Genetics Commons^™

Sars-Cov-2: An Investigation On Mutagenicity And Its Effects On Infectivity And Mortality, Tyler Elliott Silverwood

Honors Theses and Capstones

SARS-CoV-2, the etiological agent of the COVID-19 pandemic, has rapidly become a worldwide public health concern. Classified as a betacoronavirus, it is the third human coronavirus (HCoV) to emerge in the 21st century that causes severe disease, alongside SARS-CoV and MERS-CoV. The genome consists of open reading frames encoding accessory proteins and four structural proteins, including the spike protein which is a key determinant of host cell tropism. Mutations within the genome, particularly the spike gene, have been linked in-vitro to increased binding affinity to the human receptor angiotensin-converting enzyme 2 (hACE2), increased fitness in human hosts, and immune evasion. …

Creating A Georgia Southern Spider Collection: Can Dna Barcoding Help?, Guy B. Hobbs

College of Graduate Studies: Theses & Dissertations

With over 280 spider (Araneae) species recorded within the State of Georgia, USA, the need for a well-documented natural history collection with a usable voucher system is critical to continually assess spider diversity and their future ecological impact in this region. Spider identification can be daunting for the inexperienced taxonomist; it is time consuming and sometimes requires destructive procedures. Previous works have successfully used an alternative method, DNA barcoding, to correctly identify spider species while preserving their morphology. This study set forth to create the core of a well-documented spider collection within Georgia Southern University’s Institute for Coastal Plain Science …

Disease Prevalence And The Population Genetic Structure Of Crassostrea Virginica Along The Georgia Coast, Sarah Batchelor

College of Graduate Studies: Theses & Dissertations

The Eastern Oyster, Crassostrea virginica, is an ecologically important species that plays a role in protecting shorelines, water filtration, and providing habitat and food for various fish species. Perkinsus marinus and Haplosporidium nesloni are two pathogens currently affecting oyster populations. These pathogens have both been documented as causes of mass mortality events along the East coast. They greatly diminish the health of oysters, resulting in the degradation of oyster tissue, reduction in growth and reproductive ability, and may cause death. In this study, wild oysters were collected from eleven locations along the Georgia coast to investigate the presence, intensity, …

Population Genetics Of A Reintroduced Fisher (Pekania Pennanti) Population In West Virginia, Caroline E. Harms

Graduate Theses, Dissertations, and Problem Reports (ETD)

Fishers (Pekania pennanti) were reintroduced in West Virginia in 1969 with no population wide genetic analysis ever having been conducted. Genetic analysis of reintroduced populations is vital to assess genetic diversity as an indicative of population viability. My objective was to collect fisher samples throughout West Virginia, nearby states where fisher may be migrating (PA and NY), and the New Hampshire source population to provide a full genetic interpretation of the reintroduced West Virginia population. Genetic analysis was used to measure genetic diversity, admixture or delineation of subpopulations, and effective population size. Sample location and genetic data were …

In Silico Investigation Of Cardiac Arrhythmia Susceptibility In Long Qt Phenotype, Anthony Owusu-Mensah, Victoria Lam, Bright Tsevi, Michel Audette, Makarand Deo

Electrical & Computer Engineering Faculty Publications

Long QT Syndrome (LQTS) is associated with cardiac arrhythmia and sudden cardiac death. The Long QT Type 2 (LQT2) phenotype, which accounts for 35–40 % of all LQTS patients, is caused by mutations in HERG gene. The mechanisms of arrhythmia in presence of LQT2 conditions are not fully understood. We utilized anatomically and electrophysiologically realistic numerical simulations to elucidate the mechanisms of arrhythmia initiation in presence of blockade in rapid component of delayed rectifier potassium current, I_Kr. We utilized a 3D finite element model of rabbit ventricles integrated with His-purkinje network to simulate whole heart response to LQT2 …

Weak Olfactory Preferences Of The Gall Midge Asphondylia Borrichiae, Associated Fungal Endophytes And Implications On Gene Flow And Host Range Expansion, Frances S. Nagle

UNF Graduate Theses and Dissertations

Asphondylia borrichaie is a small fly (Diptera: Cecidomyiidae) that is currently undergoing host-associated sympatric divergence. Asphondylia borrichaie is an ambrosia galler, these insects utilize a host plant for oviposition, but its offspring also rely on a symbiotic fungus (or fungal community) to promote the formation of the gall as well as serve as a food source for the developing larvae. Previous studies indicate that A. borrichaie consists of two host- associated populations based on its original host plant Borrichia frutescens (Asterales: Asteraceae), and another one from the two Iva species (I. frutescens (Asterales: Asteraceae) and I. imbricata …

Statistical Methods In Genetic Studies, Cheng Gao

Dissertations, Master's Theses and Master's Reports

This dissertation includes three Chapters. A brief description of each chapter is organized as follows.

