Biology Commons^™

Community Metrics And Trophic Dynamics In Tidal Creeks In An Anthropogenically Fragmented, Coastal Landscape, Michael Robert Lowe

Dissertations

Salt marsh landscapes are among the most anthropogenically altered ecosystems in the world. Urbanization (i.e., accumulation of impervious cover and man made structrues) of the coastal landscape can disrupt the delivery of numerous ecosystem services. Among the many services provided by salt marsh habitats, they serves as the primary habitats for distinct macroinfauna (i.e., benthic and epibenthic macrofauna) and nekton (i.e., fish and decapod crustaceans) assemblages. In this dissertation, I used a number of metrics to test the overarching hypothesis that coastal urbanization has negative consequences for salt marsh faunal assemblages. Chapter I uses a landscape ecology approach to show …

Evaluation Of Human Fecal Pollution In Mississippi Coastal And Creek Waters Using Library Independent Markers, Christopher John Flood

Dissertations

The objective of this study was to determine whether statistically valid correlations could be elucidated between standard indicator bacteria (enterococci and fecal coliforms) from coastal creek and marine samples and the presence of four library independent molecular markers that are human or sewage specific. Eight hundred and nineteen samples were collected between August 2007 and July 2010 to determine enterococcal and fecal coliform counts and the presence of genetic markers for sewage indicator organisms Methanobrevibacter smithii, human specific Bacteroides sp., Bacteroides thetaiotaomicron, and Fecalibacterium sp. During the course of this study environmental parameters were measured and statistically analyzed to determine …

Characterization Of Whole Pine Tree Substrates For Adventitious Rooting Of Cuttings And Initial Growth Of Seedlings, Anthony Lynn Witcher

Dissertations

Processed whole pine (Pinus taeda L.) trees have been extensively evaluated to supplement peatmoss and pine bark usage in container substrates for greenhouse and nursery crop production. The suitability of whole pine tree (WPT) substrates for crop propagation has not been investigated. Demonstrating the versatility of WPT substrates is essential to expanding their commercial availability and use.

The objective of this work was to evaluate WPT substrates for stem cutting and seed propagation of ornamental crops, and to identify factors affecting root development. Stem cutting and seedling root development was evaluated in WPT and traditional (peatmoss and pine bark) …

A Bird In The Binoculars: Understanding Birdwatchers' Potential To Contribute To Sustainable Development And Biological Conservation, Sheri Lynn Glowinski

Dissertations

The three studies comprising this research drew from local economic development and environmental sociology to understand aspects of human dynamics that influence the conservation of birds. Using survey data collected from birdwatchers visiting coastal Alabama, the first study examined the local economic impact of birdwatching tourism and the factors that participants deemed important with respect to their recreation. Birdwatchers spent $103,305 during the four month study period. The total annual economic impact of this recreation on the area was estimated at $937,470, producing a multiplier of 1.48 and the equivalent of 20.3 full time jobs. Infrastructural variables (parking, bathrooms, site …

Investigating The Function Of The Mold Specific Gene M46, In The Pathogenic Dimorphic Fungus Histoplasma Capsulatum, Davida Lashaundra Crossley

Dissertations

Histoplasma capsulatum (Hc) is a dimorphic fungus that is the etiologic agent for the respiratory infection histoplasmosis. The fungus is found in the environment in contaminated soils of birds and bat excreta as a multi-cellular saprophytic mold. Once the soil is disturbed, spores are released and are inhaled into the lungs. In the lungs, the fungus converts to uni-cellular parasitic yeast (Maresca & Kobayashi, 1989). The conversion from mold to yeast is a requirement for pathogenesis. Previously, several mold specific genes have been isolated by our laboratory from a subtracted cDNA library. One such gene, is M46. M46 is a …

Effects Of Food Dispersion On Dominance Related Behaviors In Garnett's Bushbaby (Otolemur Garnettii)?, Kyle Daniel Edens

Dissertations

Socio-ecological theorists tie primate social structure diversity to variations in habitats within which primate species reside. This premise permits laboratory researchers to investigate specific factors that influence or relate to social structure formation and maintenance. The focus of the current investigation was three fold. We first aimed to determine the relationships between traditional and non-traditional behavioral measures of dominance, then evidence for dominance hierarchy formation was examined, and various hypotheses were tested to discern if adjustments in the foraging context altered social behaviors in Garnett’s bushbaby (Otolemur garnettii). It was determined that animals likely to displace conspecifics were …

