Gene Expression Under Combined Hypoxia And Acidosis In Chondrosarcoma, Michael Stacey, Kostika Vangjeli, Christopher Osgood

Bioelectrics Publications

Chondrosarcomas are the second most common cause of bone cancer and are removed surgically with wide margins. On recurrence, they are resistant to chemo and radiation therapy and new treatment options are critically required. This tumor type produces hyaline cartilage, a cartilage normally formed under hypoxic and acidic environment due to lack of vasculature in cartilage. Paradoxically, chondrosarcomas arise in the well vascularized, oxygen rich environment of the bone. Hypoxia and acidosis are two stressors where the cellular effects are typically reported separately even though cells experience combined effects of hypoxia and acidosis. Given the mechanistic links between hypoxia and …

Testing Evolutionary Conservation Of Sex Determination In Lepidoptera Using Crispr/Cas9 Gene Editing, Sophia Schroeder

Honors Theses

The mechanism of sex determination in Lepidoptera is largely unexplored, and limited to knowledge of only a few genes. Adult Lepidoptera have obvious sexually dimorphic qualities, such as their genitalia. However, significant sex determination genes are not imperative for the adult developmental stage. Knockouts of some sex determination genes (doublesex isoforms) are shown to be lethal in the embryonic and larval stages of development in several animals. However, it is unclear whether this is due to their respective impact on sex determination and sexual dimorphism, or the existence of another function, such as pleiotropy, within a particular gene. Moreover, …

Extracting High-Molecular Weight Dna From Cyanobacteria Using Promega's Wizard® Hmw Dna Extraction Kit With A Modified Protocol, Metis, Megan A. Hept, Lesley H. Greene

Chemistry & Biochemistry Faculty Publications

Extraction of high molecular weight (HMW) DNA for long read sequencing with little to no fragmentation and high purity is difficult to acquire from cyanobacterial species. Here we describe a modified method of extraction using Promega's Wizard® HMW DNA Extraction Kit to acquire high molecular weight DNA from cyanobacterial species. The protocol used in the kit is the “3.D. Isolating HMW DNA from Gram-Positive and Gram-Negative Bacteria” protocol. During a key step in the protocol, the lingering remnants of the mucilage layer of the cyanobacterial species is removed, preventing it from sticking to the DNA pellet produced. This customized modification …

Association Of Interpersonal Trauma And Polygenic Risk Scores With Depressive Symptoms In College Students, Rowan K. O'Hara

Theses and Dissertations

Major depression is considered a complex trait influenced by both polygenic risk factors and environmental exposures, such as childhood trauma. This study applied statistical genetic methods to calculate aggregate genetic risk for major depression to predict depressive symptoms scores in a college student sample. Data were from the Spit for Science (S4S) study in which college students from a large urban university self-reported interpersonal trauma (IPT) exposure prior to college and depressive symptoms from the past month (N = 7502; ancestry group: 20% African [AFR], 12% Admixed Americas [AMR], 10% East Asian [EAS], 49% European [EUR], 8% South Asian [SAS]). …

Evaluation Of Spliceai For Improved Genetic Variant Classification In Inherited Ophthalmic Disease Genes, Melissa Reeves

Theses and Dissertations

ABSTRACT

EVALUATION OF SPLICEAI FOR IMPROVED GENETIC VARIANT CLASSIFICATION IN INHERITED OPHTHALMIC DISEASE GENES

By Melissa Jean Reeves, Ph.D.

A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University.

Virginia Commonwealth University, 2023

Major Director: Melissa Jamerson, PhD, MLS(ASCP)

Associate Professor, Department of Medical Laboratory Sciences

Inherited ophthalmic diseases impact individuals around the globe. Inherited retinal diseases (IRDs) are the leading cause of blindness in individuals aged 15 to 45. The personal, social, and economic impact of vision loss is profound. Due to individual differences, symptoms can be variable, and …

Quantitative And Molecular Genetic Analyses Of Brain Structure, Substance Use, And Posttraumatic Stress Phenotypes: Data From Children, Adolescents And Adults, Daniel Bustamante

Theses and Dissertations

Abstract

QUANTITATIVE AND MOLECULAR GENETIC ANALYSES OF BRAIN-IMAGING, SUBSTANCE USE, AND POSTTRAUMATIC STRESS PHENOTYPES: DATA FROM CHILDREN, ADOLESCENTS AND ADULTS

By Daniel Bustamante, B.S., B.A.

