Biology Commons^™

Role Of The Orphan Crispr 2 In Enterococcus Faecalis, Andriy Barchuk

Honors College Theses

Enterococcus faecalis is a Gram-positive aerotolerant anaerobic bacterium primarily found as a member of the human and animal intestinal flora. Enterococcus faecalis along with 27 other species comprise the genus Enterococcus. Out of the whole genus E. faecalis and E. faecium are the second most common nosocomial cause for urinary tract and wound infections. The treatment of the infections is made even more complex due to E. faecalis resistance to last-resort drugs like vancomycin. An inverse relationship has been observed in the species between antibiotic resistance and presence of the CRISPR-cas locus. CRISPR-Cas (clustered, regularly interspaced short palindromic repeats and …

Paratransgenic Control Of Pierce's Disease, Arinder K. Arora

Biology ETDs

Pierce's Disease (PD) is a deadly grapevine disease, which is caused by a Gram negative bacterium, Xylella fastidiosa and transmitted by leafhoppers commonly known as sharpshooters, including the glassy-winged sharpshooter (GWSS, Homalodisca vitripennis). We developed paratransgenic control of PD using a commensal bacterium Pantoea agglomerans E325. The GWSSs acquired enhanced green fluorescent (EGFP)-expressing P. agglomerans from an artificial feeding system and the bacteria persisted within the insect foregut for two weeks. P. agglomerans was selected as the paratransgenic control agent based on its persistence within the sharpshooter foregut, a niche also inhabited by X. fastidiosa. P. agglomerans lines secreting two …

Transcriptional Regulation Of Muscle Development In Drosophila Melanogaster, Tonya M. Brunetti

Biology ETDs

The transcriptional regulation of muscle development involves several complex processes that must work together in order to form functional, syncytial muscle cells. However, when transcription is mis-regulated, muscle development is often times negatively affected and can lead to muscle diseases such as muscular dystrophy and cardiac myopathies. In order to gain more insight into how transcription is regulated, I use Drosophila melanogaster as a model for understanding muscle development. In chapter one, I use a traditional genetic screen to phenotypically and molecularly identify two Hox co-factors, extradenticle and homothorax, that have the ability to change muscle identity. Additionally, in chapter …

Flight Muscle Progenitor Populations In Drosophila Melanogaster, Elizabeth Carvosso Clarke

Biology ETDs

We use the Drosophila system to define how genes control muscle development and function. Many of the genes in the fruit fly, Drosophila melanogaster, are conserved with higher animals, and so our results can be important in understanding mechanisms of vertebrate muscle development and disease. Study of the flight muscle progenitor populations in Drosophila gives clearer understanding of the genetic regulatory networks that lead to the development of flight muscle. The direct flight muscles (DFMs) and indirect flight muscles (IFMs) arise from the myoblast population of the notal region of the Drosophila wing imaginal disc. Within the myoblast population, there …

A Life History Of The Roundnose Minnow, Dionda Episcopa, In The Middle Pecos River Valley, New Mexico, Michael A. Farrington

Biology ETDs

Life history aspects of Roundnose Minnows, Dionda episcopa, were examined for specimens collected between 2011 and 2013 in El Rito Creek, near Santa Rosa New Mexico. A recent study examining DNA suggested that, instead of supporting a widespread population of the Roundnose Minnow, New Mexico is actually home to two evolutionarily distinct Roundnose Minnow populations. This focus of this study is on the life history attributes of what may become a newly described species of Dionda. Modal class progression analysis (Bhattacharya method) documented four distinct age classes of Roundnose Minnows within El Rito Creek. Sex ratios deviated from the expected …

Gene Duplications During Experimental Evolution Of Caenorhabditis Elegans: Duplication Rates And Evolutionary Responses, James Charles Farslow

Biology ETDs

Copy-number variants (CNVs) are a ubiquitous form of genetic variation. How often this form of variation arises and its adaptive significance are active areas of contemporary research. This work presents evidence regarding both of these subjects. First, it demonstrates that gene duplications occur at a frequency two orders of magnitude greater than point mutations. Specifically, the gene duplication rate is estimated to be 1.2 x 10-7/gene/generation, compared to a point mutation rate on the order of ~10-9/site/ generation. Second, it was found that populations in a low state of fitness due to mutation accumulation could recover some or all of …

The Impact Of Temperature, Ph And Environmental Heterogeneity On Prokaryotic Diversity In Yellowstone National Park Thermal Springs, Xiaoben Jiang

Biology ETDs

Yellowstone National Park (YNP) is one of the largest and most diverse hydrothermal areas on Earth. Extensive culture-independent studies in YNP thermal springs have shown dramatic taxonomic and metabolic diversity in microbial communities. We conducted a survey of bacterial communities along temperature gradients in three alkaline springs with similar geochemistries at the local scale. With these data, we investigated the influence of environmental variables on bacterial community diversity and assemblages along a broad temperature range using high throughput 454 pyrosequencing. Previous studies have suggested that pH is the driver of microbial diversity in thermal springs among geographical regions or at …

Quantifying Temperature Sensitivity Of Soil Respiration Across A Range Of Semi-Arid Biomes, Michelle Nuanez

Biology ETDs

Soils in semi-arid regions store approximately 10% of earths soil organic carbon, the substrate which microbes oxidize, resulting in the largest source of carbon to the atmosphere from terrestrial ecosystems. Semi-arid regions are expected to experience increased temperatures and altered precipitation regimes over the next 100 years, altering soil temperature and water, the two predominant drivers in soil respiration processes. In this study we quantify the temperature sensitivity of soil respiration in five semi-arid biomes ranging from desert grassland to ponderosa pine forest along an elevational/climate gradient in central New Mexico. We measured statistically similar temperature sensitivities in 4 of …

Effects Of Stream Edges On Algal Biomass In The Middle Rio Grande, Steven Daniel Scholle

Biology ETDs

In river systems, there are many factors that impede or facilitate algal standing stock and therefore impact primary production in these environments. I am particularly interested in the influence of edges in riverine systems and how these geomorphic features affect the available surface area for algal production. This study investigates the middle Rio Grande system near Albuquerque, New Mexico, USA. The middle Rio Grande is a turbid, partially braided lotic ecosystem. Although edge characteristics can vary widely, especially between errosional and depositional banks, I hypothesize that edges become important zones of primary production, due in part to decreased water depth, …

Disturbance Events In Arid Ecosystems: Comparisons Of Enzyme Activity Profiles Across Multiple Soil Microbial Communities, Daniel Douglas Warnock

Biology ETDs

Arid ecosystems are home to approximately 35% of earth's human population, and approximately 40% of earth's terrestrial carbon. These systems are especially prone to releasing the stored carbon when under global climate change (GCC) related pressures. My goal for these studies was to expand on our already growing knowledge base of how the soil microbial communities in disturbed arid ecosystems undergo shifts in functional patterns, as they respond to a rapidly changing environment. In chapter two, I examined the overall functional activity levels and functional behaviors exhibited by both pinon and juniper supported RAM communities in the context of widespread, …

The Effect Of Dietary Salt Intake On The Subcellular Distribution Of Epithelial Na+ Channels In Vasopressin And Oxytocin Synthesizing Neurons In The Rat Hypothalamus, Richard Frank Guidry

Honors Capstones

No abstract provided.

Developing A System To Arrest Transformation Using A Zebrafish Model For Melanomagenesis, Cory Haluska

Theses, Dissertations and Culminating Projects

The recent emergence of RNA-guided CRISPR-Cas9 gene editing system adapted from the natural defense mechanism found in bacteria and archaea has made the manipulation of genetic loci more feasible than ever. Using this technique we attempted to eliminate a target sequence of about 20 nucleotides from the promoter of the protein ICER (Inducible cAMP Early Repressor) located just upstream of the start sequence. ICER is a small transcription factor and supposed tumor suppressor protein that comes from the CREM (cAMP Responsive Element) gene. ICER has been found to be absent in tumor cells, marked for degradation by the ubiquitin-proteasomal pathway. …

Modeling Trade-Offs Between Plant Fiber And Toxins: A Framework For Quantifying Risks Perceived By Foraging Herbivores, Meghan J. Camp, Lisa A. Shipley, Timothy R. Johnson, Jennifer Sorenson Forbey, Janet L. Rachlow, Miranda M. Crowell

