Genetics and Genomics Commons^™

Improving Genetic Prediction By Leveraging Genetic Correlations Among Human Diseases And Traits, Robert M. Maier, Zhihong Zhu, Sang Hong Lee, Maciej Trzaskowski, Ney Alliey Rodriguez

School of Medicine Publications

Genomic prediction has the potential to contribute to precision medicine. However, to date, the utility of such predictors is limited due to low accuracy for most traits. Here theory and simulation study are used to demonstrate that widespread pleiotropy among phenotypes can be utilised to improve genomic risk prediction. We show how a genetic predictor can be created as a weighted index that combines published genome-wide association study (GWAS) summary statistics across many different traits. We apply this framework to predict risk of schizophrenia and bipolar disorder in the Psychiatric Genomics consortium data, finding substantial heterogeneity in prediction accuracy increases …

Phylogeny And Population Genetic Analyses Reveals Cryptic Speciation In The Bombus Fervidus Species Complex (Hymenoptera: Apidae), Jonathan B. Koch, Juanita Rodriguez, James P. Pitts, James P. Strange

Ecology Center Publications

Bumble bees (Bombus Latrielle) are significant pollinators of flowering plants due to their large body size, abundant setae, and generalist foraging strategies. However, shared setal coloration patterns among closely and distantly related bumble bee species makes identification notoriously difficult. The advent of molecular genetic techniques has increased our understanding of bumble bee evolution and taxonomy, and enables effective conservation policy and management. Individuals belonging to the North American Bombus fervidus species-complex (SC) are homogenous in body structure but exhibit significant body color phenotype variation across their geographic distribution. Given the uncertainty of the genealogical boundaries within the SC, some …

Military-Related Exposures, Social Determinants Of Health, And Dysbiosis: The United States-Veteran Microbiome Project (Us-Vmp), Lisa A. Brenner, Andrew J. Hoisington, Kelly A. Stearns-Yoder, Christopher E. Stamper, Jared A. Heinze, Teodor T. Postolache, Daniel A. Hadidi, Claire A. Hoffmire, Maggie A. Stanislawski

Faculty Publications

Significant effort has been put forth to increase understanding regarding the role of the human microbiome in health- and disease-related processes. In turn, the United States (US) Veteran Microbiome Project (US-VMP) was conceptualized as a means by which to serially collect microbiome and health-related data from those seeking care within the Veterans Health Administration (VHA). In this manuscript, exposures related to military experiences, as well as conditions and health-related factors among patients seen in VHA clinical settings are discussed in relation to common psychological and physical outcomes. Upon enrollment in the study, Veterans complete psychometrically sound (i.e., reliable and valid) …

Characterization Of A Basement Membrane Associated Protein Encoding Gene In Drosophila Melanogaster, Aref Ranjbar, Ajay Srivastava

Posters-at-the-Capitol

Title: Characterization of a Basement Membrane Associated Protein Encoding Gene in Drosophila melanogaster

Authors: Aref Ranjbar, Mayank Kapadia, Ajay Srivastava, PhD(faculty member, mentor)

Basement Membranes (BM) are important for normal development and tumor progression. In order to get a better understanding of BM dynamics we identified genes that encoded BM interacting proteins. One such gene is predicted to be involved in vesicle-mediated transport in Drosophila melanogaster. Here we characterize this gene by utilizing molecular biology techniques like immunohistochemistry, RNA in situ hybridization, and Western blot analysis utilizing antibodies generated in the laboratory. Western blot analysis identified this protein to be …

New Approaches To Juvenile Age Estimation In Forensics: Application Of Transition Analysis Via The Shackelford Et Al. Method To A Diverse Modern Subadult Sample, Kelly R. Kamnikar, Nicholas P. Herrmann, Amber M. Plemons

