems: A pathway to resilience or a recipe for disaster? AU - Nowell, Branda AU - Bodkin, Candice Pippin AU - Bayoumi, Deena T2 - JOURNAL OF CONTINGENCIES AND CRISIS MANAGEMENT AB - Public management scholars have long sought to understand design principles that can promote the adaptability and resilience of complex organizational systems operating in uncertain and turbulent environments. Perhaps nowhere is this need more acute than in developing systems for responding to complex disasters. One concept that has received significant attention in discussion of resilient systems design is the notion of redundancy; however, existing literatures offer contradictory theories as to whether redundant designs enhance or undermine system resilience. Using case study data from three large‐scale wildfire events, this article extends the theoretical discussion of redundancy by developing a typology of redundancy strategies and investigating their application and associated consequences in incident response. Our findings reveal four principal ways redundancy can be integrated into system design: backup, cross‐functionality, duplication and cross‐checking. Further, each redundancy type is associated with its own capabilities for enhancing system resilience as well as its own set of risk factors that, if left unmanaged, could undermine system functioning. Findings demonstrate how understanding both the potential value and risk portfolio associated with each type of redundancy clarifies the management challenge for responders when employing these strategies. DA - 2017/9// PY - 2017/9// DO - 10.1111/1468-5973.12178 VL - 25 IS - 3 SP - 123-135 SN - 1468-5973 ER - TY - JOUR TI - Pesticides are Associated with Allergic and Non-Allergic Wheeze among Male Farmers AU - Hoppin, Jane A. AU - Umbach, David M. AU - Long, Stuart AU - London, Stephanie J. AU - Henneberger, Paul K. AU - Blair, Aaron AU - Alavanja, Michael AU - Freeman, Laura E. Beane AU - Sandler, Dale P. T2 - Environmental Health Perspectives AB - Background:Growing evidence suggests that pesticide use may contribute to respiratory symptoms.Objective:We evaluated the association of currently used pesticides with allergic and non-allergic wheeze among male farmers.Methods:Using the 2005–2010 interview data of the Agricultural Health Study, a prospective study of farmers in North Carolina and Iowa, we evaluated the association between allergic and non-allergic wheeze and self-reported use of 78 specific pesticides, reported by ≥ 1% of the 22,134 men interviewed. We used polytomous regression models adjusted for age, BMI, state, smoking, and current asthma, as well as for days applying pesticides and days driving diesel tractors. We defined allergic wheeze as reporting both wheeze and doctor-diagnosed hay fever (n = 1,310, 6%) and non-allergic wheeze as reporting wheeze but not hay fever (n = 3,939, 18%); men without wheeze were the referent.Results:In models evaluating current use of specific pesticides, 19 pesticides were significantly associated (p < 0.05) with allergic wheeze (18 positive, 1 negative) and 21 pesticides with non-allergic wheeze (19 positive, 2 negative); 11 pesticides were associated with both. Seven pesticides (herbicides: 2,4-D and simazine; insecticides: carbaryl, dimethoate, disulfoton, and zeta-cypermethrin; and fungicide pyraclostrobin) had significantly different associations for allergic and non-allergic wheeze. In exposure–response models with up to five exposure categories, we saw evidence of an exposure–response relationship for several pesticides including the commonly used herbicides 2,4-D and glyphosate, the insecticides permethrin and carbaryl, and the rodenticide warfarin.Conclusions:These results for farmers implicate several pesticides that are commonly used in agricultural and residential settings with adverse respiratory effects.Citation:Hoppin JA, Umbach DM, Long S, London SJ, Henneberger PK, Blair A, Alavanja M, Beane Freeman LE, Sandler DP. 2017. Pesticides are associated with allergic and non-allergic wheeze among male farmers. Environ Health Perspect 125:535–543; http://dx.doi.org/10.1289/EHP315 DA - 2017/4// PY - 2017/4// DO - 10.1289/ehp315 VL - 125 IS - 4 SP - 535-543 J2 - Environmental Health Perspectives LA - en OP - SN - 0091-6765 1552-9924 UR - http://dx.doi.org/10.1289/EHP315 DB - Crossref ER - TY - JOUR TI - Occupational Exposure to Pesticides and the Incidence of Lung Cancer in the Agricultural Health Study AU - Bonner, M. R. AU - Freeman, L. E. B. AU - Hoppin, Jane AU - Koutros, S. AU - Sandler, D. P. AU - Lynch, C. F. AU - Hines, C. J. AU - Thomas, K. AU - Blair, A. AU - Alavanja, M. C. R. AU - al. T2 - Environmental Health Perspectives AB - Occupational pesticide use is associated with lung cancer in some, but not all, epidemiologic studies. In the Agricultural Health Study (AHS), we previously reported positive associations between several pesticides and lung cancer incidence.We evaluated use of 43 pesticides and 654 lung cancer cases after 10 years of additional follow-up in the AHS, a prospective cohort study comprising 57,310 pesticide applicators from Iowa and North Carolina.Information about lifetime pesticide use and other factors was ascertained at enrollment (1993-1997) and updated with a follow-up questionnaire (1999-2005). Cox proportional hazards models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs), adjusting for smoking (smoking status and pack-years), sex, and lifetime days of use of any pesticides.Hazard ratios were elevated in the highest exposure category of lifetime days of use for pendimethalin (1.50; 95% CI: 0.98, 2.31), dieldrin (1.93; 95% CI: 0.70, 5.30), and chlorimuron ethyl (1.74; 95% CI: 1.02, 2.96), although monotonic exposure-response gradients were not evident. The HRs for intensity-weighted lifetime days of use of these pesticides were similar. For parathion, the trend was statistically significant for intensity-weighted lifetime days (p = 0.049) and borderline for lifetime days (p = 0.073). None of the remaining pesticides evaluated was associated with lung cancer incidence.These analyses provide additional evidence for an association between pendimethalin, dieldrin, and parathion use and lung cancer risk. We found an association between chlorimuron ethyl, a herbicide introduced in 1986, and lung cancer that has not been previously reported. Continued follow-up is warranted. DA - 2017/4// PY - 2017/4// DO - 10.1289/ehp456 VL - 125 IS - 4 SP - 544-551 J2 - Environmental Health Perspectives LA - en OP - SN - 0091-6765 1552-9924 UR - http://dx.doi.org/10.1289/EHP456 DB - Crossref ER - TY - JOUR TI - Microsatellite Markers Reveal a Predominant Sugarcane Aphid (Homoptera: Aphididae) Clone is Found on Sorghum in Seven States and One Territory of the USA AU - Harris-Shultz, Karen AU - Ni, Xinzhi AU - Wadl, Phillip A. AU - Wang, Xinwang AU - Wang, Hongliang AU - Huang, Fangneng AU - Flanders, Kathy AU - Seiter, Nicholas AU - Kerns, David AU - Meagher, Robert AU - Xue, Qingwu AU - Reisig, Dominic AU - Buntin, David AU - Cuevas, Hugo E. AU - Brewer, Michael J. AU - Yang, Xiangbing T2 - CROP SCIENCE AB - The sugarcane aphid ( Melanaphis sacchari ) has become a serious pest causing severe economic losses to sorghum [ Sorghum bicolor (L.) Moench] grown in the southern United States. Since its original detection in four states in 2013, M. sacchari on sorghum has now, in 2016, spread to 19 states. The presence of one or multiple genotypes on sorghum in the United States has not yet been established. In this study, genome sequencing of M. sacchari was used to develop microsatellite markers. A total of 8,665,267 reads and 1.44 Gb of nucleotide sequences were generated, and 79.6% of the reads were from M. sacchari . Melanaphis sacchari DNA from 46 samples from 17 locations across seven states and one US territory was polymerase chain reaction (PCR) amplified using 38 newly created microsatellite markers, as well as 14 published microsatellite markers. Genotyping with the 52 microsatellite markers indicated that the samples of M. sacchari on sorghum were all one genotype, with the exception of a single sample collected from Sinton, TX, which had the predominant genotype as well as another genotype. Genotyping of the aphid samples with 12 microsatellite markers for Buchnera aphidicola , the obligate aphid symbiont, had nearly identical results. The invasive M. sacchari on sorghum appears to be spreading in the United States on sorghum as primarily one asexual clone. DA - 2017/// PY - 2017/// DO - 10.2135/cropsci2016.12.1010 VL - 57 IS - 4 SP - 2064-2072 SN - 1435-0653 ER - TY - JOUR TI - Genome Stability in Engineered Strains of the Extremely Thermophilic Lignocellulose-Degrading Bacterium Caldicellulosiruptor bescii AU - Williams-Rhaesa, Amanda M. AU - Poole, Farris L., II AU - Dinsmore, Jessica T. AU - Lipscomb, Gina L. AU - Rubinstein, Gabriel M. AU - Scott, Israel M. AU - Conway, Jonathan M. AU - Lee, Laura L. AU - Khatibi, Piyum A. AU - Kelly, Robert M. AU - Adams, Michael W. W. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT Caldicellulosiruptor bescii is the most thermophilic cellulose degrader known and is of great interest because of its ability to degrade nonpretreated plant biomass. For biotechnological applications, an efficient genetic system is required to engineer it to convert plant biomass into desired products. To date, two different genetically tractable lineages of C. bescii strains have been generated. The first (JWCB005) is based on a random deletion within the pyrimidine biosynthesis genes pyrFA , and the second (MACB1018) is based on the targeted deletion of pyrE , making use of a kanamycin resistance marker. Importantly, an active insertion element, IS Cbe4 , was discovered in C. bescii when it disrupted the gene for lactate dehydrogenase ( ldh ) in strain JWCB018, constructed in the JWCB005 background. Additional instances of IS Cbe4 movement in other strains of this lineage are presented herein. These observations raise concerns about the genetic stability of such strains and their use as metabolic engineering platforms. In order to investigate genome stability in engineered strains of C. bescii from the two lineages, genome sequencing and Southern blot analyses were performed. The evidence presented shows a dramatic increase in the number of single nucleotide polymorphisms, insertions/deletions, and IS Cbe4 elements within the genome of JWCB005, leading to massive genome rearrangements in its daughter strain, JWCB018. Such dramatic effects were not evident in the newer MACB1018 lineage, indicating that JWCB005 and its daughter strains are not suitable for metabolic engineering purposes in C. bescii . Furthermore, a facile approach for assessing genomic stability in C. bescii has been established. IMPORTANCE Caldicellulosiruptor bescii is a cellulolytic extremely thermophilic bacterium of great interest for metabolic engineering efforts geared toward lignocellulosic biofuel and bio-based chemical production. Genetic technology in C. bescii has led to the development of two uracil auxotrophic genetic background strains for metabolic engineering. We show that strains derived from the genetic background containing a random deletion in uracil biosynthesis genes ( pyrFA ) have a dramatic increase in the number of single nucleotide polymorphisms, insertions/deletions, and IS Cbe4 insertion elements in their genomes compared to the wild type. At least one daughter strain of this lineage also contains large-scale genome rearrangements that are flanked by these IS Cbe4 elements. In contrast, strains developed from the second background strain developed using a targeted deletion strategy of the uracil biosynthetic gene pyrE have a stable genome structure, making them preferable for future metabolic engineering studies. DA - 2017/7// PY - 2017/7// DO - 10.1128/aem.00444-17 VL - 83 IS - 14 SP - SN - 1098-5336 KW - Southern blotting KW - genome sequencing KW - insertion elements KW - kanamycin resistance ER - TY - JOUR TI - Extremely thermophilic energy metabolisms: biotechnological prospects AU - Straub, Christopher T. AU - Zeldes, Benjamin M. AU - Schut, Gerrit J. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - CURRENT OPINION IN BIOTECHNOLOGY AB - New strategies for metabolic engineering of extremely thermophilic microorganisms to produce bio-based fuels and chemicals could leverage pathways and physiological features resident in extreme thermophiles for improved outcomes. Furthermore, very recent advances in genetic tools for these microorganisms make it possible for them to serve as metabolic engineering hosts. Beyond providing a higher temperature alternative to mesophilic platforms, exploitation of strategic metabolic characteristics of high temperature microorganisms grants new opportunities for biotechnological products. This review considers recent developments in extreme thermophile biology as they relate to new horizons for energy biotechnology. DA - 2017/6// PY - 2017/6// DO - 10.1016/j.copbio.2017.02.016 VL - 45 SP - 104-112 SN - 1879-0429 ER - TY - JOUR TI - Effects of nutrient additions on litter decomposition regulated by phosphorus-induced changes in litter chemistry in a subtropical forest, China AU - Zheng, Zemei AU - Mamuti, Meiliban AU - Liu, Heming AU - Shu, Yuqin AU - Hu, Shuijin AU - Wang, Xihua AU - Li, Binbin AU - Lin, Li AU - Li, Xu T2 - FOREST ECOLOGY AND MANAGEMENT AB - Nutrient additions directly alter exogenous nutrient availability in soil, and then affect endogenous nutrient concentration in litter (i.e., litter chemistry), modifying litter decomposition. However, how nutrient-induced changes in litter chemistry interacting with altered soil nutrients affect litter decomposition remain unclear. In this study, three field experiments with reciprocal transplants using litter bags were conducted in a phosphorous (P) limiting subtropical forest with control, nitrogen addition (+N), P addition (+P), and +NP treatments to examine effects of exogenous and endogenous nutrient availability on litter decomposition. Our results showed that, in Experiment I, decomposition of litter collected from the control plots was significantly inhibited by 16% under both +P and +NP treatments and reversed to become net P accumulation from P release compared to that in the control. In Experiment II, since litter collected from +P and +NP plots had higher litter P, lower C/P and N/P, its decomposition was significantly faster in the control plots by 9% and 26%, respectively, with the faster release of N and P in the litter. The in situ Experiment III found that +P and +NP treatments reduced litter decomposition by 6% and 14%, respectively, but +N did not affect it compared to the control. Our results indicate that effects of P addition on litter decomposition were mediated by P-induced changes in litter chemistry, which need to be incorporated into land surface models for predicting effects of nutrient deposition on ecosystem C cycling and assessing the climate-biosphere feedbacks. Effects of nutrient additions on litter decomposition were regulated by P-induced changes in litter chemistry. DA - 2017/9/15/ PY - 2017/9/15/ DO - 10.1016/j.foreco.2017.06.002 VL - 400 SP - 123-128 SN - 1872-7042 KW - Nutrient availability KW - P limitation KW - Litter decay KW - Fertilization ER - TY - JOUR TI - A global database of ant species abundances AU - Gibb, Heloise AU - Dunn, Rob R. AU - Sanders, Nathan J. AU - Grossman, Blair F. AU - Photakis, Manoli AU - Abril, Silvia AU - Agosti, Donat AU - Andersen, Alan N. AU - Angulo, Elena AU - Armbrecht, Inge AU - Arnan, Xavier AU - Baccaro, Fabricio B. AU - Bishop, Tom R. AU - Boulay, Raphael AU - Bruehl, Carsten AU - Castracani, Cristina AU - Cerda, Xim AU - Del Toro, Israel AU - Delsinne, Thibaut AU - Diaz, Mireia AU - Donoso, David A. AU - Ellison, Aaron M. AU - Enriquez, Martha L. AU - Fayle, Tom M. AU - Feener, Donald H., Jr. AU - Fisher, Brian L. AU - Fisher, Robert N. AU - Fitzpatrick, Matthew C. AU - Gomez, Crisanto AU - Gotelli, Nicholas J. AU - Gove, Aaron AU - Grasso, Donato A. AU - Groc, Sarah AU - Guenard, Benoit AU - Gunawardene, Nihara AU - Heterick, Brian AU - Hoffmann, Benjamin AU - Janda, Milan AU - Jenkins, Clinton AU - Kaspari, Michael AU - Klimes, Petr AU - Lach, Lori AU - Laeger, Thomas AU - Lattke, John AU - Leponce, Maurice AU - Lessard, Jean-Philippe AU - Longino, John AU - Lucky, Andrea AU - Luke, Sarah H. AU - Majer, Jonathan AU - McGlynn, Terrence P. AU - Menke, Sean AU - Mezger, Dirk AU - Mori, Alessandra AU - Moses, Jimmy AU - Munyai, Thinandavha Caswell AU - Pacheco, Renata AU - Paknia, Omid AU - Pearce-Duvet, Jessica AU - Pfeiffer, Martin AU - Philpott, Stacy M. AU - Resasco, Julian AU - Retana, Javier AU - Silva, Rogerio R. AU - Sorger, Magdalena D. AU - Souza, Jorge AU - Suarez, Andrew AU - Tista, Melanie AU - Vasconcelos, Heraldo L. AU - Vonshak, Merav AU - Weiser, Michael D. AU - Yates, Michelle AU - Parr, Catherine L. T2 - ECOLOGY AB - What forces structure ecological assemblages? A key limitation to general insights about assemblage structure is the availability of data that are collected at a small spatial grain (local assemblages) and a large spatial extent (global coverage). Here, we present published and unpublished data from 51 ,388 ant abundance and occurrence records of more than 2,693 species and 7,953 morphospecies from local assemblages collected at 4,212 locations around the world. Ants were selected because they are diverse and abundant globally, comprise a large fraction of animal biomass in most terrestrial communities, and are key contributors to a range of ecosystem functions. Data were collected between 1949 and 2014, and include, for each geo-referenced sampling site, both the identity of the ants collected and details of sampling design, habitat type, and degree of disturbance. The aim of compiling this data set was to provide comprehensive species abundance data in order to test relationships between assemblage structure and environmental and biogeographic factors. Data were collected using a variety of standardized methods, such as pitfall and Winkler traps, and will be valuable for studies investigating large-scale forces structuring local assemblages. Understanding such relationships is particularly critical under current rates of global change. We encourage authors holding additional data on systematically collected ant assemblages, especially those in dry and cold, and remote areas, to contact us and contribute their data to this growing data set. DA - 2017/3// PY - 2017/3// DO - 10.1002/ecy.1682 VL - 98 IS - 3 SP - 883-884 SN - 1939-9170 KW - abundance KW - ants KW - database KW - disturbance KW - Formicidae KW - geo-referenced KW - habitat KW - local assemblage KW - ccurrence KW - pitfall trap KW - Winkler trap ER - TY - JOUR TI - Two Distinct alpha-L-Arabinofuranosidases in Caldicellulosiruptor Species Drive Degradation of Arabinose-Based Polysaccharides AU - Abu Saleh, Mohammad AU - Han, Wen-Jie AU - Lu, Ming AU - Wang, Bing AU - Li, Huayue AU - Kelly, Robert M. AU - Li, Fu-Li T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - Species in the extremely thermophilic genus Caldicellulosiruptor can degrade unpretreated plant biomass through the action of multimodular glycoside hydrolases. To date, most focus with these bacteria has been on hydrolysis of glucans and xylans, while the biodegradation mechanism for arabinose-based polysaccharides remains unclear. Here, putative α-l-arabinofuranosidases (AbFs) were identified in Caldicellulosiruptor species by homology to less-thermophilic versions of these enzymes. From this screen, an extracellular XynF was determined to be a key factor in hydrolyzing α-1,2-, α-1,3-, and α-1,5-l-arabinofuranosyl residues of arabinose-based polysaccharides. Combined with a GH11 xylanase (XynA), XynF increased arabinoxylan hydrolysis more than 6-fold compared to the level seen with XynA alone, likely the result of XynF removing arabinofuranosyl side chains to generate linear xylans that were readily degraded. A second AbF, the intracellular AbF51, preferentially cleaved the α-1,5-l-arabinofuranosyl glycoside bonds within sugar beet arabinan. β-Xylosidases, such as GH39 Xyl39B, facilitated the hydrolysis of arabinofuranosyl residues at the nonreducing terminus of the arabinose-branched xylo-oligosaccharides by AbF51. These results demonstrate the separate but complementary contributions of extracellular XynF and cytosolic AbF51 in processing the bioconversion of arabinose-containing oligosaccharides to fermentable monosaccharides.IMPORTANCE Degradation of hemicellulose, due to its complex chemical structure, presents a major challenge during bioconversion of lignocellulosic biomass to biobased fuels and chemicals. Degradation of arabinose-containing polysaccharides, in particular, can be a key bottleneck in this process. Among Caldicellulosiruptor species, the multimodular arabinofuranosidase XynF is present in only selected members of this genus. This enzyme exhibited high hydrolysis activity, broad specificity, and strong synergism with other hemicellulases acting on arabino-polysaccharides. An intracellular arabinofuranosidase, AbF51, occurs in all Caldicellulosiruptor species and, in conjunction with xylosidases, processes the bioconversion of arabinose-branched oligosaccharides to fermentable monosaccharides. Taken together, the data suggest that plant biomass degradation in Caldicellulosiruptor species involves extracellular XynF that acts synergistically with other hemicellulases to digest arabino-polysaccharides that are subsequently transported and degraded further by intracellular AbF51 to produce short-chain arabino sugars. DA - 2017/7// PY - 2017/7// DO - 10.1128/aem.00574-17 VL - 83 IS - 13 SP - SN - 1098-5336 KW - Arabinofuranosidase KW - bioenergy KW - glycoside hydrolase KW - hyperthermophiles KW - synergism ER - TY - JOUR TI - The rice production practices of high yield and high nitrogen use efficiency in Jiangsu, China AU - Guo, Jiuxin AU - Hu, Xiangyu AU - Gao, Limin AU - Xie, Kailiu AU - Ling, Ning AU - Shen, Qirong AU - Hu, Shuijin AU - Guo, Shiwei T2 - SCIENTIFIC REPORTS AB - To face the great challenges of ensuring food security and environmental sustainability, agricultural production must be improved by high yield and high resource utilization efficiency (HYHE). We recently addressed this challenge and evaluated yield potential by surveying 735 farmers in 2008-2012 and then conducting 6 rice field experiments in 2008-2013 with large demonstration areas in 2010-2013 aimed to actualize the HYHE in Jiangsu Province, China. The survey result showed that the averaged N rate, grain yield and N partial factor productivity (PFPN) of the farmers were 336.7 kg ha-1, 8131.8 kg ha-1 and 24.2 kg kg-1, respectively. Through controlling total N rates and adjusting the application timing, the yield and the PFPN of optimal N managements (OPT) were increased by 5.9% and 37.6% with 31.4% reduction in N supply amounts for 6 experimental sites, and the yield increased by 5.6% for large demonstration areas compared with farmers' fertilizer practices (FFP), respectively. In conclusion, although the soil properties of the different regions varied, HYHE could be achieved by regulating the N management practices, thus contributing to higher rice production and lower environmental costs from intensive agriculture in Jiangsu, China. DA - 2017/5/18/ PY - 2017/5/18/ DO - 10.1038/s41598-017-02338-3 VL - 7 SP - SN - 2045-2322 ER - TY - JOUR TI - The Value of Information in Decision-Analytic Modeling for Malaria Vector Control in East Africa AU - Kim, Dohyeong AU - Brown, Zachary AU - Anderson, Richard AU - Mutero, Clifford AU - Miranda, Marie Lynn AU - Wiener, Jonathan AU - Kramer, Randall T2 - RISK ANALYSIS AB - Decision analysis tools and mathematical modeling are increasingly emphasized in malaria control programs worldwide to improve resource allocation and address ongoing challenges with sustainability. However, such tools require substantial scientific evidence, which is costly to acquire. The value of information (VOI) has been proposed as a metric for gauging the value of reduced model uncertainty. We apply this concept to an evidenced‐based Malaria Decision Analysis Support Tool (MDAST) designed for application in East Africa. In developing MDAST, substantial gaps in the scientific evidence base were identified regarding insecticide resistance in malaria vector control and the effectiveness of alternative mosquito control approaches, including larviciding. We identify four entomological parameters in the model (two for insecticide resistance and two for larviciding) that involve high levels of uncertainty and to which outputs in MDAST are sensitive. We estimate and compare a VOI for combinations of these parameters in evaluating three policy alternatives relative to a status quo policy. We find having perfect information on the uncertain parameters could improve program net benefits by up to 5–21%, with the highest VOI associated with jointly eliminating uncertainty about reproductive speed of malaria‐transmitting mosquitoes and initial efficacy of larviciding at reducing the emergence of new adult mosquitoes. Future research on parameter uncertainty in decision analysis of malaria control policy should investigate the VOI with respect to other aspects of malaria transmission (such as antimalarial resistance), the costs of reducing uncertainty in these parameters, and the extent to which imperfect information about these parameters can improve payoffs. DA - 2017/2// PY - 2017/2// DO - 10.1111/risa.12606 VL - 37 IS - 2 SP - 231-244 SN - 1539-6924 KW - Decision analysis KW - malaria control KW - value of information ER - TY - JOUR TI - TESTING A THEORY OF SENSE OF COMMUNITY AND COMMUNITY RESPONSIBILITY IN ORGANIZATIONS: AN EMPIRICAL ASSESSMENT OF PREDICTIVE CAPACITY ON EMPLOYEE WELL-BEING AND ORGANIZATIONAL CITIZENSHIP AU - Boyd, Neil M. AU - Nowell, Branda T2 - JOURNAL OF COMMUNITY PSYCHOLOGY AB - This study attempts to advance our understanding of the experience of community in organizational settings by empirically testing a theory of sense of community responsibility (SOC‐R) in relation to traditional measures of sense of community [SOC] on outcomes of employee well‐being and organizational citizenship. Findings support the notion that SOC is a better predictor of employee well‐being, while SOC‐R more strongly predicts organizational citizenship behavior. The findings add new knowledge to the literature on the experience of community in organizations, as well as representing an important contribution to our understanding of the factors that drive employee action and well‐being at work. DA - 2017/3// PY - 2017/3// DO - 10.1002/jcop.21843 VL - 45 IS - 2 SP - 210-229 SN - 1520-6629 ER - TY - JOUR TI - Simultaneous Voltammetric Measurements of Glucose and Dopamine Demonstrate the Coupling of Glucose Availability with Increased Metabolic Demand in the Rat Striatum AU - Smith, Samantha K. AU - Lee, Christie A. AU - Dausch, Matthew E. AU - Horman, Brian M. AU - Patisaul, Heather B. AU - McCarty, Gregory S. AU - Sombers, Leslie A. T2 - ACS CHEMICAL NEUROSCIENCE AB - Cerebral blood flow ensures delivery of nutrients, such as glucose, to brain sites with increased metabolic demand. However, little is known about rapid glucose dynamics at discrete locations during neuronal activation in vivo. Acute exposure to many substances of abuse elicits dopamine release and neuronal activation in the striatum; however, the concomitant changes in striatal glucose remain largely unknown. Recent developments have combined fast-scan cyclic voltammetry with glucose oxidase enzyme modified carbon-fiber microelectrodes to enable the measurement of glucose dynamics with subsecond temporal resolution in the mammalian brain. This work evaluates several waveforms to enable the first simultaneous detection of endogenous glucose and dopamine at single recording sites. These molecules, one electroactive and one nonelectroactive, were found to fluctuate in the dorsal striatum in response to electrical stimulation of the midbrain and systemic infusion of cocaine/raclopride. The data reveal the second-by-second dynamics of these species in a striatal microenvironment, and directly demonstrate the coupling of glucose availability with increased metabolic demand. This work provides a foundation that will enable detailed investigation of local mechanisms that regulate the coupling of cerebral blood flow with metabolic demand under normal conditions, and in animal studies of drug abuse and addiction. DA - 2017/2// PY - 2017/2// DO - 10.1021/acschemneuro.6b00363 VL - 8 IS - 2 SP - 272-280 SN - 1948-7193 KW - Biosensor KW - carbon fiber microelectrode KW - neuroenergetics KW - glucose oxidase KW - cocaine KW - fast-scan cyclic voltammetry ER - TY - JOUR TI - Sexting and Sexual Behavior, 2011-2015: A Critical Review and Meta-Analysis of a Growing Literature AU - Kosenko, Kami AU - Luurs, Geoffrey AU - Binder, Andrew R. T2 - JOURNAL OF COMPUTER-MEDIATED COMMUNICATION AB - Sexting and its potential links to sexual behavior, including risky sexual practices, have received scholarly scrutiny, but this literature is marked by divergent perspectives and disparate findings. To assess claims regarding the nature of the relationship between sexting and sexual behavior, we conducted a critical review of the literature and analyzed data from 15 articles via quantitative meta-analytic techniques. Sexting behavior was positively related to sexual activity, unprotected sex, and one's number of sexual partners, but the relationship was weak to moderate. Additional information, gleaned from a critical review of included studies, helped contextualize these findings and point to specific limitations and directions for future research. DA - 2017/5// PY - 2017/5// DO - 10.1111/jcc4.12187 VL - 22 IS - 3 SP - 141-160 SN - 1083-6101 UR - https://publons.com/publon/21063761/ KW - Sexting KW - Sexual Behavior KW - Text Messaging ER - TY - JOUR TI - Mosquitoes of field and forest: the scale of habitat segregation in a diverse mosquito assemblage AU - Reiskind, M. H. AU - Griffin, R. H. AU - Janairo, M. S. AU - Hopperstad, K. A. T2 - MEDICAL AND VETERINARY ENTOMOLOGY AB - Abstract Knowledge of the distribution of arthropod vectors across a landscape is important in determining the risk for vector‐borne disease. This has been well explored for ticks, but not for mosquitoes, despite their importance in the transmission of a variety of pathogens. This study examined the importance of habitat, habitat edges, and the scale at which mosquito abundance and diversity vary in a rural landscape by trapping along transects from grassland areas into forest patches. Significant patterns of vector diversity and distinct mosquito assemblages across habitats were found. The scale of individual species' responses to habitat edges was often dramatic, with several species rarely straying even 10 m from the edge. The present results suggest blood‐seeking mosquito species are faithful to certain habitats, which has consequences for patterns of vector diversity and risk for pathogen transmission. This implies that analysts of risk for pathogen transmission and foci of control, and developers of land management strategies should assess habitat at a finer scale than previously considered. DA - 2017/3// PY - 2017/3// DO - 10.1111/mve.12193 VL - 31 IS - 1 SP - 44-54 SN - 1365-2915 KW - Disease ecology KW - habitat edges KW - landscape ecology KW - vector-borne pathogens ER - TY - JOUR TI - Modeling the Growth of Archaeon Halobacterium halobium Affected by Temperature and Light AU - Lu, Hao AU - Yuan, Wenqiao AU - Cheng, Jay AU - Rose, Robert B. AU - Classen, John J. AU - Simmons, Otto D. T2 - APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY DA - 2017/3// PY - 2017/3// DO - 10.1007/s12010-016-2270-x VL - 181 IS - 3 SP - 1080-1095 SN - 1559-0291 KW - Halobacterium holobium KW - Sigmoidal model KW - Temperature effect KW - Light intensity effect KW - Bacteriorhodopsin ER - TY - JOUR TI - Identification of simple sequence repeat markers for sweetpotato weevil resistance AU - Yada, B. AU - Alajo, A. AU - Ssemakula, G. N. AU - Brown-Guedira, G. AU - Otema, M. A. AU - Stevenson, P. C. AU - Mwanga, R. O. M. AU - Yencho, G. C. T2 - Euphytica AB - Abstract The development of sweetpotato [ Ipomoea batatas (L.) Lam] germplasm with resistance to sweetpotato weevil (SPW) requires an understanding of the biochemical and genetic mechanisms of resistance to optimize crop resistance. The African sweetpotato landrace, ‘New Kawogo’, was reported to be moderately resistant to two species of SPW, Cylas puncticollis and Cylas brunneus . Resistance has been associated with the presence of hydroxycinnamic acids esters (HCAs), but the underlying genetic basis remains unknown. To determine the genetic basis of this resistance, a bi-parental sweetpotato population from a cross between the moderately resistant, white-fleshed ‘New Kawogo’ and the highly susceptible, orange-fleshed North American variety ‘Beauregard’ was evaluated for SPW resistance and genotyped with simple sequence repeat (SSR) markers to identify weevil resistance loci. SPW resistance was measured on the basis of field storage root SPW damage severity and total HCA ester concentrations. Moderate broad sense heritability (H 2 = 0.49) was observed for weevil resistance in the population. Mean genotype SPW severity scores ranged from 1.0 to 9.0 and 25 progeny exhibited transgressive segregation for SPW resistance. Mean genotype total HCA ester concentrations were significantly different (P < 0.0001). A weak but significant correlation (r = 0.103, P = 0.015) was observed between total HCA ester concentration and SPW severity. A total of five and seven SSR markers were associated with field SPW severity and total HCA ester concentration, respectively. Markers IBS11, IbE5 and IbJ544b showed significant association with both field and HCA-based resistance, representing potential markers for the development of SPW resistant sweetpotato cultivars. DA - 2017/// PY - 2017/// DO - 10.1007/s10681-017-1917-1 VL - 213 IS - 6 SP - 129 SN - 1573-5060 KW - Hydroxycinnamic acid KW - SSR markers KW - Sweetpotato weevil ER - TY - JOUR TI - Higher immunocompetence is associated with higher genetic diversity in feral honey bee colonies (Apis mellifera) AU - Lopez-Uribe, Margarita M. AU - Appler, R. Holden AU - Youngsteadt, Elsa AU - Dunn, Robert R. AU - Frank, Steven D. AU - Tarpy, David R. T2 - CONSERVATION GENETICS DA - 2017/6// PY - 2017/6// DO - 10.1007/s10592-017-0942-x VL - 18 IS - 3 SP - 659-666 SN - 1572-9737 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85013371895&partnerID=MN8TOARS KW - Microsatellites KW - Antimicrobial peptides KW - Defensin KW - Hymenoptaecin KW - Management ER - TY - JOUR TI - Genital morphology and allometry differ by species and sex in Malawi cichlid fishes AU - Moore, Emily C. AU - Roberts, Reade B. T2 - HYDROBIOLOGIA AB - The African cichlid fishes show great diversity in mating displays and reproductive strategies, yet species differences in genital morphology have been little studied. Observational notes have described broad sex differences in external genital shape between males and females, but these differences have not been quantified. We examined three aspects of genital morphology (relative anogenital distance, relative vent length, and relative external genital area) in two riverine and eleven Lake Malawi African cichlid species from eight genera. We find the most sexually distinct morphology in the Lake Malawi rock cichlids and the least sexual dimorphism in the riverine outgroup; additionally, diversity in metrics within genus indicates that these traits are recently evolving. Sexual dimorphism in morphology is present in most species, and, in the Lake Malawi species, multivariate discriminant analysis allows for accurate assignment of gonadal sex based on genital morphology and body size. This will serve as a useful method for sexing fish in a nonlethal fashion and provides a starting point for further examination of the evolution of genital morphology in this diverse group of fishes. DA - 2017/5// PY - 2017/5// DO - 10.1007/s10750-016-2912-6 VL - 791 IS - 1 SP - 127-143 SN - 1573-5117 KW - Genital morphology KW - Cichlid fishes KW - Sexual dimorphism KW - Anogenital distance KW - Genital papilla ER - TY - JOUR TI - Genetic sex determination in Astatotilapia calliptera, a prototype species for the Lake Malawi cichlid radiation AU - Peterson, Erin N. AU - Cline, Maggie E. AU - Moore, Emily C. AU - Roberts, Natalie B. AU - Roberts, Reade B. T2 - SCIENCE OF NATURE DA - 2017/6// PY - 2017/6// DO - 10.1007/s00114-017-1462-8 VL - 104 IS - 5-6 SP - SN - 1432-1904 KW - Sex chromosome KW - Genetic sex determination KW - Cichlid KW - Fish KW - Astatotilapia calliptera ER - TY - JOUR TI - Deletion of Lipoteichoic Acid Synthase Impacts Expression of Genes Encoding Cell Surface Proteins in Lactobacillus acidophilus AU - Selle, Kurt AU - Goh, Yong J. AU - Johnson, Brant R. AU - Sarah, O’Flaherty AU - Andersen, Joakim M. AU - Barrangou, Rodolphe AU - Klaenhammer, Todd R. T2 - Frontiers in Microbiology AB - Lactobacillus acidophilus NCFM is a well-characterized probiotic microorganism, supported by a decade of genomic and functional phenotypic investigations. L. acidophilus deficient in lipoteichoic acid (LTA), a major immunostimulant in Gram-positive bacteria, has been shown to shift immune system responses in animal disease models. However, the pleiotropic effects of removing LTA from the cell surface in lactobacilli are unknown. In this study, we surveyed the global transcriptional and extracellular protein profiles of two strains of L. acidophilus deficient in LTA. Twenty-four differentially expressed genes specific to the LTA-deficient strains were identified, including a predicted heavy metal resistance operon and several putative peptidoglycan hydrolases. Cell morphology and manganese sensitivity phenotypes were assessed in relation to the putative functions of differentially expressed genes. LTA-deficient L. acidophilus exhibited elongated cellular morphology and their growth was severely inhibited by elevated manganese concentrations. Exoproteomic surveys revealed distinct changes in the composition and relative abundances of several extracellular proteins and showed a bias of intracellular proteins in LTA-deficient strains of L. acidophilus. Taken together, these results elucidate the impact of ltaS deletion on the transcriptome and extracellular proteins of L. acidophilus, suggesting roles of LTA in cell morphology and ion homeostasis as a structural component of the Gram positive cell wall. DA - 2017/4/11/ PY - 2017/4/11/ DO - 10.3389/fmicb.2017.00553 VL - 8 ER - TY - JOUR TI - Cereal Leaf Beetle (Coleoptera: Chrysomelidae) Regional Dispersion and Relationship With Wheat Stand Denseness AU - Reisig, Dominic D. AU - Bacheler, Jack S. AU - Herbert, D. Ames AU - Heiniger, Ron AU - Kuhar, Thomas AU - Malone, Sean AU - Philips, Chris AU - Tilley, M. Scott T2 - ENVIRONMENTAL ENTOMOLOGY AB - Cereal leaf beetle, Oulema melanopus L., is a pest of small grains and the literature conflicts on whether it is more abundant in sparse or dense stands of wheat. Our objectives were to determine the impact of stand denseness on cereal leaf beetle abundance and to investigate the regional dispersion of cereal leaf beetles across North Carolina and Virginia. One-hundred twenty fields were sampled across North Carolina and Virginia during 2011 for stand denseness, and cereal leaf beetle eggs, larvae, and adults. Two small-plot wheat experiments were planted in North Carolina using a low and a high seeding rate. Main plots were split, with one receiving a single nitrogen application and one receiving two. Egg density, but not larva or adult density, was positively correlated with stand denseness in the regional survey. Furthermore, regional spatial patterns of aggregation were noted for both stand denseness and egg number. In the small-plot experiments, seeding rate influenced stand denseness, but not nitrogen application. In one experiment, egg densities per unit area were higher in denser wheat, while in the other experiment, egg densities per tiller were lower in denser wheat. Larvae were not influenced by any factor. Overall, there were more cereal leaf beetle eggs in denser wheat stands. Previous observations that sparse stands of wheat are more prone to cereal leaf beetle infestation can be attributed to the fact that sparser stands have fewer tillers, which increases the cereal leaf beetle to tiller ratio compared with denser stands. DA - 2017/6// PY - 2017/6// DO - 10.1093/ee/nvx034 VL - 46 IS - 3 SP - 425-433 SN - 1938-2936 KW - sampling KW - spatial distribution KW - oviposition KW - Moran's ER - TY - JOUR TI - Beyond thermal limits: comprehensive metrics of performance identify key axes of thermal adaptation in ants AU - Penick, Clint A. AU - Diamond, Sarah E. AU - Sanders, Nathan J. AU - Dunn, Robert R. T2 - FUNCTIONAL ECOLOGY AB - Summary How species respond to temperature change depends in large part on their physiology. Physiological traits, such as critical thermal limits ( CT max and CT min ), provide estimates of thermal performance but may not capture the full impacts of temperature on fitness. Rather, thermal performance likely depends on a combination of traits—including thermal limits—that vary among species. Here, we examine how thermal limits correlate with the main components that influence fitness in ants. First, we compare how temperature affected colony survival and growth in two ant species that differ in their responses to warming in the field— Aphaenogaster rudis (heat‐intolerant) and Temnothorax curvispinosus (heat‐tolerant). We then extended our study to compare CT max , thermal requirements of brood and yearly activity season among a broader set of ant species. While thermal limits were higher for workers of T. curvispinosus than A. rudis , T. curvispinosus colonies also required higher temperatures for survival and colony growth. This pattern generalized across 17 ant species, such that species whose foragers had a high CT max also required higher temperatures for brood development. Finally, species whose foragers had a high CT max had relatively short activity seasons compared with less heat‐tolerant species. The relationships between CT max , thermal requirements of brood and seasonal activity suggest two main strategies for growth and development in changing thermal environments: one where ants forage at higher temperatures over a short activity season and another where ants forage at lower temperatures for an extended activity season. Where species fall on this spectrum may influence a broad range of life‐history characteristics and aid in explaining the current distributions of ants as well as their responses to future climate change. A lay summary is available for this article. DA - 2017/5// PY - 2017/5// DO - 10.1111/1365-2435.12818 VL - 31 IS - 5 SP - 1091-1100 SN - 1365-2435 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85010641179&partnerID=MN8TOARS KW - climate change KW - critical thermal limits KW - development KW - phenology KW - social insects KW - thermal adaptation ER - TY - JOUR TI - An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid fish AU - Roberts, Reade B. AU - Moore, Emily C. AU - Kocher, Thomas D. T2 - MOLECULAR ECOLOGY AB - Despite long-standing interest in the evolution and maintenance of discrete phenotypic polymorphisms, the molecular genetic basis of such polymorphism in the wild is largely unknown. Female sex-associated blotched colour polymorphisms found in cichlids of Lake Malawi, East Africa, represent a highly successful polymorphic phenotype, found and maintained in four genera across the geographic expanse of the lake. Previously, we identified an association with an allelic variant of the paired-box transcription