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Ph-Dependent Dna Distortion And Repression Of Gene Expression By Pectobacterium Atrosepticum Pecs, Dinesh K. Deochand, Jacob K. Meariman, Anne Grove Jul 2016

Ph-Dependent Dna Distortion And Repression Of Gene Expression By Pectobacterium Atrosepticum Pecs, Dinesh K. Deochand, Jacob K. Meariman, Anne Grove

Faculty Publications

© 2016 American Chemical Society. Transcriptional activity is exquisitely sensitive to changes in promoter DNA topology. Transcription factors may therefore control gene activity by modulating the relative positioning of -10 and -35 promoter elements. The plant pathogen Pectobacterium atrosepticum, which causes soft rot in potatoes, must alter gene expression patterns to ensure growth in planta. In the related soft-rot enterobacterium Dickeya dadantii, PecS functions as a master regulator of virulence gene expression. Here, we report that P. atrosepticum PecS controls gene activity by altering promoter DNA topology in response to pH. While PecS binds the pecS promoter with high affinity …

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Phosphogenesis Associated With The Shuram Excursion: Petrographic And Geochemical Observations From The Ediacaran Doushantuo Formation Of South China, Huan Cui, Shuhai Xiao, Chuanming Zhou, Yongbo Peng, Alan J. Kaufman, Rebecca E. Plummer Jul 2016

Phosphogenesis Associated With The Shuram Excursion: Petrographic And Geochemical Observations From The Ediacaran Doushantuo Formation Of South China, Huan Cui, Shuhai Xiao, Chuanming Zhou, Yongbo Peng, Alan J. Kaufman, Rebecca E. Plummer

Faculty Publications

© 2016 Elsevier B.V. The Ediacaran Period witnessed one of the largest phosphogenic events in Earth's history. Coincidently, some phosphorite deposits in South China are associated with the largest-known carbon isotope negative excursion (i.e., Shuram Excursion), suggesting an intimate coupling of the biogeochemical carbon and phosphorous cycles. However, the geomicrobiological linkage between these anomalies remain poorly understood. In this study, we investigated the phosphorite samples from the uppermost Doushantuo Formation in South China. Carbon isotope compositions of authigenic calcite cements and nodules in the phosphorites are as low as –34‰ (VPDB). Petrographic and geochemical investigations indicate that the 13C-depleted carbonates …

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Intersystem Implications Of The Developmental Origins Of Health And Disease: Advancing Health Promotion In The 21st Century, Michael D. Barnes, Thomas L. Heaton, Michael C. Goates, Justin M. Packer Jul 2016

Intersystem Implications Of The Developmental Origins Of Health And Disease: Advancing Health Promotion In The 21st Century, Michael D. Barnes, Thomas L. Heaton, Michael C. Goates, Justin M. Packer

Faculty Publications

The developmental origins of health and disease (DOHaD) theory and life course theory (LCT) are emerging fields of research that have significant implications for the public health and health promotion professions. Using a DOHaD/LCT perspective, social determinants of health (SDH) take on new critical meaning by which health promotion professionals can implement DOHaD/LCT guided interventions, including recommended policies. Through these interventions, public health could further address the sources of worldwide chronic disease epidemics and reduce such disease rates substantially if related policy, programs, and interdisciplinary and multi-sector collaboration are emphasized. Additional characteristics of the most effective interventions involve context-specific adaptation …

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New "Light" For One-World Approach Toward Safe And Effective Control Of Animal Diseases And Insect Vectors From Leishmaniac Perspectives, Kwang Poo Chang, Bala K. Kolli, Ramesh B. Batchu, Hui Wen Chen, Larry Ming C. Chow, Robert Elliott, Jonathan F. Head, Chia Kwung Fan, Chen Hsiung Hung, Dar Der Ji, Zhao Rong Lun, Laura Manna, Yoshitsugu Matsumoto, Dennis K.P. Ng, Camila I. De Oliveira, Sayonara Melo, Yusuf Ozbel, Ahmet Özbilgin, Joseph Reynolds, Chizu Sanjoba, Shin Hong Shiao, Nang Yao Shih, Chi Wei Tsai, Maria Da Graça H. Vicente, Charles H. Barré, Petr Volf, Yueh Lung Wu, Chao Lan Yu, Xiao Nong Zhou Jul 2016

