Development Of Genomic Resources For The Evaluation Of Red Snapper, An Emerging Species Candidate For Marine Aquaculture And Stock Enhancement,
2016
University of Southern Mississippi
Development Of Genomic Resources For The Evaluation Of Red Snapper, An Emerging Species Candidate For Marine Aquaculture And Stock Enhancement, Adrienne Elise Norrell
Master's Theses
The northern red snapper (Lutjanus campechanus) is a highly targeted reef fish candidate for marine aquaculture and stock enhancement in the southern United States. This work aimed to develop genomic resources for the genetic management of aquaculture programs and to investigate population structure using high-throughput sequencing technologies. Eighty-four new microsatellite markers were developed through screening of Illumina paired-end sequencing reads. Microsatellite loci and Single Nucleotide Polymorphisms (SNPs) generated through Restriction Site Associated DNA (RAD) sequencing were assayed in 5 outbred full-sib families to construct a high-density linkage map of the red snapper genome. The map consists of 7,964 …
Development Of An In Silico Kir Genotyping Algorithm And Its Application To Population And Cancer Immunogenetic Analyses,
2016
The University of Texas Graduate School of Biomedical Sciences at Houston
Development Of An In Silico Kir Genotyping Algorithm And Its Application To Population And Cancer Immunogenetic Analyses, Howard Rosoff
Dissertations and Theses (Open Access)
Gene content determination and variant calling in the complex KIR genomic region are useful for immune system function analysis, pathogenesis and disease risk factor elucidation, immunotherapy development, evolutionary investigations, and human migration modeling. Sequence-specific oligonucleotide and sequence-specific primer PCR methods are the de facto standards for KIR presence/absence identification, but the current platforms are unsuitable for SNP calling, impractical for KIR typing large cohorts of DNA samples, and inapplicable for typing repositories in which sequence data, but not cells or cell analytes, are available. Alternative typing methods, such as in silico sequence-based typing, can address the problems associated with amplicon-based …
A Comparative Study Of K-Spectrum-Based Error Correction Methods For Next-Generation Sequencing Data Analysis,
2016
University of Southern Mississippi
A Comparative Study Of K-Spectrum-Based Error Correction Methods For Next-Generation Sequencing Data Analysis, Isaac Akogwu, Nan Wang, Chaoyang Zhang, Ping Gong
Faculty Publications
Background: Innumerable opportunities for new genomic research have been stimulated by advancement in high-throughput next-generation sequencing (NGS). However, the pitfall of NGS data abundance is the complication of distinction between true biological variants and sequence error alterations during downstream analysis. Many error correction methods have been developed to correct erroneous NGS reads before further analysis, but independent evaluation of the impact of such dataset features as read length, genome size, and coverage depth on their performance is lacking. This comparative study aims to investigate the strength and weakness as well as limitations of some newest k-spectrum-based methods and …
Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains,
2016
University of Nebraska-Lincoln
Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, Kenneth Nickerson
Kenneth Nickerson Papers
Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and metabolic …
Distribution Of Genomic Variation In The Usda Soybean Germplasm Collection And Relationship With Phenotypic Variation,
2016
University of Nebraska-Lincoln
Distribution Of Genomic Variation In The Usda Soybean Germplasm Collection And Relationship With Phenotypic Variation, Nonoy Batiller Bandillo
Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research
The USDA Soybean Germplasm Collection harbors a large stock of genetic diversity with potential to accelerate soybean cultivar development. The extent and nature of favorable alleles contained in the collection are not well known nor is the distribution of genetic variation and how it relates to phenotypic variation. The genotyping of the entire USDA Soybean Germplasm Collection marked the beginning of a systematic exploration of genetic diversity for genetic research and breeding. In this research, we conducted the first comprehensive analysis of population structure on the collection of ~14,400 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold …
Effects Of Mutating The Mrub_1345 Gene Found In Meiothermus Ruber,
2016
Augustana College, Rock Island Illinois
Effects Of Mutating The Mrub_1345 Gene Found In Meiothermus Ruber, Brandon M. Wills, Lori R. Scott
Celebration of Learning
Meiothermus ruber is a unique, red-pigmented, thermophilic bacterium that preferentially grows in high-temperature environments ranging from 35-70°C. Due to the lack of studies performed on this organism, there is quite a bit of information missing in regard to the genes found within this organism’s genome and their function. This study focuses in on the Mrub_1345 gene in M. ruber, which has been suggested to be orthologous to the proC gene found of E. coli proline biosynthesis pathway. To test if these genes are orthologs, we performed the complementation assay on wild-type proC. Next, we performed site-directed mutagenesis on amino acids …
Genome-Wide Differentiation In Closely Related Populations:
The Roles Of Selection And Geographic Isolation,
2016
University of Colorado, Boulder
Genome-Wide Differentiation In Closely Related Populations: The Roles Of Selection And Geographic Isolation, Rebecca Safran, Elizabeth Scordato, Matt Wilkins, Joanna K. Hubbard, B. R. Jenkins, Tomáš Albrecht, Samuel Flaxman, H. Karaardiç, Yoni Vortman, Arnon Lotem, Patrik Nosil, P. Pap, Sheng-Feng Shen, S.-F. Chan, T. L. Parchman, Nolan C. Kane
School of Biological Sciences: Faculty Publications
Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as “isolation by adaptation” (IBA). IBA can be complementary to the well-known pattern of “isolation by distance” (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, …
Hiv Vaccines: Progress, Limitations And A Crispr/Cas9 Vaccine,
2016
Augustana College, Rock Island Illinois
Hiv Vaccines: Progress, Limitations And A Crispr/Cas9 Vaccine, Omar A. Garcia Martinez
Biology: Student Scholarship & Creative Works
ABSTRACT: The HIV-1 pandemic continues to thrive due to ineffective HIV-1 vaccines. Historically, the world’s most infectious diseases, such as polio and smallpox, have been eradicated or have come close to eradication due to the advent of effective vaccines. Highly active antiretroviral therapy is able to delay the onset of AIDS but can neither rid the body of HIV-1 proviral DNA nor prevent further transmission. A prophylactic vaccine that prevents the various mechanisms HIV-1 has to evade and attack our immune system is needed to end the HIV-1 pandemic. Recent advances in engineered nuclease systems, like the CRISPR/Cas9 system, have …
Tropical Trees As Islands: Diversity Accumulation Of Armored Scale Insects (Hemiptera: Diaspididae) On Trees As A Function Of Forest Age,
2016
University of San Diego
Tropical Trees As Islands: Diversity Accumulation Of Armored Scale Insects (Hemiptera: Diaspididae) On Trees As A Function Of Forest Age, Hannah Shapiro
Undergraduate Honors Theses
Armored scale insects (Hemiptera: Diaspididae) are some of the most invasive insects in the world. These cryptic plant parasites are most often encountered in managed agricultural ecosystems, but very little is known about their distribution, abundance, and diversity in tropical rainforest canopies, where they are likely to have their highest diversity. Because these ubiquitous insects are extreme generalists with undirected dispersal, their diversity (alpha and beta) accumulation can conceivably be modeled according to tenets derived from island biogeography theory. For example, one expectation is that older established trees should boast a higher species diversity and abundance than younger ones. Other …
Exploring Barriers To The Adoption Of Pharmacogenomic Technology In The Clinical Setting By Clinical Healthcare Providers,
2016
Seton Hall University
Exploring Barriers To The Adoption Of Pharmacogenomic Technology In The Clinical Setting By Clinical Healthcare Providers, Jason Sudia
Seton Hall University Dissertations and Theses (ETDs)
The changing landscape of healthcare in the US has created new questions about how to best provide cost-effective, individualized care. Personalized medicine and more specifically, pharmacogenomic technology have offered new tools for healthcare providers to use to increase the efficacy, safety, and cost-effectiveness of care. However, these tools are not being utilized to their predicted extent in the clinical setting. This study utilized Rogers’ Diffusion of Innovations theory to investigate some of the reasons why. A multi-question survey, the PI-created, Pharmacogenomic Adoption Instrument (PAI) ©, was developed to assess the knowledge, attitudes and experience concerning pharmacogenetic technology in a spectrum …
