Life Sciences Commons^™

Tetrameric Structure Of Beta-Amylase 2 (Bam2) In Arabidopsis Thaliana, Lauren Elizabeth Pope

Senior Honors Projects, 2010-2019

Plants store starch during the day for use at night. This process of transitory starch degradation is mostly attributable to the β-Amylase (BAM) family, which are starch exohydrolases that cleave the penultimate α-1,4 glycosidic bonds of starch to release maltose. BAM2 was recently characterized as a catalytically active, K⁺-requiring tetramer with sigmoidal kinetics and cooperativity. All other catalytically active BAMs display Michaelis-Menten kinetics, no cooperativity, and do not require salt, making BAM2’s characteristics intriguing. Due to a lack of a crystal structure, a monomeric homology model of BAM2 was generated using I-TASSER based on a BAM5 from soybean. …

The Role Of Brain Stem 5-Ht1a And Gaba-A Receptors In The Thermoregulatory Response To Hypoxic Stress, Alexander Schmidt

Senior Honors Projects, 2010-2019

Sudden Infant Death Syndrome (SIDS) is a leading cause of infant mortality. Alterations in brainstem development of Serotonin (5HT) and γ-aminobutyric acid (GABA) are linked to its cause. The sympathetic premotor neurons located in the Nucleus of the Raphe Pallidus (NRP) in the brainstem have both 5-HT1A and GABA-A receptor subtypes that mediate protective cardiovascular responses to environmental stress. It is hypothesized that alteration in these receptors at the NRP will also modify protective thermoregulatory responses to hypoxic stress such as hypothermia. Using aseptic techniques, male and female Sprague-Dawley rats (230-385g) were instrumented with radiotelemetry probes to non-invasively measure core …

Assessing Morphological Deformities In Cetaceans: Definition Of Patterns And Quantification With A Case Study (Madeira Island, Ne Atlantic), Erich Dietterle

Masters Theses, 2010-2019

Documenting deformities in cetaceans can lead to understandings in the health of the populations, but also the state of ocean and human health in an area. Deformities like skin lesions can lead to information about local pollution levels or possible diseases, while physical impacts can give insight into vessel traffic or fishing gear entanglement information. Cetaceans encounter threats like vessel strikes and fishing gear entanglements worldwide, but less obvious activities like whale watching or pollution can also have impacts. Studies have been conducted worldwide and around the Madeira Archipelago to document deformities, but there are various descriptions for what is …

Rat Hind Limb Nociceptive Withdrawal Response To Heat And Mechanical Stimuli Depends On Initial Position Of The Paw But Not Stimulus Location, Giavanna Verdi

Senior Honors Projects, 2010-2019

Mammals rapidly withdraw their hind limb in response to noxious stimulation, which is a protective movement known as the nociceptive withdrawal response (NWR). The NWR has been previously studied in spinalized, decerebrated and anesthetized non-human and human mammals; however, there is minimal information on the NWR in intact, unanesthetized non-human mammals.

The first specific aim was to identify the factors that determine the direction and magnitude of the NWR in intact, unanesthetized rats. Based on previous studies, we hypothesized that the location of stimulation and the initial position of the paw preceding the NWR will influence the direction and magnitude …

Effects Of The Microenvironment Surrounding Cys433 In Arabidopsis Β-Amylase-1 And -3 On The Sensitivity To Glutathionylation By Nitrosoglutathione, Matthew R. Kohler

Senior Honors Projects, 2010-2019

Glutathionylation is a reversible post-translational modification of proteins involving the transfer of glutathione to the thiols of specific cysteine residues. While the mechanism behind glutathionylation is known, the specificity of cysteine glutathionylation is not understood. It is known, however, that the two main factors affecting the susceptibility to glutathionylation are the reactivity and accessibility of cysteines in proteins, which is determined by the microenvironment. Using β-amylases (BAMs) 1 and 3 from Arabidopsis thaliana, which have different sensitivities to nitrosoglutathione (GSNO), as a model, I attempted to provide insight into why some cysteines are glutathionylated by GSNO and others are …

Epigenetic Regulation Of Crx And Nrl Binding To Regulatory Elements In The Genomes Of Human Retinal Neurons, Courtney B. Stout

