Biology Commons^™

Bridging Functional Genomics And Toxicogenomics Through Dna Microarrays In A Fish Model, Shuzhao Li

Dissertations

In a case study of finding gene expression signatures for environmental stressors in Cyprinodon variegatus, this dissertation examines several important issues of applying DNA microarray technology to fish toxicogenomics. The most relevant disciplines, fish toxicogenomics and computational systems biology are reviewed in Chapter 1. Chapter 2 reviews major aspects of DNA microarray technology.

On DNA microarrays, even for probes that target the same transcript, large variations are seen in the probe signals. These variations are partly dependent and partly independent on probe sequences. Chapter 3 estimates the sequence independent variation by combining experimental and computational approaches. Chapter 4 and …

Reverse Engineering Of Gene Regulatory Networks For Discovery Of Novel Interactions In Pathways Using Gene Expression Data, Tanwir Habib

Dissertations

A variety of chemicals in the environment have the potential to adversely affect the biological systems. We examined the responses of Rat (Rattus norvegicus) to the RDX exposure and female fathead minnows (FHM, Pimephales promelas) to a model aromatase inhibitor, fadrozole, using a transcriptional network inference approach. Rats were exposed to RDX and fish were exposed to 0 or 30mg/L fadrozole for 8 days. We analyzed gene expression changes using 8000 probes microarrays for rat experiment and 15,000 probe microarrays for fish. We used these changes to infer a transcriptional network. The central nervous system is remarkably plastic in its …

Sexual Selection In A Species With Exploded Leks: The White-Crowned Manakin (Pipra Pipra), Wendy P. Tori

Dissertations

Understanding what determines male reproductive success is central to sexual selection theory. The main goal of this dissertation was to examine the processes that shape female mate choice and male reproductive success in an exploded lek species: the White-crowned Manakin (Pipra pipra). The first chapter examined if females select males with certain genetic characteristics to gain indirect fitness benefits. Specifically, it tested whether females preferentially mate with unrelated males or males with high overall heterozygosity to increase the genetic diversity of their offspring. The second chapter examined if food resources within territories affect male mating success of territory …

Puf1p-Mediated Mrna Decay And Combinatorial Control Of Mrna Stability By The Yeast Puf Proteins, Randi J. Ulbricht

Dissertations

The stability of a messenger RNA (mRNA) is a highly regulated and important aspect of gene expression. Proteins that regulate mRNA stability often bind to 3' untranslated region (UTR) sequence elements. The eukaryotic Puf proteins are one class of 3'UTR binding proteins that regulate the stability and expression of their target transcripts. Several global genome analyses have identified hundreds of potential mRNA targets of the Saccharomyces cerevisiae Puf proteins, however only three mRNA targets for these proteins have been characterized thus far. After direct testing of nearly forty candidate mRNAs, I have established three of these as true mRNA targets …

Evolution And Maintenance Of Plumage Polymorphism: The Case Of The Red-Footed Booby (Sula Sula), Patricia Carvalho Baiao

Dissertations

The red-footed booby (Sula sula) is considered one of the most polymorphic seabirds, with three recognized major adult plumage types: (1) white; (2) white-tailed brown; and (3) brown, and several degrees of intermediates. The ratio of these color morphs varies among populations, with the white morph typically predominating. However, there are a few populations that present an inversed ratio of color morphs, such as Isla Europa in the Indian Ocean and the Galapagos archipelago, with the white-tailed brown or brown morphs predominating. I studied natural populations of red-footed boobies from three geographic locations, namely, the Galapagos archipelago, Johnston Atoll in …

Closing The Seed Dispersal Loop For Guettarda Viburnoides (Rub.): Connecting Patterns Of Avian Seed Dispersal With Population Growth In A Neotropical Savanna, Andrea Patricia Loayza

Dissertations

This study connects data on frugivore activity, post-dispersal seed fate and plant population demography using stage-specific demographic modeling to examine the role of individual dispersers for plant population dynamics of the fleshy-fruited Neotropical tree Guettarda viburnoides (Rubiaceae) in northeastern Bolivian savannas. Detailed information on frugivory and seed dispersal of G. viburnoides reveals that the endocarps of this plant are dispersed mainly by two species of birds: Cyanocorax cyanomelas and Pteroglossus castanotis, which are defined as the quantitatively important dispersers of G. viburnoides. These two species differ in several qualitative aspects of seed dispersal: 1) They select fruits of …

Tritrophic Interactions In Forests: Direct And Indirect Interactions Between Birds, Insect Herbivores, And Oaks, Nicholas Anthony Barber

Dissertations

This study examines direct and indirect relationships between three trophic levels to determine effects on plant damage, herbivore abundance and community structure, and bird distribution in forest ecosystems. Exclusion experiments on white oak (Quercus alba) revealed that bird predation effects to not vary spatially despite variation in abundance of both birds and insects. Using a leaf quality manipulation, I demonstrated that bird impacts do not differ with host plant quality. Rather, birds and plant traits had additive effects on herbivore damage. Bottom-up effects of leaf quality were also more important than top-down effects of birds in structuring the insect herbivore …

Oceanic-Atmospheric Modes Of Variability And Their Effect On River Flow And Blue Crab (Callinectes Sapidus) Abundance In The Northcentral Gulf Of Mexico, Guillermo Humberto Sanchez-Rubio

Dissertations

Oceanic-atmospheric modes of variability occur on interdecadal, multidecadal, decadal, and interannual timescales and their influence on climate around the world has been confirmed. The present study investigates Mississippi River and Pascagoula River flows in response to the influence of one or more of the four oceanic-atmospheric modes of variability: the Pacific Decadal Oscillation (PDO), the Atlantic Multidecadal Oscillation (AMO), the North Atlantic Oscillation (NAO), and the El Nino Southern Oscillation (ENSO). These modes of variability are present in phases: PDO warm (PDOw) and cold (PDOc), AMO warm (AMOw) and cold (AMOc), NAO positive (NAOp) and negative (NAOn), and ENSO warm …

Yellow Head Virus: Transmission And Genome Analyses, Hongwei Ma

Dissertations

Yellow head virus (YHV) is an important pathogen to shrimp aquaculture. Among 13 species of naturally YHV-negative crustaceans in the Mississippi coastal area, the daggerblade grass shrimp, Palaemonetes pugio, and the blue crab, Callinectes sapidus, were tested for potential reservoir and carrier hosts of YHV using PCR and real time PCR. The YHV replicated in the daggerblade grass shrimp, and was still detectable on 36 d post-inoculation, causing 8% mortality after injection. However, YHV did not replicate in the blue crab. These data suggest that the daggerblade grass shrimp could act as a reservoir host for YHV. Storage conditions of …

Construction Of A New Model System In Saccharomyces Cerevisa To Study Yopo And Identify Its Targets, Laura Nejedlik

Dissertations

Yersinia species use a type three secretion system (TTSS) to inject Yersinia outer proteins (Yops) into the target cell. The effector YopO is a serine/threonine kinase which upon association with actin becomes active. However, activation of the kinase is not required for actin disruption. YopO also contains a Rho/Rac binding domain, but it is unclear how it affects these proteins.

We have established an expression system in Saccharomyces cerevisiae to study YopO. The expression vector contains a GAL1 promoter for inducible expression of YopO as well as a V5 epitope used for visualization of each Yop. We have shown that …

Characterization Of The Ap-1 And Nf-Kappa B Transcription Factors In The U-87 Mg Astrocytoma Cell Line, Denise L. Smith

Dissertations

Growth factors, signaling molecules and transcription factors are frequently mutated in cancer and platelet-derived growth factor (PDGF) has been shown to be over-expressed in most gliomas. In the astrocytoma cell line U-87 MG, the over-expression of PDGF has been shown to lead to over-expression of transcription factors activator-protein-1 (AP-1) and nuclear factor-kappa B (NF-κB), and it is believed that the individual subunits of AP-1 (c-Jun, JunB, JunD, c-Fos, FosB, Fra-1, and Fra-2) and NF-κB (c-Rel, p50, p52, p65, and RelB) play different roles in proliferation, survival and differentiation in the U-87 MG cell line.

To assess these different roles, transient …

The Role Of Msa In The Global Regulation Of Virulence In Staphylococcus Aureus, Vijayaraj Nagarajan

Dissertations

Staphylococcus aureus is an important pathogen causing life threatening diseases in humans. Previously we showed that msa modulates the activity of sarA (Staphylococcal accessory regulator), which is one of a major global regulator of virulence in S. aureus. The objective of this study is to characterize the role of msa (Modulator of SarA) in the global regulation of virulence in S. aureus. Structure and function predictions were done using several computational tools and approaches to understand the nature of msa. A novel S. aureus microarray meta-database (SAMMD) was designed and developed to compare and contrast other transcriptomes with msa transcriptome. …

Biochemical Characterization Of Two Yeast Paralogous Proteins Mth1 And Std1, Satish Pasula

Dissertations

Glucose is the most abundant monosaccharide and preferred carbon and energy source for most cells. Many organisms have evolved sophisticated means to sense glucose and respond to it appropriately. The budding yeast, Saccharomyces cerevisiae senses glucose through two transmembrane proteins, Snf3 and Rgt2. In the presence of extracellular glucose Snf3 and Rgt2 generate an intracellular signal that leads to the degradation of Mthl and Stdl, thereby inducing the expression of hexose transporter genes (EXT) by inhibiting the function of Rgtl, a transcriptional repressor of HXT genes. Mthl and Stdl are degraded via the Yckl/2 Kinase-SCFGrrl-26S proteasome pathway triggered by the …

Knowledge-Based Analysis Of Genomic Expression Data By Using Different Machine Learning Algorithms For The Purpose Of Diagnostic, Prognostic Or Therapeutic Application, Venkata Jagan Mohan Thodima

Dissertations

With more and more biological information generated, the most pressing task of bioinformatics has become to analyze and interpret various types of data, including nucleotide and amino acid sequences, protein structures, gene expression profiling and so on. In this dissertation, we apply the data mining techniques of feature generation, feature selection, and feature integration with learning algorithms to tackle the problems of disease phenotype classification, clinical outcome and patient survival prediction from gene expression profiles.

We analyzed the effect of batch noise in microarray data on the performance of classification. Batchmatch, a batch adjusting algorithm based on double scaling method …

Systematics And Floral Evolution In The Plant Genus Garcinia (Clusiaceae), Patrick Wayne Sweeney

Dissertations

The pantropical genus Garcinia (Clusiaceae), a group comprised of more than 250 species of dioecious, trees and shrubs, is a common component of lowland tropical forests and is best known by the highly prized fruit of mangosteen (G. mangostana). The genus exhibits as extreme diversity of floral form as is found anywhere in angiosperms and there are many unresolved taxonomic issues surrounding the genus. To understand patterns of floral evolution within the group and to evaluate morphology-based classification schemes involving Garcinia and its relatives, relationships among a broad sample of Garcinia and close relatives were inferred by conducting Bayesian, parsimony, …

Community Ecology And Phylogeography Of Bird Assemblages In Arid Zones Of Northern Venezuela: Implications For The Conservation Of Restricted-Range Birds, Adriana Rodriguez-Ferraro

Dissertations

Aridlands of northern Venezuela are important from an ornithological perspective because of the occurrence of habitat specialist birds that depend exclusively on desert scrubs and are endemic to this region. Currently, long-term survival of habitat specialists is threatened by ongoing changes in vegetation but the effects of such changes on bird assemblages are unknown. The goal of this study was to characterize bird assemblages found in six arid zones in northern Venezuela at both ecological and genetic levels, and to generate information relevant for conservation planning. The study involved assessments of patterns of avian species richness, abundance, community composition and …

Spatial And Temporal Dynamics Of Lekking Behavior And Female Mate Choice In The Blue-Crowned Manakin (Lepidothrix Coronata, Aves: Pipridae), Renata Duraes Ribeiro

Dissertations

In lekking species, males aggregate at display grounds (?leks?) that females visit to copulate. Lekking systems are non-resource-based and males vary widely in reproductive output. This dissertation investigates how spatial and temporal factors influence lekking dynamics and female mate choice in the blue-crowned manakin Lepidothrix coronata. The first chapter deals with spatial dynamics of lekking behavior, and investigates whether leks are formed by the establishment of males on sites of high female density (?hotspot hypothesis?). Predictive maps of female spatial distribution were built based on field data and contrasted to the lek distribution. Leks were located in sites where males …

Grassland Birds In Natural And Cultivated Grasslands In The Northern Campos Of Uruguay: Diversity Patterns, Responses To Vegetation Structure, And Nest Survival, Adrian Bruno Azpiroz

Dissertations

Grassland bird populations are declining in many regions of the world as a consequence of habitat modification but research efforts have been concentrated in North America and Europe. In the Neotropics, however, many aspects of grassland bird ecology remain virtually unexplored. The objective of this study was to examine the effects of habitat modification on the distribution, abundance, and reproductive success of grassland birds in the Northern Campos of Uruguay. The study focused on birds that inhabit four grassland habitats which differed in terms of agricultural management in the Northern Campos of Uruguay. First, distance sampling was used to characterize …

A Developmental, Phylogenetic And Taxonomic Study On The Moss Genus Taxithelium Mitt. (Pylaisiadelphaceae), Paulo Saraiva Camara

Dissertations

The family Sematophyllaceae is probably the most diverse Hypnales in the tropics and one of the most complex and taxonomically confused. This thesis comprises three parts: 1, a micromorphological study of papilla development in Taxithelium and relatives; 2, a phylogenetic study of Taxithelium; and 3, a revision of Taxithelium subgenus Vernieri. 1. I present data on the structure and development of leaf cell papillae in different Sematophyllaceae. Two kinds of papillae are recognized. One is dome-shaped to conical tapering to a firmly rounded apex (?conical?), whereas the other presents a more flaccid, baggy appearance, and is often flat-topped and wider …

Population Genetics Of Island Endemics: Neutral And Major Histocompatibility Loci, Jennifer Lynn Bollmer

Dissertations

Island archipelagoes are ideal for the study of microevolutionary forces due to their multiple, closely related but geographically disjunct populations. I used both neutral and major histocompatibility complex (MHC) loci to determine the population genetic structures of bird species endemic to the Galapagos Islands. MHC molecules recognize foreign pathogens in the body, and these loci are known for their high degree of genetic variability maintained by natural selection. Small island populations are predicted to have reduced genetic variability due to the effects of genetic drift; however, selection may be strong enough to prevent the loss of variability at MHC loci. …

Reproductive And Social Dynamics Of A Lek Breeding Bird, Thomas Brandt Ryder

Dissertations

Sociality and the unequal apportionment of reproductive success among social individuals is a common characteristic of many vertebrate taxa. To date, our understanding of what factors drive high variance in reproductive success (i.e., intra vs. inter-sexual selection) and which male attributes contribute to that variance, are still fragmentary for most species. Moreover, how social structure interacts with individual behavior and fitness remains understudied despite its potential importance to the evolution of cooperation. This dissertation research focused on understanding this complex synergistic interplay between social and reproductive dynamics in a lek-breeding bird, the wire-tailed manakin. The first chapter examines the complex …

An Analysis Of Mer1 Function During Meiotic Splicing Regulation In Saccharomyces Cerevisiae, Frederick William Scherrer

Dissertations

The transition from mitosis to meiosis in the yeast Saccharomyces cerevisiae requires a significant change to gene expression profiles. Regulation of pre-messenger RNA splicing patterns during meiosis assists in this transition by fine tuning expression of essential meiotic genes. Produced only during meiosis, Mer1p is linked to the splicing of at least three mRNAs: MER2, MER3, and AMA1. Previous evidence suggests that Mer1p activates splicing by directly recruiting snRNPs or stabilizing intermediate splicing complexes formed on pre-mRNA that contains an intronic Mer1p enhancer element. However, some splicing factors, especially accessory/non-snRNP factors, have critical roles in retaining unspliced pre-mRNAs in the …

A Systematic And Taxonomic Review Of The Family Pseudotanaidae (Crustacea: Peracarida: Tanaidacea) Based Primarily On Morphometry Cladistic Analyses, Jerry Alan Mclelland

Dissertations

Species of the tanaid family Pseudotanaidae, established by Jurgen Sieg in 1973, have been reported from all the world's oceans in depths ranging from near the surface to below 6,000 m. The family currently consists of 46 characteristically small tanaidomorph species residing in two subfamilies, the Cryptocopinae (seven species) and the Pseudotanainae (39 species). Members of the more ancestral Crytocopinae differ from the Pseudotanainae by having females with four rather than three antennule articles and a complete separation of the maxilliped endites. The primary objective of this study was to test the hypothesis that the current structure of the family …

In Vitro And In Vivo Techniques For Screening New Natural Product-Based Fungicides For Control Of Strawberry Anthracnose, Maritza Abril

Dissertations

Seven plant pathogenic fungi (Botrytis cinerea, Colletotrichum acutatum, C. fragariae, C. gloeosporioides, Fusarium oxysporum, Phomopsis obscurans, and P. viticola) valuable in screening fungicide efficacy were tested. Optimal and reproducible conditions for germination of these selected fungi were established by incorporating Roswell Park Memorial Institute 1640 (RPMI) as a medium of known composition and washing conidia to remove innate germination inhibitors. This step reduced average fungal germination times between 3.5 h and 21.2 h. The natural product-based fungicide, sampangine, seven sampangine analogs (4-bromo-sampangine, 4-methoxysampangine, benzo[4,5]sampangine, liriodenine Mel AMC-XIII-103, onychine, cryptolepine, and liriodenine CDH-II-37), plus seven conventional fungicides (benomyl, captan, cyprodinil, fenbuconazole, …

Reverse Recruitment: Activation Of Yeast Genes At The Nuclear Periphery, Terry Marvin Haley

