Long Noncoding Rna Ak001796 As A Mediator Of Epithelial-To-Mesenchymal Transition In Metastatic Breast Cancer, Sumayya Adib Alchalabi

Legacy Theses & Dissertations (2009 - 2024)

Long noncoding RNAs (lncRNAs) are emerging as key molecules regulating several cellular pathways and contributing to the development and progression of different diseases including cancer. The epithelial-to- mesenchymal transition (EMT), a molecular reprogramming process that plays a critical role in cancer metastasis, involves a complex interaction between protein coding and non-coding transcripts including lncRNAs. Understanding the biological significance of those lncRNAs of relatively unknown function, may help to uncover potential therapeutic targets for the aggressive subtypes of breast and other cancers. In this study, we examined the expression profiles of more than 17,000 lncRNAs in a large set of patients’ …

Intrabodies Reveal Critical Steps Involved In Ricin's Interactions With The Ribosome, Timothy Francis Czajka

Legacy Theses & Dissertations (2009 - 2024)

Ricin is a highly lethal protein toxin derived from the seeds of the castor plant, Ricinus communis. It is a Type II ribosome inactivating protein (RIP), meaning it is a heterodimer with one subunit, ricin toxin B (RTB), that mediates cell surface attachment and intracellular trafficking and a second subunit, ricin toxin A (RTA), that irreversibly shuts down protein synthesis in the cytosol. During trafficking, RTA and RTB necessarily separate in the endoplasmic reticulum, wherein RTA unfolds and translocates into the cytosol where it refolds into an enzymatically active conformation. RTA is remarkably fast acting and efficient, with few molecules …

Epitranscriptomic Writer Regulation Of Gene Expression In Escherichia Coli, William Eugene Gasperi

Legacy Theses & Dissertations (2009 - 2024)

The epitranscriptome is composed of enzyme catalyzed RNA modifications that can regulate tRNA, mRNA, and rRNA structure and function. RNA modifications can play key roles in regulating gene expression by controlling the when and how much of translation of specific transcripts. The SelU catalyzed tRNA wobble uridine (U) modification, occurs on tRNA lysine, glutamic acid, and glutamine. We have shown that E. coli deficient in selU gene are more sensitive to the antibiotic chloramphenicol (CAM) than their wild type counterparts. CAM works by inhibiting protein synthesis by binding to the ribosome and preventing peptide chain formation. We hypothesize that SelU …

Identification Of Ires Activity In Cellular Mrnas And Viral Rna Using A Circular Rna Construct, Priyanka Sehta

Legacy Theses & Dissertations (2009 - 2024)

Translation initiation is a critical step in the process of protein synthesis. The canonical way of translation initiation involves ribosomes being recruited to the 7-methyl guanosine cap present at the 5’end of the untranslated region (5’ UTR) of the RNAs. However, viral RNAs and some cellular mRNAs lack this 5’ cap structure and thus deploy an alternate non-canonical translation initiation mechanism. In non-canonical translation initiation, ribosome recruitment is facilitated by the RNA secondary structures called Internal Ribosome Entry Site (IRES) present most often in the 5’ UTR. To measure IRES-mediated translation, the dual luciferase assay has been the gold standard. …

Study Of Primary Cilium Structure And Intraflagellar Transport, Shufeng Sun

Legacy Theses & Dissertations (2009 - 2024)

Primary cilia are hair-like protrusions that stem from the basal bodies in the cytoplasm and extend into the extracellular space to sense signals. Intraflagellar transport (IFT) functions to transport cargo molecules into and out of the ciliary compartment to assemble, maintain, and disassemble the cilia. Accurate knowledge of the three-dimensional (3D) structure of primary cilia and precise details of the IFT profile is the foundation for understanding the sensory functions of primary cilia. This work covers three aspects of primary cilia. Firstly, we obtained and analyzed the overall 3D architecture of the complete primary cilia axoneme region using serial section …