Doctoral dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Integrative Life Sciences – Behavioral and Statistical Genetics at Virginia Commonwealth University.

Virginia Commonwealth University, 2023.

Dissertation directors: Michael C. Neale, Ph.D., Banks Distinguished Professor of Psychiatry & Human and Molecular Genetics; and, Ananda B. Amstadter, Ph.D., Professor of Psychiatry, Psychology, & Human and Molecular Genetics.

Substance use (SU) and posttraumatic stress disorder (PTSD) phenotypes are comorbid, share …

Novel Strategies In Head And Neck Tumor Therapy; Contribution Of Senescence In Therapy Response, And Resistance Development After Cisplatin Treatment, Fereshteh Ahmadinejad

Theses and Dissertations

Therapeutic outcomes achieved in head and neck squamous cell carcinoma (HNSCC) patients by concurrent cisplatin-based chemoradiotherapy initially reflect both tumor regression and tumor stasis. However, local, and distant metastasis and disease relapse as well as cisplatin-induced resistance are common in HNSCC patients. In the current work, we demonstrate that cisplatin treatment induces senescence in both p53 wild- type HN30 and p53 mutant HN12 head and neck cancer models. We also show that tumor cells can escape from senescence both in vitro and in vivo. We further established a cisplatin-resistant cell line from HN30 parental cell line that underwent brief senescence …

History, Annotated Gazetteer, And Bibliography Of Sarawak Ornithology, Frederick H. Sheldon, Dency F. Gawain, Daisy G. S. Kho, Rosalina Regai, Subir B. Shakya, Chin Aik Yeap

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

Sarawak is Malaysia’s largest state, covering most of northern Borneo. It has a remarkable history of scientific bird study, starting in the 1840s and growing ever since. To set the stage for the gazetteer, which is the core of this paper, we start with a review of this history and discuss various forces that have influenced the direction of bird research in the state. Following this introduction comes the gazetteer, which is an annotated list of c. 865 sites in Sarawak where birds have been collected, studied, or regularly observed. The gazetteer provides the latitude, longitude, and elevation of each …

Big Meadows Mountain Meadow & Aspen Restoration Project 2017 – 2023 Summary Report, Scott River Watershed Council

Aspen Bibliography

Big Meadows Mountain Meadow and Aspen Restoration Project is designed to enhance aspen and mountain meadow habitats at Big Meadows, a property that is privately owned by Ecotrust Forest Management (EFM). EFM owns approximately 40,000 acres in the Klamath Mountains of Siskiyou County, known as the Scott River Headwaters Property. The Scott River Headwaters Property Management Plan, developed by EFM, specifically identifies and prioritizes the restoration of aspen woodlands. As such, EFM and Scott River Watershed Council (SRWC) partnered with the goal of improving these critical habitats. The Big Meadows complex is one of the largest mountain meadow systems within …

Hmgb2 Regulates The Differentiation And Stemness Of Exhausted Cd8+ T Cells During Chronic Viral Infection And Cancer, Emily N. Neubert, Julia M. Derogatis, Sloan A. Lewis, Karla M. Viramontes, Pedro Ortega, Monique L. Henriquez, Rémi Buisson, Ilhem Messaoudi, Roberto Tinoco

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Chronic infections and cancers evade the host immune system through mechanisms that induce T cell exhaustion. The heterogeneity within the exhausted CD8⁺ T cell pool has revealed the importance of stem-like progenitor (Tpex) and terminal (Tex) exhausted T cells, although the mechanisms underlying their development are not fully known. Here we report High Mobility Group Box 2 (HMGB2) protein expression is upregulated and sustained in exhausted CD8⁺ T cells, and HMGB2 expression is critical for their differentiation. Through epigenetic and transcriptional programming, we identify HMGB2 as a cell-intrinsic regulator of the differentiation and maintenance of Tpex cells during …

Revolutionary Advances In The Treatment Of Genetic Disease, Emma Kaitlyn Carrigan

Honors Theses and Capstones

No abstract provided.

