Biology Commons^™

Surveying The Circular Rep Encoding Single Stranded (Cress) Dna Viral Consortium Found In Invasive Quagga Mussels (Dreissena Rostriformis Bugensis) And Sediments Of The Central Lake Michigan Benthos, Nicholas Gezon

Masters Theses

Globalization and resulting increases in international trade has allowed for the movement of species between almost all ecosystems on Earth. The Great Lakes in particular has seen a number of high impact invasive species that have moved in following the opening of the lakes to intercontinental shipping trade. This research specifically focuses on the benthic community of Lake Michigan which has seen significant community shifts including declines of the amphipods Diporeia spp. and the expansion of invasive quagga mussels (Dreissena rostriformis bugensis). Little is known about the viral community in the benthos of Lake Michigan and how …

Comparing The Effectiveness Of Alternative And Prescription Antibiotics Against Gram-Positive Bacteria, Rachel Jenkins, Roan Dickenson, Sam Turnbull, Marcela Torres

Senior Theses

The rapid emergence of antibiotic-resistant bacteria is a global public health concern that threatens the efficacy of antibiotic drugs. We found that natural remedies, specifically coconut oil, honey and cinnamon essential oil, have the potential to be used as a clinical alternative to treat antibiotic-resistant infections. In this experiment, we performed a disk diffusion test and measured the area of inhibition of each treatment to compare the effectiveness of natural and prescription antibiotics. Cinnamon essential oil showed significantly greater antibiotic activity compared to a prescription treatment, amoxicillin. With bacterial resistance continuously expanding, more work needs to be done to determine …

Species Interactions Weakly Modify Climate-Induced Tree Co-Occurrence Patterns, Paige E. Copenhaver-Parry, David M. Bell

Faculty Publications - Department of Biological & Molecular Science

Aims: Species distributions are hypothesized to be underlain by a complex association of processes that span multiple spatial scales including biotic interactions, dispersal limitation, fine-scale resource gradients and climate. Species disequilibrium with climate may reflect the effects of non-climatic processes on species distributions, yet distribution models have rarely directly considered non-climatic processes. Here, we use a Joint Species Distribution Model (JSDM) to investigate the influence of non-climatic factors on species co-occurrence patterns and to directly quantify the relative influences of climate and alternative processes that may generate correlated responses in species distributions, such as species interactions, on tree co-occurrence patterns. …

Ecology Of Hatchling Alligator Snapping Turtles (Macrochelys Temminckii), Sarah J. Spangler

Graduate Theses/Dissertations

Little is known about the first year of life for many of the world’s freshwater turtles. This is due in part to their cryptic nature and the difficulty of locating hatchlings in the wild. The lack of information about this demographically important age group has led researchers to draw conclusions from indirect inferences about survival rates and ecological roles of hatchlings that may or may not be accurate. To begin filling in some of these gaps, I focused on the first year in an alligator snapping turtle’s life. I studied: (1) circadian and circannual patterns of activity, (2) growth rates …

Genome Sequences Of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, Darthp, Hammy, Krueger, Lasthope, Peanam, Phelpsodu, Phrank, Sirphilip, Slimphazie, And Unicorn, Kirk R. Anders, Nazir Barekzi, Aaron A. Best, Gregory D. Frederick, Dmitri V. Mavrodi, Edwin Vasquez, Sea-Phages, Nana Yaa A. Amoh, Frederick N. Baliraine, William J. Buchser, Thomas P. Cast, Carmen E. Chamberlain, Hui-Min Chung, William A. D'Angelo, Christian T. Farris, Mariceli Fernandez-Martinez, Haley D. Fischman, Mark H. Forsyth, Anna G. Fortier, Kara F. Gallo, Greta J. Held, Miguel A. Lomas, Natalia Y. Maldonado-Vasquez, Claudia H. Moonsammy, Peace Namboote, Sudip Paudel, Sarah-Elizabeth Polley, Gabriella Reyes, Michael R. Rubin, Margaret S. Saha, Joseph Stukey, Tristan D. Tobias, Rebecca A. Garlena, Ty H. Stoner, Steven G. Cresawn, Deborah Jacobs-Sera, Welkin H. Pope, Daniel A. Russell, Graham F. Hatfull

Faculty Publications

We report the genome sequences of 14 cluster K mycobacteriophages isolated using Mycobacterium smegmatis mc²155 as host. Four are closely related to subcluster K1 phages, and 10 are members of subcluster K6. The phage genomes span considerable sequence diversity, including multiple types of integrases and integration sites.

