Biochemistry, Biophysics, and Structural Biology Commons^™

The Role Of Parkin In Mitochondrial Dna, Eliezer Lichter

Theses & Dissertations

Mitochondria are at the center of biological phenomena such as aging and diseases, especially neurodegenerative diseases. While the discovery of mitochondria only came approximately 200 years after the cell was discovered, a lot of progress has been made since. The mitochondrial genome encodes proteins vital for mitochondrial function. These proteins are only a subset of the proteins present in mitochondria; the rest are nuclear encoded. The nucleus also encodes cytosolic proteins vital for mitochondrial maintenance. One of these is Parkin, an E3 ubiquitin ligase that ubiquitinates mitochondrial proteins as mitochondria become depolarized. Its activity has been shown to be involved …

Caribbean Reef-Building Coral-Symbiodiniaceae Network: Identifying Symbioses Critical For System Stability In A Changing Climate, Shaman Patel

All HCAS Student Capstones, Theses, and Dissertations

Increasing global ocean temperatures and frequency of marine heatwaves pose dire consequences for coral reefs. High temperatures often lead to disruptions in coral symbiosis resulting in coral bleaching, increasing the mortality of corals. However, corals can potentially avoid bleaching peril by associating with thermally tolerant symbionts. Here we provide a tool for understanding symbiosis network stability of Caribbean reef-building corals. We created a network of Caribbean hermatypic corals and their associated Symbiodiniaceae phylotypes. A bleaching model was applied to this network to test for resilience and robustness (R50) to thermal stress. It was also layered with trait data for coral …

Dpc29 Promotes Mitochondrial Translation Post-Initation In Saccharomyces Cerevisiae, Kyle Andrew Hubble

Graduate School of Biomedical Sciences Theses and Dissertations

Although the cytosolic and bacterial translation systems are well studied, much less is known about translation in mitochondria. In the yeast Saccharomyces cerevisiae, mitochondrial gene expression is predominately regulated by translational activators. These regulators are thought to promote translation by binding the elongated 5’-UTRs on their target mRNAs. Since mammalian mitochondrial mRNAs generally lack 5’-UTRs, they must regulate translation by other mechanisms. As expected, most yeast translational activators lack orthologues in mammals. Recently, a mitochondrial gene-specific translational activator, TACO1, was reported in mice and humans. To better define its role in mitochondrial translation I examined the yeast TACO1 orthologue, DPC29. …

Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins

Masters Theses

Chemosensation is achieved through the binding of chemical signals to chemoreceptor proteins embedded in the membranes of sensory neurons. The molecular identity of these receptors, as well as the downstream processing of chemosensory signals, has been well studied in arthropods and vertebrates. However, very little is known about molluscan chemosensation. The identity of chemoreceptor proteins in the nudibranch mollusc Berghia stephanieae are unknown. Data from other protostome and molluscan studies suggest Berghia may use ionotropic receptors for some forms of chemoreception. This study used a bioinformatics approach to identify potential chemosensory ionotropic receptors in the transcriptome of Berghia. A …

The Sos Response In Escherichia Coli K12: An Exploration Of Mutations In Lexa And Reca Using Fluorescence Microscopy, Steven Van Alstine

Doctoral Dissertations

Faithful replication of the genome is paramount for maintaining the fitness of an organism. Therefore, life has evolved inducible mechanisms to be able to repair damaged DNA and maintain evolutionary fitness. The SOS response is a highly conserved DNA damage inducible response that is tightly regulated. Multiple factors contribute to the ability of the cell to perform proper DNA repair and induction of the SOS response including the amount of RecA, mutations in RecA that affect competition for DNA, and other proteins that interact with the RecA filament. The complex relationship between RecA and LexA is the subject of this …

Utilizing Rnai Technology To Develop Novel Agricultural Pesticides, Ethan B. Zand

Undergraduate Student Research Internships Conference

A general description of why RNAi based pesticide technology is a breakthrough technology able to target only pests while not harming others. This presentation gives a summary of RNAi technology, the current drawbacks of conventional pesticides, and our research on how RNAi can be used against the two-spotted spidermite; a polyphagic pest that causes significant financial damage to Canadian and worldwide agriculture

Identification And Characterization Of Genetic Elements That Regulate A C-Di-Gmp Mediated Multicellular Trait In Pseudomonas Fluorescens, Collin Kessler

Electronic Theses and Dissertations

Microbial communities contain densely packed cells where competition for space and resources are fierce. These communities are generally referred to as biofilms and provide advantages to individual cells against immunological and antimicrobial intervention, dehydration, and predation. High intracellular pools of cyclic diguanylate monophosphate (c-di-GMP) cause cells to aggregate during biofilm formation through the production of diverse extracellular polymers. Genes that encode c-di-GMP catalytic enzymes are commonly mutated during chronic infections where opportunists display enhanced resistance to phagocytosis and antibiotics. Our lab uses an emergent multicellular trait in the model organism Pseudomonas fluorescens Pf0-1 to study the emergence of c-di-GMP mutations …

