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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 …

Characterization Of Γ-Butyrolactone Autoregulatory Signaling Gene Homologs In The Angucyclinone Polyketide Ws5995b Producer Streptomyces Acidiscabies, Frank G. Healy, Kevin P. Eaton, Prajit Limsirichai, Joel F. Aldrich, Alaina K. Plowman, Russell R. King

Biology Faculty Research

Organisms belonging to the genus Streptomyces produce numerous important secondary metabolites and undergo a sophisticated morphological differentiation program. In many instances these processes are under the control of gamma-butyrolactone (GBL) autoregulatory systems. Streptomyces acidiscabies strain 84.104 produces the secondary metabolite aromatic angucyclinone polyketide WS5995B. In order to explore the role of GBL regulatory circuitry in WS5995B production and morphogenesis in S. acidiscabies, a gene cluster encoding GBL autoregulatory signaling homologs was identified and characterized. Two GBL receptor homologs, sabR and sabS, were found flanking a GBL synthase homolog sabA. Strains carrying mutations in sabS produced elevated levels …

A Proposed Syntax For Minimotif Semantics, Version 1., Jay Vyas, Ronald J. Nowling, Mark W. Maciejewski, Sanguthevar Rajasekaran, Michael R. Gryk, Martin R. Schiller

Life Sciences Faculty Research

BACKGROUND:

One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of …

Assessment Of The Endangered Species Podarcis Carbonelli On A Microgeographic Scale: A Molecular, Morphological And Physiological Approach, Maria Clara Figueirinhas Do Amaral

Masters Theses & Specialist Projects

The lizard Podarcis carbonelli is an endangered species endemic to the Iberian Peninsula. One location where this species occurs is at the Berlengas Natural Preserve, an Atlantic archipelago off the coast of Portugal. These island populations are geographically separated from nearby mainland populations. The fundamental question is, are these insular individuals distinct from the mainland populations? Four localities were chose for comparison: two island populations and two nearby coastal populations. We assessed this question using three distinct approaches: molecular, morphological and physiological approach. We sequenced the 12S RNA, the mtDNA Control Region and the 7th intron of the !-fibrinogen gene …

On The Prediction Of Extreme Ecological Events, Mark W. Denny, Luke J. H. Hunt, Luke P. Miller, Christopher D. G. Harley

Faculty Publications, Biological Sciences

Ecological studies often focus on average effects of environmental factors, but ecological dynamics may depend as much upon environmental extremes. Ecology would therefore benefit from the ability to predict the frequency and severity of extreme environmental events. Some extreme events (e.g., earthquakes) are simple events: either they happen or they don't, and they are generally difficult to predict. In contrast, extreme ecological events are often compound events, resulting from the chance coincidence of run-of-the-mill factors. Here we present an environmental bootstrap method for resampling short-term environmental data (rolling the environmental dice) to calculate an ensemble of hypothetical time series that …

Nesfatin-1 Exerts Cardiovascular Actions In Brain: Possible Interaction With The Central Melanocortin System, Gina L.C. Yosten, Willis K. Samson

Biological Sciences Faculty Research & Creative Works

Nesfatin-1 is a recently discovered hypothalamic peptide that was shown to suppress food intake through a melanocortin-3/4 receptor-dependent mechanism. Since nesfatin-1 mRNA is detected in the paraventricular nucleus of the hypothalamus, and because many peptides that alter food intake also influence cardiovascular function, we tested the ability of centrally administered nesfatin-1 to affect mean arterial pressure (MAP) in conscious, freely moving rats. Significant increases in MAP were observed following intracerebroventricular administration of nesfatin-1. Pretreatment with either the melanocortin-3/4 receptor antagonist, SHU9119 (intracerebroventricular), or the α-adrenergic antagonist, phentolamine (intra-arterial), abrogated the rise in MAP induced by nesfatin-1, indicating that nesfatin-1 may …

Phospholipase Dα1 And Phosphatidic Acid Regulate Nadph Oxidase Activity And Production Of Reactive Oxygen Species In Aba-Mediated Stomatal Closure In Arabidopsis, Xuemin Wang, Yanyan Zhang, Huiying Zhu, Qun Zhang, Maoyin Li, Min Yan, Rong Wang, Liling Wang, Ruth Welti, Wenhua Zhang

