Genetics and Genomics Commons^™

A Study On The Regulation Of Mitochondrial Biogenesis And Gluconeogenesis In S. Cerevisiae, Manika Bhondeley

LSU New Orleans Theses and Dissertations

Budding yeast has been used as a powerful model organism to study the network that communicate functions of nucleus, cytoplasm and mitochondria. Depending upon environmental cues, yeast cells regulate their metabolic programming, for example, presence of glucose repress utilization of alternate carbon source to produce energy. This phenomenon is called carbon catabolite repression, which is relieved when glucose is limiting, and alternate carbon source utilization is achieved by an increase in mitochondrial biogenesis (oxidative catabolism) and the upregulation of TCA cycle and gluconeogenesis. Most of genes involved in alternate carbon source utilization are encoded in the nucleus and undergo tight …

The Evolution Of Bivalve Shell Matrix Proteins, Mark Ira Duhon Ii

LSU Doctoral Dissertations

This dissertation focuses on the molecular underpinnings surrounding the evolution of the biomineralized shells of marine bivalves. Bivalve molluscs synthesize remarkably complex shells from calcium carbonate and an organic matrix of proteins secreted from the dorsal edge of the mantle. Molecular analyses of shell matrix proteins (SMPs) have suggested high rates of gene turnover despite the conserved nature of the shell itself. Here, I used proteomic and transcriptomic data to identify the SMPs and other biomineralization proteins from seven bivalve species that diverged 3-513 Mya. Contrary to previous studies that identified only a few shared biomineralization transcripts across the Bivalvia, …

Correction To: Small Molecule Kras Agonist For Mutant Kras Cancer Therapy., Ke Xu, Dongkyoo Park, Andrew T Magis, Jun Zhang, Wei Zhou, Gabriel L Sica, Suresh S Ramalingam, Walter J Curran, Xingming Deng

Articles, Abstracts, and Reports

An amendment to this paper has been published and can be accessed via the original article.

Sleep Modifications In A Drosophila Melanogaster Model Of Fragile X Syndrome, Morgan Mclaughlin

Undergraduate Honors Theses

Fragile X syndrome (FXS) is a neurodevelopmental disorder characterized by intellectual disabilities, disruptions in sleep, and autism in humans. Mutations in Fragile X Mental Retardation gene 1 (FMR1), which codes for a protein that modifies the expression of many target proteins, are primarily responsible for this disorder. Genetic modifications of FMR1 can increase or decrease the overall amount of sleep in humans. A potential pharmaceutical target of FXS is dopamine, a critical neurotransmitter in the regulation of sleep and wakefulness. In fruit flies (Drosophila melanogaster) dopamine has been shown to alter sleep. The mushroom body, a structure in …

Status Of The Blackstripe (Fundulus Notatus) And Blackspotted (F. Olivaceus) Topminnows In The Ozark Uplands Of Central Missouri, Nathaniel Steffensmeier, Naznin Sultana Remex, Robert Hrabik, David D. Duvernell

Southeastern Fishes Council Proceedings

The topminnow species Fundulus notatus and F. olivaceus have broadly overlapping geographic distributions that extend throughout much of the central and southern United States. In the northern portion of their respective ranges, in Missouri, the regional distributions of the two species coincide largely with recognized ecoregions. In the unglaciated southern half of Missouri, F. olivaceus is distributed throughout Ozark upland habitats while F. notatus is abundant in marginal large river and prairie habitats along the Ozark borders. An exception to this partitioning is the historical report of abundant F. notatus in the Bourbeuse and upper Meramec River drainages within the …

Proteome Profile Changes During Poly-Hydroxybutyrate Intracellular Mobilization In Gram Positive Bacillus Cereus Tsu1, Hui Li, Joshua O'Hair, Santosh Thapa, Sarabjit Bhatti, Suping Zhou, Yong Yang, Tara Fish, Theodore W. Thannhauser

Agricultural and Environmental Sciences Faculty Research

Bacillus cereus is a bacterial species which grows efficiently on a wide range of carbon sources and accumulates biopolymer poly-hydroxybutyrate (PHB) up to 80% cell dry weight. PHB is an aliphatic polymer produced and stored intracellularly as a reservoir of carbon and energy, its mobilization is a key biological process for sporulation in Bacillus spp. Previously, B. cereus tsu1 was isolated and cultured on rapeseed cake substrate (RCS), with maximum of PHB accumulation reached within 12 h, and depleted after 48 h. Fore-spore and spore structure were observed after 24 h culture.

