Life Sciences Commons^™

Kinematics And Hydrodynamics Of Cephalopod Turning Performance In Routine Swimming And Predatory Attacks, Rachel A. Jastrebsky

Biological Sciences Theses & Dissertations

Steady rectilinear swimming has received considerable attention in aquatic animal locomotion studies. Unsteady swimming movements, however, represent a large portion of many aquatic animals’ locomotive repertoire and have not been examined extensively. This study incorporates kinematic analyses of routine turning performance of brief squid Lolliguncula brevis and dwarf cuttlefish Sepia bandensis (Chapter 2), 3D velocimetry techniques to examine hydrodynamic turning performance of L. brevis (Chapter 3) and kinematic analyses of turning performance of L. brevis during predatory attacks on shrimp and fish prey (Chapter 4).

Both L. brevis and S. bandensis demonstrated high maneuverability, having the lowest measures of length-specific …

Efficient Algorithms For Prokaryotic Whole Genome Assembly And Finishing, Abhishek Biswas

Computer Science Theses & Dissertations

De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) using both overlapping reads and linked reads until the assembly runs into an ambiguous repeat region. These contigs are further bridged into scaffolds using linked read information. However, errors can be made in both phases of assembly due to high error threshold of overlap acceptance and linking based on too few mate reads. Identical as well as similar repeat regions can …

Wildlife Crime And Other Challenges To Resource System Resilience, Patricia Anne Raxter

Graduate Program in International Studies Theses & Dissertations

Although wildlife crime has exploded in Africa over the past decade —“commercial poaching” now kills an estimated eight percent of the continent’s elephant population each year—some governments have proven more successful than others at protecting wildlife and preserving habitats. To explain this variation, this study examines how the policies of three states (Kenya, Tanzania, and Botswana) have enhanced or undermined the resilience of the continent’s elephant ecosystem. Using the social-ecological system framework, the study illustrates how each state’s changing practices have either exacerbated the stresses wrought by wildlife crime or successfully protected local populations from poaching. The study finds that …

Groundwater Thresholds For Root Decomposition And The Relation To Barrier Island Ecological State Changes, Matthew Lee Smith

Biological Sciences Theses & Dissertations

Barrier islands off the eastern shore of Virginia exhibit distinct habitats that abruptly transition between periodically brackish/freshwater marshes, wooded swales, and sparsely vegetated dunes. There is strong evidence that the plant communities and ecosystem processes occurring in each habitat are primarily influenced by nutrient availability and the distance between two of the three free surfaces: land and freshwater. At the Virginia Coast Reserve-Long Term Ecological Research Site in Virginia, USA, thresholds to belowground decomposition rates were identified by measuring decay of native roots and rhizomes at 32 elevations in relation to mean annual groundwater levels (-0.356 – 1.937 m). Negative …

The Effects Of Urbanization On Tick Parasitism Rates In Birds Of Southeastern Virginia, Erin Leigh Heller

Biological Sciences Theses & Dissertations

The coastal region of southeastern Virginia is one of the largest urban areas along one of North America’s migratory flyways. Because hundreds of avian species use this flyway, understanding factors affecting birds and their health is of paramount concern. Within this region, 14 species of ticks have been documented, all of which may serve as vectors of mammal (including human) pathogens. By sampling birds at sites of varying levels of urbanization within the coastal southeastern urban matrix, I studied the relationship between ticks and their avian hosts, and how this relationship varies seasonally. Mistnets were set-up at five permanent sites …

Dna Repair Deficiency In Huntington's Disease Fibroblasts And Induced Pluripotent Stem Cells, Peter Anthony Mollica

Biological Sciences Theses & Dissertations

Mutant huntingtin protein (mhtt)– the protein responsible for cellular dysfunction in Huntington’s disease (HD) –is a product of an expanded trinucleotide repeat (TNR) cytosine-adenine-guanine (CAG) sequence in exon 1 of the huntingtin (HTT) gene. The pathology of HD has been extensively researched; however, the mechanism by which the disease-causing TNR expansions occur in somatic cells remains elusive. Interestingly, HD has often been referred to a ‘DNA repair disease’, even though DNA repair dysfunction in situ has not been identified. We hypothesized that presence of the mhtt protein affects the expression of DNA repair genes used to address DNA repair, ultimately …

A Study Of A Simulated Infectious Disease On Healthcare Workers' Reaction, Knowledge, Attitudes, And Performance Towards Hand Hygiene, Lydia Wigglesworth-Ballard

Health Services Research Dissertations

Problem Statement. The high rate of healthcare worker-patient contact provides many opportunities for exposure to pathogens, which creates challenges in assessing healthcare workers' success at preventing healthcare associated infections caused by these dangerous pathogens.