Biology Department Faculty Works

We determined the role of Phospholipase Dα1 (PLDα1) and its lipid product phosphatidic acid (PA) in abscisic acid (ABA)-induced production of reactive oxygen species (ROS) in Arabidopsis thaliana guard cells. The pldα1 mutant failed to produce ROS in guard cells in response to ABA. ABA stimulated NADPH oxidase activity in wild-type guard cells but not in pldα1 cells, whereas PA stimulated NADPH oxidase activity in both genotypes. PA bound to recombinant Arabidopsis NADPH oxidase RbohD (respiratory burst oxidase homolog D) and RbohF. The PA binding motifs were identified, and mutation of the Arg residues 149, 150, 156, and 157 in …

Fisheries Management Paper No.245 - Aquaculture Of Coral, Live Rocks And Associated Products. Aquaculture Policy, Department Of Fisheries, Western Australia

Fisheries Management Papers

Aquarium enthusiasts use corals, live rock and associated products (e.g. live sand) for display and to maintain healthy water quality conditions in their marine aquariums. There is a large and growing market for these products. While the wild harvest fisheries for aquarium products in Western Australia are sustainably managed, output is capped, so increased product is needed to meet the market demand. With a trend towards the capping of wild harvest and additional pressures, such as the introduction of Marine Parks and other marine protected areas, the aquaculture of these products is set for industry development and expansion.

The large …

Adding Upstream Sequence And A Downstream Reporter To The Bile Acid Inducible Promoter Of Clostridium Scindens Vpi 12708, Bryan Patrick Mason

Masters Theses & Specialist Projects

Bile acids in the small intestines of animals serve to breakdown fats and fatsoluble vitamins. Most of the bile acids are reabsorbed into the enterohepatic circulation, but approximately five percent of these bile acids pass into the large intestine. These bile acids are swiftly deconjugated by the bacterial population, and then subjected to further intestinal bacterial chemical modifications. The most significant of these modifications are 7α-dehydroxylations which form secondary bile acids (deoxycholate and lithocholate). Much research has illuminated the 7α-dehydroxylation pathway: of particular interest is the bile acid inducible operon, for which Clostridium scindens VPI 12708 serves as the model …

Ecological Impact Of Epigeal Termitaria On Vertebrates In The Tsavo Region Of Southeast Kenya, Margaret M. Mahan

Masters Theses & Specialist Projects

Termites ecologically engineer their environment by producing termitaria (mounds) used by many other species as dens, lookouts or food sources. The role of termite mounds in biological communities is relatively unknown, despite their ubiquitous nature. I investigated their impact on vertebrates in the Tsavo region of Kenya. Through the characterization of mounds, trapping, direct observation, and collecting microclimate data, I was able to determine the importance of mounds to vertebrates. I found uniform dispersion of mounds, that soil type is correlated with the size of mounds, and that vertebrate activity increases with mound size. I also found no significant differences …

Pestilence, Persistence And Pathogenicity: Infection Strategies Of Bartonella, Michael F. Minnick, James M. Battisti

Biological Sciences Faculty Publications

It has been nearly two decades since the discovery of Bartonella as an agent of bacillary angiomatosis in AIDS patients and persistent bacteremia and 'nonculturable' endocarditis in homeless people. Since that time, the number of Bartonella species identified has increased from one to 24, and 10 of these bacteria are associated with human disease. Although Bartonella is the only genus that infects human erythrocytes and triggers pathological angiogenesis in the vascular bed, the group remains understudied compared with most other bacterial pathogens. Numerous questions regarding Bartonella's molecular pathogenesis and epidemiology remain unanswered. Virtually every mammal harbors one or more Bartonella …

Tri-Trophic Linkages In Disease: Pathogen Transmission To Rainbow Trout Through Stonefly Prey, Sandra M. Adams, Aaron S. Adams, William E. Holben

Biological Sciences Faculty Publications

ABSTRACT Relationships between macroinvertebrates and microorganisms in aquatic environments are only poorly understood despite the fact that many aquatic macroinvertebrates feed on microbial biofilms during some life stage. Better understanding of trophic interactions between microbial biofims, macroinvertebrates, and fish may also help control fish diseases and loss of natural resources. It has also been suggested that pollution, habitat fragmentation, and poor water quality may contribute to increased pathogenesis and mortality in fish. Increased disease incidence is difficult to assess, however, in part because of the complexity of pathogen transmission dynamics. Several environmental pathogens exist whose reservoir(s) and means of transmission …

Predicting Leptodactylus (Amphibia, Anura, Leptodactylidae) Distributions: Broad-Ranging Versus Patchily Distributed Species Using A Presence-Only Environmental Niche Modeling Technique, Miguel Fernández, Daniel Cole, W. R. Heyer, Stephen Reichle, Rafael O. De Sá

Biology Faculty Publications

Locality data available for many, if not most, species of Neotropical frogs are based on written descriptions of the collecting sites, not on GPS device determined coordinate data. The pre-GPS device data are imprecise relative to GPS data. Niche modeling is a powerful technique for predicting geographic distributions that provides the best results when the locality data are precise. The purpose of this study is to determine whether imprecise historical locality data are sufficient such that niche modeling techniques can yield realistic new insights to species-level distributions. Two sets of frogs of the genus Leptodactylus that have known different kinds …

Differential Mortality Drives Life-History Evolution And Population Dynamics In The Fish Brachyrhaphis Rhabdophora, Jerald B. Johnson, J. Jaime Zuniga-Vega

Faculty Publications

Life-history theory predicts that populations experiencing different levels of extrinsic mortality will evolve divergent reproductive strategies. Previous work in the live bearing fish Brachyrhaphis rhabdophora shows that individuals from populations that occur with piscivorous fish mature earlier and at smaller sizes and have more and smaller offspring than fish from populations without predators. However, until now, there have been no data to demonstrate that differences in mortality rates actually exist between predator and predator free sites. Here we present the results of a serial mark-recapture field study designed to estimate mortality rates in natural populations of B. rhabodophora from Costa …

Assessment Of Invasive Plants Along The Upper Passaic River, Susan Marie Jankovic

Theses, Dissertations and Culminating Projects

The distribution of invasive plants was determined along the floodplain of the Passaic River in three protected park regions. Specifically, Lord Stirling Park, Hatfield Swamp, and Great Piece Meadows were assessed to determine whether or not the top 29 invasive plants as identified by Snyder and Kaufman (2004) were present. Two of the three areas are strongly affected by urbanization which may be a contributing factor to the increase of invasive plants within them. Eleven out of the top twenty nine invasive plants in New Jersey were recorded: Multiflora rose (Rosa multiflora), Lesser celandine (Ranunculus ficaria), Japanese stiltgrass (Microstegium vimineum), …

Purification And Thermodynamic Analysis Of The Stability Of Hiv-1 Reverse Transcriptase In The Presence Of Efavirenz, Chantal A. Sanmiguel

Honors Capstones

No abstract provided.

Exposure To Ultraviolet Radiation Causes Proteomic Changes In Embryos Of The Purple Sea Urchin, Strongylocentrotus Purpuratus, Joseph Paul Campanale

Master's Theses

The amount of solar ultraviolet radiation (UVR, 290-400 nm) reaching Earth’s surface is increasing due to ozone depletion and global climate change. Embryos of the purple sea urchin, Strongylocentrotus purpuratus, provide an ideal system for examining how UVR affects developing marine organisms and cells in general. To model the protein-mediated cell cycle response to UV-irradiation, six batches of S. purpuratus embryos were exposed to UVR, monitored for delays in the first mitotic division and examined for global proteomic changes. Embryos from each batch were exposed to or protected from artificial UVR for 25 or 60 min. Embryos treated with …

Rapid Evolution Of Sex-Pheromone-Producing Enzyme In Drosophila, Troy R. Shirangi, Héloïse D. Dufour, Thomas M. Williams, Sean B. Carroll

Biology Faculty Publications

A wide range of organisms use sex pheromones to communicate with each other and to identify appropriate mating partners. While the evolution of chemical communication has been suggested to cause sexual isolation and speciation, the mechanisms that govern evolutionary transitions in sex pheromone production are poorly understood. Here, we decipher the molecular mechanisms underlying the rapid evolution in the expression of a gene involved in sex pheromone production in Drosophilid flies. Long-chain cuticular hydrocarbons (e.g., dienes) are produced female-specifically, notably via the activity of the desaturase DESAT-F, and are potent pheromones for male courtship behavior in Drosophila melanogaster. We …

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 …

Fecal-Sac Ingestion By Spotted Towhees, Jenny E. Mckay, Michael T. Murphy, Sarah Bartos Smith, Jennifer K. Richardson

Biology Faculty Publications and Presentations

Altricial nestlings encase excrement in fecal sacs that parents remove by either ingesting them or transporting them away from the nest. Ingestion may allow energetically or nutritionally deprived parents to recapture energy or nutrients that might be lost because of nestlings' inefficient digestion (the "parental-nutrition hypothesis"), but ingestion may also permit parents to avoid flights from the nest that interfere with parental care (e.g., brooding young; the "economic-disposal hypothesis"). We used a hypothetico-deductive approach to test the two hypotheses' ability to account for fecal-sac ingestion by the Spotted Towhee (Pipilo maculatus). We confirmed the parental-nutrition hypothesis' predictions that …

The Role Of Temperature And Desiccation Stress In Limiting The Local-Scale Distribution Of The Owl Limpet, Lottia Gigantea, Luke P. Miller, Christopher D. G. Harley, Mark W. Denny

Faculty Publications, Biological Sciences

1 Small-scale distributions of rocky intertidal organisms may be determined in part by temperature and desiccation stress during low tide and the ability of organisms to resist such stresses. Biophysical modelling techniques, coupled with data on the physiological tolerance of organisms can be used to predict the frequency and severity of abiotic stress events.

2 The limpet Lottia gigantea is a major competitor for primary space on rocky shores along the west coast of North America. The goal of this study was to quantify the thermal and desiccation tolerance of this species and to predict the frequency of stressful events …

Seasonal Differences In Leaf-Level Physiology Give Lianas A Competitive Advantage Over Trees In A Tropical Seasonal Forest, Zhi-Quan Cai, Stefan A. Schnitzer, Frans Bongers

Biological Sciences Faculty Research and Publications

Lianas are an important component of most tropical forests, where they vary in abundance from high in seasonal forests to low in aseasonal forests. We tested the hypothesis that the physiological ability of lianas to fix carbon (and thus grow) during seasonal drought may confer a distinct advantage in seasonal tropical forests, which may explain pan-tropical liana distributions. We compared a range of leaf-level physiological attributes of 18 co-occurring liana and 16 tree species during the wet and dry seasons in a tropical seasonal forest in Xishuangbanna, China. We found that, during the wet season, lianas had significantly higher CO …

Assessing Threat Of Introduction Of The Parthenogenetic Marbled Crayfish Marmorkrebs Into North American Waters, Stephanie A. Jimenez, Zen Faulkes

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Background/Question/Methods

Marmorkrebs are parthogenetic crayfish in the genus Procambarus. Their provenance is unknown, but they were discovered in hobbyists' aquaria in Germany in the mid 1990s, and have since been introduced into the North American pet trade. Marmorkrebs are a potential invasive pest species. For example, they have already been introduced into Madagascar, where they may threaten endemic crayfish species. We are trying to estimate the risk, and possible consequences, of any accidental introduction of Marmorkrebs into North American waters. First, we conducted an online survey of hobbyists who keep Marmorkrebs as pets to estimate how widely, and how …

Serotonin Immunoreactive Cells And Nerve Fibers In The Mucosa Of The Rat Stomach, A P Gesase

