Biology Commons^™

Degenerate Oligonucleotide Primed - Polymerase Chain Reaction Evaluation And Optimization To Improve Downstream Forensic Str Analysis Of Low Quality/Low Quantity Dna, Lindsay Paige Thompson

Theses and Dissertations

When forensic biological samples yield low quality/low quantity DNA, thecurrent STR analysis methods do not generate acceptable profiles. Whole genomeamplification can be used to pre-amplify the entire genome for downstream analyses. A commercially available kit for DOP-PCR, a form of WGA, is currently being used in the clinical for downstream single locus targets. Forensic analyses utilize a multiplex amplification. This study determined that the "home brew" created by our lab performs the same as the commercially available kit. Future optimization studies of DOP-PCR can utilize this "home brew". Additionally, this research determined that a 10 second increase in electrokinetic injection …

Acquisition And Retention Of Bacterial Spores (Bacillus Atrophaeus) By Eight Insect Species, Kieron Marie Torres

Theses and Dissertations

Acquisition and retention of spores of an anthrax surrogate, Bacillus atrophaeus Nakamura ("BG") were evaluated in eight insect species. Species included: house cricket (Acheta domesticus L.), German cockroach (Blatella germanica L.), common house fly (Musca domestics L.), blue bottle fly (Calliphora vomitoria L.), hairy rove beetle Creophilus maxillosus L.), yellow mealworm (Tenebrio molitor L.), common paper wasps (Polistes exclamans exclamans Viereck), red paper wasps (Polistes Carolina L.), red harvester ant (Pogonymyrmex barbatus Smith). Individual insects were offered BG-treated food and sacrificed at specified time intervals following one, two or three meals. Resulting samples were surface-washed five consecutive times then homogenized …

Genetic Assessment Of Rare Blackbanded Sunfish (Enneacanthus Chaetodon) Populations In Virginia, Diana Marie Kercher

Theses and Dissertations

Enneacanthus chaetodon, the blackbanded sunfish, has become increasingly rare throughout its distribution in the Eastern United States. In Virginia, E. chaetodon maintains an endangered status and individuals persist in six populations. Mitochondrial DNA (mtDNA) and microsatellite data were assessed to determine the genetic characters and gene diversity of the Virginia populations. The results of these analyses were then compared to five additional populations; four from New Jersey and one from North Carolina that were known to have relatively good fitness and were not impacted severely by habitat alteration. The results of this study are relevant to selection of proper management …

Invasion Genetics Of The Blue Catfish (Ictalurus Furcatus) Range Expansion Into Large River Ecosystems Of The Chesapeake Bay Watershed, Colleen Beth Higgins

Theses and Dissertations

The blue catfish, Ictalurus furcatus (Ictaluridae), is ranked among the most invasive, nonnative species of concern in the Chesapeake Bay watershed. This species, intentionally introduced to three major tributaries and a number of impoundments between 1974 and 1989 for sport fishing, has spread into three additional tributaries. Using samples from the introduced tributary populations as a baseline, we evaluated microsatellite genetic variation in light of demographic and ecological data to elucidate the potential sources of the invasive I. furcatus populations. In general, the populations surveyed in the Chesapeake Bay watershed were considerably more inbred (F ranged from 0.03 - 0.27) …

Degenerate Oligonucleotide Primed-Pcr: Thermalcycling Modifications And Comparison Studies, Denise N. Rodier

Theses and Dissertations

Degenerate Oligonucleotide Primed-PCR (DOP-PCR) can potentially enhance analysis of low copy number DNA samples. Theoretically, this procedure replicates fragments of the genome that can then be used for downstream multiplex STR analysis. The objective of this study is to optimize DOP-PCR by examining ramplelongation times and cycle numbers in the non-specific amplification portion of DOP-PCR, and by modifying the degenerate primer. Additionally, other methods such as Multiple Displacement Amplification (MDA) and Low Copy Number PCR (LCN PCR) were examined for their ability to create accurate DNA profiles from low DNA input amounts. Increasing the ramplelongation times showed no effect on …