Senior Honors Projects, 2010-2019

The retina is a neuronal tissue lining the back of the eye containing rod and cone photoreceptors that make vision possible. Highly regulated transcriptional networks control differentiation and maintenance of photoreceptors in the retina. DNA methylation of cytosine bases in genomic DNA is an epigenetic modification correlated with repression of gene expression. Currently in our lab, the biochemical relationship between DNA methylation and the ability of retina-specific transcription factors to bind in the genome is being studied. These transcription factors, known as cone-rod homeobox (CRX) and neural leucine zipper (NRL), have been shown to act synergistically to control photoreceptor expression …

The Quadriciser’S Effect On Range Of Motion And Upper Body Motor Control In Children With Mixed Quadriplegia Due To Chromosomal Disorders, Jillian P. Serigano

Senior Honors Projects, 2010-2019

PURPOSE: The purpose of this experiment is to determine the effects that the quadriciser has on range of motion and upper body motor control in children with mixed quadriplegia due to chromosomal deletion disorders. METHODS: Two subjects with different chromosomal deletion disorders participated in this study. They completed a 10-week passive exercise intervention using the quadriciser. Range of motion of the elbow and shoulder were taken pre and post quadriciser use for both subjects. For one subject, hip and knee measurements were also taken. Both subjects also completed a timed reach task pre and post quadriciser use to test motor …

Survey Of Terrestrial Macro-Invertebrates Hg Content And Assessment Of Low Level Hg Presence On Human Health, Gregory Mansour

Senior Honors Projects, 2010-2019

Forest ecosystems in the Shenandoah Valley of Virginia are not directly exposed to major sources of Hg contamination. Rockingham Co was assumed to be suitable as a low-level control in comparison with sites exposed to major industrial contamination in Waynesboro VA for studies in the late 1900’s. Subsequently the presence of low level Hg from background sources has been demonstrated. This study was conducted from 2014-2016 and expanded from two sites in to four sites in 2016. A composite air index, soil, and decaying organic material “duff” were analyzed for total THg concentrations using a Perkin Elmer Flow Injection Spectrophotometer …

Using Ancient Practices To Fix Modern Problems: The Effect Of Biochar On Einkorn Wheat And Soil Quality, Sarah L. Miller

Senior Honors Projects, 2010-2019

As farmland soils become more and more depleted, the importance of effective soil amendments grows. Biochar is a potential soil and carbon amendment that could improve water and nutrient holding capacity and foster growth of beneficial microbes and fungi. Biochar does not contain nutrients but acts like a sponge, absorbing nutrients around it. It is so effective at holding nutrients that in the first year, if applied alone, it can make the nutrients unavailable to plants and lowers crop yields. To get the best results biochar must be saturated, also referred to as inoculated or charged, with nutrients. Once the …

Characterization Of Neuronal Specific Responses To Induced Misfolded Protein Stress In Caenorhabditis Elegans, Claire Gormley

Senior Honors Projects, 2010-2019

Abstract

Misfolded protein stress has been associated with many types of disease,

including neurodegenerative disorders like Alzheimer’s, Parkinson’s and Huntington’s

disease. When a cell accumulates misfolded proteins in the endoplasmic reticulum,

misfolded protein stress occurs and the unfolded protein response (UPR) is triggered to

induce mechanisms that will allow the cell to either survive or undergo cell death. The

nascent polypeptide associated complex (NAC) is a co-translational chaperone and α/β

heterodimer that manages protein folding and localization, and protects against misfolded

protein stress; changes in NAC function have been linked to both neurodegeneration and

cancer. In these studies, I depleted …

Construction Of A Heterologous Vaccine Against Bordetella Avium And Campylobacter Jejuni Utilizing The B. Avium Transporter, Baa1, Rachel Korba

Senior Honors Projects, 2010-2019

A Gram negative species of bacteria, Campylobacter jejuni, is the leading cause of food poisoning worldwide. Humans often contract food poisoning after ingesting contaminated poultry. Detecting the presence of C. jejuni in poultry is difficult because it is part of the natural flora and does not cause symptomatic infection. In a related manner, Bordetella avium is a Gram negative species of bacteria that causes bordetellosis in poultry. This disease is similar to whooping cough caused by the related pathogen of humans, B. pertussis. Though the mortality rate for bordetellosis is low, it weakens the birds’ immune systems, often …

Validity Of Energy Expenditure For The Garmin Vivofit During A Week Of Physical Activity, Kristen Webb

Senior Honors Projects, 2010-2019

Purpose To determine the accuracy of energy expenditure measured by the Garmin Vivofit during a 7 day period of daily living in comparison to a research grade accelerometer, Actigraph.

