Molecular Genetics Commons^™

Missense Mutation Of Msh6 Leucine 696 Has No Apparent Effect On The Dna Mismatch Repair Process, Razan H. Hammad, Rafia Rashid, Essence Tarrence, Christopher Bolden, Joanna E. Haye-Bertolozzi

XULAneXUS

Lynch Syndrome and Constitutional Mismatch Repair Deficiency are human diseases implicated in mutations of DNA mismatch repair (MMR) genes. This experiment tested a mutation of an MMR gene, MSH6, and evaluated how the mutation affected overall MMR effectiveness. Using the yeast Saccharomyces cerevisiae, we performed the CAN1 forward mutation assay to study msh6-L696F and its implications in the MMR process. We hypothesized that there would be a significant change in molecular function in the Msh6 protein in the presence of this mutation. Bioinformatic tools predicted that this amino acid change would have deleterious effects on MMR function. However, …

Life After Death: Investigating The Resistance And Recovery Of Fungal Communities To Foundation Tree Mortality, Jessie F. Marlenee

Biology ETDs

Tree mortality can have cascading effects on the composition and resilience of interacting fungal communities. Yet, little is known about the impact tree mortality, distinct from abiotic drivers (i.e., drought), has on these communities. This dissertation focuses on the resilience of fungal communities to experimental tree mortality in a piñon-juniper woodland. In chapter one, I found that piñon mortality reduced piñon fine root biomass and piñon mycorrhizal fungal diversity, whereas juniper mycorrhizal fungi were unaffected by juniper mortality. In chapter two, I revealed that piñon mortality altered the composition and spatial structure of mycorrhizal and saprotrophic fungi in the soil, …

Crispr-Induced Mutagenesis Of Arabidopsis Thaliana Gene Apetala3, Hazel Frans, Tara Phelps-Durr

SACAD: Scholarly Activities

This project aims to create CRISPR-CAS9 mutations in the APETELA3 (AP3) gene of the model plant Arabidopsis thaliana. AP3 is a class B gene critical to the petal and stamen development of Arabidopsis flowers. AP3 is defined in a MADS domain, which binds directly to DNA and may be responsible for the expression of the CaRG-box genes. AP3 works in conjunction with PISTILLATA (PI), AGAMOUS (AG), APETALA1 (AP1), and SEPALLATA (SEP) genes to specify the development in the second and third whorls of the flower. While several alleles of AP3 already exist, these alleles are strong alleles that knockout gene …

A Study To Identify The Causal Rare Genetic Variants In Primary Open And Closed Angle Glaucoma, Pseudoexfoliation Syndrome, And Associated Glaucoma, Suganya K

Theses and Dissertations

BACKGROUND: Glaucoma is the second most common cause of blindness globally typically diagnosed with a triad of clinical symptoms of increased intraocular pressure (IOP) with associated optic disc, optic nerve head (ONH) changes, and visual field defects. Genetic and environmental factors are some of the strong aetiology factors for glaucoma and identification of these factors has a potential implication in the management of the disease and its outcome. There is a paradigm shift towards understanding the genetics of glaucoma, wherein the variants in the nuclear, mitochondrial genome and other regulatory regions are being identified as contributing risk factors.

METHODOLOGY AND …

The Design, Construction, And Testing Of Mrna Vaccine Against Equine Herpes Virus, Bhawana Devkota

LSU Master's Theses

Equine Herpesvirus-1 (EHV 1) is a worldwide significant pathogen that causes respiratory illness, abortion, and neurological disorders in equine. Current vaccines, including live attenuated, inactivated, and subunit platforms, do not prevent viral latency, mucosal shedding, or cross-strain immunity, requiring alternative approaches. To address these gaps, this project explores the design, synthesis, and in vitro testing of an mRNA vaccine targeting immunogenic EHV 1 glycoprotein (gB, gC, gD, gG, and gM). Epitopes were computationally predicted using the Immune Epitope Database (IEDB), codon-optimized for Bos taurus, and cloned into pUCIDT vectors using SP6/T7 promoters. In vitro transcription (IVT) used nucleotide modifications …

The Role Of Secondary And Tertiary Structure In The Cap-Independent Translation Of Fgf-9 And Hif-1-Alpha, Amanda Michelle Whittaker