Position-Scanning Peptide Libraries As Particle Immunogens For Improving Cd8+ T-Cell Responses, Michael C. Vega

Faculty Peer-Reviewed Publications

Short peptides reflecting major histocompatibility complex (MHC) class I (MHC-I) epitopes frequently lack sufficient immunogenicity to induce robust antigen (Ag)-specific CD8⁺ T cell responses. In the current work, it is demonstrated that position-scanning peptide libraries themselves can serve as improved immunogens, inducing Ag-specific CD8⁺ T cells with greater frequency and function than the wild-type epitope. The approach involves displaying the entire position-scanning library onto immunogenic nanoliposomes. Each library contains the MHC-I epitope with a single randomized position. When a recently identified MHC-I epitope in the glycoprotein gp70 envelope protein of murine leukemia virus (MuLV) is assessed, only one …

Investigating The Antitumor Effects Of A Dsrna-Nanoparticle Complex In An In Vitro Ovarian Cancer Model, Aaron Lewis

Theses and Dissertations (Comprehensive)

An estimated 1 in 70 women will be diagnosed with ovarian cancer in their lifetime. Despite advanced detection and treatment methods, it remains a silent killer with an expected survival rate of 50%. A developing method in cancer treatment is the use of compounds that stimulate the immune system to aid in the body's fight against the disease. This project focused on the use of the potent immune stimulant double-stranded RNA (dsRNA), commercially available as polyinosinic:polycytidylic acid, poly(I:C), to induce cytotoxicity in two ovarian cancer cell lines; SKOV-3 and OVCAR-3. Some challenges exist with the delivery of dsRNA due to …

Dsrna Conjugated Phytoglycogen Nanoparticles As An Innate Immune Stimulant To Prevent Viral Infections In Rainbow Trout And Atlantic Salmon, Kayla Samms

Theses and Dissertations (Comprehensive)

Salmonids are one of the world’s most farmed fish species. These aquatic vertebrate species rely heavily on their innate immune responses to defend themselves against invading pathogens. Although commercial vaccines are available against some viral and bacterial pathogens affecting salmonids, their protective efficacy is variable. Using a prophylactic inducer of local and systemic innate immune responses could have significant implications in salmonid aquaculture. A potent inducer of the innate immune response in fish is double-stranded RNA (dsRNA), a molecule that all viruses make during their replicative cycle. Polyinosinic:polycytidylic acid (polyI:C) is a synthetic dsRNA commonly used to induce type I …

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 …

Wildlife Forage Recovery Following Boreal Wildfire, Alexis Jorgensen, Jennifer Baltzer

Theses and Dissertations (Comprehensive)

Climate change is altering the boreal wildfire regime through increases in the extent and severity of burning and reductions in fire return intervals. These changes can alter the regeneration trajectory of canopy species and ground vegetation, with implications for wildlife habitat. There is some uncertainty about the timelines of when different animal species will use burned areas as their preferred forage taxa recover following fire, and how such recovery is mediated by environmental factors. Here, we aim to address these knowledge gaps through the following questions: 1) What are the main forage types consumed by boreal wildlife and how much …

Machine Learning Applications In Microbial Ecology, Human Microbiome Studies, And Environmental Monitoring, Ryan B. Ghannam, Stephen Techtmann

Michigan Tech Publications

Advances in nucleic acid sequencing technology have enabled expansion of our ability to profile microbial diversity. These large datasets of taxonomic and functional diversity are key to better understanding microbial ecology. Machine learning has proven to be a useful approach for analyzing microbial community data and making predictions about outcomes including human and environmental health. Machine learning applied to microbial community profiles has been used to predict disease states in human health, environmental quality and presence of contamination in the environment, and as trace evidence in forensics. Machine learning has appeal as a powerful tool that can provide deep insights …