Modulation Of The Serotonin Reuptake Transporter In Raw264.7 Macrophages, Sienna Marie Arenas Malubay

Theses and Dissertations

Serotonin (5-HT) plays an important role as both a neurotransmitter and animmune modulator. The serotonin reuptake transporter (SERT) clears the extracellular space of 5-HT, which decreases the effects of 5-HT on target cells. This study demonstrated that the RAW264.7 macrophage cell line expresses SERT function, measured by assays of 3H-5HT uptake. The 5-HT uptake in RAW264.7 macrophages was more than 10-fold that of peritoneal macrophages, indicating that these cells are an excellent model for studying regulation of the SERT. Activation of macrophages with lipopolysaccharide (LPS) increased SERT activity in a time- and concentration-dependent manner and Western blots indicate that the …

Phylogeography Of Marine Meiofaunal Nemerteans Of The Ototyphlonemertes Fila Species Complex, Alexander Tulchinsky

Theses and Dissertations

Morphological conservatism combined with intraspecific variability has obstructed studies of speciation and species boundaries among marine meiofauna. Ototyphlonemertes is a genus of meiofaunal nemerteans inhabiting the interstitial spaces of marine sediments. Its members lack pelagic larvae and dispersal potential is believed to be poor. A phylogeographic study of Ototyphlonemertes fila is presented using mitochondrial (cox3) and nuclear (ISSR) molecular markers. Deep genetic divergence (approximately 18% in cox3) was observed between sympatric mitochondrial lineages in Florida. This divergence was reflected in the nuclear marker as well, suggesting the presence of two cryptic species. The first contains Florida and New England populations …

Calcium/Calmodulin Dependent Protein Kinase Type-Ii Associates With Flightless-I To Influence Its Nuclear Localization, Matthew Edward Seward

Theses and Dissertations

Ca2+/calmodulin-dependent protein kinase type-II (CaMK-II) is a Ser/Thr protein kinase regulated by Ca2+ and Calmodulin. It is a highly conserved and broadly expressed enzyme and has a unique structure and dynamic regulation. It has the ability to remain active in the absence of Ca 2+ as a result of Ca2+ dependent autophosphorylation. CaMK-II phospliorylates proteins involved in neurotransmitter secretion, long term potentiation, cytoskeletal dynamics, gene transcription, and cell motility. To support existing and identify new intracellular roles of CaMK-II, potential binding partners were identified. This was accomplished by transfecting and purifying "FLAG-tagged" CaMK-II's (α, βE, δC, and δE). CaMK-II associated …

Transforming Growth Factor-Β1 (Tgf-Β1) Induces Mast Cell Apoptosis, Farnaz Norozian

Theses and Dissertations

Mast cells are potent effectors of the inflammatory response, playing an important role in atopy, bacterial immunity, and animal models of arthritis, multiple sclerosis, and heart disease. Hence controlling mast cell numbers and responsiveness is essential for preventing inflammatory disease. This work demonstrated that the cytokine TGF-β1 is a potent inducer of mast cell apoptosis, a finding that was consistent for cultured mouse bone marrow-derived mast cells, peritoneal mast cells, and human mast cells. Cell death appeared to be the result of TGF-mediated repression of IL-3 receptor expression and function, leading to mitochondria1 damage and activation of an apoptotic cascade …

Genetic Variation Among Geographically Disparate Yellow Perch Broodstock Populations, Chandler Brooke Givens

Theses and Dissertations

As a prelude to strain selection for domestication and future marker assisted selection, genetic variation revealed by microsatellite DNA was evaluated in yellow perch, Perca flavescens, from four wild North American populations collected in 2003-2004 (Maine, ME; New York, NY; North Carolina, NC; and Pennsylvania, PA), and two captive populations (Michigan, MI; Ohio, OH). For the loci examined, levels of heterozygosity ranged from He = 0.04 to 0.88, genetic differentiation was highly significant among all population pairs, and effective migration ranged from low (Nem = 0.3) to high (Nem = 4.5). Deviation from Hardy-Weinberg 1equilibrium was regularly observed indicating significant …