Generation And Characterization Of A Rack1 Knockout Cell Line, Roy Missall

Seton Hall University Dissertations and Theses (ETDs)

The µ-opioid receptor (MOR) is an important regulator of nociception, bearing the largest role in analgesia of all opioid receptors. This function has made MOR an effective drug-target for the clinical treatment of pain. However, opioid drugs such as morphine and fentanyl are highly addictive, and prolonged abuse can be fatal due to respiratory depression. A key determinant in the cellular and systemic responses to opioids is MOR. At the transcriptional level, MOR is positively regulated by the transcription factors, including poly-C binding protein 1 (PCBP1). Using the two-hybrid screening, PCBP1 was found to interact with receptor for activated C …

The Psychosocial Effects Of Unexpected Findings On Direct To Consumer Genetic Testing, Emily Wiseman

KGI Theses and Dissertations

Direct to Consumer (DTC) genetic testing has grown in popularity since its inception in 2010. Consumers can now order DTC tests giving them more information on their ancestry, health and ethnicity than ever before. With more information and more consumers taking the tests, this has allowed for the opportunity of unexpected findings to be generated from the tests. Previous studies have shown that consumers can learn about a health risk they were previously unaware of, and this can impact the health management and surveillance practices of consumers receiving them. Additionally, studies have shown that ethnicity results can impact consumers’ previously …

Cancer Genetic Counselors’ Perceptions Of Nutritional Recommendations, Breann Reinsch

KGI Theses and Dissertations

Objective: The purpose of this research study is to understand the perspectives of genetic counselors who work with patients in the cancer setting and explore if nutrition is a consideration when counseling patients.

Background: Evidence on the influence of nutrition on cancer risk is increasing with retrospective cohort studies. The American Cancer Society states that smoking, body mass index (BMI), poor nutrition, and excess alcohol consumption are directly linked to cancer occurrences, therefore some cancers may be preventable through lifestyle changes (American Cancer Society, 2016). In cancer genetic counseling sessions, patients are often inquiring about nutritional recommendations. A majority of …

Risk Reducing Mastectomies Among Women With Mutations In Moderate Penetrance Breast Cancer Susceptibility Genes, Jacob Comeaux

KGI Theses and Dissertations

Women who harbor mutations in breast cancer susceptibility genes are at an increased lifetime risk of developing breast cancer and are faced with decisions about managing their risks, including the decision of whether to undergo a risk reducing mastectomy (RRM). While decision making for risk management has been studied extensively for BRCA1 and BRCA2 carriers, there is much less information surrounding risk management for women with mutations in moderate penetrance genes. This is a retrospective study of 280 women undergoing genetic counseling at a Los Angeles-based academic hospital between 2009 and 2019. The study used medical records to examine rates …

Which "Me" Am I Going To Be Today? Exploring Genetic Counselors' Attitudes On Expressing Their "Authentic Self" In The Workplace, Brynna Nguyenton

KGI Theses and Dissertations

While professional organizations expect their employees to adhere to a cohesive image based on the social contract of professionalism, the modern workplace is growing increasingly diverse and freedom of self-expression is challenged by these traditionally defined norms. This study seeks to define these societal expectations and their implications in the context of a rapidly changing professional landscape. Individuals portray their true identities, or “authentic selves,” through their internal beliefs and external appearance, so naturally, these expressions may contradict the expectations for their professional appearance. Previous research has investigated professionalism, authentic selfhood, and the genetic counseling profession on separate levels, but …

Statistical Inference Of Adaptation At Multiple Genomic Scales Using Supervised Classification And A Hidden Markov Model, Lauren A. Sugden

Biology and Medicine Through Mathematics Conference

No abstract provided.

