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Immediate Chromatin Immunoprecipitation And On-Bead Quantitative Pcr Analysis: A Versatile And Rapid Chip Procedure, Kayla M. Harmeyer, Paul F. South, Brett Bishop, Joe Ogas, Scott D. Briggs Mar 2015

Immediate Chromatin Immunoprecipitation And On-Bead Quantitative Pcr Analysis: A Versatile And Rapid Chip Procedure, Kayla M. Harmeyer, Paul F. South, Brett Bishop, Joe Ogas, Scott D. Briggs

Faculty Publications

© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. Genome-wide chromatin immunoprecipitation (ChIP) studies have brought significant insight into the genomic localization of chromatin-associated proteins and histone modifications. The large amount of data generated by these analyses, however, require approaches that enable rapid validation and analysis of biological relevance. Furthermore, there are still protein and modification targets that are difficult to detect using standard ChIP methods. To address these issues, we developed an immediate chromatin immunoprecipitation procedure which we call ZipChip. ZipChip significantly reduces the time and increases sensitivity allowing for rapid screening of …

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Human Adipose Tissue As A Reservoir For Memory Cd4+ T Cells And Hiv, Jacob Couturier, James W. Suliburk, Jeremy M. Brown, David J. Luke, Neeti Agarwal, Xiaoying Yu, Chi Nguyen, Dinakar Iyer, Claudia A. Kozinetz, Paul A. Overbeek, Michael L. Metzker, Ashok Balasubramanyam, Dorothy E. Lewis Mar 2015

Human Adipose Tissue As A Reservoir For Memory Cd4+ T Cells And Hiv, Jacob Couturier, James W. Suliburk, Jeremy M. Brown, David J. Luke, Neeti Agarwal, Xiaoying Yu, Chi Nguyen, Dinakar Iyer, Claudia A. Kozinetz, Paul A. Overbeek, Michael L. Metzker, Ashok Balasubramanyam, Dorothy E. Lewis

Faculty Publications

Copyright © 2015 Wolters Kluwer Health, Inc. All rights reserved. Objective: The objective of this study is to determine whether adipose tissue functions as a reservoir for HIV-1. Design: We examined memory CD4+ T cells and HIV DNA in adipose tissue-stromal vascular fraction (AT-SVF) of five patients [four antiretroviral therapy (ART)-treated and one untreated]. To determine whether adipocytes stimulate CD4+ T cells and regulate HIV production, primary human adipose cells were cocultured with HIV-infected CD4+ T cells. Methods: AT-SVF T cells were studied by flow cytometry, and AT-SVF HIV DNA (Gag and Env) was examined by nested PCR and sequence …

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Human Adipose Tissue As A Reservoir For Memory Cd4(+) T Cells And Hiv, J Couturier, J W. Suliburk, J M. Brown, D J. Luke, J Couturier, X Y. Yu, C Nguyen, D Iyer, C A. Kozinetz, P A. Overbeek, M L. Metzker, A Balasubramanyam, D E. Lewis Mar 2015

Human Adipose Tissue As A Reservoir For Memory Cd4(+) T Cells And Hiv, J Couturier, J W. Suliburk, J M. Brown, D J. Luke, J Couturier, X Y. Yu, C Nguyen, D Iyer, C A. Kozinetz, P A. Overbeek, M L. Metzker, A Balasubramanyam, D E. Lewis

Faculty Publications

Objective: The objective of this study is to determine whether adipose tissue functions as a reservoir for HIV-1. Design: We examined memory CD4(+) T cells and HIV DNA in adipose tissue-stromal vascular fraction (AT-SVF) of five patients [four antiretroviral therapy (ART)-treated and one untreated]. To determine whether adipocytes stimulate CD4(+) T cells and regulate HIV production, primary human adipose cells were cocultured with HIV-infected CD4(+) T cells. Methods: AT-SVF T cells were studied by flow cytometry, and AT-SVF HIV DNA (Gag and Env) was examined by nested PCR and sequence analyses. CD4(+) T-cell activation and HIV production were measured by …