Dual Mechanisms Implemented By Lin-28 For Positive Regulation Of Hbl-1 Are Necessary For Proper Development Of Distinct Tissues In Caenorhabditis Elegans, Madeleine Minutillo

Graduate School of Biomedical Sciences Theses and Dissertations

In Caenorhabditis elegans, the heterochronic pathway is comprised of a hierarchy of genes that control the proper timing of developmental events. hbl-1 (Hunchback Like-1) encodes an Ikaros family zinc-finger transcription factor that promotes the L2 stage cell fate events of the hypodermis. The downregulation ofhbl-1 is a crucial step for the transition from the L2 to the L3 stage. There are two known processes through which negative regulation of hbl-1 occurs: suppression of hbl-1 expression by 3 let-7 miRNAs through the hbl-1 3’UTR and inhibition of HBL-1 activity by LIN-46. The mechanisms by which hbl-1 is positively regulated have not …

The Effects Of Stress On The Mammalian Nucleolus And Ribosome Synthesis, Russell T. Sapio

Graduate School of Biomedical Sciences Theses and Dissertations

Ribosomes are responsible for translating every protein in the cell and are essential in all domains of life. Ribosome biosynthesis (RB) takes place in the nucleolus and is an intricate hierarchical process involving over 200 factors, including ribosomal proteins, ribosomal RNA (rRNA), and trans-acting ribosome biogenesis factors (RBFs). Inhibiting RB can disrupt nucleolar integrity, causing ribosomal- and nucleolar-factors to delocalize. This can stabilize the transcription factor p53, which is normally degraded rapidly, ultimately causing cell cycle arrest or apoptosis, through a mechanism termed the nucleolar stress response (NSR). This thesis explores the effects of inhibiting RB post rRNA transcription and …

Identification Of Genomic, Proteomic, And Metabolomic Signatures Associated With Pulmonary Hypertension Syndrome In Broilers, Duaa Almansaf

Graduate Theses and Dissertations

The present dissertation contains a collection of studies that examine the genomic, proteomic, and metabolomic association to pulmonary hypertension or ascites phenotype in fast-growing broilers. Pulmonary hypertension is a multifactorial metabolic disease influenced by physiological, environmental, and nutritional factors. It is characterized by a number of structural changes including, thrombosis and adverse pulmonary vascular remodeling. Thus, the atrial pressure is increased, and the right ventricle becomes hypertrophied, resulting in heart failure and the death of the bird. Pulmonary hypertension or ascites is a global problem that has negatively impacted the economy. The increased mortality rate of broilers (25%) is estimated …

Characterization Of Genetic Pathways Involved In Resistance To A Novel Antifungal Peptide, Kayla L. Haberman

Graduate Theses and Dissertations

Antibiotic resistance is increasing prevalence, particularly in Candida glabrata. This opportunistic pathogen is closely phylogenetically related to Saccharomyces cerevisiae; however, its characterization is limited. C. glabrata is only second to Candida albicans as a fungal pathogen in immunocompromised patients. Commonly resistant to azoles, the most common fungal therapy, it has become costly and challenging to treat. A histatin 5 derived antifungal peptide, KM29, has a high degree of efficacy in Candida species and S. cerevisiae. The objective of this work is to advance our understanding of the mechanism of action of KM29 against C. glabrata. Previous work in the lab …

Investigating The Biochemical Properties Of A Novel Mutation, A194v, In Human Rad51, Briana Vollbeer

All Theses

DNA double-strand breaks (DSB) are one of the most serious DNA lesions because improper repair of a DSB can lead to loss of heterozygosity, aneuploidy, and cancer. One of the primary pathways to repair DSBs is homologous recombination (HR). HR resects the DNA around the DSB and then uses homologous DNA as a template to restore the broken sequence. RAD51 has a vital function in this pathway by forming a nucleoprotein filament on a resected end of the DSB. The nucleoprotein filament searches for homology within the homologous DNA. Once homology is located, strand invasion followed by strand exchange occurs. …

Validation Of Whole Genome Resequencing For Mapping The Genetics Of Ascites In Broilers And Viral Susceptibility In Layers, Katherine Pepper Lee