Dissertations, Theses, and Capstone Projects

Under normoxic conditions, eukaryotes initiate translation of RNA through eIF4E recognition of the 5’ cap. However, under cellular stress, eukaryotic translation must be initiated through a 4E-independent, or “cap-independent” mechanism, involving eukaryotic initiation factor 4G (eIF4G) binding directly to the 5’ untranslated regions (5’ UTR) of the RNA. eIF4G binding then recruits the ribosome to the transcript. While this mechanism is useful for translation of apoptotic transcripts and transcripts involved in cell survival, cap-independent translation is also utilized by oncogenic RNA for tumorigenesis. Previous work by our lab and others has categorized this recruitment and initiation mechanism as either internal-ribosome-entry-site …

Identification Of Benzothiophene-Derived Inhibitors Of Flaviviruses By Targeting Rna-Dependent Rna Polymerase, Leah Liu Wang, Shazeed-Ul Karim, Aidan Hand, Ryan Brunkhorst, Mackenna Petersen, Sarah Altam, Yi Liu, Luwen Zhang, Fengwei Bai, Shi-Hua Xiang

School of Biological Sciences: Faculty Publications

Flaviviruses such as Dengue, West Nile, and Zika viruses are mosquito-borne RNA viruses that can cause serious diseases in humans. To develop effective drugs for treating these viruses’ infections, we create a new approach for developing common or shared drugs that may work for several different viral species of flaviviruses. It is based on the conserved RNA-dependent RNA polymerase (RdRp), which is the key enzyme for viral replication. We built up a common structure of RdRps (POLcon) from their consensus sequence. A conserved Triple-D structural motif was identified at the active site of POLcon that has been used for virtual …

‘Who’S Your Daddy?’: Ddradseq Parentage In Broodstock-Offspring Pairs Of Diadema Antillarum In A Population Restoration Initiative, Bianca R. Rosendahl

Undergraduate Scholarship and Creative Works

In the early 1980s Diadema antillarum, or the long-spined urchin, was hit by a catastrophic mass mortality event across the western Atlantic and Gulf of Mexico, inclusive of the Florida Keys. The cause of this die-off event was likely triggered by a pathogen or environmental stressor that decimated native populations by up to 98%. The species has not yet fully recovered and is struggling with recruitment success which is why it may benefit from an ex-situ recovery program. In this study, I used single nucleotide polymorphisms (SNPs) to identify genetic variation and analyze parentage in a captive population of …

Investigating Mitochondrial Stress Response Mechanisms In Aging, Aileigh E. Daniel

Theses and Dissertations

Mitochondrial dysfunction is widely recognized as a key contributor to aging and age-related diseases. The concept of mitohormesis suggests that low levels of ROS can activate stress-responsive transcription factors, promoting adaptive mechanisms that enhance longevity. We hypothesized that changes in protein abundance under conditions of mild mitochondrial stress reflect an adaptive response, and that commonly altered proteins across diverse genetic backgrounds of mitochondrial stress can help identify key regulators of stress resilience and aging. Our study identified conserved mitochondrial stress response pathways and highlighted candidate regulators for further investigation. These regulators appear to impair mitochondrial energy production by downregulating ATP …

Accurate Body Weight Class Prediction From Mirna And Gene Expression In Blood And Saliva Samples, Kimberly Lettner

Master of Science in Forensic Science Directed Research Projects

miRNA interference on protein abundance related to glucose uptake and lipid production has been evaluated in biomedical research and linked to metabolic disorders like severe obesity. The direct regulation of protein abundance caused by miRNAs on a person’s metabolism can lead to an increased weight and overall size. Body size, measured by BMI, provides additional physical descriptions that can be combined with hair color, eye color, age, and skin pigment to aid investigations of unidentified remains or unknown suspects not found in a database. The purpose of this project was to evaluate the miRNA expression of target biomarkers in dried …

Monitoring The Seasonal Presence Of The Blue Shiner, Cyprinella Caerulea, In Little River Canyon National Preserve Using Environmental Dna, Deanna Meadows

Theses

The study of environmental DNA (eDNA) has provided researchers with a more accessible and sensitive way to identify the presence of specific species compared to traditional monitoring methods. eDNA enables species detection by analyzing environmental samples such as water or soil, which contain genetic material shed by organisms in a given area. Research indicates that eDNA techniques have become a valuable method for monitoring threatened and invasive species, proving particularly reliable for detecting aquatic species compared to traditional techniques. Quantitative PCR (qPCR) has been used in numerous eDNA studies, as it provides for greater accuracy than conventional PCR. Cyprinella …

Elevating Microrna Levels By Targeting Biogenesis With Steric-Blocking Antisense Oligonucleotides, Mallory A. Havens, Anthony J. Hinrich, Frank Rigo, Michelle L. Hastings

