Genetics and Genomics Commons^™

Kaposi’S Sarcoma At The University Teaching Hospital, Lusaka, Zambia In The Antiretroviral Therapy Era, Owen Ngalamika, Veenu Minhas, Charles Wood

Nebraska Center for Virology: Faculty Publications

With great interest, we read the recent publication “Kaposi’s sarcoma in HIV-infected patients in South Africa: Multicohort study in the antiretroviral therapy era” by Bohlius et al. We congratulate the authors for their contribution to this field. In this study the authors observed a decrease in incidence of Kaposi’s sarcoma (KS) in patients treated with anti-retroviral therapy (ART) when compared to patients who are not on ART. These results are encouraging because of the ongoing HIV epidemic in sub-Saharan Africa where KS is still one of the most prevalent cancers. Also, it is a relevant topic to study in …

Activation And Degradation Of Open Reading Frame 45 By The Replication And Transcription Activator Of Kaposi's Sarcoma-Associated Herpesvirus, Ying Wang, Kai Yu, Xiuzhi Pei, Tiancheng Zhang, Yuying Guo, Charles Wood, Jinzhong Wang

Nebraska Center for Virology: Faculty Publications

The open reading frame 45 (ORF45) of the Kaposi's sarcoma-associated herpesvirus (KSHV) is an immediate-early phosphorylated tegument protein critical for viral escape from host immune surveillance. Its expression is upregulated by the viral replication and transcription activator (RTA), a key protein that controls the switch from latency to lytic replication. We report here that ORF45 expression was not only upregulated by RTA, but ORF45 could also be degraded by RTA in a proteasome-dependent manner. The ORF45 was activated by RTA via activation of the ORF45 promoter, and the promoter region from nt 69 271 to nt 69 026 was involved. …

Single-Dose Cpg Immunization Protects Against A Heterosubtypic Challenge And Generates Antigen-Specific Memory T Cells, Alexander J. Vogel, Deborah M. Brown

Nebraska Center for Virology: Faculty Publications

Despite extensive research, influenza A virus (IAV) remains a major cause of morbidity, mortality, and healthcare expenditure. Emerging pandemics from highly pathogenic IAV strains, such as H5N1 and pandemic H1N1, highlight the need for universal, crossprotective vaccines. Current vaccine formulations generate strain-specific neutralizing antibodies primarily against the outer coat proteins, hemagglutinin and neuraminidase. In contrast to these highly mutable proteins, internal proteins of IAV are more conserved and are a favorable target for developing vaccines that induce strong T cell responses in addition to humoral immunity. Here, we found that intranasal administration with a single dose of CpG and inactivated …

Long-Acting Parenteral Combination Antiretroviral Loaded Nano-Drug Delivery System To Treat Chronic Hiv-1 Infection: A Humanized Mouse Model Study, Subhra Mandal, Guobin Kang, Pavan Kumar Prathipati, Wenjin Fan, Qingsheng Li, Christopher J. Destache

Nebraska Center for Virology: Faculty Publications

Human immunodeficiency virus (HIV) patients are often diagnosed in the chronic stage of HIV/AIDS. Combination antiretroviral therapy (cART) has improved quality of life for HIV-infected patients. Present study describes a novel long-acting parenteral formulation of combination antiretroviral (cARV) loaded nano-drugs for treating chronic HIV-1 (cHIV) in a humanized-BLT (hu-BLT) mice model. The cARV (elvitegravir + tenofovir alafenamide + emtricitabine; EVG + TAF + FTC) drugs (mimicking marketed Genvoy® one-pill for HIV-treatment) were encapsulated in poly (lactic-co-glycolic acid) nanoparticles (NPs). To establish cHIV, hu-BLT mice were intravaginally challenged with HIV-1 and maintained for 15 weeks. Plasma viral load (pVL) was monitored …