Interrelationships Between Testosterone, Aggression, And Parental Care Of A Temperate-Zone, Resident Songbird, The Northern Cardinal (Cardinalis Cardinalis), Margaret Susan Devries

Dissertations

Interrelationships among testosterone (T), aggression, and parental care have received much investigative attention. Within birds, many studies have focused on examining such relationships using species characterized by relatively brief periods of territoriality and breeding. Few have investigated links between circulating T and reproductive behavior in birds that are year-round territorial residents and have lengthy breeding seasons, such as the Northern Cardinal (Cardinalis cardinalis). The following six chapters report and discuss findings from this dissertation’s examination of aspects of T production and potential interconnections with circulating T, aggression, and parental care in male and female cardinals. This work suggests …

Accessing Learning In The Adult Zebrafish With A Novel Associative Learning Task, David Joseph Jouandot Ii

Dissertations

The zebrafish (Danio rerio) is accepted in the developmental and genomic communities as a model organism. However, the capacity for the zebrafish as a behavioral model has yet to be fully acknowledged. The research presented provides evidence validating the novel task, aids in gaining a better understanding of the learning processes, and identifies individual differences. The novel associative learning task differs from any present well established behavioral model and lends itself to future development. The task provides the zebrafish community with a high output behavioral task which is readily replicated and allows one researcher to test between eight …

Diversification And Coexistence In The Madagascar Olive (Noronhia, Oleaceae), Cynthia Hong-Wa

Dissertations

The long-isolated island of Madagascar provides a suitable setting for studying species diversification, with most groups of organisms there both radiating and showing a high level of endemism. Noronhia is one of these groups and represents the most successful radiation of the olive family (Oleaceae) in Madagascar, with ca. 80 species. In this study, using plastid and nuclear DNA sequences obtained from a comprehensive sampling both within Noronhia and the family, I show that Noronhia, together with Indian Ocean species of Chionanthus, form a monophyletic clade sister to African Chionanthus. The diversification of Noronhia followed a likely Cenozoic dispersal from …

Astrocytes Modulate Microglial Phenotype And Dendritic Cell-Like Properties, Nischal K. Padala

Dissertations

Microglia are the resident immune cells of the CNS. In the healthy CNS, they express negligible levels of MHC II molecules as well as co-stimulatory molecules CD40, CD80 and CD86 necessary for antigen presentation to and activation of T cells. Co-stimulatory molecule expression can be induced in isolated microglia in vitro by sequential treatment with granulocyte monocyte colony-stimulating factor (GM-CSF) followed by lipopolysaccharide (LPS). Upon such treatment, they become mature dendritic cells (DCs), capable of activating T cells. However, microglia are not isolated in life, but rather exist in an environment enriched by other cells, notably astrocytes.

Therefore, to determine …

Coexistence Of Sympatric Taxa Of Chamaecrista Section Xerocalyx: Addressing The Interplay Between Morphology And Biotic Interactions, Beatriz Baker-Méio

Dissertations

Animal-plant interactions may prevent gene flow and promote divergent selection among closely related plants, ultimately leading to formation of new species. This may be the case for Chamaecrista sect. Xerocalyx, in which two or more of the 24 varieties often are encountered in the same area, with marked morphological and phenological differences among them. Over a broad geographical range, however, the morphological gaps among varieties disappear. Several biotic interactions contribute to the fitness of Chamaecrista species. Their flowers are pollinated by bees, and herbivores attack their leaves, flowers, fruits, and seeds. In addition, all species produce extrafloral nectar, which …

Marine Fungi Of U.S. Gulf Of Mexico Barrier Island Beaches: Biodiversity And Sampling Strategy, Allison Kathleen Walker

Dissertations

Marine fungi are an important but often overlooked component of marine ecosystems. Primarily saprotrophic, they are vital to coastal nutrient cycling processes and food webs. However, basic marine fungal distribution data are lacking in many parts of the world, as is knowledge of the sampling intensity required to characterize the biodiversity of these communities. The roles of substrate, season and latitude in shaping intertidal ascomycete community structure were examined for the U.S. Gulf of Mexico, and the role of sampling frequency on species richness estimates was also addressed. Best sampling practices were developed and 750 collections of beach detritus, sand …

Management Of Biological And Chemical Constituents For The Advancement Of Intensive, Minimal-Exchange, Biofloc-Based Shrimp (Litopenaeus Vannamei) Aquaculture, Andrew James Ray

Dissertations

Intensive, minimal-exchange, biofloc-based shrimp aquaculture systems may provide a sustainable alternative to traditional shrimp culture. Through a series of experiments, this document explores the effects of several key management strategies on water quality, isotopic distribution, and shrimp production.