Biology Department Faculty Articles

MicroRNAs (miRNAs) are regulators of gene expression, and their dysregulation is linked to cancer and other diseases, making them important therapeutic targets. Several strategies for targeting and modulating miRNA activity are being explored. For example, steric-blocking antisense oligonucleotides (ASOs) can reduce miRNA activity by either blocking binding sites on specific mRNAs or base-pairing to the miRNA itself to prevent its interaction with the target mRNAs. ASOs have been less explored as a tool to elevate miRNA levels, which could also be beneficial for treating disease. In this study, using the PKD1/miR-1225 gene locus as an example, where miR-1225 is located …

From Turf To Turf: Fungal Invasion Of Ascocoryne Turficola In A Northern Michigan Bog, Evan L. Coscarelli-Trott

All NMU Master's Theses

This is the first paper to report Ascocoryne turficola Boud. 1905 (Helotiales: Ascomycota) within the United States. It is an obligate bog fungus native to Europe and Siberia, where it is extremely rare across most of its range. A. turficola appeared at Lily Pond Bog in Marquette, Michigan (87.47º W, 46.59º N) in 2019, almost contemporaneous with anecdotal reports in Minnesota and Ontario. Since 2019, the Lily Pond population has exploded and become the dominant fungus in this bog but has yet to spread to similar bogs nearby. This species is adapted to long distance dispersal and carries the potential …

The Seat Of Singular Gene Choice: Dissecting The Role Of Odorant Receptor Enhancer Elements That Lead To Mammalian Olfactory System Expression, Alessandro M. Rosa

Dissertations, Theses, and Capstone Projects

Odorant receptors (ORs) were first identified in 1991 and the initial data strongly suggested that ORs were part of a large superfamily of G-protein-coupled receptors. Within a few years of the discovery of the OR superfamily, it became clear that each OR allele was exclusively expressed in olfactory sensory neurons (OSN), and that this singular expression leads to cellular identity. Many studies over the past thirty years have sought to unlock the mysteries of the mechanism for monoallelic and monogenic OR gene activation and expression in OSNs, however no definitive model for singular gene expression has emerged.

Using a series …

Early Onset Alzheimer’S Disease Markers In Mouse Hippocampus Unveiled By Single-Cell Transcriptomic Analysis Following Cranial Radiotherapy, Tuba Aksoy

Dissertations and Theses (Open Access)

Cranial radiation therapy plays an integral role in the treatment of brain tumors but can lead to progressive cognitive deficits in survivors by mechanisms that are poorly understood. To develop preventive or mitigative strategies, it is crucial to better understand the underlying pathogenesis of radiation-induced cognitive impairments. The study investigated single-cell transcriptomics and DNA methylation changes as potential drivers of persistent cellular dysfunction after radiation exposure, specifically concentrating on the CA1-3 regions of the hippocampus and the prefrontal cortex due to their role in cognitive functions. Thirteen-week-old mice underwent whole-brain radiation at clinically relevant doses. Following whole-brain radiation, an assessment …

Conservation Genomic Investigation Of A Threatened Trout Species Endemic To The Gila River, David Thomas Camak

Biology ETDs

Climate change is a looming threat to the persistence of species, especially aquatic, imperiled species. Species native to desert streams are at a particular disadvantage, as many species already face drought, floods, wildfires, and threats from nonnative species, all of which are thought to be exacerbated by climate change. Species such as the threatened Gila Trout (Oncorhynchus gilae) already have small ranges and persist in fragmented and isolated habitats that limits gene flow between populations. Therefore, it is important to understand the current genomic status of such populations to be able to predict the future effects of climate …

Role Of Sds-22/Pp1 Phosphatase In Polarizing The Germplasm Of Caenorhabditis Elegans Embryo, Aparna Nurni Ravi

Dartmouth College Ph.D Dissertations

During asymmetric cell division, cell polarity and cell cycle are tightly coupled to ensure robust segregation of cell fate determinants and generation of cellular diversity. In the one-cell C. elegans embryo, multiple cell cycle kinases regulate cell polarization and posterior segregation of germline fate determinants (germplasm). For example, PLK-1 kinase inhibits the retention of its germplasm substrate POS-1 in the anterior, driving POS-1 segregation to the posterior (Han et al., 2018). Additionally, MBK-2 kinase disassembles P granules in the anterior through phosphorylation of the P granule scaffold MEG-3, helping to drive P granule segregation to the posterior (Wang et al., …

