Genetics and Genomics Commons^™

Review Of "Race Unmasked: Biology And Race In The Twentieth Century" By M. Yudell, John B. Jenkins

Biology Faculty Works

No abstract provided.

Expression Of Insulin Responsive Genes In Insulin Resistant Conditions, And The Effect Of Selenium On Gene Expression, David L. Ruff

Masters Theses

Chronically high blood glucose levels lead to many problems, such as insulin resistance, the hallmark of Type II diabetes. Increased flux through the hexosamine biosynthesis pathway is one mechanism by which high glucose as well as glucosamine has been shown to induce insulin resistance. This study tests the effects of glucosamine induced insulin resistance on insulin regulation of the metabolic genes glucose-6-phosphate dehydrogenase (G6PDH) and fatty acid synthase (FAS) as well as insulin responsive proteins tribbles homolog (TRIB3) and sterol regulatory element binding protein (SERBP-1c) 1c.

Selenium, a micronutrient has been shown to be an effective insulin mimetic in Type …

Role Of B Cell Receptor Signaling In Il-10 Production By Normal And Malignant B-1 Cells., Sara S Alhakeem, Vishal J Sindhava, Mary K Mckenna, Beth W Gachuki, John C Byrd, Natarajan Muthusamy, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

B-1 cells are considered innate immune cells, which produce the majority of natural antibodies. B-1 cell responses to B cell receptor (BCR) and Toll-like receptor ligation are tightly regulated owing to the cross-reactivity to self-antigens. CD5 has been shown to play a major role in downregulation of BCR responses in B-1 cells. Here, we provide evidence for another mechanism by which BCR response is regulated in B-1 cells. B-1 cells, as well as their malignant counterpart, B cell chronic lymphocytic leukemia (B-CLL) cells, produce interleukin-10 (IL-10) constitutively. IL-10 secretion by normal B-1 cells downregulates their proliferation responses to BCR ligation. …

Post Operative Fungal Endopthalmitis Due To Geotrichum Candidum, Thein Myint, Matthew J. Dykhuizen, Carolyn H. Mcdonald, Julie A. Ribes

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Geotrichum species have been rarely reported as the cause of sepsis, disseminated infection in immunosuppressed patients. The patient we describe developed indolent endophthalmitis four months after her routine right eye cataract surgery. The intraoperative sample from right vitreous fluid grew Geotrichum candidum. The patient underwent vitrectomy, artificial lens explantation and intravitreal injection of amphotericin B followed by oral voriconazole. Despite these interventions, she underwent enucleation. This is the first published case of Geotrichum candidum endophthalmitis.

Atmospheric Nitrogen Assimilation In Ustilago Maydis., Michael Cooper

Electronic Theses and Dissertations

Nitrogen is an essential nutrient for all living creatures. Ammonium is one of the most efficiently used and thus preferred, sources of nitrogen. As with other dimorphic fungi, yeast-like cells of Ustilago maydis, a fungal pathogen of maize, switches to filamentous growth when starved for nitrogen/ammonium. U. maydis carries two genes, ump1 and ump2, encoding ammonium transporters that facilitate both uptake of ammonium and the filamentous response to its absence. While no obvious phenotype is observed when ump1 is deleted, cells without ump2 are unable to filament in response to low ammonium, although they can still grow. Surprisingly, …

Genomic And Transcriptomic Analyses Of Microbotryum Lychnidis-Dioicae Provide Insights Into The Biology Of A Fascinating Fungal Phytopathogen., Su San Toh

Electronic Theses and Dissertations

This study made use of the Silene latifolia/Microbotryum lychnidis-dioicae phytopathogen system as the focal system to establish the first reference genome for Microbotryum violaceum sensu lato. In silico analysis was performed on the genome assembly to identify various characteristics of the genome. Using RNA-Sequencing technologies on the Illumina platform, we collected transcriptomic data for both in vitro and in planta life stages of the fungus, providing the most comprehensive look at the gene expression and regulation of this fungus. Due to a lack of identifiable domains on the predicted genes, gene set enrichment analysis was done in …

Genome Rearrangements Can Make And Break Small Rna Genes, Rahul Raghavan, Fenil R. Kacharia, Jess A. Millar, Christine Demko Sislak, Howard Ochman

Biology Faculty Publications and Presentations

Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in …

A Survey Of The Common Loon (Gavia Immer) Genome Reveals Patterns Of Natural Selection, Zach G. Gayk

All NMU Master's Theses

With rapid advances in Next-Generation Sequencing technology, comparative genomics has become a viable method for studying the adaptation of species to their environment at the genome level. I investigated this in common loons (Gavia immer)—for which molecular adaptation has not been characterized—by finding signatures of positive selection as evidence for genomic adaptation.

