Genetics and Genomics Commons^™

Forensic Genealogy: A Tool In Dna Analysis, Samantha Olsen

Undergraduate Honors College Theses 2016-

DNA is the basic unit of which differentiates one individual to the next. Short Tandem Repeats and Single Nucleotide Polymorphisms are two locations of DNA that have been the most successful in DNA analysis. Unique DNA profiles can be created so that interpretations can be made about the individual who contributed to the DNA sample. Systems like STRmix are currently being employed to give unbiased assumptions about the DNA profiles. There are several different statistical approaches in assigning probabilities to DNA evidence, likelihood ratio and random match probability are two common approaches. After assumptions are made, comparisons can be made …

A Zugunruhe Data Collection System Using Passive Infrared Sensors, Ryan Terry, Luis E. Ramirez, Carol Carrera, Abigail Kimmitt, Kira Delmore, Ana Goulart

Pursue: Undergraduate Research Journal

When engineers and biologists work together, there is a lot to learn on both sides. For instance, our work introduced us to zugunruhe, which is a German word that means “unrest”. It is used in the context of migratory birds, as they become restless at night, inside their cages, during their migratory period. When does zugunruhe start? It usually starts when the weather becomes cold and the days shorter, but it varies for different bird species. Moreover, global warming has caused changes in zungunruhe’s timing, which made it even harder to predict. Another question is about genetics: is …

Viropana (Vna) 5, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 5

• ID – vna 5
• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens
• Base pairs – 391

Viropana (Vna) 1, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 1

• ID – vna 1

• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens

• Base pairs – 492

Efficacy Of Aav-Mediated Gene Replacement Therapy For Mybpc3- Associated Hcm In Ipscms, Marian Henderson, Josh Meisner, Sabrina Friedline, Yao-Chang Tsan, Adam Helms

Summer Research

• Hypertrophic cardiomyopathy (HCM) is a highly morbid myocardial disease occurring in 1:200 people in the general population
• Most common genetic cause of HCM are mutations in MYBPC3, encoding for MyBP-C, a critical protein for regulating cardiac muscle contractility
• Limited treatments available primarily focus on symptomatic management and cannot reverse cardiomyopathy
• Haploinsufficiency - one allele is unable to produce sufficient protein to maintain normal cardiac function
• Adeno-associated virus (AAV) mediated gene replacement therapy recently emerged as a therapeutic option for genetic diseases due to loss of function variants causing haploinsufficiency

Viropana (Vna) 2, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 2

• ID – vna 2
• Details – Gene from a novel protein family belonging to the regeneration tool kit of Notophthalmus viridescens
• Base pairs – 396

Viropana (Vna) 4, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 4

• ID – vna 4
• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens
• Base pairs – 501

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, …

Investigation Into The Genetic Provenance Of Three Rare Plants With East-West Disjunction Patterns In Pennsylvania., Scott Schuette, Christopher T. Martine

Other Faculty Research and Publications

Rare plant conservation relies on an understanding of the natural history, biology and ecology, and real and potential threats to their populations to inform state regulations that serve to protect the species from extirpation. This work often involves extensive field surveys over several years to determine population sizes and whether those populations are seeing reductions in number of individuals necessary to maintain the genetic diversity within and between those populations. Species and populations with high genetic diversity are better equipped to withstand sudden changes to their habitats that derive from land use changes and changing climate. There are a variety …

Attitudes And Opinions About Direct-To-Consumer Genetic Testing In Undergraduate Science Students, Morgan N. Driver, Sally I-Chun Kuo, Olivia Nayeri, Chloe J. Walker, Chelsea Derlan Willians, Tricia Smith, Amy E. Adkins, Danielle M. Dick

Graduate Research Posters

Background: There has been exponential growth in the number of direct-to-consumer genetic testing kits sold in the past decade. Consumers utilize direct-to-consumer genetic tests for a number of reasons which include learning about one’s ancestry and potential ways to manage health. Emerging adults tend to be early adopters of new technologies; however, there has been little research regarding the opinions about direct-to-consumer genetic testing in emerging adults.