The Complexities Of Female Mate Choice And Male Polymorphisms: Elucidating The Role Of Genetics, Age, And Mate-Choice Copying, Kasey D. Fowler-Finn, Laura Sullivan-Beckers, Amy M. Runck, Eileen A. Hebets

Eileen Hebets Publications

Genetic, life history, and environmental factors dictate patterns of variation in sexual traits within and across populations, and thus the action and outcome of sexual selection. This study explores patterns of inheritance, diet, age, and mate-choice copying on the expression of male sexual signals and associated female mate choice in a phenotypically diverse group of Schizocosa wolf spiders. Focal spiders exhibit one of two male phenotypes: ‘ornamented’ males possess large black brushes on their forelegs, and ‘non-ornamented’ males possess no brushes. Using a quantitative genetics breeding design in a mixed population of ornamented/non-ornamented males, we found a strong genetic basis …

Octopamine Levels Relate To Male Mating Tactic Expression In The Wolf Spider Rabidosa Punctulata, Eileen A. Hebets, Matthew Hansen, Thomas C. Jones, Dustin J. Wilgers

Eileen Hebets Publications

In the wolf spider Rabidosa punctulata, upon encountering a female, males use one of two distinct strategies: (1) they court the female in an attempt to elicit a mating, or (2) they engage in a direct-mount tactic that involves extensive grappling with the female until a mating is achieved. The latter tactic appears more sexually aggressive, and both tactics come with the risk of being cannibalized. We explored the physiological mechanisms underlying this behavioral variation by assessing the relationship between circulating levels of the biogenic amine octopamine (OA), a neuromodulator suggested to play a role in “fight or flight” responses …

Functional Approach To Condition, Dustin J. Wilgers, Eileen A. Hebets

Eileen Hebets Publications

Animal signaling is commonly thought to be costly. Signaling costs can arise via a variety of avenues, including energy expenditure, predator attraction, and so on (reviews in Zuk and Kolluru, 1998; Kotiaho, 2001), and are predicted to increase with signal expression (e.g., size, amplitude, and intensity; Johnstone, 1997). Due to these costs, signaler condition, which is hypothesized to be a reflection of a signaler’s genetic quality, is expected to influence the level of signal expression one can afford (Zahavi, 1975), resulting in a positive correlation between signaler condition and signal expression – that is, condition-dependent signaling (Zahavi, 1977; West-Eberhard, 1979; …

Oxygenation Properties And Isoform Diversity Of Snake Hemoglobins, Jay F. Storz, Chandrasekhar Natarajan, Hideaki Moriyama, Federico G. Hoffmann, Tobias Wang, Angela Fago, Hans Malte, Johannes Overgaard, Roy E. Weber

Jay F. Storz Publications

Available data suggest that snake hemoglobins (Hbs) are characterized by a combination of unusual structural and functional properties relative to the Hbs of other amniote vertebrates, including oxygenation-linked tetramer-dimer dissociation. However, standardized comparative data are lacking for snake Hbs, and the Hb isoform composition of snake red blood cells has not been systematically characterized. Here we present the results of an integrated analysis of snake Hbs and the underlying α- and β-type globin genes to characterize 1) Hb isoform composition of definitive erythrocytes, and 2) the oxygenation properties of isolated isoforms as well as composite hemolysates. We used species from …

Generation Of An Attenuated, Cross-Protective Pepino Mosaic Virus Variant Through Alignment-Guided Mutagenesis Of The Viral Capsid Protein, Godwill M. Chewachong, Sally A. Miller, Joshua J. Blakeslee, David M. Francis, Thomas Jack Morris, Feng Qu

School of Biological Sciences: Faculty Publications

Mild variants of many viruses are able to protect infected plants from subsequent invasion by more severe variants of the same viruses through a process known as cross-protection. In the past, the cross-protective viral variants were commonly derived from mild field isolates that were sometimes genetically heterogeneous, providing variable levels of crossprotection. Here, we report a novel approach to rapidly generate crossprotective variants of the tomato-infecting Pepino mosaic virus (PepMV) independently of the availability of mild field isolates. Our approach sought to attenuate PepMV by mutating less conserved amino acid residues of the abundantly produced capsid protein (CP). These less-conserved …

