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Genomic Tools And Models For Investigating The Role Of Germline Diversity In Mouse Antibody Repertoire Development., Justin T. Kos 2022 University of Louisville

Genomic Tools And Models For Investigating The Role Of Germline Diversity In Mouse Antibody Repertoire Development., Justin T. Kos

Electronic Theses and Dissertations

Given the diversity and complexity within immunoglobulin (IG) loci, effective mouse models first require characterization of intra-strain differences and construction of high-quality reference assemblies for IG loci in several representative strains. To understand light chain germline diversity across biomedically significant mouse strains, we profiled the expressed IGK and IGL repertoires of 18 commonly used laboratory mouse strains using AIRR-seq. Across strains, we observed germline IGKV sequences shared by three different IGK haplotypes and a more conserved IGLV germline repertoire among common laboratory strains. Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing was used to sequence and assemble bacterial artificial chromosomes (BAC) …


Discovering The Pathways And Go Terms Associated With Mettl3 Modified Circular Rnas In The Embryonic Cerebral Cortex Of Mice., Dunia Zedan 2022 University of Louisville

Discovering The Pathways And Go Terms Associated With Mettl3 Modified Circular Rnas In The Embryonic Cerebral Cortex Of Mice., Dunia Zedan

Electronic Theses and Dissertations

Circular RNAs (cirRNAs) are a class of RNA molecules that result from the alternative back-splicing events that join the 3’ and 5’ ends normally present in the linear RNA molecules. It has been published that cirRNAs can function as gene regulators and as “microRNA sponges” to negatively control the functions of microRNAs. While many studies have been conducted to understand the regulatory roles of Mettl3 in linear messenger RNAs, fewer contributions were applied to understand the impact of Mettl3 modified cirRNAs on gene expression and on the regulation of different KEGG biological pathways and GO terms. This thesis was conducted …


Using Thermography To Determine Mechanisms Of Heat Loss In The Southern Flying Squirrel (Glaucomys Volans), Colin Flynn 2022 University of Maine - Main

Using Thermography To Determine Mechanisms Of Heat Loss In The Southern Flying Squirrel (Glaucomys Volans), Colin Flynn

Honors College

Climate change is one of the biggest factors currently affecting the health and energetics of animals. Species evolve to operate optimally under certain environmental conditions and changes in those conditions can be detrimental to the species. Previous studies have shown increased evaporative cooling in flying squirrels at higher temperatures but not much is known about their ability to use other avenues of heat loss such as thermal windows; areas of the body that exchange heat with the environment via convection. For example, the patagium of southern flying squirrels may also serve as a thermal window to aid in heat dissipation. …


Quantifying Equine Behavior Utilizing Gps, Vanessa M. Cote 2022 University of Maine - Main

Quantifying Equine Behavior Utilizing Gps, Vanessa M. Cote

Honors College

GPS tracking systems have been around for many years and are used to track, map, determine precise locations, navigate, and get precise time measurements on a number of different animals, devices, vehicles, and much more. The use of GPS tracking systems on animals has been a huge breakthrough in the cattle industry since this means farmers no longer have to monitor their cattle manually, but can do remotely. The research that has previously been done on cattle tracking can now be applied to horses, although as horses are used in a much different manner than cattle the data will go …


An Investigation Of Epigenetic Mechanisms Driving The Biology Of Head And Neck Squamous Cell Carcinoma, Scot Carson Callahan 2022 The Texas Medical Center Library

An Investigation Of Epigenetic Mechanisms Driving The Biology Of Head And Neck Squamous Cell Carcinoma, Scot Carson Callahan

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Head and neck squamous cell carcinoma (HNSCC) is the 6th most common cancer worldwide and is associated with significant morbidity and mortality. To date, the majority of work in the field has focused on genomic alterations such as mutations and copy number alterations. However, the clinical success of targeted therapies that exploit known genomic alterations, such as EGFR mutations, has remained mixed. Over the past decade, the importance of epigenetic regulators has come to the forefront, with the realization that many of these genes are mutated in cancer. Despite this realization, the role of epigenetics in regulating tumorigenesis, progression and …


Extracting Dna From Embalmed Tissue To Study Genetic Predisposition To Degenerative Disc Disease, Conner Lynn 2022 Bellarmine University