In Chapter 1, we proposed a new method, called MF-TOWmuT, for genome-wide association studies with multiple genetic variants and multiple phenotypes using family samples. MF-TOWmuT uses kinship matrix to account for sample relatedness. It is worth mentioning that in simulations, we considered hidden polygenic effects and varied the proportion of variance contributed by it to generate phenotypes. Simulation studies show that MF-TOWmuT can preserve the type I error rates and is more powerful than several existing methods in different simulation scenarios, MFTOWmuT is also quite …

The Effect Of Nutrition On Longevity And Fertility In Diverse Drosophila: A Tor-Mediated Process, Tessa E. Steenwinkel

Dissertations, Master's Theses and Master's Reports

Nutrition and growth are strongly linked, but not much is known about how nutrition leads to growth. To understand the connection between nutrition through diet, growth and/or proliferation, we need to study the phenotypes resulting from the activation and inhibition of central metabolic pathways. Here I use the model organism Drosophila melanogaster (D. mel.) and three non-model Drosophila species with different dietary needs, Drosophila guttifera (D. gut.), Drosophila deflecta (D. def.), and Drosophila tripunctata (D. tri.), to study the effects of dietary amino acid availability in these diverse flies on fecundity and …

Construction And Analysis Of Genetic Regulatory Networks With Rna-Seq Data From Arabidopsis Thaliana, Tessa Kriz

Dissertations, Master's Theses and Master's Reports

Reconstruction of gene regulatory networks (GRNs) is a fundamental aspect of genetic engineering and provides a deeper understanding of the biological processes of an organism. Two methods were implemented to reconstruct the gene regulatory networks of Arabidopsis thaliana under two treatments: methyl jasmonate (MeJa) and salicylic acid (SA). The Joint Reconstruction of multiple Gene Regulatory Networks (JRmGRN) method was utilized to construct a joint network for identifying hub genes common to both conditions in addition to networks specific to each condition. The Differential Network Analysis with False Discover Rate Control method constructed a network of connections unique to only one …

การศึกษาการแสดงออกของ Efflux Pump ในเชื้อ Acinetobacter Baumannii ที่ถูกเหนี่ยวนำให้ดื้อยา Amikacin, ณัฐนิชา บัวงามดี

Chulalongkorn University Theses and Dissertations (Chula ETD)

เชื้อแบคทีเรียแกรมลบ Acinetobacter baumannii เป็นเชื้อฉวยโอกาส ที่ก่อให้เกิดการติดเชื้อในโรงพยาบาล และมีการดื้อต่อยาปฏิชีวนะหลายชนิด จากหลายกลไกการดื้อยา รวมถึงการใช้ efflux pump ขับยาออกนอกเซลล์ การศึกษาครั้งนี้ผู้วิจัยได้ทดสอบหาค่าความเข้มข้นต่ำสุดที่ยับยั้งการเจริญเติบโตของเชื้อ (MIC) ต่อยา amikacin ในเชื้อ A. baumannii ทั้งหมด 8 ตัวอย่าง ที่ได้จากสิ่งส่งตรวจของผู้ป่วย และเชื้อสายพันธุ์มาตรฐาน ATCC 19606 พบว่าเชื้อ A. baumannii 7 ตัวอย่างมีค่า MIC อยู่ในช่วง 0.25 – 4 µg/mL (ไวต่อยา) และเชื้ออีก 2 ตัวอย่างมีค่า MIC เท่ากับ 64 และมากกว่า 256 µg/mL (ดื้อต่อยา) เมื่อเหนี่ยวนำเชื้อด้วยยา amikacin โดยเพาะเลี้ยงเชื้อในสภาวะที่มียา amikacin ความเข้มข้นเพิ่มขึ้นเป็นสองเท่า ทุก 48 ชั่วโมง ติดต่อกันเป็นเวลาหลายวัน พบว่าเชื้อ A. baumannii หลังเหนี่ยวนำด้วยยา amikacin ทั้ง 8 ตัวอย่าง มีค่า MIC เพิ่มขึ้นอยู่ในช่วง 32 ถึงมากกว่า 256 µg/mL ผลการศึกษาการใช้สารยับยั้ง efflux pump ได้แก่ สาร carbonylcyanide m-chlorophenylhydrazone (CCCP) พบว่าเชื้อ A. baumannii หลังเหนี่ยวนำด้วยยา amikacin ทั้ง 8 ตัวอย่าง มีค่า MIC ต่อยา amikacin เมื่อมีสาร CCCP ลดลงมากกว่าหรือเท่ากับ 4 เท่าของค่า MIC ต่อยา amikacin ที่ไม่มีสาร …