Genetically Based Low Oxygen Affinities Of Felid Hemoglobins: Lack Of Biochemical Adaptation To High-Altitude Hypoxia In The Snow Leopard, Jan E. Janecka, Simone S. E. Nielsen, Sidsel D. Andersen, Federico G. Hoffmann, Roy E. Weber, Trevor Anderson, Jay F. Storz, Angela Fago

School of Biological Sciences: Faculty Publications

Genetically based modifications of hemoglobin (Hb) function that increase blood–O₂ affinity are hallmarks of hypoxia adaptation in vertebrates. Among mammals, felid Hbs are unusual in that they have low intrinsic O₂ affinities and reduced sensitivities to the allosteric cofactor 2,3-diphosphoglycerate (DPG). This combination of features compromises the acclimatization capacity of blood–O2 affinity and has led to the hypothesis that felids have a restricted physiological niche breadth relative to other mammals. In seeming defiance of this conjecture, the snow leopard (Panthera uncia) has an extraordinarily broad elevational distribution and occurs at elevations above 6000 m in the Himalayas. Here, …

Characterization Of The Ecological Role Of Genes Mediating Acid Resistance In Lactobacillus Reuteri During Colonization Of The Gastrointestinal Tract, Janina A. Krumbeck, Nathan L Marsteller, Steven Frese, Daniel A. Peterson, Amanda Ramer-Tait, Robert W. Hutkins, Jens Walter

Department of Food Science and Technology: Faculty Publications

Rodent-derived strains of Lactobacillus reuteri densely colonize the forestomach of mice and possess several genes whose predicted functions constitute adaptations towards an acidic environment. The objective of this study was to systematically determine which genes of L. reuteri 100-23 contribute to tolerance towards host gastric acid secretion. Genes predicted to be involved in acid resistance were inactivated, and their contribution to survival under acidic conditions was confirmed in model gastric juice. Fitness of five mutants that showed impaired in vitro acid resistance were then compared through competition experiments in ex-germ-free mice that were either treated with omeprazole, a proton-pump inhibitor …

Steps In Metagenomics: Let’S Avoid Garbage In And Garbage Out, Jacques Izard

Department of Food Science and Technology: Faculty Publications

Is metagenomics a revolution or a new fad? Metagenomics is tightly associated with the availability of next-generation sequencing in all its implementations. The key feature of these new technologies, moving beyond the Sanger-based DNA sequencing approach, is the depth of nucleotide sequencing per sample.Knowing much more about a sample changes the traditional paradigms of “What is the most abundant?” or “What is the most significant?” to “What is present and potentially sig­nificant that might influence the situation and outcome?” Let’s take the case of identifying proper biomarkers of disease state in the context of chronic disease prevention. Prevention has been …

Gene Expression And Alzheimer's Disease: Evaluation Of Gene Expression Patterns In Brain And Blood For An Alzheimer's Disease Mouse Model, Amanda Hazy

Senior Honors Theses

Previous studies have established a causative role for altered gene expression in development of Alzheimer’s disease (AD). These changes can be affected by methylation and miRNA regulation. In this study, expression of miRNA known to change methylation status in AD was assessed by qPCR. Genome-wide expression changes were determined by RNA-sequencing of mRNA from hippocampus and blood of control and AD mice. The qPCR data showed significantly increased expression of Mir 17 in AD, and sequencing data revealed 230 genes in hippocampus, 58 genes in blood, and 8 overlapping genes showing significant differential expression (p value ≤ 0.05). Expression data …

