Life Sciences Commons^™

Toxicogenomics Analysis Of Non-Model Transcriptomes Using Next-Generation Sequencing And Microarray, Arun Rawat

Dissertations

With the advent of next generation technologies like Roche/454 Life Sciences that require low cost and less time for sequencing will help in providing a workable draft of non-model species genomes. Availability of high throughput microarray technologies for gene expression profiling provides low-cost tools for investigation of highly-integrated responses to various stimuli. These advancements along with bioinformatics processing have led to an increasing number of non-model species having well-annotated transcriptomes. The project focuses on the life cycle of development, functional annotation, and utilization of genomic tools for the avian wildlife species to determine the molecular impacts of exposure to munitions …

Regulation Of Biofilm And Antibiotic-Resistance By The Modulator Of Sara (Msa) In Staphylococcus Aureus, Antony Schwartz

Dissertations

Staphylococcus aureus is an important human pathogen that is the causative agent of life-threatening diseases such as endocarditis and osteomyelitis. The ability of S. aureus to thrive as a successful pathogen can be partially attributed to its ability to form biofilm. Biofilm is an extracellular polysaccharide, protein, and DNA-based slime layer that protects the bacterial community. The global regulator sarA is essential for biofilm formation. Since the modulator of sarA (msa) gene regulates several virulence factors and is required for the full expression of sarA, the capacity of the msa mutant to form a biofilm was examined. The mutation of …

A Comprehensive Uncertainty Analysis And Method Of Geometric Calibration For A Circular Scanning Airborne Lidar, Michael Oliver Gonsalves

Dissertations

This dissertation describes an automated technique for ascertaining the values of the geometric calibration parameters of an airborne lidar. A least squares approach is employed that adjusts the point cloud to a single planar surface which could be either a narrow airport runway or a dynamic sea surface. Going beyond the customary three boresight angles, the proposed adjustment can determine up to eleven calibration parameters to a precision that renders a negligible contribution to the point cloud’s positional uncertainty.

Presently under development is the Coastal Zone Mapping and Imaging Lidar (CZMIL), which, unlike most contemporary systems that use oscillating mirrors …

Global Protein Interactome Exploration Through Mining Genome-Scale Data In Arabidopsis Thaliana, Feng Xu, Guang Li, Chen Zhao, Yuhua Li, Peng Li, Jian Cui, Youping Deng, Tieliu Shi

Faculty Publications

Background

Many essential cellular processes, such as cellular metabolism, transport, cellular metabolism and most regulatory mechanisms, rely on physical interactions between proteins. Genome-wide protein interactome networks of yeast, human and several other animal organisms have already been established, but this kind of network reminds to be established in the field of plant.

Results

We first predicted the protein protein interaction in Arabidopsis thaliana with methods, including ortholog, SSBP, gene fusion, gene neighbor, phylogenetic profile, coexpression, protein domain, and used Naïve Bayesian approach next to integrate the results of these methods and text mining data to build a genome-wide protein interactome …

Nucleosome Structure Incorporated Histone Acetylation Site Prediction In Arabidopsis Thaliana, Chen Zhao, Hui Liu, Youping Deng, Tieliu Shu

Faculty Publications

Background

Acetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few researches have focused on prediction of lysine acetylation sites. Several systematic prediction studies have been conducted for human and yeast, but less for Arabidopsis thaliana.

Results

Concerning the insufficient observation on acetylation site, we analyzed contributions of the peptide-alignment-based distance definition and 3D structure factors in acetylation prediction. We found that traditional structure contributes little to acetylation site prediction. Identified acetylation sites of histones in Arabidopsis thaliana …

Time Lagged Information Theoretic Approaches To The Reverse Engineering Of Gene Regulatory Networks, Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng, Chaoyang Zhang

Faculty Publications

Background: A number of models and algorithms have been proposed in the past for gene regulatory network (GRN) inference; however, none of them address the effects of the size of time-series microarray expression data in terms of the number of time-points. In this paper, we study this problem by analyzing the behaviour of three algorithms based on information theory and dynamic Bayesian network (DBN) models. These algorithms were implemented on different sizes of data generated by synthetic networks. Experiments show that the inference accuracy of these algorithms reaches a saturation point after a specific data size brought about by …

Quail Genomics: A Knowledgebase For Northern Bobwhite, Arun Rawat, Kurt A. Gust, Mohamed O. Elasri, Edward J. Perkins

Faculty Publications

Background

The Quail Genomics knowledgebase (http://www.quailgenomics.info) has been initiated to share and develop functional genomic data for Northern bobwhite (Colinus virginianus). This web-based platform has been designed to allow researchers to perform analysis and curate genomic information for this non-model species that has little supporting information in GenBank.