A Comparison Of Divergence In Non-Introgressing Genes Across A Chickadee Hybrid Zone, Eliana K. Lowe

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Hybridization between species plays a very important role in the overall evolutionary history of many taxa. The study of hybrid zones can also provide insight into how species are responding to environmental factors such as climate change and changes in species interactions. The hybrid zone between the northern black-capped chickadee (Poecile atricapillus) and the southern Carolina chickadee (Poecile carolinensis) provides an insight into how hybridization is affecting two distinct species. Black-capped and Carolina hybrids have reduced fitness in the wild. Hybrids tend to have higher basal metabolic rates, less muscle growth, and less neuron growth to …

Campylobacter Vaccination Reduces Diarrheal Disease And Infant Growth Stunting Among Rhesus Macaques, Sara M. Hendrickson, Archana Thomas, Hans-Peter Raué, Kamm Prongay, Andrew J. Haertel, Nicholas S. Rhoades, Jacob F. Slifka, Lina Gao, Benjamin K. Quintel, Ian J. Amanna, Ilhem Messaoudi, Mark K. Slifka

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Campylobacter-associated enteric disease is estimated to be responsible for more than 160 million cases of gastroenteritis each year and is linked to growth stunting of infants living under conditions of poor sanitation and hygiene. Here, we examine naturally occurring Campylobacter-associated diarrhea among rhesus macaques as a model to determine if vaccination could reduce severe diarrheal disease and infant growth stunting. Compared to unvaccinated controls, there are no Campylobacter diarrhea-associated deaths observed among vaccinated infant macaques and all-cause diarrhea-associated infant mortality is decreased by 76% (P = 0.03). By 9 months of age, there is a 1.3 cm increase in dorsal …

Chronic Alcohol Consumption Dysregulates Innate Immune Response To Sars-Cov-2 In The Lung, Sloan A. Lewis, Isaac R. Cinco, Brianna M. Doratt, Madison B. Blanton, Cherise Hoagland, Natali Newman, Michael Davies, Kathleen A. Grant, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Background Alcohol consumption is widespread with over half of the individuals over 18 years of age in the U.S. reporting alcohol use in the last 30 days. Moreover, 9 million Americans engaged in binge or chronic heavy drinking (CHD) in 2019. CHD negatively impacts pathogen clearance and tissue repair, including in the respiratory tract, thereby increasing susceptibility to infection. Although, it has been hypothesized that chronic alcohol consumption negatively impacts COVID-19 outcomes; the interplay between chronic alcohol use and SARS-CoV-2 infection outcomes has yet to be elucidated.

Methods In this study we employed luminex, scRNA sequencing, and flow cytometry to …

Monoclonal Antibody Therapy Of Breastfeeding Patient Infected With Sars-Cov-2: A Case Report, Nicole E. Marshall, Madison B. Blanton, Brianna M. Doratt, Delphine C. Malherbe, Monica Rincon, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Introduction: Although safety data demonstrated the efficacy and effectiveness of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination for all individuals over 6 months of age, including pregnant and breastfeeding individuals, optimal treatment courses for symptomatic pregnant and lactating individuals infected with SARS-CoV-2 remain to be defined. Case Description: A coronavirus disease 2019 (COVID-19)-vaccinated breastfeeding woman received anti-SARS-CoV-2 monoclonal antibody treatment casirivimab–imdevimab 5 days after diagnosis of a symptomatic breakthrough SARS-CoV-2 infection. Results and Conclusions: The patient did not present with obvious defects in innate or adaptive cellular subsets, but compared with controls had minimal maternal antibody response to recommended …