An experiment evaluated the effects of managing suspended solids (biofloc) concentration at two levels. It was found that using a higher flow rate to larger settling chambers resulted in significantly lower biofloc and nitrate concentrations, and significantly improved shrimp growth rate. A second experiment compared systems with clear water and systems with biofloc. The filters in the clear water systems prevented biofloc …

A Time Series Analysis Method Using Hidden Variables For Gene Network Reconstruction, Xi Wu

Dissertations

The DNA microarray technology can be applied to obtain time series data which contains thousands of genes and tens of time points. When confront the great amount of data points a fast and effective method must be constructed to extract useful information. The assumption that the interactions between genes are static in the time series data is made. After made the assumption how to reconstruct those interactions becomes a difficulty problem. Since the underlying interactions between genes are complicated, which involve transcription, translation and protein-protein interaction, to construct a model from physicochemistry is almost impossible/effortless. The popular methods constructed from …

The Role Of The Cysteine/Glutathione Regulatory Genes Cdo1, Gsh1, And Gsh2 In Yeast-Mold Dimorphism Of The Pathogenic Fungus Histoplasma Capsulatum, Melissa Anne Adams

Dissertations

The dimorphism of Histoplasma capsulatum (Hc) from a mold to yeast is regulated by many environmental factors such as temperature and thiol concentrations. Histoplasma exists in the soil (or in vitro at 25ºC) as a multicellular saprophytic mold. In the lungs of an infected host (or in vitro at 37ºC), a shift to the unicellular parasitic yeast occurs. Sulfhydryl groups (-SH), especially cysteine, are necessary in the culture medium for the mold to yeast transition. Cysteine is the precursor for the synthesis of glutathione. Enzymes involved in the cysteine metabolism pathway are being studied in order to evaluate …

Urban Development In Costa Rica: The Direct And Indirect Impacts On Local And Regional Avian Assemblages, Jeff L. Norris

Dissertations

Urban development, the pinnacle of human land use, has drastic effects on native ecosystems and the species they contain. For the first time in recorded history there are more people living in cities than in the rural areas surrounding them. Furthermore, the global rate of urbanization continues increasing; raising serious concerns for earth's tropical regions as they harbor a disproportionate amount of the earth's species, and where the impacts of urban development on natural communities are poorly known. Therefore, for my dissertation research I investigated the impacts of urban development on avian community structure and organization at both local and …

Discrete Targeting Of Peptide And Non-Peptide Neurotransmitters By A Single Neuron, Daniel Kueh

Dissertations

The heart excitor (HE) motor neuron in the medicinal leech, Hirudo, releases acetylcholine (ACh) and a peptide, FMRFamide, to regulate the contractile activity of the heart tube and associated side vessels. Consistent with Dale’s Principle, it was assumed that both neurotransmitters were coreleased by all presynaptic varicosities. However, discrete peptide-positive and peptide-negative varicosities can be found consistently at particular sites of innervation on the heart tube. Dual-labeled HE neurons were produced by pressure injecting Neurobiotin into single HE neurons and applied antibodies against FMRFamide on the same preparations. Consistent with initial expectations, peptide-labeled varicosities were numerous and widely distributed …

The Effect Of Photoperiod On Regulation Of Key Components Of The Life Cycle In The Bumble Bee Bombus Impatiens L. (Hymenoptera: Apidae)., Edgar Javier Hernandez

Dissertations

This study investigates how photoperiod affects internal characteristics of colonies of the temperate bumble bee Bombus impatiens particularly; development, reproduction, and social behavior. To answer this question I used an experimental approach using commercially obtained colonies of B. impatiens kept under controlled environmental conditions, and using the exposure to photoperiod as the only variable. Eight different photoperiod treatments were evaluated over the social phase of the colony’s life cycle. Colonies exposed to photoperiods that simulate the species natural temperate photoperiod exhibited larger growth rates, higher, oviposition rates, and higher brood survival than colonies exposed to constant photoperiods. Similarly, colonies exposed …