Methods Participants wore a research grade accelerometer (Actigraph GT3X+) and a Garmin Vivofit device for 7 straight days, 24 hours a day. Paired t-tests were used to examine mean differences in 7-day mean energy expenditure and step values obtained between the devices, as well as the mean energy expenditure values for each day. Pearson correlation was used to assess the relationship of energy expenditure between the devices. Statistical significance was set …

The Effect Of Incline On Caloric Expenditure Measured By A Wrist-Worn Commercial Activity Monitor, Kaitlin M. Bickel

Senior Honors Projects, 2010-2019

Purpose Physical activity monitors have become popular among the general public to monitor steps, floors climbed, active minutes, and energy expenditure (EE). While there is evidence to support that these devices are accurate in counting steps, there is limited and inconclusive research regarding how accurate they are in measuring EE. This study aimed to test the accuracy of a newer commercial physical activity monitor, the Fitbit Charge (FC), in reporting EE compared to a research-grade accelerometer (GT3X), and indirect calorimetry (IC) while walking on a treadmill with and without incline.

Methods 30 subjects (22 female and 8 male) walked on …

Studies Into The Structure And Function Of Various Domains Of Obscurin And Titin, Rachel A. Policke

Senior Honors Projects, 2010-2019

Muscles give our bodies the ability to move by stretching and contracting. While contraction is accomplished by the well-known actin-myosin interaction, not much is known about stretch. Two integral muscle proteins involved in stretch are titin and obscurin; both are long rope-like protein molecules that seem to act as molecular springs. Mutations in these two proteins can lead to diseases such as hypertrophic cardiomyopathy and muscular dystrophy, as well as a variety of cancers. In an effort to understand muscle stretch and signaling on a more fundamental level, here we present the high resolution structure of obscurin Ig59, a domain …

Energy Poverty: Sos, Kaitlin Tomlinson

Senior Honors Projects, 2010-2019

This honors thesis is a part of a larger ISAT Senior Capstone project with partner Rachel Stukenborg. The purpose of the collaborative ISAT Capstone Project was to develop a set of university-level teaching and learning resources about energy poverty that incorporate a spherical display system, Science On a Sphere (S.O.S.). Four lesson “packages” were created regarding energy poverty for the ISAT Capstone. The first three incorporate Science On a Sphere while the fourth delves into the social, political, economic and cultural dynamics of sustainable solutions, without S.O.S. images. Each lesson package includes a background analysis, a comprehensive lesson plan, supporting …

Repeaterator: A Tool For Visualizing Dna Repeat Motifs In Actinobacteriophage Genomes, Grant A. Rybnicky

Senior Honors Projects, 2010-2019

Horizontal gene transfer plays a large role in microbial genetic diversity. Bacteriophages can mediate diversity within their hosts through transduction, the uptake and dispersal of microbial host DNA between bacterial hosts. However, bacteriophages themselves experience horizontal gene transfer through mobile genetic elements and recombination. Unlike their hosts, bacteriophages cannot easily be mapped onto a phylogenic tree as they do not all possess a common trait like the 16s RNA gene. However, their genomes are typically small enough to be analyzed usingThere are tools to compare bacteriophages such as Gepard and Phamerator that compare nucleotide identity across bacteriophage entire genomes. However, …

The Effects Of Ocular Dominance On Visual Processing In College Students, William A. Holland

Senior Honors Projects, 2010-2019

V. Abstract

The role of ocular dominance in processing visual memory and analytic tasks is unknown. Previous research variably showed both significant effects and no effect of ocular dominance on visual perception, motor control and sports performance. Consequently, the goal of this study was to determine if there is a relationship between ocular dominance and visual processing under a variety of computer gaming tasks. This was accomplished by first determining subjects’ ocular dominance through the use of the Miles test, and then proceeding to examine the subjects’ visual performance on four different Lumosity games under three conditions: left eye, right …

Turning The Tables: A Student’S Study Into The Frequency Of Physical Activity Among University Faculty And Staff, Julianna M. Detrane

Senior Honors Projects, 2010-2019

The purpose of this study was to examine the relationship between physical activity and gender, position, social support, and motivation. The researcher conducted an observational, cross-sectional study of James Madison University faculty and staff (n=423) through the use of SurveyPlanet. The survey was adapted from the 2002 International Physical Activity Questionnaire (IPAQ), and participants responded to items regarding their current moderate and vigorous physical activity level based on the previous seven days, as well as items assessing level of motivation and sources of social support. Results of a multiple regression analysis, F(4, 412) = 6.811, p < .001, adj. R² = …