New "Light" For One-World Approach Toward Safe And Effective Control Of Animal Diseases And Insect Vectors From Leishmaniac Perspectives, Kwang Poo Chang, Bala K. Kolli, Ramesh B. Batchu, Hui Wen Chen, Larry Ming C. Chow, Robert Elliott, Jonathan F. Head, Chia Kwung Fan, Chen Hsiung Hung, Dar Der Ji, Zhao Rong Lun, Laura Manna, Yoshitsugu Matsumoto, Dennis K.P. Ng, Camila I. De Oliveira, Sayonara Melo, Yusuf Ozbel, Ahmet Özbilgin, Joseph Reynolds, Chizu Sanjoba, Shin Hong Shiao, Nang Yao Shih, Chi Wei Tsai, Maria Da Graça H. Vicente, Charles H. Barré, Petr Volf, Yueh Lung Wu, Chao Lan Yu, Xiao Nong Zhou

Faculty Publications

© 2016 The Author(s). Light is known to excite photosensitizers (PS) to produce cytotoxic reactive oxygen species (ROS) in the presence of oxygen. This modality is attractive for designing control measures against animal diseases and pests. Many PS have a proven safety record. Also, the ROS cytotoxicity selects no resistant mutants, unlike other drugs and pesticides. Photodynamic therapy (PDT) refers to the use of PS as light activable tumoricides, microbicides and pesticides in medicine and agriculture. Here we describe "photodynamic vaccination" (PDV) that uses PDT-inactivation of parasites, i.e. Leishmania as whole-cell vaccines against leishmaniasis, and as a universal carrier to …

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Calling In Sick: Impacts Of Fever On Intra-Urban Human Mobility, T. Alex Perkins, Valerie A. Paz-Soldan, Steven T. Stoddard, Amy C. Morrison, Brett M. Forshey, Kanya C. Long, Eric S. Halsey, Tadeusz J. Kochel, John P. Elder, Uriel Kitron, Thomas W. Scott, Gonzalo M. Vazquez-Prokopec Jul 2016

Calling In Sick: Impacts Of Fever On Intra-Urban Human Mobility, T. Alex Perkins, Valerie A. Paz-Soldan, Steven T. Stoddard, Amy C. Morrison, Brett M. Forshey, Kanya C. Long, Eric S. Halsey, Tadeusz J. Kochel, John P. Elder, Uriel Kitron, Thomas W. Scott, Gonzalo M. Vazquez-Prokopec

Faculty Publications

© 2016 The Author(s) Published by the Royal Society. All rights reserved. Pathogens inflict a wide variety of disease manifestations on their hosts, yet the impacts of disease on the behaviour of infected hosts are rarely studied empirically and are seldom accounted for in mathematical models of transmission dynamics. We explored the potential impacts of one of the most common disease manifestations, fever, on a key determinant of pathogen transmission, host mobility, in residents of the Amazonian city of Iquitos, Peru. We did so by comparing two groups of febrile individuals (dengue-positive and dengue-negative) with an afebrile control group. A …

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Tools And Techniques For Computational Reproducibility, Stephen Piccolo, Michael B. Frampton Jul 2016

Tools And Techniques For Computational Reproducibility, Stephen Piccolo, Michael B. Frampton

Faculty Publications

When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. The deterministic nature of most computer programs means that the same analysis tasks, applied to the same data, will …

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Food Habits, Lifestyle Factors, And Risk Of Prostate Cancer In Central Argentina: A Case Control Study Involving Self-Motivated Health Behavior Modifications After Diagnosis, Winston J. Craig, Sandaly O. S. Pacheco, Fabio J. Pacheco, Gimena M. J. Zapata, Julieta M. E. Garcia, Carlos A. Previale, Hector E. Cura Jul 2016

Food Habits, Lifestyle Factors, And Risk Of Prostate Cancer In Central Argentina: A Case Control Study Involving Self-Motivated Health Behavior Modifications After Diagnosis, Winston J. Craig, Sandaly O. S. Pacheco, Fabio J. Pacheco, Gimena M. J. Zapata, Julieta M. E. Garcia, Carlos A. Previale, Hector E. Cura

Faculty Publications

Cancer is the second most important non-communicable disease worldwide and disproportionately impacts low- to middle-income countries. Diet in combination with other lifestyle habits seems to modify the risk for some cancers but little is known about South Americans. Food habits of Argentinean men pre- and post-diagnosis of prostate cancer (n = 326) were assessed along with other lifestyle factors. We studied whether any of the behaviors and risk factors for prostate cancer were found in men with other cancers (n = 394), compared with control subjects (n = 629). Before diagnosis, both cases reported a greater mean consumption of meats …