Breaking The Chain – The Role Of Intersexual Genetic Correlations In Sexual Dimorphism And The Consequences And Limits Of Their Evolution, Matthew Ma Maoloni, Tara Newman, Tristan Af Long Dr.

Theses and Dissertations (Comprehensive)

In many sexually reproducing species, males and females often differ in countless ways beyond their primary sexual organs. This phenomenon is known as sexual dimorphism, and it is generally considered to be an adaptive response to differences in the selection pressures experienced by males and females. Despite the advantages associated with sexual dimorphism, it does not evolve completely unhindered – there are plenty of biological effects that can limit the extent and rate of divergence between the sexes. This research project focusses on the potential role of the intersexual genetic correlation (r_mf­) – which describes the …

Composition And Homology In The Taxonomic Classification Of Escherichia Coli, Tanya Irani

Theses and Dissertations (Comprehensive)

As new techniques have been introduced, specifically the possibility of complete genome sequencing, better methods of defining bacterial species have also been proposed. One of the most recently proposed methods, using bioinformatic techniques, is to calculate the average nucleotide identity (ANI) between the homologous genome segments of different isolates. Another method for species discrimination that has been tested successfully is the similarity of DNA compositional signatures. However, in a recent update, DNA signatures split the available Escherichia coli complete genomes into three groups. To check if this result was consistent with such genomes belonging to different species, we tested methods …

Joint Modeling Of Rnaseq And Radiomics Data For Glioma Molecular Characterization And Prediction, Zeina A. Shboul, Norou Diawara, Arastoo Vossough, James Y. Chen, Khan M. Iftekharuddin

Electrical & Computer Engineering Faculty Publications

RNA sequencing (RNAseq) is a recent technology that profiles gene expression by measuring the relative frequency of the RNAseq reads. RNAseq read counts data is increasingly used in oncologic care and while radiology features (radiomics) have also been gaining utility in radiology practice such as disease diagnosis, monitoring, and treatment planning. However, contemporary literature lacks appropriate RNA-radiomics (henceforth, radiogenomics) joint modeling where RNAseq distribution is adaptive and also preserves the nature of RNAseq read counts data for glioma grading and prediction. The Negative Binomial (NB) distribution may be useful to model RNAseq read counts data that addresses potential shortcomings. …

Lepidopteran Granivory Reduces Seed Counts In A Rare Species Of Riparian Scour Prairies, Cheyenne Moore, Angela J. Mcdonnell, Scott Schuette, Christopher T. Martine

Faculty Journal Articles

In Pennsylvania Baptisia australis var. australis is found along only four waterways: the Allegheny River, Youghiogheny River, Clarion River, and Red Bank Creek. Because of its limited distribution and small number of extant populations, the species is considered state-threatened in Pennsylvania. In addition, the riparian prairie habitat that Pennsylvania Baptisia australis var. australis is restricted to is also in decline and considered vulnerable. Because of these conservation concerns, insights into the natural history of the taxon in the state is valuable and will inform conservation efforts. Field surveys and fruit collections along the Allegheny River and herbarium collections were used …