factor gene pax7a and blotched colour morphs in Lake Malawi cichlid fishes. Although a diverse range of blotched phenotypes are present in Lake Malawi cichlid species, they all appeared to result from an allele of pax7a that produces increased levels of transcript. Here, we examine the developmental and genetic basis of variation among blotched morphs. First, we confirm that pax7a-associated blotch morphs result primarily from modulation of melanophore development and survival. From laboratory crosses and natural population studies, we identify at least three alleles of pax7a associated with discrete subtypes of blotched morphs, in addition to the ancestral pax7a allele. Genotypes at pax7a support initial evolution of a novel pax7a allele to produce the blotched class of morphs, followed by subsequent evolution of that pax7a blotched allele to produce additional alleles associated with discrete colour morphs. Variant alleles of pax7a produce different levels of pax7a transcript, correlating with pigmentation phenotype at the cellular level. This naturally selected allelic series should serve as a case study for understanding the molecular genetic control of pax7a expression and the evolution of sex-associated alleles. DA - 2017/5// PY - 2017/5// DO - 10.1111/mec.13975 VL - 26 IS - 10 SP - 2625-2639 SN - 1365-294X KW - allelic series KW - cichlid fish KW - colour morphs KW - pax7 KW - pigmentation ER - TY - JOUR TI - Variation in Recombination Rate: Adaptive or Not? AU - Ritz, Kathryn R. AU - Noor, Mohamed A. F. AU - Singh, Nadia D. T2 - TRENDS IN GENETICS AB - Rates of meiotic recombination are widely variable both within and among species. However, the functional significance of this variation remains largely unknown. Is the observed within-species variation in recombination rate adaptive? Recent work has revealed new insight into the scale and scope of population-level variation in recombination rate. These data indicate that the magnitude of within-population variation in recombination is similar among taxa. The apparent similarity of the variance in recombination rate among individuals between distantly related species suggests that the relative costs and benefits of recombination that establish the upper and lower bounds may be similar across species. Here we review the current data on intraspecific variation in recombination rate and discuss the molecular and evolutionary costs and benefits of recombination frequency. We place this variation in the context of adaptation and highlight the need for more empirical studies focused on the adaptive value of variation in recombination rate. DA - 2017/5// PY - 2017/5// DO - 10.1016/j.tig.2017.03.003 VL - 33 IS - 5 SP - 364-374 SN - 1362-4555 ER - TY - JOUR TI - To Disclose or Not to Disclose: When Fear of Nocebo Effects Infringes Upon Autonomy AU - Bryan, Hadley AU - Dubljevic, Veljko T2 - AMERICAN JOURNAL OF BIOETHICS AB - Fortunato and colleagues (2017) provide an interesting perspective on nocebo effects in clinical contexts, and propose selective withholding of information during the informed consent process for a... DA - 2017/// PY - 2017/// DO - 10.1080/15265161.2017.1314045 VL - 17 IS - 6 SP - 50-52 SN - 1536-0075 UR - https://doi.org/10.1080/15265161.2017.1314045 ER - TY - JOUR TI - Temperature-related changes of Ca and P release in synthesized hydroxylapatite, geological fluorapatite, and bone bioapatite AU - Chen, Weikun AU - Wang, Quanzhi AU - Meng, Shiting AU - Yang, Ping AU - Jiang, Liu AU - Zou, Xiang AU - Li, Zhen AU - Hu, Shuijin T2 - CHEMICAL GEOLOGY AB - Solubility of apatite is highly addressed in mineralogical and material studies. Heating is one of the major processes in apatite industry. In this study, synthesized hydroxylapatite (HAp), geological fluorapatite (FAp), and bone bioapatite (BAp) were heated at various temperatures (100–900 °C) for analyses. The mineralogy and solubility of the three apatites were analyzed by XRD, ATR–IR, and ICP. Release of Ca and P in water for BAp reaches the maximum when heated at 200 °C, i.e., 0.215 mmol/L for Ca and 0.106 mmol/L for P. The value is higher than the maximum values (heated at 900 °C) of the solubility for HAp and FAp. The heating temperature at 600 °C is a re-crystallization point for all the three types of apatites. Especially, the crystallinity of BAp is significantly elevated at > 600 °C. Phase of geological FAp is relatively stable during heating up to 900 °C. Phase of β-TCP is present when heating HAp at 800 to 900 °C. In addition, BAp is transformed to the resemblance of HAp. However, no β-TCP was detected for BAp during heating between 800 and 900 °C, which is probably due to its Ca-deficiency. This study elucidates the correlation of phase changes of BAp and its solubility during heating, which sheds the light on its application as materials and fertilizer. DA - 2017/2/20/ PY - 2017/2/20/ DO - 10.1016/j.chemgeo.2017.01.014 VL - 451 SP - 183-188 SN - 1878-5999 KW - Heating KW - Hydroxylapatite KW - Fluorapatite KW - Bioapatite KW - Dissolution ER - TY - PCOMM TI - Sry Gene Drive for Rodent Control: Reply to Gemmell and Tompkins AU - Kanavy, Dona AU - Serr, Megan AB - We would like to thank Gemmell and Tompkins for their interest and comments on the article by Piaggio et al. [ 1 Piaggio A.J. et al. Is it time for synthetic biodiversity conservation?. Trends Ecol. Evol. 2016; 32: 97-107 Abstract Full Text Full Text PDF PubMed Scopus (108) Google Scholar ]. The issues raised by Gemmell and Tompkins [ 2 Gemmell N.J. Tompkins D.M. Gene drives and rodent control: response to Piaggio et al.. Trends Ecol. Evol. 2017; 32: 314-315 Abstract Full Text Full Text PDF PubMed Scopus (10) Google Scholar ] are very pertinent, and they correctly identified that the format of the article did not lend itself to a comprehensive discussion of the ideas of using gene drives in mice. The method being considered in the Piaggio et al. article is to utilize a naturally occurring t-allele transgene (Tg) to sex-bias a mouse population, causing it to crash. Inserting the sex-determining region on the Y chromosome (Sry) into the Tg allows biased inheritance where the majority of the offspring born are phenotypically male. DA - 2017/5// PY - 2017/5// DO - 10.1016/j.tree.2017.03.006 SP - 315-316 ER - TY - JOUR TI - Sexual plasticity: A fishy tale AU - Liu, Hui AU - Todd, Erica V. AU - Lokman, P. Mark AU - Lamm, Melissa S. AU - Godwin, John R. AU - Gemmell, Neil J. T2 - MOLECULAR REPRODUCTION AND DEVELOPMENT AB - SUMMARY Teleost fish exhibit remarkably diverse and plastic patterns of sexual development. One of the most fascinating modes of plasticity is functional sex change, which is widespread in marine fish including species of commercial importance; however, the regulatory mechanisms remain elusive. In this review, we explore such sexual plasticity in fish, using the bluehead wrasse ( Thalassoma bifasciatum ) as the primary model. Synthesizing current knowledge, we propose that cortisol and key neurochemicals modulate gonadotropin releasing hormone and luteinizing hormone signaling to promote socially controlled sex change in protogynous fish. Future large‐scale genomic analyses and systematic comparisons among species, combined with manipulation studies, will likely uncover the common and unique pathways governing this astonishing transformation. Revealing the molecular and neuroendocrine mechanisms underlying sex change in fish will greatly enhance our understanding of vertebrate sex determination and differentiation as well as phenotypic plasticity in response to environmental influences. Mol. Reprod. Dev. 84: 171–194, 2017. © 2016 Wiley Periodicals, Inc . DA - 2017/2// PY - 2017/2// DO - 10.1002/mrd.22691 VL - 84 IS - 2 SP - 171-194 SN - 1098-2795 ER - TY - JOUR TI - Pedigree Reconstruction with Genome-Wide Markers in Potato AU - Endelman, Jeffrey B. AU - Carley, Cari A. Schmitz AU - Douches, David S. AU - Coombs, Joseph J. AU - Bizimungu, Benoit AU - De Jong, Walter S. AU - Haynes, Kathleen G. AU - Holm, David G. AU - Miller, J. Creighton, Jr. 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 T2 - AMERICAN JOURNAL OF POTATO RESEARCH DA - 2017/4// PY - 2017/4// DO - 10.1007/s12230-016-9556-y VL - 94 IS - 2 SP - 184-190 SN - 1874-9380 KW - Pedigrees KW - SNPs KW - Solanum tuberosum ER - TY - JOUR TI - Mineral Availability as a Key Regulator of Soil Carbon Storage AU - Yu, Guanghui AU - Xiao, Jian AU - Hu, Shuijin AU - Polizzotto, Matthew L. AU - Zhao, Fangjie AU - McGrath, Steve P. AU - Li, Huan AU - Ran, Wei AU - Shen, Qirong T2 - ENVIRONMENTAL SCIENCE & TECHNOLOGY AB - Mineral binding is a major mechanism for soil carbon (C) stabilization, and mineral availability for C binding critically affects C storage. Yet, the mechanisms regulating mineral availability are poorly understood. Here, we showed that organic amendments in three long-term (23, 154, and 170 yrs, respectively) field experiments significantly increased mineral availability, particularly of short-range-ordered (SRO) phases. Two microcosm studies demonstrated that the presence of roots significantly increased mineral availability and promoted the formation of SRO phases. Mineral transformation experiments and isotopic labeling experiments provided direct evidence that citric acid, a major component of root exudates, promoted the formation of SRO minerals, and that SRO minerals acted as "nuclei" for C retention. Together, these findings indicate that soil organic amendments initialize a positive feedback loop by increasing mineral availability and promoting the formation of SRO minerals for further C binding, thereby possibly serving as a management tool for enhancing carbon storage in soils. DA - 2017/5/2/ PY - 2017/5/2/ DO - 10.1021/acs.est.7b00305 VL - 51 IS - 9 SP - 4960-4969 SN - 1520-5851 ER - TY - JOUR TI - Longevity and fecundity of the egg parasitoid Telenomus podisi provided with different carbohydrate diets AU - Lahiri, S. AU - Orr, D. AU - Cardoza, Y. J. AU - Sorenson, C. T2 - Entomologia Experimentalis et Applicata AB - Abstract In order for successful biological pest control using parasitoids, the most suitable naturally available food resources, as well as the fitness of parasitoids feeding on these resources, need to be ascertained. The goal of this study was to improve the understanding of the ecological requirements and consequent fitness of one such parasitoid, T elenomus podisi A shmead ( H ymenoptera: Platygastridae), a predominant stink bug ( H eteroptera: P entatomidae) egg parasitoid native to southeastern USA . We assessed the effects of carbohydrate resources readily available in the wasp's natural habitat on longevity and fecundity of female T . podisi under laboratory conditions. Carbohydrate diets included in the study were buckwheat, F agopyrum esculentum M oench ( P olygonaceae) nectar and honeydew from cowpea aphid, A phis craccivora K och ( H emiptera: A phididae), compared with honey or water controls, which are normally used for laboratory rearing of this species. Eggs of P odisus maculiventris S ay ( H emiptera: P entatomidae) were provided as hosts for oviposition. Honeydew of cowpea aphid proved to be as good a nutrition source as buckwheat nectar, in enhancing wasp longevity and fecundity. We also assessed the importance of honeydew freshness on the biological attributes of T . podisi , as honeydew becomes crystallized or highly viscous on drying up and therefore may pose an issue for uptake by parasitoids. We found that fresh honeydew of the pea aphid, A cyrthosiphon pisum H arris ( H emiptera: A phididae) significantly enhanced wasp longevity when compared to a diet of 1‐day‐old honeydew and the fava bean leaf (control). However, fresh honeydew of green peach aphid, M yzus persicae S ulzer ( H emiptera: A phididae) had the same effect on wasp longevity, fecundity, and proportion of male progeny as radish leaf (control). The potential of certain ubiquitously available food resources, in enhancing biological control of economically damaging pests by parasitoids, is being highlighted in this study; information which could be valuable in similar parasitoid‐host systems as well. DA - 2017/// PY - 2017/// DO - 10.1111/eea.12531 VL - 162 IS - 2 SP - 178-187 ER - TY - JOUR TI - Impacts of tillage, maturity group, and insecticide use on Megacopta cribraria (Hemiptera: Plataspidae) populations in double cropped soybean AU - Del Pozo-Valdivia, A.I. AU - Reisig, D.D. AU - Bacheler, J.S. T2 - J. Econ. Entomol AB - Megacopta cribraria (F.), also known as the kudzu bug, is a soybean pest in the United States, and it can cause up to a 60% yield reduction if not controlled. Insecticides are commonly used to manage this pest in commercial soybean fields. However, other soybean production practices may also affect kudzu bug populations. This study investigated the effect of soil tillage, maturity group selection, and insecticide use on kudzu bug densities in soybean. During 2012 and 2013, at two locations each year in North Carolina, four varieties of soybean maturity groups were planted in June into conventionally tilled plots and into plots with cereal crop residue under reduced tillage conditions (mimicking double-crop production). Plots were further split as insecticide-protected and untreated. Four times more kudzu bugs were found in conventionally tilled than reduced till plots throughout the growing season. Selection of the maturity group influenced the attractiveness of the kudzu bug to oviposit on soybean. A 56% reduction of kudzu bug densities was achieved through insecticide treatment, with an ∼6% increase in yield. Information on how production practices, including soil tillage, affect kudzu bug populations in soybean may help growers select practices to minimize kudzu bug injury and protect yield. Megacopta cribraria (F.), conocido como el bicho del kudzu, es una plaga de la soja en los Estados Unidos que puede reducir el rendimiento hasta un 60% si no es controlado oportunamente con insecticidas en campos comerciales de soja. Sin embargo, otras prácticas de producción en la soja pueden afectar las poblaciones del bicho del kudzu. El presente estudio investigó el efecto de la labranza del campo, la selección del grupo de madurez en soja, y el uso de insecticidas en la densidad del bicho del kudzu. Durante el 2012 y el 2013, cuatro diferentes grupos de madurez de soja fueron plantados en Junio bajo el sistema tradicional de labranza y con labranza reducida que incluyó residuos del cultivo anterior, en dos lugares de Carolina del Norte. Parcelas experimentales fueron divididas en las que recibieron insecticida y las parcelas control. Se encontró cuatro veces más bichos del kudzu en parcelas donde el suelo fue labrado tradicionalmente, comparado con las parcelas con labranza reducida a lo largo de toda la temporada. La selección del grupo de madurez influyó la atractividad para la oviposición del bicho del kudzu en la soja. El bicho del kudzu fue reducido en un 56% y el rendimiento de soja se incrementó en un 6% por las aplicaciones de insecticidas. Información de cómo las prácticas de producción de soja, incluyendo la labranza del suelo, afectan las poblaciones del bicho del kudzu ; podrían ayudar a los agricultores a seleccionar prácticas que minimizen el daño de ésta plaga, protegiendo el rendimiento de éste cultivo. DA - 2017/// PY - 2017/// DO - 10.1093/jee/tow288 VL - 110 IS - 1 SP - 168-176 SN - 1938-291X KW - Soil preparation KW - kudzu bug KW - cumulative insect day KW - Glycine max KW - cultural control ER - TY - JOUR TI - Feeding preference and performance of Helicoverpa zea (Lepidoptera: Noctuidae) larvae on different soybean (Fabales: Fabaceae) tissue types AU - Suits, R. AU - Reisig, D.D. AU - Burrack, H. T2 - Fla. Entomol AB - Helicoverpa zea Boddie (Lepidoptera: Noctuidae) feeding preference and performance on soybean tissue types is poorly understood. We assessed preference by looking at feeding behavior and resulting performance of 2nd and 4th instar H. zea larvae on leaves, flowers, and pods in no-choice and choice assays. Consumption indices were calculated and observed feeding behaviors were used to indicate preference; survival, growth rate, and larval body mass were recorded as measures of performance. Second instars performed better when fed leaf tissue than when fed other tissue types. In no-choice assays, 32% of 2nd instars that fed exclusively on newly emerging trifoliates reached the pupal stage, and 50% of those that fed exclusively on fully emerged leaf trifoliates survived to pupation. Early instar survival was poor (ranging from 0 to 3%) on all other tissue types, including flowers, stems, and pods. However, when given a choice of tissue types throughout their larval lifetime, 2nd instars preferred to feed on newly emerging trifoliates and early developing pods, consuming on average 51 and 38%, respectively, of each tissue type. In no-choice assays, 4th instars performed best on pods with fully developed seeds; however, when presented with a choice throughout their lifetime, late instars did not feed at a higher rate on any single tissue type. If H. zea exhibits similar behavior under field conditions, information on preference can be used to inform management practices and may aid in the development of conventionally bred and transgenic varieties. DA - 2017/// PY - 2017/// DO - 10.1653/024.100.0123 VL - 100 IS - 1 SP - 162–167 ER - TY - JOUR TI - Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid(1) AU - Spooner, David M. AU - Ruess, Holly AU - Iorizzo, Massimo AU - Senalik, Douglas AU - Simon, Philipp T2 - AMERICAN JOURNAL OF BOTANY AB - We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences.We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP).Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named DcMP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations.Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid. DA - 2017/2// PY - 2017/2// DO - 10.3732/ajb.1600415 VL - 104 IS - 2 SP - 296-312 SN - 1537-2197 KW - Apiaceae KW - carrot KW - Daucus KW - DcMP KW - germplasm KW - mitochondria KW - next-generation sequencing KW - nuclear-to-plastid DNA transfer KW - plastid phylogeny ER - TY - JOUR TI - Enhancing genomic prediction with genome-wide association studies in multiparental maize populations AU - Bian, Y. AU - Holland, J. B. T2 - HEREDITY AB - Genome-wide association mapping using dense marker sets has identified some nucleotide variants affecting complex traits that have been validated with fine-mapping and functional analysis. However, many sequence variants associated with complex traits in maize have small effects and low repeatability. In contrast to genome-wide association study (GWAS), genomic prediction (GP) is typically based on models incorporating information from all available markers, rather than modeling effects of individual loci. We considered methods to integrate results of GWASs into GP models in the context of multiple interconnected families. We compared association tests based on a biallelic additive model constraining the effect of a single-nucleotide polymorphism (SNP) to be equal across all families in which it segregates to a model in which the effect of a SNP can vary across families. Association SNPs were then included as fixed effects into a GP model that also included the random effects of the whole genome background. Simulation studies revealed that the effectiveness of this joint approach depends on the extent of polygenicity of the traits. Congruent with this finding, cross-validation studies indicated that GP including the fixed effects of the most significantly associated SNPs along with the polygenic background was more accurate than the polygenic background model alone for moderately complex but not highly polygenic traits measured in the maize nested association mapping population. Individual SNPs with strong and robust association signals can effectively improve GP. Our approach provides a new integrative modeling approach for both reliable gene discovery and robust GP. DA - 2017/6// PY - 2017/6// DO - 10.1038/hdy.2017.4 VL - 118 IS - 6 SP - 585-593 SN - 1365-2540 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85012882558&partnerID=MN8TOARS ER - TY - JOUR TI - Effects of Postharvest Cold Storage on the Development and Survival of Immature Drosophila suzukii (Diptera: Drosophilidae) in Artificial Diet and Fruit AU - Aly, Marwa F. K. AU - Kraus, Dylan A. AU - Burrack, Hannah J. T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) attacks a wide range of host plants, including crops such as blueberries, cherries, caneberries, and strawberries. We evaluated the influence of three temperatures (1.1, 3.9, and 5.0 °C) and four exposure durations (6, 12, 24, and 72 h) that were selected to represent typical grower practices on survival and development time of immature D. suzukii in artificial diet and one temperature and duration (1.67 °C for 72 h) in fruit (blueberries and raspberries). Cold storage at 1.1 °C for 24 h decreased larval survival, but shorter durations generally did not affect larval survival. No eggs or young larvae survived when held for 72 h at 1.1 °C, and fewer older larvae survived after 72 h at 1.1, 3.9, and 5.0 °C than at 20 °C (control). Development time in diet was longer for all life stages following at least 12 h at any of the storage temperatures. In blueberries, no eggs survived to pupation when stored at 1.67 °C for 72 h, and survival of third instars was reduced by 41%. In raspberries, egg, second instar, and third instar survival was significantly reduced following storage at 1.67 °C for 72 h. Drosophila suzukii larval development time was shorter in raspberry than in blueberry, but it was significantly longer in both fruits when stored at 1.67 °C for 72 h. Our results indicate that cold storage can reduce survival and increase development time of immature D. suzukii, and it could be a useful part of an integrated program to manage D. suzukii infestation. DA - 2017/2// PY - 2017/2// DO - 10.1093/jee/tow289 VL - 110 IS - 1 SP - 87-93 SN - 1938-291X KW - Spotted wing drosophila KW - blueberry KW - raspberry KW - postharvest ER - TY - JOUR TI - Effect of Simulated Anthonomus signatus (Coleoptera: Curculionidae) Injury on Strawberries (Fragaria X ananassa) Grown in Southeastern Plasticulture Production AU - McPhie, Douglas AU - Burrack, Hannah J. T2 - JOURNAL OF ECONOMIC ENTOMOLOGY AB - Female strawberry bud weevils (Anthonomus signatus Say) oviposit in developing flower buds of strawberries (Fragaria spp.), caneberries (Rubus spp.), and red bud (Cercis canadensis). After laying a single egg, weevils will girdle or “clip” the buds at the pedicel, killing the bud and preventing fruit development. This injury is of concern to commercial strawberry growers, who typically assume the loss of one clipped bud is the loss of one average sized fruit, causing the economic threshold to be set extremely low. There is evidence of compensation in some cultivars of strawberries, but research has previously only been conducted in perennial strawberry production. The majority of strawberries in the southeastern United States are grown in annual plasticulture systems. We assessed the ability of five strawberry cultivars commonly grown in annual plasticulture to compensate for A. signatus injury by removing buds at different growth stages. There was no effect of bud removal on total yield in any of the cultivars tested. Harvest timing was affected by simulated A. signatus damage in some cultivars, which may be an important consideration for direct market strawberry growers. DA - 2017/2// PY - 2017/2// DO - 10.1093/jee/tow266 VL - 110 IS - 1 SP - 208-212 SN - 1938-291X KW - Anthonomus signatus KW - strawberry KW - host plant resistance KW - HPR KW - compensation ER - TY - JOUR TI - Does florivory by Helicoverpa zea cause yield loss in soybeans? AU - Reisig, D. AU - Suits, R. AU - Burrack, H. AU - Bacheler, J. AU - Dunphy, J.E. T2 - J. Econ. Entomol AB - Helicoverpa zea (Boddie), corn earworm, is a damaging insect pest of many crops, including soybeans. An economic threshold for soybeans during the pod-filling stages exists to prevent economic damage to seeds. However, the impact of florivory (flower feeding) by H. zea larvae on seed yield is poorly understood and there is no economic threshold for flowering-stage soybeans. Four small plot experiments were conducted in North Carolina during 2011 and 2012 to assess the impact of H. zea feeding during the flowering stages of determinate soybeans on various yield components. Helicoverpa zea densities were manipulated with insecticides and various planting dates of soybeans and monitored weekly. Helicoverpa zea naturally infested the plots after flowering began and were allowed to feed until R3; they were eliminated from all plots from R3 to maturity. In some sites, H. zea densities exceeded the podding economic threshold during the flowering stages, but yield did not differ among treatments. During 2012, florivory from H. zea was measured directly by counting injured flowers. There was a negative yield relationship between both injured flower number and cumulative flower number. Moreover, H. zea densities were related to both a decrease in cumulative flowers and an increase in injured flowers, even though a direct linkage between H. zea density and yield loss was not observed. Without knowing the preferred tissue types and performance of early-instar larvae on soybeans, it is possible that H. zea density may not be the best measurement for developing an economic threshold in flowering soybeans. DA - 2017/// PY - 2017/// DO - 10.1093/jee/tow312 VL - 110 IS - 2 SP - 464-470 SN - 1938-291X KW - corn earworm KW - economic threshold KW - flowering-stage soybean ER - TY - JOUR TI - Building early-larval sexing systems for genetic control of the Australian sheep blow fly Lucilia cuprina using two constitutive promoters AU - Yan, Ying AU - Linger, Rebecca J. AU - Scott, Maxwell J. T2 - Scientific Reports AB - Transgenic sexing strains (TSS) that carry conditional female lethal genes are advantageous for genetic control programs based on the sterile insect technique (SIT). It is desirable if females die early in development as larval diet is a major cost for mass production facilities. This can be achieved by using a gene promoter that is only active in embryos to drive expression of the tetracycline transactivator (tTA), the transcription factor commonly used in two-component TSS. While an embryo-specific promoter is ideal it may not be essential for assembling an effective TSS as tTA can be repressed by addition of tetracycline to the diet at larval and/or adult stages. Here we have investigated this idea by isolating and employing the promoters from the Lucilia spitting image and actin 5C genes to drive tTA expression in embryos and later stages. L. cuprina TSS with the tTA drivers and tTA-regulated tetO-Lshid effectors produced only females when raised on a limited tetracycline diet. The Lshid transgene contains a sex-specific intron and as a consequence only females produce LsHID protein. TSS females died at early larval stages, which makes the lines advantageous for an SIT program. DA - 2017/5/31/ PY - 2017/5/31/ DO - 10.1038/s41598-017-02763-4 VL - 7 IS - 1 SP - J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-017-02763-4 DB - Crossref ER - TY - JOUR TI - Bio-organic Fertilizer Promotes Plant Growth and Yield and Improves Soil Microbial Community in Continuous Monoculture System of Chrysanthemum morifolium cv. Chuju AU - Wang, Jianfei AU - Li, Xiaoliang AU - Xing, Suzhi AU - Ma, Zhongyou AU - Hu, Shuijin AU - Tu, Cong T2 - INTERNATIONAL JOURNAL OF AGRICULTURE AND BIOLOGY DA - 2017/// PY - 2017/// DO - 10.17957/ijab/15.0339 VL - 19 IS - 3 SP - 563-568 SN - 1814-9596 KW - Monocropping system KW - Soil sickness KW - Soil pathogen KW - Sustainable production KW - Yield reduction ER - TY - JOUR TI - Amino Acids Are an Ineffective Fertilizer for Dunaliella spp. Growth AU - Murphree, C. A. AU - Dums, J. T. AU - Jain, S. K. AU - Zhao, C. S. AU - Young, D. Y. AU - Khoshnoodi, N. AU - Tikunov, A. AU - Macdonald, J. AU - Pilot, G. AU - Sederoff, Heike AU - al. T2 - FRONTIERS IN PLANT SCIENCE AB - Autotrophic microalgae are a promising bioproducts platform. However, the fundamental requirements these organisms have for nitrogen fertilizer severely limit the impact and scale of their cultivation. As an alternative to inorganic fertilizers, we investigated the possibility of using amino acids from deconstructed biomass as a nitrogen source in the genus Dunaliella. We found that only four amino acids (glutamine, histidine, cysteine, and tryptophan) rescue Dunaliella spp. growth in nitrogen depleted media, and that supplementation of these amino acids altered the metabolic profile of Dunaliella cells. Our investigations revealed that histidine is transported across the cell membrane, and that glutamine and cysteine are not transported. Rather, glutamine, cysteine, and tryptophan are degraded in solution by a set of oxidative chemical reactions, releasing ammonium that in turn supports growth. Utilization of biomass-derived amino acids is therefore not a suitable option unless additional amino acid nitrogen uptake is enabled through genetic modifications of these algae. DA - 2017/5/26/ PY - 2017/5/26/ DO - 10.3389/fpls.2017.00847 VL - 8 SP - SN - 1664-462X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85021390666&partnerID=MN8TOARS KW - Dunaliella KW - nitrogen recycling KW - lipids KW - biofuel KW - amino acids KW - sustainability ER - TY - JOUR TI - Translation regulation in plants: an interesting past, an exciting present and a promising future AU - Merchante, Catharina AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - PLANT JOURNAL AB - Summary Changes in gene expression are at the core of most biological processes, from cell differentiation to organ development, including the adaptation of the whole organism to the ever‐changing environment. Although the central role of transcriptional regulation is solidly established and the general mechanisms involved in this type of regulation are relatively well understood, it is clear that regulation at a translational level also plays an essential role in modulating gene expression. Despite the large number of examples illustrating the critical role played by translational regulation in determining the expression levels of a gene, our understanding of the molecular mechanisms behind such types of regulation has been slow to emerge. With the recent development of high‐throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein–RNA interactions and ribosome occupancy at the genome level, a renewed enthusiasm toward studying translation regulation is warranted. The use of these new powerful technologies in well‐established and uncharacterized translation‐dependent processes holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation. DA - 2017/5// PY - 2017/5// DO - 10.1111/tpj.13520 VL - 90 IS - 4 SP - 628-653 SN - 1365-313X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85017002891&partnerID=MN8TOARS KW - translation KW - upstream open reading frames KW - internal ribosomal entry sites KW - gene-specific translation KW - global regulation of translation KW - RNA-binding protein ER - TY - JOUR TI - Transcriptomic analysis in strawberry fruits reveals active auxin biosynthesis and signaling in the ripe receptacle AU - Estrada-Johnson, E. AU - Csukasi, F. AU - Pizarro, C. M. AU - Vallarino, J. G. AU - Kiryakova, Y. AU - Vioque, A. AU - Brumos, J. AU - Medina-Escobar, N. AU - Botella, M. A. AU - Alonso, J. M. AU - Fernie, A. R. AU - Sanchez-Sevilla, J. F. AU - Osorio, S. AU - Valpuesta, V. T2 - Frontiers in Plant Science DA - 2017/// PY - 2017/// VL - 8 ER - TY - JOUR TI - Season-long programs for control of Drosophila suzukii in southeastern US blackberries AU - Diepenbrock, Lauren M. AU - Hardin, Jesse A. AU - Burrack, Hannah J. T2 - CROP PROTECTION AB - Drosophila suzukii is an invasive insect pest which impacts small fruit production throughout much of the world. Current management programs use regular applications of broad-spectrum insecticides which must be rotated for resistance management. This study examined the efficacy of rotational treatment programs designed to meet the needs of commercial growers in the southeastern United States, a region which experiences frequent rainfall during the growing season. In bioassays, all insecticides in our programs killed at least 50% of all female flies. Despite this good efficacy and weekly applications, infestation still occurred within fields. Our findings demonstrate the necessity of a comprehensive management strategy for blackberries, requiring additional efforts to current chemical-intensive management regimes, including cultural management practices such as pruning, harvest frequency, and post-harvest cooling. DA - 2017/8// PY - 2017/8// DO - 10.1016/j.cropro.2017.03.022 VL - 98 SP - 149-156 SN - 1873-6904 KW - Drosophila suzukii KW - Season-long treatment program KW - Integrated pest management KW - Resistance management ER - TY - JOUR TI - Science hobbyists: active users of the science-learning ecosystem AU - Corin, Elysa N. AU - Jones, M. Gail AU - Andre, Thomas AU - Childers, Gina M. AU - Stevens, Vanessa T2 - INTERNATIONAL JOURNAL OF SCIENCE EDUCATION PART B-COMMUNICATION AND PUBLIC ENGAGEMENT AB - Science hobbyists engage in self-directed, free-choice science learning and many have considerable expertise in their hobby area. This study focused on astronomy and birding hobbyists and examined how they used organizations to support their hobby engagement. Interviews were conducted with 58 amateur astronomers and 49 birders from the midwestern and southeastern United States. A learning ecology framework was used to map the community contexts with which the hobbyists acted. Results indicated seven contexts that supported the participants’ hobby involvement over time: home, K-12 schools, universities, informal learning institutions, hobby clubs, conferences, and community organizations. Three themes emerged that described how hobbyists interacted with organizations in their communities: (1) organizations provided multiple points of entrance into the science-learning ecosystem, (2) organizations acted as catalysts to facilitate a hobbyist’s development in their hobby, and (3) the relationship between hobbyists and organizations they used for learning eventually became bidirectional. Results showed that both astronomy and birding hobbyists used science-learning organizations to meet their hobby-related learning goals. Most hobbyists in the sample (90% astronomers, 78% birders) also engaged in outreach and shared their hobby with members of their community. Patterns of interaction of the astronomy and birding hobbyists within the seven contexts are discussed. DA - 2017/6// PY - 2017/6// DO - 10.1080/21548455.2015.1118664 VL - 7 IS - 2 SP - 161-180 SN - 2154-8463 KW - Hobby KW - free-choice learning KW - adult learners ER - TY - JOUR TI - Reconstructing larval growth and habitat use in an amphidromous goby using otolith increments and microchemistry AU - Hogan, J. D. AU - Kozdon, R. AU - Blum, M. J. AU - Gilliam, J. F. AU - Valley, J. W. AU - McIntyre, P. B. T2 - JOURNAL OF FISH BIOLOGY AB - High‐resolution analysis of growth increments, trace element chemistry and oxygen isotope ratios ( δ 18 O ) in otoliths were combined to assess larval and post‐larval habitat use and growth of Awaous stamineus , an amphidromous goby native to Hawai‘i. Otolith increment widths indicate that all individuals experience a brief period of rapid growth during early life as larvae and that the duration of this growth anomaly is negatively correlated with larval duration. A protracted high‐growth period early in larval life is associated with a lower ratio of Sr:Ca, which may reflect low salinity conditions in nearshore habitats. A distinct shift in δ 18 O (range: 4–5‰) is closely associated with the metamorphic mark in otoliths, indicating that larval metamorphosis occurs promptly upon return to fresh water. Strontium and other trace elements are not as tightly coupled to the metamorphosis mark, but confirm the marine‐to‐freshwater transition. Integration of microstructural and microchemical approaches reveals that larvae vary substantially in growth rate, possibly in association with habitat differences. Although time and financial costs make it difficult to achieve large sample sizes, present results show that examining even a small number of individuals can lead to novel inferences about early life history in diadromous fishes and illustrates the value of integrating analyses. DA - 2017/4// PY - 2017/4// DO - 10.1111/jfb.13240 VL - 90 IS - 4 SP - 1338-1355 SN - 1095-8649 KW - Awaous stamineus KW - LA-ICP-MS KW - migration KW - otolith ageing KW - SIMS KW - Sr:Ca ER - TY - JOUR TI - Process-based modelling shows how climate and demography shape language diversity AU - Michael, Gavin C. AU - Rangel, Thiago F. AU - Bowern, Claire AU - Colwell, Robert K. AU - Kirby, Kathryn R. AU - Botero, Carlos A. AU - Dunn, Michael AU - Dunn, Robert R. AU - McCarter, Joe AU - Coelho, Marco Tulio Pacheco AU - Gray, Russell D. T2 - GLOBAL ECOLOGY AND BIOGEOGRAPHY AB - Abstract Aim Two fundamental questions about human language demand answers: why are so many languages spoken today and why is their geographical distribution so uneven? Although hypotheses have been proposed for centuries, the processes that determine patterns of linguistic and cultural diversity remain poorly understood. Previous studies, which relied on correlative, curve‐fitting approaches, have produced contradictory results. Here we present the first application of process‐based simulation modelling, derived from macroecology, to examine the distribution of human groups and their languages. Location The Australian continent is used as a case study to demonstrate the power of simulation modelling for identifying processes shaping the diversity and distribution of human languages. Methods Process‐based simulation models allow investigators to hold certain factors constant in order to isolate and assess the impact of modelled processes. We tested the extent to which a minimal set of processes determines the number and spatial distribution of languages on the Australian continent. Our model made three basic assumptions based on previously proposed, but untested, hypotheses: groups fill unoccupied spaces, rainfall limits population density and groups divide after reaching a maximum population. Results Remarkably, this simple model accurately predicted the total number of languages (average estimate 406, observed 407), and explained 56% of spatial variation in language richness on the Australian continent. Main conclusions Our results present strong evidence that current climatic conditions and limits to group size are important processes shaping language diversity patterns in Australia. Our study also demonstrates how simulation models from macroecology can be used to understand the processes that have shaped human cultural diversity across the globe. DA - 2017/5// PY - 2017/5// DO - 10.1111/geb.12563 VL - 26 IS - 5 SP - 584-591 SN - 1466-8238 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85008474181&partnerID=MN8TOARS KW - Culture KW - language diversity KW - macroecology KW - simulation modelling ER - TY - JOUR TI - Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms AU - Counts, James A. AU - Zeldes, Benjamin M. AU - Lee, Laura L. AU - Straub, Christopher T. AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE AB - The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as ‘extreme thermophiles’ and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs—basically, anywhere there is hot water. Initial efforts to study extreme thermophiles faced challenges with their isolation from difficult to access locales, problems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermophiles were among the first organisms to be sequenced, thereby opening up the application of systems biology‐based methods to probe their unique physiological, metabolic and biotechnological features. The bacterial genera Caldicellulosiruptor , Thermotoga and Thermus , and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermophiles to date. The recent emergence of genetic tools for many of these organisms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering. WIREs Syst Biol Med 2017, 9:e1377. doi: 10.1002/wsbm.1377 This article is categorized under: Biological Mechanisms > Metabolism DA - 2017/5// PY - 2017/5// DO - 10.1002/wsbm.1377 VL - 9 IS - 3 SP - SN - 1939-005X ER - TY - JOUR TI - Impact of imidacloprid treated seed and foliar insecticide on Hessian fly abundances in wheat (Triticum aestivum L.) AU - Howell, F. C. AU - Reisig, D. D. AU - Burrack, H. J. AU - Heiniger, R. T2 - CROP PROTECTION AB - Wheat, Triticum aestivum L., is a major crop of economic importance throughout the United States. The Hessian fly, Mayetiola destructor (Say), is a common economically important pest, feeding on wheat in the larval stage through the southeastern US. It is a multi-voltine species, with generation number dependent on temperature. Growers rely on various management approaches such as resistant wheat varieties, crop rotation, timely plantings, and insecticide treatments to control this destructive pest. The objectives for this research were to show the efficacy of a common insecticide seed treatment (imidacloprid) and a common foliar insecticide spray (lambda-cyhalothrin) on Hessian fly abundance in wheat. Four experiments were conducted over two years in North Carolina, in order to manipulate Hessian fly abundance. Small plot studies were designed with whole plot treatments including non-treated and imidacloprid treated wheat seed, and subplots split with a semi-monthly foliar lambda-cyhalothrin application or no foliar insecticide. The number of Hessian fly eggs present on leaves, number of larvae, number of pupae, and tiller density were counted for the fall generation(s) and all plots were sprayed with foliar insecticide during the spring. Wheat seed treated with imidacloprid had fewer eggs, larvae, and pupae compared to other non-treated seed. With one exception during 2014, foliar spray applications did not reduce egg, larvae, and pupae abundance. Warmer temperatures during 2015 experiments provided conditions that extended Hessian fly presence, allowing multiple fall generations to infest wheat. Unlike 2014 experiments, foliar sprays in 2015 experiments provided some protection from Hessian fly. DA - 2017/8// PY - 2017/8// DO - 10.1016/j.cropro.2017.03.007 VL - 98 SP - 46-55 SN - 1873-6904 KW - Cecidomyiidae KW - Mayetiola destructor KW - Wheat KW - Imidacloprid KW - Insecticidal seed treatment ER - TY - JOUR TI - House Dust Endotoxin Levels Are Associated with Adult Asthma in a U.S. Farming Population AU - Carnes, Megan Ulmer AU - Hoppin, Jane A. AU - Metwali, Nervana AU - Wyss, Annah B. AU - Hankinson, John L. AU - O’Connell, Elizabeth Long AU - Richards, Marie AU - Long, Stuart AU - Freeman, Laura E. Beane AU - Sandler, Dale P. AU - Henneberger, Paul K. AU - Barker-Cummings, Christie AU - Umbach, David M. AU - Thorne, Peter S. AU - London, Stephanie J. T2 - Annals of the American Thoracic Society AB - Endotoxin initiates a proinflammatory response from the innate immune system. Studies in children suggest that endotoxin exposure from house dust may be an important risk factor for asthma, but few studies have been conducted in adult populations.To investigate the association of house dust endotoxin levels with asthma and related phenotypes (wheeze, atopy, and pulmonary function) in a large U.S. farming population.Dust was collected from the bedrooms (n = 2,485) of participants enrolled in a case-control study of current asthma (927 cases) nested within the Agricultural Health Study. Dust endotoxin was measured by Limulus amebocyte lysate assay. Outcomes