The Cost Of Roaming Free: Assessing The Effects Of Plant Secondary Metabolites On Diet Selection And Nutritional Condition In A Free-Ranging Generalist Herbivore, Daniel Patrick Melody

Boise State University Theses and Dissertations

Large vertebrate herbivores have a wide variety of browsing options available. However, most plants contain a suite of plant secondary metabolites (PSMs) that can have toxic effects when ingested. Herbivores must therefore make dietary choices that minimize the potentially harmful effects of PSM ingestion and maximize the use of available nutrients and protein. During winter months, in northern latitudes, climatological factors restrict browsing options and many populations of herbivores must subsist primarily on forage that is relatively poor in nutritional quality and high in PSMs. Many species of herbivores have developed a suite of behavioral and physiological adaptations to cope …

Analyzing Coxsackievirus B3 Genomic Rna By Site Directed Mutagenesis And Shape Analysis, Sara Smith

Theses/Capstones/Creative Projects

Virulent Coxsackievirus B3 (CVB3) is linked to myocarditis, pancreatitis, and type I diabetes. Avirulent CVB3 doesn’t cause disease. CVB3 possesses a positive, single-stranded ribonucleic acid (RNA) genome containing 7,400 nucleotides, organized into four sections: a 5’ untranslated region (5’ UTR), a single open reading frame, a 3’ untranslated region, and a poly-A tail. The 5’ UTR is 743 nucleotides divided into 7 domains. Mutations within the 5’ UTR can alter RNA structure, and thus alter virulence. Nucleotide associations responsible for higher level RNA folding patterns and structure haven’t been defined. We are investigating the 5’ UTR by selective 2’ hydroxyl …

Behavioral Ecology And Associated Virology Of Mosquito-Host Interactions In Southern California, Oliver Eshun

Loma Linda University Electronic Theses, Dissertations & Projects

Elucidating characteristics of mosquito-host interactions are critical for understanding the ecology and epidemiology of mosquito-borne diseases. In this dissertation, I conducted three studies to explore potential mosquito-host interactions and associated virus infection rates. I first demonstrated that mosquito captures at CO2-baited traps decreased most markedly with height above ground, and also decreased with distance from water at a riparian area but not at an open water source lacking a vegetated border. Birds might therefore prefer elevated nests or roosts to avoid mosquitoes. The second study examined the anti-mosquito behaviors of budgerigars (Melopsittacus undulatus) in a laboratory study. The birds defended …

A Comparative Microbial Composition Assessment Of Stormwater, Urban Runoff And Wastewater, Rose Syomiti Mutiso

Loma Linda University Electronic Theses, Dissertations & Projects

The goal of this study was to compare two methods for assessment of fecal indicator bacteria (FIB) in urban runoff (n = 96), stormwater (n = 8), and wastewater (n = 16). We quantified the densities and reductions of E. coli and Enterococcus, in raw stormwater, treated urban off from the Santa Monica Urban Runoff Recycling Facility (SMURRF) and wastewater from the Eastern Municipal Water District’s (EMWD) Moreno Valley water reclamation facility. We compared the overall FIB recovery efficiency by two varieties of USEPA-approved, culture-based laboratory methods in each type of water. The two types of methods were the IDEXX …

Yeast Dynamin And Ypt6 Converge On The Garp For Endosome-To-Golgi Trafficking, Pelin Makaraci