Recurrent Mutations Of T-Cell Receptor And Co-Stimulatory Signaling Proteins In Peripheral T-Cell Lymphomas,
2016
University of Nebraska Medical Center
Recurrent Mutations Of T-Cell Receptor And Co-Stimulatory Signaling Proteins In Peripheral T-Cell Lymphomas, Joseph Rohr
Theses & Dissertations
Peripheral T-cell lymphomas (PTCLs) comprise a heterogeneous group of mature T-cell neoplasms with a poor prognosis. Recently, mutations in TET2 and other epigenetic modifiers as well as RHOA have been identified in these diseases, particularly in angioimmunoblastic T-cell lymphoma (AITL). CD28 is the major co-stimulatory receptor in T-cells which, upon binding ligand, induces sustained T-cell proliferation and cytokine production when combined with T-cell receptor stimulation, through many signaling molecules including VAV1. This thesis identifies recurrent mutations in CD28 in PTCLs, as well as mutations in VAV1. Two residues of CD28 – D124 and T195 – were recurrently mutated in 11.3% …
The Effects Of Chronic Partial Sleep Deprivation And Chronic Voluntary Alcohol Consumption On Δfos B Accumulation,
2016
James Madison University
The Effects Of Chronic Partial Sleep Deprivation And Chronic Voluntary Alcohol Consumption On Δfos B Accumulation, Kristian Ponder
Masters Theses, 2010-2019
The present study explores the relation between sleep restriction and alcohol use and the neural substrates that result from chronic behaviors. Accumulation of the transcription factors ΔFosB is suggested as a possible outcome of chronic behaviors, such as addiction. Sleep is discussed as possible mediating factor in the relationship between ΔFosB and chronic alcohol consumption. There were four experimental groups in this study: Control (C), Sleep Deprivation only (SD), Alcohol Exposure only (AO), and both sleep deprivation and alcohol exposure (B). Levels of ΔFosB accumulation in the Nucleus Accumbens (NAc) revealed a significant main effect of sleep deprivation, but no …
Mrub_2874 Is Homologous To B3386 And Mrub_1349 Is Homologous To B2914, But Mrub_1349 Is Not Homologous To B4090,
2016
Augustana College, Rock Island Illinois
Mrub_2874 Is Homologous To B3386 And Mrub_1349 Is Homologous To B2914, But Mrub_1349 Is Not Homologous To B4090, Samantha Murad, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
ABSTRACT. This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2874 and Mrub_1349. We predict that Mrub_2874 encodes the enzyme ribulose-5-phosphate 3-epimerase (DNA coordinates 2912530..2913204 on the reverse strand), which is the first step of the pentose phosphate pathway (KEGG map number 00030). It catalyzes the conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3386, which has the gene …
Genomic Drivers Of Cutaneous Squamous Cell Carcinoma Development,
2016
The University of Texas Graduate School of Biomedical Sciences at Houston
Genomic Drivers Of Cutaneous Squamous Cell Carcinoma Development, Vida Chitsazzadeh
Dissertations and Theses (Open Access)
Skin cancer is the most common malignancy in humans. Annually, in U.S. there are over 3 million cases with an estimated overall economic impact of $2 billion. Cutaneous Squamous Cell Carcinoma (cuSCC) comprises 15-20% of all skin cancers. cuSCC has the best-defined progression from a distinct precancerous lesion, the Actinic Keratosis (AK), to invasive cuSCC. Destructive therapies for AK treatment must be used repetitively, causing significant morbidity. There is a tremendous need for targeted diagnostics and therapy for AKs, representing an important opportunity for secondary skin cancer prevention. Our knowledge of the molecular and cellular events that lead to the …
Investigating Metastatic Lineage In Colorectal Cancer By Single Cell Dna Sequencing,
2016
The University of Texas Graduate School of Biomedical Sciences at Houston
Investigating Metastatic Lineage In Colorectal Cancer By Single Cell Dna Sequencing, Marco Leung
Dissertations and Theses (Open Access)
Metastasis is the primary cause of human cancer deaths. Patients with metastatic colorectal cancer (mCRC) show only an 11% 5-year survival rate, compared to those without local or distant metastases (92% 5-year survival rate). Understanding the CRC tumor evolution may provide valuable insights on how to improve treatment in patients with mCRC. However, the genomic basis of metastasis has been difficult to study, in part due to the extensive intratumor heterogeneity at both the primary and metastatic tumor sites, and the low frequency of subclones with metastatic potential. Previous studies have applied conventional bulk next-generation sequencing (NGS) methods, which have …