Methods: Data came from a study conducted in an upper-level biology course focusing on understanding undergraduate science students’ overall experiences with receiving personalized genetic testing results from 23andMe. The present study used data …

A Multispecies Perspective Into Dietary Genetic Adaptations And Ancient Migration In The Peruvian Andes, Kelsey Jorgensen

Wayne State University Dissertations

Successful adaptation to the high-elevation Andes would have required both cultural and biological adaptations by early human populations. These past adaptations continue to shape the evolutionary outcomes of both humans and non-human species today. A multispecies perspective was used to examine how humans and non-human creatures, specifically insects, were shaped by past human adaptations. This dissertation asked two primary questions: 1) Given the importance and evolutionary history of potato consumption in the Peruvian Andes, is a genetic adaptation to better digest potato starch detectable in present-day Peruvians? and 2) Using the Andean Potato Weevil (APW) phylogeny as a proxy, what …

Examining A Functional Interaction Between Chromatin Remodeler Chd1 And Histone H1 In D. Melanogaster, Breanna Kim

Scripps Senior Theses

Chromodomain-helicase-DNA-binding-protein-1 (CHD1) is a highly conserved ATP- dependent remodeling protein. It is localized to active genes and directs nucleosome spacing, while its loss has been linked to various human diseases, such as human prostate cancer. In Drosophila, CHD1 is important for fertility and wing development, and overexpression of CHD1 leads to severe wing vein defect phenotypes. The Linker Histone H1, which is known for maintaining heterochromatin and is associated with inactive genes, had been previously identified as a possible functional partner of CHD1, though the exact nature of their interaction is unclear. I undertook a genetic approach to examining the …

Retrotransposon-Mediated Transduction Of An Environmental Cue To Regulate Centrosome Fate, Shawn Patrick Murphy

Legacy Theses & Dissertations (2009 - 2024)

In 1969, the enrichment of mobile element repeat sequences led Britton and Davidson to propose the hypothesis that gene expression in higher eukaryotes is regulated through the exaptation of mobile elements. In this work, I have explored the hypothesis that mobile elements can also be harnessed by the host to regulate asymmetric cell division, thereby determining cell fate. Retrotransposons are ubiquitous eukaryotic mobile elements that transpose through an RNA intermediate. They are often active in cell types that divide asymmetrically to yield daughter cells with different fates, such as embryonic stem cells, germline stem cells, neuronal stem cells and 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 …

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. …

Mimicking The Effect Of Prolactin On Stat3/Stat5 Activity In Breast Cancer, Jennifer N. Barbuto, Sarah R. Walker

Honors Theses and Capstones

Signal transducers and activators of transcription (STAT) 3 and 5 are commonly constitutively activated in breast cancer. STAT5 can outcompete STAT3 and reduce cell proliferation and metastasis. STAT5 activation is stimulated by prolactin, a natural hormone that can be harmful at high levels. The aim of this study is to identify some possible previously developed drugs that mimic the effect of prolactin and STAT5 without the added risk in MDA-MB231 breast cancer cells. Using the CLUE database query app and STAT5 up- and downregulation signatures, three drugs (X, K, and M) were chosen based on their similarity in signatures to …

Functional Characterization Of Threonine 49 Phosphorylation Of Cytochrome C, Antoine Khobeir

Wayne State University Theses

Cytochrome c (Cytc) is a pivotal multifunctional mitochondrial protein that serves as a single electron carrier between complexes III and IV of the electron transport chain. It has important roles in both cellular respiration and apoptosis. The novel Thr49 (T49) phosphorylation of Cytc likely affects mitochondrial respiration, membrane potential, ROS production, ATP production, and apoptosis. Based on the functional characterization of previously mapped phosphorylation sites (Tyr97, Tyr48, Thr28, Ser47, Thr58) of the lab, we hypothesize that T49 phosphorylation will lead to controlled respiration, optimal intermediate mitochondrial membrane potential, lower ROS production, and inhibition of apoptosis compared to unphosphorylated Cytc. Here …

Novel Role Of Endoplasmic Reticulum-Associated Degradation In The Regulation Of Ceruloplasmin, Stephen William Hippleheuser