I used Illumina short read sequencing data from a single female common loon to produce a fragmented assembly of the common loon (Gavia immer) genome. The resulting assembly had a contig N50 of 814 bp, a total length of 767,326,331 bp, and 45.7 % …

Preventing Thymus Involution In K5.Cyclin D1 Transgenic Mice Sustains The Naïve T Cell Compartment With Age, Michelle L. Bolner

Dissertations and Theses (Open Access)

The thymus maintains T cell receptor (TCR) repertoire diversity through perpetual release of self-MHC restricted naive T cells. However, thymus involution during the aging process reduces naïve T cell output, leading to defective immune responsiveness to newly encountered antigens. We have found that early thymus involution precipitates the age-associated shift favoring memory T cell dominancy in young control mice. Furthermore, we have shown that age-related thymus involution is prevented in mice expressing a keratin 5 promoter-driven Cyclin D1 (K5.D1) transgene in thymic epithelial cells (TECs). Thymopoiesis occurs normally in K5.D1 transgenic thymi and sustains T cell output to prevent the …

A Platform For Fast Detection Of Let-7 Micro Rna Using Polyaniline Fluorescence And Image Analysis Techniques, Partha P. Sengupta

Master's Theses

The project describes a new strategy for transducing hybridization events through modulating intrinsic properties of the electroconductive polymer polyaniline (PANI). When DNA based probes electrostatically interact with PANI, its fluorescence properties are increased, a phenomenon that can be enhanced by UV irradiation. Hybridization of target nucleic acids results in dissociation of probes causing PANI fluorescence to return to basal levels. By monitoring restoration of base PANI fluorescence as little as 10^-11 M (10 pM) of target oligonucleotides could be detected within 15 minutes of hybridization. Detection of complementary oligos was specific, with introduction of a single mismatch failing to …

In Vivo Functional Significance Of Ccat2 Long Non-Coding Rna In Myelodysplastic Syndrome, Maitri Y. Shah

Dissertations and Theses (Open Access)

Long non-coding RNAs form the largest part of the mammalian non-coding transcriptome and control gene expression at various levels including chromatin modification, transcriptional and post-transcriptional processing. Although the underlying molecular mechanisms are not yet entirely understood, lncRNAs are implicated in initiation and progression of several cancers. CCAT2 is a lncRNA that spans the highly conserved 8q24 region associated with increased risk for various cancers. CCAT2 has been shown to play an important role in inducing chromosomal instability and supporting cell proliferation and cell cycle arrest. However, a causal role of CCAT2 in initiation of tumorigenesis and the importance of G/T …

Apply Data Clustering To Gene Expression Data, Abdullah Jameel Abualhamayl Mr.

Electronic Theses, Projects, and Dissertations

Data clustering plays an important role in effective analysis of gene expression. Although DNA microarray technology facilitates expression monitoring, several challenges arise when dealing with gene expression datasets. Some of these challenges are the enormous number of genes, the dimensionality of the data, and the change of data over time. The genetic groups which are biologically interlinked can be identified through clustering. This project aims to clarify the steps to apply clustering analysis of genes involved in a published dataset. The methodology for this project includes the selection of the dataset representation, the selection of gene datasets, Similarity Matrix Selection, …

Microrna-Mediated Plant Development And Response To Environmental Stress In Perennial Grasses, Shuangrong Yuan

All Dissertations

World population will pass nine billion by 2050, while the agricultural land area will not increase dramatically in the coming decades. To meet the ever-increasing food demand, genetically engineered crops have been rapidly adopted for crop productivity. MicroRNAs have become increasingly attractive as targets in crop genetic modification due to their regulatory role in fine-tuning many essential biological processes. My research explores the potentials of microRNA528 (miR528) and miR396 for use in genetic modifications of the important agronomic traits of plant development, abiotic stress response, and/or flowering time control in an economically and environmentally important perennial monocot species, creeping bentgrass …