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Human Adipose Tissue As A Reservoir For Memory Cd4(+) T Cells And Hiv, J Couturier, J W. Suliburk, J M. Brown, D J. Luke, J Couturier, X Y. Yu, C Nguyen, D Iyer, C A. Kozinetz, P A. Overbeek, M L. Metzker, A Balasubramanyam, D E. Lewis Mar 2015

Human Adipose Tissue As A Reservoir For Memory Cd4(+) T Cells And Hiv, J Couturier, J W. Suliburk, J M. Brown, D J. Luke, J Couturier, X Y. Yu, C Nguyen, D Iyer, C A. Kozinetz, P A. Overbeek, M L. Metzker, A Balasubramanyam, D E. Lewis

Faculty Publications

Objective: The objective of this study is to determine whether adipose tissue functions as a reservoir for HIV-1. Design: We examined memory CD4(+) T cells and HIV DNA in adipose tissue-stromal vascular fraction (AT-SVF) of five patients [four antiretroviral therapy (ART)-treated and one untreated]. To determine whether adipocytes stimulate CD4(+) T cells and regulate HIV production, primary human adipose cells were cocultured with HIV-infected CD4(+) T cells. Methods: AT-SVF T cells were studied by flow cytometry, and AT-SVF HIV DNA (Gag and Env) was examined by nested PCR and sequence analyses. CD4(+) T-cell activation and HIV production were measured by …

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Sequencing, Identification And Mapping Of Primed L1 Elements (Simple) Reveals Significant Variation In Full Length L1 Elements Between Individuals, Vincent A. Streva, Vallmer E. Jordan, Sara Linker, Dale J. Hedges, Mark A. Batzer, Prescott L. Deininger Mar 2015

Sequencing, Identification And Mapping Of Primed L1 Elements (Simple) Reveals Significant Variation In Full Length L1 Elements Between Individuals, Vincent A. Streva, Vallmer E. Jordan, Sara Linker, Dale J. Hedges, Mark A. Batzer, Prescott L. Deininger

Faculty Publications

© Streva et al. Background: There are over a half a million copies of L1 retroelements in the human genome which are responsible for as much as 0.5% of new human genetic diseases. Most new L1 inserts arise from young source elements that are polymorphic in the human genome. Highly active polymorphic "hot" L1 source elements have been shown to be capable of extremely high levels of mobilization and result in numerous instances of disease. Additionally, hot polymorphic L1s have been described to be highly active within numerous cancer genomes. These hot L1s result in mutagenesis by insertion of new …

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A Meta-Analysis Of Gene Expression Signatures Of Blood Pressure And Hypertension, Tianxiao Huan, Tõnu Esko, Marjolein J. Peters, Luke C. Pilling, Katharina Schramm, Claudia Schurmann, Brian H. Chen, Chunyu Liu, Roby Joehanes, Andrew D. Johnson, Chen Yao, Sai Xia Ying, Paul Courchesne, Lili Milani, Nalini Raghavachari, Richard Wang, Poching Liu, Eva Reinmaa, Abbas Dehghan, Albert Hofman, André G. Uitterlinden, Dena G. Hernandez, Stefania Bandinelli, Andrew Singleton, David Melzer, Andres Metspalu, Maren Carstensen, Harald Grallert, Christian Herder, Thomas Meitinger, Annette Peters, Michael Roden, Melanie Waldenberger Mar 2015

A Meta-Analysis Of Gene Expression Signatures Of Blood Pressure And Hypertension, Tianxiao Huan, Tõnu Esko, Marjolein J. Peters, Luke C. Pilling, Katharina Schramm, Claudia Schurmann, Brian H. Chen, Chunyu Liu, Roby Joehanes, Andrew D. Johnson, Chen Yao, Sai Xia Ying, Paul Courchesne, Lili Milani, Nalini Raghavachari, Richard Wang, Poching Liu, Eva Reinmaa, Abbas Dehghan, Albert Hofman, André G. Uitterlinden, Dena G. Hernandez, Stefania Bandinelli, Andrew Singleton, David Melzer, Andres Metspalu, Maren Carstensen, Harald Grallert, Christian Herder, Thomas Meitinger, Annette Peters, Michael Roden, Melanie Waldenberger