Novel Characteristics Of Murine Bone Marrow-Derived Macrophages And Human Macrophage-Like Cells, George Tharwat Georges

Theses and Dissertations

These studies provide evidence for novel properties of macrophages derived from bone marrow stem cells. In study 1, treatment of activated mouse bone marrow-derived macrophages (BMM) with either catecholamine synthesis inhibitors (α-methyl-para-tyrosine and fusaric acid) or the β2 adrenergic receptor antagonist ICI 118,551 demonstrated that BMM produce catecholamines. The catecholamines modulated macrophage cytokine production through autocrine actions on adrenergic receptors. In study II, undifferentiated human bone marrow cells were incubated in 30% mouse L929 fibroblast conditioned medium and generated adherent cells within three days. The cells were clearly identifiable as macrophages based on surface proteins and phagocytic activity but produced …

Autocrine Effects Of Catecholamines On Macrophage Release Of Interleukin-6 (Il-6), Shaunta D. Poe

Theses and Dissertations

Effects of norepinephrine (NE) on macrophage cytokine release are complex because the cells have both α2 and β2 adrenergic receptors, which mediate opposing actions. Furthermore, β2-adrenergic agonists are reported to have both stimulatory and inhibitory effects on interleukin-6 (IL-6). This study was designed to clarify the autocrine role of macrophage-derived NE on IL-6 production in activated peritoneal macrophages. Effects of NE on IL-6 production in the RAW264.7 macrophage cell-line also were investigated. Treatment of activated peritoneal macrophages with endotoxin, the α2-adrenergic antagonists yohimbine or RS79948 revealed that the α2-adrenergic receptor mediates a stimulatory autocrine action of catecholamines on IL-6 production. …

Reaction Of Tardigrades (Hypsibius) To Physical And Chemical Extremes, Limor Raz

Theses and Dissertations

The process of cryptobiosis is characterized by a complete state of body water dehydration and undetectable metabolic activity, which allows tardigrades {Hypsibius) to escape environmental stress when conditions become unfavorable. In our research, Hypsibius was tested in a laboratory under pH levels of 3 to 10 and a salinity concentration gradient. In the pH experiment, we placed tardigrades in petri dishes with agar solution in an experimental pH and measured the average distance traveled. We expected them to respond favorably to a neutral pH of 7 which is common in most living organisms by showing increased movement. In the salinity …

Phylogeny And Biogeography Of Ice Crawlers (Insecta: Grylloblattodea): Evidence From Six Molecular Loci, Karl J. Jarvis

Theses and Dissertations

Ice crawlers (Insecta: Grylloblattodea) are rarely encountered insects that consist of five genera representing 26 species from North America and Asia. Asian grylloblattids are the most diverse, but North American ice crawlers (genus Grylloblatta) are known for their adaptation to cold conditions. Phylogenetic relationships among grylloblattid species and genera are not known. Late Pleistocene glaciations had a major effect on the current Grylloblatta distribution, because their specific habitat requirements restrict them to small geographical areas. Six genes were sampled in 37 individuals for 18S rRNA, 28S rRNA, histone 3, 12S rRNA, 16S rRNA, and cytochrome oxidase II (COII) from 27 …

Digestibility, Nitrogen Balance, And Blood Metabolites In Llama And Alpaca Fed Barley And Barley Alfalfa Forages., Heather Loree Davies

Theses and Dissertations

These projects were conducted to determine the digestibility of forage diets with differing CP levels in llamas and alpacas. The Utah study was designed to compare llama and alpaca nutritional parameters to determine if nutritional recommendations for llamas can be directly extrapolated to alpacas. The first study evaluated the effects of forage quality on blood metabolites and nitrogen balance in mature, intact male llamas (n = 4, 36 ± 4.4 months, 87 ± 17 kg) at high altitude in Letanias, Bolivia (4,267 m = aprox.14,000 ft above sea level). A second experiment was conducted with eight adult gelded camelids (n …

