Life Sciences Commons^™

The Stability Of Epigenetic Variants That Can Act As Loci Causing Phenotypic Change, Raul Faburrieta

Biology Theses

Epigenetic variations are a possible source of heritable phenotypic variation. In this study I focus on phenotypic alterations seen in epigenetic Recombinant Inbred Lines (epiRILs) of Arabidopsis thaliana. These epiRILs allow me to study the effects differentially methylated regions (DMRs) have on phenotypic variance. In a study performed in 2014 by Cortijo et al., they found that DMR’s affect flowering time and root length when grown under greenhouse conditions. In this study, I replicated the Cortijo et al. (2014) study, with some changes, to see whether the same significant eQTL regions are found. I found that, some of the eQTLs …

Ecological Niche Modeling Of Endemic Texas Crayfish Species Under Current Conditions, Sarah A. Burgett

Biology Theses

Crayfish play many important roles in freshwater ecosystems such as ecosystem engineering, bioindicator, and food resource. Even though they are important to ecosystems, they are highly understudied. There has been previous work done on ecological niche modeling on Texas crayfish species, but this study takes it a step further by combining soil, climate, and hydrology variables to model the ecological niches of three endemic species: Procambarus texanus, Procambarus nueces, and Procambarus fayettei. Ecological niche models were created for the three species of interest using the program Maxent. I found that P. texanus and P. fayettei have indistinguishable …

Status Survey Of Eight Rare Aquatic Macroinvertebrates In East Texas, Alexandra Randall

Biology Theses

Freshwater is essential to human existence. The health of each freshwater source is connected to the survival of pollution intolerant species of aquatic macroinvertebrates in the orders Ephemeroptera, Plecoptera, and Trichoptera (EPT taxa). A higher presence of EPT taxa equates to better water quality because their water bound larvae assist in maintaining clean freshwater environments and will not survive in highly polluted water. Human disruption to natural environments is causing increases in polluted freshwater, leading to decreases in the presence of EPT taxa. Texas Parks and Wildlife Department documentation shows major concern for the populations of eight EPT species of …

Modeling A Parkinson’S Disease Like State In Zebrafish Larvae Utilizing 6-Hydroxydopamine, Adrian Romero

Biology Theses

Parkinson's’ disease (PD) is a neurodegenerative disorder characterized by the loss of midbrain dopaminergic (mDA) neurons that currently has no cure. It is primarily characterized in patients by motor symptoms that include but are not limited to: tremor at rest, rigidity, akinesia, and postural instability affecting the quality of life for over 8.5 million people worldwide. The neurotoxin 6-hydroxydopamine (6-OHDA) has been used to induce a Parkinson’s disease-like state in several animal models; however, assessment of 6-OHDA use in zebrafish demonstrated a lack of consensus on method and utility. We determined an optimized protocol utilizing 6-OHDA to produce a PD-like …

Identification Of Biomarkers Of Sub-Lethal Algal Toxin Exposure In Atlantic Salmon (Salmo Salar) And Chinook Salmon (Oncorhynchus Tshawytscha) Using Differential Gene Expression Analysis, Brandon Ellingson

Biology Theses

Atlantic Salmon (Salmo salar) and Chinook Salmon (Oncorhynchus tshawytscha) are important culturally, recreationally, economically, and are a common aquaculture species in Canada and the United States. In the Pacific Northwest, blooms of toxic algae result in millions of dollars annually in losses for salmonid aquaculture producers. Blooms of harmful cyanobacteria produce microcystins which have been linked to net-pen liver disease which has large financial impacts on net pen salmon operations. Microcystin-LR, the most toxic variant, bioaccumulates in the liver and disrupts normal cellular activity by inhibiting protein phosphatases leading to deleterious effects on growth, immune status, and liver function. To …

Heterogeneity Among Harveyi Clade-Specific Virulence Genes And Attribution Of These Genes To Possible Environmental Carriers, Cameron Brown

Biology Theses

In the face of global warming, waterborne pathogens are evolving rapidly and expanding geographically. The Vibrio Harveyi clade encompasses a number of human and aquatic organism pathogens, and due to their physiology, they may benefit from ongoing changes in the temperature, pH, and salinity of the global Ocean. With this, the Southeastern United States might become an accommodating environment for Harveyi clade species, and it is imperative to monitor for their abundance and distribution in the environment. A qPCR assay was developed for the detection and quantification of clade-specific virulence genes toxRvh, hly, toxR, luxR, srp, vhha, vhh, and vhp …

An Ecological Survey Of East Texas Salamanders Across The Camp Tyler Outdoor Field School In Smith County, Texas, Justin C. Hunt

Biology Theses

Amphibians are a unique class of organisms with a very long and storied evolutionary history of survival. Many modern amphibian clades occupy several vital ecological roles within their native freshwater environments. One of these roles, typically includes functioning as an ecological indicator species, whereby the presence of stable and diverse populations of many amphibian species, including salamanders, within a freshwater ecosystem have long been considered ecological indicators of good habitat quality and stable ecosystem health. Similarly, salamanders also function as important members of their local food webs and act as valuable mediators of complex trophic hierarchies to facilitate nutrient cycling …

Monitoring The Effects Of Poultry Waste On Fishes And Macroinvertebrates In The Sabine River, Karley R. Parker

Biology Theses

Freshwater is a vital resource that provides life and sustainability for almost all organisms on Earth. It is important to maintain its health and protect it from emerging pollutants that pose a threat to the organisms that use it. Pollution continues to threaten the well-being of the environment’s freshwater sources all around the world that could lead to damaging effects in the future. The Sabine River is a major freshwater resource in the east Texas and western Louisiana areas that provides a habitat for thousands of organisms as well as other domestic uses for humans. In 2019, a waste discharge …

Examining Protein Localization Via Fluorescence Microscopy In Saccharomyces Cerevisiae, Lewis Barr, Richard H. Adams, Ellen France Phd

Biology Theses

Twenty-seven years ago, Saccharomyces cerevisiae became the first eukaryote to have its full genome sequenced, thus leading to the discovery that 30% of genes related to human diseases are orthologous to those in S. cerevisiae. Since then, 75% of the proteome has had its localization classified, and we sought to fill the remaining gaps of knowledge by identifying the localization of three proteins: Fsh3, Gid10, and Ade13, which function as a serine hydrolase, ubiquitin ligase, and adenylosuccinate lyase, respectively. To visualize cellular localization, we used a C-terminal GFP tagging strategy and subsequent fluorescence microscopy. Through colocalization analyses, we identified …

Toward Accelerometer Recording Of Pit Viper Foraging Behavior In Nature: Validation And Case Study With Timber Rattlesnakes (Crotalus Horridus), Morgan L. Thompson

Biology Theses

Accelerometer dataloggers are becoming increasingly common in field studies of animal behavior. Among the most difficult study subjects, and consequently, the most ideal candidates for accelerometer applications, are those for which simultaneous observation of key fitness-determining behaviors, such as foraging, across a sample of individuals in the wild is traditionally impossible or restricted to the use of proxy measures. This is the case for many solitary vertebrate predators, such as all pit vipers (Viperidae; Crotalinae). Large-bodied pit vipers are ambush (sit-and-wait) specialists that represent uniquely challenging and intriguing study subjects in predator ecology. Unlike many comparable avian or mammalian terrestrial …

Niche Modeling Of Eight Crayfish Species In Texas, Nathan Schubert

Biology Theses

Freshwater species make up ~10% of all known species and occupy less than one percent of earth’s habitat, which is being degraded by human usage. Crayfish have a large impact on their aquatic or terrestrial environment and can serve as a health indicator of aquatic environments, as they generally require undegraded environments. In many habitats, crayfish make up more than half of the macroinvertebrate biomass, and play important ecological roles, as a food resource for both aquatic and terrestrial species, as predators of fish and invertebrates, and as bioprocessors of vegetation and detritus. The objective of this project was to …

Differential Expression Of Photosynthetic Genes In Cryptophyte Algae (Hemiselmis Cryptochromatica Ccmp 1181), Chastity D. Aguilar

Biology Theses

Cryptophytes are a group of freshwater algae that have acquired photosynthesis through secondary endosymbiosis with a red alga and an unknown eukaryote heterotroph. Cryptophytes possess photosynthetic pigment-protein structures called phycobiliproteins (PBPs). Cryptophyte phycobiliproteins are composed of α and β-protein subunits and four chromophores (bilins). There are nine classes of cryptophyte PBPs that absorb different wavelengths of light based on the type of bilins covalently bound to the protein subunits. Three cryptophyte PBPs are phycoerythrins that give the algae a red appearance and six are phycocyanins that give the algae a blue to green appearance. Hemiselmis cryptochromatica (CCMP 1181) is a …

Round Goby (Neogobius Melanostomus) Seasonal Diet, Drift Impacts, And Influence On Stream Connectivity In Great Lakes Tributary Streams, Kyle R. Glenn Mr

Biology Theses

Seasonality, energy recruitment, and food web position dictate the degree of impact fish impose on their surrounding environment. In the Great Lakes, the round goby (Neogobius melanostomus) is known to out-migrate from nearshore habitat to offshore depths in the winter months. However, in Great Lake tributaries, round goby populations were found up to 25 km upstream during winter months, and distance upstream was a predictor of out-migration propensity; populations farthest upstream did not out-migrate. Seasonal resources shaped the diet and condition of these fish thus creating inland populations with different average lengths, diets, and body condition compared to …

Temperature Affects Nest Box Occupancy, Nest Success, And Nestling Size In A Southeastern Population Of Eastern Bluebirds (Sialia Sialis), Christopher G. Horacek

Biology Theses

Given the critical role that temperature plays in avian reproductive biology, rising temperatures as a result of global climate change will likely impact reproductive success of many bird populations. Secondary cavity nesting birds, many of which rely on artificial nest boxes to maintain population levels, may be particularly at risk because increased temperatures inside nest boxes can determine whether nest boxes are selected, reduce nest success, and/or negatively affect the growth and survival of offspring. We examined the effect of nest box color on nest box temperature and the influence of nest box temperature, nest box color, entrance orientation, and …

Filamentous Green Algae (Cladophora Glomerata) In Near Shore Lake Ontario: An Investigation Of Tissue And Water Nutrient Dynamics Through A Period Of Growth And Decomposition., James L. Wagner Jr

Biology Theses

Cladophora glomerata, a filamentous green alga abundant in the Laurentian Great Lakes, has long been considered a nuisance throughout the region. Previous phosphorus (P) abatement practices and legislation successfully reduced the abundance of the algae, but with the introduction of dreissenid mussels, a resurgence has been observed. Though there is substantial literature and modeling of the growth cycle of Cladophora, relatively little research has been dedicated to the decomposition stage of the algae, a period which may contribute to a substantial influx of nutrients to near-shore environmental regions. By first examining a period of in-situ growth within Lake …

Niche Partitioning Of Food Resources By Freshwater Mussels In A Multispecies Mussel Bed In The Sabine River, Marissa Netti

Biology Theses

Freshwater mussels (Unionids) are a very diverse group of bivalves, with about 300 species in the United States. Although freshwater mussels are very diverse, they are also critically endangered and are declining at extremely high rates. In fact, the U.S. Fish and Wildlife Service proposed excluding eight freshwater mussel species from the Endangered Species Act (ESA) in 2021 because they went extinct. Mussels play a key role in keeping our water systems healthy because of their filter feeding method. Filter feeding influences the rest of the ecosystem through the transfer of energy, cycling of nutrients, and purification of the surrounding …

Associations Of Rare Caddisflies With The Western Dwarf Salamander Eurycea Paludicola, Lillie Hawkins

Biology Theses

There is limited information on the three species of caddisflies Philopotamidae Chimarra holzenthali, Hydropsychidae Cheumatopsyche morsei, Hydroptilidae Hydroptila ouachita and the western dwarf salamander Eurycea paludicola. In particular, there is a lack of any habitat associations between these caddisflies and the western dwarf salamander. Museum specimens of the caddisflies are scarce; however, the literature suggests they are spring dwelling like the western dwarf salamander. The goal of this project was to sample previously known and new habitats where these organisms might be found and report overall quality of the habitats and whether the caddisflies were associated with …

Regional-Scale Climate-Induced Variation In Ant Physiology And Morphology, Daniel E. Murphy

Biology Theses

The biology of ectotherms such as insects is influenced by ambient thermal conditions. Ants are a ubiquitous and ecologically important group of insects and are well-established as bioindicators of thermal conditions. Ants are sensitive to the thermal extremes that vary with latitude, elevation, and land use, and these thermal gradients influence their spatial and temporal distributions. As a result, ants have evolved physiological and morphological thermal adaptations in response to the thermal environment of their habitats. These adaptations include increased physiological and morphological tolerance for temperature extremes. In Western New York (WNY), temperatures are temporally and spatially heterogeneous, changing with …

Combining Historic Records And Multi-Criteria Habitat Suitability Analysis For The Potential Reintroduction Of Lake Sturgeon (Acipenser Fulvescens Rafinesque) Into Tributaries Of Lake Erie, Kylie P. Wirebach, Christopher Pennuto, Dimitry Gorsky

Biology Theses

Predicting the location and quality of habitat for imperiled species is an increasingly important application of modeling technology. The Lake Sturgeon (Acipenser fulvescens) is a widely-extirpated fish of the Laurentian Great Lakes whose recovery is dependent on the availability and connectivity of suitable stream habitat today. This is especially true in Lake Erie, where the largest Lake Sturgeon fishery was once found. I predicted that modern habitat suitability would be dependent on land use legacies from the past 200 years, with western Lake Erie tributaries having less suitable habitat compared to the eastern Lake Erie tributaries. I developed a multi-criteria …

Rhizosphere-Competent Actinobacterial Isolates With Acc Deaminase Activity Alleviate Salt Stress In Tomato Plants In The Uae, Alaa Ahmed Abbas Elbadawi

Biology Theses

Tomato (Solanum lycopersicum) is one of the most popular vegetables in the world, including the United Arab Emirates (UAE). Salinity is a global menace to plant growth and development, causing significant economic losses to tomato and other crop plants. It is well-known that 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD) can increase plant tolerance to environmental stresses. This can be attributed to the increased activity of the enzyme ACCD, which breaks down ACC [the immediate precursor of ethylene (ET)] to ammonia and α-ketobutyrate, to lower the overproduction of ET levels in planta and to reduce the damages caused …

Integrating Radio Telemetry And Accelerometry To Evaluate The Scale-Dependent Effects Of Roadways On The Movement Patterns Of Timber Rattlesnakes (Crotalus Horridus), Anna F. Tipton

Biology Theses

Roadways are among the most widespread and disruptive anthropogenic land use features that influence the behavior and movement of wildlife. Negative impacts such as vehicle-induced mortality, habitat destruction and fragmentation, and the creation of barriers to movement have been well documented across taxa, but the fine-scale behavioral impact of roadways on smaller, cryptic species has yet to be directly examined. Using a novel integration of radio telemetry and tri-axial accelerometry, we evaluated the movement response of Timber Rattlesnakes (Crotalus horridus) to roadways in central Georgia. We quantified individual C. horridus movement and space use with both radio telemetry …

The Impact Of Processing Body Proteins On An Adenovirus Infection, La`Quita Randolph

Biology Theses

Adenovirus is a nonenveloped, double-stranded DNA virus that contains a 36 Kbp genome. The E4 ORF3 region of its genome consists of an E4 11k protein that can reorganize host cell components by relocalizing cellular proteins. One such cellular component is the cytoplasmic processing body, which consists of proteins involved in translational repression of mRNA and mRNA degradation. During an adenovirus infection, processing body proteins Ddx6 and Pat1b have been shown to colocalize and form aggresomes. Aggresomes induced by E4 11k are specific to the adenovirus serotype 5 (Ad 5). In this study, cytoplasmic Pat1b foci were observed and quantified …

The Phylogeography And Invasion History Of Jumping Worms On The Hamilton College Campus Inferred Through Populations Genetics, Dylan Morse '22

Biology Theses

Phylogeographic studies are helpful in reconstructing invasion history and population dynamics. Since the first introduction of Amynthas species into the United States in the 1930’s, Amynthas species (invasive jumping worms) have spread throughout the eastern United States and into Canada. Three Amynthas species, Amynthas agrestis, Amynthas tokioensis, and Metaphire hilgendorfi, all affect productivity and nutrient cycling in soil and forested ecosystems. Recent studies have used the COI barcoding region to track invading taxa and elucidate cryptic diversity.

This study investigates populations of Amynthas species on the Hamilton College campus. Using the COI barcoding region to conduct a …

Native And Non-Native Ant Impacts On Soil Microbes, Hannah A. Stewart

Biology Theses

Organisms produce chemical weapons for defense, but target organisms can develop resistance. In their introduced range, non-native species may bring “novel weapons” against which native organisms have not co-evolved resistance. The invasive European fire ant (Myrmica rubra) may have brought antimicrobial secretions to the Northeastern United States that are novel weapons against native fungal and bacterial soil organisms. I hypothesized that M. rubra would better inhibit seed pathogens resulting in greater emergence of native myrmecochorous Viola sororia seeds and, as a side effect, more strongly inhibit arbuscular mycorrhizal fungi than a native seed dispersing ant (Aphaenogaster picea …

The Effects Of Hydrologic Heterogeneity On Harmful Algal Blooms In Freshwater Reservoir, Lake Sinclair, Georgia, Margaret Blackledge

Biology Theses

Aquatic habitats are frequently studied after a major water quality problem like the occurrence of an algal bloom. In this study, A proactive rather than a reactive response was considered, where the complexity of conditions conducive to uncontrolled cell growth were studied before a bloom took place by sampling regularly. This study aimed to monitor water quality by monthly sampling of algal communities for approximately one year. As the base of the aquatic food web, algae are a highly diverse group of organisms with varying sensitivity to physical and chemical changes in the environment. Four shallow sites were monitored at …

Shell Calcification And Growth Of The Aquatic Snail Planorbella Trivolvis Under Low Calcium Conditions Typical Of Decalcified Northern Lakes, Shawn A. Witte

Biology Theses

The water calcium concentration of northern softwater lakes has declined to critically low levels due to numerous anthropogenic stressors, and the availability of calcium is expected to decline further. To assess the impact that critically low water calcium has on aquatic snail shell calcification and growth, juvenile Planorbella trivolvis were raised for 60 days in one of four treatments, each containing a different amount of dissolved calcium (0.64, 1.3, 2.5, and 5.1 mg/L). There was no difference in tissue weight or shell size among treatments, suggesting low water calcium concentrations do not impact adult body mass or size. However, snails …

Developmental And Behavioral Responses Of Early Life Stages Of Fathead Minnows (Pimephales Promelas) To Urban Effluents Treated With Advanced-Oxidation Processes, Amy Cavanaugh

Biology Theses

Wastewater Treatment Plants (WWTP) are the main vector for pharmaceutical and personal care products (PPCPs) to enter waterways. Many PPCPs are lipophilic, allowing them to bioaccumulate and biomagnify within aquatic organisms. PPCPs have been known to alter fish behavior and physiological processes, such as nesting defense and sex ratios, and produce an increase in deformities. Advanced oxidation processes (AOPs) are novel ways for treating WWTPs effluents that use hydroxyl radicals to indiscriminately breakdown PPCPs. In this study, fathead minnows (Pimephales promelas) were used to examine the biological effects of AOP-treated municipal effluent as they developed from eggs to …

Assesment Of Antibiotic Resistant Gene Expression In Clinical Isolates Of Pseudomonas Aeruginosa, Dustin Esmond

Biology Theses

Increasing prevalence of nosocomial infections by antimicrobial resistant pathogens resulting in higher mortality rates and financial burden is of great concern. Pseudomonas aeruginosa represents one of six highly virulent “ESKAPE” pathogens that exhibit considerable intrinsic drug resistance as well as mechanisms for acquiring further resistance. As many of these mechanisms are regulated through gene expression, we sought to identify regulatory strategies and patterns at play in 23 clinical isolates collected from Baku, Azerbaijan and Tyler, Texas, USA. Real-time quantitative polymerase chain reaction was performed on six gene targets implicated in resistance and contrasted with antibiotic phenotypes. We found AmpC cephalosporinase …

Water Quality Assessment Of The Neches River And Anyalysis Of Pathogenic Bacterial Contaminants, Samantha J. Rowe

Biology Theses

Several waterways have been flagged in East Texas as being bacterially impaired (containing fecal indicator bacteria), including portions of the upper Neches River. Water quality is important to support healthy aquatic ecosystems as well as the well-being of inhabitants near or downstream of a water body. Many factors can contribute to the water quality of rivers, such as agriculture, recreational use, and urban and industrial growth. This study examined the water quality of specific branches in the Upper Neches River including the Neches River above Lake Palestine and Black Fork Creek. All sample sites were visited during the months of …

Comparative Microbiome Analysis Of The Funfus Gardening Ant Species Trachymyrmex Arizonensis, Chase D. Rowan

Biology Theses

Fungus-growing ants (Attini: Formicidae) and their fungal cultivars participate in ant-fungus mutualism that share a 50-million-year-old coevolutionary history. Fungal cultures are grown in gardens alongside ants and a diverse collection of microbes that interact with both species in mutualistic, commensal, and antagonistic relationships. These microbes aid in digestion and detoxification of food, provide essential nutrients, help in nest hygiene, and play a dominant role in defense against pathogens and disease. Microbial communities of many model species have been shown to change in a laboratory setting as compared to their natural environment. High-throughput 16s sequencing of the V4 variable region was …