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Planning For Sustainability In Small Municipalities: The Influence Of Interest Groups, Growth Patterns, And Institutional Characteristics, Vanessa R. Levesque, Kathleen P. Bell, Aram J. K. Calhoun Jul 2016

Planning For Sustainability In Small Municipalities: The Influence Of Interest Groups, Growth Patterns, And Institutional Characteristics, Vanessa R. Levesque, Kathleen P. Bell, Aram J. K. Calhoun

Faculty Publications

How and why small municipalities promote sustainability through planning efforts is poorly understood. We analyzed ordinances in 451 Maine municipalities and tested theories of policy adoption using regression analysis.We found that smaller communities do adopt programs that contribute to sustainability relevant to their scale and context. In line with the political market theory, we found that municipalities with strong environmental interests, higher growth, and more formal governments were more likely to adopt these policies. Consideration of context and capacity in planning for sustainability will help planners better identify and benefit from collaboration, training, and outreach opportunities.

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Geospatial Modeling Approach To Monument Construction Using Michigan From A.D. 1000–1600 As A Case Study, Meghan L. Howey, Michael W. Palace, Crystal H. Mcmichael Jul 2016

Geospatial Modeling Approach To Monument Construction Using Michigan From A.D. 1000–1600 As A Case Study, Meghan L. Howey, Michael W. Palace, Crystal H. Mcmichael

Faculty Publications

Building monuments was one way that past societies reconfigured their landscapes in response to shifting social and ecological factors. Understanding the connections between those factors and monument construction is critical, especially when multiple types of monuments were constructed across the same landscape. Geospatial technologies enable past cultural activities and environmental variables to be examined together at large scales. Many geospatial modeling approaches, however, are not designed for presence-only (occurrence) data, which can be limiting given that many archaeological site records are presence only. We use maximum entropy modeling (MaxEnt), which works with presence-only data, to predict the distribution of monuments …

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Book Review: Madness In Civilization: A Cultural History Of Insanity From The Bible To Freud, From The Madhouse To Modern Medicine, Edward Cohen Jul 2016

Book Review: Madness In Civilization: A Cultural History Of Insanity From The Bible To Freud, From The Madhouse To Modern Medicine, Edward Cohen

Faculty Publications

A review of: Scull, Andrew. (2015). Madness in civilization: A cultural history of insanity from the Bible to Freud, from the madhouse to modern medicine. Princeton, NJ: Princeton University Press. 448 pp. $39.50 (Hardback), ISBN 978-0-691-16615-5.

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Attending To Scientific Practices Within Undergraduate Research Experiences, Gina Quan, Chandra Turpen, Andrew Elby Jul 2016

Attending To Scientific Practices Within Undergraduate Research Experiences, Gina Quan, Chandra Turpen, Andrew Elby

Faculty Publications

Ford (2015) argues for viewing “scientific practice” not as a list of particular skills, but rather, more holistically as “sets of regularities of behaviors and social interactions” among scientists. This conceptualization of scientific practices foregrounds how they meaningfully connect to one another and are purposefully employed in order to explain nature. We apply this framework in the context of undergraduate research experiences (UREs) to understand the early forms of student engagement in scientific practices, and how these specific forms of engagement may be consequential for students’ future participation. Using video from interviews with students and research mentors, we argue that …

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The Misidentification Of Children With Disabilities: A Harm With No Foul, Claire Raj Jul 2016

The Misidentification Of Children With Disabilities: A Harm With No Foul, Claire Raj

Faculty Publications

Special education, despite being a uniform federal mandate, is often implemented drastically differently depending on the school system delivering services, the particular category of disability, and the race or ethnicity of students. Affluent white children who attend well-managed school districts tend to benefit from special education services. In the under-funded and over-tasked districts where most minorities attend school, the special education system does not always provide the same benefits. In these schools, special education, too often, operates as a dumping ground for those students the general education system cannot or refuses to serve. In these instances, the label of “special …

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A New Genus And Species Of Blind Sleeper (Teleostei: Eleotridae) From Oaxaca, Mexico: First Obligate Cave Gobiiform In The Western Hemisphere, Stephen J. Walsh, Prosanta Chakrabarty Jul 2016

A New Genus And Species Of Blind Sleeper (Teleostei: Eleotridae) From Oaxaca, Mexico: First Obligate Cave Gobiiform In The Western Hemisphere, Stephen J. Walsh, Prosanta Chakrabarty