Faculty Publications

Genome-wide association studies (GWAS) have uncovered numerous genetic variants (SNPs) that are associated with blood pressure (BP). Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression, which in turn affect BP variability. Therefore, characterizing genes whose expression is associated with BP may reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. A meta-analysis of results from six studies of global gene expression profiles of BP and hypertension in whole blood was performed in 7017 individuals who were not …

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Yy1 Gene Dosage Effect And Bi-Allelic Expression Of Peg3, Bambarendage P.U. Perera, Ryoichi Teruyama, Joomyeong Kim Mar 2015

Yy1 Gene Dosage Effect And Bi-Allelic Expression Of Peg3, Bambarendage P.U. Perera, Ryoichi Teruyama, Joomyeong Kim

Faculty Publications

© 2015 Perera et al. In the current study, we tested the in vivo effects of Yy1 gene dosage on the Peg3 imprinted domain with various breeding schemes utilizing two sets of mutant alleles. The results indicated that a half dosage of Yy1 coincides with the up-regulation of Peg3 and Zim1, suggesting a repressor role of Yy1 in this imprinted domain. This repressor role of Yy1 is consistent with the observations derived from previous in vitro studies. The current study also provided an unexpected observation that the maternal allele of Peg3 is also normally expressed, and thus the expression of …

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Analysis Of The Radiation-Damage-Free X-Ray Structure Of Photosystem Ii In Light Of Exafs And Qm/Mm Data, Mikhail Askerka, David J. Vinyard, Jimin Wang, Gary W. Brudvig, Victor S. Batista Mar 2015

Analysis Of The Radiation-Damage-Free X-Ray Structure Of Photosystem Ii In Light Of Exafs And Qm/Mm Data, Mikhail Askerka, David J. Vinyard, Jimin Wang, Gary W. Brudvig, Victor S. Batista

Faculty Publications

© 2015 American Chemical Society. A recent femtosecond X-ray diffraction study produced the first high-resolution structural model of the oxygen-evolving complex of photosystem II that is free of radiation-induced manganese reduction (Protein Data Bank entries 4UB6 and 4UB8). We find, however, that the model does not match extended X-ray absorption fine structure and QM/MM data for the S1 state. This is attributed to uncertainty about the positions of oxygen atoms that remain partially unresolved, even at 1.95 Å resolution, next to the heavy manganese centers. In addition, the photosystem II crystals may contain significant amounts of the S0 state, because …

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Elevated Hypertension Risk For African-Origin Populations In Biracial Societies: Modeling The Epidemiologic Transition Study, Richard S. Cooper, Terrence E. Forrester, Jacob Plange-Rhule, Pascal Bovet, Estelle V. Lambert, Lara R. Dugas, Kathryn E. Cargill, Ramon A. Durazo-Arvizu, David A. Shoham, Liping Tong, Guichan Cao, Amy Luke Mar 2015

Elevated Hypertension Risk For African-Origin Populations In Biracial Societies: Modeling The Epidemiologic Transition Study, Richard S. Cooper, Terrence E. Forrester, Jacob Plange-Rhule, Pascal Bovet, Estelle V. Lambert, Lara R. Dugas, Kathryn E. Cargill, Ramon A. Durazo-Arvizu, David A. Shoham, Liping Tong, Guichan Cao, Amy Luke

Faculty Publications

OBJECTIVES:: Blood pressures in persons of African descent exceed those of other racial/ethnic groups in the United States. Whether this trait is attributable to the genetic factors in African-origin populations, or a result of inadequately measured environmental exposures, such as racial discrimination, is not known. To study this question, we conducted a multisite comparative study of communities in the African diaspora, drawn from metropolitan Chicago, Kingston, Jamaica, rural Ghana, Cape Town, South Africa, and the Seychelles. METHODS:: At each site, 500 participants between the age of 25 and 49 years, with approximately equal sex balance, were enrolled for a longitudinal …

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Concerted Motions Networking Pores And Distant Ferroxidase Centers Enable Bacterioferritin Function And Iron Traffic, Huili Yao, Huan Rui, Ritesh Kumar, Kate Eshelman, Scott Lovell, Kevin P. Battaile, Wonpil Im, Mario Rivera Mar 2015