Graduate Theses/Dissertations

Protein recycling is an important cellular process required for cell homeostasis. Results from prior studies demonstrated that Vps1, a dynamin homologue in yeast, is implicated in protein recycling from the endosome to the trans-Golgi Network (TGN). However, the function of Vps1 in relation to Ypt6, a master GTPase in the recycling pathway, remains unknown. The present study reveals that Vps1 physically interacts with Ypt6 if at least one of them is full-length. It was found that overexpression of full-length Vps1, but not GTP hydrolysis-defective Vps1 mutants, is sufficient to rescue abnormal phenotypes in membrane trafficking pathways provoked by loss …

Heat And Mass Transfer Effects Of Peristaltic Transport Of A Nano Fluid In Peripheral Layer, K. M. Prasad, N. Subadra, M, A. S. Srinivas

Applications and Applied Mathematics: An International Journal (AAM)

This paper deals with a theoretical investigation of heat and mass transfer effects of peristaltic transport of a nanofluid in peripheral layer. By using appropriate methods, the velocity in the core region as well as in the peripheral region, pressure drop, time averaged flux, frictional force, temperature profile, nanoparticle phenomenon, heat transfer coefficient and mass transfer coefficient of the fluid are investigated, using lubrication theory. Effects of different physical parameters like viscosity ratio, mean radius of the central layer, Brownian motion parameter, thermophoresis parameter, local temperature Grashof number as well as local nanoparticle Grashof number on pressure rise characteristics, frictional …

Draft Genome Sequence Of A Monokaryotic Model Brown-Rot Fungus Postia (Rhodonia) Placenta Sb12, Jill Gaskell, Phil Kersten, Luis F. Larrondo, Paulo Canessa, Diego Martinez, David Hibbett, Monika Schmoll, Christian P. Kubicek, Angel T. Martinez, Jagjit Yadav, Emma Master, Jon Karl Magnuson, Debbie Yaver, Randy Berka, Kathleen Lail, Cindy Chen, Kurt Labutti, Matt Nolan, Anna Lipzen, Andrea Aerts, Robert Riley, Kerrie Barry, Bernard Henrissat, Robert Blanchette, Igor V. Grigoriev, Dan Cullen

Biology

We report the genome of Postia (Rhodonia) placenta MAD-SB12, a homokaryotic wood decay fungus (Basidiomycota, Polyporales). Intensively studied as a representative brown rot decayer, the gene complement is consistent with the rapid depolymerization of cellulose but not lignin.

Ecological And Oceanographic Influences On Leatherback Turtle Behavior And Scyphozoan Jellyfish Distributions In The Gulf Of Mexico, Katrina Aleksa

Dissertations

Leatherback turtles (Dermochelys coriacea) are a wide-ranging, oceanic species that feed exclusively on gelatinous zooplankton. Leatherback have been spotted in the Gulf of Mexico (GoM) for several decades and consistently had a high level of interactions with longline fisheries. However, no quantitative studies have been performed to address the spatiotemporal distribution of these turtles in the GoM. This research determines 1) leatherback movements and high-use areas in the GoM, 2) their association with oceanographic features, 3) the distribution and density of two abundant medusae in the northern GoM and any association with biophysical parameters, and 4) the body …

Delayed Effects Of Sub-Lethal Lampricide, 3-Trifluoromethyl-4-Nitrophenol (Tfm), Exposure On The Metabolic Physiology Of Juvenile Lake Sturgeon (Acipenser Fulvescens), Matthew J. Symbal

All NMU Master's Theses

The lampricide 3-trifluoromethyl-4-nitrophenol (TFM) can be lethal to juvenile lake sturgeon (Acipenser fulvescens) at high concentrations used to control invasive sea lamprey (Petromyzon marinus). Little is known about how TFM would affect juvenile lake sturgeon (age-0) at the sub-lethal concentrations encountered during routine lampricide treatments; specifically, its effects on growth, stress response, and metabolism. Age-0 lake sturgeon were exposed to TFM concentrations at levels 0.0x, 0.5x, and 1.0x the minimum lethal concentration (mlc) of TFM required to kill 99.9% of sea lamprey larvae during a routine stream treatment. The mlc was estimated based on pH and alkalinity …

The Relative Importance Of Fire History, Management Treatments, Biotic, And Abiotic Factors On The Abundance Of Key Vegetative Components In An Endangered Sagebrush-Steppe Ecosystem, Ann Marie Raymondi