Mild/Asymptomatic Covid-19 In Unvaccinated Pregnant Mothers Impairs Neonatal Immune Responses, Brianna M. Doratt, Suhas Sureshchandra, Heather E. True, Monica Rincon, Nicole E. Marshall, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Maternal SARS-CoV-2 infection triggers placental inflammation and alters cord blood immune cell composition. However, most studies focus on outcomes of severe maternal infection. Therefore, we analyzed cord blood and chorionic villi from newborns of unvaccinated mothers who experienced mild/asymptomatic SARS-CoV-2 infection during pregnancy. We investigated immune cell rewiring using flow cytometry, single-cell RNA sequencing, and functional readouts using ex vivo stimulation with TLR agonists and pathogens. Maternal infection was associated with increased frequency of memory T and B cells and nonclassical monocytes in cord blood. Ex vivo T and B cell responses to stimulation were attenuated, suggesting a tolerogenic state. …

Integrated Single Cell Analysis Shows Chronic Alcohol Drinking Disrupts Monocyte Differentiation In The Bone Marrow, Sloan A. Lewis, Brianna M. Doratt, Qi Qiao, Madison B. Blanton, Kathleen A. Grant, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Chronic heavy alcohol drinking (CHD) rewires monocytes and macrophages toward heightened inflammatory states with compromised antimicrobial defenses that persist after 1-month abstinence. To determine whether these changes are mediated through alterations in the bone marrow niche, we profiled monocytes and hematopoietic stem cell progenitors (HSCPs) from CHD rhesus macaques using a combination of functional assays and single cell genomics. CHD resulted in transcriptional profiles consistent with increased activation and inflammation within bone marrow resident monocytes and macrophages. Furthermore, CHD resulted in transcriptional signatures associated with increased oxidative and cellular stress in HSCP. Differentiation of HSCP in vitro revealed skewing toward …

Multimodal Profiling Of Term Human Decidua Demonstrates Immune Adaptations With Pregravid Obesity, Suhas Sureshchandra, Brianna M. Doratt, Heather E. True, Norma Mendoza, Monica Rincon, Nicole E. Marshall, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Leukocyte diversity of the first-trimester maternal-fetal interface has been extensively described; however, the immunological landscape of the term decidua remains poorly understood. We therefore profiled human leukocytes from term decidua collected via scheduled cesarean delivery. Relative to the first trimester, our analyses show a shift from NK cells and macrophages to T cells and enhanced immune activation. Although circulating and decidual T cells are phenotypically distinct, they demonstrate significant clonotype sharing. We also report significant diversity within decidual macrophages, the frequency of which positively correlates with pregravid maternal body mass index. Interestingly, the ability of decidual macrophages to respond to …

Statistical Analyses To Identify Genetic Variants Associated With Neuropathological And Mri-Based Endophenotypes Of Alzheimer’S Disease, Lincoln M. P. Shade

Theses and Dissertations--Epidemiology and Biostatistics

Aged individuals often accumulate multiple brain pathologies that contribute individually and synergistically to cognitive decline and dementia. Alzheimer’s disease (AD) is the most commonly diagnosed form of dementia, constituting over 50% of dementia diagnoses, and poses an enormous burden on human health and well-being. In the United States alone, over six million individuals are living with AD, and the disease imposes financial costs of treatment and care of over $300 billion annually. The most common form of AD, late-onset AD (LOAD), presents in individuals aged 65 years and older and is highly heritable, with twin and family studies estimating its …

Foraging Behavior In The Eastern Subterranean Termite, Reticulitermes Flavipes (Kollar) (Isoptera: Rhinotermitidae), Anugerah Fajar