Efficacy Of Galactooliosaccharide (Gos) And/Or Rhamnose-Based Synbiotics In Enhancing Ecological Performance Of Lactobacillus Reuteri In The Human Gut And Characterization Of Its Gos Metabolic System, Monchaya Rattanaprasert

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Probiotic L. reuteri has potential to produce antimicrobial compounds and secrete immunosuppressive factors. These metabolic attributes could benefit the human host by providing colonization resistance (competitive and metabolic exclusion) against enteropathogens and mitigating inflammation. As metabolically active cells are fundamental to such probiotic properties, synbiotic approaches that supply L. reuteri with a source(s) of carbon, energy, and/or external electron acceptor for cell growth in the gut environment could therefore prompt the probiotic to engage in beneficial activities. In this study, the efficacy of GOS and/or rhamnose-based synbiotic approaches in promoting colonization persistence and metabolic activity of L. reuteri was evaluated. …

Genetic Analyses Determine Connectivity Among Cave And Surface Populations Of The Jamaican Endemic Freshwater Crab Sesarma Fossarum In The Cockpit Country, Manuel Stemmer, Christoph D. Schubart

International Journal of Speleology

The Jamaican freshwater crab Sesarma fossarum (Decapoda: Brachyura: Sesarmidae) is endemic to western central Jamaica where it occurs in cave and surface streams of karst regions. In the present study, we examine the population genetic structure of the species, providing evidence for intraspecific differentiation and genetic substructure among twelve sampled populations. Interestingly, crabs from caves appear genetically undistinguishable from representatives of nearby surface waters, despite previously observed and described morphometric differentiation. In contrast, genetic isolation takes place among populations from rivers and caves belonging to different watersheds. In one case, even populations from different tributaries of the same river were …

Effects Of Shade And Feeding Zilpaterol Hydrochloride To Finishing Steers On Performance, Carcass Quality, Heat Stress, Mobility, And Body Temperature, Bradley M. Boyd, Steven D. Shackelford, Kristin E. Hales, Tami M. Brown-Brandl, Meredith L. Bremer, Matthew L. Spangler, T. L. Wheeler, D. A. King, Galen Erickson

Department of Animal Science: Faculty Publications

Steers (n = 480; 22% with black hides and 78% with red hides) were used to study the effects of shade and feeding zilpaterol hydrochloride (ZH) on performance, carcass quality, heat stress, mobility, and body temperature (BT). A randomized block design with a 2 × 2 factorial treatment arrangement was used with 4 replicates per treatment. Factors included housing type (open or shaded pens) and the feeding of ZH (0 or 8.33 mg/kg DM) the last 21 d on feed with a 3-d withdrawal. Cattle were blocked by BW into a heavy or light block and randomly assigned to pen …

Meta-Analysis Of Genome-Wide Association Studies With Correlated Individuals: Application To The Hispanic Community Health Study/Study Of Latinos (Hchs/Sol), Tamar Sofer, John R. Shaffer, Misa Graff, Qibin Qi, Adrienne M. Stilp, Stephanie M. Gogarten, Kari E. North, Carmen R. Isasi, Cathy C. Laurie, Adam A. Szpiro

UW Biostatistics Working Paper Series

Investigators often meta-analyze multiple genome-wide association studies (GWASs) to increase the power to detect associations of single nucleotide polymorphisms (SNPs) with a trait. Meta-analysis is also performed within a single cohort that is stratified by, e.g., sex or ancestry group. Having correlated individuals among the strata may complicate meta-analyses, limit power, and inflate Type 1 error. For example, in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), sources of correlation include genetic relatedness, shared household, and shared community. We propose a novel mixed-effect model for meta-analysis, “MetaCor", which accounts for correlation between stratum-specific effect estimates. Simulations show that MetaCor controls …

A Forward Genetic Screen Reveals Novel Independent Regulators Of Ulbp1, An Activating Ligand For Natural Killer Cells, Benjamin G Gowen, Bryan Chim, Caleb D. Marceau, Trever T Greene, Patrick Burr, Jeanmarie R. Gonzalez, Charles Hesser, Peter A. Dietzen, Teal Russell, Alexandre Iannello, Laurent Coscoy, Charles L. Sentman