Boise State University Theses and Dissertations

Dryland ecosystems are globally distributed and occupy nearly half of Earth’s terrestrial surface. Drylands are particularly vulnerable to degradation and their restoration has become a global concern. Sagebrush-steppe ecosystems in the intermountain western United States have been subject to decades of active management efforts to address invasive species and restore plant communities, and can serve as a relevant case study to investigate dynamics between fire, invasive species, and management treatments in a representative dryland system. My objective was to determine the relative importance of fire history, management treatment history, abiotic, and biotic factors in relation to the abundance of key …

Characterization Of Notch1 And Pi3k-Pten-Akt/Mtor Pathway Interaction In Head And Neck Squamous Cell Carcinoma, Kyriante' Henry

Dissertations and Theses (Open Access)

Head and neck squamous cell carcinoma (HNSCC) affects various mucosal sites of the upper aerodigestive tract, including the nasal and oral cavities, the nasopharynx, and the oropharynx. More than five hundred thousand new cases of HNSCC occurred in 2011 alone, with 50,000 reported cases in the United States. This trend made HNSCC the seventh most common non-skin cancer worldwide (Ferlay et al., 2015). Although significant epidemiological and pathological advancements have been made, survival rates have not improved much over the last 40 years, leaving a mortality rate that remains at approximately 50%. An unbiased drug screen demonstrated that HNSCC cell …

Insights Into The Therapeutic Potential Of Salt Inducible Kinase 1: A Novel Mechanism Of Metabolic Control, Randi Fitzgibbon

Dissertations and Theses (Open Access)

Salt inducible kinase 1 (SIK1) has been considered a stress-inducible kinase since it was first cloned in 1999. Continued efforts since this time have been dedicated to characterizing the structure and function of SIK1. Such research has laid the ground work for our understanding of SIK1 action and regulation in tissue and stimuli dependent manners. The fundamental findings of this dissertation continue in this tradition and include investigations of SIK1 regulatory mechanisms in skeletal muscle cells, the cellular and physiological effects of SIK1 loss of function in vitro and in vivo, and intracellular metabolic and mitochondrial regulation by this …

Examining The Understanding Of Inquiry-Based Learning And Teaching Among Undergraduate Teachers And Students, Maren Hudson

Electronic Theses and Dissertations

One of the main aims of inquiry is to engage students as active, not passive, participants in science. The purpose of this study is to describe science educators’ and students’ views about inquiry-based instruction in order to better understand and improve implementation of evidence-based teaching strategies. Inquiry-based techniques have been shown to improve student understanding of scientific concepts, yet, there continue to be challenges in implementing these techniques. This research project utilizes Q Methodology, a research method that captures both common and disparate measures of subjectivity, to identify commonalities and defining viewpoints about inquiry-based teaching and learning. Three significantly different …

Small Rna-Dependent Gene Silencing In The Green Alga Chlamydomonas Reinhardtii: Functions And Mechanisms, Eun Jeong Kim

School of Biological Sciences: Dissertations, Theses, and Student Research

Small RNAs (sRNAs), ~20-30 nucleotides in length, are non-coding RNAs that play essential roles in the regulation of gene expression in eukaryotes. They lead to inactivation of cognate sequences at the post-transcriptional level via a variety of mechanisms involved in translation inhibition and/or RNA degradation.

In the Chlorophyta Chlamydomonas reinhardtii, however, the molecular machinery responsible for sRNA-mediated translational repression remains unclear. To address the mechanisms of translation inhibition by sRNA, we have isolated an RNAi defective mutant (Mut26), which contains a deletion of the gene encoding the homolog of CCR4 in Chlamydomonas. We investigated the expression …

Genetic Diversity Of Kemp's Ridley (Lepidochelys Kempii) Sea Turtles On South Padre Island, Texas, Hilary R. Frandsen

Theses and Dissertations

In 2010, researchers observed an abrupt decline in nesting numbers of the Kemp’s ridley following 35 years of positive growth. In wake of this halt, and subsequent lowered nesting averages, evaluation of the genetic diversity of remaining individuals is relevant to investigate the plausibility of a genetic bottleneck, and determine the reproductive stability of the Kemp’s ridley.

