Genetics and Genomics Commons^™

Genomic Sequencing Data Analysis Workflow For Bioinformatics Core Facilities, Selen A. Yilmaz, Jie Zhang, Gulcin Ozer

Learning Showcase 2014

Next Generation Sequencing (NGS) is becoming a common tool in the practice of biomedical research and the future of how medicine will be practiced. To keep up with the explosion in new NGS experiments and the growing need in data analysis, we identified bottlenecks of our NGS data analysis workflow, evaluated and tested feasibility of solutions. To address main bottlenecks we incorporated two solutions into our

workflow: (1) Globus Genomics, a well-maintained cloud based sequencing data analysis framework which leverage advanced tools and data management, and (2) GenomAnalytics from GenomOncology, an interactive platform for data integration, annotation, filtering an interpretation. …

Ploidy Number For Panicum Virgatum (Switchgrass) From The Long Island Sound Coastal Lowland Compared To Upland And Lowland Cultivars., Tanisha Williams, Carol Auer

Plant Science Articles

Panicum virgatum L. (switchgrass) is a native, perennial grass in North America with important ecological function in ecoregions including the Long Island Sound Coastal Lowland in the Northeastern United States. In recent decades, switchgrass has become a model lignocellulosic bioenergy crop with a large research portfolio describing its distribution, genetics, genomics, phenology, traits, gene flow, and cultivation. Switchgrass has been divided into two ecotypes, the Lowland ecotype which is tetraploid (2n= 4x= 36 chromosomes) and the Upland ecotype which is tetraploid or octaploid (2n= 8x= 72). While most switchgrass research has focused on genotypes from the Midwest or Southeastern regions, …

Caspase-3 Mediates The Pathogenic Effect Of Yersinia Pestis Yopm In Liver Of C57bl/6 Mice And Contributes To Yopm's Function In Spleen, Zhan Ye, Amanda A. Gorman, Annette M. Uittenbogaard, Tanya Myers-Morales, Alan M. Kaplan, Donald A. Cohen, Susan C. Straley

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The virulence protein YopM of the plague bacterium Yersinia pestis has different dominant effects in liver and spleen. Previous studies focused on spleen, where YopM inhibits accumulation of inflammatory dendritic cells. In the present study we focused on liver, where PMN function may be directly undermined by YopM without changes in inflammatory cell numbers in the initial days of infection, and foci of inflammation are easily identified. Mice were infected with parent and ΔyopM-1 Y. pestis KIM5, and effects of YopM were assessed by immunohistochemistry and determinations of bacterial viable numbers in organs. The bacteria were found …

Gwatch: A Web Platform For Automated Gene Association Discovery Analysis, Anton Svitin, Sergey Malov, Nikolay Cherkasov, Paul Geerts, Mikhail Rotkevich, Pavel Dobrynin, Andrey Shevchenko, Li Guan, Jennifer L. Troyer, Sher L. Hendrickson, Holli Hutcheson Dilks, T. K. Oleksyk, Sharyne Donfield, Edward Gomperts, Douglas A. Jabs, Efe Sezgin, Mark Van Natta, P. Richard Harrigan, Zabrina L. Brumme, Stephen J. O'Brien

Biology Faculty Articles

Background: As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations.

Findings: Here we present a dynamic web-based platform – GWATCH – that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication …

Cloning And Characterization Of Il-1Β, Il-8, Il-10, And Tnfα From Golden Tilefish (Lopholatilus Chamaeleonticeps) And Red Snapper (Lutjanus Campechanus), Kristina L. Deak

USF Tampa Graduate Theses and Dissertations

Cytokines are pleiotropic and redundant signaling molecules that govern the inflammatory response and immunity, a critical ecological parameter for organism success and population growth. Produced at the site of injury or pathogen intrusion by a variety of cell types, cytokines mediate cell-signaling in either an autocrine or paracrine manner. The type and magnitude of the cytokine milieu produced subsequently dictates the strength and form of immune response. As the most diverse vertebrate group, with a high sensitivity to contaminants, fish represent an important foci for the evaluation of immune system evolution, function, and alteration upon toxicant exposure. While many cytokines …

Autoantibodies To The Ny-Eso-1 Tumor Antigen In Metastatic Melanoma: Sialylation Of The Fc Region Of Immunoglobulin G Induces Differential Expression Signatures Of Inflammatory Molecules During Dendritic Cell Differentiation And Maturation, Martin Oaks, Nathaniel Rein, John O. Richards, James Shaffer

Journal of Patient-Centered Research and Reviews

Purpose: We tested the hypothesis that different glycoforms of antibodies from patients with metastatic melanoma have different functional effects on human dendritic cell differentiation and maturation.