Dissertations

The regulation of genes at the nuclear periphery is an evolutionarily conserved phenomenon in eukaryotes. The reverse-recruitment model of transcriptional activation postulates that genes are activated by moving to and contacting transcription machinery located at subnuclear structures. In Saccharomyces cerevisiae it has been reported that this platform for gene regulation may reside at the nuclear periphery. To test this hypothesis, I utilized a GFP-gene tagging technique, which uses LacI-GFP to visualize a tandem array of its DNA-binding sequence, to monitor localization ofSUC2 and GALL I found that both genes preferentially localized to the nuclear periphery when transcriptionally active. By developing …

Use Of Monoclonal ∆-9-Tetrahydrocannabinol Antibodies Chemically Bound To A Polystyrene Surface Using Glutaraldehyde For The Purpose Of Extracting ∆-9-Tetrahydrocannabinol And ∆-9-Tetrahydrocannabinol Carboxylic Acid From Postmortem Whole Blood Samples For Analysis By Gas Chromatography Mass Spectrometry, Thomas Sidney Pittman

Dissertations

Quantitations of drugs and their respective metabolites in postmortem blood samples using gas chromatographic instrumentation is a primary analytical practice used to determine if drugs played a role in or were the cause of a victim's death. Postmortem blood samples often prove difficult to work with due to interfering substances formed during the putrefaction process. Attempts to eliminate interfering substances with present day extraction methods can be time-consuming, costly and often ineffective when dealing with drugs that exhibit toxicity or impairment at very low concentrations. This study was conducted using monoclonal antibodies chemically bound to a polystyrene surface to extract …

Roosting Ecology Of Rafinesque's Big-Eared Bat, Corynorhinus Rafinesquii, In Southeastern Mississippi, Austin Webb Trousdale Iii

Dissertations

Rafinesque's big-eared bat, Corynorhinus rafinesquii, is considered rare and/or declining throughout its range. Concrete bridges are potentially important roosts for C. rafinesquii, especially in the Gulf Coastal Plain where the species' natural roosts (caves and large hollow trees) are inherently scarce. Successful efforts to monitor and conserve this species must account for its movements among multiple roosts and determine the duration of its roost use (including bridges) at different temporal scales. Therefore, I investigated roosting ecology of C. rafinesquii from 2000-2005 within a mixed hardwood-pine (Pinus spp.) system in southeastern Mississippi. I conducted surveys of concrete bridges to determine phenological …

Mechanisms Of Ionic Current Changes Underlying Rhythmic Activity Recovery After Decentralization, Olga E. Khorkova Sherman

Dissertations

Neuronal networks capableof generating rhythmic output in the absence of patterned sensory or central inputs are widely represented in the nervous system where they support a variety of functions, from learning and memory to rhythmic motor activity such as breathing. To perfectly function in a living organism, rhythm-generating networks have to combine the capability of producing a stable output with the plasticity needed to adapt to the changing demands of the organism and environment. This dissertation used the pyloric network of the crab Cancer borealis to identify potential mechanisms that ensure stability and adaptation of rhythm generation by neuronal networks …

Natal Dispersal And New Group Formation In Capybaras (Hydrochoerus Hydrochaeris) In A Seasonally Flooded Savanna Of Venezuela, Elizabeth Rae Congdon

Dissertations

This study examines natal dispersal and new group formation in capybaras (Hydrochoerus hydrochaeris) in a seasonally flooded savanna in Venezuela. The first section describes a novel approach to the study of dispersal that could be applied to many taxa. Dispersal is considered in three stages (emigration, transience, and immigration) and its proximate and ultimate mechanisms are clearly differentiated. The second chapter describes dispersal behavior in capybaras, including which individuals disperse, when, and to where. In the third chapter, I evaluate dispersal in capybaras with respect to social subordination and social cohesion hypotheses. In this population, some support was …

Mapk Survival Signaling In Melanoma, Matthew W. Vanbrocklin

Dissertations

Extracellular signals activate mitogen-activated protein kinase (MAPK) cascades potentiating biological activities such as cell proliferation, differentiation, and survival. Constitutive activation of MAPK signaling pathways is implicated in the development and progression of many human cancers, including melanoma. Mutually exclusive activating mutations in NRAS or BRAF are found in ∼85% of all melanomas resulting in constitutive activation of the MAPK pathway (RAS-BRAF-MEK-ERK-RSK). We have previously demonstrated that inhibition of this pathway with small molecule MEK inhibitors selectively induces apoptosis in human melanoma cells both in vitro and in vivo, but not in normal melanocytes. These results support the notion that the …