Graduate Theses and Dissertations

This dissertation focused on the efficacy and validity of whole genome resequencing (WGR) for fine mapping genetic determinants of particular traits in a given organism. Previously, our research group used WGR to identify haplotype blocks of single nucleotide polymorphisms associated with ascites resistance with some as strong candidates for use in marker-assisted selection (MAS). Chapter 2 discusses the completion of a MAS project through evaluation of ascites incidence as well as production traits of economic value to poultry producers. Thus, the MAS project also covered viability of this methodology in the industry. The MAS significantly reduced ascites incidence in broilers …

Investigating The Role Of The Cholesterol Recognition/Interaction Amino-Acid Consensus Sequence In Follicle Stimulating Hormone Receptor Function And Structure, Tatyana Lynn

Honors Theses

Human infertility is a complex disorder that can often be attributed to a dysfunction of the endocrine system. Follicle-stimulating hormone (FSH) is one of many hormones that participate in a complex process in both women and men to regulate normal reproduction. The dysfunction of this hormone and its receptor are some of the many causes of infertility. FSH is secreted by the anterior pituitary and, in women, initiates a cascade of biological events that enable ovulation. FSH carries out its function by binding and activating specific receptors. The FSH receptor (FSHR) is a G protein-coupled receptor (GPCR) that is located …

Cdc6 Is Sequentially Regulated By Pp2a-Cdc55, Cdc14, And Sic1 For Origin Licensing In S. Cerevisiae, Jasmin Philip

Dissertations, Theses, and Capstone Projects

Control of DNA replication is critical for progression of the cell cycle and genomic stability. Cyclin-dependent kinases (CDKs) coordinate numerous phosphorylation events to accomplish two biological tasks for all living organisms: DNA replication and cell division. One CDK, Cyclin-Cdc28, is responsible for cell cycle progression in budding yeast. DNA replication requires a stepwise assembly of the pre-replicative complex on DNA, including Orc1-6, Cdc6, Cdt1 and Mcm2-7, during M-G1 phase. Cdc6 contains eight Cdc28 consensus sites, SP or TP motifs. Clb5-Cdc28 phosphorylates Cdc6-T7 to recruit Cks1, the Cdc28 phospho-adaptor, for subsequent multisite phosphorylation during S phase. There are two phospho-degrons at …

A Review Of Current Methods In Avian Dietary Analysis And Their Integrated Application To Characterize The Trophic Niche Of Louisiana Waterthrush (Parkesia Motacilla)., Brandon Hoenig

Electronic Theses and Dissertations

Characterizing a species’ dietary composition presents an avenue to understand many facets of its ecological niche and can provide essential information for the species’ long-term conservation. To date, the vast majority of diet studies have relied on direct identification of prey during foraging observations or from diet samples to characterize the dietary habits of birds. However, advancements in laboratory-based approaches have revolutionized the field of trophic ecology by allowing researchers to indirectly infer dietary habits with higher resolution across greater time scales. Here, I apply two of these laboratory-based techniques, namely DNA metabarcoding and stable isotope analysis, to characterize the …

Investigation Of Dna Variability And Phylogenetic Relationships Of Perlesta (Plecoptera: Perlidae) In Mississippi, James C. Valentine, Mac H. Alford

Master's Theses

The genus Perlesta Banks, 1906 (Plecoptera: Perlidae) consists of 35 species, 33 native to the United States and Canada and two native to China. For over a century these small, brown stonefly adults and freckled yellow nymphs have gone by the name of the type species of the genus, Perlesta placida, but taxonomic work in the genus since 1989 has resulted in the recognition of additional species. These species were mostly recognized and described using morphological characteristics, but two areas that are lacking include (1) linking nymphs to adults and (2) phylogenetic analysis of all species occurring in Mississippi …

Extracellular Mechanotransduction In Marfan Syndrome: An Equivalence Principle, Stephen Haller

Theses & Dissertations

Biological tissues continuously experience mechanical stress and have evolved sophisticated mechanisms to sense mechanical stimuli. While traditional viewpoints regard cells as the ultimate sensors and processors of mechanical information, compounding evidence demonstrates that extracellular matrix, the structural component of tissues, also exhibits evolved molecular responses to force. This led us to propose a new paradigm termed extracellular mechanotransduction, in which matrix orchestrates a complementary form of force integration distinct from traditional cellular and extracellular viewpoints. We thus propose that force-sensitive signaling mechanisms evolved within the extracellular space to help cells maintain mechanical homeostasis in tissues. In this dissertation, we apply …

Novel Regulators Of Cellular Secretion Alter The Tumor Microenvironment To Drive Metastasis, Rakhee Bajaj

Dissertations & Theses (Open Access)