Concerted Motions Networking Pores And Distant Ferroxidase Centers Enable Bacterioferritin Function And Iron Traffic, Huili Yao, Huan Rui, Ritesh Kumar, Kate Eshelman, Scott Lovell, Kevin P. Battaile, Wonpil Im, Mario Rivera

Faculty Publications

© 2015 American Chemical Society. X-ray crystallography, molecular dynamics (MD) simulations, and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe2+-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB …

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Strain-Dependence Of The Structure And Ferroic Properties Of Epitaxial Ni1 - Xti1 - Yo3 Thin Films Grown On Sapphire Substrates, Tamas Varga, Timothy C. Droubay, Mark E. Bowden, Sean A. Stephens, Sandeep Manandhar, Vaithiyalingam Shutthanandan, Robert J. Colby, Dehong Hu, William A. Shelton, Scott A. Chambers Mar 2015

Strain-Dependence Of The Structure And Ferroic Properties Of Epitaxial Ni1 - Xti1 - Yo3 Thin Films Grown On Sapphire Substrates, Tamas Varga, Timothy C. Droubay, Mark E. Bowden, Sean A. Stephens, Sandeep Manandhar, Vaithiyalingam Shutthanandan, Robert J. Colby, Dehong Hu, William A. Shelton, Scott A. Chambers

Faculty Publications

Polarization-induced weak ferromagnetism has been predicted a few years back in compounds MTiO3 (M = Fe, Mn, Ni) (Fennie, 2008). We set out to stabilize this metastable, distorted perovskite structure by growing NiTiO3 epitaxially on sapphire Al2O3 (001) substrate, and to control the polar and magnetic properties via strain. Epitaxial Ni1 - xTi1 - yO3 films of different Ni/Ti ratios and thicknesses were deposited on Al2O3 substrates by pulsed laser deposition at different temperatures, and characterized using several techniques. The effect of film thickness, deposition temperature, and film stoichiometry on lattice strain, film structure, and physical properties was investigated. Our …

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The Structural Basis For Specificity In Lipoxygenase Catalysis, Marcia E. Newcomer, Alan R. Brash Mar 2015

The Structural Basis For Specificity In Lipoxygenase Catalysis, Marcia E. Newcomer, Alan R. Brash

Faculty Publications

© 2014 The Protein Society. Many intriguing facets of lipoxygenase (LOX) catalysis are open to a detailed structural analysis. Polyunsaturated fatty acids with two to six double bonds are oxygenated precisely on a particular carbon, typically forming a single chiral fatty acid hydroperoxide product. Molecular oxygen is not bound or liganded during catalysis, yet it is directed precisely to one position and one stereo configuration on the reacting fatty acid. The transformations proceed upon exposure of substrate to enzyme in the presence of O2 (RH + O2 → ROOH), so it has proved challenging to capture the precise mode of …

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Examining Evolutionary Relationships And Shifts In Depth Preferences In Batfishes (Lophiiformes: Ogcocephalidae), Valerie Derouen, William B. Ludt, Hsuan Ching Ho, Prosanta Chakrabarty Mar 2015

Examining Evolutionary Relationships And Shifts In Depth Preferences In Batfishes (Lophiiformes: Ogcocephalidae), Valerie Derouen, William B. Ludt, Hsuan Ching Ho, Prosanta Chakrabarty

Faculty Publications

© 2014 Elsevier Inc. Batfishes (Ogcocephalidae) are an understudied, group of marine anglerfishes that are dorsoventrally flattened and have an illicium and esca (terminal lure) used to attract prey. The family contains 10 genera and 75 recognized species from nearly all tropical and subtropical seas. Relationships among these taxa, as well as the position of Ogcocephalidae within Lophiiformes, remain poorly understood with previous studies showing conflicting, and poorly resolved results. The timing of divergence and depth of origination in the water column have also not been explored in any detail. In this study a concatenated nuclear (three genes) and mitochondrial …

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Fall Armyworm (Lepidoptera: Noctuidae) Ecology In Southeastern Cotton, Jarrod T. Hardke, Gus M. Lorenz, B. Rogers Leonard Mar 2015

Fall Armyworm (Lepidoptera: Noctuidae) Ecology In Southeastern Cotton, Jarrod T. Hardke, Gus M. Lorenz, B. Rogers Leonard

Faculty Publications

The fall armyworm, Spodoptera frugiperda (J. E. Smith), is a sporadic pest with a diverse host range. This insect occasionally causes damage to cotton across the United States from the Rocky Mountains to the East Coast. Fall armyworm has been problematic in cotton due to its overall tolerance to many insecticide use strategies and difficulty in finding and surveying field infestations with sampling protocols. A review of insect biology, description of life stages, behavior and host strain identification, injury to cotton, and potential management options for the southeastern United States are presented.