Accurate Mutation Annotation And Functional Prediction Enhance The Applicability Of -Omics Data In Precision Medicine,
2016
The University of Texas Graduate School of Biomedical Sciences at Houston
Accurate Mutation Annotation And Functional Prediction Enhance The Applicability Of -Omics Data In Precision Medicine, Tenghui Chen
Dissertations and Theses (Open Access)
Clinical sequencing has been recognized as an effective approach for enhancing the accuracy and efficiency of cancer patient management and therefore achieve the goals of personalized therapy. However, the accuracy of large scale sequencing data in clinics has been constrained by many different aspects, such as clinical detection, annotation and interpretation of the variants that are observed in clinical sequencing data. In my Ph.D thesis work, I mainly investigated how to comprehensively and efficiently apply high dimensional -omics data to enhance the capability of precision cancer medicine. Following this motivation, my dissertation has been focused on two important topics in …
The Microbiome Of The Built Environment: A Large-Scale Citizen Science Genomics Project,
2016
University of Alabama in Huntsville
The Microbiome Of The Built Environment: A Large-Scale Citizen Science Genomics Project, Christopher Garrett Wilson
Honors Capstone Projects and Theses
No abstract provided.
Biology, Gene Flow, And Management Of Glyphosate-Resistant Common Waterhemp (Amaranthus Rudis Sauer) In Nebraska,
2016
University of Nebraska-Lincoln
Biology, Gene Flow, And Management Of Glyphosate-Resistant Common Waterhemp (Amaranthus Rudis Sauer) In Nebraska, Debalin Sarangi
Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research
Common waterhemp is the most troublesome weed in the midwestern United States. Growers from Nebraska reported failure to control common waterhemp following sequential applications of glyphosate in glyphosate-tolerant corn and soybean, which led to moderate to severe yield loss; justifying the need to confirm resistance and study the biology and management of common waterhemp. The objectives of this research were: 1) to confirm the presence of glyphosate-resistant (GR) common waterhemp biotypes in Nebraska and to evaluate their sensitivity to herbicides belonging to alternative sites-of-action; 2) to evaluate the response of common waterhemp to water stress; 3) to quantify pollen-mediated gene …
The Effects Of Chronic Partial Sleep Deprivation On Alcohol Consumption And Delta Fos B Accumulation,
2016
James Madison University
The Effects Of Chronic Partial Sleep Deprivation On Alcohol Consumption And Delta Fos B Accumulation, Kristian Ponder
Showcase of Graduate Student Scholarship and Creative Activities
The present study explores the relation between sleep restriction and alcohol use and the neural substrates that result from chronic behaviors, such as transcription factors. Transcription factor activity is suggested as a possible outcome of chronic behaviors, such as addiction. Sleep is discussed as possible mediating factor in the relationship between specific transcription factors and alcohol. Analysis will focus on brain areas related to both sleep and reward.
The Genomic Cds Sandbox: An Assessment Among Domain Experts.,
2016
Children's Mercy Kansas City
The Genomic Cds Sandbox: An Assessment Among Domain Experts., Ayesha Aziz, Kensaku Kawamoto, Karen Eilbeck, Marc S Williams, Robert R Freimuth, Mark A Hoffman, Luke V Rasmussen, Casey L Overby, Brian H Shirts, James M Hoffman, Brandon M Welch
Manuscripts, Articles, Book Chapters and Other Papers
Genomics is a promising tool that is becoming more widely available to improve the care and treatment of individuals. While there is much assertion, genomics will most certainly require the use of clinical decision support (CDS) to be fully realized in the routine clinical setting. The National Human Genome Research Institute (NHGRI) of the National Institutes of Health recently convened an in-person, multi-day meeting on this topic. It was widely recognized that there is a need to promote the innovation and development of resources for genomic CDS such as a CDS sandbox. The purpose of this study was to evaluate …