Hif-Independent Responses In Hypoxia, Divya Padmanabha

Theses and Dissertations

The adaptive response to hypoxia is accompanied by widespread transcriptional changes that allow for prolonged survival in low oxygen. Many of these changes are directly regulated by the conserved hypoxia-inducible factor-1 (HIF-1) complex; however, even in its absence, many oxygen-sensitive transcripts in Caenorhabditis elegans are appropriately regulated in hypoxia. To identify mediators of these non-HIF-dependent responses, I established a hif-1 mutant reporter line that expresses GFP in hypoxia or when worms are treated with the hypoxia mimetic cobalt chloride (cobalt chloride). The reporter is selective and HIF-independent, in that it remains insensitive to a number of cellular stresses, but is …

Global Analysis Of Gene Expression And Projection Target Correlations In The Mouse Brain, Ahmed Fakhry, Tao Zeng, Hanchuan Peng, Shuiwang Ji

Computer Science Faculty Publications

Recent studies have shown that projection targets in the mouse neocortex are correlated with their gene expression patterns. However, a brain-wide quantitative analysis of the relationship between voxel genetic composition and their projection targets is lacking to date. Here we extended those studies to perform a global, integrative analysis of gene expression and projection target correlations in the mouse brain. By using the Allen Brain Atlas data, we analyzed the relationship between gene expression and projection targets. We first visualized and clustered the two data sets separately and showed that they both exhibit strong spatial autocorrelation. Building upon this initial …

Smoking Patterns Among Vcu Students, Jasmine Saini

UROP Posters

For some individuals, college can be a high risk time for the development of problems associated with alcohol use and other substances. The purpose of this study is to examine these initiation and use patterns as they relate to nicotine use among college students 18 years of age and older enrolled in Spit for Science: The VCU Student Survey. The Spit for Science research project evaluates how genetic and environmental factors contribute to substance use and emotional health among college students at VCU. This study uses data from the Spit for Science 2011 cohort (n=2007) to investigate smoking patterns among …

Increasing Knowledge About Alpha-1 Antitrypsin Deficiency In The Chronic Obstructive Pulmonary Disease Population, Maureen Ann Wentink Barta

Walden Dissertations and Doctoral Studies

The purpose of the project was to increase awareness about alpha-1 antitrypsin deficiency (AATD) in chronic obstructive pulmonary disease (COPD), particularly among those with a familial history of genetic factor AATD; an additional goal was to understand its relationship to COPD. COPD is the third leading cause of death in the United States, with more than half of COPD patients experiencing significant disabilities. Major causes for COPD include smoking, air pollution, secondary smoke, upper respiratory infections, hereditary factors, occupational factors, environmental factors, and socioeconomic factors. Genetic factors, however, also play a significant role in early onset COPD and in those …

Hash-Map-Eradicator: Filtering Non-Target Sequences From Next Generation Sequencing Reads, Jonathon Brenner, Catherine Putonti

Bioinformatics Faculty Publications

Contemporary DNA sequencing technologies are continuously increasing throughput at ever decreasing costs. Moreover, due to recent advances in sequencing technology new platforms are emerging. As such computational challenges persist. The average read length possible has taken a giant leap forward with the PacBio and Nanopore solutions. Regardless of the platform used, impurities within the DNA preparation of the sample - be it from unintentional contaminants or pervasive symbiots - remains an issue. We have developed a new tool, HAsh-MaP-ERadicator (HAMPER), for the detection and removal of non-target, contaminating DNA sequences. Integrating hash-based and mapping-based strategies, HAMPER is both memory and …

Characterization Of Suspected Cyclic Di-Gmp Metabolizing Genes In Streptomyces Scabies, Bridget N. Bickers

Undergraduate Honors Thesis Projects

Streptomyces scabies is a bacterial plant pathogen responsible for a condition known as common scab in potatoes and other tuber crops. Aerial hyphae and spore development have been shown to be regulated by cyclic di-GMP (c-di-GMP) signaling in the non-pathogenic species Streptomyces coelicolor and Streptomyces venezuelae. The second messenger c-di-GMP is ubiquitous among bacteria and is connected to many functions such as: motility, virulence, and biofilm formation, but the effects of c-di-GMP signaling in other streptomycetes are unknown. The purpose of this study is to elucidate the function of the suspected S. scabies c-di-GMP phosphodiesterase genes SCAB11501 and SCAB27241 …