Faculty Publications

© 2016 by the American Society of Ichthyologists and Herpetologists. Caecieleotris morrisi, new genus and species of sleeper (family Eleotridae), is described from a submerged freshwater cave in a karst region of the northern portion of the State of Oaxaca, Mexico, Río Papaloapan drainage, Gulf of Mexico basin. The new species represents the first cave-adapted sleeper known from the Western Hemisphere and is one of only 13 stygobitic gobiiforms known worldwide, with all others limited in distribution to the Indo-Pacific region. The new taxon represents a third independent evolution of a hypogean lifestyle in sleepers, the others being two species …

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References To Television Programming In Judicial Opinions And Lawyers’ Advocacy, Douglas E. Abrams Jul 2016

References To Television Programming In Judicial Opinions And Lawyers’ Advocacy, Douglas E. Abrams

Faculty Publications

"Think of the poor judge who is reading ... hundreds and hundreds of these briefs," says Chief Justice John G. Roberts, Jr. "Liven their life up just a little bit. . . with something interesting." Lawyers can "liven up" their briefs with references to television shows generally known to Americans who have grown up watching the small screen. After discussing television's pervasive effect on American culture since the early 1950s, this Article surveys the array of television references that appear in federal and state judicial opinions. In cases with no claims or defenses concerning the television industry, judges often help …

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A Single Amino-Acid Substitution In The Sodium Transporter Hkt1 Associated With Plant Salt Tolerance, Akhtar Ali, Natalia Raddatz, Rashid Aman, Songmi Kim, Hyeong Cheol Park, Masood Jan, Dongwon Baek, Irfan Ullah Khan, Dong Ha Oh, Sang Yeol Lee, Ray A. Bressan, Keun Woo Lee, Albino Maggio, Jose M. Pardo, Hans J. Bohnert, Dae Jin Yun Jul 2016

A Single Amino-Acid Substitution In The Sodium Transporter Hkt1 Associated With Plant Salt Tolerance, Akhtar Ali, Natalia Raddatz, Rashid Aman, Songmi Kim, Hyeong Cheol Park, Masood Jan, Dongwon Baek, Irfan Ullah Khan, Dong Ha Oh, Sang Yeol Lee, Ray A. Bressan, Keun Woo Lee, Albino Maggio, Jose M. Pardo, Hans J. Bohnert, Dae Jin Yun

Faculty Publications

© 2016 American Society of Plant Biologists. All rights reserved. A crucial prerequisite for plant growth and survival is the maintenance of potassium uptake, especially when high sodium surrounds the root zone. The Arabidopsis HIGH-AFFINITY K+ TRANSPORTER1 (HKT1), and its homologs in other salt-sensitive dicots, contributes to salinity tolerance by removing Na+ from the transpiration stream. However, TsHKT1;2, one of three HKT1 copies in Thellungiella salsuginea, a halophytic Arabidopsis relative, acts as a K+transporter in the presence of Na+ in yeast (Saccharomyces cerevisiae). Amino-acid sequence comparisons indicated differences between TsHKT1;2 and most other published HKT1 sequences with respect to an …

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Perchlorate And Volatiles Of The Brine Of Lake Vida (Antarctica): Implication For The In Situ Analysis Of Mars Sediments, Fabien Kenig, Luoth Chou, Christopher P. Mckay, W. Andrew Jackson, Peter T. Doran, Alison E. Murray, Christian H. Fritsen Jul 2016

Perchlorate And Volatiles Of The Brine Of Lake Vida (Antarctica): Implication For The In Situ Analysis Of Mars Sediments, Fabien Kenig, Luoth Chou, Christopher P. Mckay, W. Andrew Jackson, Peter T. Doran, Alison E. Murray, Christian H. Fritsen

Faculty Publications

©2016. American Geophysical Union. All Rights Reserved. The cold (−13.4°C), cryoencapsulated, anoxic, interstitial brine of the >27 m thick ice of Lake Vida (Victoria Valley, Antarctica) contains 49 µg · L−1of perchlorate and 11 µg · L−1of chlorate. Lake Vida brine (LVBr) may provide an analog for potential oxychlorine-rich subsurface brine on Mars. LVBr volatiles were analyzed by solid-phase microextraction (SPME) gas chromatography–mass spectrometry (GC-MS) with two different SPME fibers. With the exception of volatile organic sulfur compounds, most other volatiles observed were artifacts produced in the GC injector when the thermal decomposition products of oxychlorines reacted with reduced carbon …

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Cobalt Chloride Treatment Used To Ablate The Lateral Line System Also Impairs The Olfactory System In Three Freshwater Fishes, Julie M. Butler, Karen E. Field, Karen P. Maruska Jul 2016