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Mobilization Of Alu Elements Throughout Papio And Theropithecus Genomes, Emily Bennett Mar 2015

Mobilization Of Alu Elements Throughout Papio And Theropithecus Genomes, Emily Bennett

Honors Capstones

No abstract provided.

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Existence Of Lévy's Area And Pathwise Integration, Peter Imkeller, David J Prömel Mar 2015

Existence Of Lévy's Area And Pathwise Integration, Peter Imkeller, David J Prömel

Communications on Stochastic Analysis

No abstract provided.

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On The Transport Modes Of Fine Sediment In The Wave Boundary Layer Due To Resuspension/Deposition: A Turbulence-Resolving Numerical Investigation, Zhen Cheng, Xiao Yu, Tian Jian Hsu, Celalettin E. Ozdemir, S. Balachandar Mar 2015

On The Transport Modes Of Fine Sediment In The Wave Boundary Layer Due To Resuspension/Deposition: A Turbulence-Resolving Numerical Investigation, Zhen Cheng, Xiao Yu, Tian Jian Hsu, Celalettin E. Ozdemir, S. Balachandar

Faculty Publications

Previous field observations revealed that the wave boundary layer is one of the main conduits delivering fine sediments from the nearshore to continental shelves. Recently, a series of turbulence-resolving simulations further demonstrated the existence of a range of flow regimes due to different degrees of sediment-induced density stratification controlled by the sediment availability. In this study, we investigate the scenario in which sediment availability is governed by the resuspension/deposition from/to the bed. Specifically, we focus on how the critical shear stress of erosion and the settling velocity can determine the modes of transport. Simulations reveal that at a given wave …

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Robustness Of Target Dose Coverage To Motion Uncertainties For Scanned Carbon Ion Beam Tracking Therapy Of Moving Tumors, John Gordon Eley, Wayne David Newhauser, Daniel Richter, Robert Lüchtenborg, Nami Saito, Christoph Bert Feb 2015

Robustness Of Target Dose Coverage To Motion Uncertainties For Scanned Carbon Ion Beam Tracking Therapy Of Moving Tumors, John Gordon Eley, Wayne David Newhauser, Daniel Richter, Robert Lüchtenborg, Nami Saito, Christoph Bert

Faculty Publications

Beam tracking with scanned carbon ion radiotherapy achieves highly conformal target dose by steering carbon pencil beams to follow moving tumors using real-time magnetic deflection and range modulation. The purpose of this study was to evaluate the robustness of target dose coverage from beam tracking in light of positional uncertainties of moving targets and beams. To accomplish this, we simulated beam tracking for moving targets in both water phantoms and a sample of lung cancer patients using a research treatment planning system. We modeled various deviations from perfect tracking that could arise due to uncertainty in organ motion and limited …

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Toll-Like Receptor 4 Inhibition Within The Paraventricular Nucleus Attenuates Blood Pressure And Inflammatory Response In A Genetic Model Of Hypertension, Rahul B. Dange, Deepmala Agarwal, Ryoichi Teruyama, Joseph Francis Feb 2015

Toll-Like Receptor 4 Inhibition Within The Paraventricular Nucleus Attenuates Blood Pressure And Inflammatory Response In A Genetic Model Of Hypertension, Rahul B. Dange, Deepmala Agarwal, Ryoichi Teruyama, Joseph Francis

Faculty Publications

© 2015 Dange et al. Background: Despite the availability of several antihypertensive medications, the morbidity and mortality caused by hypertension is on the rise, suggesting the need for investigation of novel signaling pathways involved in its pathogenesis. Recent evidence suggests the role of toll-like receptor (TLR) 4 in various inflammatory diseases, including hypertension. The role of the brain in the initiation and progression of all forms of hypertension is well established, but the role of brain TLR4 in progression of hypertension has never been explored. Therefore, we investigated the role of TLR4 within the paraventricular nucleus (PVN; an important cardioregulatory …