Wayne State University Theses

Ceruloplasmin (Cp) is a secreted ferroxidase produced by the hepatocytes that assists in the transport of iron throughout the human body. In human aceruloplasminemia patients, due to Cp deficiency excess intracellular iron buildup leads to ailments like liver cirrhosis, neurodegeneration, and blindness. We recently found that the biogenesis of Cp in the endoplasmic reticulum (ER) is regulated by a principal ER quality-control process, ER-associated degradation (ERAD). ERAD clears misfolded ER proteins for cytosolic proteasomal degradation, with the Sel-1 suppressor of lin-12-like (Sel1L)-HMG-CoA reductase degradation 1 (Hrd1) protein complex representing the most conserved branch in mammals. Interestingly, we found that Sel1L-Hrd1 …

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 …

Viropana (Vna) 3, Abijeet Singh Mehta, Panagiotis A. Tsonis, Amit Singh

Components of a Regeneration Toolkit: Notophthalmus viridescens

Viropana (vna) 3

• ID – vna 3
• Details – Gene from a novel protein family belonging to the regeneration toolkit of Notophthalmus viridescens
• Base pairs – 426

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 …

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 …

Transactivation And Mitochondrial Activity Are Affected By High Temperature In C. Elegans Sperm, Jacqueline Mcvay

Scripps Senior Theses

Sexual reproduction has a conserved flaw in that it is temperature sensitive. Exposure to high temperature leads to male infertility, but little is known about the underlying mechanism. Understanding these mechanisms is important for agriculture and reproductive medicine. Using C. elegans, we investigated two potential aspects of male fertility that may be affected by high temperature conditions: activation of sperm by seminal fluid and sperm mitochondrial activity. There are two pathways for sperm activation in C. elegans: the SPE-8 pathway in hermaphrodites and the TRY-5 pathway in male seminal fluid. Hermaphrodite sperm with a mutation in spe-8 can …

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 …

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 …

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. …

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 …

Using Genetic Approaches To Understand Tumorigenesis In Drosophila, Shawna Defreitas

College of Graduate Studies: Theses & Dissertations

The large number of conserved molecular and signaling pathways between Drosophila melanogaster and humans, makes Drosophila an effective model organism to better understand human diseases, including cancers. Previous studies by clinicians and researchers have identified PTEN, BRCA2, P53, NF1, and RB1 as key mutational drivers in High Grade Serous Ovarian Cancer (HGSOC), the most malignant form of ovarian cancer in humans. The objective of this study was to develop a tumor model in the follicle cell epithelium of the Drosophila ovary and to use immunohistochemistry to study the molecular mechanisms behind tumor development. First, the Drosophila …

Exploring The Genetic Variability Of Zebra Mussels Dreisenna Polymoprha, Maxwell Carr

Journal of Earth and Life Science

Zebra Mussels Dreisenna polymorpha are one of the most well-known invasive species here in the United States. This species can take over watersheds very quickly, causing damage to both the ecosystem and man-made structures. The basic physical behavior of this species has been well documented, but the invasive North American Zebra Mussel is much more aggressive and therefore causes more damage in the Great Lakes region compared to its native waters. Genetic variation may be playing a very large role in how and why D. polymorpha is causing such large problems for stakeholders in the United States. This review cites …

Microbiomes Of Blood-Feeding Arthropods: Genes Coding For Essential Nutrients And Relation To Vector Fitness And Pathogenic Infections. A Review, Daniel E. Sonenshine, Philip E. Stewart

Biological Sciences Faculty Publications

Blood-feeding arthropods support a diverse array of symbiotic microbes, some of which facilitate host growth and development whereas others are detrimental to vector-borne pathogens. We found a common core constituency among the microbiota of 16 different arthropod blood-sucking disease vectors, including Bacillaceae, Rickettsiaceae, Anaplasmataceae, Sphingomonadaceae, Enterobacteriaceae, Pseudomonadaceae, Moraxellaceae and Staphylococcaceae. By comparing 21 genomes of common bacterial symbionts in blood-feeding vectors versus non-blooding insects, we found that certain enteric bacteria benefit their hosts by upregulating numerous genes coding for essential nutrients. Bacteria of blood-sucking vectors expressed significantly more genes (p < 0.001) coding for these essential nutrients than those of non-blooding insects. Moreover, compared to endosymbionts, the genomes of enteric bacteria also contained significantly more genes (p < 0.001) that code for the synthesis of essential amino acids and proteins that detoxify reactive oxygen species. In contrast, microbes in non-blood-feeding insects expressed few gene families coding for these nutrient categories. We also discuss specific midgut bacteria essential for the normal development of pathogens (e.g., Leishmania) versus …