Biology Commons^™

Platform Effects On Optical Variability And Prediction Of Underwater Visibility, Grace Chang, Michael S. Twardowski, Yu You, Mark A. Moline, Peng-Wang Zhai, Scott Freeman, Matthew Slivkoff, Francesco Nencioli, George W. Kattawar

Biological Sciences

We present hydrographic and optical data collected concurrently from two different platforms, the R/P FLoating Instrument Platform and the R/V Kilo Moana, located about 2km apart in the Santa Barbara Channel in California. We show that optical variability between the two platforms was due primarily to platform effects, specifically the breakdown of stratification from mixing by the hull of R/P FLIP. Modeled underwater radiance distribution differed by as much as 50% between the two platforms during stratified conditions. We determine that the observed optical variability resulted in up to 57% differences in predicted horizontal visibility of a black target.

Genomic Organization And Molecular Phylogenies Of The Beta (Β) Keratin Multigene Family In The Chicken (Gallus Gallus) And Zebra Finch (Taeniopygia Guttata): Implications For Feather Evolution, Matthew J. Greenwold, Roger H. Sawyer

Faculty Publications

Background: The epidermal appendages of reptiles and birds are constructed of beta (β) keratins. The molecularphylogeny of these keratins is important to understanding the evolutionary origin of these appendages, especially feathers. Knowing that the crocodilian β-keratin genes are closely related to those of birds, the published genomes ofthe chicken and zebra finch provide an opportunity not only to compare the genomic organization of their β- keratins,but to study their molecular evolution in archosaurians.

Results: The subfamilies (claw, feather, feather-like, and scale) of β-keratin genes are clustered in the same 5' to 3' orderon microchromosome 25 in chicken and zebra finch, …

Microbial Stoichiometry And Homeostasis Of Nutrient Ratios In Fungi, Desiree Leach

Honors Theses

Stoichiometry is the ratio of elements in a substance or microbial biomass. This paper investigates microbial stoichiometry and the responses of microbes to dissolved nutrient concentrations and ratios. The current work assesses both autrotrophic and heterotrophic responses to nutrient enrichment: autotrophic and heterotrophic states are defined mainly by ecosystem primary production and respiration. In ecosystems dominated by autotrophic microbes, nutrient enrichment can lead to increased biomass and biomass-specific rates of primary production. Heterotrophic ecosystems rely on subsides of organic carbon from outside the system. Their enrichment with N and/or P can accelerate microbial respiration rates and result in carbon losses …

Growth Rate Of Mugil Cephalus From Two Isolated Ponds In Huntington Beach State Park, South Carolina, Matthew Vincent

Honors Theses

Measurement of growth of the euryhaline teleost Mugil cephalus is quite common in open ocean settings, but growth rates of M. cephalus in isolated areas is non-existent. Two isolated ponds in Huntington Beach State, Horry County, South Carolina were selected to study the growth rate of M. cephalus; Sandpiper Pond with virtual no hydrologic connection to the ocean and Jetty Pond with adequate hydrologic connection to the ocean were the sites of sample collection. Scales from M. cephalus in both ponds were collected then aged by two readers, where agreeing ages were kept in the dataset. A von Bertalanffy growth …

Cell Culture Models Of Genetic Variation, Joshua T. Witten

Arts & Sciences Graduate Student Theses and Dissertations

Studying genetic variation presents a dilemma. While the genetic variation of greatest interest is that causing variation in traits and disease risk in natural populations, natural populations have characteristics that make them challenging to study. In this work, I have assessed the use of cell culture methods as a solution to some of these challenges. In particular, I studied genetic variation in the budding yeast Saccharomyces cerevisiae that was generated by selection in the lab as a model for natural genetic variation. I have found that even simplistic selection programs in the laboratory, including the use of chemical mutagenesis to …

Individuals Differences In Exploratory Behavior Of Prairie Voles, Microtus Ochrogaster, Danielle N. Lee

Dissertations

Individual differences in behavior are significant because they serve as the substrate for natural selection. Within the Behavioral Syndromes framework, researchers study individual differences in behavior of animals. Behavioral Syndromes are defined as correlations between behaviors in different environmental contexts or testing situations. In this study, I examined the effects of litter size and sex ratio, familial relationships, and age and sex on exploratory behavior of prairie voles, Microtus ochrogaster. Exploratory behavior, defined as spontaneous behavioral responses to unfamiliar stimuli, was examined in three novel situations: an open-field with novel objects, a two-way novel choice apparatus, and a complex maze. …

Student Content Knowledge Increases After Participation In A Hands-On Biotechnology Intervention, Amber L. Bigler