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Oncostatin M Modulation Of Lipid Storage, Carrie M. Elks, Jacqueline M. Stephens, Jacqueline M. Stephens Feb 2015

Oncostatin M Modulation Of Lipid Storage, Carrie M. Elks, Jacqueline M. Stephens, Jacqueline M. Stephens

Faculty Publications

© 2015 by the authors; licensee MDPI, Basel, Switzerland. Oncostatin M (OSM) is a cytokine belonging to the gp130 family, whose members serve pleiotropic functions. However, several actions of OSM are unique from those of other gp130 cytokines, and these actions may have critical roles in inflammatory mechanisms influencing several metabolic and biological functions of insulin-sensitive tissues. In this review, the actions of OSM in adipose tissue and liver are discussed, with an emphasis on lipid metabolism.

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Impaired Gamma Delta T Cell-Derived Il-17a And Inflammasome Activation During Early Respiratory Syncytial Virus Infection In Infants, Huaqiong Huang, Jordy Saravia, Dahui You, Aaron J. Shaw, Stephania A. Cormier Feb 2015

Impaired Gamma Delta T Cell-Derived Il-17a And Inflammasome Activation During Early Respiratory Syncytial Virus Infection In Infants, Huaqiong Huang, Jordy Saravia, Dahui You, Aaron J. Shaw, Stephania A. Cormier

Faculty Publications

© 2015 Australasian Society for Immunology Inc. Respiratory syncytial virus (RSV) infection remains a significant global health burden disproportionately affecting infants and leading to long-term lung disease. Interleukin (IL)-17A has been shown to be involved in regulating viral and allergic lung inflammatory responses, which has led to a more recent interest in its role in RSV infection. Using a neonatal mouse model of RSV, we demonstrate that neonates fail to develop IL-17A responses compared with adult mice; the main immediate IL-17A contributor in adults were γδ T cells. Antibody neutralization of IL-17A in adult mice caused increased lung inflammation and …

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New Genetic Loci Link Adipose And Insulin Biology To Body Fat Distribution, D. Shungin, T. W. Winkler, D. C. Croteau-Chonka, T. Ferreira, A. E. Locke, R. Mägi, R. J. Strawbridge, T. H. Pers, K. Fischer, A. E. Justice, T. Workalemahu, J. M.W. Wu, M. L. Buchkovich, N. L. Heard-Costa, T. S. Roman, A. W. Drong, C. Song, S. Gustafsson, F. R. Day, T. Esko, T. Fall, Z. Kutalik, J. Luan, J. C. Randall, A. Scherag, S. Vedantam, A. R. Wood, J. Chen, R. Fehrmann, J. Karjalainen, B. Kahali, C. T. Liu, E. M. Schmidt Feb 2015

New Genetic Loci Link Adipose And Insulin Biology To Body Fat Distribution, D. Shungin, T. W. Winkler, D. C. Croteau-Chonka, T. Ferreira, A. E. Locke, R. Mägi, R. J. Strawbridge, T. H. Pers, K. Fischer, A. E. Justice, T. Workalemahu, J. M.W. Wu, M. L. Buchkovich, N. L. Heard-Costa, T. S. Roman, A. W. Drong, C. Song, S. Gustafsson, F. R. Day, T. Esko, T. Fall, Z. Kutalik, J. Luan, J. C. Randall, A. Scherag, S. Vedantam, A. R. Wood, J. Chen, R. Fehrmann, J. Karjalainen, B. Kahali, C. T. Liu, E. M. Schmidt

Faculty Publications

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, we conducted genome-wide association meta-analyses of waist and hip circumference-related traits in up to 224,459 individuals. We identified 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (WHRadjBMI) and an additional 19 loci newly associated with related waist and hip circumference measures (P<5×10-8). Twenty of the 49 WHRadjBMI loci showed significant sexual dimorphism, 19 of which displayed a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation, and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.