Human Biology Open Access Pre-Prints

Dental development is one of the most widely utilized and accurate methods available for estimating age in subadult skeletal remains. The timing of tooth growth and development is regulated by genetics and less affected by external factors, allowing reliable estimates of chronological age. Traditional methodology focuses on comparing tooth developmental scores to corresponding age charts. Using the Moorrees, Fanning, and Hunt (MFH) developmental scores, Shackelford and colleagues embed the dental development method in a statistical framework based on transition analysis. They generated numerical parameters underlining each “stage” and age-at-death distribution and applied them to fossil hominins and Neanderthals with limited …

Thinking Computationally About Forensics: Anthropological Perspectives On Advancements In Technologies, Data, And Algorithms, Bridget F.B. Algee-Hewitt, Jieun Kim, Cris E. Hughes

Human Biology Open Access Pre-Prints

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Improved Reference Genome For The Domestic Horse Increases Assembly Contiguity And Composition, Theodore S. Kalbfleisch, Edward S. Rice, Michael S. Depriest Jr., Brian P. Walenz, Matthew S. Hestand, Joris R. Vermeesch, Brendan L. O'Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E Mccue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Richard E. Green, Donald C. Miller, Douglas F. Antczak, James N. Macleod

Maxwell H. Gluck Equine Research Center Faculty Publications

Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of …

Who Needs Data? I’Ve Got Experience!, Dawnie Wolfe Steadman

Human Biology Open Access Pre-Prints

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Waardenburg Syndrome And Left Persistent Superior Vena Cava, Driss Raissi, Alexander Christie, Kimberly Applegate

Radiology Faculty Publications

Waardenburg syndrome (WS) is a rare genetic disorder secondary to neural crest cell developmental abnormalities. It is predominantly described as an auditory-pigmentary syndrome with diverse patient presentation, typically involving congenital sensorineural hearing loss and pigmentation abnormalities of the skin, hair, and iris. Other developmental abnormalities that may be associated with this syndrome are Hirschsprung's disease and a myriad of cardiovascular congenital defects. We present a case of a young girl with WS who found to have a persistent left superior vena cava (PLSVC) draining into the coronary sinus. The prevalence of PLSVC is increased in patients with chromosomal and genetic …

Hnrnpa2 Mediated Acetylation Reduces Telomere Length In Response To Mitochondrial Dysfunction, Manti Guha, Satish Srinivasan, F. Bradley Johnson, Gordon Ruthel, Kip Guja, Miguel Garcia-Diaz, Brett A. Kaufman, M. Rebecca Glineburg, Jikang Fang, Hiroshi Nakagawa, Jeelan Basha, Tapas Kundu, Narayan G. Avadhani

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Telomeres protect against chromosomal damage. Accelerated telomere loss has been associated with premature aging syndromes such as Werner’s syndrome and Dyskeratosis Congenita, while, progressive telomere loss activates a DNA damage response leading to chromosomal instability, typically observed in cancer cells and senescent cells. Therefore, identifying mechanisms of telomere length maintenance is critical for understanding human pathologies. In this paper we demonstrate that mitochondrial dysfunction plays a causal role in telomere shortening. Furthermore, hnRNPA2, a mitochondrial stress responsive lysine acetyltransferase (KAT) acetylates telomere histone H4at lysine 8 of (H4K8) and this acetylation is associated with telomere attrition. Cells containing dysfunctional mitochondria …

Speciation And Hybridization In Jamaican-Endemic Streamertail Hummingbirds (Trochilus Polytmus And T. Scitulus), Caroline D. Judy

LSU Doctoral Dissertations

Streamertails hummingbirds (Trochilus polytmus and T. scitulus) are recently diverged sister taxa that appear to have speciated in situ on the island of Jamaica. They are distinguished by male bill color, a secondary sexual trait that is coral red in T. polytmus and jet black in T. scitulus. They hybridize in a narrow zone where their ranges meet in eastern Jamaica. In Chapter 2, I performed a formal population survey of T. scitulus to determine the size of the population, which was unknown. I determined that the total population contains well over 100,000 individuals despite its limited …