Theses and Dissertations

Hands-on learning is at the heart of science learning. This study examined increased changes of student content knowledge in biology, particularly biotechnology, after a hands-on biotechnology intervention was implemented into a secondary school. A traditional learning school was selected for a control. Both teachers had participated in a biotechnology professional development program called Project Crawfish. Students from both schools took the same assessment before and after their respective units (biotechnology intervention and genetics unit), and the classroom was the unit of analysis (n=5, n=6, respectively). The assessment was compared as a whole and then divided into five components, eight questions …

Comparative Transcriptional Profiling Identifies Takeout As A Gene That Regulates Life Span, Johannes Bauer, Michael Antosh, Chengyi Chang, Christoph Schorl, Santharam Kolli, Nicola Neretti, Stephen L. Helfand

Biosciences Research

A major challenge in translating the positive effects of dietary restriction (DR) for the improvement of human health is the development of therapeutic mimics. One approach to finding DR mimics is based upon identification of the proximal effectors of DR life span extension. Whole genome profiling of DR in Drosophila shows a large number of changes in gene expression, making it difficult to establish which changes are involved in life span determination as opposed to other unrelated physiological changes. We used comparative whole genome expression profiling to discover genes whose change in expression is shared between DR and two molecular …

Assessing The Phylogenetic Utility Of Dna Barcoding Using The New Zealand Cicada Genus Kikihia, Megan Ribak

Honors Scholar Theses

DNA Barcoding (Hebert et al. 2003) has the potential to revolutionize the process of identifying and cataloguing biodiversity; however, significant controversy surrounds some of the proposed applications. In the seven years since DNA barcoding was introduced, the Web of Science records more than 600 studies that have weighed the pros and cons of this procedure. Unfortunately, the scientific community has been unable to come to any consensus on what threshold to use to differentiate species or even whether the barcoding region provides enough information to serve as an accurate species identification tool. The purpose of my thesis is to analyze …

The Effect Of Heavy Metal Stress On Avian Proximal Tubule Urate Secretion, Carla L. Maffeo

Honors Scholar Theses

In both humans and birds, urate is an important antioxidant when maintained at normal plasma concentrations. Though human kidneys primarily reabsorb filtered urate, while those of birds perform mostly secretion, both maintain urate levels at ~300microM. The importance of maintaining urate levels within the homeostatic range was observed when the study of several prominent diseases revealed an association with hyperuricemia.

This study examined the effect of elevated zinc concentration on avian urate secretion. Here, acute exposure of chicken proximal tubule epithelial cells (cPTCs) to zinc stress had no effect on urate secretion, but prolonged zinc-induced cellular stress inhibited active transepithelial …

Changes In Light Levels With Loss Of Eastern Hemlock (Tsuga Canadensis) At A Southern Appalachian Headwater Stream: Implications For Brook Trout (Salvelinus Fontinalis), Leigh A. Siderhurst

Masters Theses, 2010-2019

The exotic invasive insect, hemlock woolly adelgid (Adelges tsugae Annand), is causing mortality in eastern hemlocks (Tsuga canadensis [L.] Carr.) throughout the eastern U. S. Hemlocks are being replaced by hardwood species that cannot fill the structural and functional role of hemlock in forest ecosystems. Because hemlocks produce dense shade, their loss may increase understory light levels. In the southern Appalachians, increases in understory light could cause changes in stream ecosystems because riparian hemlocks may help maintain cool stream temperatures for cold water species such as brook trout (Salvelinus fontinalis). I studied changes in light levels with eastern hemlock decline …

Investigation Of The Roles Of Kinesin-5 Motor Protein Family Members In Arabidopsis Thaliana, Bareza Abbas Rasoul

Masters Theses, 2010-2019

Eukaryotic cells contain a cytoskeleton that performs a range of essential functions, including intracellular transport, nuclear division and shaping the cell. There are various kinesin motor proteins involved in organizing the microtubule cytoskeleton during interphase and mitosis. The plant Arabidopsis thaliana has the largest number of kinesins amongst all sequenced organisms. Many of those kinesins have not been studied. Members of the Kinesin-5 family cross link microtubules and are crucial for separation of mitotic spindle poles. There are 4 members of this family in Arabidopsis: Kinesin-5 A, B, C and D, but only Kinesin-5 C has been studied previously. Each …

Chemotaxis Of Amphibian Pathogen Batrachochytrium Dendrobatidis In The Presence And Absence Of Antifungal Metabolites Produced By Amphibian Skin Bacteria, Brianna Ashlyn Lam