Methods. This study explored the effects of a simulated infectious disease on healthcare workers' hand hygiene knowledge, attitudes, performance, and reactions using Kirkpatrick's Four levels of Evaluation. The study utilized a mixed method pre-test – 2 post-test design. The dependent variables were hand hygiene knowledge, attitudes toward hand hygiene guidelines, hand hygiene performance, and reaction to the overall experience. Data was collected three times over a …

Lower Extremity Biomechanics In Individuals With And Without Previous Hamstring Injury, Jessica A. Mutchler

Human Movement Sciences Theses & Dissertations

Primary risk factors for hamstrings strains such as fatigue, previous injury and strength deficits have been identified in the research, yet re-injury rates remain high among the physically active. Sub-acute analysis of the hip, knee and ankle biomechanics following a hamstrings strain have been largely overlooked and may provide additional insight into re-injury risks. It was the aim of this dissertation to explore long-term adaptations in walking and running tasks following a hamstrings strain, and to develop a hip endurance test that could be used in future studies.

Project one used a cross-sectional study with test-retest design to develop and …

The Effects Of Pre-Maximal Exertion Inhalation Of Ammonia And The Performance Effects During Deadlift Maximal Tests, Justin Nicholas Vigil

Human Movement Sciences Theses & Dissertations

The purpose of this study was to investigate the effects of ammonia as a stimulant on athletic performance during a deadlift one maximal repetition (1-RM) absolute strength test. It was hypothesized that ammonia inhalation would result in a larger 1-RM, possibly due to immediate catecholamine release attributed to the fight-or-flight response. If proven effective, ammonia inhalation would present an option to increase power and strength performance during training and competition based on an acute manipulation of natural occurring hormones, eliminating the side effects attributed to other supplementation methods. Subjects (n = 10 males, X±SD age = 21±1 years, mass = …

Determining The Prevalence And Distribution Of Tick-Borne Pathogens In Southeastern Virginia And Exploring The Transmission Dynamics Of Rickettsia Parkeri In Amblyomma Maculatum, Chelsea L. Wright Thompson

Biological Sciences Theses & Dissertations

Tick-borne pathogens are an increasing threat to human and animal health worldwide. In the United States, cases of Lyme disease, spotted fever rickettsioses, ehrlichiosis and anaplasmosis are on the rise. Factors related to emergence include appearance of a new pathogen, recognition of an existing pathogen and environmental changes that result in new exposure events. Despite the rise in tick-borne disease incidence within many states, including Virginia, there is a paucity of data related to the prevalence and distribution of ticks and tick-borne pathogens.

The first aim of this dissertation research was to determine the tick-borne pathogen composition within tick populations …

Molecular Phylogeny Of The Genus Houstonia And Allies In Rubiaceae, Hunter Lee Shanks

Biological Sciences Theses & Dissertations

Houstonia (Rubiaceae) is a strictly North American genus of 24 species distributed from Mexico, throughout the United States, up to Canada. Houstonia has proven to be a taxonomically difficult genus since the Linnaean description of Houstonia and the related genera: Hedyotis and Oldenlandia in 1753. For over 250 years botanists have lumped and separated Houstonia from Hedyotis and Oldenlandia based on various morphological characters. The most recent circumscription of Houstonia (Terrell 1996) separated the genus into two subgenera with each subgenus containing two sections. Nuclear (ITS) and plastid (trnL-F, rps16) DNA sequences were used to build a molecular phylogeny depicting …