Methods: Antibodies to the cancer antigen NY-ESO-1 were affinity-purified from patients with melanoma and further fractionated into different glycoforms by lectin chromatography. Sialic acid-rich and sialic acid-poor fractions of these immunoglobulin G antibodies (IgG) were added to dendritic cell cultures during both differentiation and maturation, and the resulting cellular messenger RNA (mRNA) and culture supernatants were tested by microarray and enzyme-linked immunoassay for molecules related to inflammatory pathways.

Results: We identified unique mRNA and …

Fisheries Management Paper No.266 - Exmouth Gulf Prawn Managed Fishery Bycatch Action Plan 2014-2019. Version 1.0, Department Of Fisheries, Western Australia

Fisheries Management Papers

Bycatch is described as the part of the catch which is returned to the sea (usually referred to as non-retained or discarded) either because it has no commercial value or because legislative requirements preclude it being retained. Thus, this Bycatch Action Plan (BAP) includes unmarketable finfish and invertebrate species, along with endangered, threatened and protected (ETP) species, such as marine mammals, reptiles and some elasmobranchs.

It is Government policy to minimise bycatch in all commercial fisheries. This BAP details a program of actions to address bycatch issues in the Exmouth Gulf Prawn Managed Fishery (EGPMF), in accordance with the EGPMF …

Phylogenetic Analysis Of Algal Symbionts Associated With Four North American Amphibian Egg Masses, Eunsoo Kim, Yuan Lin, Ryan R. Kerney, Lili Blumenberg, Cory Bishop

Biology Faculty Publications

Egg masses of the yellow-spotted salamander Ambystoma maculatum form an association with the green alga “Oophila amblystomatis” (Lambert ex Wille), which, in addition to growing within individual egg capsules, has recently been reported to invade embryonic tissues and cells. The binomial O. amblystomatis refers to the algae that occur in A. maculatum egg capsules, but it is unknown whether this population of symbionts constitutes one or several different algal taxa. Moreover, it is unknown whether egg masses across the geographic range of A. maculatum, or other amphibians, associate with one or multiple algal taxa. To address these …

Draft Genome Sequences Of Antibiotic-Resistant Commensal Escherichia Coli, Meghan Garrett, Jennifer Parker, Craig M. Stephens

Biology

Antimicrobial resistance is a significant public health issue. We report here the draft genome sequences of three drug-resistant strains of commensal Escherichia coli isolated from a single healthy college student. Each strain has a distinct genome, but two of the three contain an identical large plasmid with multiple resistance genes.

Intercellular Cooperation And Competition In Brain Cancers: Lessons From Drosophila And Human Studies, Indrayani Waghmare, Austin Roebke, Mutsuko Minata, Madhuri Kango-Singh, Ichiro Nakano

Biology Faculty Publications

Glioblastoma (GBM) is a primary brain cancer with an extremely poor prognosis. GBM tumors contain heterogeneous cellular components, including a small subpopulation of tumor cells termed glioma stem cells (GSCs). GSCs are characterized as chemotherapy- and radiotherapy-resistant cells with prominent tumorigenic ability. Studies in Drosophila cancer models demonstrated that interclonal cooperation and signaling from apoptotic clones provokes aggressive growth of neighboring tumorigenic clones, via compensatory proliferation or apoptosis induced proliferation. Mechanistically, these aggressive tumors depend on activation of Jun-N-terminal kinase (upstream of c-JUN), and Drosophila Wnt (Wg) in the apoptotic clones. Consistent with these nonmammalian studies, data from several mammalian …

Genome-Wide Association Study Of Saturated, Mono- And Polyunsaturated Red Blood Cell Fatty Acids In The Framingham Heart Offspring Study, Nathan L. Tintle, James V. Pottala, Sean Lacey, Vasan Ramachandran, Jason Westra, Ally Rogers, Jake Clark, Ben Olthoff, Martin Larson, William Harris, Gregory C. Shearer

Faculty Work Comprehensive List

Most genome-wide association studies have explored relationships between genetic variants and plasma phospholipid fatty acid proportions, but few have examined apparent genetic influences on the membrane fatty acid profile of red blood cells (RBC). Using RBC fatty acid data from the Framingham Offspring Study, we analyzed over 2.5 million single nucleotide polymorphisms (SNPs) for association with 14 RBC fatty acids identifying 191 different SNPs associated with at least 1 fatty acid. Significant associations (p<1×10⁻⁸) were located within five distinct 1 MB regions. Of particular interest were novel associations between (1) arachidonic acid and PCOLCE2 (regulates apoA-I maturation …