Characterization Of Transfer Of The Mobile Genomic Island Encoding Methicillin Resistance Among Staphylococci, Melissa D. Ray

Theses and Dissertations

The gene encoding methicillin resistance in Staphylococcus aureus (MRSA) is carried in the chromosome on a large genomic island called SCCmec and is always inserted at the att site within orfX. SCCmec has been designated a mobile genetic element but a mechanism by which it moves among different strains and species of staphylococci has never been demonstrated. This work shows that bacteriophage 80α is capable of transducing SCCmec into a recipient cell, after which it can integrate into the bacterial chromosome via homologous recombination. More importantly, this work characterizes a conjugative mechanism of SCCmec transfer. …

Investigating The Role Of The Nucleosome Remodeling Factor Nurf As A Regulator Of Gene Expression, Aiman S. Alhazmi

Theses and Dissertations

The nucleosome remodeling factor (NURF) is an evolutionary conserved ATP-dependent chromatin remodeling factor. It was first isolated from Drosophila as a complex with enzymatic activity that once recruited to nucleosome, it slides the nucleosome to provide accessibility for transcription factors. Since then, numerous works from animal models and cell lines show the role of NURF as a regulator of gene expression. NURF interacts with H3K4me3 and sequence specific transcription factors that recruit the complex to promoter regions. Whether this is the only mechanism by which NURF regulates gene expression is not known. However, other ATP-dependent chromatin remodeling complexes are known …

Phenotypic Characterization Of Pnpase Knockdown In C. Elegans, Laura A. Lambert

Theses and Dissertations

The multifunctional exoribonuclease protein PNPase is implicated as a potential target for cancer therapy as well as causing mitochondrial disorders in humans, but there has yet to be a whole animal knockdown model created. In this study, C. elegans was used to investigate the effect of knocking down pnpt-1, the gene that encodes PNPase. It was discovered that pnpt-1 knockdown significantly extends lifespan via an increase in superoxide production similar to other known mitochondrial lifespan extension pathways. Additionally, mitochondrial networks, size and respiration are affected indication of other mitochondrial dysfunction..

PNPase is also known to transport small RNAs into the …

Investigation Into The Specification Of Nurf Recruitment To The Genome, Marissa Mack

Theses and Dissertations

The nucleosome remodeling factor (NURF) is a mutli-protein complex that plays a role in the regulation of gene expression through its ability to remodel nucleosomes. The largest subunit of this complex, Bptf (Bromodomain PHD Finger Transcription Factor) is important for many cellular processes as a transcriptional regulator and improper function results in disease or malignancy. To further understand the genome-wide recruitment of the NURF complex, the interaction partner for the N-terminal PHD finger domain of Bptf was investigated through pull down assays followed by mass spectrometry. It was determined that this domain does not recognize histones; instead it recognizes a …

Functional Analysis Of The Ovarian Cancer Susceptibility Locus At 9p22.2 Reveals A Transcription Regulatory Network Mediated By Bnc2 In Ovarian Cells, Melissa Buckley

USF Tampa Graduate Theses and Dissertations

GWAS have identified several chromosomal loci associated with ovarian cancer risk. However, the mechanism underlying these associations remains elusive. We identify candidate functional Single Nucleotide Polymorphisms (SNPs) at the 9p22.2 ovarian cancer susceptibility locus, several of which map to transcriptional regulatory elements active in ovarian cells identified by FAIRE-seq (Formaldehyde assisted isolation of regulatory elements followed by sequencing) and ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) in relevant cell types. Reporter and electrophoretic mobility shift assays (EMSA) determined the extent to which candidate SNPs had allele specific effects. Chromosome conformation capture (3C) reveals a physical association between Basonuclin 2 (BNC2) and …