Perch Selection By Male Dragonflies (Odonata, Anisoptera) Related To Competitive Ability And Species Composition, Jessica L. Beard

Biological Sciences Theses & Dissertations

Males of many species of dragonflies (Odonata, Anisoptera) establish territories in aquatic habitats where they compete with other males for access to food and females. Territorial males typically perch on emergent vegetation and chase rival males who intrude into their territories. This dissertation research examined the role of male size in perch height selection, position on the perch, and competitive ability. Four hypotheses were tested: 1) Dragonfly species would vary by size and that territorial species would show sexual size dimorphism (SSD), 2) Perch height selection would be related to dragonfly size, 3) Position on the perch would be related …

Blue Carbon In Freshwater / Brackish Marshes On The Barrier Islands Of Virginia Aboveground Net Primary Productivity And Carbon Pools, Emily Caitlin Adams

Biological Sciences Theses & Dissertations

"Blue carbon" is a relatively new concept describing carbon distributed tidally and sequestered via net production within coastal ecosystems, including seagrass beds, mangrove forests, and salt-water marshes. These systems sequester carbon at least 10 times faster than terrestrial systems. Fresh to brackish wetlands that receive irregular tidal influence due to overwash and storm events have not been typically studied as blue carbon systems. My objective was to quantify carbon pools within four interdunal fresh to brackish marshes on Hog Island, Virginia to determine their blue carbon potential. Marshes 1 and 2 were farthest from the ocean, below and above a …

The Effects Of Propofol, Sodium Pentobarbital, And Ketamine Hydrochloride On In Vitro Mouse Embryonic Development, Tyler C. Balak

Theses and Dissertations in Biomedical Sciences

Every year more than 75,000 pregnant women are exposed to teratogenic medications or general anesthesia during non-obstetric surgery in the US,1-4 and embryonic effects of general anesthesia are of particular interest in laboratory research and veterinary medicine. The mouse system is used to screen potential toxic effects of anesthetics used in egg retrieval for in vitro fertilization (IVF), or those of pharmacologic agents which may come in contact with the egg or early embryo. Mouse preimplantation 2-cell embryos were exposed in vitro to incremental concentrations of common general anesthetics within and exceeding the normal clinical dosage range for mice (propofol …

Exploring The Neuropeptides, Neuropeptide Receptors And Neurotransmitter Receptors In The Synganglia Of Part-Fed Females Of Ornithodoros Turicata (Argasidae) And Ixodes Scapularis (Ixodidae) With Insights Into Their Roles In Contrasting Biology, Noble I. Egekwu

Theses and Dissertations in Biomedical Sciences

The neurobiology of the synganglion (central nervous system) of the Lyme disease tick, Ixodes scapularis and the soft tick Ornithodoros turicata was evaluated using Illumina GAII high throughput sequencing which generated high coverage cDNA libraries (transcriptomes). These ticks exhibit different biological patterns of feeding, blood meal water, and salt elimination, cuticle plasticity versus cuticle synthesis, development and reproduction. RNA sequencing of I. scapularis, and Ornithodoros turicata yielded a total of 117,900,476 raw reads which were assembled to 30,838 contigs and a total of 63,528,102 also assembled to 132,258 contigs, respectively. Comparison of Gene Ontology (GO) mapping success for genes …

Educational Practices And Attainment Of Competency In The Professional Preparation Of An Athletic Trainer, Julie M. Cavallario

Human Movement Sciences Theses & Dissertations

The professional education of athletic trainers will continue to evolve as the needs of the profession, and the healthcare system, change. In current educational practices the educational preparation of an athletic trainer can take place at the undergraduate or post-baccalaureate level. Additionally, there are no universally applicable outcome measures for comparison of student performance in the clinical education portion of existing curriculums.

The purpose of this dissertation was to explore the existing education practices, especially relevant to clinical education, currently in place for athletic training (AT) at the professional level. The purpose of the literature review was to historically examine, …

Plasma Activated Air Mediates Gene Transfer, Chelsea M. Edelblute

Biological Sciences Theses & Dissertations

Cold plasma is produced when strong applied electric fields accelerate free electrons, which dissociate, excite, or ionize gaseous molecules [1]. The deposition of ions from the plasma source is dependent on power generation, input gas composition, and gas flow rate. In the presence of reactive species, the membrane of eukaryotic cells is compromised allowing for otherwise impermeant molecules, such as DNA, to enter the inner-cell milieu [2].