Chlorovirus Atcv-1 Is Part Of The Human Oropharyngeal Virome And Is Associated With Changes In Cognitive Functions In Humans And Mice, Robert H. Yolken, Lorraine Jones-Brando, David D. Dunigan, Geetha Kannan, Faith Dickerson, Emily Severance, Sarven Sabunciyan, C. Conover Talbot Jr., Emese Prandovszky, James R. Gurnon, Irina V. Agarkova, Flora Leister, Kristin L. Gressitt, Ou Chen, Bryan Deuber, Fangrui Ma, Mikhail V. Pletnikov, James L. Van Etten

James Van Etten Publications

Chloroviruses (family Phycodnaviridae) are large DNA viruses known to infect certain eukaryotic green algae and have not been previously shown to infect humans or to be part of the human virome. We unexpectedly found sequences homologous to the chlorovirus Acanthocystis turfacea chlorella virus 1 (ATCV-1) in a metagenomic analysis of DNA extracted from human oropharyngeal samples. These samples were obtained by throat swabs of adults without a psychiatric disorder or serious physical illness who were participating in a study that included measures of cognitive functioning. The presence of ATCV-1 DNA was confirmed by quantitative PCR with ATCV-1 DNA being …

Eight Legged Encounters, Eileen A. Hebets

Eileen Hebets Publications

This program was funded in part by a National Science Foundation grant (DRL–1241482 to EAH). Material was developed in collaboration with Marie- Claire Chelini, Jessie Rose Storz, Cody Storz, and Malcolm Rosenthal. Steven Schwartz, Jason Stafstrom, Kathy French, Priscilla Grew, and Judy Diamond were all extremely helpful in grant writing, facilitating the first live event, and/or discussions. Pawl Tisdale (artist) was phenomenal to work with on all aspects of the project!

TABLE OF CONTENTS

CLASSIFICATION & TAXONOMY STATIONS
I. WHAT IS AN ARTHROPOD? page 4 a. The goal of this station is to introduce the audience to some basic information …

A Consensus Taxonomy For The Hawaiian Honeycreepers, H. Douglas Pratt

Occasional Papers of the Museum of Natural Science, Louisiana State University

No abstract provided.

Characterization Of The Transcriptome, Nucleotide Sequence Polymorphism, And Natural Selection In The Desert Adapted Mouse Peromyscus Eremicus, Matthew D. Macmanes, Michael B. Eisen

Molecular, Cellular & Biomedical Sciences

As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal, Peromyscus eremicus, is native to the desert regions of the southwest United States and may live its entire life without oral fluid intake. As a first step toward understanding the genetics that underlie this phenotype, we present a characterization of the …

Legume Crops Phylogeny And Genetic Diversity For Science And Breeding, Petr Smýkal, Clarice J. Coyne, Mike J. Ambrose, Nigel Maxted, Hanno Schaefer, Matthew W. Blair

Agricultural and Environmental Sciences Faculty Research

Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal feed. Fabaceae, the third largest family of flowering plants, has traditionally been divided into the following three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae, all together with 800 genera and 20,000 species. The latter subfamily contains most of the major cultivated food and feed crops. Among the grain legumes are some of mankind's earliest crop plants, …

Revisiting The Vanishing Refuge Model Of Diversification, Robert Damasceno, Maria L. Strangas, Ana C. Carnaval, Miguel T. Rodrigues, Craig Moritz

Publications and Research

Much of the debate around speciation and historical biogeography has focused on the role of stabilizing selection on the physiological (abiotic) niche, emphasizing how isolation and vicariance, when associated with niche conservatism, may drive tropical speciation. Yet, recent re-emphasis on the ecological dimensions of speciation points to a more prominent role of divergent selection in driving genetic, phenotypic, and niche divergence. The vanishing refuge model (VRM), first described by Vanzolini and Williams (1981), describes a process of diversification through climate-driven habitat fragmentation and exposure to new environments, integrating both vicariance and divergent selection. This model suggests that dynamic climates and …

Scalable Combinatorial Tools For Health Disparities Research, Michael A. Langston, Robert S. Levine, Barbara J. Kilbourne, Gary L. Rogers Jr., Anne D. Kershenbaum, Suzanne H. Baktash, Steven S. Coughlin, Arnold M. Saxton, Vincent K. Agboto, Darryl B. Hood, Maureen Y. Litchveld, Tonny J. Oyana, Patricia Matthews-Juarez, Paul D. Juarez