Dartmouth Scholarship

Recognition and elimination of tumor cells by the immune system is crucial for limiting tumor growth. Natural killer (NK) cells become activated when the receptor NKG2D is engaged by ligands that are frequently upregulated in primary tumors and on cancer cell lines. However, the molecular mechanisms driving NKG2D ligand expression on tumor cells are not well defined. Using a forward genetic screen in a tumor-derived human cell line, we identified several novel factors supporting expression of the NKG2D ligand ULBP1. Our results show stepwise contributions of independent pathways working at multiple stages of ULBP1 biogenesis. Deeper investigation of selected hits …

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Biology Faculty Articles

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon …

The Genome Russia Project: Closing The Largest Remaining Omission On The World Genome Map, T. K. Oleksyk, Vladimir Brukhin, Stephen J. O'Brien

Biology Faculty Articles

We are witnessing the great era of genome exploration of the world, as genetic variation in people is being detailed across multiple varied world populations in an effort unprecedented since the first human genome sequence appeared in 2001. However, these efforts have yet to produce a comprehensive mapping of humankind, because important regions of modern human civilization remain unexplored. The Genome Russia Project promises to fill one of the largest gaps, the expansive regions across the Russian Federation, informing not just medical genomics of the territories, but also the migration settlements of historic and pre-historic Eurasian peoples.

Evidence Of Field-Evolved Resistance To Bifenthrin In Western Corn Rootworm (Diabrotica Virgifera Virgifera Leconte) Populations In Western Nebraska And Kansas, Adriano E. Pereira, Haichuan Wang, Sarah N. Zukoff, Lance Meinke, B. Wade French, Blair Siegfried

Department of Entomology: Faculty Publications

Pyrethroid insecticides have been used to control larvae or adults of the western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, a key pest of field corn in the United States. In response to reports of reduced efficacy of pyrethroids in WCR management programs in southwestern areas of Nebraska and Kansas the present research was designed to establish a baseline of susceptibility to the pyrethroid insecticide, bifenthrin, using susceptible laboratory populations and to compare this baseline with susceptibility of field populations. Concentration-response bioassays were performed to estimate the baseline susceptibility. From the baseline data, a diagnostic concentration (LC99) was determined and …

Effect Of Genetic Background On The Dystrophic Phenotype In Mdx Mice., William D Coley, Laurent Bogdanik, Maria Candida Vila, Qing Yu, Terence A Partridge, Kanneboyina Nagaraju, +12 Additional Authors

Genomics and Precision Medicine Faculty Publications

Genetic background significantly affects phenotype in multiple mouse models of human diseases, including muscular dystrophy. This phenotypic variability is partly attributed to genetic modifiers that regulate the disease process. Studies have demonstrated that introduction of the γ-sarcoglycan null allele onto the DBA/2J background confers a more severe muscular dystrophy phenotype than the original strain, demonstrating the presence of genetic modifier loci in the DBA/2J background. To characterize the phenotype of dystrophin deficiency on the DBA/2J background, we created and phenotyped DBA/2J-congenic Dmdmdx mice (D2-mdx) and compared them to the original, C57BL/10ScSn-Dmdmdx (B10-mdx) model. These strains were compared to their respective …

Age-Associated Methylation Suppresses Spry1, Leading To A Failure Of Re-Quiescence And Loss Of The Reserve Stem Cell Pool In Elderly Muscle., Anne Bigot, William J Duddy, Zamalou G Ouandaogo, Elisa Negroni, Virginie Mariot, Svetlana Ghimbovschi, Brennan Harmon, Aurore Wielgosik, Camille Loiseau, Joseph Devaney, Julie Dumonceaux, Gillian Butler-Browne, Vincent Mouly, Stéphanie Duguez

Genomics and Precision Medicine Faculty Publications

The molecular mechanisms by which aging affects stem cell number and function are poorly understood. Murine data have implicated cellular senescence in the loss of muscle stem cells with aging. Here, using human cells and by carrying out experiments within a strictly pre-senescent division count, we demonstrate an impaired capacity for stem cell self-renewal in elderly muscle. We link aging to an increased methylation of the SPRY1 gene, a known regulator of muscle stem cell quiescence. Replenishment of the reserve cell pool was modulated experimentally by demethylation or siRNA knockdown of SPRY1. We propose that suppression of SPRY1 by age-associated …

Playing God, Jeff Ploegstra

Faculty Work Comprehensive List

"Technically speaking, animals and plants that we have selectively bred are genetically modified organisms (GMOs)."