Cobalt Chloride Treatment Used To Ablate The Lateral Line System Also Impairs The Olfactory System In Three Freshwater Fishes, Julie M. Butler, Karen E. Field, Karen P. Maruska

Faculty Publications

© 2016 Butler et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Fishes use multimodal signals during both inter- and intra-sexual displays to convey information about their sex, reproductive state, and social status. These complex behavioral displays can include visual, auditory, olfactory, tactile, and hydrodynamic signals, and the relative role of each sensory channel in these complex multi-sensory interactions is a common focus of neuroethology. The mechanosensory lateral line system of fishes detects …

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Mitogen-Dependent Regulation Of Dusp1 Governs Erk And P38 Signaling During Early 3t3-L1 Adipocyte Differentiation, Bradley S. Ferguson, Heesun Nam, Jacqueline M. Stephens, Ron F. Morrison Jul 2016

Mitogen-Dependent Regulation Of Dusp1 Governs Erk And P38 Signaling During Early 3t3-L1 Adipocyte Differentiation, Bradley S. Ferguson, Heesun Nam, Jacqueline M. Stephens, Ron F. Morrison

Faculty Publications

© 2015 Wiley Periodicals, Inc. Knowledge concerning mechanisms that control proliferation and differentiation of preadipocytes is essential to our understanding of adipocyte hyperplasia and the development of obesity. Evidence has shown that temporal regulation of mitogen-activated protein kinase (MAPK) phosphorylation and dephosphorylation is critical for coupling extracellular stimuli to cellular growth and differentiation. Using differentiating 3T3-L1 preadipocytes as a model of adipocyte hyperplasia, we examined a role for dual-specificity phosphatase 1 (DUSP1) on the timely modulation of MAPK signaling during states of growth arrest, proliferation, and differentiation. Using real-time reverse transcription PCR (qRT-PCR), we report that DUSP1 is induced during …

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Geauxdock: Accelerating Structure-Based Virtual Screening With Heterogeneous Computing, Ye Fang, Yun Ding, Wei P. Feinstein, David M. Koppelman, Juana Moreno, Mark Jarrell, J. Ramanujam, Michal Brylinski Jul 2016

Geauxdock: Accelerating Structure-Based Virtual Screening With Heterogeneous Computing, Ye Fang, Yun Ding, Wei P. Feinstein, David M. Koppelman, Juana Moreno, Mark Jarrell, J. Ramanujam, Michal Brylinski

Faculty Publications

© 2016 Fang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Computational modeling of drug binding to proteins is an integral component of direct drug design. Particularly, structure-based virtual screening is often used to perform large-scale modeling of putative associations between small organic molecules and their pharmacologically relevant protein targets. Because of a large number of drug candidates to be evaluated, an accurate and fast docking engine is a critical element of …

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Comparative Transcriptome Analysis Of Resistant And Susceptible Common Bean Genotypes In Response To Soybean Cyst Nematode Infection, Shalu Jain, Kishore Chittem, Robert Brueggeman, Juan M. Osorno, Jonathan Richards, Berlin D. Nelson Jul 2016

Comparative Transcriptome Analysis Of Resistant And Susceptible Common Bean Genotypes In Response To Soybean Cyst Nematode Infection, Shalu Jain, Kishore Chittem, Robert Brueggeman, Juan M. Osorno, Jonathan Richards, Berlin D. Nelson

Faculty Publications

Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) reproduces on the roots of common bean (Phaseolus vulgaris L.) and can cause reductions in plant growth and seed yield. The molecular changes in common bean roots caused by SCN infection are unknown. Identification of genetic factors associated with SCN resistance could help in development of improved bean varieties with high SCN resistance. Gene expression profiling was conducted on common bean roots infected by SCN HG type 0 using next generation RNA sequencing technology. Two pinto bean genotypes, PI533561 and GTS-900, resistant and susceptible to SCN infection, respectively, were used as RNA sources …

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Fine Mapping Of The Barley Chromosome 6h Net Form Net Blotch Susceptibility Locus, Jonathan Richards, Shiaoman Chao, Timothy Friesen, Robert Brueggeman Jul 2016

Fine Mapping Of The Barley Chromosome 6h Net Form Net Blotch Susceptibility Locus, Jonathan Richards, Shiaoman Chao, Timothy Friesen, Robert Brueggeman

Faculty Publications

Net form net blotch, caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres, is a destructive foliar disease of barley with the potential to cause significant yield loss in major production regions throughout the world. The complexity of the host-parasite genetic interactions in this pathosystem hinders the deployment of effective resistance in barley cultivars, warranting a deeper understanding of the interactions. Here, we report on the high-resolution mapping of the dominant susceptibility locus near the centromere of chromosome 6H in the barley cultivars Rika and Kombar, which are putatively targeted by necrotrophic effectors from P. teres f. teres isolates …

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Meta-Analysis Of 49 549 Individuals Imputed With The 1000 Genomes Project Reveals An Exonic Damaging Variant In Angptl4 Determining Fasting Tg Levels, Elisabeth M. Van Leeuwen, Aniko Sabo, Joshua C. Bis, Jennifer E. Huffman, Ani Manichaikul, Albert V. Smith, Mary F. Feitosa, Serkalem Demissie, Peter K. Joshi, Qing Duan, Jonathan Marten, Jan B. Van Klinken, Ida Surakka, Ilja M. Nolte, Weihua Zhang, Hamdi Mbarek, Ruifang Li-Gao, Stella Trompet, Niek Verweij, Evangelos Evangelou, Leo Pekka Lyytikäinen, Bamidele O. Tayo, Joris Deelen, Peter J. Van Der Most, Sander W. Van Der Laan, Dan E. Arking, Alanna Morrison, Abbas Dehghan, Oscar H. Franco, Albert Hofman, Fernando Rivadeneira, Eric J. Sijbrands, Andre G. Uitterlinden Jul 2016

Meta-Analysis Of 49 549 Individuals Imputed With The 1000 Genomes Project Reveals An Exonic Damaging Variant In Angptl4 Determining Fasting Tg Levels, Elisabeth M. Van Leeuwen, Aniko Sabo, Joshua C. Bis, Jennifer E. Huffman, Ani Manichaikul, Albert V. Smith, Mary F. Feitosa, Serkalem Demissie, Peter K. Joshi, Qing Duan, Jonathan Marten, Jan B. Van Klinken, Ida Surakka, Ilja M. Nolte, Weihua Zhang, Hamdi Mbarek, Ruifang Li-Gao, Stella Trompet, Niek Verweij, Evangelos Evangelou, Leo Pekka Lyytikäinen, Bamidele O. Tayo, Joris Deelen, Peter J. Van Der Most, Sander W. Van Der Laan, Dan E. Arking, Alanna Morrison, Abbas Dehghan, Oscar H. Franco, Albert Hofman, Fernando Rivadeneira, Eric J. Sijbrands, Andre G. Uitterlinden

Faculty Publications

Background So far, more than 170 loci have been associated with circulating lipid levels through genomewide association studies (GWAS). These associations are largely driven by common variants, their function is often not known, and many are likely to be markers for the causal variants. In this study we aimed to identify more new rare and low-frequency functional variants associated with circulating lipid levels. Methods We used the 1000 Genomes Project as a reference panel for the imputations of GWAS data from ~60 000 individuals in the discovery stage and ~90 000 samples in the replication stage. Results Our study resulted …

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Quantifying The Spatiotemporal Dynamics In A Chorus Frog (Pseudacris) Hybrid Zone Over 30 Years, Kristin N. Engebretsen, Lisa N. Barrow, Eric N. Rittmeyer, Jeremy M. Brown, Emily Moriarty Lemmon Jul 2016

Quantifying The Spatiotemporal Dynamics In A Chorus Frog (Pseudacris) Hybrid Zone Over 30 Years, Kristin N. Engebretsen, Lisa N. Barrow, Eric N. Rittmeyer, Jeremy M. Brown, Emily Moriarty Lemmon

Faculty Publications

© 2016 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Although theory suggests that hybrid zones can move or change structure over time, studies supported by direct empirical evidence for these changes are relatively limited. We present a spatiotemporal genetic study of a hybrid zone between Pseudacris nigrita and P. fouquettei across the Pearl River between Louisiana and Mississippi. This hybrid zone was initially characterized in 1980 as a narrow and steep “tension zone,” in which hybrid populations were inferior to parentals and were maintained through a balance between selection and dispersal. We reanalyzed historical tissue …

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Identiication Of Essential Arginine Residues Of Escherichia Coli Deda/Tvp38 Family Membrane Proteins Yqja And Yghb, Sujeet Kumar, Cersten L. Bradley, Patience Mukashyaka, William T. Doerrler Jul 2016

Identiication Of Essential Arginine Residues Of Escherichia Coli Deda/Tvp38 Family Membrane Proteins Yqja And Yghb, Sujeet Kumar, Cersten L. Bradley, Patience Mukashyaka, William T. Doerrler