Identifying The Gap: Cancer Genetic Counseling And Testing For Underinsured Patients, Bailey Sanderson

KGI Theses and Dissertations

Background: Health care costs have increased faster than Consumer Price Index leading to patients weighing their options of medical treatment and services. One such service, genetic counseling, has grown 20% annually, in part due to the increased demand of genetic testing. Oncology care is one need for testing because 5-15% of all cancer diagnoses in the United States are inherited. Due to the fact that the Affordable Care Act does not cover all genetic counseling testing needs, and ethnic minorities are less likely to seek testing due to insurance coverage and costs, an increased effort is needed to reach …

Identification Of Clinically-Relevant Sequence Variants Within The Human Reference Genome, Lisa A. Lansdon

Research Days

No abstract provided.

Performance Analysis Of Three Bioinformatic Variant Callers Using A Somatic Reference Standard, Binu Porath, Binu Porath

Research Days

No abstract provided.

Multi-Omic Single-Cell Snapshots Reveal Multiple Independent Trajectories To Drug Tolerance In A Melanoma Cell Line., Yapeng Su, Melissa E Ko, Hanjun Cheng, Ronghui Zhu, Min Xue, Jessica Wang, Jihoon W Lee, Luke Frankiw, Alexander Xu, Stephanie Wong, Lidia Robert, Kaitlyn Takata, Dan Yuan, Yue Lu, Sui Huang, Antoni Ribas, Raphael Levine, Garry P Nolan, Wei Wei, Sylvia K Plevritis, Guideng Li, David Baltimore, James R Heath

Articles, Abstracts, and Reports

The determination of individual cell trajectories through a high-dimensional cell-state space is an outstanding challenge for understanding biological changes ranging from cellular differentiation to epigenetic responses of diseased cells upon drugging. We integrate experiments and theory to determine the trajectories that single BRAFV600E mutant melanoma cancer cells take between drug-naive and drug-tolerant states. Although single-cell omics tools can yield snapshots of the cell-state landscape, the determination of individual cell trajectories through that space can be confounded by stochastic cell-state switching. We assayed for a panel of signaling, phenotypic, and metabolic regulators at points across 5 days of drug treatment to …

The Embark® Protocol: Dog Genomics In Genetics Laboratories, Alexandra Kissel

Honors Theses

In a world of ever-advancing technology, it is imperative that young pre-health professionals are educated according to the most relevant research. One of the most fundamental, foundational concepts of health is genetics. This field is rapidly expanding, and quickly engraining itself into the realm of healthcare. Genetic testing and gene therapies, once subjects of science fiction, have become commonplace. It is more important than ever that health professionals have a concrete knowledge of genetics, and this begins with the proper education of pre-health students.

With this idea in mind, a laboratory protocol was designed for students of the Bisc 336 …

Population Genetics Of A Recent Range Expansion By The Southern Pine Beetle, Dendroctonus Frontalis, Into The Northeastern United States, Megan Stubbs

Honors Theses

Population genetics as a field of study aims to determine the genetic variation among individuals in a population, and differences among populations. Certain population genetic analyses can provide such information and be used to better understand the biological aspects to a species’ expansion beyond its native range. The southern pine beetle (SPB), Dendroctonus frontalis, has become an invasive pest to pine forests in northeastern United States with its recent range expansion. Nine microsatellite loci were first developed and then used in analyses. To determine what the genetic variation is among individuals in SPB populations across its entire range, including …

Use Of Embark Database And An Active Learning Protocol In A High School Classroom, Landon Goodreau

Honors Theses

With advances in technology, personal genome sequencing has become more affordable than ever before. With this wealth of genetic information come new individualized approaches to medicine and pharmacology, along with moral, legal, and ethical issues to carefully consider. Yet studies suggest that most members of the general public do not have the genetic literacy required to understand the implications of genomic data. It is important that today’s students are able to grasp concepts relating to their own genome to make informed medical decisions in the future. Here I describe an active learning-based activity designed to enhance high school students’ understanding …