Genetic Variation Within A Species Of Parasitic Nematode, Skrjabingylus Chitwoodorum, In Skunks, Allie N. Denham, Malorri R. Hughes, Robert C. Dowler, Nicholas J. Negovetich, Loren K. Ammerman

Biology Faculty Publications and Presentations

Carnivores in the families Mustelidae and Mephitidae are essential hosts for the cranial roundworm genus Skrjabingylus. A high prevalence of Skrjabingylus chitwoodorum has been observed in the striped skunk, Mephitis mephitis. Genetic barcoding studies of other nematodes have successfully used the cytochrome oxidase I (COI) mitochondrial gene to analyze genetic variation and divergence. We tested the hypothesis that low population structuring occurs within S. chitwoodorum because M. mephitis is widespread across much of North America and has high levels of gene flow. We extracted DNA from 38 samples of Skrjabingylus removed from the sinuses of M. mephitis and one from …

Bacterial Viruses Subcommittee And Archaeal Viruses Subcommittee Of The Ictv: Update Of Taxonomy Changes In 2021, Mart Krupovic, Dann Turner, Vera Morozova, Mike L. Dyall-Smith, Hanna M. Oksanen, Rob Edwards, Bas E. Dutilh, Kenneth M. Stedman, Multiple Additional Authors

Biology Faculty Publications and Presentations

In this article, we – the Bacterial Viruses Subcommittee and the Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) – summarise the results of our activities for the period March 2020 – March 2021. We report the division of the former Bacterial and Archaeal Viruses Subcommittee in two separate Subcommittees, welcome new members, a new Subcommittee Chair and Vice Chair, and give an overview of the new taxa that were proposed in 2020, approved by the Executive Committee and ratifed by vote in 2021. In particular, a new realm, three orders, 15 families, 31 subfamilies, 734 …

A Bioinformatic Analysis Of The Biosynthesis Of Carotenoids In The Copepod Tigriopus Californicus, Anchalya Balasubramaniam

Theses and Dissertations (Comprehensive)

Abstract

Biological pigments, also called biochromes, are coloured compounds which are displayed by a variety of life forms, including animals, due to selective colour absorption. The combination of light absorption and reflection enables each pigment to portray a distinct colour which results in the broad spectrum of colours we observe in our surroundings. Carotenoids are a large group of yellow, orange, and red biological pigments found in living organisms. Our current biomolecular knowledge of carotenoids is heavily derived from studying the pathway in photosynthetic prokaryotes, bacteria, fungi, and plants. Carotenoid pigments are exceptionally multifunctional as they act as photo-protectors against …

Phylogeography, Diversification, And Historical Demography Of The White-Toothed Rats (Berylmys) In Indochina, Kristy Lee Tuttle

Graduate Research Theses & Dissertations

Berylmys, the White-toothed rats, and other members of the Rattus sl (Rattus, Maxomys, Leopoldamys, Niviventer, Bandicota, and Sundamys) evolved from 3-5 million years ago during a period of dynamic landscape change in Indochinese south Asia wherein climatically stable, warm forests of Miocene and Pliocene Indochina transitioned to a modern landscape regime. From the late Pliocene through the terminal Pleistocene, climate changes, ecological shifts, rising and falling sea levels, and tectonic uplift drove adaptive radiation within Rattus sl, in complex interactions that are still not completely understood. The goal of this study is to understand species relationships and population structure in …

Novel Quantification And Localization Of Water And Solute Transporters In The Tissues Of The Spiney Dogfish (Squalus Acanthias), Tolulope B. Ojo

Electronic Theses and Dissertations

The dogfish, Squalus acanthias is a marine cartilaginous elasmobranch found in the North Atlantic and Pacific oceans. Dogfish synthesize and excrete urea as a product of nitrogen metabolism. They also convert ammonia into urea and retain this urea, such that their plasma is isosmotic or slightly hyperosmotic to the surrounding seawater. To facilitate the regulation of body fluid and to maintain ionic concentrations and osmotic pressure, Dogfish use ion and solute transporters (e.g., NCC, UT-1) and aquaporin water channel proteins. Studies have identified some of the aquaporin genes in the elasmobranch genome, but their functions are mostly uncharacterized. Recent transcriptomic …