Extracting Dna From Embalmed Tissue To Study Genetic Predisposition To Degenerative Disc Disease, Conner Lynn

Undergraduate Theses

INTRODUCTION. According to a prominent study, 80-90% of people will show some evidence of degenerative disc disease (DDD) by age 50. Researchers have proposed that a Q326W substitution in the COL9A2 gene increases susceptibility to DDD. The role of collagen IX in intervertebral discs is not completely known, but due to its increased flexibility compared to other types of collagens, it is thought to connect collagen II with other components of the cartilage which are important to the integrity of the disc. Collagen II can be found within the nucleus pulposus and the inner portion of the annulus fibrosis. Researchers …


Exploration Of Genes Controlling Grain Yield Heterosis In Hybrid Wheat (Triticum Aestivum L.) Utilizing 3ʹ Rna Sequencing, Nichole Miller 2022 University of Nebraska-Lincoln

Exploration Of Genes Controlling Grain Yield Heterosis In Hybrid Wheat (Triticum Aestivum L.) Utilizing 3ʹ Rna Sequencing, Nichole Miller

Theses, Dissertations, and Student Research in Agronomy and Horticulture

The implementation and future success of hybrid wheat (Triticum aestivum L.) is impacted by breeders’ inability to create consistent high yielding, high heterosis hybrids. This research addresses this problem by conducting an exploration of transcriptomes from hybrids and parent lines to determine what genes are active in heterotic or non-heterotic hybrids and how their level of expression can explain the phenotype of grain yield heterosis. Using hybrids that showed positive mid-parent heterosis (MPH), classified as heterotic in our study, and negative or no difference MPH hybrids, classified as non-heterotic, differentially expressed genes (DEGs) potentially related to heterosis and hybrid …


Genomic Analysis Of Metabolic Differences Found In Clostridium Perfringens That Cause Necrotic Enteritis In Poultry, Connor Aylor 2022 University of Nebraska-Lincoln

Genomic Analysis Of Metabolic Differences Found In Clostridium Perfringens That Cause Necrotic Enteritis In Poultry, Connor Aylor

Dissertations & Theses in Veterinary and Biomedical Science

Clostridium perfringens is a common member of gut microbiota in healthy animals, but can also be an important pathogen in human and veterinary medicine. It produces several protein toxins that contribute to both histotoxic and enteric diseases in animals. Necrotic enteritis in poultry has been associated with the NetB toxin of C. perfringens; however, this toxin alone is insufficient to cause disease in infected chickens. While considerable research has focused on the presence of toxins and virulence factors, little has been done to assess the function of metabolic factors on the ability of the bacteria to cause disease. In …


Diversity Of Bacteriophage In Burkholderia Species, Abigail Price 2022 Bowling Green State University

Diversity Of Bacteriophage In Burkholderia Species, Abigail Price

Honors Projects

Bacteriophages are viruses that infect and replicate within bacteria and offer the potential of a therapeutic alternative to chronic infections that do not respond to antibiotic-based therapies. B. vietnamiensis is one of a number of Burkholderia species involved with chronic drug resistant infections in the lungs of individuals with compromised respiratory systems, as found in those with chronic obstructive pulmonary disease and, most especially, are of particular significance in patients with cystic fibrosis. The diversity of the Burkholderia species is explored by using online databases and looking at bacteriophage or phage-encoding viruses found in B. vietnamiensis. The open reading frames …


Identification Of Dna Methylation Episignatures For Classification And Phenotype/Genotype Correlation In Mendelian Neurodevelopmental Disorders, John Reilly 2022 The University of Western Ontario

Identification Of Dna Methylation Episignatures For Classification And Phenotype/Genotype Correlation In Mendelian Neurodevelopmental Disorders, John Reilly

Electronic Thesis and Dissertation Repository

ABSTRACT: Diagnosis for neurodevelopmental disorders poses numerous challenges, related to the lack of specific findings and limited understanding of clinical impact of the majority of genetic variation. Epigenomics mechanisms involve chemical modifications in DNA that involve a range of cellular mechanisms. DNA methylation is an epigenetic mechanism involving addition and removal of methyl groups to cytosine residues. These methylation signals form episignatures; patterns of methylation that can be used as biomarkers capable of differentiating neurodevelopmental disorders. EpiSigns have enabled molecular diagnosis of a number of genetic conditions, classification of variants of unknown significance, and provided insights into the pathophysiology of …


