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Investigating The Role Of Small Noncoding Rnas In Vertebrate Anoxia Tolerance, Claire Louise Riggs

Dissertations and Theses

Very few vertebrates survive extended periods of time without oxygen. Entry into metabolic depression is central to surviving anoxia, which is supported by overall suppression of protein synthesis, yet requires increased expression of specific proteins. Studying the rapid and complex regulation of gene expression associated with survival of anoxia may uncover new mechanisms of cellular biology and transform our understanding of cells, as well as inform prevention and treatment of heart attack and stroke in humans. Small non-coding RNAs (sncRNAs) have emerged as regulators of gene expression that can be rapidly employed, can target individual genes or suites of genes, …

Mechanism Of Gene Regulation By Coding Polya Tracks, Laura Lea Arthur

Arts & Sciences Electronic Theses and Dissertations

Regulation of gene expression is essential for cellular development and survival. The great variety and complexity of regulatory mechanisms underscores this fact. Messenger RNA stability and translational efficiency are often key determinants of gene expression. mRNA surveillance pathways, discovered for their role in degradation of aberrant mRNA, are now known to be instrumental in the regulation of physiologically correct mRNA stability. Thus, the study of cis elements in a transcript that can induce mRNA surveillance pathways has become an area of particular interest.

Here I report on the mechanism of gene regulation by coding polyA tracks, defined as a sequence …

Morphological And Gene Expression Plasticity In Neotropical Cichlid Fishes, Sharon Fern Clemmensen

Doctoral Dissertations

Trophic divergence in cichlid fish is linked to morphological shifts in the pharyngeal jaw apparatus. For instance, in the Heroine cichlids of Central America, the ability to crush hard-shelled mollusks is a convergent phenotype with multiple evolutionary origins. These durophagous species often have very similar pharyngeal jaw morphologies associated with the pharyngeal jaw apparatus and some of these similarities could be due to phenotypically plastic responses to mechanical stress. I examined the durophagous cichlid Vieja maculicauda for differences in pharyngeal osteology, dentition, and soft tissues when exposed to different diet regimes. Here I discuss the effect on the morphology and …

Impacts Of Oil Exposure During Early Life Development Stages In Sheepshead Minnows (Cyprinodon Variegatus) Under Different Environmental Factors, Danielle Simning

Master's Theses

The release of approximately 5 million barrels of crude oil into the northern Gulf of Mexico during the 2010 Deepwater Horizon oil spill jeopardized estuarine ecosystem health from Texas to Florida. These estuarine habitats, which serve as nurseries for many important fisheries are also prone to rapid fluctuations in environmental stressors such as oxygen concentration, and salinity. The consequence of combined exposure to crude oil and suboptimal environmental factors during early life stage development of fish is still largely unknown. The objective of this project was to investigate the impacts of exposure to crude oil in combination with varying environmental …

Chromatin Accessibility Dynamics In The Arabidopsis Root Epidermis And Endodermis During Cold Acclimation, Shawn Hoogstra

Electronic Thesis and Dissertation Repository

Understanding cell-type specific transcriptional responses to environmental conditions is limited by a lack of knowledge of transcriptional control due to epigenetic dynamics. Additionally, cell-type analyses are limited by difficulties in applying current technologies to single cell-types. A novel DNase-seq protocol and analysis procedure, deemed DNase-DTS, was developed to identify DHSs in the Arabidopsis epidermis and endodermis under control and cold acclimation conditions. Results identified thousands of DHSs within each cell-type and experimental condition. DHSs showed strong association to gene expression, DNA methylation, and histone modifications. A priori mapping of existing DNA binding motifs within accessible genes and the cold C-repeat/dehydration …

Transcriptomic Regulation Of Alternative Phenotypic Trajectories In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Amie L. Romney

Dissertations and Theses

The Annual Killifish, Austrofundulus limnaeus, survives the seasonal drying of their pond habitat in the form of embryos entering diapause midway through development. The diapause trajectory is one of two developmental phenotypes. Alternatively, individuals can "escape" entry into diapause and develop continuously until hatching. The alternative phenotypes of A. limnaeus are a form of developmental plasticity that provides this species with a physiological adaption for surviving stressful environments. The developmental trajectory of an embryo is not distinguishable morphologically upon fertilization and phenotype is believed to be influenced by maternal provisioning within the egg based on observations of offspring phenotype …

Characterizing Mekk1: Candidate Behavioural Isolation Gene, Caryn Dooner

Electronic Thesis and Dissertation Repository

Behavioural isolation can occur due to divergence in aspects of courtship and mating, and can contribute to reproductive isolation. The purpose of this study is to determine how a gene, Mekk1, contributes to female rejection behaviour between D. melanogaster and D. simulans. Unique polymorphisms were identified within D. simulans Mekk1 that could contribute to behaviour, most of which are non-coding. Both transcripts of Mekk1 appear to be expressed at similar levels in D. simulans and D. melanogaster. These data also indicate that Mekk1 may be expressed in a specific region of the brain called the mushroom body, …

Ecological Epigenetics Of Avian Range Expansions, Holly J. Kilvitis

USF Tampa Graduate Theses and Dissertations

In light of human-mediated environmental change, a fundamental goal for biologists is to determine which phenotypic characteristics enable some individuals, populations or species to be more adept at coping with such change, while rendering others more vulnerable. Studying ongoing range expansions provide a unique opportunity to address this question by allowing documentation of how novel environments shape phenotypic variation on ecological timescales. At range-edges, individuals are exposed to strong selective pressures and population genetic challenges (e.g. bottlenecks and/or founder effects), which make genetic adaptation difficult. Nevertheless, certain species, such as the house sparrow (Passer domesticus), seem to thrive in their …

