Genetics and Genomics Commons^™

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 …

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 …

Characterization Of Cell Type-Specific Molecular Heterogeneity In Cancer Using Multi-Omic Approaches, Min Kyung Lee

Dartmouth College Ph.D Dissertations

Tumors are composed of heterogeneous cell types each with its own unique molecular profiles. Recent advances in single cell genomics technologies have begun to increase our understanding of the molecular heterogeneity that exists in tumors with particular focus on gene expression and chromatin accessibility profiles. However, due to limitations in methods for certain sample types and high cost for single cell genomics, bulk tumor molecular profiling has been and remains widely used. In addition, other facets of single cell epigenomic profiling, particularly methylation and hydroxymethylation, remains underexplored. Thus, investigations to understand the cell type specific epigenetic heterogeneity and the cooperation …

Comparative Genomics Of The Putatively Asexual Powder Lichens Lepraria And Other Lecanoromycete Lichens, Bubba Pfeffer

EWU Masters Thesis Collection

No abstract provided.

Intraspecific Hybrid Identification Of Black Walnuts Via Marker Assisted Selection, Makenna B. Thompson

Graduate Theses/Dissertations

The improvement of Eastern black walnut (Juglans nigra L.) cultivars could increase market expansion. Improved cultivars with superior qualities would increase profitability for both the seller and the buyer. Agronomically and economically important traits such as heavier nut weight, disease resistance, tree structure integrity, and yearly nut production can be efficiently improved by breeding black walnuts via marker-assisted selection. Microsatellite/simple sequence repeat markers were used in this research to determine potential intraspecific hybrids between ‘Football’ and ‘Sparrow’ cultivars. Intraspecific is defined as of the same genus and species. This quality makes it more difficult to identify hybrids because the parent …

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 …

Methylation Patterns Across Tissue Type And Time In Peromyscus Leucopus: A Targeted Museum Study, Loryn Smith

Master's Theses or Doctor of Nursing Practice

Museum specimens are a vital data source for many types of studies. One relatively new use includes studying methylation patterns. Methylation patterns are a form of epigenetics or how gene expression changes without alteration of the genetic code. These patterns have been examined in many mammals. However, the focus has previously been on overall epigenetic patterns. Few studies have investigated whether methylation patterns differ across tissue types, time, or preservation method. In this study, I compared methylation patterns in muscle, liver, toe pads, and nasal bones from Peromyscus leucopus (white-footed mouse) museum specimens collected in 2022, 2018, 2014, and 2008 …

Anti-Tick Vaccine Candidate Subolesin Is Important For Blood Feeding And Innate Immune Gene Expression In Soft Ticks, Krittika Nandy, Comfort Tamakloe, Daniel E. Sonenshine, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Subolesin is a conserved molecule in both hard and soft ticks and is considered as an effective candidate molecule for the development of anti-tick vaccine. Previous studies have reported the role of subolesin in blood feeding, reproduction, development, and gene expression in hard ticks. However, studies addressing the role of subolesin in soft ticks are limited. In this study, we report that subolesin is not only important in soft tick Ornithodoros turicata americanus blood feeding but also in the regulation of innate immune gene expression in these ticks. We identified and characterized several putative innate immune genes including Toll, Lysozyme …

Biodiversity Of Philippine Marine Fishes: A Dna Barcode Reference Library Based On Voucher Specimens, Katherine E. Bemis, Matthew G. Girard, Mudjekeewis D. Santos, Kent E. Carpenter, Jonathan R. Deeds, Diane E. Pitassy, Nicko Amor L. Flores, Elizabeth S. Hunter, Amy C. Driskell, Kenneth S. Macdonald Iii, Lee A. Weigt, Jeffrey T. Williams

Biological Sciences Faculty Publications

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased …

Therapeutic Neutralizing Monoclonal Antibody Administration Protects Against Lethal Yellow Fever Virus Infection, Michael J. Ricciardi, Lauren N. Rust, Nuria Pedreño-Lopez, Sofiya Yusova, Sreya Biswas, Gabriela M. Webb, Lucas Gonzalez-Nieto, Thomas B. Voigt, Johan J. Louw, Fernanda D. Laurino, John R. Dibello, Hans-Peter Raué, Aaron M. Barber-Axthelm, Kimberly Chun, Samantha Uttke, Lidiane M. S. Raphael, Aaron Yrizarry-Medina, Brandon C. Rosen, Rebecca Agnor, Lina Gao, Caralyn Labriola, Michael Axthelm, Jeremy Smedley, Justin G. Julander, Myrna C. Bonaldo, Laura M. Walker, Ilhem Messaoudi, Mark K. Slifka, Dennis R. Burton, Esper G. Kallas, Jonah B. Sacha, David I. Watkins, Benjamin J. Burwitz