Here, I evaluate the genetic diversity within a sampling of the Kemp’s ridleys on South Padre Island using two methods: targeting the mitochondrial control region and targeting the complete mitochondrial genome. Opportunistic samples were donated from juvenile ridleys on the East coast, and …

Foxo3 Regulation Of Stem Cell Markers Oct4 And Sox2 In Pten-Null Glioblastomas, Eduardo Martinez

Theses and Dissertations

The PI3K pathway controls many cellular processes such as cell growth, survival, metabolism, apoptosis, and differentiation. Canonically, PI3K activates AKT leading to subsequent nuclear exportation of FOXO transcription factors. Dysregulation of the PI3K pathway is a hallmark in many cancers and often is attributable to a null mutation in PTEN. PTEN is a phosphatase that reverses the reactions catalyzed by PI3K. Loss of PTEN leads to constitutive inactivation of tumor suppressor FOXO proteins. However, there is increasing evidence that FOXO may still reside and promote transcriptional activity in the nucleus despite high PI3K output within certain advance cancers and …

Genetic Differentiation Of Two Species Of Buckwheat (Eriogonum), Jenessa Blotter Lemon

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Limestone mining in the San Franicso Mountain Range of west central Utah threatens the survival of a rare endemic species of buckwheat (Eriogonum soredium). This species is an edaphic endemic, only found growing on the outcrops of the Ordovician limestone mines in the area. Eriogonum soredium is a candidate for governmental protection under the Endangered Species Act (ESA). However, a common, widespread buckwheat (Eriogonum shockleyi) appears to be closely related to the narrow endemic. The genetic relatedness of the rare and and common species will greatly influence the decision of United States Fish and Wildlife Service …

Phylogeography Of An Estuarian Calanoid Copepod; Acartia Tonsa In The Texas Gulf Of Mexico, Nicole J. Figueroa

Theses and Dissertations

The calanoid copepod, Acartia tonsa is one of the most abundant and well-studied estuarian species. However, the idea that this cosmopolitan species has unrestricted dispersal and high gene flow has been challenged. In this study, a more holistic picture of the phylogeography of A. tonsa was developed using the mitochondrial gene cytochrome oxidase one (mtCOI). Multiple new lineages were found in the Texas Gulf of Mexico that are basal to Northeastern Atlantic lineages. Connectivity was also observed between Brazil and the Texas Gulf of Mexico. The revised phylogeny shows a clear pattern of cryptic speciation as the species made a …

Intraspecific Differences In Molecular Stress Responses And Coral Pathobiome Contribute To Mortality Under Bacterial Challenge In Acropora Millepora, Rachel M. Wright, Carly D. Kenkel, Carly E. Dunn, Erin N. Shilling, Line K. Bay, Mikhail V. Matz

Biological Sciences: Faculty Publications

Disease causes significant coral mortality worldwide; however, factors responsible for intraspecific variation in disease resistance remain unclear. We exposed fragments of eight Acropora millepora colonies (genotypes) to putatively pathogenic bacteria (Vibrio spp.). Genotypes varied from zero to >90% mortality, with bacterial challenge increasing average mortality rates 4-6 fold and shifting the microbiome in favor of stress-associated taxa. Constitutive immunity and subsequent immune and transcriptomic responses to the challenge were more prominent in high-mortality individuals, whereas low-mortality corals remained largely unaffected and maintained expression signatures of a healthier condition (i.e., did not launch a large stress response). Our results suggest that …

Understanding Community And Ecophysiology Of Plant Species On The Colorado Plateau, Hannah Elizabeth Yokum

Theses and Dissertations

The intensification of aridity due to anthropogenic climate change is likely to have a large impact on the growth and survival of plant species in the southwestern U.S. where species are already vulnerable to high temperatures and limited precipitation. Global climate change impacts plants through a rising temperature effect, CO2 effect, and land management. In order to forecast the impacts of global climate change, it is necessary to know the current conditions and create a baseline for future comparisons and to understand the factors and players that will affect what happens in the future. The objective of Chapter 1 is …