Phylogenetic Relationship Of Forest Spiny Pocket Mice (Genus Heteromys) Inferred From Mitochondrial And Nuclear Markers With Implications For Species Boundaries, Malinda Wallentine Gonzalez

Theses and Dissertations

I constructed a best estimate phylogeny based on congruence of multiple data sources. In recent years molecular data has been used both to construct phylogenies of taxonomic groups and to aid in the delimitation of new species. I generated and analyzed sequence data for forest spiny pocket mice (Genus Heteromys) for the mitochondrial gene cyt b (1143 bp) and two nuclear gene segments MYH2 (252 bp) and EN2 (189 bp). I used maximum parsimony and Bayesian analyses to infer relationships among species and to provide a framework for using a species delimitation method to investigate the possibility of multiple …

Vegetation Response Of A Wyoming Big Sagebrush (Artemisia Tridentata Ssp. Wyomingensis) Community To 6 Mechanical Treatments In Rich County, Utah, Daniel David Summers

Theses and Dissertations

In recent years, the importance of sagebrush to shrub-steppe ecosystems and associated plant and animal species has been recognized. The historical removal of herbaceous species by excessive and uncontrolled livestock grazing on many of our sagebrush ecosystems has resulted in a stagnant state where dense, competitive stands of sagebrush prevent herbaceous species from recovering. Most early research on sagebrush control was directed toward eradication to increase herbaceous forage for livestock production, rather than sagebrush thinning to improve shrub vigor and understory production for wildlife habitat and community diversity. Mechanical treatments have the ability to retain shrub and herbaceous components, while …

Phylogenetic History, Morphological Parallelism, And Speciation In A Complex Of Appalachian Salamanders (Genus: Desmognathus), Nathan D. Jackson

Theses and Dissertations

Understanding the mechanisms that generate shared morphologies across closely related taxa is important when identifying distinct evolutionary lineages using morphological characters. Desmognathus salamanders are an ideal group for testing hypotheses concerning the correlation between morphological similarity and genetic exchange within and among nominal species due to a pattern of high discordance between the two. Phylogeographic hypotheses are tested for populations of the D. quadramaculatus species complex throughout southern Appalachia by combining phylogenetic and population genetic methods with geographical information. Phylogenetic and phylogeographic inferences are then assessed in conjunction with morphological characteristics that have traditionally diagnosed taxonomic entities to understand the …

Biochemical And Molecular Nutrition Blocks As Dietary Supplements In Llamas (Lama Glama) In The Last Third Of The Gestation Period Of The Ceac, Janette Illanes Callejas

Theses and Dissertations

The present work consisted in the use of biochemical and molecular nutrition blocks (BMN) in llamas during the last third of the gestation period, at the Agricultural Experiment Center of Condori (CEAC), located 49 km north of the city of Oruro, and 12 km north of the Caracollo population, in the province of Cercado. For this research work, we used 20 pregnant llamas in the last third of their gestation period, between the ages of 2 and 3 years old, 10 of which belonged to the Khara breed, and 10 to the Thampulli breed. Two corrals of 7 x 7 …

Seasonal And Spatial Variation In Leaf Area Index, Litter Production, And Light Levels In Myrica Cerifera,Shrub Thickets Across A Barrier Island Chronsequence, Steven T. Brantley

Theses and Dissertations

Leaf area index (LAI), litter production and understory light levels of Myrica cergera shrub thickets were assessed on Hog Island, Virginia to quantify spatial and seasonal variations in leaf area and light attenuation among four thickets representing a successional chronosequence and compare methods of estimating LA1 in shrub- dominated systems. Seasonal LA1 estimates were made seven times throughout the year with a portable integrating radiometer (Li-Cor LAI-2000) and three times by measurement of photosynthetically active radiation (PAR) and use of the Beer-Larnbert law. Leaf area index was also estimated through leaf litter collection and use of allometric relationships between stem …