Description

A multi-tissue, normalized cDNA library generated for Northern bobwhite was sequenced using 454 Life Sciences next generation sequencing. The Quail Genomics knowledgebase represents the 478,142 raw ESTs generated from the sequencing effort in addition to assembled nucleotide and protein sequences including 21,980 unigenes annotated with meta-data. A …

Dynamics Of Protofibril Elongation And Association Involved In Aβ42 Peptide Aggregation In Alzheimer's Disease, Preetam Ghosh, Amit Kumar, Bhaswati Datta, Vijayaraghavan Rangachari

Faculty Publications

Background: The aggregates of a protein called, ‘Aβ’ found in brains of Alzheimer’s patients are strongly believed to be the cause for neuronal death and cognitive decline. Among the different forms of Aβ aggregates, smaller aggregates called ‘soluble oligomers’ are increasingly believed to be the primary neurotoxic species responsible for early synaptic dysfunction. Since it is well known that the Aβ aggregation is a nucleation dependant process, it is widely believed that the toxic oligomers are intermediates to fibril formation, or what we call the ‘on-pathway’ products. Modeling of Aβ aggregation has been of intense investigation during the last …

Biocompatibility Of Synthetic Poly(Ester Urethane)/Polyhedral Oligomeric Silsesquioxane Matrices With Embryonic Stem Cell Proliferation And Differentiation, Yan-Lin Guo, Wenshou Wang, Joshua U. Otaigbe

Faculty Publications

Incorporation of polyhedral oligomeric silsesquioxanes (POSS) into poly(ester urethanes) (PEU) as a building block results in a PEU/POSS hybrid polymer with increased mechanical strength and thermostability. An attractive feature of the new polymer is that it forms a porous matrix when cast in the form of a thin film, making it potentially useful in tissue engineering. In this study, we present detailed microscopic analysis of the PEU/POSS matrix and demonstrate its biocompatibility with cell culture. The PEU/POSS polymer forms a continuous porous matrix with open pores and interconnected grooves. From SEM image analysis, it is calculated that there are about …

Stable Isotope Analysis Reveals Detrital Resource Base Sources Of The Tree Hole Mosquito, Aedes Triseriatus, Michael G. Kaufman, Kirsten S. Pelz-Stelinski, Donald A. Yee, Steven A. Juliano, Peggy H. Ostrom, Edward D. Walker

Faculty Publications

1. Detritus that forms the basis for mosquito production in tree hole ecosystems can vary in type and timing of input. We investigated the contributions of plant‐ and animal‐derived detritus to the biomass of Aedes triseriatus (Say) pupae and adults by using stable isotope (¹⁵N and ¹³C) techniques in laboratory experiments and field collections.
2. Laboratory‐reared mosquito isotope values reflected their detrital resource base, providing a clear distinction between mosquitoes reared on plant or animal detritus.
3. Isotope values from field‐collected pupae were intermediate between what would be expected if a single (either plant or animal) detrital source dominated the …

Integrating Concepts And Technologies To Advance The Study Of Bird Migration, W. Douglas Robinson, Melissa Bowlin, Isabelle Bisson, Judy Shamoun-Barnes, Kasper Thorup, Robert H. Diehl, Thomas H. Kunz, Sarah Mabey, David W. Winkler

Faculty Publications

Recent technological innovation has opened new avenues in migration research - for instance, by allowing individual migratory animals to be followed over great distances and long periods of time, as well as by recording physiological information. Here, we focus on how technology - specifically applied to bird migration - has advanced our knowledge of migratory connectivity, and the behavior, demography, ecology, and physiology of migrants. Anticipating the invention of new and smaller tracking devices, in addition to the ways that technologies may be combined to measure and record the behavior of migratory animals, we also summarize major conceptual questions that …