Factors Affecting Trailer Thermal Environment Experienced By Market Pigs Transported In The Us, Y Xiong, Richard S. Gates, Angela R. Green-Miller

Department of Animal Science: Faculty Publications

Extreme weather conditions challenge pig thermoregulation during transport and are addressed by the National Pork Board (NPB) Transport Quality Assurance® (TQA) program that provides guidelines for trailer boarding, bedding, and misting. These guidelines are widely applied, yet very little is known about the microenvironment within the trailer. In this study, TQA guidelines (V4) were evaluated via extensive thermal environment measurements during transport in order to evaluate spatial variability and implications on ventilation pattern. Effects of trailer management strategies including bedding, boarding, and misting were examined and the trailer was monitored for interior temperature rise and THI responses within six separate …

A Common Genetic Mechanism Underlies Morphological Diversity In Fruits And Other Plant Organs, Shan Wu, Biyao Zhang, Neda Keyhaninejad, Gustavo R. Rodríguez, Hyun Jung Kim, Manohar Chakrabarti, Eudald Illa-Berenguer, Nathan K. Taitano, M. J. Gonzalo, Aurora Díaz, Yupeng Pan, Courtney P. Leisner, Dennis Halterman, C. Robin Buell, Yiqun Weng, Shelley H. Jansky, Herman Van Eck, Johan Willemsen, Antonio J Monforte, Tea Meulia, Esther Van Der Knaap

Plant and Soil Sciences Faculty Publications

Shapes of edible plant organs vary dramatically among and within crop plants. To explain and ultimately employ this variation towards crop improvement, we determined the genetic, molecular and cellular bases of fruit shape diversity in tomato. Through positional cloning, protein interaction studies, and genome editing, we report that OVATE Family Proteins and TONNEAU1 Recruiting Motif proteins regulate cell division patterns in ovary development to alter final fruit shape. The physical interactions between the members of these two families are necessary for dynamic relocalization of the protein complexes to different cellular compartments when expressed in tobacco leaf cells. Together with data …

Embryonic Origin And Genetic Basis Of Cave Associated Phenotypes In The Isopod Crustacean Asellus Aquaticus., Hafasa Mojaddidi, Franco Fernandez, Priscilla A. Erickson, Meredith E. Protas

Natural Sciences and Mathematics | Faculty Scholarship

Characteristics common to animals living in subterranean environments include the reduction or absence of eyes, lessened pigmentation and enhanced sensory systems. How these characteristics have evolved is poorly understood for the majority of cave dwelling species. In order to understand the evolution of these changes, this study uses an invertebrate model system, the freshwater isopod crustacean, Asellus aquaticus, to examine whether adult differences between cave and surface dwelling individuals first appear during embryonic development. We hypothesized that antennal elaboration, as well as eye reduction and pigment loss, would be apparent during embryonic development. We found that differences in pigmentation, eye …

How Does Antibiotic Resistance Spread In Tuberculosis?, Julie A. Spencer

Shared Knowledge Conference

The ancient bacterial disease of tuberculosis (TB) is curable with antibiotics, but according to the World Health Organization, in 2016 over 10 million people became infected with the disease. 600,000 of these cases were resistant to antibiotics, yet the worldwide treatment success rate for drug resistant TB is only 54%. Furthermore, strains exist now that are resistant to all known antibiotics. In the current environment of global travel, this poses a risk for emergent epidemics of drug resistant TB. In this study, I asked: after an antibiotic resistant strain has evolved in someone’s lungs, how does it spread? It is …

Mechanisms For The Spread Of Antibiotic Resistance In Tuberculosis, Julie Allison Spencer