Theses and Dissertations--Entomology

Foraging is essential for survival, but it can be unpredictably dangerous due to organismal interactions like competition and predation to various environmental factors. Animals have come up with strategies to safeguard foraging. Social insects, with their elaborate division of labor, have developed sophisticated systems of foraging task allocation that allow them to capitalize resources beyond their competitors. In this thesis, I delve into the subjects of foraging behavior, allocation strategies, and the genetic basis of foraging in the eastern subterranean termite, Reticulitermes flavipes, the most widely distributed termite species in North America and one of the most economically important …

Functional Residues Of Cjpata, Robert Lamont

Theses and Dissertations (Comprehensive)

Antibiotic resistance in pathogenic bacteria continues to challenge clinicians and threaten the lives of infected individuals. For this reason, new classes of antibiotics or new targets for antibiotic therapy are needed to circumvent this global health crisis. In Gram-negative bacteria, the enzymes peptidoglycan O-acetyltransferase A and B (PatA and PatB), are responsible for adding acetyl groups to the C-6 hydroxyl group of N-acetyl muramic acid (MurNAc) in peptidoglycan (PG). These acetyl groups are responsible for inhibiting the activity of lysozyme from host organisms that hydrolyze the β1-4 glycosidic linkage between MurNAc and N-acetylglucosamine (GlcNAc). The acetyl groups …

Dfhic: A Dilated Full Convolution Model To Enhance The Resolution Of Hi-C Data, Bin Wang, Kun Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Hi-C technology has been the most widely used chromosome conformation capture(3C) experiment that measures the frequency of all paired interactions in the entire genome, which is a powerful tool for studying the 3D structure of the genome. The fineness of the constructed genome structure depends on the resolution of Hi-C data. However, due to the fact that high-resolution Hi-C data require deep sequencing and thus high experimental cost, most available Hi-C data are in low-resolution. Hence, it is essential to enhance the quality of Hi-C data by developing the effective computational methods.

Results: In this work, we propose …

Intergenic Transcription In In Vivo Developed Bovine Oocytes And Pre-Implantation Embryos, Saurav Ranjitkar, Mohammad Shiri, Jiangwen Sun, Xiuchun Tian

Computer Science Faculty Publications

Background

Intergenic transcription, either failure to terminate at the transcription end site (TES), or transcription initiation at other intergenic regions, is present in cultured cells and enhanced in the presence of stressors such as viral infection. Transcription termination failure has not been characterized in natural biological samples such as pre-implantation embryos which express more than 10,000 genes and undergo drastic changes in DNA methylation.

Results

Using Automatic Readthrough Transcription Detection (ARTDeco) and data of in vivo developed bovine oocytes and embryos, we found abundant intergenic transcripts that we termed as read-outs (transcribed from 5 to 15 kb after TES) and …

Cellbrf: A Feature Selection Method For Single-Cell Clustering Using Cell Balance And Random Forest, Yunpei Xu, Hong-Dong Li, Cui-Xiang Lin, Ruiqing Zheng, Yaohang Li, Jinhui Xu, Jianxin Wang

Computer Science Faculty Publications

Motivation

Single-cell RNA sequencing (scRNA-seq) offers a powerful tool to dissect the complexity of biological tissues through cell sub-population identification in combination with clustering approaches. Feature selection is a critical step for improving the accuracy and interpretability of single-cell clustering. Existing feature selection methods underutilize the discriminatory potential of genes across distinct cell types. We hypothesize that incorporating such information could further boost the performance of single cell clustering. Results

We develop CellBRF, a feature selection method that considers genes’ relevance to cell types for single-cell clustering. The key idea is to identify genes that are most important for discriminating …

A Single-Cell Atlas Of Bovine Skeletal Muscle Reveals Mechanisms Regulating Intramuscular Adipogenesis And Fibrogenesis, Leshan Wang, Peidong Gao, Chaoyang Li, Qianglin Liu, Zeyang Yao, Yuxia Li, Xujia Zhang, Jiangwen Sun, Constantine Simintiras, Matthew Welborn, Kenneth Mcmillin, Stephanie Oprescu, Shihuan Kuang, Xing Fu

Computer Science Faculty Publications

Background

Intramuscular fat (IMF) and intramuscular connective tissue (IMC) are often seen in human myopathies and are central to beef quality. The mechanisms regulating their accumulation remain poorly understood. Here, we explored the possibility of using beef cattle as a novel model for mechanistic studies of intramuscular adipogenesis and fibrogenesis.