Lung cancer is a highly aggressive disease responsible for ~25% of all cancer-related deaths, due in part to its proclivity to metastasize. Treating metastasis holds potential for improving patient survival but requires a deeper investigation into the underlying mechanisms. Some of these processes that can regulate metastasis are: (1) Oncogenic targets of epithelial micro-RNAs (miRNAs) are epigenetically de-repressed upon loss of the miRNAs during epithelial-to-mesenchymal transition (EMT) and in cancer. EMT confers plasticity and fitness to cancer cells promoting their survival through the metastatic cascade. This cascade and EMT are initiated by loss of the miRNA200 family (miR-200) and the …

The Role Of Ccaat Binding Factor In The Regulation Of Catalase Gene Expression In Candida Albicans, Zahra Al-Rumaih

Graduate Theses and Dissertations

Candida albicans is a fungal opportunistic human pathogen. Its infections range from surficial infections like skin rash to fatal systemic infections. Filamentation growth mode is associated with C. albicans virulence because it helps penetration of the host’s epithelial cells. The CCAAT-binding factor (CBF) is a conserved heterooligomeric transcription factor found in 30% of eukaryotes genes. In C. albicans it is composed of 4 major subunits, including Hap2, Hap3, Hap4, and Hap5. Hap2 and Hap5 are essential for DNA binding and function. Hap4 has 3 homologous subunits: Hap41 and Hap42 are putative subunits of CBP. Hap43 is the only Hap4 subunit …

Mutations In The N-Terminus Of The Mod(Mdg4) Btb Domain Reveal An Unexpected Role Of Mod(Mdg4) In Chromosome Segregation In Female Meiosis, Gwyneth D E Walker, Bruce D. Mckee

Chancellor’s Honors Program Projects

No abstract provided.

Proteomic Analysis Of The Expression Of Masp1 Dragline Silk Protein In E. Coli, Sophie Rae Pazzo, Rajan Amit Patel, Kamrin Athwal, Edward Kim

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

A Patient-Derived Ipsc Model To Study Glutamate Deficiency By Shank-3 Mutation In Autism Spectrum Disorder, Tiffany Berry, Courtney Caccia

Biology Student Scholarship

Tiffany Berry ’22, Majors: Biology and Psychology

Courtney Caccia ’22, Majors: Biology and Psychology

Faculty Mentor: Dr. Charles Toth, Biology

The use of human stem cell lines derived from persons with Autism Spectrum Disorder (ASD) provides a unique opportunity to model brain growth and potential to regain brain activity for treatment. Our lab has previously used stem cells to derive 3D cardiomyocytes to examine cardiovascular disease as well as kidney organoids and macrophages to study kidney disease. Using techniques our lab has learned using these stem cell models have prepared us to examine cell communication in mutated neurons. We will …

Salicylic Acid And N-Hydroxypipecolic Acid At The Fulcrum Of The Plant Immunity-Growth Equilibrium, Alyssa Shields, Vanessa Shivnauth, Christian Danve M. Castroverde

Biology Faculty Publications

Salicylic acid (SA) and N-hydroxypipecolic acid (NHP) are two central plant immune signals involved in both resistance at local sites of pathogen infection (basal resistance) and at distal uninfected sites after primary infection (systemic acquired resistance). Major discoveries and advances have led to deeper understanding of their biosynthesis and signaling during plant defense responses. In addition to their well-defined roles in immunity, recent research is emerging on their direct mechanistic impacts on plant growth and development. In this review, we will first provide an overview of how SA and NHP regulate local and systemic immune responses in plants. We …

Amelioration Of Mitochondrial Bioenergetic Dysfunction In Diabetes Mellitus: Delving Into Specialized And Non-Specific Therapeutics For The Ailing Heart, Andrya Jean Durr

Graduate Theses, Dissertations, and Problem Reports

Morbidity and mortality of the diabetic population is influenced by many confounding factors, but cardiovascular disease (CVD), remains the leading cause of death. Mitochondrial dysfunction is central in the development of cardiac contractile dysfunction, with decreased mitochondrial bioenergetic function, increased dependence on free fatty acid utilization, and a decrease in glucose utilization having been shown to contribute to contractile dysfunction. Strategies targeting the amelioration of mitochondrial bioenergetic function are attractive for limiting diabetes-induced heart failure, and preserving health-span. The goals of this dissertation were to assess two mitochondrial-centric approaches for the amelioration of mitochondrial and cardiac contractile dysfunction in diabetes …

Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum, Farren Smith

Graduate Theses, Dissertations, and Problem Reports

Plants are some of the most diverse organisms on earth, consisting of more than 350,000 different species. To understand the underlying processes that contributed to plant diversification, it is fundamental to identify the genetic and genomic components that facilitated various adaptations over evolutionary history. Most studies to date have focused on the underlying controls of above-ground traits such as grain and vegetation; however, little is known about the “hidden half” of plants. Root systems comprise half of the total plant structure and provide vital functions such as anchorage, resource acquisition, and storage of energy reserves. The execution of these key …