Masters Theses, 2010-2019

Chytridiomycosis is an amphibian skin disease that threatens amphibian biodiversity worldwide. The infectious fungal agent of chytridiomycosis, Batrachochytrium dendrobatidis, can affect amphibians differently in that some amphibian populations can co-exist with the fungus and others quickly succumb to disease. Amphibians in populations that co-exist with the B. dendrobatidis are shown to have sub-lethal infections on their skins. Several co-existing populations have also been shown to have higher proportions of individuals with antifungal skin bacteria suggesting the role of skin bacteria in disease outcome. Little is known about the mechanism(s) that antifungal skin bacteria use to ameliorate the effects of B. …

Activation Of Gabaa And 5ht1a Receptors In The Raphe Pallidus Abolish The Cardiovascular Responses To Stress In Conscious Rats, Nhut Minh Pham Le

Masters Theses, 2010-2019

Serotonergic neurons of the raphe pallidus area of the brainstem are involved in the cardiovascular responses to stress. However, the manner in which they mediate these responses is not well understood and severe abnormalities in this system have been associated with Sudden Infant Death Syndrome. In the current study, microinjections of muscimol and 8-OH-DPAT (GABAA and 5HT1A receptor agonists, respectively) into the raphe pallidus abolished the increase in mean arterial pressure and the tachycardiac responses following air jet, handing, and restraint stress that were observed following microinjections of artificial cerebrospinal fluid. The stress responses following muscimol microinjections suggest that this …

Fish Community Response To The Addtion Of Wood In Smith Creek, Virginia, Chastine Daniel Kyger

Masters Theses, 2010-2019

Large woody debris (LWD) is an important component of healthy stream ecosystems. LWD shapes stream physical habitat features, captures and stores organic matter, and serves as shelter, feeding sites, and reproductive substrate for fish and other aquatic organisms. Loss of in-stream LWD and sources of LWD as a result of human activities has negatively impacted many streams. Recently, restoration of in-stream LWD and riparian sources of LWD have become important facets of stream restoration, though many projects involving LWD restoration lack monitoring and evaluation. I evaluated the effects of adding LWD on the fish community in Smith Creek, a small …

Investigation Of The Role Of Bam9 In Starch Metabolism In Arabidopsis Thaliana, Elizabeth Ann Steidle

Masters Theses, 2010-2019

Beta-amylases play an essential role in night time starch degradation in leaves. There are nine known beta-amylases (BAMs) in Arabidopsis thaliana. This research is focused on BAM9, which is localized in the chloroplasts but is unique compared to active BAM proteins. First, alignments of BAM9 orthologs and catalytically active paralogs suggest that BAM9 may not be catalytically active and may not bind to starch, but it may bind to another molecule at a remote site. Secondly, microarray data shows a peak of BAM9 expression at the dark/light transition which is contradictory to what one would expect for an active BAM …

Mutant Huntingtin Fragments Form Oligomers In A Polyglutamine Length-Dependent Manner In Vitro And In Vivo, Justin Legleiter, Emily M. Sontag, Gregor P. Lotz, Ellen Sapp, Cheping Ng, Marian Difiglia, Leslie M. Thompson, Paul J. Muchowski

Biological Sciences Faculty Research and Publications

Huntington disease (HD) is caused by an expansion of more than 35–40 polyglutamine (polyQ) repeats in the huntingtin (htt) protein, resulting in accumulation of inclusion bodies containing fibrillar deposits of mutant htt fragments. Intriguingly, polyQ length is directly proportional to the propensity for htt to form fibrils and the severity of HD and is inversely correlated with age of onset. Although the structural basis for htt toxicity is unclear, the formation, abundance, and/or persistence of toxic conformers mediating neuronal dysfunction and degeneration in HD must also depend on polyQ length. Here we used atomic force microscopy to demonstrate mutant htt …

Long-Term Spatial And Temporal Variability Of Benthic Macroinvertebrate Communities: Implications For Bioassessment Of Lotic Systems, Eve O'Connor

Theses and Dissertations

The structure and composition of benthic macroinvertebrate communities can vary spatially and over time. Spatial and temporal variation along a stream has many implications for population and community dynamics, which may influence bioassessment programs. I examined variability in the benthic community of eight streams within the Polecat Creek, Virginia watershed. These streams vary in size from 1st to 4th order. The streams were sampled once every season for eleven years using standard bioassessment protocols. Macroinvertebrates were sampled from both sediment and submerged wood habitats at each site. The coefficient of variation (CV) was used to quantify among season, among year …

Scaling Of Feeding Performance In Panther Grouper, Cromileptes Altivelis, Candace R. Read