Host-Parasite Interactions In Galapagos Seabirds, Iris Ilena Levin

Dissertations

Parasites exhibit a wide range of life history strategies that contribute to different dispersal abilities, host specialization, transmission modes, life-cycle complexity and population structure. Understanding dispersal rates in hosts and parasites is instrumental in defining the scale at which coevolution may be occurring. In order to better understand how and when parasites move between different hosts, I studied a seabird – Hippoboscid fly ectoparasite (and vector) – Haemosporidian parasite system in the Galapagos Islands. I began by describing the Haemosporidian parasites of Galapagos seabirds, discovering a Plasmodium species parasite in Galapagos Penguins (Sphensicus mendiculus), and a new clade of Hippoboscid-vectored …

Evolution And Biogeography Of Fire-Eye Antbirds (Genus Pyriglena): Insights From Molecules And Songs, Marcos Maldonado Coelho

Dissertations

The importance of climatic and geologic factors as drivers of population differentiation and speciation in the Neotropical region has long been appreciated. However, many questions remain regarding their roles underlying the processes and patterns of diversification. Studies conducted in distinct regions containing a suite of geological and ecological conditions constitute ideal scenarios to assess the role of Pleistocene climatic changes, rivers, and mountain building as historical diversification mechanisms. In chapters 1 and 2, I used an integrative approach combining molecular phylogenetics, phylogeography and population genetics to elucidate the importance of climatic and geological factors as engines of diversification. I focused …

Genetic Variation In Potentially Virulent Vibrio Parahaemolyticus From The Northern Gulf Of Mexico, Nicholas Felix Noriea Iii

Dissertations

Vibrio parahaemolyticus (V_p) is a gram-negative bacterium found naturally in marine and estuarine environments. V_p is found in oysters including those which are later consumed by the public. Sub-populations of potentially virulent Vp contain specific virulence factors and are relevant human pathogens capable of causing gastroenteritis, wound infection, and death. The tdh and trh genes, both encoding hemolysins, have been correlated with the majority of clinical V_p isolates but have not been shown to be the definitive virulence factors.

A total of 146 V_p isolates from the northern Gulf of Mexico were collected and probed …

Clam (Corbicula Fluminea) As A Potential Sentinel Of Human Norovirus Contamination In Freshwater, Xunyan Ye

Dissertations

The purpose of this study was to evaluate and validate the use of the clam Corbicula fluminea as a sentinel of human noroviruses (HuNoV) contamination in freshwater. The first specific aim was to develop a new method to extract HuNoV RNA from contaminated bivalves (e.g. oysters, clams) that would be much faster than existing methods. The procedure developed includes an initial total RNA extraction using TRI Reagent, followed by HuNoV RNA concentration and purification using biotinylated probe-capture technology. HuNoV RNA is finally detected by real-time RT-PCR. Using bivalve homogenates spiked with HuNoV, 100 PCR detection units of the virus was …

Application Of A Hybrid 3d-Var Data Assimilation System In The Monterey Bay To Study Regional Dynamics Of The California Current System, Chudong Pan

Dissertations

A data assimilation system combining 3-dimensional variational scheme and Navy Coastal Ocean Model was applied to the Monterey Bay area to assimilate temperature and salinity glider data collected in August 2003. The hybrid background error covariance model in the present 3-dimensional variational system incorporates both the static and the flow-dependent background error covariance. To explore the impact of high temporal resolution on the overall skill of the assimilation system, the intended data assimilation interval was set to 1 hour in the present study. A Floating Temporal Window approach is designed to keep the computational efficiency of the scheme and to …

Analysis Of The Condition-Specific Regulation Of Puf3p Activity And Puf3p-Mediated Translational Repression Of Mrna In Saccharomyces Cerevisiae, Melanie A. Miller

Dissertations

The Puf family of proteins regulates aspects of eukaryotic development such as embryonic development, and memory formation by promoting translational repression and/or degradation of targeted mRNAs in the cytoplasm. Yeast Puf3p regulates mitochondria biogenesis and function by modulating the stabilities of nuclear-transcribed mitochondrial mRNAs in response to different carbon sources. Dextrose simulates rapid Puf3p-mediated degradation of its mRNA targets via decay complex recruitment. Ethanol, galactose, or raffinose promotes stabilization of mRNA targets, as Puf3p-mediated decay activity is severely inhibited or abolished. In this work, I have established that carbon source-induced inhibition of Puf3p activity is not due to decreased transcription …