were measured by questionnaire, spirometry, and blood draw. We evaluated associations using linear and logistic regression.Endotoxin was significantly associated with current asthma (odds ratio [OR], 1.30; 95% confidence interval [CI], 1.14-1.47), and this relationship was modified by early-life farm exposure (born on a farm: OR, 1.18; 95% CI, 1.02-1.37; not born on a farm: OR, 1.67; 95% CI, 1.26-2.20; Interaction P = 0.05). Significant positive associations were seen with both atopic and nonatopic asthma. Endotoxin was not related to either atopy or wheeze. Higher endotoxin was related to lower FEV1/FVC in asthma cases only (Interaction P = 0.01). For asthma, there was suggestive evidence of a gene-by-environment interaction for the CD14 variant rs2569190 (Interaction P = 0.16) but not for the TLR4 variants rs4986790 and rs4986791.House dust endotoxin was associated with current atopic and nonatopic asthma in a U.S. farming population. The degree of the association with asthma depended on early-life farm exposures. Furthermore, endotoxin was associated with lower pulmonary function in patients with asthma. DA - 2017/3// PY - 2017/3// DO - 10.1513/annalsats.201611-861oc VL - 14 IS - 3 SP - 324-331 J2 - Annals ATS LA - en OP - SN - 2329-6933 2325-6621 UR - http://dx.doi.org/10.1513/AnnalsATS.201611-861OC DB - Crossref KW - pulmonary function KW - atopy KW - wheeze KW - CD14 KW - TLR4 ER - TY - JOUR TI - Genetic analysis and association of simple sequence repeat markers with storage root yield, dry matter, starch and β-carotene content in sweetpotato AU - Yada, Benard AU - Brown-Guedira, Gina AU - Alajo, Agnes AU - Ssemakula, Gorrettie N. AU - Owusu-Mensah, Eric AU - Carey, Edward E. AU - Mwanga, Robert O.M. AU - Yencho, G. Craig T2 - Breeding Science AB - Molecular markers are needed for enhancing the development of elite sweetpotato (Ipomoea batatas (L.) Lam) cultivars with a wide range of commercially important traits in sub-Saharan Africa. This study was conducted to estimate the heritability and determine trait correlations of storage root yield, dry matter, starch and β-carotene content in a cross between 'New Kawogo' × 'Beauregard'. The study was also conducted to identify simple sequence repeat (SSR) markers associated with these traits. A total of 287 progeny and the parents were evaluated for two seasons at three sites in Uganda and genotyped with 250 SSR markers. Broad sense heritability (H2) for storage root yield, dry matter, starch and β-carotene content were 0.24, 0.68, 0.70 and 0.90, respectively. Storage root β-carotene content was negatively correlated with dry matter (r = -0.59, P < 0.001) and starch (r = -0.93, P < 0.001) content, while storage root yield was positively correlated with dry matter (r = 0.57, P = 0.029) and starch (r = 0.41, P = 0.008) content. Through logistic regression, a total of 12, 4, 6 and 8 SSR markers were associated with storage root yield, dry matter, starch and β-carotene content, respectively. The SSR markers used in this study may be useful for quantitative trait loci analysis and selection for these traits in future. DA - 2017/// PY - 2017/// DO - 10.1270/jsbbs.16089 VL - 67 IS - 2 SP - 140-150 J2 - Breed. Sci. LA - en OP - SN - 1344-7610 1347-3735 UR - http://dx.doi.org/10.1270/jsbbs.16089 DB - Crossref KW - sweetpotato KW - SSR marker KW - heritability KW - yield ER - TY - JOUR TI - Generation of LIF-independent induced pluripotent stem cells from canine fetal fibroblasts AU - Gonçalves, N.J.N. AU - Bressan, F.F. AU - Roballo, K.C.S. AU - Meirelles, F.V. AU - Xavier, P.L.P. AU - Fukumasu, H. AU - Williams, C. AU - Breen, M. AU - Koh, S. AU - Sper, R. AU - Piedrahita, J. AU - Ambrósio, C.E. T2 - Theriogenology AB - Takahashi and Yamanaka established the first technique in which transcription factors related to pluripotency are incorporated into the genome of somatic cells to enable reprogramming of these cells. The expression of these transcription factors enables a differentiated somatic cell to reverse its phenotype to an embryonic state, generating induced pluripotent stem cells (iPSCs). iPSCs from canine fetal fibroblasts were produced through lentiviral polycistronic human and mouse vectors (hOSKM/mOSKM), aiming to obtain pluripotent stem cells with similar features to embryonic stem cells (ESC) in this animal model. The cell lines obtained in this study were independent of LIF or any other supplemental inhibitors, resistant to enzymatic procedure (TrypLE Express Enzyme), and dependent on bFGF. Clonal lines were obtained from slightly different protocols with maximum reprogramming efficiency of 0.001%. All colonies were positive for alkaline phosphatase, embryoid body formation, and spontaneous differentiation and expressed high levels of endogenous OCT4 and SOX2. Canine iPSCs developed tumors at 120 days post-injection in vivo. Preliminary chromosomal evaluations were performed by FISH hybridization, revealing no chromosomal abnormality. To the best of our knowledge, this report is the first to describe the ability to reprogram canine somatic cells via lentiviral vectors without supplementation and with resistance to enzymatic action, thereby demonstrating the pluripotency of these cell lines. DA - 2017/4// PY - 2017/4// DO - 10.1016/j.theriogenology.2017.01.013 VL - 92 SP - 75-82 J2 - Theriogenology LA - en OP - SN - 0093-691X UR - http://dx.doi.org/10.1016/j.theriogenology.2017.01.013 DB - Crossref KW - iPSC KW - Canine KW - Stem cells KW - Pluripotency KW - Cellular reprogramming ER - TY - JOUR TI - Differential responses of soil bacterial communities to long-term N and P inputs in a semi-arid steppe AU - Ling, Ning AU - Chen, Dima AU - Guo, Hui AU - Wei, Jiaxin AU - Bai, Yongfei AU - Shen, Qirong AU - Hu, Shuijin T2 - GEODERMA AB - Both nitrogen (N) and phosphorus (P) may limit plant production in steppes and affect plant community structure. However, few studies have explored in detail the differences and similarities in the responses of belowground microbial communities to long-term N and P inputs. Using a high-throughput Illumina Miseq sequencing platform, we characterized the bacterial communities in a semi-arid steppe subjected to long-term N or P additions. Our results showed that both the Chao richness and Shannon's diversity were negatively correlated to N input rate, while only Chao richness was significantly and negatively correlated to P input rate. Also, both N and P additions altered the bacterial community structure. The bacterial community between plots of the same N or P input rate was much more dissimilar with the higher input level, indicating more severe niche differentiation in pots with higher N or P input. N Inputs significantly increased the relative abundance of the predicted copiotrophic groups (Proteobacteria and Firmicutes) but reduced the predicted oligotrophic groups (Acidobacteria, Nitrospirae, Chloroflexi), with the order Rhizobiales being most affected. P additions significantly affected only two phyla (Armatimonadetes and Chlorobi), which were positively correlated with P source. Results from the structural equation modelling (SEM) showed that N additions affected the bacterial community primarily by changing the pH, while P additions did so mainly by improving P availability. Our results suggest that the below-ground bacterial communities are more sensitive to N inputs, but P inputs can also play an important role in bacterial niche differentiation. These findings improve our understanding of bacterial responses to N and P inputs, and their impacts on bacterial-mediated processes, especially in the context of increasing anthropogenic nutrient inputs. DA - 2017/4/15/ PY - 2017/4/15/ DO - 10.1016/j.geoderma.2017.01.013 VL - 292 SP - 25-33 SN - 1872-6259 KW - Semi-arid steppe KW - Nor P inputs KW - Soil bacterial diversity KW - Soil bacterial community structure KW - Illumine Miseq sequencing ER - TY - JOUR TI - Deciphering the routes of invasion of Drosophila suzukii by means of ABC random forest AU - Fraimout, A. AU - Debat, V. AU - Fellous, S. AU - Hufbauer, R. A. AU - Foucaud, J. AU - Pudlo, P. AU - Marin, J. M. AU - Price, D. K. AU - Cattel, J. AU - Chen, X. AU - Depra, M. AU - Duyck, P. F. AU - Guedot, C. AU - Kenis, M. AU - Kimura, M. T. AU - Loeb, G. AU - Loiseau, A. AU - Martinez-Sanudo, I. AU - Pascual, M. AU - al., T2 - Molecular Biology and Evolution DA - 2017/// PY - 2017/// VL - 34 IS - 4 SP - 980-996 ER - TY - JOUR TI - Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping AU - Schlautman, Brandon AU - Covarrubias-Pazaran, Giovanny AU - Diaz-Garcia, Luis AU - Iorizzo, Massimo AU - Polashock, James AU - Grygleski, Edward AU - Vorsa, Nicholi AU - Zalapa, Juan T2 - G3-GENES GENOMES GENETICS AB - The American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. DA - 2017/4// PY - 2017/4// DO - 10.1534/g3.116.037556 VL - 7 IS - 4 SP - 1177-1189 SN - 2160-1836 KW - centromere region KW - genetic map KW - simple sequence repeat KW - single nucleotide polymorphism KW - Vaccinium ER - TY - JOUR TI - Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain AU - Whitham, Jason M. AU - Schulte, Mark J. AU - Bobay, Benjamin G. AU - Bruno-Barcena, Jose M. AU - Chinn, Mari S. AU - Flickinger, Michael C. AU - Pawlak, Joel J. AU - Grunden, Amy M. T2 - APPLIED MICROBIOLOGY AND BIOTECHNOLOGY DA - 2017/2// PY - 2017/2// DO - 10.1007/s00253-016-7978-6 VL - 101 IS - 4 SP - 1615-1630 SN - 1432-0614 UR - https://doi.org/10.1007/s00253-016-7978-6 KW - Acetyl-coA KW - Carbon monoxide dehydrogenase KW - Clostridium ljungdahlii KW - Ethanol KW - Wood-Ljungdahl pathway ER - TY - JOUR TI - CRISPR-Cas Technologies and Applications in Food Bacteria AU - Stout, Emily AU - Klaenhammer, Todd AU - Barrangou, Rodolphe T2 - ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 8 AB - Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity. DA - 2017/// PY - 2017/// DO - 10.1146/annurev-food-072816-024723 VL - 8 IS - 1 SP - 413-437 SN - 1941-1421 KW - probiotics KW - cultures KW - strain-typing KW - phage resistance KW - plasmid vaccination KW - antimicrobial KW - genome editing ER - TY - JOUR TI - Behavior of Telenomus podisi (Hymenoptera: Platygastridae) Adults under Overwintering Conditions(1) AU - Lahiri, Sriyanka AU - Orr, David AU - Sorenson, Clyde AU - Cardoza, Yasmin J. T2 - JOURNAL OF ENTOMOLOGICAL SCIENCE AB - Abstract  To assess overwintering refuge preferences by Telenomus podisi Ashmead, artificial refuges of varying geometries and composition were provided to wasps when exposed to overwintering conditions in an environmental chamber. Field sampling of leaf-litter and tree bark was also used in an effort to determine site preference of overwintering wasps. Under artificial overwintering conditions, wasps preferred to hang inverted while quiescent, regardless of the refuge design, indicating behavior that avoids precipitation or extreme temperature fluctuations during overwintering in field conditions. Wasps preferred refuges with wider gaps between upper and lower surfaces, avoiding spaces that were narrower than their standing height. Parasitoids also preferred settling at least 60 mm from refuge edges. Results suggest that T. podisi has a preference for the type of overwintering refuge that leaf-litter may offer. DA - 2017/1// PY - 2017/1// DO - 10.18474/jes16-06.1 VL - 52 IS - 1 SP - 15-28 SN - 0749-8004 KW - Platygastridae KW - overwintering KW - biocontrol ER - TY - JOUR TI - Variation in the Fusarium verticilloides-maize pathosystem and implications for sorting mycotoxin-contaminated maize grain AU - Morales, L. AU - Wenndt, A. AU - Marino, T. AU - Holland, J. AU - Nelson, R. T2 - Phytopathology DA - 2017/// PY - 2017/// VL - 107 IS - 2 SP - 11-11 ER - TY - JOUR TI - The renaissance of life near the boiling point - at last, genetics and metabolic engineering AU - Adams, Michael W. W. AU - Kelly, Robert M. T2 - MICROBIAL BIOTECHNOLOGY AB - We discuss here the prospects for biotechnology of extreme thermophilic microorganisms. Imagine microbial biology and biotechnology without genome sequences and genetic tools. On top of that, consider working with microorganisms that do not grow at ambient temperatures or on solid media. Yet another challenge – these microorganisms inhabit extreme thermal environments that can be dangerous and expensive to access (Fig. 1). These were the challenges facing pioneering microbiologists, such as Thomas Brock, Holger Jannasch, Wolfram Zillig and Karl Stetter, in the latter half of the 20th century as they established extreme thermophily in the lexicon of modern microbiology. By the end of the century, numerous microbes had been described which could grow near, and even above, the boiling point of water (see Fig. 2). They were isolated from continental hot springs and shallow marine vents, and many were discovered in deep sea hydrothermal environments several kilometres below sea level (Stetter et al., 1990). Moreover, most of these microbes were classified as archaea, with only a very few bacterial species known able to grow optimally at temperatures above 80°C. These organisms encompass a range of metabolic modes. They include those capable of aerobic and anaerobic respiration; autotrophic and heterotrophic metabolism; sugar and peptide fermentation; reduction in elemental sulfur, sulfate, thiosulfate, ferric iron, arsenate and nitrate; oxidation of metals and metal oxides; and the conversion of hydrogen gas and carbon dioxide to methane. In the mid-1990s, the enormous interest in these extremely thermophilic microbes, and also in the archaeal domain of life, is well illustrated by the fact that three of the first dozen genomes to be sequenced were from thermophilic archaea (Methanococus, Archaeoglobus and Methanobacterium), with those of the most thermophilic bacteria determined shortly thereafter (Thermotoga and Aquifex). Their genomes were typically smaller (~2 Mb) than those of the model mesophilic bacteria (3–4 Mb), and their sequences provided insights into how these microbes from odd places fit into the evolutionary scheme of life. They also enabled the expression of numerous genes from these organisms in microbial models, such as Escherichia coli, opening up the window on studies of protein stability and enzyme catalysis at temperatures even above 100°C. Genome sequences enabled global transcriptional studies that, coupled with biochemical analyses, provided many novel physiological and metabolic details of extreme thermophily, although general rules of life at extreme temperature remained elusive and still do to this day. Stabilizing a protein above the boiling point involves rather minor changes relative to its mesophilic counterpart, and the mechanisms involved are generally unique to a particular protein. Moreover, even with genome sequence information in hand, biotechnological opportunities at extreme temperatures were restricted to single-step biocatalysis using recombinant enzymes. Realizing the true biotechnological potential of microbes that thrive near above the boiling point of water has been greatly hampered by the inability to genetically manipulate them, but this has recently changed. Specifically, genetic systems reproducible in more than one laboratory have now been developed for two genera that grow optimally above 80°C, the anaerobic archaea Thermococcus and Pyrococcus (see Fig. 2), both of which grow by fermenting sugars and peptides. Techniques to grow these organisms on plates at high temperature in the absence of oxygen were developed with T. kodakorenesis (Topt ~85°C) over a decade ago through the pioneering work of Imanaka and Atomi (Sato et al., 2003). More recently, these methods have been applied to other Thermococcus species (Kim et al., 2010; Lim et al., 2014) and to P. furiosus (Topt ~100°C), the first for a microbe to grow at or above the boiling point of water (Bridger et al., 2012). Genetic studies to date with Thermococcus and Pyrococcus have mainly focused on providing insights into their physiology and metabolism and the homologous overproduction of affinity-tagged enzymes (McTernan et al., 2014). However, recent reports demonstrate metabolic engineering of these organisms for biotechnological purposes. For example, heterologous gene expression in Pyrococcus has enabled it to use carbon monoxide as an energy source (Schut et al., 2016) and to generate from sugars the biofuel n-butanol (Keller et al., 2015) and the industrial building block 3-hydroxypropionate (3HP) (Keller et al., 2013). Through bioengineering approaches, 3HP production near the gram per litre scale is now possible (Hawkins et al., 2015; Lian et al., 2016). Kinetic modelling promises to further increase bioproduct formation (Loder et al., 2016). In addition, the first example of the industrial application of a genetically engineered extreme thermophile, T. onnurineus (Topt ~85°C), was recently reported: a recombinant strain of this organism was optimized for the conversion of carbon monoxide produced from processing steel into hydrogen gas at very high efficiency (Simon et al., 2015). These studies demonstrate what can be achieved when prior extensive studies on the metabolism and enzymology of life near 100°C are utilized for biotechnological purposes and the production of useful products. Bioprocessing at temperature near and above 80°C can have important advantages over near-ambient operations. Highly genetically modified microorganisms usually have a fitness disadvantage and can be easily overtaken in culture when contaminating microbes are present. The high growth temperature of extreme thermophiles precludes growth or survival of virtually any contaminating organism. This reduces operating costs associated with reactor sterilization and maintaining a sterile facility. In addition, at industrial scales, heat production from microbial metabolic activity vastly outweighs heat loss through bioreactor walls such that cooling is required. Extreme thermophiles have the advantage that non-refrigerated cooling water can be used if needed, and heating requirements can be met with low-grade steam typically in excess capacity on plant sites. In fact, in the process in which the metabolically engineered T. onnurineus, which produces at 85°C hydrogen gas from the CO generated in steel mills, has no sterilization requirements, no cooling needs, and uses waste heat from the plant site and uses sea water to make up water losses (T. onnurineus is of marine origin). In fact, in a process based on metabolically engineered T. onnurineus, production of hydrogen gas at 85°C from CO generated in steel mills has no sterilization requirements, no cooling needs, uses waste heat from the plant site, and uses sea water to make up water losses (T. onnurineus of a marine organism). Genetic systems are also available for four genera of microbes that grow optimally in the 70 – 80°C range (see Fig. 2), and these offer a wider spectrum of metabolic diversity than Thermococcus and Pyrococcus species. All are heterotrophs and include the aerobe Thermus, the acidophilic aerobe Sulfolobus, and the anaerobes Thermoanerobacterium and Caldicellulosiruptor. Of these, Caldicellulosiruptor species probably have the most potential in the biotechnological field because of their ability to break down and grow on the carbohydrate polymers cellulose and hemicellulose (xylan), the primary components of plant biomass. Indeed, these organisms can degrade wood and grasses without any thermochemical pre-treatment (Kataeva et al., 2009; Zurawski et al., 2015). Recent advances in the genetic system for these organisms (Lipscomb et al., 2016) bode well for their future utilization in biomass to biofuel conversion processes. So, a renaissance of sorts is at hand in the field of extreme thermophily that offers engineering these organisms for biotechnological processes. One can anticipate that this field will soon take advantage of the latest developments in genetic manipulations, such as Tnseq and CRISPR, as well as the full spectrum of tools in systems biology. The future looks bright for these remarkable organisms that thrive at the upper temperature limits of life. This work was supported by grants to RMK and MWWA by the US Department of Energy Research ARPA-E Electrofuels Program (DE-AR0000081), the US National Science Foundation (CBET-1264052, CBET-1264053), the US Air Force Office of Scientific Research (AFOSR) (FA9550-13-1-0236) and the BioEnergy Science Center (BESC), a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. DA - 2017/1// PY - 2017/1// DO - 10.1111/1751-7915.12463 VL - 10 IS - 1 SP - 37-39 SN - 1751-7915 ER - TY - JOUR TI - The contribution of theory and experiments to conservation in fragmented landscapes AU - Resasco, Julian AU - Bruna, Emilio M. AU - Haddad, Nick M. AU - Banks-Leite, Cristina AU - Margules, Christopher R. T2 - ECOGRAPHY AB - The clearing and fragmentation of terrestrial ecosystems is commonly acknowledged as a major cause of the decline of biodiversity. These and other predicted responses to habitat fragmentation are derived from theory, which ecologists have tested with empirical approaches ranging from observations to experimental manipulations. These empirical approaches have also identified areas of theory in need of additional development. For example, experimental studies of fragmentation have provided insights such as the key role played by the matrix surrounding fragments, the importance of edge effects, and the impacts of corridors linking fragments with one another. Much less clear, however, is the extent to which these theoretical and empirical studies – while advancing our conceptual understanding of ecological responses to landscape change – help guide management and conservation practice. We review lessons learned from landscape‐scale fragmentation experiments and observational studies, present the results of a survey of fragmentation and conservation experts which probed for links and mismatches between fragmentation studies and conservation practice, and discuss how future studies can