Posting about the benefits and dangers of genetic modification from In All Things - an online hub committed to the claim that the life, death, and resurrection of Jesus Christ has implications for the entire world.

http://inallthings.org/playing-god/

Population Genetics And Epigenetics Of Two Salt Marsh Plant Species Along An Environmental Gradient, Christy M. Foust

USF Tampa Graduate Theses and Dissertations

Phenotypic plasticity is the ability of a given genotype to exhibit different phenotypes in response to environmental variables, which can impact population level processes. Plasticity of ecologically-relevant traits is important to an organism’s environmental response; however, the underlying mechanisms of plasticity are largely unknown. Ecological epigenetics may offer mechanisms (e.g. DNA methylation) underlying phenotypic plasticity. Epigenetics can be defined as the underlying molecular mechanisms that allow one genotype to exhibit different phenotypes. Differential DNA methylation is one epigenetic mechanism that has been correlated with a number of ecologically-relevant traits; including, differential herbivory in Viola cazorlensis, spinescence in Ilex aquifolium …

Complete Genome Sequences Of Four Escherichia Coli St95 Isolates From Bloodstream Infections, Craig M. Stephens, Jeffrey M. Skerker, Manraj S. Sekhon, Adam P. Arkin, Lee W. Riley

Biology

Finished genome sequences are presented for four Escherichia coli strains isolated from bloodstream infections at San Francisco General Hospital. These strains provide reference sequences for four major fimH-identified sublineages within the multilocus sequence type (MLST) ST95 group, and provide insights into pathogenicity and differential antimicrobial susceptibility within this group.

Vegfa: Just One Of Multiple Mechanisms For Sex-Specific Vascular Development Within The Testis?, Kevin M. Sargent, Renee M. Sargent, Renata Spuri Gomes, Andrea S. Cupp

Department of Animal Science: Faculty Publications

Testis development from an indifferent gonad is a critical step in embryogenesis. A hallmark of testis differentiation is sex-specific vascularization which occurs as endothelial cells migrate from the adjacent mesonephros into the testis to surround Sertoli-germ cell aggregates and induce seminiferous cord formation. Many in vitro experiments have demonstrated that Vascular Endothelial Growth Factor A (VEGFA) is a critical regulator of this process. Both inhibitors to VEGFA signal transduction and excess VEGFA isoforms in testis organ cultures impaired vascular development and seminiferous cord formation. However, in vivo models using mice which selectively eliminated all VEGFA isoforms: in Sertoli and germ …

Evaluating Equations Estimating Change In Swine Feed Intake During Heat And Cold Stress, R. R. White, P. S. Miller, M. D. Hanigan

Department of Animal Science: Faculty Publications

The objectives of this study were to evaluate heat stress feed intake models for growing swine using a data set assembled from the literature and to develop a series of new equations modeling the influence of the thermal environment and interactions between the thermal environmental and other factors on feed intake. A literature survey was conducted to identify studies assessing intake responses to temperature. The resulting data set comprised 35 studies containing 120 comparisons to thermoneutral intake. Intake as a fraction of thermoneutral intake (FFI) was the primary response variable, where a value of 1 represented no change from thermoneutral …

Tuberculosis And Cardiovascular Disease: Linking The Epidemics, Moises A. Huaman, David Henson, Eduardo Ticona, Timothy R. Sterling, Beth A. Garvy

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The burden of tuberculosis and cardiovascular disease (CVD) is enormous worldwide. CVD rates are rapidly increasing in low- and middle-income countries. Public health programs have been challenged with the overlapping tuberculosis and CVD epidemics. Monocyte/macrophages, lymphocytes and cytokines involved in cellular mediated immune responses against Mycobacterium tuberculosis are also main drivers of atherogenesis, suggesting a potential pathogenic role of tuberculosis in CVD via mechanisms that have been described for other pathogens that establish chronic infection and latency. Studies have shown a pro-atherogenic effect of antibody-mediated responses against mycobacterial heat shock protein-65 through cross reaction with self-antigens in human vessels. Furthermore, …

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulos, Konstantin Laufer, George K. Thiruvathukal, Catherine Putonti

Bioinformatics Faculty Publications

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …