Genetics and Genomics Commons^™

Transcriptome Analysis Of Sea Lamprey Embryogenesis, Zakary Ilya Yermolenko

Seton Hall University Dissertations and Theses (ETDs)

The sea lamprey (Petromyzon marinus) has survived throughout evolution for hundreds of millions of years. It is considered an invasive species to the Great Lakes that has caused dramatic changes in the ecosystem for fish communities resulting in the collapse of a fishing industry that was previously valued at billions of dollars. Successful management of the sea lamprey is essential to a sustainable fishing industry and biodiversity. Therefore sea lamprey embryos were studied at various stages of development by growing them in a simulated habitat. RNAs from adult female ovaries and embryos at different time points during embryogenesis …

Earthworm Remyelination Gene Expression Analysis, Shelby Shevik

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

The Development Of A Comprehensive Antifungal Susceptibility Testing Assay For Vulvovaginal Candidiasis Therapy, David Hardaker

Graduate School of Biomedical Sciences Theses and Dissertations

Vulvovaginal candidiasis is the most common fungal infection of the female urogenital tract, commonly caused by Candida albicans and C. glabrata. However, treatment can be difficult when caused by non-albicans strains due to resistance to the oral antifungal drug fluconazole. The mechanism through which strains of Candida, particularly C. glabrata, develop resistance to different antifungal classes has not been completely characterized. The ergosterol biosynthesis pathway, an important component of the cell membrane, is the major target of antifungals such as fluconazole, an inhibitor of the ERG 11 gene. Current research shows that an upregulation of specific genes in C. glabrata …

Evaluation Of Select Publicly Available In Silico Methods For Predicting Functional Effects Of Missense Mutations In The Galns Gene, Kathryn Davidson

Dissertations, Masters Theses, Capstones, and Culminating Projects

The ability to sequence patient DNA has led to an explosion in the reports of mutations for a number of diseases. Frequently, published reports include in silico predictions of the probability that the mutations are disease-associated. The question asked here is how well these in silico methods predict the effects of new mutations, i.e., mutations not included in the dataset(s) used for training and testing the in silico method. To address this question, we examined mutations associated, or potentially associated, with Morquio A (MPS IVA), a rare, autosomal recessive lysosomal storage disorder (LSD) caused by a deficiency of lysosomal enzyme …

Modeling The Adaptive Immune Response To Mutation-Generated Antigens, Rory J. Geyer

University Scholar Projects

Somatic mutations may drive tumorigenesis or lead to new, immunogenic epitopes (neoantigens). The immune system is thought to represses neoplastic growths through the recognition of neoantigens presented only by tumor cells. To study mutations as well as the immune response to mutation-generated antigens, we have created a conditional knockin mouse line with a gene encoding, 5’ to 3’, yellow fluorescent protein (YFP), ovalbumin (which is processed to the immunologically recognizable peptide, SIINFEKL), and cyan fluorescent protein (CFP), or, YFP-ovalbumin-CFP. A frame shift mutation has been created at the 5’ end of the ovalbumin gene, hence YFP should always be expressed, …

Tactical Adjustment Of Signaling Leads To Increased Mating Success And Survival, Laura Sullivan-Beckers, Eileen A. Hebets

Eileen Hebets Publications

Most sexually reproducing animals overcome the challenge of searching for and attracting mates by utilizing signals that are broadcast through a spatially and temporally varying environment. A diverse suite of behavioral solutions exist for overcoming such environmental variability, including the adjustment of signaling behavior based upon receiver feedback. Few studies have directly examined the relationship between such tactical signaling adjustments and proxies of male fitness; the few that have, failed to find a relationship. Using the wolf spider, Schizocosa rovneri, we set out to first quantify among-male variation in the form and degree of responsiveness to female feedback. Following …

The Reference Transcriptome Of The Adult Female Biting Midge (Culicoides Sonorensis) And Differential Gene Expression Profiling During Teneral, Blood, And Sucrose Feeding Conditions, Dana Nayduch, Matthew B. Lee, Christopher Saski

Publications

Unlike other important vectors such as mosquitoes and sandflies, genetic and genomic tools for Culicoides biting midges are lacking, despite the fact that they vector a large number of arboviruses and other pathogens impacting humans and domestic animals world-wide. In North America, female Culicoides sonorensis midges are important vectors of bluetongue virus (BTV) and epizootic hemorrhagic disease virus (EHDV), orbiviruses that cause significant disease in livestock and wildlife. Libraries of tissue-specific transcripts expressed in response to feeding and oral orbivirus challenge in C. sonorensis have previously been reported, but extensive genome-wide expression profiling in the midge has not. Here, we …

Lifecycle Efficiency Of Mice Divergently Selected For Heat Loss, Adrienne Bhatnagar

Department of Animal Science: Dissertations, Theses, and Student Research

Divergent selection for heat loss as an indication of maintenance energy requirements in mice resulted in a low (ML) and high maintenance line (MH), and an intermediate control line (MC). Improved feed efficiency has been observed in ML mice, which would be economically beneficial in livestock species. However, previous work showed evidence of unfavorable correlated responses to selection in ML mice compared to MH mice. Therefore, the objective of this study was to model a lifecycle similar to a livestock production system using these lines and determine if these correlated responses diminish the benefit of improved feed efficiency by calculating …

Mapping Quantitative Trait Loci Associated With Alternaria Leaf Blight Resistance And Elemental Sulfur Tolerance In Melon, James Daley

All Theses

Melon (Cucumis melo L.) production is significantly affected by Alternaria leaf blight, caused by Alternaria cucumerina. Fungicide application is the primary control method; however, this could be mitigated through the increased use of resistant varieties. USDA-ARS breeding line MR-1 has been shown to have a high level of resistance to Alternaria cucumerina. However, molecular markers linked MR-1 Alternaria resistance have yet to be identified. In order in identify QTL associated with Alternaria resistance MR-1 x Ananas Yokneum (AY) derived recombinant inbred lines (RILs) were phenotyped using a modified wounded-leaf assay. Elemental sulfur is an effective fungicide for several foliar pathogens …

Modulated Functions Of The Fanconi Anemia Core Complex, Yaling Huang

Dissertations and Theses (Open Access)

Cells derived from Fanconi anemia (FA) patients are characterized by hypersensitivity to DNA interstrand crosslinks (ICLs), suggesting that FA genes play a role in ICL repair. Fanconi anemia core complex (including A, B, C, E, F, G, L, FAAP20, and FAAP100) activates the Fanconi pathway by providing the essential E3 ligase activity for FANCD2 mono-ubiquitination. Previous studies suggested the existence of three protein-protein interaction groups. However, the functions of most FA core complex protein are still limited to their presence in the complex. How the spatially-defined FANCD2 ubiquitination is accomplished by the core complex remains unknown.

To elucidate the roles …

Natural And Exogenous Genome Editing In Wiskott-Aldrich Syndrome Patient Cells, Tamara J. Laskowski

Dissertations and Theses (Open Access)

Wiskott-Aldrich syndrome (WAS) is an X-linked primary immunodeficiency disease characterized by thrombocytopenia, recurrent infections and increased autoimmunity. This disease is caused by mutations in the WAS gene (WAS) which encodes for the WAS protein (WASp), exclusively expressed in hematopoietic cells and required for proper platelet production and lymphoid cell function. Approximately 11% of patients with WAS exhibit a phenomenon called Somatic Revertant Mosaicism which is characterized by the presence of lymphocytes which naturally revert back to normal phenotype by restoring WASp expression. To date, the mechanisms of this naturally-occurring gene therapy remains poorly understood, and the full extent …

Modeling The Adaptive Immune Response To Mutation-Generated Antigens, Rory J. Geyer

Honors Scholar Theses

Somatic mutations may drive tumorigenesis or lead to new, immunogenic epitopes (neoantigens). The immune system is thought to represses neoplastic growths through the recognition of neoantigens presented only by tumor cells. To study mutations as well as the immune response to mutation-generated antigens, we have created a conditional knockin mouse line with a gene encoding, 5’ to 3’, yellow fluorescent protein (YFP), ovalbumin (which is processed to the immunologically recognizable peptide, SIINFEKL), and cyan fluorescent protein (CFP), or, YFP-ovalbumin-CFP. A frame shift mutation has been created at the 5’ end of the ovalbumin gene, hence YFP should always be expressed, …

The Association Between The Il-1 Pathway, Isaac C. Wun

Dissertations and Theses (Open Access)

Cutaneous malignant melanoma (CMM) is a potentially lethal malignancy that warrants attention and further research, as it is known to that there is an increasing rate of incidence in theUnited States, and it is also known that exposure to UV light is its most crucial risk factor, and family history of melanoma is also an important risk factor. Melanoma is an aggressive and lethal cancer in humans. There are an estimated new 132,000 melanoma cases annually worldwide, and the trend has doubled in the past 20 years. However, attempts to treat melanoma have encountered considerable resistance and remained ineffective. The …

Characterization Of Ftsa-Ftsn Interaction During Escherichia Coli Cell Division, [email protected] K. Busiek

Dissertations and Theses (Open Access)

Division of a bacterial cell into two equal daughter cells requires precise assembly and constriction of the division machinery, or divisome. The Escherichia coli divisome includes nearly a dozen essential cell division proteins that assemble at midcell between segregating sister chromosomes. FtsZ, a homolog of eukaryotic tubulin, is the first essential cell division protein to localize at midcell where it polymerizes into a ring-shaped scaffold (Z ring). Establishment of the Z ring is required for recruitment of downstream cell division proteins including FtsA, a cytoplasmic protein that tethers the Z ring to the inner membrane. Following localization of FtsA and …

P53 Maintains Hepatic Cell Identity During Liver Regeneration, Zeynep Hande Coban Akdemir

Dissertations and Theses (Open Access)

p53 MAINTAINS HEPATIC CELL IDENTITY DURING LIVER REGENERATION

Zeynep Hande Coban Akdemir, B.S.,M.A.

Advisory Professor: Michelle Craig Barton, Ph.D.

p53 is a tumor suppressor that has been well studied in tumor-derived, cultured cells. However, its functions in normal proliferating cells and tissues are generally overlooked. We propose that p53 functions during the G1-S transition can be studied in normal, differentiated cells during surgery-induced liver regeneration. Two-thirds partial hepatectomy (PH) of mouse liver offers a unique model to compare p53 functions in regenerating versus sham (control) cells. My hypothesis is that intersection of global expression analyses (microarray and RNA sequencing) and …

The Mechanism Of Small Rna Biogenesis, Degradation, And Function In Arabidopsis, Meng Xie

School of Biological Sciences: Dissertations, Theses, and Student Research

Eukaryotic small RNAs play important roles in many biological processes through sequence-specific RNA silencing. In plants, there are mainly two small RNAs triggering gene silencing: microRNAs (miRNAs) and small interfering RNAs (siRNAs). The biogenesis and precise regulation of small RNA abundance are crucial for plant growth, development, genomic stability, and the resistance to both abiotic and biotic stresses. In this study, we used Arabidopsis thaliana, the model plant, to study the mechanism of RNA-directed DNA methylation (RdDM), in which siRNAs can trigger DNA methylation and gene silencing. In addition, we investigated the mechanism of miRNA biogenesis and degradation. For …

Clpxp Modulates Cell Growth And Morphology In Cell Shape Mutants Of E.Coli, Ryann Murphy

Senior Honors Projects

ClpXP modulates cell growth and morphology in cell shape mutants of E. coli

Ryann Murphy¹ and Jodi L. Camberg¹

¹University of Rhode Island, Department of Cell and Molecular Biology, Kingston, RI, 02881

Penicillin Binding Proteins (PBPs) are a family of prokaryotic membrane proteins named for their propensity to bind the antibiotic penicillin and are involved in remodeling and deposition of peptidoglycan. In wild type Escherichia coli cells, the uniform rod shape is conserved across generations. E.coli cells containing multiple deletions of Low Molecular Weight (LMW) PBPs exhibit irregular shapes. LMW PBP5 (dacA) is a potential …

Investigations Into Sensory Ecology And Gene Evolution Of The Pea Aphid (Acyrthosiphon Pisum), Swapna R. Purandare

School of Biological Sciences: Dissertations, Theses, and Student Research

Organisms use environmental cues to gather information required to perform activities that are essential for their survival and reproduction, such as searching for food, avoiding danger, and finding mates. They respond to the acquired information by changing their behavior or physiology, which may result in increased fitness. Due to the fundamental importance of information in an organism’s life, it is important to understand its acquisition, processing, and the organism’s response to it. In the work presented here, we used the pea aphid (Acyrthosiphon pisum), an insect that produces multiple phenotypes, or morphs, that are genetically identical, but differ …

Teaching Gene Regulation In The High School Classroom, Ap Biology,, Stefanie H. Baker, Marie Fox, Leigh Smith

Arthur Vining Davis High Impact Fellows Projects

This project sought to enhance high school students’ understanding of gene regulation as taught in an Advanced Placement Biology course. We accomplished this by designing and implementing a lab module that included a pre-lab assessment, a hands-on classroom experiment, and a post-lab assessment in the form of a lab poster. Students developed lab skills while simultaneously learning about course content. Students’ progress was evaluated through a multiple choice/essay test and their lab posters that they created on the lab experiment.

Combined Metagenomic And Phenomic Approaches Identify A Novel Salt Tolerance Gene From The Human Gut Microbiome, Eamon Culligan, Julian R. Marchesi, Colin Hill, Roy D. Sleator

Department of Biological Sciences Publications

In the current study, a number of salt-tolerant clones previously isolated from a human gut metagenomic library were screened using Phenotype MicroArray (PM) technology to assess their functional capacity. PM's can be used to study gene function, pathogenicity, metabolic capacity and identify drug targets using a series of specialized microtitre plate assays, where each well of the microtitre plate contains a different set of conditions and tests a different phenotype. Cellular respiration is monitored colorimetrically by the reduction of a tetrazolium dye. One clone, SMG 9, was found to be positive for utilization/transport of L-carnitine (a well-characterized osmoprotectant) in the …