contribute to conservation practice. Our survey showed that respondents consider fragmentation theory and empirical studies and their findings important for guiding conservation and management practices. The survey also identified that there are disconnects between what is typically studied by fragmentation ecologists and factors that are central to the practice of biodiversity conservation, notably, community‐based human dimensions (e.g. economic, social, health issues), policy and governance, ecosystem services, eco‐evolutionary responses of species, and interaction of multiple threats to biodiversity and ecosystem processes. We discuss how these disconnects can present opportunities for experiments to continue to provide valuable recommendations for conservation practice in fragmented landscapes. DA - 2017/1// PY - 2017/1// DO - 10.1111/ecog.02546 VL - 40 IS - 1 SP - 109-118 SN - 1600-0587 ER - TY - JOUR TI - The Global Synanthrome Project: A Call for an Exhaustive Study of Human Associates AU - Dunn, Robert R. AU - Nunn, Charles L. AU - Horvath, Julie E. T2 - TRENDS IN PARASITOLOGY AB - Here we coin the term synanthrome to describe all of the species we interact with. We propose that the time is now here for The Global Synanthrome Project to describe all of our interacting species and how they have changed through time and across space. This effort must involve natural history, ecology, and evolutionary biology in addition to genomics studies that are already underway. DA - 2017/1// PY - 2017/1// DO - 10.1016/j.pt.2016.09.007 VL - 33 IS - 1 SP - 4-7 SN - 1471-5007 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85001090545&partnerID=MN8TOARS ER - TY - JOUR TI - Molecular analysis of environmental plant DNA in house dust across the United States AU - Craine, Joseph M. AU - Barberan, Albert AU - Lynch, Ryan C. AU - Menninger, Holly L. AU - Dunn, Robert R. AU - Fierer, Noah T2 - AEROBIOLOGIA DA - 2017/3// PY - 2017/3// DO - 10.1007/s10453-016-9451-5 VL - 33 IS - 1 SP - 71-86 SN - 1573-3025 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84979255882&partnerID=MN8TOARS KW - Environmental DNA KW - Plant allergens KW - Geography KW - Next-generation sequencing ER - TY - JOUR TI - Incidence and titer of viral infections within soybean cyst nematode culture collections and field populations AU - Ruark, C. AU - Koenning, S. AU - Davis, E. AU - Opperman, C. AU - Lommel, S. AU - Mitchum, M. G. AU - Sit, T. T2 - Phytopathology DA - 2017/// PY - 2017/// VL - 107 IS - 1 SP - 7-7 ER - TY - JOUR TI - Experimental evidence does not support the Habitat Amount Hypothesis AU - Haddad, Nick M. AU - Gonzalez, Andrew AU - Brudvig, Lars A. AU - Burt, Melissa A. AU - Levey, Douglas J. AU - Damschen, Ellen I. T2 - ECOGRAPHY AB - For a half century, habitat configuration – the arrangement of habitat patches within a landscape – has been central to theories of landscape ecology, population dynamics, and community assembly, in addition to conservation strategies. A recent hypothesis advanced by Fahrig (2013) would, if supported, greatly diminish the relevance of habitat configuration as a predictor of diversity. The Habitat Amount Hypothesis posits that the sample area effect overrides patch size and patch isolation effects of habitat fragmentation on species richness. It predicts that the amount of habitat in a local landscape, regardless of configuration, is the main landscape‐level determinant of species richness. If habitat amount is indeed the major, landscape‐level driver of species richness, the slopes of the species–area relationship (SAR) for otherwise similar fragmented and unfragmented landscapes should be indistinguishable. We tested the Habitat Amount Hypothesis with data from two replicated and controlled habitat fragmentation experiments that disentangle the effects of habitat amount and configuration. One experiment provided time‐series data on plant species richness and the other on micro‐arthropod species richness. We found that, relative to less fragmented habitats, the SARs for fragmented habitats have significantly higher slopes and that the magnitude of the difference in slopes increased over time. Relatively more species were lost in smaller areas when fragments were more isolated. In both experiments, the proportion of species lost due to increased habitat fragmentation was nearly identical to the proportion lost due to reduced habitat amount. Our results provide a direct and experimentally derived refutation of the Habitat Amount Hypothesis, supporting the long‐held view that in addition to area, patch isolation and configuration are important determinants of species richness. Differences in species richness between fragmented and non‐fragmented habitats increase over time, demonstrating that long‐term studies are needed to understand the effects of fragmentation, above and beyond the amount of habitat lost. DA - 2017/1// PY - 2017/1// DO - 10.1111/ecog.02535 VL - 40 IS - 1 SP - 48-55 SN - 1600-0587 ER - TY - JOUR TI - Expanding the CRISPR Toolbox: Targeting RNA with Cas13b AU - Barrangou, Rodolphe AU - Gersbach, Charles A. T2 - MOLECULAR CELL AB - In this issue of Molecular Cell, Smargon et al., 2017Smargon A. Cox D.B.T. Pyzocha N.K. Zheng K. Slaymaker I.M. Gootenberg J.S. Abudayyeh O.A. Essletzbichler P. Shmakov S. Makarova K.S. et al.Mol. Cell. 2017; 65 (this issue): 618-630Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar unearth Cas13b from type VI-B CRISPR-Cas immune systems and characterize its RNA-guided, RNA-targeting activity, including regulation by the novel co-factors Csx27 and Csx28, as well as non-specific collateral RNA damage. In this issue of Molecular Cell, Smargon et al., 2017Smargon A. Cox D.B.T. Pyzocha N.K. Zheng K. Slaymaker I.M. Gootenberg J.S. Abudayyeh O.A. Essletzbichler P. Shmakov S. Makarova K.S. et al.Mol. Cell. 2017; 65 (this issue): 618-630Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar unearth Cas13b from type VI-B CRISPR-Cas immune systems and characterize its RNA-guided, RNA-targeting activity, including regulation by the novel co-factors Csx27 and Csx28, as well as non-specific collateral RNA damage. CRISPR and associated sequences (Cas) together constitute CRISPR-Cas systems that provide adaptive immunity against invasive nucleic acids via DNA-encoded, RNA-mediated, sequence-specific targeting. Several molecular machines derived from CRISPR-Cas systems have been very successfully repurposed as technologies for editing the genome, controlling the transcriptome, and altering the epigenome (Barrangou and Doudna, 2016Barrangou R. Doudna J.A. Nat. Biotechnol. 2016; 34: 933-941Crossref PubMed Scopus (537) Google Scholar). Indeed, Cas9 has enabled the democratization of genome editing in the past 3 years, with great promise for versatile cell engineering. Despite the transformative impact of CRISPR-based technologies in recent years, only a small fraction of CRISPR-Cas systems have yet to be explored in any detail. Consequently, several recent efforts have focused on mining microbial genomes to unearth programmable Cas effector proteins able to expand the molecular biology toolkit, with recent additions such as Cpf1 (now Cas12a) (Zetsche et al., 2015Zetsche B. Gootenberg J.S. Abudayyeh O.O. Slaymaker I.M. Makarova K.S. Essletzbichler P. Volz S.E. Joung J. van der Oost J. Regev A. et al.Cell. 2015; 163: 759-771Abstract Full Text Full Text PDF PubMed Scopus (2500) Google Scholar), C2c2 (now Cas13a) (Shmakov et al., 2015Shmakov S. Abudayyeh O.O. Makarova K.S. Wolf Y.I. Gootenberg J.S. Semenova E. Minakhin L. Joung J. Konermann S. Severinov K. et al.Mol. Cell. 2015; 60: 385-397Abstract Full Text Full Text PDF PubMed Scopus (714) Google Scholar), CasX, and CasY (Burstein et al., 2016Burstein D. Harrington L.B. Strutt S.C. Probst A.J. Anantharaman K. Thomas B.C. Doudna J.A. Banfield J.F. Nature. 2016; (Published online December 22, 2016)https://doi.org/10.1038/nature21059Crossref Scopus (323) Google Scholar). The featured study by Smargon et al., 2017Smargon A. Cox D.B.T. Pyzocha N.K. Zheng K. Slaymaker I.M. Gootenberg J.S. Abudayyeh O.A. Essletzbichler P. Shmakov S. Makarova K.S. et al.Mol. Cell. 2017; 65 (this issue): 618-630Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar reports that Cas13b (previously C2c6) from type VI-B CRISPR-Cas systems is an RNA-guided RNase with an idiosyncratic mechanism of action that could be repurposed to target RNA in a programmable manner (Figure 1). In the past decade, CRISPR-Cas systems have been established as the drivers of adaptive immunity in bacteria and repurposed as a revolutionary genome-editing technology (Barrangou and Doudna, 2016Barrangou R. Doudna J.A. Nat. Biotechnol. 2016; 34: 933-941Crossref PubMed Scopus (537) Google Scholar). Our appreciation for the natural diversity of CRISPR-Cas systems has yielded several rounds of classification and nomenclature evolution, and there are currently two major classes distinguished by single versus complexed effector proteins, which are further divided into six major types and 19 subtypes (Makarova et al., 2015Makarova K.S. Wolf Y.I. Alkhnbashi O.S. Costa F. Shah S.A. Saunders S.J. Barrangou R. Brouns S.J. Charpentier E. Haft D.H. et al.Nat. Rev. Microbiol. 2015; 13: 722-736Crossref PubMed Scopus (1462) Google Scholar, Shmakov et al., 2017Shmakov S. Smargon A. Scott D. Cox D. Pyzocha N. Yan W. Abudayyeh O.O. Gootenberg J.S. Makarova K.S. Wolf Y.I. et al.Nat. Rev. Microbiol. 2017; (Published online January 23, 2017)https://doi.org/10.1038/nrmicro.2016.184Crossref PubMed Scopus (555) Google Scholar). The most effective strategy to uncover the next Cas effector protein is to develop sophisticated and creative in silico analyses to parse through the ever-increasing numbers of sequenced microbial genomes. To find a new subtype of CRISPR-Cas systems, Smargon et al., 2017Smargon A. Cox D.B.T. Pyzocha N.K. Zheng K. Slaymaker I.M. Gootenberg J.S. Abudayyeh O.A. Essletzbichler P. Shmakov S. Makarova K.S. et al.Mol. Cell. 2017; 65 (this issue): 618-630Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar used a computational database mining approach to search for single large effector proteins associated with CRISPR arrays that did not contain the nearly universal markers cas1 and cas2 and identified Cas13b. Two distinct classes were detected repeatedly among a total of 105 genomic loci identified and were particularly enriched in Bacteriodetes, such as Porphyromonas and Prevotella. Though Cas13b has a novel sequence, it carries two HEPN domains (RxxxxH), somewhat similar to the architecture of Cas13a, the signature RNase from the type VI-A CRISPR-Cas system (Shmakov et al., 2015Shmakov S. Abudayyeh O.O. Makarova K.S. Wolf Y.I. Gootenberg J.S. Semenova E. Minakhin L. Joung J. Konermann S. Severinov K. et al.Mol. Cell. 2015; 60: 385-397Abstract Full Text Full Text PDF PubMed Scopus (714) Google Scholar, Shmakov et al., 2017Shmakov S. Smargon A. Scott D. Cox D. Pyzocha N. Yan W. Abudayyeh O.O. Gootenberg J.S. Makarova K.S. Wolf Y.I. et al.Nat. Rev. Microbiol. 2017; (Published online January 23, 2017)https://doi.org/10.1038/nrmicro.2016.184Crossref PubMed Scopus (555) Google Scholar). Genetically, the CRISPR array is reminiscent of other class 2 systems, with a 36 nt, partially palindromic repeat sequence and spacers with homology to phage genome sequences. Mechanistically, two mature CRISPR RNA (crRNA) species were identified, a “short” 66 nt crRNA and a “long” 118 nt crRNA with an extended CRISPR repeat portion. After porting the systems into E. coli, Smargon et al., 2017Smargon A. Cox D.B.T. Pyzocha N.K. Zheng K. Slaymaker I.M. Gootenberg J.S. Abudayyeh O.A. Essletzbichler P. Shmakov S. Makarova K.S. et al.Mol. Cell. 2017; 65 (this issue): 618-630Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar showed knockdown of essential genes when Cas13b was heterologously expressed with targeted crRNAs. By studying strongly depleted sequences, Smargon et al., 2017Smargon A. Cox D.B.T. Pyzocha N.K. Zheng K. Slaymaker I.M. Gootenberg J.S. Abudayyeh O.A. Essletzbichler P. Shmakov S. Makarova K.S. et al.Mol. Cell. 2017; 65 (this issue): 618-630Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar revealed that heavily targeted sequences are typically flanked by a peculiar double-sided protospacer flanking sequence (PFS), akin to the protospacer-associated motif (PAM). Focusing on the Bergeyella zoohelcum BzCas13b, Smargon et al., 2017Smargon A. Cox D.B.T. Pyzocha N.K. Zheng K. Slaymaker I.M. Gootenberg J.S. Abudayyeh O.A. Essletzbichler P. Shmakov S. Makarova K.S. et al.Mol. Cell. 2017; 65 (this issue): 618-630Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar showed sequence-specific single-stranded RNA (ssRNA) targeting. Furthermore, this activity was associated with non-specific RNA cleavage, dubbed “collateral” RNase activity, albeit only in the presence of target RNA, similar to what has been previously described for Cas13a (Abudayyeh et al., 2016Abudayyeh O.O. Gootenberg J.S. Konermann S. Joung J. Slaymaker I.M. Cox D.B. Shmakov S. Makarova K.S. Semenova E. Minakhin L. et al.Science. 2016; 353: aaf5573Crossref PubMed Scopus (1146) Google Scholar, East-Seletsky et al., 2016East-Seletsky A. O’Connell M.R. Knight S.C. Burstein D. Cate J.H. Tjian R. Doudna J.A. Nature. 2016; 538: 270-273Crossref PubMed Scopus (592) Google Scholar). HEPN-dependent interference was confirmed by resistance against lytic phage MS2, with reduced plaque formation in the presence of targeting spacers, involving conserved catalytic arginines and histidines (R116/H121 and R1177/H1182). Additionally, the study investigated other novel cas genes they found typically associated with cas13b, Csx27, and Csx28, which were determined to be a repressor and an enhancer of Cas13b activity, respectively. Mechanistically, the absence of the nearly universal CRISPR markers cas1 and cas2 is intriguing given their implication in novel spacer acquisition during the immunization process, though they could be provided in trans given the frequent occurrence of other CRISPR-Cas systems in genomes that carry cas13b. This is somewhat contradictory with the typical orthogonality of different CRISPR-Cas systems, and future studies should investigate whether Cas1 and Cas2 can interact with type VI-B CRISPR arrays and determine how acquisition occurs in this subtype. The potential for cross-reactivity of acquisition machinery across systems may help with understanding the currently mysterious mechanisms of immunization. Arguably the most novel insight provided by this new system is the discovery of the co-regulatory molecules Csx27 and Csx28. The dual control options afforded by Csx27 inhibition and Csx28 activation of Cas13b beg the question as to whether there is control of cas13b transcription prior to interference and/or post-transcriptional control by direct interaction with Cas13b (or possibly crRNA) following invasive RNA targeting. Smargon et al., 2017Smargon A. Cox D.B.T. Pyzocha N.K. Zheng K. Slaymaker I.M. Gootenberg J.S. Abudayyeh O.A. Essletzbichler P. Shmakov S. Makarova K.S. et al.Mol. Cell. 2017; 65 (this issue): 618-630Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar’s demonstration of Csx27- and Csx28-based regulation in non-native hosts from heterologous systems indicates that the latter is at least one contributing factor, but this should certainly be a necessary area of future work. The mechanism of Csx27 and Csx28 action also determines how they might interplay with the putative target phages, including potential roles in the rise of phage resistance via invader transcript destruction or possibly triggering of host death via collateral RNA targeting. The former would enable the host to thrive, whereas the latter would drive suicide of infected cells for the benefit of the rest of the population, akin to the abortive infection system. It will be important to define the role of these new regulatory control systems in determining the cellular outcome of Cas13b activity and the impact at the population levels for both hosts and phages. Additionally, similar to recent analyses of Cas9 and other Cas effector proteins, biochemical and structural studies will also be necessary, to provide critical insights into their biology, as well as a basis to enhance their functions and optimize their activity and specificity by engineering. Given the potential repurposing of these molecular machines in eukaryotes, it is intriguing to ponder how effectively and specifically RNA targeting will be for either RNA-virus eradication or promoting programmed cell death by exploiting collateral RNase activity. Actually, it is still unclear whether this system naturally targets RNA viruses and/or the RNA transcripts of DNA viruses. Although CRISPR-Cas systems are potent antivirals by nature, they could also be reprogrammed to drive the death of the host when it is desirable to do so. Indeed, an endogenous lethal self-targeting pathway could be hijacked to drive cell suicide by exploiting the collateral RNA damage mechanism, leading to systemic RNA degradation and programmed cell death. This is reminiscent of the repurposing of self-targeting CRISPR-Cas systems as antimicrobials (Gomaa et al., 2014Gomaa A.A. Klumpe H.E. Luo M.L. Selle K. Barrangou R. Beisel C.L. MBio. 2014; 5: e00928-13Crossref PubMed Scopus (245) Google Scholar). Overall, this study illustrates how mining dark matter in obscure bacterial genomes is continuing to yield novel Cas-based molecular machines that advance our understanding of the interplay between bacteria and their predators and open new avenues for the development of new tools that expand the molecular biology toolbox for genome, transcriptome, and epigenome engineering. R.B. and C.A.G. are inventors on patents related to CRISPR-Cas systems and their various uses. R.B. is a co-founder and SAB member of Intellia Therapeutics and Locus Biosciences; C.A.G. is a co-founder and SAB member of Locus Biosciences and Element Genomics. Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28Smargon et al.Molecular CellJanuary 5, 2017In BriefSmargon et al. identify and characterize two class 2 type VI-B CRISPR systems lacking Cas1 and Cas2 and containing the RNA-guided RNase Cas13b, differentially regulated by Csx27 and Csx28. Through an E. coli essential gene screen they show that Cas13b RNA targeting is dependent on a double-sided PFS and RNA accessibility. Full-Text PDF Open Archive DA - 2017/2/16/ PY - 2017/2/16/ DO - 10.1016/j.molcel.2017.02.002 VL - 65 IS - 4 SP - 582-584 SN - 1097-4164 ER - TY - JOUR TI - Connecting models, data, and concepts to understand fragmentation's ecosystem-wide effects AU - Haddad, Nick M. AU - Holt, Robert D. AU - Fletcher, Robert J., Jr. AU - Loreau, Michel AU - Clobert, Jean T2 - ECOGRAPHY DA - 2017/1// PY - 2017/1// DO - 10.1111/ecog.02974 VL - 40 IS - 1 SP - 1-8 SN - 1600-0587 ER - TY - JOUR TI - Biochar amendments increase the yield advantage of legume-based intercropping systems over monoculture AU - Liu, Ling AU - Wang, Yanfang AU - Yan, Xinwei AU - Li, Jiwei AU - Jiao, Nianyuan AU - Hu, Shuijin T2 - AGRICULTURE ECOSYSTEMS & ENVIRONMENT AB - Biochar soil amendments are receiving increased attention as one strategy to improve soil quality and crop productivity. However, studies about how biochar affects crop productivity so far have mainly focused on single cropping systems. Few have examined the effects of biochar additions on intercrops. We conducted a field experiment that investigated the effects of biochar amendments on yield and nutrient uptake in an intercropping system where maize (Zea mays L.) was intercropped with either soybean (Glycine max L.) or peanut (Arachis hypogaea L.). The relative advantages of both yield and total nutrient content were calculated as land equivalent ratios (LER). Biochar amendments significantly increased the yield advantage in both maize/soybean and maize/peanut systems over the single crops. Similarly, they significantly enhanced the relative N and P uptake advantage. Using the 15N isotope dilution method, we examined the effect of biochar amendments on peanut N2-fixation and subsequent N transfer from peanut to maize in a root-box experiment. Biochar amendments of 10 and 20 g kg−1 soil increased peanut N fixation by 15.52% and 14.11%, and increased N transfer from peanut to maize by 32.66% and 36.07%, respectively. These results indicate that amending soil with biochar can amplify the benefits of legume-based intercropping by enhancing legume N fixation and facilitating N transfer from legume plants to co-existing cereal crops. DA - 2017/1/16/ PY - 2017/1/16/ DO - 10.1016/j.agee.2016.12.026 VL - 237 SP - 16-23 SN - 1873-2305 KW - Biochar KW - Legume-based intercropping KW - Yield and nutrient uptake KW - N-15-dilution KW - N fixation and N transfer ER - TY - JOUR TI - A Nonparametric survival function estimator via censored kernel quantile regressions AU - Shin, S. J. AU - Zhang, H. H. AU - Wu, Y. C. T2 - Statistica Sinica DA - 2017/// PY - 2017/// VL - 27 IS - 1 SP - 457-478 ER - TY - JOUR TI - tDCS for Memory Enhancement: Analysis of the Speculative Aspects of Ethical Issues AU - Voarino, Nathalie AU - Dubljević, Veljko AU - Racine, Eric T2 - Frontiers in Human Neuroscience AB - Transcranial direct current stimulation (tDCS) is a promising technology to enhance cognitive and physical performance. One of the major areas of interest is the enhancement of memory function in healthy individuals. The early arrival of tDCS on the market for lifestyle uses and cognitive enhancement purposes lead to the voicing of some important ethical concerns, especially because, to date, there are no official guidelines or evaluation procedures to tackle these issues. The aim of this article is to review ethical issues related to uses of tDCS for memory enhancement found in the ethics and neuroscience literature and to evaluate how realistic and scientifically well-founded these concerns are? In order to evaluate how plausible or speculative each issue