Faculty Publications

© 2016 FEMS. Escherichia coli DedA/Tvp38 family proteins YghB and YqjA are putative membrane transporters with 62% amino acid identity and overlapping functions. An E. coli strain (BC202) with nonpolar ΔyghB and ΔyqjA mutations displays cell-division defects and temperature sensitivity and is sensitive to antibiotics and alkaline pH. In this study, we performed site-directed mutagenesis on conserved, charged amino acids of YqjA and YghB. We discovered two conserved predicted membrane-embedded arginines (R130 and R136) that are critical for function in both proteins as deined by their ability to complement BC202 phenotypes, when expressed from a plasmid. Lysine can substitute for …

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Be-Breeder - Learning: A New Tool For Teaching And Learning Plant Breeding Principles, Roberto Fritsche-Neto, Filipe Inácio Matias Jul 2016

Be-Breeder - Learning: A New Tool For Teaching And Learning Plant Breeding Principles, Roberto Fritsche-Neto, Filipe Inácio Matias

Faculty Publications

The Be-Breeder application is an on-line tool constructed through the R software for the purpose of assisting in some of the main genetic and statistical analyses related to the area of plant breeding. In addition, Be-Breeder provides a section called “Learning”, which in a simple click-point manner allows explanation of theories related to the effect of inbreeding, population structure, qualitative and quantitative traits, heterosis, population size, effect of selection, and composition of hybrids. Be-Breeder is available for network use on the website of the Allogamous Plant Breeding Laboratory (Laboratório de Melhoramento de Plantas Alógamas) of ESALQ-USP through the link: http:// …

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Population Genomics Related To Adaptation In Elite Oat Germplasm, Kathy Esvelt Klos, Yung Fen Huang, Wubishet A. Bekele, Don E. Obert, Ebrahiem Babiker, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael Bonman, Martin L. Carson, Shiaoman Chao, Belaghihalli N. Gnanesh, Irene Griffiths, Stephen A. Harrison, Catherine J. Howarth, Gongshe Hu, Amir Ibrahim, Emir Islamovic, Eric W. Jackson, Jean Luc Jannink, Frederic L. Kolb, Michael S. Mcmullen, Jennifer Mitchell Fetch, J. Paul Murphy, Herbert W. Ohm, Howard W. Rines, Brian G. Rossnagel, Jessica A. Schlueter, Mark E. Sorrells, Charlene P. Wight, Weikai Yan, Nicholas A. Tinker Jul 2016

Population Genomics Related To Adaptation In Elite Oat Germplasm, Kathy Esvelt Klos, Yung Fen Huang, Wubishet A. Bekele, Don E. Obert, Ebrahiem Babiker, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael Bonman, Martin L. Carson, Shiaoman Chao, Belaghihalli N. Gnanesh, Irene Griffiths, Stephen A. Harrison, Catherine J. Howarth, Gongshe Hu, Amir Ibrahim, Emir Islamovic, Eric W. Jackson, Jean Luc Jannink, Frederic L. Kolb, Michael S. Mcmullen, Jennifer Mitchell Fetch, J. Paul Murphy, Herbert W. Ohm, Howard W. Rines, Brian G. Rossnagel, Jessica A. Schlueter, Mark E. Sorrells, Charlene P. Wight, Weikai Yan, Nicholas A. Tinker

Faculty Publications

Six hundred thirty five oat (Avena sativa L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype-phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from K = 1 to 20 model-based analyses suggested a structured population. However, the PC and K = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation (p < 0.0001). Single-locus F-statistic (FST) in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of r2 = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24.

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Population Genomics Related To Adaptation In Elite Oat Germplasm, Kathy Esvelt Klos, Yung Fen Huang, Wubishet A. Bekele, Don E. Obert, Ebrahiem Babiker, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael Bonman, Martin L. Carson, Shiaoman Chao, Belaghihalli N. Gnanesh, Irene Griffiths, Stephen A. Harrison, Catherine J. Howarth, Gongshe Hu, Amir Ibrahim, Emir Islamovic, Eric W. Jackson, Jean Luc Jannink, Frederic L. Kolb, Michael S. Mcmullen, Jennifer Mitchell Fetch, J. Paul Murphy, Herbert W. Ohm, Howard W. Rines, Brian G. Rossnagel, Jessica A. Schlueter, Mark E. Sorrells, Charlene P. Wight, Weikai Yan, Nicholas A. Tinker Jul 2016