Free-Roaming Cat Abundance Across A Habitat Gradient, Rachel E. Bird

Electronic Theses and Dissertations

There are an estimated 172 million owned and feral cats in the United States, and wildlife enthusiasts and cat owners are often at odds over how best to manage free-roaming cats. Management is needed because of the documented impacts of free-ranging cats on wildlife. Targeting these management efforts, however, is hampered by an imperfect understanding of cat distribution in the landscape. My study used game cameras and capture-recapture sampling to estimate abundance of free-roaming cats across a habitat gradient in Bulloch County, Georgia, USA. In all, I detected cats at 51% (25/49) sites with a mean of 2.1 cats per …

Predation Threat In A Variable Landscape: Connecting Predation Risk To Nesting Success For The Seaside Sparrow (Ammospiza Maritima Macgilivraii), Corina D. Newsome

Electronic Theses and Dissertations

Predation, the leading cause of nest-failure in birds, not only exists as a direct threat to nesting success, but may exacerbate other sources of nest mortality. Birds inhabiting Atlantic coastal marshes, such as Seaside Sparrows (Ammospiza maritima; hereafter SESP), are experiencing significant and rapid changes to their habitat, particularly sea level rise (SLR) and encroaching urbanization, that may affect the relative influence of nest predation on overall productivity. For SESPs, SLR presents an inherent threat to nest success in its potential to increase the frequency of nest flooding. In addition to this direct threat, the ability of SESPs …

Alternative Promoter Use Governs The Expression Of Iglon Cell Adhesion Molecules In Histogenetic Fields Of The Embryonic Mouse Brain, T. Jagomäe, K. Singh, M.-A. Philips, M. Jayaram, K. Seppa, T. Tekko, Scott F. Gilbert, E. Vasar, K. Lilleväli

Biology Faculty Works

The members of the IgLON superfamily of cell adhesion molecules facilitate fundamental cellular communication during brain development, maintain functional brain circuitry, and are associated with several neuropsychiatric disorders such as depression, autism, schizophrenia, and intellectual disabilities. Usage of alternative promoter-specific 1a and 1b mRNA isoforms in Lsamp, Opcml, Ntm, and the single promoter of Negr1 in the mouse and human brain has been previously described. To determine the precise spatiotemporal expression dynamics of Lsamp, Opcml, Ntm isoforms, and Negr1, in the developing brain, we generated isoform-specific RNA probes and carried out in situ hybridization in the developing (embryonic, E10.5, E11.5, …

Sperm Fate Is Promoted By The Mir-44 Microrna Family In The Caenorhabditis Elegans Hermaphrodite Germline, Katherine Ann Maniates, Benjamin S. Olson, Allison L. Abbott

Biological Sciences Faculty Research and Publications

Posttranscriptional regulation of gene expression, typically effected by RNA-binding proteins, microRNAs (miRNAs), and translation initiation factors, is essential for normal germ cell function. Numerous miRNAs have been detected in the germline; however, the functions of specific miRNAs remain largely unknown. Functions of miRNAs have been difficult to determine as miRNAs often modestly repress target mRNAs and are suggested to sculpt or fine tune gene expression to allow for the robust expression of cell fates. In Caenorhabditis elegans hermaphrodites, cell fate decisions are made for germline sex determination during larval development when sperm are generated in a short window before the …

Sex Chromosome Turnover In Bent-Toed Geckos (Cyrtodactylus), Shannon E. Keating, Madison Blumer, L. Lee Grismer, Aung Lin, Stuart V. Nielsen, Myint Kyaw Thura, Perry L. Wood Jr., Evan S.H. Quah, Tony Gamble