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Yellow fever virus (YFV) is a reemerging global health threat, driven by several factors, including increased spread of the mosquito vector and rapid urbanization. Although a prophylactic vaccine exists, vaccine hesitancy, supply deficits, and distribution difficulties leave specific populations at risk of severe YFV disease, as evidenced by recent outbreaks in South America. To establish a treatment for patients with severe YFV infection, we tested 37 YFV-specific monoclonal antibodies isolated from vaccinated humans and identified two capable of potently neutralizing multiple pathogenic primary YFV isolates. Using both hamster and nonhuman primate models of lethal YFV infection, we demonstrate that a …

Genetic And Pharmacogenetics Associations Of Cancer Disparities In Appalachia, Nan Lin

Theses and Dissertations--Pharmacy

Individuals residing in Appalachian regions have significant health disparities, including higher cancer incidence and mortality rates. Previous studies have addressed the impact of socioeconomic status and environmental risk factors on Appalachia cancer disparities, while few studies have evaluated genetic risk factors.

Germline whole exome sequencing samples from 7,078 individuals with cancer (759 Appalachians) were evaluated. Demographics and relatedness were assessed using KING. Ethnicity was verified by principal component analysis using TRACE, which included 6,034 individuals (85%) of European genetic ancestry. After QC filtering, 5,980 individuals were analyzed. To assess the overall predisposition of hereditary disease, gene level frequency of likely …

Molecular Genetic Studies Of Horses, Especially With Reference To Aggrecan And Dwarfism, John Edmund Eberth

Theses and Dissertations--Veterinary Science

This work consists of studies on dwarfism in Miniature horses and a study on breakdowns in Thoroughbreds in relation to gene aggrecan. A correction of the description and designation of D3 dwarf variant in aggrecan (ACAN) from the master’s thesis Chondrodysplasia-like dwarfism in the Miniature horse (2013). Commercial sequencing showed previous sequencing reads presented an artifact and not a single base deletion. Analysis showed a single base missense mutation in exon 8 identified as D3* was the actual cause. Multiple alleles of ACAN associated with chondrodysplastic dwarfism in Miniature horses by Eberth et al. (2018), corrected the …

Use Of Molecular Genetics To Investigate Population Structure And Swayback In Horses, Navid Yousefimashouf

Theses and Dissertations--Veterinary Science

The present research incorporated molecular genetic methods to 1) investigate the genetic basis of Juvenile Onset Lordosis or Swayback in the American Saddlebred horses; and 2) conduct a population genetic study to compare the Persian Kurdish, Persian Arabian and American Thoroughbred horse populations.

Juvenile-onset lordosis, or swayback, is a condition in horses where the conformational topline back curvature drops significantly within the first two years of life. The trait has a higher prevalence in Saddlebreds (5%). Prior research on them quantified the trait using a Measurement of Back Contour (MBC), defining an MBC of >7.0 centimeters as swayback, and8.0) MBC …

Biomarker Identification For Breast Cancer Types Using Feature Selection And Explainable Ai Methods, David E. La Rosa Giraud

Honors Undergraduate Theses

This paper investigates the impact the LASSO, mRMR, SHAP, and Reinforcement Feature Selection techniques on random forest models for the breast cancer subtypes markers ER, HER2, PR, and TN as well as identifying a small subset of biomarkers that could potentially cause the disease and explain them using explainable AI techniques. This is important because in areas such as healthcare understanding why the model makes a specific decision is important it is a diagnostic of an individual which requires reliable AI. Another contribution is using feature selection methods to identify a small subset of biomarkers capable of predicting if a …

Enhancing Tomato Fruit Quality: Application Of Crispr/Dcas9-Mediated Methylation On The Pg Gene Promoter Region, Irena Komninakas

Holster Scholar Projects

Commercially produced tomatoes are typically harvested well before maturation in order to withstand domestic and international distribution. While this process ensures unspoiled goods, the nutritional value of the fruits have been curtailed as a result of premature harvesting. Previous research has found that the polygalacturonase gene (PG gene) is responsible for cell wall degradation of the tomato. In this study, CRISPR/dCas9 technology was employed to increase methylation levels in the promoter regions of the PG gene. This method is significant in that it epigenetically modifies the tomato genome using a technique that has the potential to develop non-genetically modified progeny …