Mahurin Honors College Capstone Experience/Thesis Projects

Fishes demonstrate the greatest change throughout ontogeny in body size of all vertebrates, some becoming twelve times their original length. Panther groupers, Cromileptes altivelis, are no exception. This vast size change influences other aspects of their lives including their feeding behavior, the prey they consume, and the capabilities of the mechanisms they use to capture prey. The change in the feeding performance of the panther grouper, Cromileptes altivelis, was quantified through buccal pressure recordings and high-speed videography. From this data, we can deduce that the larger juvenile was able to generate greater negative pressure within the mouth. It appears that …

Assessing Scientific Inquiry: Teacher Beliefs And Practices, Adam James Mitchell

Theses and Dissertations

Science education reform movements have long urged the use of inquiry methods in all science instruction. More recently, standards and accountability reform efforts have emphasized measuring and improving student science achievement. Researchers have questioned the alignment and balance between these reforms (Lane, 2004; Yeh, 2001). This study addresses issues faced by secondary science teachers as they simultaneously meet the goals of these reform movements. Mixed methods were used to answer the questions: 1) Can a teacher's beliefs and practices regarding inquiry teaching methods be correlated with his/her assessment practices?; 2) What item types are most commonly employed by teachers that …

Mutation Of The Vesicular Monoamine Transporter-1 Gene Alters Its Protein Product, Abena Watson-Siriboe

Theses and Dissertations

The vesicular monoamine transporter 1 (VMAT1) is essential for storage of monoamines, such as epinephrine and serotonin, in secretory vesicles of neuroendocrine cells. Recently the VMAT1 protein was detected in human and mouse brain, and mutations of the VMAT1 gene at single DNA nucleotides (single nucleotide polymorphisms or SNPs) were associated with schizophrenia. In this study, Chinese hamster ovarian cells were stably transfected with either human VMAT1 DNA (GenBank: #NM_003053.1 or DNA with the Thr4Pro SNP, which results in a threonine to proline change in amino acid number 4 of the VMAT1 protein. Western blot analysis revealed that cells with …

Investigation Of High Salt Intake And Adipogenesis In Rats, May Yong

Biological Sciences

Sodium chloride has been scrutinized of late, not only for its liberal use as a food preservative but for its contribution to disease states. The causal role of habitual high salt intake in increasing blood pressure and exacerbating hypertension has been established. A growing body of evidence strongly suggests that hypertension contributes to other conditions such as cardiovascular disease, obesity, stroke, and type II diabetes. Rates of hypertension are significantly higher in obese individuals. These comorbidities have been positively associated with the modern Western diet. Worldwide, many government and health organizations have called for public policy measures to mandate sodium …

Development Of Representative Species-Level Molecular Markers And Morphological Character Analysis Of Leucothoid Amphipods (Crustacea: Amphipoda), Kristine Nicolle White

Dissertations

Leucothoid amphipods were investigated using morphology and molecular rDNA gene sequence fragments. The morphological diagnostic characters for traditional taxonomy have been clarified, a molecular marker for representative species has been developed, and one of the current anamorph-leucomorph connections has been confirmed with molecular sequence data. Ultimately this study has combined traditional morphological and modern molecular methods to clarify the taxonomy and to propose a preliminary phylogeny of the Leucothoidae. Analysis of 18S rDNA gene fragments from 13 species in two genera supported the current morphological species designations and the separation of the family into two clades. Combined analysis of 18S …

Systematic Revision Of The Kalliapseudidae (Crustacea: Peracarida: Tanaidacea) And The Population Genetic Structure And Phylogeography Of A Species Along The Southeastern And Gulf Coasts Of North America, David Thomas Drumm

Dissertations

The Kalliapseudidae is a family of shallow burrow-dwelling marine and estuarine tanaidaceans. There are currently 39 known species of 12 genera and three subfamilies. They are primarily circumtropical in distribution; however, several species are found in temperate waters. The phylogeny of Kalliapseudidae is assessed to test the monophyly of currently accepted subfamilies and genera, based largely on examination of material loaned from various museums and institutions. Multiple exemplars from other apseudomorph families were also included in the ingroup to test the monophyly of the family. Parsimony analyses included 41 terminal taxa and 64 binary and multistate morphological characters. Analyses based …

Correlated Evolution Of Defensive And Nutritional Traits In Native And Non-Native Plants, Nicole Molinari, Charles A. Knight

Biological Sciences

We performed a comparative analysis of defensive and nutritional plant traits responsible for differential herbivory in a series of experimental feeding trials with generalist herbivores. We measured three defensive traits (leaf strength, leaf mass per unit area and endophytic fungal infection) and two nutritional traits (foliar nitrogen and water) for 26 native and eight non-native plant species from coastal California shrublands. Our feeding trials involved three species of generalist herbivore (beet armyworm, cabbage looper and the garden snail) in two types of laboratory feeding trial (single plant species and preference tests). All traits were significantly related to the amount of …