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Genetic Studies Of Body Mass Index Yield New Insights For Obesity Biology, A. E. Locke, B. Kahali, S. I. Berndt, A. E. Justice, T. H. Pers, F. R. Day, C. Powell, S. Vedantam, M. L. Buchkovich, J. Yang, D. C. Croteau-Chonka, T. Esko, T. Fall, T. Ferreira, S. Gustafsson, Z. Kutalik, J. Luan, R. Mägi, J. C. Randall, T. W. Winkler, A. R. Wood, T. Workalemahu, J. D. Faul, J. A. Smith, J. H. Zhao, W. Zhao, J. Chen, R. Fehrmann, K. Hedman, J. Karjalainen, E. M. Schmidt, D. Absher, N. Amin Feb 2015

Genetic Studies Of Body Mass Index Yield New Insights For Obesity Biology, A. E. Locke, B. Kahali, S. I. Berndt, A. E. Justice, T. H. Pers, F. R. Day, C. Powell, S. Vedantam, M. L. Buchkovich, J. Yang, D. C. Croteau-Chonka, T. Esko, T. Fall, T. Ferreira, S. Gustafsson, Z. Kutalik, J. Luan, R. Mägi, J. C. Randall, T. W. Winkler, A. R. Wood, T. Workalemahu, J. D. Faul, J. A. Smith, J. H. Zhao, W. Zhao, J. Chen, R. Fehrmann, K. Hedman, J. Karjalainen, E. M. Schmidt, D. Absher, N. Amin

Faculty Publications

Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10-8), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ∼2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20 % of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.

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Predicting Protein Interface Residues Using Easily Accessible On-Line Resources, Surabhi Maheshwari, Michal Brylinski Feb 2015

Predicting Protein Interface Residues Using Easily Accessible On-Line Resources, Surabhi Maheshwari, Michal Brylinski

Faculty Publications

© The Author 2015. Published by Oxford University Press. It has beenmore than a decade since the completion of the Human Genome Project that provided us with a complete list of human proteins. The next obvious task is to figure out how various parts interact with each other. On that account, we re- view 10methods for protein interface prediction, which are freely available as web servers. In addition, we comparatively evaluate their performance on a common data set comprising different quality target structures. We find that using experi- mental structures and high-quality homology models, structure-basedmethods outperformthose using only protein se- …

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Exposure To Electronic Cigarettes Impairs Pulmonary Anti-Bacterial And Anti-Viral Defenses In A Mouse Model, Thomas E. Sussan, Sachin Gajghate, Rajesh K. Thimmulappa, Jinfang Ma, Jung Hyun Kim, Kuladeep Sudini, Nicola Consolini, Stephania A. Cormier, Slawo Lomnicki, Farhana Hasan, Andrew Pekosz, Shyam Biswal Feb 2015

Exposure To Electronic Cigarettes Impairs Pulmonary Anti-Bacterial And Anti-Viral Defenses In A Mouse Model, Thomas E. Sussan, Sachin Gajghate, Rajesh K. Thimmulappa, Jinfang Ma, Jung Hyun Kim, Kuladeep Sudini, Nicola Consolini, Stephania A. Cormier, Slawo Lomnicki, Farhana Hasan, Andrew Pekosz, Shyam Biswal

Faculty Publications

© 2015 Sussan et al. Electronic cigarettes (E-cigs) have experienced sharp increases in popularity over the past five years due to many factors, including aggressive marketing, increased restrictions on conventional cigarettes, and a perception that E-cigs are healthy alternatives to cigarettes. Despite this perception, studies on health effects in humans are extremely limited and in vivo animal models have not been generated. Presently, we determined that E-cig vapor contains 7x1011 free radicals per puff. To determine whether E-cig exposure impacts pulmonary responses in mice, we developed an inhalation chamber for E-cig exposure. Mice that were exposed to E-cig vapor contained …

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Variants For Hdl-C, Ldl-C, And Triglycerides Identified From Admixture Mapping And Fine-Mapping Analysis In African American Families, Priya B. Shetty, Hua Tang, Tao Feng, Bamidele Tayo, Alanna C. Morrison, Sharon L.R. Kardia, Craig L. Hanis, Donna K. Arnett, Steven C. Hunt, Eric Boerwinkle, Dabeeru C. Rao, Richard S. Cooper, Neil Risch, Xiaofeng Zhu Feb 2015