Population Genomics Related To Adaptation In Elite Oat Germplasm, Kathy Esvelt Klos, Yung Fen Huang, Wubishet A. Bekele, Don E. Obert, Ebrahiem Babiker, Aaron D. Beattie, Åsmund Bjørnstad, J. Michael Bonman, Martin L. Carson, Shiaoman Chao, Belaghihalli N. Gnanesh, Irene Griffiths, Stephen A. Harrison, Catherine J. Howarth, Gongshe Hu, Amir Ibrahim, Emir Islamovic, Eric W. Jackson, Jean Luc Jannink, Frederic L. Kolb, Michael S. Mcmullen, Jennifer Mitchell Fetch, J. Paul Murphy, Herbert W. Ohm, Howard W. Rines, Brian G. Rossnagel, Jessica A. Schlueter, Mark E. Sorrells, Charlene P. Wight, Weikai Yan, Nicholas A. Tinker

Faculty Publications

Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype-phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24.

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The Contribution Of The Pineal Gland On Daily Rhythms And Masking In Diurnal Grass Rats, Arvicanthis Niloticus, Dorela D. Shuboni, Amna A. Agha, Thomas K. H. Groves, Andrew J. Gall Jul 2016

The Contribution Of The Pineal Gland On Daily Rhythms And Masking In Diurnal Grass Rats, Arvicanthis Niloticus, Dorela D. Shuboni, Amna A. Agha, Thomas K. H. Groves, Andrew J. Gall

Faculty Publications

Melatonin is a hormone rhythmically secreted at night by the pineal gland in vertebrates. In diurnal mammals, melatonin is present during the inactive phase of the rest/activity cycle, and in primates it directly facilitates sleep and decreases body temperature. However, the role of the pineal gland for the promotion of sleep at night has not yet been studied in non-primate diurnal mammalian species. Here, the authors directly examined the hypothesis that the pineal gland contributes to diurnality in Nile grass rats by decreasing activity and increasing sleep at night, and that this could occur via effects on circadian mechanisms or …

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Environmental Context For The Terminal Ediacaran Biomineralization Of Animals, H. Cui, A. J. Kaufman, S. Xiao, S. Peek, H. Cao, X. Min, Y. Cai, Z. Siegel, X. M. Liu, Y. Peng, J. D. Schiffbauer, A. J. Martin Jul 2016

Environmental Context For The Terminal Ediacaran Biomineralization Of Animals, H. Cui, A. J. Kaufman, S. Xiao, S. Peek, H. Cao, X. Min, Y. Cai, Z. Siegel, X. M. Liu, Y. Peng, J. D. Schiffbauer, A. J. Martin

Faculty Publications

© 2016 John Wiley & Sons Ltd In terminal Ediacaran strata of South China, the onset of calcareous biomineralization is preserved in the paleontological transition from Conotubus to Cloudina in repetitious limestone facies of the Dengying Formation. Both fossils have similar size, funnel-in-funnel construction, and epibenthic lifestyle, but Cloudina is biomineralized, whereas Conotubus is not. To provide environmental context for this evolutionary milestone, we conducted a high-resolution elemental and stable isotope study of the richly fossiliferous Gaojiashan Member. Coincident with the first appearance of Cloudina is a significant positive carbonate carbon isotope excursion (up to +6‰) and an increase in …

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Structural Characterization Of Tick Cement Cones Collected From In Vivo And Artifical Membrane Blood-Fed Lone Star Ticks (Ambylomma Americanum), Rebekah Bullard, Paige Allen, Chien-Chung Chao, Jessica Douglas, Pradipta K. Das, Sarah E. Morgan, Wei-Mei Ching, Shahid Karim Jul 2016

Structural Characterization Of Tick Cement Cones Collected From In Vivo And Artifical Membrane Blood-Fed Lone Star Ticks (Ambylomma Americanum), Rebekah Bullard, Paige Allen, Chien-Chung Chao, Jessica Douglas, Pradipta K. Das, Sarah E. Morgan, Wei-Mei Ching, Shahid Karim

Faculty Publications

The Lone Star tick, Amblyomma americanum, is endemic to the southeastern United States and capable of transmitting pathogenic diseases and causing non-pathogenic conditions. To remain firmly attached to the host, the tick secretes a proteinaceous matrix termed the cement cone which hardens around the tick’s mouthparts to assist in the attachment of the tick as well as to protect the mouthparts from the host immune system. Cement cones collected from ticks on a host are commonly contaminated with host skin and hair making analysis of the cone difficult. To reduce the contamination found in the cement cone, we have adapted …

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