The efficacy of a novel cold plasma reactor based on shielded sliding discharge for the delivery of plasmid DNA was assessed. The device is entirely non-contact, wherein the plasma never directly touches the …

Blue Carbon In Coastal Freshwater/Brackish Marshes On The Barrier Islands Of Virginia: Belowground Carbon Dynamics, Nathan M. Sedghi

Biological Sciences Theses & Dissertations

Some coastal ecosystems sequester substantially more carbon (blue carbon) than land locked systems due to high net primary production and deposition associated with oceanic influences. Most blue carbon research has focused on mangroves, seagrass beds, and salt marshes. Studies on blue carbon potential of coastal freshwater marshes are less common. Barrier islands frequently flood, with seawater reaching interior ecosystems. I examined brackish/freshwater marshes on Virginia barrier islands for possible roles as blue carbon systems. I studied four interior marshes on Hog Island, which varied in proximity to a direct overwash path and protection by a trail berm that divides northern …

Molecular Phylogenetics And Historical Biogeography Of The Tribe Chiococceae (Rubiaceae), Sushil Kumar Paudyal

Biological Sciences Theses & Dissertations

Chiococceae are a monophyletic assemblage of morphologically very diverse groups of plants ranging in habit from subshrubs to shrubs to tall trees exhibiting an astonishing variation in shapes and sizes of corolla, and kinds of fruits and seeds. They are primarily distributed in the Neotropics but also occur in the West Pacific islands; thus exhibiting amphi-Pacific tropical disjunction. This study addresses the phylogenetic relationships and biogeography of the Chiococceae using molecular DNA sequence data, and presents novel data on the tribal and generic delimitations, intergeneric relationships, and the origin and dispersal of this group.

In the most recent tribal delimitations …

Computational Development For Secondary Structure Detection From Three-Dimensional Images Of Cryo-Electron Microscopy, Dong Si

Computer Science Theses & Dissertations

Electron cryo-microscopy (cryo-EM) as a cutting edge technology has carved a niche for itself in the study of large-scale protein complex. Although the protein backbone of complexes cannot be derived directly from the medium resolution (5-10 Å) of amino acids from three-dimensional (3D) density images, secondary structure elements (SSEs) such as alpha-helices and beta-sheets can still be detected. The accuracy of SSE detection from the volumetric protein density images is critical for ab initio backbone structure derivation in cryo-EM. So far it is challenging to detect the SSEs automatically and accurately from the density images at these resolutions. This dissertation …

Zero-Inflated Models To Identify Transcription Factor Binding Sites In Chip-Seq Experiments, Sameera Dhananjaya Viswakula

Mathematics & Statistics Theses & Dissertations

It is essential to determine the protein-DNA binding sites to understand many biological processes. A transcription factor is a particular type of protein that binds to DNA and controls gene regulation in living organisms. Chromatin immunoprecipitation followed by highthroughput sequencing (ChIP-seq) is considered the gold standard in locating these binding sites and programs use to identify DNA-transcription factor binding sites are known as peak-callers. ChIP-seq data are known to exhibit considerable background noise and other biases. In this study, we propose a negative binomial model (NB), a zero-inflated Poisson model (ZIP) and a zero-inflated negative binomial model (ZINB) for peak-calling. …

Exploring The Effect Of Climate Change On Biological Systems, Nardos Sori

Chemistry & Biochemistry Theses & Dissertations

The present and potential future effect of global warming on the ecosystem has brought climate change to the forefront of scientific inquiry and discussion. For our investigation, we selected two organisms, one from cyanobacteria and one from a cereal plant to determine how climate change may impact these biological systems. The study involved understanding the physiological and adaptive responses at both the genetic and protein function levels to counteract environmental stresses. An increase in atmospheric carbon dioxide is a key factor in global climate change and can lead to alterations in ocean chemistry. Cyanobacteria are important, ancient and ubiquitous organisms …