A Genomic Analysis Of Bobcat Populations In North America With A Comparison To The Canada Lynx: An Assessment Of Local Adaptation To Unique Ecoregions And Phylogeography, Jennifer C. Broderick

Electronic Theses and Dissertations

Bobcats (Lynx rufus) are an ecologically and genetically diverse species with a large contiguous range throughout North America. The species not only has a wide array of phenotypic variation compared to other mammals, but shows marked adaptability across ecozones with differing ecological influences. It is these various selective pressures in distinctive parts of the continent that have likely led to localized adaptations within the bobcat metapopulations. The species is also marked by its ability to maintain connectivity and populations in anthropogenically developed areas, an advantage it has over other felids, including its close relative the Canada lynx ( …

Do Innexins Function In The Extreme Cold Response Of Drosophila Melanogaster, Madison A. Ward

Masters Theses, 2020-current

Nociception is an organism’s ability to detect, process and reflexively respond to potentially damaging stimuli. While the process of nociception has clear, protective advantages, inappropriate and prolonged signaling can lead to chronic pain in humans. Nociception is a vital and genetically conserved process, thus cold nociception in Drosophilaprovides a model for identifying molecular components required for nociceptor function in vertebrates. Drosophila Class III dendritic arborization (da) neurons have previously been shown to be involved in the cold nociceptive response. Due to the importance of fast response to damaging stimuli, we hypothesize that electrical synapses are involved in cold nociception. …

Multi-Generational Effects Of ∆9-Tetrahydrocannabinol Exposure On Gene Expression In Liver Tissue, Kayla Lovitt

Honors Theses

Cannabis is the most commonly used, cultivated, and trafficked illicit drug worldwide. Increased availability and acceptance of cannabis and cannabinoid-containing products provide the necessity for understanding how these substances influence aging. In this study, zebrafish (Danio rerio) were exposed to concentrations of Δ⁹-tetrahydrocannabinol (THC) (0.08, 0.4, 2 µM) during embryonic-larval development, the effects on aging were measured 30 months later and in the offspring of the exposed fish (F1 generation. We observed results indicating a biphasic and hormetic effect. Treatment with the lowest concentration of THC significantly increased egg production, while higher concentrations resulted in impaired …

A Goldenbraid Cloning System For Synthetic Biology In Social Amoebae, Peter Kundert, Alejandro Sarrion-Perdigones, Yezabel Gonzalez, Mariko Katoh-Kurasawa, Shigenori Hirose, Peter Lehmann, Koen J T Venken, Gad Shaulsky

Faculty, Staff and Students Publications

GoldenBraid is a rapid, modular, and robust cloning system used to assemble and combine genetic elements. Dictyostelium amoebae represent an intriguing synthetic biological chassis with tractable applications in development, chemotaxis, bacteria-host interactions, and allorecognition. We present GoldenBraid as a synthetic biological framework for Dictyostelium, including a library of 250 DNA parts and assemblies and a proof-of-concept strain that illustrates cAMP-chemotaxis with four fluorescent reporters coded by one plasmid.

Using A Novel Cell- Penetrating Peptide Technology To Induce Pluripotency, Laura-Maria Oja

Master of Science in Chemical Sciences Theses

Somatic stem cells have been used as a regenerative medicine tool to treat diseases like leukemia for decades, but they are limited in their ability to self-renew and differentiate. A better alternative, induced pluripotent stem cells (iPSCs), has the ability to generate cells from all three germ layers and avoid tissue rejection as well as bypass the ethical concerns related to embryonic stem cells. In 2006, Takahashi and Yamanaka discovered that only four genes were required to induce pluripotency: Oct4, Sox2, Klf4, and c-Myc (OSKM). Since then, pluripotency has been induced with OSKM most effectively by transfection or transduction. However, …

Using Genetic Panels To Predict Tenderness In Beef Cattle, Tanya M. Weber, Michael J. Colle, Gordon K. Murdoch, B J. Buseman, Jessica M. Lancaster, Jessie B. Van Buren, James A. Nasados, Phillip D. Bass