Sociology Faculty Research

Despite staggering investments made in unraveling the human genome, current estimates suggest that as much as 90% of the variance in cancer and chronic diseases can be attributed to factors outside an individual’s genetic endowment, particularly to environmental exposures experienced across his or her life course. New analytical approaches are clearly required as investigators turn to complicated systems theory and ecological, place-based and life-history perspectives in order to understand more clearly the relationships between social determinants, environmental exposures and health disparities. While traditional data analysis techniques remain foundational to health disparities research, they are easily overwhelmed by the ever-increasing size …

Genetic Analysis Of Ton2 Dependent Processes In Microtubule Organization In Arabidopsis Thaliana, Samantha Nicole Atkinson

Theses and Dissertations

Microtubules carry out many functions within the cell. They're used during mitosis and meiosis to move chromosomes to opposite sides of the cell so that cell division can occur. They're also used as structural support for the cell and are involved in establishing the cell shape. Microtubules are also able to reorient from a longitudinal orientation to a transverse orientation in response to gibberellic acid and auxin (two hormones that are involved in cell elongation). The mechanism for how this reorientation occurs is unknown. The TONNEAU2 (TON2) protein is necessary for proper microtubule organization. We looked at how TON2 affects …

Analysis Of Differential Mrna And Mirna Expression In An Alzheimer’S Disease Mouse Model, Amanda Hazy, Matthew Dalton

Other Undergraduate Scholarship

Research has shown that changes in gene expression play a critical role in the development of Alzheimer’s Disease (AD). Our project will evaluate genome-wide RNA expression patterns from brain and blood in an AD mouse model. This analysis will provide insight regarding the mechanisms of AD pathology as well as determine a possible diagnostic tool utilizing RNA expression patterns found in the blood as biomarkers for AD.

Integrated Transcriptome Analysis Reveals Mirna-Mrna Crosstalk In Laryngeal Squamous Cell Carcinoma., Yang Zhang, Yong Chen, Jinhai Yu, Guiming Liu, Zhigang Huang

College of Science & Mathematics Departmental Research

Next generation sequencing (NGS) has proven to be a powerful tool in delineating myriads of molecular subtypes of cancer, as well as in revealing accumulation of genomic mutations throughout cancer progression. Whole genome microRNA (miRNA) and mRNA expression profiles were obtained from patients with laryngeal squamous cell carcinoma (LSCC) using deep sequencing technology, and were analyzed by utilizing integrative computational approaches. A large number of protein-coding and non-coding genes were detected to be differentially expressed, indicating a functional switch in LSCC cells. A total of 127 mutated genes were detected to be significantly associated with ectoderm and epidermis development. Eleven …

Editorial Overview: Environmental Physiology: Insect Environmental Physiology, Brent J. Sinclair

Biology Publications

No abstract provided.

The Peopling Of The African Continent And The Diaspora Into The New World, Michael Campbell, Jibril Hirbo, Jeffrey Peter Townsend, Sarah Tishkoff

Department of Biology Faculty Publications

Africa is the birthplace of anatomically modern humans, and is the geographic origin of human migration across the globe within the last 100,000 years. The history of African populations has consisted of a number of demographic events that have influenced patterns of genetic and phenotypic variation across the continent. With the increasing amount of genomic data and corresponding developments in computational methods, researchers are able to explore long-standing evolutionary questions, expanding our understanding of human history within and outside of Africa. This review will summarize some of the recent findings regarding African demographic history, including the African Diaspora, and will …

Altered Theca And Cumulus Oocyte Complex Gene Expression, Follicular Arrest And Reduced Fertility In Cows With Dominant Follicle Follicular Fluid Androgen Excess, Adam F. Summers, William E. Pohlmeier, Kevin M. Sargent, Brizett D. Cole, Rebecca J. Vinton, Scott G. Kurz, Renee M. Mcfee, Robert A. Cushman, Andrea S. Cupp, Jennifer R. Wood

Department of Animal Science: Faculty Publications

Aspiration of bovine follicles 12–36 hours after induced corpus luteum lysis serendipitously identified two populations of cows, one with High androstenedione (A4; >40 ng/ml; mean = 102) and another with Low A4 (/ml; mean = 9) in follicular fluid. We hypothesized that the steroid excess in follicular fluid of dominant follicles in High A4 cows would result in reduced fertility through altered follicle development and oocyte maternal RNA abundance. To test this hypothesis, estrous cycles of cows were synchronized and ovariectomy was performed 36 hours later. HPLC MS/MS analysis of follicular fluid showed increased dehydroepiandrosterone (6-fold), A4 (158-fold) and testosterone …