Shared Knowledge Conference

Tuberculosis (TB) is currently the ninth leading cause of death for humans worldwide, causing 10.4 million new infections in 2016. According to the World Health Organization, of these infections, 600,000 were antibiotic resistant. However, the treatment success rate for resistant TB was only 54%. The potential for emergent epidemics of drug resistant TB highlights the need to understand the mechanisms for the spread of resistance. Mycobacterium tuberculosis, the bacterium that causes TB, evolves resistant strains within individuals who are being treated with antibiotics. It has been assumed previously that the resistant characteristics of these strains are spread primarily by the …

Molecular Structure Of Promoter-Bound Yeast Tfiid., Olga Kolesnikova, Adam Ben-Shem, Jie Luo, Jeff Ranish, Patrick Schultz, Gabor Papai

Articles, Abstracts, and Reports

Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID …

South American Leaf-Cutter Bees (Genus Megachile) Of The Subgenera Rhyssomegachile And Zonomegachile, With Two New Subgenera (Hymenoptera: Megachilidae), Víctor H. González, Terry Griswold, Michael S. Engel

All PIRU Publications

Leaf-cutter bees (genus Megachile Latreille) are among the most common and diverse group of bees. However, the identity and taxonomic placement of many species are problematic and species identification is often difficult. Some species are known only from a single specimen or from one of the sexes, and identification keys are not available for many groups. We address these taxonomic issues for the subgenera Rhyssomegachile Mitchell and Zonomegachile Mitchell, two poorly known South American lineages of leaf-cutter bees. We provide comparative diagnoses, redescriptions, illustrated identification keys, new geographical records, and designate needed neotypes for Megachile cara Mitchell, M. gigas Schrottky, …

The Impact Of Selective Genotyping On The Response To Selection Using Single-Step Genomic Best Linear Unbiased Prediction, Jeremy T. Howard, Thomas A. Rathje, Caitlyn E. Bruns, Danielle F. Wilson-Wells, Stephen D. Kachman, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Across the majority livestock species, routinely collected genomic and pedigree information has been incorporated into evaluations using single-step methods. As a result, strategies that reduce genotyping costs without reducing the response to selection are important as they could have substantial economic impacts on breeding programs. Therefore, the objective of the current study was to investigate the impact of selectively genotyping selection candidates on the selection response using simulation. Populations were simulated to mimic the genome and population structure of a swine and cattle population undergoing selection on an index comprised of the estimated breeding values (EBV) for 2 genetically correlated …

Population Genetics Of The Eastern Subterranean Termite, Reticulitermes Flavipes, In The Southern Appalachian Mountains, Lee Ann Passarella

Honors Theses

As an area rich in biodiversity, the Appalachian Mountains are an ideal place for biological research. The pronounced impacts of Pleistocene climatic cycles on forest distributions over time have shaped the evolutionary history of animals that depend on these habitats, underpinning the research that is presented here. The present study on the eastern subterranean termite, Reticulitermes flavipes, was conducted to better understand the spatial distribution of genetic diversity within and among populations of this species in the context of the aforementioned historical climatic changes in the southern Appalachian Mountain region. I hypothesized that there would be geographically localized, distinct genetic …

Genetic Variants In The Sirt6 Transcriptional Regulatory Region Affect Gene Activity And Carcass Quality Traits In Indigenous Chinese Beef Cattle (Bos Taurus), Lin-Sheng Gui, Sayed Haidar Abbas Raza, Matthew Garcia, Yong-Gang Sun, Irfan Ullah, Yin-Cang Han

Animal, Dairy, and Veterinary Science Faculty Publications

Background: The aim of this study was to analyze potential influences of polymorphisms within the regulatory region of the bovine SIRT6 gene on carcass quality traits. Expression analyses suggested that SIRT6 gene is predominately expressed in kidney, compared with other tissues. In 535 indigenous Chinese beef cattle, two novel single nucleotide polymorphisms (SNPs) were identified within the promoter region of the SIRT6 gene.