Methods

Skeletal muscle single-cell RNAseq was performed on three cattle breeds, including Wagyu (high IMF), Brahman (abundant IMC but scarce IMF), and Wagyu/Brahman cross. Sophisticated bioinformatics analyses, including clustering analysis, gene set enrichment analyses, gene regulatory network construction, RNA velocity, pseudotime analysis, and cell-cell communication analysis, were performed to elucidate …

An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …

Taxonomic Classification Of Viral And Bacterial Dna Following 2021 Avian Mass Mortality Event, Tessa Baillargeon

Honors Theses and Capstones

From May through July 2021, an unusual mortality event occurred along the eastern coast and Midwest of the United States. Thousands of birds, mostly from the order Passeriformes, were part of the die-off including blue jays (Cyanocitta cristata), common grackles (Quiscalus quiscula), European starlings (Sturnus vulgaris), American robins (Turdus migratorius). Clinical signs included crusted eyes, swollen conjunctiva, otitis, seizures, and ataxia.

The New Hampshire Veterinary Diagnostic Laboratory (NHVDL) received over 100 affected birds from various collaborators throughout the United States including Washington DC, NJ, CT, MD, and OH. Given the timing and geologic …

Investigation Of The Function Of Protein Acyl Transferases Using Crispr-Cas9 To Create Null Mutants, Claire E. Christopher

Honors Theses and Capstones

24 Protein Acyl Transferases (PATs) have been identified in the model organism Arabidopsis thaliana. Despite knowing the enzymatic function of these genes (palmitoylation), the specific subcellular pathways, protein targets, and cellular activities of these proteins remain unknown. To investigate the pathways that PAT genes are involved in, deletion mutations were created in several genes and the phenotype of the organisms carrying homozygous mutations was observed. To introduce mutations, the CRISPR/Cas9 system was inserted into the plant’s genome using Agrobacterium tumefaciens to cause deletions in PAT genes of interest. To date, no CRISPR-induced pat mutants have a noticeable phenotype. These …

Investigating The Role Of Bromodomain Proteins On Histone Post-Translational Modifications In Toxoplasma Gondii, Joshua Steven Berthiaume

Honors Theses and Capstones

Toxoplasma gondii is a prevalent pathogenic parasite that infects approximately 25 percent of the US population. For the parasite to successfully establish and maintain infection in its host, properly controlled regulation of gene expression is critical. One way Toxoplasma regulates gene expression is through modification of histone proteins that bind to DNA and can control gene accessibility. Acetylation is a modification that is added to histones that changes chromatin structure to enhance gene activation. Histone acetylation can also regulate gene expression by recruitment of important regulators such as bromodomain proteins (BDP). A previous study showed that loss of the bromodomain …

Identification Of Novel Biosynthetic Gene Clusters Encoding For Polyketide/Nrps-Producing Chemotherapeutic Compounds From Marine-Derived Streptomyces Hygroscopicus From A Marine Sanctuary, Hannah Ruth Flaherty

Honors Theses and Capstones

Nearly one out of six deaths in 2020, around ten million people, were caused by cancer, making it a leading cause of death worldwide (WHO, 2022). This major public health issue, in addition to the rise of multidrug-resistant (MDR) pathogens, provides a high demand for the discovery of new pharmaceutical drugs to be used clinically to treat these conditions. The Streptomyces genus accounts to produce 39% of all microbial metabolites currently approved for human health, indicating its potential as an important species to study for antimicrobial and anticancer agents. The long linear genome of Streptomyces contains specialized sequences known as …