Avoidance Of Skeletal Muscle Atrophy In Spontaneous And Facultative Hibernators, Clark Cotton, Henry J. Harlow

Biology Faculty Publications

Smooth and skeletal muscle changes were compared from overwintering white-tailed prairie dogs, spontaneous hibernators that undergo regular, low-temperature torpor bouts, and black-tailed prairie dogs, facultative hibernators that use sporadic, moderate-temperature torpor bouts. The objectives were to assess the abilities of these two species with dramatically different torpor patterns (1) to conserve skeletal muscle morphology, protein, and strength and (2) to use labile protein in the small intestine and liver during the winter season of reduced activity and food intake. Mass and protein concentration of the extensor digitorum longus (EDL), soleus, liver, and small intestine, as well as skeletal muscle strength …

The Relationship Between Plasma Steroid Hormone Concentrations And The Reproductive Cycle In The Northern Pacific Rattlesnake, Crotalus Oreganus, Craig M. Lind, Jerry F. Husak, Cas Eikenaar, Ignacio T. Moore, Emily N. Taylor

Biological Sciences

We describe the reproductive cycle of Northern Pacific rattlesnakes (Crotalus oreganus) by quantifying steroid hormone concentrations and observing reproductive behaviors in free-ranging individuals. Additionally, we examined reproductive tissues from museum specimens. Plasma steroid hormone concentrations were quantified for both male and female snakes throughout the active season (March–October). We measured testosterone (T), 5α-dihydrotestosterone (DHT), and corticosterone (B) concentrations in both sexes and 17β-estradiol (E2) and progesterone (P) in females only. We observed reproductive behaviors (e.g., consortship, courtship, and copulation) in the field and measured testis and follicle size in male and female snakes from museum collections to relate …

An Antibody Directed Against The Fusion Peptide Of Junin Virus Envelope Glycoprotein Gpc Inhibits Ph-Induced Membrane Fusion, Joanne York, Jody D. Berry, Ute Stroeher, Qunnu Li, Heinz Feldmann, Min Lu, Meg Trahey, Jack H. Nunberg

Biological Sciences Faculty Publications

The arenavirus envelope glycoprotein (GPC) initiates infection in the host cell through pH-induced fusion of the viral and endosomal membranes. As in other class I viral fusion proteins, this process proceeds through a structural reorganization in GPC in which the ectodomain of the transmembrane fusion subunit (G2) engages the host cell membrane and subsequently refolds to form a highly stable six-helix bundle structure that brings the two membranes into apposition for fusion. Here, we describe a G2-directed monoclonal antibody, F100G5, that prevents membrane fusion by binding to an intermediate form of the protein on the fusion pathway. Inhibition of syncytium …

Zebrafish-Encoded 3- O -Sulfotransferase-3 Isoform Mediates Herpes Simplex Virus Type 1 Entry And Spread, Kevin Jones

Department of Biology Faculty Publications

Heparan sulfate proteoglycans modified by human glucosaminyl 3-O-sulfotransferase-3 (3-OST-3) isoform generates the cellular receptor for herpes simplex virus type 1 (HSV-1). Interestingly, the ability of zebrafish (ZF)-encoded 3-OST-3 isoform to modify heparan sulfate to mediate HSV-1 entry and cell-cell fusion has not been determined although it is predominantly expressed in ZF, a popular model organism to study viral infections. Here, we demonstrate that expression of ZF-encoded 3-OST-3 isoform renders the resistant Chinese hamster ovary (CHO-K1) cells to become susceptible for HSV-1 entry. The following lines of evidence support the important role of ZF-encoded 3-OST-3 isoform as the mediator of HSV-1 …

The Fox In The Henhouse: Responses Of Chickens (Gallus Domesticus) To The Scent Of A Predator, Andrew C. Alba, Gregory B. Cunningham

Biology Faculty/Staff Publications

Domestic chickens (Gallus domesticus) are often used as a model species in testing bird olfaction. Previous studies have indicated that domestic chicks can discriminate between various odors, are attracted to familiar odors, and use olfactory cues during food selection. Additionally, studies have indicated that olfaction plays an important role in predator recognition in a variety of songbirds. It has yet to be demonstrated, however, whether chickens can detect predators using olfactory cues. To address this, we tested 1-2 day old naïve chicks with undiluted fox urine and found that they were able to detect this scent. This could …