Incorporating Genomics And Bioinformatics Across The Life Sciences Curriculum, Jayna L. Ditty, Christopher A. Kvaal, Brad Goodner, Sharyn K. Freyermuth, Cheryl Bailey, Robert A. Britton, Stuart G. Gordon, Sabine Heinhorst, Kelyenne Reed, Zhaohui Xu, Erin R. Sanders-Lorenz, Seth Axen, Edwin Kim, Mitrick Johns, Kathleen Scott, Cheryl A. Kerfeld

Faculty Publications

No abstract provided.

Alteration Of Microbial Communities Colonizing Leaf Litter In A Temperate Woodland Stream By Growth Of Trees Under Conditions Of Elevated Atmospheric Co2, John J. Kelly, Amit Bansal, Jonathan Winkelman, Lori R. Janus, Shannon Hell, Marie Wencel, Patricia Belt, Kevin A. Kuehn, Steven T. Rier, Nancy C. Tuchman

Faculty Publications

Elevated atmospheric CO₂ can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. Fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. This study tested the hypothesis that changes in leaf chemistry caused by elevated atmospheric CO₂ would result in changes in the size and …

Algal Community Structure In Water Bodies Of Mississippi: The Role Of Environmental Factors In Its Spatial And Temporal Dynamics, Nestor Raul Anzola

Dissertations

A meta-analysis was done on studies that included six major taxa groups: Cyanobacteria, Chlorophyta, Chrysophyta (primarily diatoms), Euglenophyta, Pyrrophyta, and Rhodophyta and six aquatic habitats of Mississippi to determine the abundance and richness of the algal community and to identify relevant environmental drivers of algal assemblage composition. Twenty algae data sets on small order streams, large streams and rivers, lakes and reservoirs, fish production ponds, brackish water, and marine water were analyzed. Chlorophyta was dominant in lakes and reservoirs and was the most diverse taxa in the phytoplankton of small order streams and large streams and rivers. Cyanobacteria were the …

Burrowing Behavior Of The Fiddler Crab Uca Panacea In Relation To Food Availability, Jennifer A. Mraz

Master's Theses

Much of fiddler crab behavior is regulated by the tides and centers around their burrows. Field and laboratory studies were conducted to assess the effect of food availability on burrowing in the Gulf coast fiddler crab, Vea panacea. In the field, crabs were observed for droving behavior through visual observations; evidence for this behavior was assessed further by determining sediment organic content. Although the organic content did increase significantly as distance increased from the edge of the water, fiddler crabs did not exhibit droving behavior at my study site. Field burrows were cast and measured for depth, diameter and volume …

Information Acquisition And Sociality Among Migratory Birds, Zoltán Németh

Dissertations

Information use is a key feature of adaptive behavior: the better informed an individual, the better it is able to adjust its behavior to meet the demands of a variable world. Therefore, most animals attempt to reduce environmental uncertainty by gathering information when it is available. However, tracking unpredictable ecological factors may carry costs as individuals invest valuable time and energy in the process of information acquisition. Social learning (i.e., use of social information inadvertently produced by other individuals) enables the individual to gain rapid and more complete assessment of its novel environment. This process may be particularly important for …

Patterns Of Diversity, Zoogeography, And Ecological Gradients In Honduran Freshwater Fishes, Wilfredo Antonio Matamoros

Dissertations

Nineteen major river drainages across Honduras were sampled from 2005-2009 in order to understand Honduran geographical patterns of freshwater fish distribution, to delineate the Honduran freshwater fishes ichthyographical provinces, and to understand patterns of species assemblage at the drainage level. A total of 166 species of freshwater fishes were sampled, a 64% increase over previously published reports. Eight species belong to primary freshwater families, 47 to secondary, and 111 to peripherals. In order to understand the species-drainages relationships, a presence-absence matrix was built for the 19 major drainages and 55 primary and secondary freshwater fishes. Correspondence and cluster analysis clearly …

Evaluating Ecosystem Response To Oyster Restoration And Nutrient Load Reduction With A Multispecies Bioenergetics Model, Richard S. Fulford, Denise L. Breitburg, Mark Luckenbach, Roger I.E. Newell