Biological Sciences Faculty Research and Publications

Lizards and snakes (squamates) are known for their varied sex determining systems, and gecko lizards are especially diverse, having evolved sex chromosomes independently multiple times. While sex chromosomes frequently turnover among gecko genera, intrageneric turnovers are known only from Gekko and Hemidactylus. Here, we used RADseq to identify sex-specific markers in two species of Burmese bent-toed geckos. We uncovered XX/XY sex chromosomes in Cyrtodactylus chaunghanakwaensis and ZZ/ZW sex chromosomes in Cyrtodactylus pharbaungensis. This is the third instance of intrageneric turnover of sex chromosomes in geckos. Additionally, Cyrtodactylus are closely related to another genus with intrageneric turnover, Hemidactylus. …

Phage Antibiotic Antagonism Of Escherichia Coli B And T4 Phage, Mikaela Griechen, Miranda Griechen, Tyler Mueller

Student Academic Conference

Antibiotic resistance has resulted in researchers finding new methods for treating diseases caused by pathogenic bacteria. Antibiotic resistance forms due to the presence of plasmids and mutations in the bacterial genome. Phage Antibiotic synergy has been reported when exposing bacteria to phages in previous studies. Bacterial immune mechanisms, specifically those that aid against bacteriophages, have been exploited by researchers as a potential treatment for infection and diseases. These mechanism includes Superinfection (Sie), Abortive infection, surface modification, etc. Escherichia coli B is a bacteria that contains an outer membrane with receptors, porins, lipopolysaccharides, and other surface molecules that aid in defense …

Stable Isotope Analysis Of An Invasive Crab Species, Charybdis Hellerii, In The Indian River Lagoon, Justin R. Meyer

Honors Undergraduate Theses

The world has never been more connected than it is today. While this is true for people, it is also true for Earth's flora and fauna. Unfortunately, this connectedness has contributed to unprecedented invasive species introductions around the world. Most introductions result in an introduced species dying out in the newly invaded territory and never becoming established. Other introduced species establish and persist for years, but never have a noticeable effect on local ecosystems. However, occasionally, an invasive species gets introduced to a new area and has negative impacts on native plant and animal life. The Indo-Pacific swimming crab, Charybdis …

Assessing The Utility Of Environmental Dna Techniques To Monitor White Shrimp (Litopenaeus Setiferus) Abundance On The Georgia Coast, Raven Hurt

Electronic Theses and Dissertations

Environmental DNA (eDNA) surveys have developed over the last decade from once being a novel tool to now acting as an effective technology often used in complement to traditional capture surveys for assessing the distribution of organisms in freshwater and marine environments. However, many uncertainties on how to properly develop, operate, and analyze eDNA based techniques still hinder this technology effectiveness in the field. The white shrimp, Litopenaeus setiferus, is a common, commercially and recreationally important species in the United States, with landings exceeding $254 million in 2020. L. setiferus is also used as a key indicator species to changes …

Reproductive Biology Of The Spinner Shark Carcharhinus Brevipinna, Off The Southeast U.S. Coast, Kristin K. Palmrose

UNF Graduate Theses and Dissertations

The spinner shark, Carcharhinus brevipinna, is a large coastal shark species that is common on the U.S. southeast coast and caught in both commercial and recreational fisheries. Little research has been conducted on the life history of C. brevipinna in the Northwestern Atlantic, presenting challenges for fishery management. This is especially true for reproductive biology, warranting a need to determine how rapidly individuals are reproducing and contributing to the population. This study aimed to characterize reproduction in C. brevipinna by determining size-at-maturity, reproductive seasonality, periodicity, and fecundity. This was accomplished by analyzing changes in reproductive tract morphology and histology, …

Interleukin-2 Receptor Alpha Nuclear Localization Impacts Vascular Smooth Muscle Cell Function And Phenotype, Kristie Nhi Dinh