Microbial Diversity And Community Structure In Sediments Associated With The Seagrass (Thallassia Testudinum) In Apalachicola Bay, Florida, Rahma Ahmed, Thomas McElroy, Troy Mutchler 2022 Kennesaw State University

Microbial Diversity And Community Structure In Sediments Associated With The Seagrass (Thallassia Testudinum) In Apalachicola Bay, Florida, Rahma Ahmed, Thomas Mcelroy, Troy Mutchler

Symposium of Student Scholars

Seagrass is an angiosperm which provides many ecosystem services in coastal areas, such as providing food, shelter and nurseries for many species, and decreasing the impact of waves on shorelines. A global assessment reported that 29% of known seagrass meadows are in a state of decline due to the effects of human activity. Seagrass is commonly found in shallow marine waters where they form meadows containing a microbiome that plays an important role in providing nutrients for seagrass growth, though little is known about the microorganisms within the seagrass meadow sediments. Our project collected sediments from seagrass meadows and adjacent …


Identifying Molecular Markers For Early Detection Of Toxic Cyanobacteria And Dinoflagellate, Shafqat F. Ehsan 2022 St. Mary's University

Identifying Molecular Markers For Early Detection Of Toxic Cyanobacteria And Dinoflagellate, Shafqat F. Ehsan

St. Mary's University Honors Theses and Projects

Harmful algal Blooms (HABs) develop when algal colonies grow out of control, causing toxicity or injury to humans, fish, shellfish, marine mammals, and birds. Most HABs of public health concern in saltwater generally are caused by eukaryotic dinoflagellates and diatoms. Prokaryotic cyanobacteria are usually responsible for freshwater blooms although they can contribute to saltwater and brackish blooms too. A common monitoring target of both groups is the saxitoxin-encoding genes. Saxitoxin(STX) is responsible for Paralytic shellfish poisoning, a foodborne illness developed from consumption of STX contaminated shellfish. Each cyanobacterial SXT gene cluster contains a set of core genes, common to all …


Commercially Geneticizing Race, Ethnicity, And Nation: The Implications Of The Discourse Surrounding Commercialized Genetic Tests On Identity, Kiara Jacoby 2022 Arcadia University

Commercially Geneticizing Race, Ethnicity, And Nation: The Implications Of The Discourse Surrounding Commercialized Genetic Tests On Identity, Kiara Jacoby

The Compass

No abstract provided.


Ubjective Information And Survival In A Simulated Biological System, Tyler S. Barker, Massimiliano Pierobon, Peter J. Thomas 2022 University of Nebraska-Lincoln

Ubjective Information And Survival In A Simulated Biological System, Tyler S. Barker, Massimiliano Pierobon, Peter J. Thomas

CSE Journal Articles

Information transmission and storage have gained traction as unifying concepts to characterize biological systems and their chances of survival and evolution at multiple scales. Despite the potential for an information-based mathematical framework to offer new insights into life processes and ways to interact with and control them, the main legacy is that of Shannon’s, where a purely syntactic characterization of information scores systems on the basis of their maximum information efficiency. The latter metrics seem not entirely suitable for biological systems, where transmission and storage of different pieces of information (carrying different semantics) can result in different chances of survival. …


Host-Pathogen Coevolution Between Tasmanian Devils (Sarcophilus Harrisii) And Devil Facial Tumor Disease, Dylan Garret Gallinson 2022 University of South Florida

Host-Pathogen Coevolution Between Tasmanian Devils (Sarcophilus Harrisii) And Devil Facial Tumor Disease, Dylan Garret Gallinson

USF Tampa Graduate Theses and Dissertations

Coevolution is a driving force of rapid evolution, yet the complexity of coevolutionary interactions has made it difficult to characterize the genomic basis of traits mediating such relationships. Coevolutionary dynamics are especially important in host-pathogen systems where the host and pathogen must constantly adapt to one another. The Tasmanian devil and its species-specific transmissible cancer, devil facial tumor disease (DFTD), provide the rare opportunity to study host-pathogen coevolution in a complex natural system. Extensive spatiotemporal devil sampling, high linkage disequilibrium in devils, and a large selective pressure imposed by DFTD facilitate a system tractable for study. Here, we characterized devil …