Department of Animal Science: Faculty Publications

Genetic panel use as a selection tool has grown in popularity in the beef industry. The objective of the study was to determine whether beef cattle genetically selected for tenderness generated a tender product. Igenity® (IT) panel results were provided by a cattle producer for 52 steers, which were harvested at a commercial harvest facility. Boneless strip loins (Institutional Meat Purchase Specifications #180; United States Department of Agriculture [USDA] Choice, n = 32; USDA Prime n = 20) were collected from the left side of each carcass and transported to the University of Idaho Meat Science Laboratory. Four steaks were …

Status Of The Blackstripe (Fundulus Notatus) And Blackspotted (F. Olivaceus) Topminnows In The Ozark Uplands Of Central Missouri, Nathaniel Steffensmeier, Naznin Sultana Remex, Robert Hrabik, David D. Duvernell

Biological Sciences Faculty Research & Creative Works

The topminnow species Fundulus notatus and F. olivaceus have broadly overlapping geographic distributions that extend throughout much of the central and southern United States. In the northern portion of their respective ranges, in Missouri, the regional distributions of the two species coincide largely with recognized ecoregions. In the unglaciated southern half of Missouri, F. olivaceus is distributed throughout Ozark upland habitats while F. notatus is abundant in marginal large river and prairie habitats along the Ozark borders. An exception to this partitioning is the historical report of abundant F. notatus in the Bourbeuse and upper Meramec River drainages within the …

Investigating The Redox Sensitivity Of Mitf Splice Variants, Rachel Berryman

Senior Theses

Within pigment-producing cells known as melanocytes, the transcription factor MITF is intimately involved in regulating genes associated with cell cycle maintenance and melanocyte differentiation. Research, however, has provided conflicting results on the relationship between the expression levels of MITF and melanocyte cell fate. To complicate matters, two splice variants of MITF exist, differing by only 18 base pairs. These variants have been observed at variable levels of expression in melanocyte and melanoma cells, raising the question as to their functional purpose. Building upon previous research by the Leachman/Cassidy lab that identified the redox sensitivity of MITF while additionally establishing a …

The Ecology And Evolutionary History Of Two Musk Turtles In The Southeastern United States, Grover Brown

Dissertations

Turtles are among one of the most imperiled vertebrate groups on the planet with more than half of all species worldwide listed as threatened, endangered or extinct by the International Union of the Conservation of Nature. The Southeastern United States is a global biodiversity hotspot for turtles, and it likely represents the last area on the planet of both high diversity and high abundance of turtle species. In the past century, there has been an exponential increase in the number of publications on turtles in the United States and Canada, however a recent review of the literature suggests that this …

Genetic Analysis Of Flower Color Differences Between A Hummingbird-Pollinated And A Self-Pollinated Monkeyflower (Mimulus) Species, Caitlin Foster

University Scholar Projects

Flower color plays an important role in pollinator discrimination and speciation. Understanding the genetic contributions to flower color differences between two closely related species, Mimulus cardinalis and Mimulus parishii, can improve understanding of how they developed different pollination syndromes and diverged from a recent common ancestor. M. cardinalis is hummingbird-pollinated and has large, bright red flowers while M. parishii is self-pollinated and has small, pale pink flowers. An F2 hybrid population between these two species was created to establish a platform for analysis of the genetic architecture controlling the differences in anthocyanin pigmentation. Statistical analysis of anthocyanin concentration distribution …

Comparative Analysis Of Metabolic Pathways Of Bacteria Used In Fermented Food, Keanu Hoang, Kiran Bastola

Theses/Capstones/Creative Projects

This study presents a novel methodology for analyzing metabolic pathways. Utilizing KEGG REST API through a Biopython package and file parser, data about whether or not a bacteria has an enzyme or not was extracted. The results found that differences in metabolic pathway enrichment values follow along the lines of genera and pathway type. In particular, bacteria found in food spoilage and commercial nitrogen fixing products had high values of enrichment.