The Development Of A Specific Pathogen Free (Spf) Barrier Colony Of Marmosets (Callithrix Jacchus) For Aging Research, Corinna N. Ross, Steven Austad, Kathy Brasky, Celeste J. Brown, Larry J. Forney, Jonathan A. Gelfond, Robert Lanford, Arlan Richardson, Suzette D. Tardif

Biology Faculty Publications (Archived)

A specific pathogen free (SPF) barrier colony of breeding marmosets (Callithrix jacchus) was established at the Barshop Institute for Longevity and Aging Studies. Rodent and other animal models maintained as SPF barrier colonies have demonstrated improved health and lengthened lifespans enhancing the quality and repeatability of aging research. The marmosets were screened for two viruses and several bacterial pathogens prior to establishing the new SPF colony. Twelve founding animals successfully established a breeding colony with increased reproductive success, improved health parameters, and increased median lifespan when compared to a conventionally housed, open colony. The improved health and longevity of marmosets …

Predatory Capacity Of King Crabs In Antarctica, Brittan V. Steffel

Theses and Dissertations

For millions of years, cold water temperatures have excluded shell-crushing (durophagous) predators from continental-shelf environments off the western Antarctic Peninsula. Recently, however, king crabs, Paralomis birsteini, have been found in dense, reproductively viable populations on the upper continental slope, and rapid warming might enable them to expand to the shelf. King crabs are crushing shelled invertebrates on the slope, but calcification of sturdy, shell-crushing chelae is likely inhibited by the low saturation state of high-Mg calcite in the deep Southern Ocean. The objectives of this study were to better understand the predatory capacity of P. birsteini by estimating the potential …

Utilizing Accelerometer Telemetry Tags To Compare Red Snapper (Lutjanus Campechanus) Behavior On Artificial And Natural Reefs, Ethan T. Getz

Theses and Dissertations

The Texas Parks and Wildlife Department Artificial Reef Program has deployed over 2,800 hectares of reefing area composed of petroleum platforms, steel vessels, and concrete. Artificial reefs have been shown to support many important reef fishes such as red snapper (Lutjanus campechanus), however, few studies have compared fish behavior on artificial reefs and natural habitats. We examined activity levels, behavioral patterns and habitat preferences of red snapper over natural reefs, oil platforms and submerged ships. Telemetry tags (Sonotronics model MTT) with tri-axial acceleration range, average depth, and average temperature were programmed to optimize data collection and tag life. …

An Analysis Of The Spatial, Temporal, And Functional Role Of Key Proteins In The Drosophila Melanogaster Salivary Gland During Exocrine Secretion, Kathryn Lantz

UNLV Theses, Dissertations, Professional Papers, and Capstones

For over 60 years, the larval salivary gland of Drosophila melanogaster has been the ultimate model for elucidating how steroid hormones trigger genome-wide changes in gene expression in a specific target tissue. Because of the unusual interphase chromosomes of the salivary gland, the regions of the genome that are being induced by the steroid/receptor complex actually form puffs that are easily visible in compound microscopy. Despite the importance of this system, little has been elucidated over the years regarding how the hormone exposure actually changes the physiological activity of this secretory system. The work presented in this dissertation makes a …

Software For Sequence Analysis Of Variants In Functional Screening Libraries And Personalized Genome Files, Jacklyn Michelle Newsome

UNLV Theses, Dissertations, Professional Papers, and Capstones

Detailed knowledge of protein function is critical for both the study of protein interactions and the development of drugs which target specific proteins. Currently, there are few techniques that directly examine protein function. The techniques that are available are time consuming and can only address one variant of a protein at a time. Our laboratory has designed 3 high throughput protein function screens. We hypothesize that these will address this shortfall.

The first screen is the Chimeric Minimotif Decoy (CMD) Assay. For this screen, we constructed red fluorescent proteins with one or more C-terminal minimotifs. Minimotifs are short, contiguous amino …