Contribution Of The Mnr2 Protein To Magnesium Homeostasis In Saccharomyces Cerevisiae, Nilambari Prafulla Pisat

Dissertations

Magnesium is an essential metal nutrient with diverse roles in biology. To maintain the optimal function of key biological processes, intracellular Mg2+ concentration is tightly regulated. Despite the importance of this process however, relatively little is known about mechanisms of Mg2+ homeostasis in eukaryotic cells. An understanding of homeostasis starts with defining the function of key transport proteins that allow the passage of Mg2+ ions across the membranes. Yeast geneticists have identified four proteins from Bakers' yeast (Saccharomyces cerevisiae) involved in regulating the accumulation of Mg2+ within the cell (Alr1 and Alr2) and within the mitochondrial compartment (Mrs2 and Lpe10). …

Consequences Of Stochastic Mrna Synthesis In A Gene Regulatory Pathway, Khyati Shah

Dissertations

Gene expression is a stochastic process, with elements of randomness present in both transcription and translation. This stochasticity results in cell-to-cell variation in the amounts of gene products, mRNAs and proteins, and is observed in organisms ranging from bacteria and yeast to higher eukaryotes. Randomness in the activation and inactivation of a gene is the preliminary cause of this variation. At the level of proteins, these variations are buffered compared to levels of mRNA, due to the longer lifespan of proteins. Nevertheless, there is substantial variation observed at the level of proteins, resulting in phenotypic diversity among genetically identical cells. …

Role Of Pseudomonas Produced Hydrogen Cyanide In Biological Control Of Plant-Parasitic Nematodes, Haytham Aly

Dissertations

Plant-parasitic nematodes are among the most devastating pests world-wide, causing extensive damage to important agriculture crops. The management of nematodes is challenging. Current methods used for nematode control rely mostly on using chemical nematicides and naturally resistant plants. Because of serious health and environmental problems associated with chemical control and over use of resistant plants resulting in resistant breaking strains of nematodes, alternative nematode-control methods are needed. Several potential nematode-biocontrol agents, including bacteria and fungi, have been studied for their antagonistic effect toward plant-parasitic nematodes. However, a concise picture about the biological agent’s mechanisms used to antagonize nematodes remains elusive. …

Effects Of The Exotic Shrub Lonicera Maackii On The Plant Animal Interactions In The Invaded Habitat, Humberto De Paula Dutra

Dissertations

Invasive plants are an economical, political, social, and ecological problem. Some invasive species are a serious concern for society because some of them are diseases, some are agricultural pests, and some become major threats to the ecosystems. Most studies with invasive species are limited because they measure only the impact of the invasion via direct pathways. Unfortunately, the potential for non-native plant species to alter ecosystem functions via indirect pathways mediated by interactions with animals just recently became broadly recognized. This research investigates the interactions of Amur honeysuckle with native fauna and how these interactions indirectly affect other trophic levels …

Elucidating Matrix Protein Import And Beta-Oxidation Pathways In Plant Peroxisomes, Bibi Rafeiza Khan

Dissertations

Plant peroxisomes function in fatty acid β-oxidation, jasmonic acid (JA) synthesis, and conversion of indole-3-butyric acid (IBA) to indole-3-acetic acid (IAA). Peroxisomes lack genetic material; proteins required for peroxisomal processes are imported posttranslationally. The PEX5 and PEX7 receptors import proteins containing one of two peroxisomal targeting signals (PTS1 or PTS2). I took a genetic approach to better understand protein import and to elucidate the role of Acyl-CoA Oxidase (ACX) enzymes in the model plant Arabidopsis thaliana. ACX enzymes catalyze the first step in β-oxidation. There are six ACX genes in Arabidopsis and each ACX enzyme acts on specific chain-length targets, …

Movement Ecology Of An Intercontinental Migratory Bird During Spring Stopover, Emily Beth Cohen

Dissertations

Movement ecology is a component of nearly all aspects of animal behavior and an animal’s decision to move is likely influenced by a complex combination of exogenous and endogenous factors. Therefore, an examination of the causes and consequences of organismal movement provides a conceptual framework for understanding complex behavioral strategies. My dissertation research is focused on the movement ecology of an intercontinental migratory songbird during spring migration. I adopted experimental approaches to study the factors influencing how a songbird migrant, red-eyed vireos (Vireo olivaceus), makes decisions in unfamiliar landscapes from the initiation of spring stopover.

I simulated the …