Coffee Carbon Stocks, Pest And Diseases Under Varied Shade Management: A Review, Anna E. Nordseth

Senior Honors Projects, 2010-2019

Coffee agroforestry systems have received increased attention in recent decades because of their capacity to improve agricultural sustainability. Coffee (Coffea arabica), one of the most economically important crops, is widespread throughout the tropics and can have serious environmental impacts. To ensure sustainable coffee production, it is critical that coffee systems are maintained to maximize carbon storage and minimize susceptibility to pests and diseases. This study reviews the history of coffee production, from forested coffee systems to industrial coffee monocultures. We describe the five classifications for coffee systems, and use them as a framework to compare aboveground carbon stocks …

Topical Administration Of Lacritin Peptide For The Treatment Of Canine Keratoconjunctivitis Sicca, Eliza A. Gaylord

Senior Honors Projects, 2010-2019

Keratoconjunctivitis sicca (KCS), also known as dry-eye disease, causes a deficiency of tears in both humans and canines. Due to the lack of effective therapeutics for the treatment of dry-eye disease, there is a market potential for a novel secretion enhancing factor. Lacritin, a naturally occurring tear glycoprotein, increases basal tearing in rabbits when topically applied to the ocular surface and shows potential as a dry-eye therapeutic. This study aims to characterize Lacritin as a biomarker of dry-eye disease in canines with KCS. A total of 46 canine tear samples, 24 normal and 22 diagnosed with KCS, were obtained through …

Obscurin Acts As A Variable Force Resistor, Aidan M. Willey

Senior Honors Projects, 2010-2019

Obscurin (800-900 kDa) is a giant cytoskeletal protein important to muscle cell maintenance and organization. One of its functions is to connect distal regions within the cell. The protein architecture suggests this role; obscurin consists of dozens of individually-folded domains linked together. Given obscurin’s shape and position in the cell, it likely responds to cell motion and stretch by itself stretching and compressing. One outstanding question is how obscurin accomplishes this. Here, we begin to probe the molecular mechanism and outcomes of obscurin stretch resistance. We hypothesize that obscurin could either act like a rope, only resisting stretch when fully …

Survey Of Microbial Urea Degrader Diversity In Two Freshwater Ecosystems: Lake Shenandoah And The Shenandoah River, Naomi E. Gilbert

Senior Honors Projects, 2010-2019

One of the primary drivers of cyanobacterial harmful algal blooms (cHABs) in freshwater systems is nutrient loading, particularly of nitrogen and phosphorus. There has been an increased focus on assessing the role of nitrogen (N) in freshwater lakes and rivers that suffer cHABs. Urea, a widely-used, N-rich fertilizer, is a source of interest due to its abundance in freshwater ecosystems, primarily caused by anthropogenic nutrient loading. While recent work has shown that cHAB population succession may favor the toxic cyanobacterium Microcystis in urea-rich waters, the diversity of the associated bacterial community capable of degrading urea has yet to be determined. …

Searching For Sex Differences In Snake Skin, Sydney E. Ashton

Senior Honors Projects, 2010-2019

The production of many secondary sexual signals, including pheromones, is controlled by sex hormone action at the sites of signal synthesis. The red-garter snake (Thamnophis sirtalis parietalis) is an ideal vertebrate for studying the interaction between steroids and sexual signals: males exclusively rely on skin-based female pheromones during courtship, and pheromone composition is augmented by treatment with sex steroids (e.g., males produce female pheromone if implanted with estrogen). But how do steroid hormones promote pheromone expression at the molecular level in snake skin? Feminizing effects of estrogens on sexual signals are known to result from activation of estrogen …

Complementary Multimodal Compartments In The Developing Inferior Colliculus, Roxana Behrooz

Senior Honors Projects, 2010-2019

The auditory system is responsible for detecting, encoding, and deciphering hearing. The inferior colliculus (IC) is a major relay hub situated in the midbrain, that is subdivided into a central nucleus, and surrounding dorsal and lateral cortices. The central nucleus of the inferior colliculus (CNIC) is organized tonotopically based on a frequency gradient and strictly processes auditory information. In contrast, recent studies show that the lateral cortex of the inferior colliculus (LCIC) is actually multimodal, receiving inputs from not just auditory sources, but also somatosensory and visual structures. The precise organization of patterned inputs to the LCIC and their development …

The Effects Of Coffee Ingestion On The Acute Testosterone Response To Exercise, Taylor Landry