Generating A Colorimetric Ssa4 Transcript Export Reporter For Multicopy Suppression Screen In S. Cerevisiae, Zaid Hatem 2022 Belmont University

Generating A Colorimetric Ssa4 Transcript Export Reporter For Multicopy Suppression Screen In S. Cerevisiae, Zaid Hatem

Belmont University Research Symposium (BURS)

The export of mRNA from the nucleus to the cytoplasm is a regulatory point that is essential to the pathway of gene expression in eukaryotic cells. The export of mRNA transcripts is mediated through selective doorways called the nuclear pore complexes (NPC). Additionally, there are proteins associated with the nuclear pore complex that assist in facilitating the export. This includes association with the export receptor, Mex67, which binds to the transcript and ferries it through NPCs. During cellular stress, such as heat shock, the export of housekeeping mRNA transcripts is halted, forcing these transcripts to remain inside the nucleus and …


Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk 2022 Belmont University

Exploring The Functionality Of Putative Bop3 Post-Translational Modifications, Liliya Tkachuk

Honors Scholars Collaborative Projects

All eukaryotic cells require that transcribed mRNAs undergo export form the nucleus to the cytoplasm where they can be translated into proteins. This process requires a host of proteins which are conserved between the unicellular budding yeast, S. cerevisiae, and humans. During this process, Mex67 and other associated proteins facilitate the mRNA to travel across the nuclear pore complex (NPC), doorways embedded in the nuclear envelope. Upon the exit of mRNA, Mex67 is released and recycled back into the nucleus to facilitate the export of more mRNA. This occurs through the action of Dbp5, whose activity is regulated through …


Assessing The Threat Of Coral Decline On Fish Diversity In Response To Temperature, Ryland Talmadge 2022 SIT Study Abroad

Assessing The Threat Of Coral Decline On Fish Diversity In Response To Temperature, Ryland Talmadge

Independent Study Project (ISP) Collection

Misali, a PECCA-protected island off the east coast of Pemba, Tanzania, is considered to be a marine biodiversity hotspot with a protected Non-Extractive Zone (NEZ) and remaining Extractive Zone (EZ). Upon protection, the island’s fringe reefs faced severe coral bleaching during the 1998 bleaching event, estimated to kill up to 70% of corals. Since the event, several others have occurred in addition to restructuring the management plan in 2006 to expand the region to 1000km. While the damage from the most recent coral bleaching event in 2020 has yet to be surveyed, this study investigates the current reef health in …


Comparative Modeling And Evolutionary Comparison Of Serine Protease, A Timber Rattlesnake Venom Protein, Qawer Ayaz 2022 Jacksonville State University

Comparative Modeling And Evolutionary Comparison Of Serine Protease, A Timber Rattlesnake Venom Protein, Qawer Ayaz

Theses

The aim of this study is to create a homology model of VG35 serine protease and evaluate the evolutionary comparison of secondary structure on basis of protein model using YASARA. This method was furthermore used to predict the potential epitopes which can help in the investigation of future studies.

The VG35 was used to run a BLAST search which gave most resembled serine protease of different species which was then translated and modeled in YASARA. The modeled protein data was then used to determine the secondary structure. This was then used for evolutionary comparison of all proteins to VG35. Then …


The Development Of Inhibitors For Sars-Cov-2 Orf8, My Thanh Thao Nguyen 2022 College of Saint Benedict/Saint John's University

The Development Of Inhibitors For Sars-Cov-2 Orf8, My Thanh Thao Nguyen

CSBSJU Distinguished Thesis

An unexpected outbreak of SARS-CoV-2 caused a worldwide pandemic in 2020. Many repurposed drugs were tested, but there are currently only three FDA approved antivirals (Merck’s antiviral Molnupiravir, Pfizer’s antiviral Paxlovid, and Remdisivir).1 Most of the antiviral drugs tested SARS-CoV-2 main protease and RNA-dependent RNA polymerase. However, it is important to explore different drug targets of SARS-CoV-2 to prepare for the virus mutations of the future. This research looks at an alternative approach in which SARSCoV- 2 Open Reading Frame 8 (ORF8), which has been shown to be a rapidly evolving hypervariable gene, was chosen to be the protein of …


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