Multichannel Characterization Of Brain Activity In Neurological Impairments, Yalda Shahriari

Biomedical Engineering Theses & Dissertations

Hundreds of millions of people worldwide suffer from various neurological and psychiatric disorders. A better understanding of the underlying neurophysiology and mechanisms for these disorders can lead to improved diagnostic techniques and treatments. The objective of this dissertation is to create a novel characterization of multichannel EEG activity for selected neurological and psychiatric disorders based on available datasets. Specifically, this work provides spatial, spectral, and temporal characterizations of brain activity differences between patients/animal models and healthy controls, with focus on modern techniques that quantify cortical connectivity, which is widely believed to be abnormal in such disorders. Exploring the functional brain …

Development Of A Practical Visual-Evoked Potential-Based Brain-Computer Interface, Nicholas R. Waytowich

Biomedical Engineering Theses & Dissertations

There are many different neuromuscular disorders that disrupt the normal communication pathways between the brain and the rest of the body. These diseases often leave patients in a `locked-in" state, rendering them unable to communicate with their environment despite having cognitively normal brain function. Brain-computer interfaces (BCIs) are augmentative communication devices that establish a direct link between the brain and a computer. Visual evoked potential (VEP)- based BCIs, which are dependent upon the use of salient visual stimuli, are amongst the fastest BCIs available and provide the highest communication rates compared to other BCI modalities. However. the majority of research …

Potential For Biocontrol Of Environmental Vibrio Spp. By Predatory Bacteria Bacteriovorax, Patrick Tennis

OES Theses and Dissertations

The scale of predator-prey interactions varies from the iconic (e.g., lions and gazelles) to the microscopic (e.g., protists and bacteria). Bdellovibrio-and-like-organisms (BALOs) are bacteria that prey upon other Gram-negative bacteria, including pathogens. In particular, the halophilic genus Vibrio, many species of which are disease agents, has been shown to be susceptible to attack by BALOs. One motivation of the present research is to assess the potential for biocontrol of Vibrio by Bacteriovorax. This investigation is the first to test the susceptibility of Vibrio strains (n = 26) originating from a variety of geographic locations to predation by …

The Behavioral Causes Of Reproductive Skew In Cooperatively Polygynandrous Acorn Woodpeckers (Melanerpes Formicivorus), Anna C. Brownson

Biological Sciences Theses & Dissertations

Reproductive skew, the degree to which reproduction is shared among same-sex individuals in a social group, is a pattern affected by ecological conditions, sociality, cooperation, and the inter- and intrasexual behavior of individuals in complex animal societies. Transactional and compromise skew models assume that high skew is the product of dominance hierarchies among cobreeders, yet this has rarely been tested. Both model types fail to incorporate the decisions of more than two individuals, generally overlooking the effect of female behavior on male reproductive success in multi-male groups, and are ineffective at predicting skew in larger groups characterized by more than …

A Framework And System For A Multi-Model Decision Aid For Sustainable Farming Practices, Kasi Bharath Vegesana

Computational Modeling & Simulation Engineering Theses & Dissertations

Decision support systems (DSS) for farmers address the need for modeling multiple processes and scenarios that affect farmer decision making. Existing DSS have various drawbacks that stop them from being deployed as decision support tools. This research proposes a multi-model simulation framework that can be used to analyze farm management practices at the crop level, individual farm level and at the community level to show the impact and alternatives for smallholder farming practices. A generic crop growth model is proposed, based on existing equations. We run sensitivity analysis on the model to identify important variables. The outputs from the crop …

De Novo Protein Structure Modeling And Energy Function Design, Lin Chen

Computer Science Theses & Dissertations

The two major challenges in protein structure prediction problems are (1) the lack of an accurate energy function and (2) the lack of an efficient search algorithm. A protein energy function accurately describing the interaction between residues is able to supervise the optimization of a protein conformation, as well as select native or native-like structures from numerous possible conformations. An efficient search algorithm must be able to reduce a conformational space to a reasonable size without missing the native conformation. My PhD research studies focused on these two directions.

A protein energy function—the distance and orientation dependent energy function of …