A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel

Biology Theses

Fungus-growing ants (Tribe Attini) and their fungal cultivars share a 50-million-year coevolutionary history. Large scale phylogenetic analyses depict a strong co-phyletic signal among ants and their farmed fungi yet fungus sharing among unrelated ant lineages is somewhat widespread. An overview of sharing has been hampered by a lack of genetic markers that exhibit intraspecific variation and surveys across geographic regions. For example, previous studies have shown similar sequences of the internal transcribed spacer (ITS) region of fungus in different species of Trachymyrmex, suggesting that these ant species are farming the same fungal clone. To examine whether this was a …

A Molecular Toolset For The In Vivo Detection Of A Sulfolobus Islandicus Leucyl Trna Synthetase Paralog, Nicholas Michael Bretz

Theses and Dissertations

An ancient and ubiquitous set of enzymes known as the aminoacyl-tRNA synthetases are required for the viability of all organisms. The aminoacyl-tRNA synthetases catalyze the attachment of amino acids onto tRNA molecules. The aminoacylated, or charged, tRNA is then transported and utilized at the ribosome for the synthesis of proteins. The genome of the hyperthermophilic microorganism Sulfolobus islandicus (S. islandicus) harbors a unique leucyl-tRNA synthetase paralog, LeuRS-I, of unknown function. While its duplicate, LeuRS-F, carries out all the classical functions of LeuRS-family enzymes, LeuRS-I fails to charge leucine onto tRNALeu, despite its ability to activate this amino acid and bind …

Dna Polymerase Ε: Replication Error Prevention And Consequences Of A Cancer-Associated Mutation, Chelsea R. Bulock

Theses & Dissertations

Genome integrity is necessary to prevent mutations and disease. During eukaryotic DNA replication, DNA polymerases ε (Polε) and δ (Polδ) synthesize the leading and lagging strand, respectively. Polε and Polδ also have exonuclease activity that acts in series with post-replicative mismatch repair (MMR) to remove replication errors. Defects in proofreading and MMR lead to an increase in mutations and cause cancer in humans. This dissertation focuses on several unresolved issues involving the relationship between Polε and Polδ in replication error avoidance. First, despite an abundance of data supporting the one-strand-one-polymerase replication fork model, defects in the fidelity of Polε have …

Single-Fluorophore Sensors For Mechanical Force In Living Cells, Sarah Kricheff

Honors Scholar Theses

Mechanotransduction is the process by which a mechanical stimulus is converted to a cellular signal. This process is heavily influential of cell morphology, differentiation, and behavior. However, altered levels of mechanical stimuli are also found in many pathological contexts. For example, cancerous cells have stiffer surrounding tissue than healthy cells, and research suggests that this alters cell behavior and promotes metastasis. Despite these findings, the cellular processes behind these signaling alterations remain widely unknown. Understanding these cascades is critical, as involved proteins can give us a deeper understanding of the role of mechanotransduction, and certain proteins can potentially be targeted …

An Examination Of The Influence Of Multi-Scale Processes And Connectivity On The Population And Assemblage Dynamics Of Headwater Fishes, Josh P. Hubbell

Dissertations

Typified by their branching pattern, headwaters are numerically abundant as the density of these habitats increases with increasing distance from the base of a dendritic river system. Connectivity among headwaters is complex, resulting in the spatial isolation of populations. Headwater specialists have evolved a suite of traits that permit these species to permanently reside within these habitats. The spatial configuration and connectivity of headwaters has repercussions for metapopulations and meta-assemblages. I investigated how multi-scale processes and connectivity influenced the patch occupancy, coexistence, movement ecology, population structure, and gene flow of headwater specialists. In chapter two, I used occupancy modeling to …

Modeling Neurofibromatosis Type Ii In Zebrafish, Hannah Nuszen

University Honors Program Senior Projects

Neurofibromatosis Type 2 (NF2) is a rare genetic disorder, classified as a neurocutaneous syndrome inherited through an autosomal dominant genetic mutation or deletion of the NF2 gene in humans. The tumor suppressor gene NF2 encodes the cytoskeletal protein MERLIN to promote apoptosis and inhibit abnormal cellular proliferation. Mutations in NF2 lead to a deficiency of functional MERLIN in humans and can result in hearing loss, disability, and premature death. These symptoms are due to uncontrollable growth of schwann cells generating bilateral benign tumors (schwannomas) within the nerve sheath of cranial nerve VIII. Here we seek to understand the function of …