Postmitotic Expression Of Sod1g93a Gene Affects The Identity Of Myogenic Cells And Inhibits Myoblasts Differentiation, M. Martini, G. Dobrowolny, M. Aucello, Antonio Musaro

Research outputs 2014 to 2021

To determine the role of mutant SOD1 gene (SOD1G93A) on muscle cell differentiation, we derived C2C12 muscle cell lines carrying a stably transfected SOD1G93A gene under the control of a myosin light chain (MLC) promoter-enhancer cassette. Expression of MLC/SOD1G93A in C2C12 cells resulted in dramatic inhibition of myoblast differentiation. Transfected SOD1G93A gene expression in postmitotic skeletal myocytes downregulated the expression of relevant markers of committed and differentiated myoblasts such as MyoD, Myogenin, MRF4, and the muscle specific miRNA expression. The inhibitory effects of SOD1G93A gene on myogenic program perturbed Akt/p70 and MAPK signaling pathways which promote differentiation cascade. Of note, …

Carnivore Diet Identification Through Scat And Genetic Analysis In Namibia, Africa, Alicia J. Walsh

Honors Theses and Capstones

Worldwide the cheetah population is declining making them Africa’s most endangered large cat. Namibia, Africa currently has the largest population of cheetahs in the world. During the summer of 2014, I did scat analysis of carnivores on the property of the Cheetah Conservation Fund (CCF) in Namibia in order to better understand the predators that compete with the cheetah and how the ecosystem works as a whole. I worked at CCF for nine weeks to analyze the diets of carnivores in the area through genetic and scat analysis. Analyzing carnivore feces would ultimately identify the diet of various carnivores in …

Fungicide Resistance Genetics Of Apple Scab Fungus Venturia Inaequalis, Alexis Lt Reddel

Honors Theses and Capstones

Apple scab, caused by the ascomycete fungus Venturia inaequalis, is considered the most devastating disease on domestic apple crops. Apples are the most important cultivated crop in temperate regions and the United States produced about 4.6 million tons of apples in 2010. Traditional methods to control fungal plant diseases like apple scab are based on the use of chemical compounds that may produce serious negative effects, mainly related with environmental pollution and the development of fungicide resistance. Identifying genes and mechanisms of fungicide resistance in V. inaequalis is imperative to developing new and more effective defenses against the spread …

The Significance Of Crispr/Cas9-Directed Cul3 Knockout On Human Colorectal Cancer Cells, Zoe A. Lautz

Departmental Honors Projects

Cancer, the second leading cause of death in the US, is caused by mutations in select genes that alter cellular function leading to uncontrolled proliferation. Understanding the specific genes that drive cancer can lead to the generation of novel cancer therapies. To identify novel genes that drive cancer in the colon (CRC), lungs, and ovaries in mice, Starr et al. employed a transposon-based insertional mutagenesis system. One of the genes identified, APC, is mutated in 70-80% of human CRCs. CUL3, suspected to be a general driver gene, was discovered in the lung cancer screen. CUL3 was analyzed for its role …

Primer Efficacy In The Dna Barcoding Of Spiders, Rhennetta Jo Bork

Honors Program Theses

DNA barcoding is the process of amplifying a 650 base pair segment of the sequence of the mitochondrial gene cytochrome c oxidase (COI), and amplifying this gene with a polymerase chain reaction (PCR). It is used to help identify and distinguish animal species and also to help determine genetic differences in species. DNA barcoding can be especially useful when working with spiders since they tend to be very small and hard to distinguish. However, achieving a DNA barcode can be difficult and thus techniques to improve the method of DNA barcoding can be helpful. This research looked into the different …

Drosophila Muller F Elements Maintain A Distinct Set Of Genomic Properties Over 40 Million Years Of Evolution, Wilson Leung, Christopher D. Shaffer, Laura K. Reed, Sheryl T. Smith, Randall J. Dejong, Arlene J. Hoogewerf

University Faculty Publications and Creative Works

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have …