Contributions Of Gene Copy Number Variation To Genome Evolution And Local Adaptation Of The Cyanobacterium Acaryochloris,
2017
University of Montana, Missoula
Contributions Of Gene Copy Number Variation To Genome Evolution And Local Adaptation Of The Cyanobacterium Acaryochloris, Amy L. Gallagher
Graduate Student Theses, Dissertations, & Professional Papers
Acaryochloris is a recently discovered genus of cyanobacteria, unique in its use of an uncommon chlorophyll as its major photosynthetic pigment, and in its peculiar genome dynamics. Members of this genus exhibit increased genic copy number variation (CNV), which is thought to be primarily derived from gene duplications and horizontal gene transfer (HGT). Acaryochloris provides an ideal system to explore mechanisms behind maintenance of gene duplicates and the influence of CNV in local adaptation. Here, I propose a mechanism for retention of gene duplicates of the bacterial recombinase, RecA, in Acaryochloris genomes and provide preliminary evidence that these paralogs are …
Improvement Of Milling And Nutritional Quality Characteristics Of Oats Through Genomic Selection,
2017
South Dakota State University
Improvement Of Milling And Nutritional Quality Characteristics Of Oats Through Genomic Selection, Sudha Neupane Adhikari
Electronic Theses and Dissertations
Oats can lower cholesterol, reduce risks of type-2 diabetes, and help prevent heart diseases when consumed daily. Therefore, it is important to evaluate and select breeding lines with desirable milling and nutritional quality traits. Genomic selection, which uses genotyping data to predict the breeding value of an individual, is a promising method to increase genetic gain by selecting for quality traits earlier in the line development process. In this study, we collected phenotypic data for three nutritional traits (protein, β- glucan, and fat content) and five milling quality traits (percent plumps, percent thins, percent plump groat, groat percent and thousand …
Characterization Of A Large Vertebrate Genome And Homomorphic Sex Chromosomes In The Axolotl, Ambystoma Mexicanum,
2017
University of Kentucky
Characterization Of A Large Vertebrate Genome And Homomorphic Sex Chromosomes In The Axolotl, Ambystoma Mexicanum, Melissa Keinath
Theses and Dissertations--Biology
Changes in the structure, content and morphology of chromosomes accumulate over evolutionary time and contribute to cell, developmental and organismal biology. The axolotl (Ambystoma mexicanum) is an important model for studying these changes because: 1) it provides important phylogenetic perspective for reconstructing the evolution of vertebrate genomes and amphibian karyotypes, 2) its genome has evolved to a large size (~10X larger than human) but has maintained gene orders, and 3) it possesses potentially young sex chromosomes that have not undergone extensive differentiation in the structure that is typical of many other vertebrate sex chromosomes (e.g. mammalian XY chromosomes …
Complete Genome Sequences Of Cluster A Mycobacteriophages Bobswaget, Fred313, Kady, Lokk, Myradee, Stagni, And Stepmih,
2017
Seton Hill University
Complete Genome Sequences Of Cluster A Mycobacteriophages Bobswaget, Fred313, Kady, Lokk, Myradee, Stagni, And Stepmih, Kristen A. Butela, Susan M. R. Gurney, Heather L. Hendrickson, Janine M. Leblanc-Straceski, Anastasia M. Zimmerman, Stephanie B. Conant, Nikki E. Freed, Olin K. Silander, Joshua J. Thomson, Charlotte A. Berkes, Cristina Bertolez, Courtney G. Davies, Amber Elinsky, Alison J. Hanlon, Juliette Nersesyan, Payal Patel, John Sherwood, Tiffany Tieu Ngo, Kathryn A. Wisniewski, Kathrine Yacoo, Paul M. Arendse, Nathan W. Bowlen, Jasmina Cunmulaj, Julie L. Downs, Charlee A. Ferrenberg, Alexandra E. Gassman, Cody E. R. Gilligan, Emily Gorkiewicz, Christopher Harness, Anthony Huffman, Christina Jones, Anna Julien, Alexis E. Kupic, Sayonara F. Latu, Thomas J. Manning, Danielle Maxwell, Merrimack College Sea-Phages Annotators 2016, Catherine E. Meyer, Madeleine Reardon, Matthew Slaughter, Royce Swasey, Rebecca I. Tennent, Victoria Torres, Tamia Waller, Rachel M. Worcester, Brooke L. Yost, Steven G. Cresawn, Rebecca A. Garlena, Deborah Jacobs-Sera, Welkin H. Pope, Daniel A. Russell, Graham F. Hatfull, Jacob D. Kagey
Biology Faculty Publications
Seven mycobacteriophages from distinct geographical locations were isolated, using Mycobacterium smegmatis mc2155 as the host, and then purified and sequenced. All of the genomes are related to cluster A mycobacteriophages, BobSwaget and Lokk in subcluster A2; Fred313, KADY, Stagni, and StepMih in subcluster A3; and MyraDee in subcluster A18, the first phage to be assigned to that subcluster.