Variants For Hdl-C, Ldl-C, And Triglycerides Identified From Admixture Mapping And Fine-Mapping Analysis In African American Families, Priya B. Shetty, Hua Tang, Tao Feng, Bamidele Tayo, Alanna C. Morrison, Sharon L.R. Kardia, Craig L. Hanis, Donna K. Arnett, Steven C. Hunt, Eric Boerwinkle, Dabeeru C. Rao, Richard S. Cooper, Neil Risch, Xiaofeng Zhu

Faculty Publications

Background - Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African Americans. Methods and Results - The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. The analysis was performed in 1905 unrelated African American subjects from the National Heart, Lung and Blood Institute's Family Blood Pressure Program (FBPP). Regions showing admixture evidence were followed-up with family-based association analysis in 3556 African American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age2, sex, body mass index, …

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A Moonlighting Function Of Mycobacterium Smegmatis Ku In Zinc Homeostasis?, Ambuj K. Kushwaha, Dinesh K. Deochand, Anne Grove Feb 2015

A Moonlighting Function Of Mycobacterium Smegmatis Ku In Zinc Homeostasis?, Ambuj K. Kushwaha, Dinesh K. Deochand, Anne Grove

Faculty Publications

© 2014 The Protein Society. Ku protein participates in DNA double-strand break repair via the nonhomologous end-joining pathway. The three-dimensional structure of eukaryotic Ku reveals a central core consisting of a β-barrel domain and pillar and bridge regions that combine to form a ring-like structure that encircles DNA. Homologs of Ku are encoded by a subset of bacterial species, and they are predicted to conserve this core domain. In addition, the bridge region of Ku from some bacteria is predicted from homology modeling and sequence analyses to contain a conventional HxxC and CxxC (where x is any residue) zinc-binding motif. …

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Faculty Senate Newsletter, February 2015, Louisiana State University And Agricultural & Mechanical College Feb 2015

Faculty Senate Newsletter, February 2015, Louisiana State University And Agricultural & Mechanical College

LSU Faculty Senate Publications

Message from President: An ivy-league legend holds that early twentieth-century literary scholar George Lyman Kittredge once passed a doctoral student who had flubbed his dissertation defense when, upon asking the candidate about his smoking preferences, Kittredge discovered that the lad had a keen eye for quality cigars. Although we can thank our lucky stars that Kittredge’s kind of benevolent autocracy—his readiness to use unchecked authority to show off his combined power and tastefulness—is a thing of the past, we can also at least minimally mourn the passing of eccentricity and of the mix of moxie and eagerness that induces acts …

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Genomic Variation In A Widespread Neotropical Bird (Xenops Minutus) Reveals Divergence, Population Expansion, And Gene Flow, Michael G. Harvey, Robb T. Brumfield Feb 2015

Genomic Variation In A Widespread Neotropical Bird (Xenops Minutus) Reveals Divergence, Population Expansion, And Gene Flow, Michael G. Harvey, Robb T. Brumfield

Faculty Publications

© 2014 Elsevier Inc. The demographic and phylogeographic histories of species provide insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of species histories with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited …

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Simulation Modelling Of High-Throughput Cryopreservation Of Aquatic Germplasm: A Case Study Of Blue Catfish Sperm Processing, E. Hu, Thunshun Warren Liao, Terrence R. Tiersch Feb 2015

Simulation Modelling Of High-Throughput Cryopreservation Of Aquatic Germplasm: A Case Study Of Blue Catfish Sperm Processing, E. Hu, Thunshun Warren Liao, Terrence R. Tiersch

Faculty Publications

Emerging commercial-level technology for aquatic sperm cryopreservation has not been modelled by computer simulation. Commercially available software (ARENA, Rockwell Automation, Inc. Milwaukee, WI) was applied to simulate high-throughput sperm cryopreservation of blue catfish (Ictalurus furcatus) based on existing processing capabilities. The goal was to develop a simulation model suitable for production planning and decision making. The objectives were to: (1) predict the maximum output for 8-h workday; (2) analyse the bottlenecks within the process, and (3) estimate operational costs when run for daily maximum output. High-throughput cryopreservation was divided into six major steps modelled with time, resources, and logic structures. …

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