Results: Association analysis indicated that G allele of the c.-1100 A > G had a positive effect on fat deposition, and the Hap4/4 diplotype had more favourable results than other dipoltypes with respect to the evaluation of carcass …

Kaposi’S Sarcoma-Associated Herpesvirus Seropositivity Is Associated With Type 2 Diabetes Mellitus: A Case–Control Study In Xinjiang, China, Meng Cui, Qiwen Fang, Jun Zheng, Zhanjun Shu, Yin Chen, Yage Fan, Juan Zhao, Charles Wood, Tiejun Zhang, Yan Zeng

Nebraska Center for Virology: Faculty Publications

Objective: To assess the potential relationship between Kaposi’s sarcoma-associated herpesvirus (KSHV) infection and type 2 diabetes mellitus (DM-2) in Xinjiang, China.

Methods: A case–control study of consecutively included DM-2 patients and normal controls was conducted among the Uygur and Han populations in Xinjiang Uygur Autonomous Region, China. Blood samples were collected and KSHV seroprevalence, antibody titers, and viral load were investigated. Logistic regression analysis and multiple linear regression analysis were applied to explore determinants of the main outcome measures.

Results: A total of 324 patients with DM-2 and 376 normal controls were included. The seroprevalence of KSHV was 49.1% (95% …

A Novel Tetracycline-Responsive Transgenic Mouse Strain For Skeletal Muscle-Specific Gene Expression, Masahiro Iwata, Davis A. Englund, Yuan Wen, Cory M. Dungan, Kevin A. Murach, Ivan J. Vechetti Jr., Christopher B. Mobley, Charlotte A. Peterson, John J. Mccarthy

Center for Muscle Biology Faculty Publications

Background: The tetracycline-responsive system (Tet-ON/OFF) has proven to be a valuable tool for manipulating gene expression in an inducible, temporal, and tissue-specific manner. The purpose of this study was to create and characterize a new transgenic mouse strain utilizing the human skeletal muscle α-actin (HSA) promoter to drive skeletal muscle-specific expression of the reverse tetracycline transactivator (rtTA) gene which we have designated as the HSA-rtTA mouse.

Methods: To confirm the HSA-rtTA mouse was capable of driving skeletal muscle-specific expression, we crossed the HSA-rtTA mouse with the tetracycline-responsive histone H2B-green fluorescent protein (H2B-GFP) transgenic mouse in order to label myonuclei.

Results: …

The Mitochondrial Genome Of The Endemic Brazilian Paradoxial Frog Pseudis Tocantins (Hylidae), Kaleb Pretto Gatto, Jeramiah J. Smith, Luciana Bolsoni Lourenço

Biology Faculty Publications

In this work, we present for the first time the mitochondrial genome of a paradoxical frog (Pseudis tocantins). This genome is 15.56 kb, excluding the control region, and is similar in gene content to other hylid mitogenomes. Maximum likelihood analysis, using the mitogenomes of several anurans, indicated P. tocantins as closely related to other hylid species.

Integrating Multiple Genetic Detection Methods To Estimate Population Density Of Social And Territorial Carnivores, Sean M. Murphy, Ben C. Augustine, Jennifer R. Adams, Lisette P. Waits, John J. Cox

Forestry and Natural Resources Faculty Publications

Spatial capture–recapture models can produce unbiased estimates of population density, but sparse detection data often plague studies of social and territorial carnivores. Integrating multiple types of detection data can improve estimation of the spatial scale parameter (σ), activity center locations, and density. Noninvasive genetic sampling is effective for detecting carnivores, but social structure and territoriality could cause differential detectability among population cohorts for different detection methods. Using three observation models, we evaluated the integration of genetic detection data from noninvasive hair and scat sampling of the social and territorial coyote (Canis latrans). Although precision of estimated density was …

Repeat Elements Organise 3d Genome Structure And Mediate Transcription In The Filamentous Fungus Epichloë Festucae, David J. Winter, Austen R. D. Ganley, Carolyn A. Young, Ivan Liachko, Christopher L. Schardl, Pierre-Yves Dupont, Daniel Berry, Arvina Ram, Barry Scott, Murray P. Cox