is, we applied the methodological framework described by Racine et al. (2014) for "informed and reflective" speculation in bioethics. This framework could be succinctly presented as requiring: (1) the explicit acknowledgment of factual assumptions and identification of the value attributed to them; (2) the validation of these assumptions with interdisciplinary literature; and (3) the adoption of a broad perspective to support more comprehensive reflection on normative issues. We identified four major considerations associated with the development of tDCS for memory enhancement: safety, autonomy, justice and authenticity. In order to assess the seriousness and likelihood of harm related to each of these concerns, we analyzed the assumptions underlying the ethical issues, and the level of evidence for each of them. We identified seven distinct assumptions: prevalence, social acceptance, efficacy, ideological stance (bioconservative vs. libertarian), potential for misuse, long term side effects, and the delivery of complete and clear information. We conclude that ethical discussion about memory enhancement via tDCS sometimes involves undue speculation, and closer attention to scientific and social facts would bring a more nuanced analysis. At this time, the most realistic concerns are related to safety and violation of users' autonomy by a breach of informed consent, as potential immediate and long-term health risks to private users remain unknown or not well defined. Clear and complete information about these risks must be provided to research participants and consumers of tDCS products or related services. Broader public education initiatives and warnings would also be worthwhile to reach those who are constructing their own tDCS devices. DA - 2017/1/11/ PY - 2017/1/11/ DO - 10.3389/fnhum.2016.00678 VL - 10 SP - J2 - Front. Hum. Neurosci. OP - SN - 1662-5161 UR - http://dx.doi.org/10.3389/fnhum.2016.00678 DB - Crossref KW - memory enhancement KW - cognitive enhancement KW - brain stimulation KW - tDCS KW - ethics ER - TY - JOUR TI - Societal Risk Evaluation Scheme (SRES): Scenario-Based Multi-Criteria Evaluation of Synthetic Biology Applications AU - Cummings, Christopher L. AU - Kuzma, Jennifer T2 - PLOS ONE AB - Synthetic biology (SB) applies engineering principles to biology for the construction of novel biological systems designed for useful purposes. From an oversight perspective, SB products come with significant uncertainty. Yet there is a need to anticipate and prepare for SB applications before deployment. This study develops a Societal Risk Evaluation Scheme (SRES) in order to advance methods for anticipatory governance of emerging technologies such as SB. The SRES is based upon societal risk factors that were identified as important through a policy Delphi study. These factors range from those associated with traditional risk assessment, such as health and environmental consequences, to broader features of risk such as those associated with reversibility, manageability, anticipated levels of public concern, and uncertainty. A multi-disciplinary panel with diverse perspectives and affiliations assessed four case studies of SB using the SRES. Rankings of the SRES components are compared within and across the case studies. From these comparisons, we found levels of controllability and familiarity associated with the cases to be important for overall SRES rankings. From a theoretical standpoint, this study illustrates the applicability of the psychometric paradigm to evaluating SB cases. In addition, our paper describes how the SRES can be incorporated into anticipatory governance models as a screening tool to prioritize research, information collection, and dialogue in the face of the limited capacity of governance systems. To our knowledge, this is the first study to elicit data on specific cases of SB with the goal of developing theory and tools for risk governance. DA - 2017/1/4/ PY - 2017/1/4/ DO - 10.1371/journal.pone.0168564 VL - 12 IS - 1 SP - SN - 1932-6203 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85008354426&partnerID=MN8TOARS ER - TY - JOUR TI - Relative Contributions of Agricultural Drift, Para-Occupational, and Residential Use Exposure Pathways to House Dust Pesticide Concentrations: Meta-Regression of Published Data AU - Deziel, Nicole C. AU - Freeman, Laura E. Beane AU - Graubard, Barry I. AU - Jones, Rena R. AU - Hoppin, Jane A. AU - Thomas, Kent AU - Hines, Cynthia J. AU - Blair, Aaron AU - Sandler, Dale P. AU - Chen, Honglei AU - Lubin, Jay H. AU - Andreotti, Gabriella AU - Alavanja, Michael C. R. AU - Friesen, Melissa C. T2 - Environmental Health Perspectives AB - Background:Increased pesticide concentrations in house dust in agricultural areas have been attributed to several exposure pathways, including agricultural drift, para-occupational, and residential use.Objective:To guide future exposure assessment efforts, we quantified relative contributions of these pathways using meta-regression models of published data on dust pesticide concentrations.Methods:From studies in North American agricultural areas published from 1995 to 2015, we abstracted dust pesticide concentrations reported as summary statistics [e.g., geometric means (GM)]. We analyzed these data using mixed-effects meta-regression models that weighted each summary statistic by its inverse variance. Dependent variables were either the log-transformed GM (drift) or the log-transformed ratio of GMs from two groups (para-occupational, residential use).Results:For the drift pathway, predicted GMs decreased sharply and nonlinearly, with GMs 64% lower in homes 250 m versus 23 m from fields (interquartile range of published data) based on 52 statistics from seven studies. For the para-occupational pathway, GMs were 2.3 times higher [95% confidence interval (CI): 1.5, 3.3; 15 statistics, five studies] in homes of farmers who applied pesticides more recently or frequently versus less recently or frequently. For the residential use pathway, GMs were 1.3 (95% CI: 1.1, 1.4) and 1.5 (95% CI: 1.2, 1.9) times higher in treated versus untreated homes, when the probability that a pesticide was used for the pest treatment was 1–19% and ≥ 20%, respectively (88 statistics, five studies).Conclusion:Our quantification of the relative contributions of pesticide exposure pathways in agricultural populations could improve exposure assessments in epidemiologic studies. The meta-regression models can be updated when additional data become available.Citation:Deziel NC, Beane Freeman LE, Graubard BI, Jones RR, Hoppin JA, Thomas K, Hines CJ, Blair A, Sandler DP, Chen H, Lubin JH, Andreotti G, Alavanja MC, Friesen MC. 2017. Relative contributions of agricultural drift, para-occupational, and residential use exposure pathways to house dust pesticide concentrations: meta-regression of published data. Environ Health Perspect 125:296–305; http://dx.doi.org/10.1289/EHP426 DA - 2017/3// PY - 2017/3// DO - 10.1289/ehp426 VL - 125 IS - 3 SP - 296-305 J2 - Environmental Health Perspectives LA - en OP - SN - 0091-6765 1552-9924 UR - http://dx.doi.org/10.1289/EHP426 DB - Crossref ER - TY - JOUR TI - More than meets the eye: Emergent properties of transcription factors networks in Arabidopsis AU - Muhammad, Durreshahwar AU - Schmittling, Selene AU - Williams, Cranos AU - Long, Terri A. T2 - BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS AB - Uncovering and mathematically modeling Transcription Factor Networks (TFNs) are the first steps in engineering plants with traits that are better equipped to respond to changing environments. Although several plant TFNs are well known, the framework for systematically modeling complex characteristics such as switch-like behavior, oscillations, and homeostasis that emerge from them remain elusive. This review highlights literature that provides, in part, experimental and computational techniques for characterizing TFNs. This review also outlines methodologies that have been used to mathematically model the dynamic characteristics of TFNs. We present several examples of TFNs in plants that are involved in developmental and stress response. In several cases, advanced algorithms capture or quantify emergent properties that serve as the basis for robustness and adaptability in plant responses. Increasing the use of mathematical approaches will shed new light on these regulatory properties that control plant growth and development, leading to mathematical models that predict plant behavior. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer. DA - 2017/1// PY - 2017/1// DO - 10.1016/j.bbagrm.2016.07.017 VL - 1860 IS - 1 SP - 64-74 SN - 0006-3002 KW - Transcription factor networks (TFNs) KW - Emergent properties KW - Mathematical modeling ER - TY - JOUR TI - High-Throughput Resequencing of Maize Landraces at Genomic Regions Associated with Flowering Time AU - Jamann, Tiffany M. AU - Sood, Shilpa AU - Wisser, Randall J. AU - Holland, James B. T2 - PLOS ONE AB - Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions. We report the use of a multiplexed panel of 319 PCR assays that target 20 candidate loci associated with photoperiod sensitivity in maize while requiring 25 ng or less of starting DNA per sample. Enriched regions had an average on-target sequence read depth of 105 with 98% of the sequence data mapping to the maize 'B73' reference and 80% of the reads mapping to the target interval. Sequence reads were aligned to B73 and 1,486 and 1,244 variants were called using SAMtools and GATK, respectively. Of the variants called by both SAMtools and GATK, 30% were not previously reported in maize. Due to the high sequence read depth, heterozygote genotypes could be called with at least 92.5% accuracy in hybrid materials using GATK. The genetic data are congruent with previous reports of high total genetic diversity and substantial population differentiation among maize landraces. In conclusion, semiconductor sequencing of highly multiplexed PCR reactions is a cost-effective strategy for resequencing targeted genomic loci in diverse maize materials. DA - 2017/1/3/ PY - 2017/1/3/ DO - 10.1371/journal.pone.0168910 VL - 12 IS - 1 SP - SN - 1932-6203 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85008367807&partnerID=MN8TOARS ER - TY - JOUR TI - GlobalAnts: a new database on the geography of ant traits (Hymenoptera: Formicidae) AU - Parr, Catherine L. AU - Dunn, Robert R. AU - Sanders, Nathan J. AU - Weiser, Michael D. AU - Photakis, Manoli AU - Bishop, Tom R. AU - Fitzpatrick, Matthew C. AU - Arnan, Xavier AU - Baccaro, Fabricio AU - Brandao, Carlos R. F. AU - Chick, Lacy AU - Donoso, David A. AU - Fayle, Tom M. AU - Gomez, Crisanto AU - Grossman, Blair AU - Munyai, Thinandavha C. AU - Pacheco, Renata AU - Retana, Javier AU - Robinson, Andrew AU - Sagata, Katayo AU - Silva, Rogerio R. AU - Tista, Melanie AU - Vasconcelos, Heraldo AU - Yates, Michelle AU - Gibb, Heloise T2 - INSECT CONSERVATION AND DIVERSITY AB - Abstract In recent years the focus in ecology has shifted from species to a greater emphasis on functional traits. In tandem with this shift, a number of trait databases have been developed covering a range of taxa. Here, we introduce the GlobalAnts database. Globally, ants are dominant, diverse and provide a range of ecosystem functions. The database represents a significant tool for ecology in that it (i) contributes to a global archive of ant traits (morphology, ecology and life history) which complements existing ant databases and (ii) promotes a trait‐based approach in ant and other insect ecology through a broad set of standardised traits. The GlobalAnts database is unique in that it represents the largest online database of functional traits with associated georeferenced assemblage‐level data (abundance and/or occupancy) for any animal group with 9056 ant species and morphospecies records for entire local assemblages across 4416 sites. We describe the structure of the database, types of traits included and present a summary of data coverage. The value of the database is demonstrated through an initial examination of trait distributions across subfamilies, continents and biomes. Striking biogeographic differences in ant traits are highlighted which raise intriguing questions as to the mechanisms generating them. DA - 2017/1// PY - 2017/1// DO - 10.1111/icad.12211 VL - 10 IS - 1 SP - 5-20 SN - 1752-4598 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85008262955&partnerID=MN8TOARS KW - Assemblages KW - ecology KW - functional trait KW - morphology KW - online database ER - TY - JOUR TI - First Report of Raspberry leaf mottle virus in Blackberry in the United States. AU - Thekke-Veetil, T. AU - Khadgi, A. AU - Johnson, D. AU - Burrack, H. AU - Sabanadzovic, S. AU - Tzanetakis, I. E. T2 - PLANT DISEASE AB - HomePlant DiseaseVol. 101, No. 1First Report of Raspberry leaf mottle virus in Blackberry in the United States PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Raspberry leaf mottle virus in Blackberry in the United StatesT. Thekke-Veetil, A. Khadgi, D. Johnson, H. Burrack, S. Sabanadzovic, and I. E. TzanetakisT. Thekke-VeetilSearch for more papers by this author, A. KhadgiSearch for more papers by this author, D. JohnsonSearch for more papers by this author, H. BurrackSearch for more papers by this author, S. SabanadzovicSearch for more papers by this author, and I. E. TzanetakisSearch for more papers by this authorAffiliationsAuthors and Affiliations T. Thekke-Veetil A. Khadgi , Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701 D. Johnson , Department of Entomology, University of Arkansas, Fayetteville, AR 72701 H. Burrack , Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 S. Sabanadzovic , Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762 I. E. Tzanetakis , Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701. Published Online:17 Oct 2016https://doi.org/10.1094/PDIS-07-16-1014-PDNAboutSections ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Raspberry leaf mottle virus (RLMV) is the most widespread virus in raspberry in the Pacific Northwest (Quito-Avila et al. 2014). The virus has been reported in the U.K. in blackberry (Jones and McGavin 1998) but its presence in the host in the United States is unknown. A survey was carried out in the Southeast and Midwest to ascertain whether the virus infects commercial and wild blackberries, and to evaluate its potential role in the recent outbreak of blackberry yellow vein disease (BYVD; Martin et al. 2013). A total of 247 BYVD-affected plants, collected from Arkansas, Florida, Georgia, Illinois, North Carolina, South Carolina, and West Virginia between 2008 and 2011 were screened by RT-PCR for the presence of RLMV as described in Tzanetakis et al. (2007). Four plants tested positive, two cultivated (Arkansas and North Carolina), and two wild blackberries from Arkansas. All amplicons (452 bp) were sequenced to confirm their identity and revealed 99 to 100% identity between each other at the nucleotide and amino acid levels (GenBank accessions KX431258 to 61), as well as with the type isolate (DQ357218). Additionally, the presence of RLMV was confirmed by RNA blot hybridization (Thekke Veetil and Tzanetakis 2016). The PCR amplicons were cloned into a Topo2.1 cloning vector and an insert was subjected to digoxigenin probe synthesis and used for virus detection according to manufacturer’s protocol (DIG High Prime DNA Labeling and Detection Starter Kit II, Roche Life Science), by blotting total nucleic acids (900 ng) from all infected and healthy blackberry controls onto a positively charged nylon membrane (GE Healthcare Life Sciences). This is the first report of RLMV in blackberry in the United States. Its low incidence in commercial fields and wild blackberries indicates that RLMV is not a major player in the BYVD outbreak. The apparently low incidence of RLMV in commercial blackberry plantings suggests that RLMV does not circulate in propagation material. The virus is transmitted by the large raspberry aphid (Amphorophora agathonica Hottes) and because of the low incidence of the vector in the areas assayed (Johnson and Burrack, unpublished), RLMV is not expected to be a major risk factor for the industry.References:Jones, A. T., and McGavin, W. J. 1998. Ann. Appl. Biol. 132:239. Crossref, ISI, Google ScholarMartin, R. R., et al. 2013. Plant Dis. 97:168. https://doi.org/10.1094/PDIS-04-12-0362-FE Link, ISI, Google ScholarQuito-Avila, D. F., et al. 2014. Plant Dis. 98:176. https://doi.org/10.1094/PDIS-05-13-0562-RE Link, ISI, Google ScholarThekke Veetil, T., and Tzanetakis, I. E. 2016. Plant Dis. 100:867. Link, ISI, Google ScholarTzanetakis, I. E., et al. 2007. Virus Res. 127:26. https://doi.org/10.1016/j.virusres.2007.03.010 Crossref, ISI, Google ScholarDetailsFiguresLiterature CitedRelated Vol. 101, No. 1 January 2017SubscribeISSN:0191-2917e-ISSN:1943-7692 Metrics Article History Issue Date: 22 Dec 2016Published: 17 Oct 2016First Look: 29 Aug 2016Accepted: 19 Aug 2016 Pages: 265-265 Information© 2017 The American Phytopathological SocietyCited byRaspberry leaf mottle virusCABI Compendium, Vol. CABI CompendiumA synthesis of virus-vector associations reveals important deficiencies in studies on host and vector manipulation by plant virusesVirus Research, Vol. 285Rubus spp. (Blackberry, Blackraspberry, Caneberry, Raspberry, Redraspberry, Wineberry)6 June 2020 DA - 2017/1// PY - 2017/1// DO - 10.1094/pdis-07-16-1014-pdn VL - 101 IS - 1 SP - 265-265 SN - 1943-7692 ER - TY - JOUR TI - Characterization of a Genomic Region under Selection in Cultivated Carrot (Daucus carota subsp sativus) Reveals a Candidate Domestication Gene AU - Macko-Podgorni, Alicja AU - Machaj, Gabriela AU - Stelmach, Katarzyna AU - Senalik, Douglas AU - Grzebelus, Ewa AU - Iorizzo, Massimo AU - Simon, Philipp W. AU - Grzebelus, Dariusz T2 - FRONTIERS IN PLANT SCIENCE AB - Carrot is one of the most important vegetables worldwide, owing to its capability to develop fleshy, highly nutritious storage roots. It was domesticated ca. 1,100 years ago in Central Asia. No systematic knowledge about the molecular mechanisms involved in the domestication syndrome in carrot are available, however, the ability to form a storage root is undoubtedly the essential transition from the wild Daucus carota to the cultivated carrot. Here, we expand on the results of a previous study which identified a polymorphism showing a significant signature for selection upon domestication. We mapped the region under selection to the distal portion of the long arm of carrot chromosome 2, confirmed that it had been selected, as reflected in both the lower nucleotide diversity in the cultivated gene pool, as compared to the wild (πw/πc = 7.4 vs. 1.06 for the whole genome), and the high FST (0.52 vs. 0.12 for the whole genome). We delimited the region to ca. 37 kb in length and identified a candidate domestication syndrome gene carrying three non-synonymous single nucleotide polymorphisms and one indel systematically differentiating the wild and the cultivated accessions. This gene, DcAHLc1, belongs to the AT-hook motif nuclear localized (AHL) family of plant regulatory genes which are involved in the regulation of organ development, including root tissue patterning. AHL genes work through direct interactions with other AHL family proteins and a range of other proteins that require intercellular protein movement. Based on QTL data on root thickening we speculate that DcAHLc1 might be involved in the development of the carrot storage root, as the localization of the gene overlapped with one of the QTLs. According to haplotype information we propose that the 'cultivated' variant of DcAHLc1 has been selected from wild Central Asian carrot populations upon domestication and it is highly predominant in the western cultivated carrot gene pool. However, some primitive eastern landraces and the derived B7262 purple inbred line still carry the 'wild' variant, reflecting a likely complexity of the genetic determination of the formation of carrot storage roots. DA - 2017/1/18/ PY - 2017/1/18/ DO - 10.3389/fpls.2017.00012 VL - 8 SP - SN - 1664-462X KW - AT-hook motif nuclear localized (AHL) KW - domestication syndrome KW - genotyping-by-sequencing KW - linkage disequilibrium KW - single nucleotide polymorphism KW - storage root ER - TY - JOUR TI - CO2-induced alterations in plant nitrate utilization and root exudation stimulate N2O emissions AU - Wu, Keke AU - Chen, Dima AU - Tu, Cong AU - Qiu, Yunpeng AU - Burkey, Kent O. AU - Reberg-Horton, S. Chris AU - Peng, Shaolin AU - Hu, Shuijin T2 - SOIL BIOLOGY & BIOCHEMISTRY AB - Atmospheric carbon dioxide enrichment (eCO2) often increases soil nitrous oxide (N2O) emissions, which has been largely attributed to increased denitrification induced by CO2-enhancement of soil labile C and moisture. However, the origin of the N remains unexplained. Emerging evidence suggests that eCO2 alters plant N preference in favor of ammonium (NH4+-N) over nitrate (NO3−-N). Yet, whether and how this attributes to the enhancement of N2O emissions has not been investigated. We conducted a microcosm experiment with wheat (Triticum aestivum L.) and tall fescue (Schedonorus arundinaceus (Schreb.) Dumort.) to examine the effects of eCO2 on soil N2O emissions in the presence of two N forms (NH4+-N or NO3−-N). Results obtained showed that N forms dominated eCO2 effects on plant and microbial N utilization, and thus soil N2O emissions. Elevated CO2 significantly increased the rate and the sum of N2O emissions by three to four folds when NO3−-N, but not NH4+-N, was supplied under both wheat and tall fescue. While enhanced N2O emission was more related to the reduced plant NO3−-N uptake under wheat, it concurred with increased labile C under tall fescue. In the presence of NO3−-N, significantly lower shoot biomass N and 15N, but higher plant biomass C:N ratio, microbial biomass C and N, and/or soil extractable C indicated that eCO2 constrained plant NO3−-N utilization and likely stimulated root exudation. We propose a new conceptual model in which eCO2-inhibition of plant NO3−-N uptake and/or CO2-enhancement of soil labile C enhances the N and/or C availability for denitrifiers and increases the intensity and/or the duration of N2O emissions. Together, these findings indicate that CO2-enhancement of soil N and labile C favors denitrification, suggesting that management of N fertilizers in intensive systems will likely become more challenging under future CO2 scenarios. DA - 2017/3// PY - 2017/3// DO - 10.1016/j.soilbio.2016.11.018 VL - 106 SP - 9-17 SN - 0038-0717 KW - Elevated CO2 KW - Root exudation KW - Nitrous oxide KW - N-15 tracer KW - Ammonium nitrogen (NH4+-N) KW - Nitrate nitrogen (NO3--N) KW - Fertilization management ER - TY - JOUR TI - Taxonomic resolution is a determinant of biodiversity effects in arbuscular mycorrhizal fungal communities AU - Yang, Haishui AU - Zhang, Qian AU - Koide, Roger T. AU - Hoeksema, Jason D. AU - Tang, Jianjun AU - Bian, Xinmin AU - Hu, Shuijin AU - Chen, Xin T2 - JOURNAL OF ECOLOGY AB - Summary Arbuscular mycorrhizal fungi ( AMF ) are key regulators of ecosystem processes, yet how their biodiversity works in ecosystems remains poorly understood. We documented the extent to which taxonomic resolution influenced the effect of biodiversity of AMF taxa on plant performance (growth, nutrient uptake and stress tolerance) in a meta‐analysis of 902 articles. We found that the effect of biodiversity of AMF taxa depended on taxonomic resolution. Plant performance was positively promoted by AMF family richness, while no effect was found for fungal species richness. In addition, negative effect was found between AMF phylogenetic diversity and plant growth. This pattern can be explained by functional conservatism within AMF families and functional differentiation among AMF families. Synthesis . Conservation of AMF communities to maintain a full complement of ecosystem functions requires the presence of diverse families and not simply diverse species within a family. This finding may be of key importance for the function of ecosystems under various environmental perturbations to which AMF families may respond differently. DA - 2017/1// PY - 2017/1// DO - 10.1111/1365-2745.12655 VL - 105 IS - 1 SP - 219-228 SN - 1365-2745 KW - arbuscular mycorrhiza KW - competition KW - diversity KW - ecosystem function KW - functional complementarity KW - niche KW - taxonomic level ER - TY - JOUR TI - Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.) AU - Andres, R. J. AU - Coneva, V. AU - Frank, M. H. AU - Tuttle, J. R. AU - Samayoa, L. F. AU - Han, S. W. AU - Kaur, B. AU - Zhu, L. L. AU - Fang, Hui AU - Bowman, D. T. AU - Rojas-Pierce, Marcela AU - Haigler, Candace H. AU - Jones, D. C. AU - Holland, James AU - Chitwood, D. H. AU - Kuraparthy, Vasu T2 - Proceedings of the National Academy of Sciences of the United States of America AB - Abstract Leaf shape is spectacularly diverse. As the primary source of photo-assimilate in major crops, understanding the evolutionary and environmentally induced changes in leaf morphology are critical to improving agricultural productivity. The role of leaf shape in cotton domestication is unique, as breeders have purposefully selected for entire and lobed leaf morphs resulting from a single locus, okra ( L-D 1 ). The okra locus is not only of agricultural importance in cotton ( Gossypium hirsutum L.), but through pioneering chimeric and morphometric studies it has contributed to fundamental knowledge about leaf development. Here we show that the major leaf shapes of cotton at the L-D 1 locus are controlled by a HD-Zip transcription factor most similar to Late Meristem Identity1 (LMI1) gene. The classical okra leaf shape gene has133-bp tandem duplication in the promoter, correlated with elevated expression, while an 8-bp deletion in the third exon of the presumed wild-type normal leaf causes a frame-shifted and truncated coding sequence. Virus-induced gene silencing (VIGS) of this LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. An intermediate leaf shape allele, sub-okra , lacks both the promoter duplication and the exonic deletion. Our results indicate that sub-okra is the ancestral leaf shape of tetraploid cotton and normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. DA - 2017/// PY - 2017/// DO - 10.1101/062612 VL - 114 IS - 1 SP - E57–66 ER - TY - JOUR TI - Integrating Criminological and Decision Research Theory: Implications for Understanding and Addressing Crime in Marginalized Communities AU - Rivers, Louie, III AU - Gibbs, Carole AU - Paternoster, Raymond T2 - DEVIANT BEHAVIOR AB - Minority groups are significantly overrepresented in crime. Theories of racial differences in crime developed using two separate and distinct approaches that highlight either increased exposure to criminogenic factors at the individual level or greater risk of crime due to disadvantaged neighborhood conditions. Neighborhood theories describe how structural disadvantage disrupts neighborhood social processes and produces oppositional street cultures. In the article, we advance theorizing on race and crime by linking the neighborhood experience to individual-level decision making via new conceptualizations of culture. Rather than a “values as goals” view of culture, culture may include a “tool kit” of ways to solve problems and this cultural toolkit may, in turn, influence how an individual makes decisions. Specifically, culturally learned toolkits may increase flaws in the decision process (e.g., fast and intuitive rather than deliberate decision processes, the use of decision heuristics) to produce more crime, which would explain the association between race and crime. We integrate this conceptualization of culture and these flaws in the decision-making process into rational choice theory at the individual level and describe how they may be exacerbated in disadvantaged neighborhood contexts. Implications for understanding race and crime and directions for future research are discussed. DA - 2017/// PY - 2017/// DO - 10.1080/01639625.2016.1196948 VL - 38 IS - 1 SP - 74-93 SN - 1521-0456 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84979049920&partnerID=MN8TOARS ER - TY - JOUR TI - Dynamical behavior of an epidemiological model with a demographic Allee effect AU - Usaini, Salisu AU - Lloyd, Alun L. AU - Anguelov, Roumen AU - Garba, Salisu M. T2 - Mathematics and Computers in Simulation AB - As the Allee effect refers to small density or population size, it cannot be deduced whether or not the Allee mechanisms responsible for an Allee effect at low population density or size will affect the dynamics of a population at high density or size as well. We show using susceptible–exposed–infectious (SEI) model that such mechanisms combined with disease pathogenicity have a detrimental impact on the dynamics of a population at high population level. In fact, the eventual outcome could be an inevitable population crash to extinction. The tipping point marking the unanticipated population collapse at high population level is mathematically associated with a saddle–node bifurcation. The essential mechanism of this scenario is the simultaneous population size depression and the increase of the extinction threshold owing to disease virulence and the Allee effect. Using numerical continuation software MatCont another saddle–node bifurcation is detected, which results in the re-emergence of two non-trivial equilibria since highly pathogenic species cause their own extinction but not that of their host. DA - 2017/3// PY - 2017/3// DO - 10.1016/j.matcom.2016.04.010 VL - 133 SP - 311-325 J2 - Mathematics and Computers in Simulation LA - en OP - SN - 0378-4754 UR - http://dx.doi.org/10.1016/j.matcom.2016.04.010 DB - Crossref KW - Allee effect KW - Threshold KW - Extinction KW - Saddle-node bifurcation ER - TY - JOUR TI - Variation of within-crop microhabitat use by Drosophila suzukii (Diptera: Drosophilidae) in blackberry AU - Diepenbrock, L. M. AU - Burrack, H. J. T2 - JOURNAL OF APPLIED ENTOMOLOGY AB - Abstract Drosophila suzukii Matsumara (Diptera: Drosophilidae) is an invasive vinegar fly that infests ripe and ripening soft skinned fruits. In the south‐eastern United States, blackberry ( Rubus spp.) crops are heavily impacted by D. suzukii , and current management tactics rely on the use of broad‐spectrum insecticides targeted to adult populations. An improved understanding of D. suzukii biology and ecology are necessary to create sustainable management options. Knowledge of how D. suzukii interacts with resources will enable targeted management actions in the future. In this present study, we monitored larval infestation throughout the blackberry canopy and found that infestation was highest in the inner portion of the canopy and lower in more exposed locations. We also documented higher humidity within the cane canopy relative to the edge of the field. A difference in abiotic conditions may create within‐crop microhabitats that D. suzukii is able to exploit. Future research will explore how to take advantage of these microhabitats in pest management programs. DA - 2017/2// PY - 2017/2// DO - 10.1111/jen.12335 VL - 141 IS - 1-2 SP - 1-7 SN - 1439-0418 KW - Drosophila suzukii KW - invasive species KW - microhabitat KW - pest management ER - TY - JOUR TI - Soybean cyst nematode culture collections and field populations from North Carolina and Missouri reveal high incidences of infection by viruses AU - Ruark, Casey L. AU - Koenning, Stephen R. AU - Davis, Eric L. AU - Opperman, Charles H. AU - Lommel, Steven A. AU - Mitchum, Melissa G. AU - Sit, Tim L. T2 - PLOS ONE AB - Five viruses were previously discovered infecting soybean cyst nematodes (SCN; Heterodera glycines) from greenhouse cultures maintained in Illinois. In this study, the five viruses [ScNV, ScPV, ScRV, ScTV, and SbCNV-5] were detected within SCN greenhouse and field populations from North Carolina (NC) and Missouri (MO). The prevalence and titers of viruses in SCN from 43 greenhouse cultures and 25 field populations were analyzed using qRT-PCR. Viral titers within SCN greenhouse cultures were similar throughout juvenile development, and the presence of viral anti-genomic RNAs within egg, second-stage juvenile (J2), and pooled J3 and J4 stages suggests active viral replication within the nematode. Viruses were found at similar or lower levels within field populations of SCN compared with greenhouse cultures of North Carolina populations. Five greenhouse cultures harbored all five known viruses whereas in most populations a mixture of fewer viruses was detected. In contrast, three greenhouse cultures of similar descent to one another did not possess any detectable viruses and primarily differed in location of the cultures (NC versus MO). Several of these SCN viruses were also detected in Heterodera trifolii (clover cyst) and Heterodera schachtii (beet cyst), but not the other cyst, root-knot, or reniform nematode species tested. Viruses were not detected within soybean host plant tissue. If nematode infection with viruses is truly more common than first considered, the potential influence on nematode biology, pathogenicity, ecology, and control warrants continued investigation. DA - 2017/1/31/ PY - 2017/1/31/ DO - 10.1371/journal.pone.0171514 VL - 12 IS - 1 SP - SN - 1932-6203 ER - TY - PCOMM TI - Rethinking biosecurity AU - Kuzma, J. DA - 2017/// PY - 2017/// SP - 12-12 ER - TY - JOUR TI - Responses of arthropod populations to warming depend on latitude: evidence from urban heat islands AU - Youngsteadt, Elsa AU - Ernst, Andrew F. AU - Dunn, Robert R. AU - Frank, Steven D. T2 - GLOBAL CHANGE BIOLOGY AB - Biological effects of climate change are expected to vary geographically, with a strong signature of latitude. For ectothermic animals, there is systematic latitudinal variation in the relationship between climate and thermal performance curves, which describe the relationship between temperature and an organism's fitness. Here, we ask whether these documented latitudinal patterns can be generalized to predict arthropod responses to warming across mid- and high temperate latitudes, for taxa whose thermal physiology has not been measured. To address this question, we used a novel natural experiment consisting of a series of urban warming gradients at different latitudes. Specifically, we sampled arthropods from a single common street tree species across temperature gradients in four US cities, located from 35.8 to 42.4° latitude. We captured 6746 arthropods in 34 families from 111 sites that varied in summer average temperature by 1.7-3.4 °C within each city. Arthropod responses to warming within each city were characterized as Poisson regression coefficients describing change in abundance per °C for each family. Family responses in the two midlatitude cities were heterogeneous, including significantly negative and positive effects, while those in high-latitude cities varied no more than expected by chance within each city. We expected high-latitude taxa to increase in abundance with warming, and they did so in one of the two high-latitude cities; in the other, Queens (New York City), most taxa declined with warming, perhaps due to habitat loss that was correlated with warming in this city. With the exception of Queens, patterns of family responses to warming were consistent with predictions based on known latitudinal patterns in arthropod physiology relative to regional climate. Heterogeneous responses in midlatitudes may be ecologically disruptive if interacting taxa respond oppositely to warming. DA - 2017/4// PY - 2017/4// DO - 10.1111/gcb.13550 VL - 23 IS - 4 SP - 1436-1447 SN - 1365-2486 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85006106453&partnerID=MN8TOARS KW - arthropods KW - climate change KW - ectotherms KW - global warming KW - latitude KW - thermal tolerance KW - urban heat island KW - urbanization ER - TY - JOUR TI - Recommendations for the Implementation of Telehealth in Cardiovascular and Stroke Care A Policy Statement From the American Heart Association AU - Schwamm, Lee H. AU - Chumbler, Neale AU - Brown, Ed AU - Fonarow, Gregg C. AU - Berube, David AU - Nystrom, Karin AU - Suter, Robert AU - Zavala, Mirian AU - Polsky, Daniel AU - Radhakrishnan, Kavita AU - Lacktman, Nathaniel AU - Horton, Katherine AU - Malcarney, Mary-Beth AU - Halamka, John AU - Tiner, A. Colby T2 - CIRCULATION AB - The aim of this policy statement is to provide a comprehensive review of the scientific evidence evaluating the use of telemedicine in cardiovascular and stroke care and to provide consensus policy suggestions. We evaluate the effectiveness of telehealth in advancing healthcare quality, identify legal and regulatory barriers that impede telehealth adoption or delivery, propose steps to overcome these barriers, and identify areas for future research to ensure that telehealth continues to enhance the quality of cardiovascular and stroke care. The result of these efforts is designed to promote telehealth models that ensure better patient access to high-quality cardiovascular and stroke care while striving for optimal protection of patient safety and privacy. DA - 2017/2/14/ PY - 2017/2/14/ DO - 10.1161/cir.0000000000000475 VL - 135 IS - 7 SP - E24-E44 SN - 1524-4539 KW - AHA Scientific Statements KW - cardiovascular diseases KW - health services KW - stroke KW - telemedicine ER - TY - JOUR TI - High pesticide exposure events and DNA methylation among pesticide applicators in the agricultural health study AU - Rusiecki, Jennifer A. AU - Freeman, Laura E. Beane AU - Bonner, Matthew R. AU - Alexander, Melannie AU - Chen, Ligong AU - Andreotti, Gabriella AU - Barry, Kathryn H. AU - Moore, Lee E. AU - Byun, Hyang-Min AU - Kamel, Freya AU - Alavanja, Michael AU - Hoppin, Jane A. AU - Baccarelli, Andrea T2 - ENVIRONMENTAL AND MOLECULAR MUTAGENESIS AB - Pesticide exposure has been associated with acute and chronic adverse health effects. DNA methylation (DNAm) may mediate these effects. We evaluated the association between experiencing unusually high pesticide exposure events (HPEEs) and DNAm among pesticide applicators in the Agricultural Health Study (AHS), a prospective study of applicators from Iowa and North Carolina. DNA was extracted from whole blood from male AHS pesticide applicators ( n = 695). Questionnaire data were used to ascertain the occurrence of HPEEs over the participant's lifetime. Pyrosequencing was used to quantify DNAm in CDH1 , GSTp1 , and MGMT promoters, and in the repetitive element, LINE‐1 . Linear and robust regression analyses evaluated adjusted associations between HPEE and DNAm. Ever having an HPEE ( n = 142; 24%) was associated with elevated DNAm in the GSTp1 promoter at CpG7 (chr11:67,351,134; P < 0.01) and for the mean across the CpGs measured in the GSTp1 promoter ( P < 0.01). In stratified analyses, elevated GSTP1 promoter DNAm associated with HPEE was more pronounced among applicators >59 years and those with plasma folate levels ≤16.56 ng/mL (p‐interaction <0.01); HPEE was associated with reduced MGMT promoter DNAm at CpG2 (chr10:131,265,803; P = 0.03), CpG3 (chr10:131,265,810; P = 0.05), and the mean across CpGs measured in the MGMT promoter ( P = 0.03) among applicators >59 years and reduced LINE‐1 DNAm ( P = 0.05) among applicators with ≤16.56 ng/mL plasma folate. Non‐specific HPEEs may contribute to increased DNAm in GSTp1 , and in some groups, reduced DNAm in MGMT and LINE‐1 . The impacts of these alterations on disease development are unclear, but elevated GSTp1 promoter DNAm and subsequent gene inactivation has been consistently associated with prostate cancer. Environ. Mol. Mutagen. 58:19–29, 2017. © 2016 Wiley Periodicals, Inc. DA - 2017/1// PY - 2017/1// DO - 10.1002/em.22067 VL - 58 IS - 1 SP - 19-29 SN - 1098-2280 KW - DNA methylation KW - pesticides KW - exposure KW - Agricultural Health Study KW - epigenetics ER - TY - JOUR TI - Accumulation of medium-chain, saturated fatty acyl moieties in seed oils of transgenic Camelina sativa AU - Hu, Zhaohui AU - Wu, Qian AU - Dalal, Jyoti AU - Vasani, Naresh AU - Lopez, Harry O. AU - Sederoff, Heike W. AU - Qu, Rongda T2 - PLOS ONE AB - With its high seed oil content, the mustard family plant Camelina sativa has gained attention as a potential biofuel source. As a bioenergy crop, camelina has many advantages. It grows on marginal land with low demand for water and fertilizer, has a relatively short life cycle, and is stress tolerant. As most other crop seed oils, camelina seed triacylglycerols (TAGs) consist of mostly long, unsaturated fatty acyl moieties, which is not desirable for biofuel processing. In our efforts to produce shorter, saturated chain fatty acyl moieties in camelina seed oil for conversion to jet fuel, a 12:0-acyl-carrier thioesterase gene, UcFATB1, from California bay (Umbellularia californica Nutt.) was expressed in camelina seeds. Up to 40% of short chain laurate (C12:0) and myristate (C14:0) were present in TAGs of the seed oil of the transgenics. The total oil content and germination rate of the transgenic seeds were not affected. Analysis of positions of these two fatty acyl moieties in TAGs indicated that they were present at the sn-1 and sn-3 positions, but not sn-2, on the TAGs. Suppression of the camelina KASII genes by RNAi constructs led to higher accumulation of palmitate (C16:0), from 7.5% up to 28.5%, and further reduction of longer, unsaturated fatty acids in seed TAGs. Co-transformation of camelina with both constructs resulted in enhanced accumulation of all three medium-chain, saturated fatty acids in camelina seed oils. Our results show that a California bay gene can be successfully used to modify the oil composition in camelina seed and present a new biological alternative for jet fuel production. DA - 2017/2/17/ PY - 2017/2/17/ DO - 10.1371/journal.pone.0172296 VL - 12 IS - 2 SP - SN - 1932-6203 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85013067776&partnerID=MN8TOARS ER - TY - JOUR TI - A longitudinal study of human milk composition in the second year postpartum: implications for human milk banking AU - Perrin, Maryanne T. AU - Fogleman, April D. AU - Newburg, David S. AU - Allen, Jonathan C. T2 - MATERNAL AND CHILD NUTRITION AB - Abstract While the composition of human milk has been studied extensively in the first year of lactation, there is a paucity of data regarding human milk composition beyond one year postpartum. Policies vary at milk banks around the world regarding how long lactating women are eligible to donate their milk. The primary purpose of this study is to describe longitudinal changes in human milk composition in the second year postpartum to support the development of evidence based guidelines regarding how long lactating women can donate human milk to a milk bank. Nineteen lactating women in North Carolina provided monthly milk samples from 11 months to 17 months postpartum ( N = 131), and two non‐profit milk banks provided ( N = 33) pooled, unpasteurized milk samples from 51 approved donors less than one year postpartum. There was a significant increase ( P < 0.05) in the concentration of total protein, lactoferrin, lysozyme, Immunoglobulin A, oligosaccharides and sodium in longitudinal samples of mother's milk between 11 and 17 months postpartum, while zinc and calcium concentrations declined, and no changes were observed in lactose, fat, iron and potassium. Human milk in the second year postpartum contained significantly higher concentrations of total protein, lactoferrin, lysozyme and Immunoglobulin A, than milk bank samples, and significantly lower concentrations of zinc, calcium, iron and oligosaccharides. Accepting milk bank donations beyond one year postpartum is a potential strategy for increasing the supply of donor milk, but may require mineral fortification. DA - 2017/1// PY - 2017/1// DO - 10.1111/mcn.12239 VL - 13 IS - 1 SP - SN - 1740-8709 KW - human milk KW - milk banking KW - lactation KW - pasteurized donor milk ER -