Ocular Gene Transfer In The Spotlight: Implications Of Newspaper Content For Clinical Communications, Shelly Benjaminy, Tania M. Bubela

Office of the Provost

Background: Ocular gene transfer clinical trials are raising hopes for blindness treatments and attracting media attention. News media provide an accessible health information source for patients and the public, but are often criticized for overemphasizing benefits and underplaying risks of novel biomedical interventions. Overly optimistic portrayals of unproven interventions may influence public and patient expectations; the latter may cause patients to downplay risks and over-emphasize benefits, with implications for informed consent for clinical trials. We analyze the news media communications landscape about ocular gene transfer and make recommendations for improving communications between clinicians and potential trial participants in light of …

New Insights On Hybridization In Potamogeton Floridanus (The Florida Pondweed), Kaitlyn R. Sampson

Graduate Theses and Dissertations (2019 - present)

Freshwater ecosystems are some of the most important and highest threatened habitats in the world, and aquatic plants play an important, but often-overlooked, role in maintaining them. Potamogeton is a diverse and ecologically important aquatic plant genus well known for taxonomic difficulty and rampant hybridization. lbis study aimed to 1) test the hypothesis that Potamogeton jloridanus (Florida pondweed) is a hybrid between P. oakesianus and P. pulcher, and 2) to investigate correlations in ecological conditions for the focal species. This study revealed the discovery of a new population of P. jloridanus in Big Coldwater Creek in Santa Rosa Co., FL, …

Mutating Lysine 336 In Msh6 Does Not Appear To Affect Dna Mismatch Repair In Saccharomyces Cerevisiae, Anthony Thompson, Daniel Reese, Noa Bennafield, Kalila Daveron, Christopher Bolden, Joanna E. Haye-Bertolozzi

XULAneXUS

Defects in the DNA mismatch repair process results in the accumulation of mutations and disease. Mutations in MSH6 and MSH2, encoding for the subunits of the MutSα complex, are often responsible for Constitutional Mismatch Repair Deficiency (CMMRD) and Lynch Syndrome (LS), respectively. This work focused on DNA mismatch repair through analysis of the MSH6 missense variant msh6-K336T. The mutation examined in this study is msh6-K336T in Saccharomyces cerevisiae, which is equivalent to msh6-K431T in humans. The mutation results in the replacement of lysine with threonine, an amino acid with different properties. It was therefore hypothesized that the mutation …

The Tissue-Specific Role Of Smn-1 In C. Elegans, Lindsey Philips

Biological Sciences Theses and Dissertations

Spinal muscular atrophy (SMA) is an autosomal recessive disease that results from mutations in the Survival Motor Neuron (SMN-1) gene. Although SMN is a ubiquitously expressed protein that acts as an RNA-binding protein (RBP), SMA is characterized by the selective degeneration of motor neurons of the lower spinal cord. Despite a clear understanding of the genetic causes underlying SMA, the mechanisms associated with low SMN levels to disease pathogenesis remains unclear. Here, we investigate the role SMN-1 has in different tissues to begin understanding possible mechanisms. This project has three aims that has guided our experiments. The first aim is …

Omani Camels From A Cultural And Genomics Perspective, Al Muatasim Al Zadjali

Electronic Theses and Dissertations

The Dromedarian camel, Camelus dromedarius, is native to the Arabian Peninsula, including the Sultanate of Oman. These camels are used for food, milk, as well as show and racing competitions. Despite their economic and cultural importance research on camels in Oman is limited. The goal of this study was to examine their genomic variation, relationship with camels in other parts of the Arabian Peninsula, and to determine if selective breeding has led to the establishment of distinct breeds in Oman. Information was compiled from multiple sources to produce a comprehensive review on the breeding, management, economic and cultural use, …

Characterizing The Expression Of The Sphingosine 1-Phosphate Pathway In Injury And Post-Traumatic Fibrosis, Nicole Cubbage

Masters Theses, 2020-current

Following injury, tissue repair allows for the restoration of the architecture and function of the injured tissue, while tissue replacement is characterized by severely damaged or non-regenerable tissue that is repaired by the laying down of extensive connective tissue, also known as fibrosis. The fibrotic process should be arrested at its early stage to have the greatest impact on preventing or reversing associate sequelae and promoting the regeneration of normal tissue. Sphingosine 1-phosphate (S1P), a metabolic product of cell membrane sphingolipids, has emerged as a pathway that may be involved in fibrosis. Most of S1P’s actions are mediated through the …