Kernel-Based Whole-Genome Prediction Of Complex Traits: A Review, Gota Morota, Daniel Penagaricano

Department of Animal Science: Faculty Publications

Prediction of genetic values has been a focus of applied quantitative genetics since the beginning of the 20th century, with renewed interest following the advent of the era of whole genome-enabled prediction. Opportunities offered by the emergence of high-dimensional genomic data fueled by post-Sanger sequencing technologies, especially molecular markers, have driven researchers to extend Ronald Fisher and Sewall Wright’s models to confront new challenges. Inparticular, kernel methods are gaining consideration as a regression method of choice for genome-enabled prediction. Complex traits are presumably influenced by many genomic regions working in concert with others (clearly so when considering pathways), thus generating …

Identification And Characterization Of Factors Involved In Dna Demethylation And Anti-Silencing In Arabidopsis, Zhaobo Lang

Open Access Dissertations

DNA methylation is a key epigenetic mark for transcriptional gene silencing in many eukaryotes. DNA methylation status can be dynamically controlled by methylation and active demethylation processes. Compared to the well-known mechanisms of DNA methylation, the mechanisms of DNA demethylation and its regulation are poorly understood. In order to better understand the DNA demethylation pathway, we developed two genetic screening systems in Arabidopsis to identify new components involved in the DNA demethylation. In the first system, which is based on 35S promoter driven SUC2 (sucrose transporter 2) transgene, a mutant (91-1) was isolated and map-based cloning identified the …

Associated Behavioral, Genetic, And Gene Expression Variation With Alternative Life History Tactics In Salmonid Fishes, Ashley Chin-Baarstad

Open Access Dissertations

Individual differences in behavior can have potential fitness consequences and often reflect underlying genetic variation. My research focuses on three objectives related to individual level variation: 1) evaluating the innate behavioral variation within and between individuals, families, and progeny of different life-history types across time; 2) testing for differences in gene expression within the brain associated with this behavioral variation; and 3) using genetic polymorphisms to test for associations with ecotype, as well as population structure, in polymorphic populations. First, we evaluated the variation in a suite of ecologically relevant behaviors across time in juvenile progeny produced from crosses within …

Data Completion Methods For Improved Developmental Stage Annotation Of Drosophila Embryos In Images, Chitsanu Janyalikit

Electrical & Computer Engineering Theses & Dissertations

Drosophila melanogaster is a dominant model organism for studying the function of animal genes in initial stages of embryogenesis. Usually, images containing Drosophila gene expression patterns are captured at different developmental stages to study the interconnection of animal genes. To achieve most biologically meaningful results, gene expression images from a similar stage should be compared. Currently, biologists manually classify embryos in images into different stages, which is time intensive and infeasible for current massively produced gene expression images. Therefore, there is a need to develop an automatic system for the annotation.

Gene expression information in embryo images usually appears as …

An Rnai-Based Suppressor Screen Identifies Interactors Of The Myt1 Ortholog Of Caenorhabditis Elegans, Anna Allen, Jessica Nesmith, Andy Golden

Department of Biology Faculty Publications

Oocyte maturation in all species is controlled by a protein complex termed the maturation promoting factor (MPF). MPF is comprised of a cyclin-dependent kinase (CDK) and its partner cyclin, and is regulated by dueling regulatory phosphorylation events on the CDK. In Caenorhabditis elegans, the Wee1/Myt1 ortholog WEE-1.3 provides the inhibitory phosphorylations on CDK-1 that keep MPF inactive and halts meiosis. Prior work has shown that depletion of WEE-1.3 in C. elegans results in precocious oocyte maturation in vivo and a highly penetrant infertility phenotype. This study sought to further define the precocious maturation phenotype and to identify novel interactors with …

Advancing The Microbiome Research Community, Curtis Huttenhower, Rob Knight, C. Titus Brown, J. Gregory Caporaso, Jose C. Clemente, Dirk Gevers, Eric A. Franzosa, Scott T. Kelley, Dan Knights, Ruth E. Ley, Anup Mahurkar, Jacques Ravel, Scientists For Advancement Of Microbiome Research, Owen White, Jacques Izard

Department of Food Science and Technology: Faculty Publications

The human microbiome has become a recognized factor in promoting and maintaining health. We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. Advances in these aspects of the research community may in turn advance our understanding of human microbiome biology.

It is now widely recognized that disturbances in our normal microbial populations may be linked to acute infections such as Clostridium difficile and to chronic diseases such as heart disease, cancer, obesity, and autoimmune disorders. This has prompted substantial interest in the microbiome from both basic and clinical perspectives. …