Investigation On Genetic Modifiers Of Age At Onset Of Major Depressive Disorder,
2017
Virginia Commonwealth University
Investigation On Genetic Modifiers Of Age At Onset Of Major Depressive Disorder, Huseyin Gedik
Theses and Dissertations
Major Depressive Disorder (MDD) is a complex multifactorial disorder, which would lead to disability. Environmental and genetic factors are involved in MDD etiology. The aim of this project was to identify loci modifying age at onset (AAO) of MDD using survival models after adjusting for Childhood Sexual Abuse (CSA). To achieve this aim, a dataset was made available by the China Oxford and VCU Experimental Research on Genetic Epidemiology (CONVERGE) consortium. The study population had 5,220 controls and 5,282 cases with MDD. We performed two univariate association analyses using Cox Proportional Hazard (Cox PH) models. These two are Full Sample …
Hyper-Activation Of Pp60(Src) Limits Nitric Oxide Signaling By Increasing Asymmetric Dimethylarginine Levels During Acute Lung Injury,
2017
Old Dominion University
Hyper-Activation Of Pp60(Src) Limits Nitric Oxide Signaling By Increasing Asymmetric Dimethylarginine Levels During Acute Lung Injury, Sanjiv Kumar, Xutong Sun, Satish Kumar Noonepalle, Qing Lu, Evgeny Zemskov, Ting Wang, Saurabh Aggarwal, Christine Gross, Shruti Sharma, Ankit A. Sesai, John D. Catravas
Bioelectrics Publications
The molecular mechanisms by which the endothelial barrier becomes compromised during lipopolysaccharide (LPS) mediated acute lung injury (ALI) are still unresolved. We have previously reported that the disruption of the endothelial barrier is due, at least in part, to the uncoupling of endothelial nitric oxide synthase (eNOS) and increased peroxynitrite-mediated nitration of RhoA. The purpose of this study was to elucidate the molecular mechanisms by which LPS induces eNOS uncoupling during ALI. Exposure of pulmonary endothelial cells (PAEC) to LPS increased pp60Src activity and this correlated with an increase in nitric oxide (NO) production, but also an increase in …
Evolution Of Molt Phenology In Dwarf Hamsters,
2017
University of Montana, Missoula
Evolution Of Molt Phenology In Dwarf Hamsters, Zachary Clare-Salzler
Graduate Student Theses, Dissertations, & Professional Papers
Environmental seasonality presents many challenges for survival. In response, organisms from across the tree of life exhibit adaptive phenology, which can facilitate survival from season to season. In particular, many species are white in the winter and brown in the summer where winter snow cover alters the visual environment. There is an extensive body of literature describing the physiological and cellular regulation of this trait in the Siberian dwarf hamster (Phodopus sungorus), but there are major shortcomings in our understanding concerning the evolution and molecular regulation of mammalian skin phenology. Notably, little is known about the genetic basis …
Differential Activity And Content Of High-Affinity Glutamate Transporters, Content Of Their Regulatory Proteins, And Capacity For Glutamine And Glutathione Synthesis In Tissues Of Finished Versus Growing Steers,
2017
University of Kentucky
Differential Activity And Content Of High-Affinity Glutamate Transporters, Content Of Their Regulatory Proteins, And Capacity For Glutamine And Glutathione Synthesis In Tissues Of Finished Versus Growing Steers, Jing Huang
Theses and Dissertations--Animal and Food Sciences
Improvement of feeding regimens for production animals has been hindered by a lack of fundamental knowledge about how the capacity to regulate nutrient absorption across cell membranes affects the function of nutrient metabolizing enzymes. The objective is to determine if the activities and protein content of system X-AG glutamate transporter, its regulatory protein (GTRAP3-18 and ARL6IP1), glutamine synthetase (GS) and glutathione (GSH) content, changes in liver (Experiment 1), longissimus dorsi (LM) and subcutaneous adipose tissue (SF) (Experiment 2) as beef steers transitioned from predominantly-lean (growing) to -lipid (finished) tissue accretion phases. In liver (Experiment 1), system X- …
Genomic Perspectives On Amphibian Evolution Across Multiple Phylogenetic Scales,
2017
University of Kentucky
Genomic Perspectives On Amphibian Evolution Across Multiple Phylogenetic Scales, Paul Michael Hime
Theses and Dissertations--Biology
Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation exert strong effects on the resulting inferences. Genome scans are employed to test hypotheses about the mechanisms of genetic sex determination in …
Metagomics: A Web-Based Tool For Peptide-Centric Functional And Taxonomic Analysis Of Metaproteomics Data,
2017
Old Dominion University
Metagomics: A Web-Based Tool For Peptide-Centric Functional And Taxonomic Analysis Of Metaproteomics Data, Michael Riffle, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, Daniel Jaschob, William S. Noble, Brook L. Nunn
OES Faculty Publications
Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the …
High-Throughput Single-Molecule Mapping Links Subtelomeric Variants And Long-Range Haplotypes With Specific Telomeres,
2017
Old Dominion University
High-Throughput Single-Molecule Mapping Links Subtelomeric Variants And Long-Range Haplotypes With Specific Telomeres, Eleanor Young, Steven Pastor, Ramakrishnan Rajagopalan, Jennifer Mccaffrey, Justin Sibert, Angel C. Y. Mak, Pui-Yan Kwok, Harold Riethman, Ming Xiao
School of Medical Diagnostics & Translational Sciences Publications
Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomereterminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technology in nano-channel arrays to analyze large terminal human chromosome segments extending from chromosome-specific subtelomere sequences through subtelomeric repeat regions to terminal (TTAGGG) n repeat tracts. We establish detailed maps for subtelomere gap regions in the human reference sequence, detect many new large subtelomeric variants and demonstrate the feasibility of long-range haplotyping through segmentally duplicated subtelomere regions. …
Complete Genome Sequences Of 38 Gordonia Sp. Bacteriophages,
2017
University of Pittsburgh
Complete Genome Sequences Of 38 Gordonia Sp. Bacteriophages, Welkin H. Pope, Matthew T. Montgomery, Randall J. Dejong
University Faculty Publications and Creative Works
We report here the genome sequences of 38 newly isolated bacteriophages using Gordonia terrae 3612 (ATCC 25594) and Gordonia neofelifaecis NRRL59395 as bacterial hosts. All of the phages are double-stranded DNA (dsDNA) tail phages with siphoviral morphologies, with genome sizes ranging from 17,118 bp to 93,843 bp and spanning considerable nucleotide sequence diversity.
Comparative Genomic Analysis Of Two Serotype 1/2b Listeria Monocytogenes Isolates From Analogous Environmental Niches Demonstrates The Influence Of Hypervariable Hotspots In Defining Pathogenesis,
2016
Teagasc Food Research Centre, Fermoy, Ireland and Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Ireland
Comparative Genomic Analysis Of Two Serotype 1/2b Listeria Monocytogenes Isolates From Analogous Environmental Niches Demonstrates The Influence Of Hypervariable Hotspots In Defining Pathogenesis, Aidan Casey, Kieran Jordan, Aidan Coffey, Edward M. Fox, Olivia Mcauliffe
Department of Biological Sciences Publications
The vast majority of clinical human listeriosis cases are caused by serotype 1/2a, 1/2b, 1/2c, and 4b isolates of Listeria monocytogenes. The ability of L. monocytogenes to establish a systemic listeriosis infection within a host organism relies on a combination of genes that are involved in cell recognition, internalization, evasion of host defenses, and in vitro survival and growth. Recently, whole genome sequencing and comparative genomic analysis have proven to be powerful tools for the identification of these virulence-associated genes in L. monocytogenes. In this study, two serotype 1/2b strains of L. monocytogenes with analogous isolation sources, but …
Evolution In Light Of Mitonuclear Landscapes: An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.),
2016
University of Southern Mississippi
Evolution In Light Of Mitonuclear Landscapes: An Examination Of Mitochondrial Replacement In Killifish (Fundulus Spp.), Stephen D. Flanagan
Dissertations
The mitochondria are responsible for the bulk of energy production in eukaryotes. They possess their own genome that works in conjunction with the nuclear genome to accomplish the extraordinarily important task of energy conversion. When species hybridize there will be a mismatch in evolutionary histories between these two genomes. The deleterious interactions of these genomes have been studied in great detail (i.e. hybrid breakdown). However, little work has been conducted to understand the population genetic, and morphological consequences of wide-ranging replacement. The Fundulus notatus complex is comprised of 3 species: F. notatus, F. olivaceus, and F. euryzonus. …
Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry,
2016
University of California, San Francisco
Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry, Shea T. Lance, David J. Sukovich, Kenneth M. Stedman, Adam R. Abate
Biology Faculty Publications and Presentations
Background: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the …
Investigating The Functional Role Of Tick Antioxidants In Hematophagy And Vector Competence,
2016
University of Southern Mississippi
Investigating The Functional Role Of Tick Antioxidants In Hematophagy And Vector Competence, Deepak Kumar
Dissertations
Ticks are obligate hematophagous arthropods and harbor several pathogens which transmit various diseases to humans and their domesticated animals. Host blood- digestion in a tick midgut (MG) generates several reactive oxygen species (ROS), which are extremely toxic to essential macromolecules (e.g. DNA, proteins, and lipids) within the cell, resulting in high oxidative stress. Thus, this dissertation focuses on the questions of how tick homeostasis responds to high oxidative stress, and how ticks and their harbored pathogens survive the high surge of oxidative stress during blood digestion. We are specifically interested in the tick-pathogen, Rickettsia parkeri (R. parkeri, Rp), harbored by …
Concomitant Targeting Of The Mtor/Mapk Pathways: Novel Therapeutic Strategy In Subsets Of Non-Small Cell Lung Cancer,
2016
The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Concomitant Targeting Of The Mtor/Mapk Pathways: Novel Therapeutic Strategy In Subsets Of Non-Small Cell Lung Cancer, Dennis Ruder
Dissertations and Theses (Open Access)
Over the last decade, a paradigm-shift in lung cancer therapy has evolved into targeted-driven medicinal approaches. However, patients frequently relapse and develop resistance to available therapies. Herein, we utilized genomic mutation data from advanced chemorefractory non-small cell lung cancer (NSCLC) patients enrolled in the Biomarker-Integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE-2) clinical trial to characterize novel actionable genomic alterations potentially of clinical relevance. We identified RICTOR alterations (mutations, amplifications) in 17% of lung adenocarcinomas and found RICTOR expression correlates to worse overall survival. There was enrichment of MAPK pathway genetic aberrations in key oncogenes (e.g. KRAS, BRAF, …
First Occurrence Of The Invasive Hydrozoan Gonionemus Vertens A. Agassiz, 1862 (Cnidaria: Hydrozoa) In New Jersey, Usa,
2016
Montclair State University
First Occurrence Of The Invasive Hydrozoan Gonionemus Vertens A. Agassiz, 1862 (Cnidaria: Hydrozoa) In New Jersey, Usa, John J. Gaynor, Paul A.X. Bologna, Dena J. Restaino, Christie Barry
Department of Biology Faculty Scholarship and Creative Works
Gonionemus vertens A. Agassiz, 1862 is a small hydrozoan native to the Pacific Ocean. It has become established in the northern and southern Atlantic Ocean as well as the Mediterranean Sea. We report on the first occurrence of this species in estuaries in New Jersey, USA,and confirm species identification through molecular sequence analysis. Given the large number of individuals collected, we contend that this is a successful invasion into this region with established polyps. The remaining question is the vector and source of these newly established populations.
Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome,
2016
Loyola University Chicago
Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti
Bioinformatics Faculty Publications
Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates …
Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae,
2016
Loyola University Chicago
Draft Genome Sequence For A Urinary Isolate Of Nosocomiicoccus Ampullae, Evann Elizabeth Hilt, Travis Kyle Price, Katherine Diebel, Catherine Putonti, Alan J. Wolfe
Bioinformatics Faculty Publications
A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was investigated. The size of the genome was 1,578,043 bp, with an observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA genes, and 1,532 protein-coding sequences. Genome coverage was 727× and consisted of 32 contigs, with an N50 of 109,831 bp.