Correlation Between Bioassessments Of Macroinvertebrates And Fishes And Natural Land Cover In Virginia Coastal Plain Watersheds, Warren Hunter Smigo

Theses and Dissertations

Twenty five first through third order streams in the Coastal Plain of Virginia were sampled for benthic macroinvertebrates and fishes to determine whether a predictable relationship between areas of Unfragmented Natural Land Cover (UNLC) and biotic integrity could be established. I hypothesized that as the area of UNLC increased in a watershed at either the whole catchment or riparian scale, biotic indices measuring stream water and habitat quality would increase. Biotic integrity was measured through the scores from the Coastal Plain Macroinvertebrate Index (CPMI) for benthic macroinvertebrates and the VCU Index of Biotic Integrity (IBI) for fishes. Using GIS, the …

Genetic Variability, Pathogen Susceptibility, Subspecies Identity And Conservation Of The Endangered Northern Flying Squirrel (Glaucomys Sabrinus) In Virginia, James Lincoln Sparks Jr.

Theses and Dissertations

I examined the population genetic structure of three known subspecies of Glaucomys sabrinus from Appalachia, Washington State, and two previously unexamined populations from Mount Rogers National Recreation Area (MRNRA) in Southwestern Virginia. Mean FST (0.107) and an AMOVA (P G. sabrinus subspecies populations in the southern Appalachians are genetically differentiated. Glaucomys sabrinus at MRNRA were less inbred than expected. Gene flow, a consensus tree based on Nei's genetic distance, elevated heterozygosity and morphometric data suggest that the MRNRA G. sabrinus population is an intergrade of the two recognized Appalachian subspecies, G. s. fuscus and G. s. coloratus. I compared inbreeding …

Material And Acoustic Properties Of Swimbladders Of Tilapia And Channel Catfish, Mohammed Ali Nawaz

Theses and Dissertations

Acoustically, teleost swimbladders have been considered resonant underwater bubbles. Contrary results indicating that bladders are tuned less sharply than such a bubble have been explained by damping of surrounding fish tissue. Recent findings in toadfish and weakfish, however, suggest that the bladder is a highly damped structure and that the frequency of the fish sounds is deternlined as a forced response to sonic muscle movement rather than by resonance of the bladder. In this study I examined acoustics and material properties of swimbladders in Tilapia (an auditory generalist) and the channel catfish (an auditory specialist). The swimbladder was struck with …

Habitat Selection In Four Sympatric Small Mammal Species And The Effects Of Potential Predators On Peromyscus Leucopus, Adam Daniel Chupp

Theses and Dissertations

I examined the effects of potential predators in relation to habitat selection in Peromyscus leucopus. I also examined habitat selection in three other sympatric species (Blarina brevicauda, Blarina carolinensis, Sorex longirostris). I utilized data fiom 49 sampling sites on National Park Service land; Petersburg National Battlefield Eastern Front Unit (15), Five-Forks Unit (17), Appomattox Court House National Historical Park (15) and Booker T. Washington National Monument (12). Sites were categorized by location (park unit) and habitat type (i.e. bottom-land hardwood), and the microhabitat within each sampling site was characterized by four variables (% cover of grasses, herbs, shrubs, and volume …

Distribution Of Chemistry And Sexual Fecundity In The Lichenized-Fungi, Xanthoparmelia Cumberlandia And Xanthoparmelia Coloradoensis On Boulder Mountain, Aquarius Plateau, Ut, Heather Bird Jackson

Theses and Dissertations

Three aspects of Xanthoparmelia cumberlandia and Xanthoparmelia coloradoënsis populations found at two elevations are explored: clustering of secondary chemicals and the resulting implications for taxonomic distinctions, the usefulness of thallus size as an indirect measure of sexual fecundity, and the frequency of sexual reproduction.