Regulation Of Intracellular Sorting Of The Bruno Protein In Drosophila Flight Muscles, Travis Main

Master's Theses

Understanding mechanisms of intracellular sorting is a fundamental inquiry of cell biology. We used the B-body and protein Bruno (Bru) as a model to study the formation of nuclear domains that are membraneless organelles inside the cell nucleus. Specifically, we sought to identify protein sequences that regulate Bru's affinity to B-bodies and protein aggregation. We generated various Bru mutants and subsequently tested them in vivo using fluorescence microscopy. We found that the protein solubility of Bru is determined through an interplay of RNA recognition motifs (RRMs) and intrinsically disordered regions (IDRs). Using truncation analysis, we identified a 31-amino acid region …

Towards Understanding The Function Of An Ets-Like Gene In Nematostella Vectensis: Generation Of A Knockout Mutant Line And A Transgenic Reporter Line, Emily Bullock

Biological Sciences Undergraduate Honors Theses

Due to their unique phylogenic position as sister to Bilateria, Cnidaria are often credited with the utility of allowing for reconstruction of ancestral biology based on characteristics shared with bilaterians and other animals. This factor makes investigation into the nervous systems of cnidarians critical in understanding early neural evolution. Wamides, a class of neuropeptides, have been shown to play a regulatory role in life cycle transitions across many different species. The cnidarian specific Wamide neuropeptide, GLWamide, has previously been identified to play an accelerator role in the metamorphic timing of a specific species of sea anemone, Nematostella vectensis. However, …

Annotation Of Hypothetical Genes In Lactococcus Lactis Ssp. Il403, Jennifer A. Tangires

Student Scholar Showcase

The human gastrointestinal tract (GIT) harnesses various microbial organisms involved in almost all processes of physiological homeostasis, among these are lactic acid bacteria (LAB). These bacteria, almost all of which belong to the order Lactobacillales, are able to produce lactic acid, and play an important role in food preservation because they produce bacteriocins. Bacteriocins are antimicrobial proteins that are used to fight off related bacteria in their environment that are competing for the same resources. This study focuses on a specific LAB strain, Lactococcus lactis ssp. IL1403 where 21.9% of its predicted genes have not yet been assigned a function. …

Comparative Genomics Of Selected Lactobacillus Helveticus Strains, Cain Petty

Undergraduate Research Conference

My research is to compare two strains (D76 and H10) of Lactobacillus helveticus and a shared gene between them. I would want to experiment with overexpression to test for any difference in the regulatory function of genes associated with CggR - the central glycolytic genes regulator. The poster I am presenting would outline this and provide a clearer understanding of genes and potential overexpression.

The Plant Disease Triangle Facing Climate Change: A Molecular Perspective, Charles Roussin-Léveillée, Christina A. M. Rossi, Christian Castroverde, Peter Moffett

Biology Faculty Publications

No abstract provided.

Managing Stress: A Study Of Stress Response Mechanisms In Mycobacteria, Augusto C. Hunt Serracin

Biology Dissertations - Archive

Mycobacteria encompass many pathogenic species known to cause severe disease in humans. A well-known example is Mycobacterium tuberculosis (Mtb), the causative agent of the lung disease tuberculosis, which kills millions of humans worldwide yearly. Pathogenic mycobacteria like Mtb are challenging to treat because of their innate ability to adapt to environmental stress. Their unique cell physiology and conserved stress responses allow them to combat biological insults, regulate growth, and regulate genes involved in stress; all these responses increase tolerance to antibiotics. The current therapies to treat mycobacterial infections are lengthy and, at times, unsuccessful, partly due to antibiotic tolerance. A …

Tim/Tam Receptors: A Potential Biomarker For Predicting Sensitivity To Zika Virus-Induced Oncolysis In Non-Small Cell Lung Cancers, Shankari Somasekar

Honors Undergraduate Theses

Non-small cell lung cancers (NSCLC) constitute 80-85% of lung cancers and are the leading cause of cancer-related deaths globally. The most common cause is prolonged smoking. Current treatment options for NSCLC include surgery, radiation, chemotherapy, targeted drug therapy, and immunotherapy. Although these medications are effective in the short term, patients often face issues of drug resistance and debilitating side effects with prolonged use. Currently, the use of Zika virus (ZIKV) is being researched as a possible alternative treatment for cancer, which minimizes side effects and the risk of drug resistance. TIM/TAM proteins are identified as the putative ZIKV receptors on …