Plant Pathology Faculty Publications

Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C …

Identification And Heterologous Reconstitution Of A 5-Alk(En)Ylresorcinol Synthase From Endophytic Fungus Shiraia Sp. Slf14, Huiwen Yan, Lei Sun, Jinge Huang, Yixing Qiu, Fuchao Xu, Riming Yan, Du Zhu, Wei Wang, Jixun Zhan

Biological Engineering Faculty Publications

A new type III polyketide synthase gene (Ssars) was discovered from the genome of Shiraia sp. Slf14, an endophytic fungal strain from Huperzia serrata. The intron-free gene was cloned from the cDNA and ligated to two expression vectors pET28a and YEpADH2p-URA3 for expression in Escherichia coli BL21(DE3) and Saccharomyces cerevisiae BJ5464, respectively. SsARS was efficiently expressed in E. coli BL21(DE3), leading to the synthesis of a series of polyketide products. Six major products were isolated from the engineered E. coli and characterized as 1,3-dihydroxyphenyl-5-undecane, 1,3-dihydroxyphenyl-5-cis-6'-tridecene,1,3-dihydroxyphenyl-5-tridecane, 1,3-dihydroxyphenyl-5-cis-8'-pentadecene, 1,3-dihydroxyphenyl-5-pentadecane and 1,3-dihydroxyphenyl-5-cis-10'-heptadecene, respectively, …

Synergistic Effects Of Temperature And Salinity On The Gene Expression And Physiology Of Crassostrea Virginica, Hollis Jones

LSU Master's Theses

Crassostrea virginica, the eastern oyster, forms reefs that provide critical services and benefits to the resiliency of the surrounding ecosystem. Changes in environmental conditions, including salinity and temperature, can dramatically alter the services oysters provide by affecting their population dynamics. Climate warming may further exacerbate the effects of salinity changes as precipitation events increase in frequency, intensity, and duration. Temperature and salinity independently and synergistically influence gene expression and physiology in marine organisms. We used comparative transcriptomics, physiology, and a field assessment experiment to investigate whether Louisianan oyster are changing their phenotypes to cope with increased temperature and salinity …

Genome Wide Association Studies For Identification Of Markers Linked To Sucrose Traits In Sugarcane, Nathanael Darrell Fickett

LSU Doctoral Dissertations

Sugarcane, being a complex aneu-polyploid, poses unique challenges to fine mapping of quantitative trait loci (QTL) controlling agronomic traits of interest. Genome-wide association studies (GWAS) could be a better alternative to identify molecular markers associated with specific traits due to high linkage disequilibrium in sugarcane. In the first study, marker-trait associations (MTAs) were evaluated for three sucrose traits, Brix, total recoverable sugar (TRS), and percent sucrose on 48 elite and historic Louisiana breeding clones using 1,062 alleles. These sucrose traits were highly correlated (P-value < 0.0001) at >0.96. TASSEL 5.1 and JMP Genomics 8.0 were compared with eight models run in each program. …

Hominoid Intraspecific Cranial Variation Mirrors Neutral Genetic Diversity, Julia M. Zichello, Karen L. Baab, Kieran P. Mcnulty, Christopher J. Raxworthy, Michael E. Steiper

Publications and Research

Natural selection, developmental constraint, and plasticity have all been invoked as explanations for intraspecific cranial variation in humans and apes. However, global patterns of human cranial variation are congruent with patterns of genetic variation, demonstrating that population history has influenced cranial variation in humans. Here we show that this finding is not unique to Homo sapiens but is also broadly evident across extant ape species. Specifically, taxa that exhibit greater intraspecific cranial shape variation also exhibit greater genetic diversity at neutral autosomal loci. Thus, cranial shape variation within hominoid taxa reflects the population history of each species. Our results suggest …