First, we use clustering of 46 chemicals produced by X. cumberlandia and X. coloradoënsis to evaluate the adequacy of the current taxonomic distinction between them. Using principal components analysis and UPGMA, we find that the currently recognized species boundaries indicated by the presence of stictic acid in X. cumberlandia and salazinic acid in X. coloradoënsis are …

Density Effects On Growth, Survival And Diet Of June Sucker (Chasmistes Liorus): A Component Allee Effect In An Endangered Species., David Barrett Gonzalez

Theses and Dissertations

Density-dependence is considered one of the most important regulators of population growth, and it has been documented across a wide variety of species. Typically, population growth rate and components thereof decline with increasing density (i.e., negative density-dependence); however, in species that exhibit high population densities and social behavior, positive density-dependence (i.e., Allee effect) may occur at low density. June sucker, a federally endangered lake sucker endemic to Utah Lake, Utah, USA, occurred historically at high density, and it exhibits coordinated feeding behavior. These characteristics indicate a potential for the existence of an Allee effect at current low population densities. To …

Evolution And Phylogeny Of Basal Winged Insects With Emphasis On Mayflies (Ephemeroptera), Thomas H. Ogden

Theses and Dissertations

Ephemeroptera (mayflies) is a monophyletic group of semi-aquatic pterygote insects, comprising 3083 species, 376 genera, and 37 described families and are present on all continents, excluding Antarctica, being associated with freshwater and brackish water habitats. The order is unique among pterygote insects in possessing functional wings at the penultimate molt (subimago stage), prior to the full development of genitalia; in all other insects the presence of functional wings occurs only after the final molt. The purpose of this dissertation is to use molecular and morphological data, in order to investigate the position of the order Ephemeroptera among other insect orders, …

Prevalence Of Teleological And Lamarckian Misconceptions Of Natural Selection Among College Students, Bryce T. Battisti

Theses and Dissertations

Science teachers and researchers note that students must correctly understand the role of natural selection in evolution to make sense of biology. The level of understanding of natural selection can be assessed using the Conceptual Inventory of Natural Selection (CINS) which is a 20-item multiple-choice test that incorporates student misconceptions as distractors. In the present study, Item Response Theory (IRT) was used to analyze the occurance of misconceptions on the CINS among 1192 students in an introductory non-majors biology course. The four most difficult topics in the CINS are: (a) how change occurs in a population; (b) origin of variation; …

Phylogeny Of The Polyneopterous Insects With Emphasis On Plecoptera: Molecular And Morpological Evidence, Matthew Dana Terry

Theses and Dissertations

Polyneoptera is an assemblage of eleven insect orders comprising the "orthopteroid" insects. It includes familiar insects such as grasshoppers, roaches, termites, earwigs and preying mantises; as well as the more obscure web-spinners, angel insects and ice-crawlers. We present a phylogenetic analysis of the polyneopteran orders based on 18S rDNA, 28S rDNA, Histone 3, and a coded morphology matrix for an extensive sampling of taxa. We investigate the use of congruence between separate datasets as an a priori measure of alignment quality. Our results support the paraphyly of Polyneoptera, the monophyly of Dictyoptera, sister taxon relationships between Embiidina + Phasmatodea and …

Phylogenetic Systematics And Evolution Within The Family Scincidae, Alison Swindle Whiting

Theses and Dissertations

Scincidae (skinks) comprise one of the largest families of lizards, and the more than 1300 species show great variation in body size and form, and are found worldwide in a diversity of habitats. The group presents many interesting questions ranging from the colonization of oceanic islands, to the evolution of limb loss, yet most of these and other questions remain understudied. The purpose of this dissertation is to use multiple mitochonidrial and nuclear DNA markers in connection with current cladistic methods to address evolutionary questions at many levels within Scincidae. In chapter one, a molecular phylogenetic study, based on six …