Masters Theses, 2010-2019

Abstract

This study investigated the effects of coffee ingestion (COF) on serum testosterone responses to exercise in recreationally weight-trained males. Subjects ingested either 12 ounces of 6mg/kg caffeinated coffee (COF), decaffeinated coffee (DEC), or water (PLA) one hour prior to exercise in a randomized, within-subject, crossover design. The exercise session consisted of 21 minutes of high intensity interval cycling (alternating intensities corresponding to two minutes at power outputs associated with 2.0 mmol/L lactate and 4.0 mmol/L lactate) followed by resistance exercise (7 exercises, 3 sets of 10 repetitions, 65% 1RM, 1-minute rest periods). Subjects also completed repetitions to fatigue tests …

Relationship Between Breakfast And Basketball Shooting Accuracy, Dimitrije Cabarkapa

Masters Theses, 2010-2019

Purpose: The purpose of this study was to determine if collegiate and recreational basketball players shooting accuracy improved after consumption of breakfast (BF) compared to no-breakfast (No-BF).

Methods: 24 male and female collegiate and recreational basketball players completed a three-week intervention study with a crossover design. Subjects were randomly assigned to a four-day BF or No-BF treatment starting on Monday and completed testing that included a free-throw drill and timed 2-point and 3-point drills on day four. Treatment switched the following Monday. Food intake records were collected during each treatment phase.

Results: There was no difference between BF and No-BF …

The Effect Of Ambient Temperature On Recovery Of Surgical Stress In Sprague-Dawley Rats, Romie D. Powell

Masters Theses, 2010-2019

Laboratory animals are housed at ambient temperatures ranging from 20°C – 26°C per recommended guidelines. Rats in particular typically prefer ambient temperatures (Tamb) of ~27°C (Brown et al, 2011). When rats undergo surgical instrumentation for experimental use, they often recover at normal room temperature (~21°C). While this is comfortable to those maintaining them, it may lead to a cold thermal stress for the rats. It is hypothesized that housing rats at ambient temperatures away from their preferred Tamb could lead to a thermal stress, which adversely affects surgical recovery. To address this, rats (220g-350g) were surgically instrumented with a radiotelemetry …

The Effect Of Calcium In Artificial Substrates For Oyster Restoration: Implications For The Mitigation Of Oyster Population Decline, Jessie Mandirola

Masters Theses, 2010-2019

Oyster populations in the Chesapeake Bay have declined by 99% over the past 150 years due to overharvesting, disease, ocean acidification, and poor water quality. Restoration efforts are needed to reestablish native oyster populations. Current restoration efforts utilize natural oyster shells but these methods are expensive and unsustainable. Therefore, restoration is starting to use artificial substrates instead. Concrete has been successfully used in previous research; spat will attach and oysters will grow. However, there is a lack of knowledge about how the composition of concrete effects oyster larval recruitment. We tested concrete made with limestone sand (“special concrete”) to increase …

Impact Of Pre-Exercise Feedings With A Low Or High Glycemic Index On The Ergogenic Effects Of Carbohydrate Mouth-Rinsing During Cycling, Nikolai J. Hladick

Masters Theses, 2010-2019

Purpose: Carbohydrate (CHO) ingestion during exercise enhances performance in short endurance events (~ 1 hr) due to neural influences, as demonstrated by the efficacy of CHO mouth-rinsing during cycling. However, the magnitude of these neural effects may be blunted following pre-exercise CHO feedings. This study examined whether the glycemic index (GI) of a pre-exercise meal affected time-trial (TT) performance in cyclists using a CHO mouth-rinse during exercise. Methods: Eight cyclists (age: 24 ± 6 yr; VO_2max: 61 ± 8 ml×kg^-1×min^-1) completed 4 exercise trials, consisting of 15 min of constant-load cycling followed by a …

The Effects Of Caffeine Ingestion On The Hemostatic Response To Simulated Firefighting Activities, Sierra D. Wassell

Masters Theses, 2010-2019

Sudden cardiac events are the leading cause of death among firefighters, and it is acknowledged that most ischemic events are due to an occlusive thrombus formation. In addition, due to the demanding job requirements and shift work, firefighters commonly overuse caffeine. The purpose of this study was to examine the potential effects of caffeine on the hemostatic response to simulated firefighting activity. Twelve healthy male firefighters (age, 31.3 ± 5.4 yrs; weight, 94.2 ± 13.1 kg; BMI, 28.7 ± 2.9 kg·m^-2) participated in this study, wearing full personal protective equipment (PPE) and self-contained breathing apparatus (SCBA). Subjects completed …