Browse all Theses and Dissertations

Atherosclerosis is responsible for 50% of all deaths in western society and is the main cause of cardiovascular diseases (Pahwa et al. 2020). Vascular smooth muscle cells (VSMC) play a vital role in the development of atherosclerotic plaques; this is due to their ability to proliferate and migrate in response to inflammation and damage to arteries’ inner linings. To further understand what causes these cells to proliferate and migrate, our lab has previously found that VSMC express all three subunits of the IL-2 receptor (IL-2R). Out of these three subunits, IL-2Rα appeared to change the most depending on the phenotype …

Functional Characterization Of Infectious Hematopoietic Necrosis Virus Matrix Protein In Host Cellular Responses, Jeffery Ringiesn

Browse all Theses and Dissertations

Infectious hematopoietic necrosis virus (IHNV) is a deadly fish pathogen that poses a global threat to aquatic ecosystems and the aquaculture industry. For decades, research has focused on developing vaccine therapeutics utilizing a variety of techniques and strategies. While these studies have met with some success in identifying potential vaccine targets that provided protective immunity, a commercially viable IHNV vaccine is currently unavailable. Here we explore the relationship between the structure and function of the IHNV matrix (M) protein through the introduction of mutations that reduce anti-host effects, with the goal of developing a novel recombinant IHNV with reduced pathogenicity …

Characterizing The Effects Of 14-3-3 Isoforms On Alpha-Synuclein Toxicity In A Yeast Model, Angela Marie Braunschweiger

Browse all Theses and Dissertations

The presynaptic protein alpha-synuclein encoded by SNCA is the primary component of Lewy bodies and Lewy neurites which are the histopathological hallmarks of Parkinson’s disease. While the etiology of Parkinson’s remains unclear, SNCA mutations and copy number variations are one of several genes linked to Parkinson’s. The family of highly conserved chaperone proteins 14-3-3 have been shown to co-aggregate and share regions of 40% homology with alpha-synuclein. Mitochondrial dysfunction also plays a role in Parkinson’s disease with abnormalities in mitochondrial respiration due to interference of complex I in the electron transport chain being found in Parkinson’s patients. Alpha-synuclein increases fragmentation …

Neuroprotective And Neurotherapeuticeffects Of Dihydrotestosterone,17Β-Estradiol, And Pueraria Mirifica Extract On Cognitive Impairment In Androgen Deficient Rats, Taratorn Fainanta

Chulalongkorn University Theses and Dissertations (Chula ETD)

This study aims to understand the mechanism of action of androgen deficiency, which usually occurs in elderly men, and the neuroprotective and neurotherapeutic effects of dihydrotestosterone (DHT), 17β-estradiol (E2) and Pueraria mirifica extract (PME) on cognitive impairment in male rats. Four series of experiments were conducted. Experiment I was to understand the mechanism of action of androgen deficiency on cognitive impairment. Rats at the age of 4 months old were orchidectomized (ODX) or sham-operated (SH), kept for 3 days, 2, 4, 6, and 8 months (M0, M2, M4, M6 and M8, respectively), determined spatial learning behavior and memory capacity, and …

Unique Genomic And Phenotypic Responses To Extreme And Variable Ph Conditions In Purple Urchin Larvae, Strongylocentrotus Purpuratus, April Dawn Garrett

Graduate College Dissertations and Theses

Given the unprecedented increases in atmospheric carbon dioxide and its projected negative impacts on organismal ecology and physiology, it is crucial to understand if and how organisms will withstand such environmental changes. Due to the oceans’ service as a carbon sink, marine organisms face the added stressor of ocean acidification (OA), the process by which carbon dioxide mixes with water and decreases pH while simultaneously depleting the seawater of calcium carbonate. Marine organisms that rely on calcium carbonate for exoskeleton development are considered particularly vulnerable to OA, though previous results vary among species, leading to the question of who the …