Divergent Responses Of Larval And Juvenile Blue Mussels To Low Salinity Exposure, Melissa A. May

Electronic Theses and Dissertations

In this study, we compared the osmotic stress response of larval and juvenile blue mussels (Mytilus edulis) at the transcriptomic, metabolomic, and whole organism levels. Blue mussels inhabit coastal areas, where they face climate-induced reductions in nearshore salinity. Despite their ecological and economic importance, scientists do not fully understand the underlying transcriptomic and cellular mechanisms of the osmotic stress response in blue mussels or how the ability to respond to stress changes throughout development. Blue mussels spend the first weeks of life developing through several larval stages in the plankton. These early life history stages are more vulnerable …

Elucidating The Interplay Between Sodium Selenite On The Tick Amblyomma Maculatum Selenoprotein Gene Expression, Afnan M. Beauti

Honors Theses

Selenium (Se) is an element recognized as an essential micronutrient in eukaryote organisms. Selenoproteins contain selenium as selenocysteine, the 21st amino acid. Selenium plays a role in cell growth and functioning. At low concentrations, it can induce growth and at high concentrations, it can cause a cell to stop growing and potentially have toxic effects on the cell and organism. When selenium levels are high, oxidative stress results by the production of reactive oxidative species. Selenoproteins, however, can aid the antioxidant response in the cell. Ticks are arthropods of interest, as they are one of few that contain many selenogenes, …

Statistical Methods For Two Problems In Cancer Research: Analysis Of Rna-Seq Data From Archival Samples And Characterization Of Onset Of Multiple Primary Cancers, Jialu Li

Dissertations & Theses (Open Access)

My dissertation is focused on quantitative methodology development and application for two important topics in translational and clinical cancer research.

The first topic was motivated by the challenge of applying transcriptome sequencing (RNA-seq) to formalin-fixation and paraffin-embedding (FFPE) tumor samples for reliable diagnostic development. We designed a biospecimen study to directly compare gene expression results from different protocols to prepare libraries for RNA-seq from human breast cancer tissues, with randomization to fresh-frozen (FF) or FFPE conditions. To comprehensively evaluate the FFPE RNA-seq data quality for expression profiling, we developed multiple computational methods for assessment, such as the uniformity and continuity …

Hippocampal Epigenetic Changes In A Mouse Model Of Fetal Alcohol Spectrum Disorders, Eric J. Chater-Diehl

Electronic Thesis and Dissertation Repository

Fetal alcohol spectrum disorders (FASD) refers to the neurological, developmental, and behavioural abnormalities arising from in utero ethanol exposure. These abnormities included attention deficit, anxiety, and learning and memory impairment persisting into adulthood. The molecular mechanisms of such persistent behavioural changes remain unknown and are an area of intense research. In this thesis, mice were exposed to ethanol during the third trimester equivalent, the peak of synaptic development. Following this exposure, genome-wide epigenetic and gene expression and changes in the hippocampus were assessed in adult (70 day old) mice.

In the first experiment, genome-wide trimethylation of histone H3 at histone …

Age And Sex-Specific Effect Of Caloric Restriction On Circadian Clock And Longevity-Associated Gene Expression, Arten Andreyevich Astafev

ETD Archive

The rhythms in the expression of circadian clock genes are affected by calorie restriction (CR), a dietary paradigm known to increase lifespan. In our current study, we show that circadian rhythms are influenced by sex and the effects of CR are different between males and females. In particular, we found a group of clock genes which showed a sex-dependent difference in expression, as well as in response to CR (Rev-Erb α, Ror γ and both Cryptochromes: Cry1 and Cry2 genes). Two clock genes showed no difference in expression but their response to CR showed sexual dimorphism (Ror α and Rev-Erb …

Network-Based Approaches To Identify The Impacted Genes And Active Interactions, Sahar Ansari

Wayne State University Dissertations

A very important step in system biology is the identification of the networks that are most impacted in the given phenotype.

Such networks explain where the target genes are affected by some other genes, and therefore describe the mechanisms involved in a biological process.

The identified networks are used to: 1) predict the disease or the responses of the system to a specific impact, 2) find the subset of genes that interact with each other and play an important role in the condition of interest, and 3) understand the mechanisms involved in that condition.

In this thesis, we propose an …

The Role Of N-Myc Downstream Regulated Gene 1 In Breast Cancer Lipid Metabolism, Christopher James Sevinsky

Legacy Theses & Dissertations (2009 - 2024)

Altered carbohydrate and lipid metabolism are increasingly well characterized hallmarks of aggressive breast cancers. While aerobic glycolysis, or “the Warburg effect”, is a well-established metabolic adaptation exploited by tumor cells, the understanding of unique aspects of cancer lipid metabolism lags behind. This is especially true regarding the coordination of complex lipid synthesis and trafficking pathways, which remains poorly understood. N-Myc Downstream Regulated Gene1 (NDRG1) is overexpressed in many solid tumors, but its function is unclear. The importance of NDRG1 is best exemplified by the effect of null mutations on human physiology: inactivating mutations give rise to the severe autosomal recessive …