Faculty Publications

Many of the world's coastal ecosystems are impacted by multiple stressors each of which may be subject to different management strategies that may have overlapping or even conflicting objectives. Consequently, management results may be indirect and difficult to predict or observe. We developed a network simulation model intended specifically to examine ecosystem-level responses to management and applied this model to a comparison of nutrient load reduction and restoration of highly reduced stocks of bivalve suspension feeders (eastern oyster, Crassostrea virginica) in an estuarine ecosystem (Chesapeake Bay, USA). Model results suggest that a 50% reduction in nutrient inputs from the watershed …

Chemical Inhibition Of Caax Protease Activity Disrupts Yeast Ras Localization, Surya P. Mandahar, Emily R. Hildebrandt, William H. Jacobsen, George M. Santangelo, Walter K. Schmidt

Faculty Publications

Proteins possessing a C-terminal CaaX motif, such as the Ras GTPases, undergo extensive post-translational modification that includes attachment of an isoprenoid lipid, proteolytic processing and carboxylmethylation. Inhibition of the enzymes involved in these processes is considered a cancer-therapeutic strategy. We previously identified nine in vitro inhibitors of the yeast CaaX protease Rce1p in a chemical library screen (Manandhar et al., 2007). Here, we demonstrate that these agents disrupt the normal plasma membrane distribution of yeast GFP-Ras reporters in a manner that pharmacologically phenocopies effects observed upon genetic loss of CaaX protease function. Consistent with Rce1p being the in vivo target …

Natural Selection On Testosterone Production In A Wild Songbird Population, Joel W. Mcglothlin, Danielle J. Whittaker, Sara E. Schrock, Nicole M. Gerlach, Jodie M. Jawor, Eric A. Snajdr, Ellen D. Ketterson

Faculty Publications

Because of their role in mediating life-history trade-offs, hormones are expected to be strongly associated with components of fitness; however, few studies have examined how natural selection acts on hormonal variation in the wild. In a songbird, the dark-eyed junco (Junco hyemalis), field experiments have shown that exogenous testosterone alters individuals' resolution of the survival-reproduction trade-off, enhancing reproduction at the expense of survival. Here we used standardized injections of gonadotropin-releasing hormone (GnRH) to assay variation in the testosterone production of males. Using measurements of annual survival and reproduction, we found evidence of strong natural selection acting on GnRH-induced …

A Novel Gene Network Inference Algorithm Using Predictive Minimum Description Length Approach, Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng, Chaoyang Zhang

Faculty Publications

Background: Reverse engineering of gene regulatory networks using information theory models has received much attention due to its simplicity, low computational cost, and capability of inferring large networks. One of the major problems with information theory models is to determine the threshold which defines the regulatory relationships between genes. The minimum description length (MDL) principle has been implemented to overcome this problem. The description length of the MDL principle is the sum of model length and data encoding length. A user-specified fine tuning parameter is used as control mechanism between model and data encoding, but it is difficult to …

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

Dissertations

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

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

Dissertations

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

Relationships Between Particle Properties And Scattering In Coastal Waters Of The Northern Gulf Of Mexico Influenced By The Mississippi River, Bruce Alan Spiering

Dissertations

This study was conducted to determine how the characteristics of an assemblage of suspended particles, including their composition and size affect the relationship between the optical scattering coefficient b (m-1), and the dry mass of the particles in suspension. Knowledge of the scattering to total suspended matter (TSM) ratio, i.e. the mass specific scattering coefficient b* (m2/g), is important because the light detected by optical imaging sensors used for remote sensing is the light that has been scattered by particles back through the water surface. If this ratio is not known or varies within the region of interest, accurate estimates …

Conservation And Ecology Of The Yellow-Blotched Sawback (Graptemys Flavmaculata), William Winsyl Selman Ii

Dissertations

The role of species conservation is becoming increasingly important due to the mounting pressures from humans on habitats and populations of organisms. This is particularly evident in riverine ecosystems throughout the world where the human demand for freshwater resources is increasing, and consequently, the number of imperiled aquatic organisms is also growing. The seven chapters of this dissertation primarily focus on the Yellow-blotched Sawback, Graptemys flavimaculata, an endangered riverine turtle that is endemic to the Pascagoula River system of southeast Mississippi, USA. At the population level, we aimed to study the impacts of Hurricane Katrina on two study populations within …