Biology Faculty Publications and Presentations

When selecting habitats, herbivores must weigh multiple risks, such as predation, starvation, toxicity, and thermal stress, forcing them to make fitness trade-offs. Here, we applied the method of paired comparisons (PC) to investigate how herbivores make trade-offs between habitat features that influence selection of food patches. The method of PC measures utility and the inverse of utility, relative risk, and makes trade-offs and indifferences explicit by forcing animals to make choices between two patches with different types of risks. Using a series of paired-choice experiments to titrate the equivalence curve and find the marginal rate of substitution for one risk …

An Epigenetic Toolkit Allows For Diverse Genome Architectures In Eukaryotes, Xyrus X. Maurer-Alcalá, Laura A. Katz

Biological Sciences: Faculty Publications

Genome architecture varies considerably among eukaryotes in terms of both size and structure (e.g. distribution of sequences within the genome, elimination of DNA during formation of somatic nuclei). The diversity in eukaryotic genome architectures and the dynamic processes are only possible due to the well-developed epigenetic toolkit, which probably existed in the Last Eukaryotic Common Ancestor (LECA). This toolkit may have arisen as a means of navigating the genomic conflict that arose from the expansion of transposable elements within the ancestral eukaryotic genome. This toolkit has been coopted to support the dynamic nature of genomes in lineages across the eukaryotic …

Sex-Associated Mitochondrial Genes: Tools For Understanding Unionid Reproduction And Development, Amy Louise Maynard

Graduate Theses/Dissertations

Gonochoristic species of the bivalve order Unionida possess two types of mitochondria. The female-inherited mitochondria (F-mt) is found in the somatic cells of both sexes, while male-inherited mitochondria (M-mt) is found in the male gonad. These mitochondria possess different open reading frames (M-ORF or F-ORF respectively). Previous studies suggested that two types of sperm might exist, each carrying one or the other mitochondrial haplotype, and it was hypothesized that the presence of either F-mt or M-mt in sperm may be involved in determination of offspring sex. I investigated this hypothesis in Bleedingtooth (Venustaconcha pleasii). Sperm samples were obtained from field-collected …

Gut Microbiota Of Migratory Passerines At Stopover, William Bagley Lewis

Master's Theses

Although the gut microbiota provides many beneficial functions to animal hosts, relatively little is known about the gut microbiota of passerines. It is likely that gut microbes are especially important during the migratory phase; however gut atrophy experienced during prolonged migratory flight may cause disruptions of the stable microbiota. Fecal samples were collected from several species of passerine after crossing the Gulf of Mexico during spring migration and before crossing during fall, and microbiota communities were analyzed using next-generation sequencing. Despite showing large inter-individual variation, a core microbiota composed largely of Firmicutes and Proteobacteria was identified in all birds. Microbiota …

The Vascular Flora Of Wayne County, Mississippi, Daniel M. Mcnair

Master's Theses

The vascular flora of Wayne County, Mississippi, was surveyed from 2013–2015, and the species of native and naturalized plants are listed. In total, 1,135 species were identified from field collections, previously collected herbarium specimens, and field observations. These belong to 556 genera and 165 families. Four of these species represent first recorded occurrences in the state of Mississippi: Blyxa aubertii Rich., Gomphrena serrata Pav. ex Moq., Isoetes valida (Engelm.) Clute, and Polypogon interruptus Kunth. GPS coordinates are given for important collection sites representing the diversity of plant communities in the county. All voucher specimens from the survey are deposited in …

High Resolution Melt Analysis Of Samples With Differential Dna Methylation To Identify Tissue Source Of Origin, Stephanie M. Ledgerwood

Master's Theses

In Forensic Science casework, identifying the source of a tissue can assist in crime scene reconstruction. Currently, presumptive testing methods to identify tissue type are utilized in crime scene laboratories, but there is a need for a more reliable confirmatory test for tissue type identification. High Resolution Melt (HRM) analysis is an innovative technology that has the potential to determine tissue types through variations in DNA methylation patterns. Recently, DNA methylation patterns have been found to correspond with specific tissue types in particular regions of DNA. Two markers, B_SPTB_03 and DDX4 have been effective in differentiating sperm from other tissue …

Maternal Effects And Offspring Behavior: Potential Contributors To The Lack Of Recruitment In Mississippi Gopher Tortoises (Gopherus Polyphemus), Aaron L. Holbrook

Master's Theses

Federally threatened in Mississippi, gopher tortoise (Gopherus polyphemus) populations within the state have strongly variable recruitment and are generally in decline. Hatching success is significantly lower in Mississippi than in any other part of the species’ range , and most hatchlings die within the first year. There are few refuges where survival and hatching success is high. Here I compare two populations that differ in recruitment and offspring survival for differences in corticosterone. Corticosterone is a hormone that influences both energy availability and is released in elevated levels during stressful events, like living in poor quality habitat. Prolonged corticosterone elevation …

Temporal And Spatial Dynamics Of Scaling-Specific Features Of A Gene Regulatory Network In Drosophila, Honggang Wu, Renjie Jiao, Manu, Jun Ma

Biology Faculty Publications

A widely appreciated aspect of developmental robustness is pattern formation in proportion to size. But how such scaling features emerge dynamically remains poorly understood. Here we generate a data set of the expression profiles of six gap genes in Drosophila melanogasterembryos that differ significantly in size. Expression patterns exhibit size-dependent dynamics both spatially and temporally. We uncover a dynamic emergence of under-scaling in the posterior, accompanied by reduced expression levels of gap genes near the middle of large embryos. Simulation results show that a size-dependent Bicoid gradient input can lead to reduced Krüppel expression that can have long-range and …

Dynamics Of An Sir Model With Nonlinear Incidence And Treatment Rate, Balram Dubey, Preeti Dubey, Uma S. Dubey

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, global dynamics of an SIR model are investigated in which the incidence rate is being considered as Beddington-DeAngelis type and the treatment rate as Holling type II (saturated). Analytical study of the model shows that the model has two equilibrium points (diseasefree equilibrium (DFE) and endemic equilibrium (EE)). The disease-free equilibrium (DFE) is locally asymptotically stable when reproduction number is less than one. Some conditions on the model parameters are obtained to show the existence as well as nonexistence of limit cycle. Some sufficient conditions for global stability of the endemic equilibrium using Lyapunov function are obtained. …

Effects Of Shrub Encroachment And Removal On South Texas Coastal Prairie Flora, Parker Alex Watson

Theses and Dissertations

Watson, Parker Alex, Effects of shrub encroachment and removal on South Texas coastal prairie flora. Master of Science, December, 2015. 60 pages, 14 tables, 11 figures, 47 references, 5 appendices. Native-invasive honey mesquite (Prosopis glandulosa) and huisache (Acacia farnesiana) are aggressively encroaching onto South Texas coastal prairies, outcompeting Gulf cordgrass (Spartina spartinae) and associated prairie vegetation with potential legacy effects on the landscape. To measure conditions in the presence of shrubs, data loggers were installed for 16 mos in shrub understories and grass cover to monitor light, soil and air temperatures. Vegetation and canopy surveys were also conducted to evaluate …

Does Gut Microbiota Affect The Diet Preference In Anurans?, Jordan A. Rice

Honors Theses

Gut microbiota is a community of bacteria that live in the digestive track of a host. These microbes assist in the breakdown of indigestible materials as food passes through the alimentary canal. Metabolites from bacteria may play a role cell to cell communication with their host and thus gut microbiota may affect the diet preference of the animal host. Southern Leopard frogs (Rana sphenocephala) and Green Tree frogs (Hyla cinerea) were used as focal species to test whether gut microbiota affect their diet preference. Three groups of tadpoles were tested. The control group was fed a …

Biomechanical Performances Of Networked Polyethylene Glycol Diacrylate: Effect Of Photoinitiator Concentration, Temperature, And Incubation Time, Morshed Khandaker, Albert Orock, Stefano Tarantini, Jeremiah White, Ozlem Yasar

Publications and Research

Nutrient conduit networks can be introduced within the Polyethylene Glycol Diacrylate (PEGDA) tissue construct to enable cells to survive in the scaffold. Nutrient conduit networks can be created on PEGDA by macrochannel to nanochannel fabrication techniques. Such networks can influence the mechanical and cell activities of PEGDA scaffold. There is no study conducted to evaluate the effect of nutrient conduit networks on the maximum tensile stress and cell activities of the tissue scaffold.The study aimed to explore the influence of the network architecture on the maximum tensile stress of PEGDA scaffold and compared with the nonnetworked PEGDA scaffold. Our study …

Expression Of Insulin Responsive Genes In Insulin Resistant Conditions, And The Effect Of Selenium On Gene Expression, David L. Ruff

Masters Theses

Chronically high blood glucose levels lead to many problems, such as insulin resistance, the hallmark of Type II diabetes. Increased flux through the hexosamine biosynthesis pathway is one mechanism by which high glucose as well as glucosamine has been shown to induce insulin resistance. This study tests the effects of glucosamine induced insulin resistance on insulin regulation of the metabolic genes glucose-6-phosphate dehydrogenase (G6PDH) and fatty acid synthase (FAS) as well as insulin responsive proteins tribbles homolog (TRIB3) and sterol regulatory element binding protein (SERBP-1c) 1c.

Selenium, a micronutrient has been shown to be an effective insulin mimetic in Type …

Water Use Of Four Commonly Planted Landscape Tree Species In A Semi-Arid Suburban Environment, Michael Cameron Bunnell

Theses and Dissertations

Native plant communities and agricultural land are commonly converted to urban areas as cities across the Western United States continue to grow and expand. This expansion is typically accompanied by afforestation where a common goal among communities is to maximize shade tree composition. Planted forests in these regions are commonly composed of introduced tree species native to mesic environments and their ability to persist is dependent on consistent irrigation inputs. Many potential ecosystem services may be derived from planting trees in urban and suburban areas; however, there are also costs associated with extensive afforestation, and shade tree cover may have …

Virulence Of Photorhabdus Spp.: Examining The Roles Of Environment, Evolution, And Genetics In Insect Mortality, Dana Blackburn

Theses and Dissertations

Entomopathogenic nematodes (EPNs) (genera Heterorhabditis and Steinernema) kill their invertebrate hosts with the aid of a mutualistic bacterium. The bacteria (Xenorhabdus spp. for steinernematids and Photorhabdus spp. for heterorhabditids) are primarily responsible for killing the host and providing the nematodes with nutrition and defense against secondary invaders. Photorhabdus is a Gram-negative bacterium in the Enterobacteriaceae family with high virulence towards their insect hosts. To achieve high mortality rates Photorhabdus produces a variety of virulence factors such as toxins, lipases, proteases, secretion systems, and fimbriae. EPNs are amenable to laboratory rearing and mass production for biocontrol applications against insects …

Validating Side Scan Sonar As A Fish Survey Tool, Michael A. Bollinger

Theses and Dissertations

Hydroacoustic methods can be used to answer a variety of questions regarding fish populations and behavior. In this study, side scan sonar methodology was developed to quantify abundance and biomass and compared to established visual observation methods on SCUBA over artificial reef structures in the western Gulf of Mexico. Side scan sonar methods were equivalent to SCUBA surveys for measuring fish abundance over the same reef areas, however, abundances were significantly higher when the larger area sampled by side scan was utilized. Side scan sonar methods were also more time efficient than SCUBA, ROV and long line fishing methods (66.7%, …

Examination Of The Chagas Disease Vector, Triatoma Gerstackeri, In The Lower Rio Grande Valley, Alfredo Flores

Theses and Dissertations

Chagas disease is caused by the protozoan parasite Trypanosoma cruzi, which is carried by an insect vector of the family Reduviidae, and of the subfamily Triatomina. The species Triatoma gerstaeckeri is identified as the primary vector of T. cruzi within the Rio Grande Valley. Species of Triatoma gerstaeckeri were trapped in La Sal del Rey National Refuge in 2012 and 2013.

Data indicates a seasonal dispersal pattern of activity for T. gerstaeckeri. Optimal time of capture was between 1-2 hours after sunset. Different methods were utilized to determine the best combination of lures. Results indicate that the UV-light alone is …

Decomposition And Nitrogen Dynamics Of Turtle Grass (Thalassia Testudinum) In A Subtropical Estuarine System, Monica Delgado

Theses and Dissertations

Seagrass beds are pivotal in the functioning of coastal ecosystems in terms of productivity, organic matter turnover and nutrient cycling. Aiming to document decay and nitrogen (N) dynamics of turtle grass (Thalassia testudinum) in a subtropical estuarine system, decomposition patterns of leaves and rhizomes were characterized and compared. Nitrogen usage during decomposition of tissues, and of live tissues and epiphytes growing on live leaves, was also quantified and compared. Stable isotope ratios allowed tracing N within the seagrass bed, following N incorporation into seagrass tissues from the surrounding media (water, sediment). Leaves had a higher N content and decomposed at …