Determining The Relationship Of Human Enteric Viruses In Clinical, Wastewater, And Environmental Samples Utilizing Molecular And Cell Culture Techniques, Jacquelina Susann Williams Woods

Dissertations

This study was the first to examine five significant enteric viruses in human fecal material, sewage, and oysters to show a genetic relationship between human enteric viruses and different sample matrices. Fecal samples were collected from an area hospital and examined for norovirus genotype I (NoV GI), norovirus genotype II (NoV Gil), hepatitis A virus (HA V), adenovirus (ADV), and enteroviruses. During this study, sewage samples were collected from a Waster Water Treatment Plant (WWTP) in Mobile, ALand oyster sentinels were placed at 0.1 nautical miles (nm) (station 1 ), 0.2nm (station 2}, 1.5nm (station 3), and 4nm (station 4) …

The Natural Provenance: Ecoliteracy In Higher Education In Mississippi, Sarah Elizabeth Wheeless

Dissertations

Researchers have suggested that there is an increasing apathy in the study of natural history both in academic settings and in the scientific community (Schmidly, 2005). Natural history is the cornerstone of ecological literacy. However, most studies of environmental knowledge do not directly address knowledge of local natural history. Instead, they concern knowledge of human environmental issues, environmental concepts, or broad ecological knowledge. Ecoliteracy established the study of natural history as fundamental to environmental knowledge and seeks to determine levels of knowledge of local environments and factors associated with that knowledge (Pilgrim et al., 2007).

This study investigated ecoliteracy in …

Soccer Penalty Kick Pre-Impact Cues Of Male Right-Footed High School Soccer Players, Jason Ryan Jones

Dissertations

The purpose of this study was to use direct observation methods to collect evidence of pre-impact cues in a soccer penalty kick and to analyze their predictive powers in determining shot direction. The five pre-impact cues were position of the approachru n, alignmento f the hips,leano ftrunk, placemenot f non-kickingf oot, and actiono f the non-kickings idea rm.V ideo wasc ollecteda ndt hena nalyzedu singa Dartfishrn tagging panel. There were a total of fifty male high school right-footed participants.C oachesfr om areah igh schools occert eamsp rovidedt heir top penaltyk ick takerst o participatein the study.V ideo wasc ollectedo n …

Role Of Casein Kinase 1 In The Glucose Sensor-Mediated Signaling Pathway In Yeast, Satish Pasula, Samujjwal Chakraborty, Jae H. Choi, Jeong-Ho Kim

Faculty Publications

Background

In yeast, glucose-dependent degradation of the Mth1 protein, a corepressor of the glucose transporter gene (HXT) repressor Rgt1, is a crucial event enabling expression of several HXT. This event occurs through a signaling pathway that involves the Rgt2 and Snf3 glucose sensors and yeast casein kinase 1 and 2 (Yck1/2). In this study, we examined whether the glucose sensors directly couple with Yck1/2 to convert glucose binding into an intracellular signal that leads to the degradation of Mth1.

Results

High levels of glucose induce degradation of Mth1 through the Rgt2/Snf3 glucose signaling pathway. Fluorescence microscopy analysis …

Beyond Affymetrix Arrays: Expanding The Set Of Known Hybridization Isotherms And Observing Pre-Wash Signal Intensities, Alexander Pozhitkov, Idrissa Boube, Marius Brouwer, Peter A. Noble

Faculty Publications

Microarray hybridization studies have attributed the nonlinearity of hybridization isotherms to probe saturation and post-hybridization washing. Both processes are thought to distort 'true' target abundance because immobilized probes are saturated with excess target and stringent washing removes loosely bound targets. Yet the paucity of studies aimed at understanding hybridization and dissociation makes it difficult to align physicochemical theory to microarray results. To fill the void, we first examined hybridization isotherms generated on different microarray platforms using a ribosomal RNA target and then investigated hybridization signals at equilibrium and after stringent wash. Hybridization signal at equilibrium was achieved by treating the …