Tanzania Journal of Science

The current study has showed the morphological features of serotonin (5-hydroxytryptamine) immunoreactivity in the pyloric mucosa of the rat stomach. The immunoreactive elements included the endocrine cells, mast cells and mucosal nerve fibers in the lamina propria. The immunopositive endocrine cells were oval in shape and located mostly in the basal part of the gastric glands. The cell contained a central non-staining area and the peripheral staining zone. The mast cells stained homogenously and appeared to be oval-round in shape. They were located in the upper, middle and basal parts of the mucosa. Serotonin immunoreactive nerve fibers with varicosities were …

Morphological Features Of Tyrosine Hydroxylase Immunoreactive Cells In The Mouse Islets Of Langerhans, A P Gesase, Y -I Satoh

Tanzania Journal of Science

The current immunohistochemical study used the antibody against tyrosine hydroxylase (TH) to observe the immunoreactive elements in the mouse pancreas. The results indicated the presence of immunoreactive nerve fibers and endocrine cells. The immunopositive nerve fibers appeared as thick and thin bundles; thick bundles were seen to run along the blood vessels giving out fine fibers to the wall. Varicose nerve fibers were seen in the islets of Langerhans and also in close association with the exocrine endpieces. The TH immunoreactive cells were oval-round in shape and some showed the central non-staining area and the dense staining peripheral zone. More …

Effects Of Biofilm Age And Composition On Oyster Larval Setting, Alaina Hart

Theses and Dissertations

The lack of success in restoring oyster, Crassostrea virginica, populations to Chesapeake Bay and its tributaries has raised many questions about why many restoration efforts have failed. A number of studies have focused on the larval stage of oysters and considered the variables that impact oyster setting behavior in an effort to understand why oyster populations have not recovered. Studies that have examined setting surfaces suggest that biofilms promote oyster larval settlement; however, similar studies with barnacle larvae have found an inhibitory relationship. The present study utilized field-produced biofilms of different ages to determine if natural biofilms inhibit or promote …

Genetic Differentiation Of The Parasitoid, Cotesia Congregata (Say), Based On Host-Plant Complex, Georgia Karns

Theses and Dissertations

Endoparasitoids of herbivorous lepidopterans have intimate relationships with their host species as well as the plant on which their host develops. Characteristics of both hosts and plants can affect parasitoid success in tri-trophic systems and thus, drive diversification. Genetic differentiation was estimated for Cotesia congregata (Say) collected from two distinct host-plant complexes, Manduca sexta L. on tobacco (Nicotiana tabacum L.) and Ceratomia catalpae, (Haworth) on catalpa (Catalpa bignonioides Walker), in the mid-Atlantic region of North America using seven microsatellite loci and the mitochondrial COI locus. Microsatellite allele frequencies were differentiated based on host-plant complex, and COI haplotypes from individuals on …

Assessment Of Pre-Pcr Whole Genome Amplification Of Single Pollen Grains Using Flowering Dogwood (Cornus Florida), Candace Dillon

Theses and Dissertations

Studies of gene flow in natural plant populations often focus on either historical or abiotic dispersal methods (e.g. wind, water, gravity), but there is little information available on contemporary, animal-mediated pollen dispersal patterns. Emerging molecular laboratory techniques allow unprecedented insights into spatial patterns of pollen-mediated gene flow. However, to date, technical challenges have limited their widespread application. The genome of a pollen grain can be amplified via whole genome amplification (WGA) prior to traditional amplification via polymerase chain reaction (PCR) to prevent the stochastic effects associated with low copy number amplification. Even still, WGA can suffer from low success rates …

Understanding The Genetic Consequences Of Rapid Range Expansion: A Case Study Using The Invasive Microstegium Vimineum Trin. (Poaceae), Stephen Baker

Theses and Dissertations

Global temperature changes are predicted to influence the distributions of plants and can have significant consequences for population genetic structure. Both the nature of these consequences and the processes that shape them are of interest for both conservation genetics and the development of realistic management programs. Rapid range expansion occurs on short temporal scales not conducive to conventional phylogeographical analyses. This paper presents the findings from a population genetic study of the invasive grass Microstegium vimineum Trin. A. Camus throughout the James River Basin of Virginia. Genotypic analysis using Amplified Fragment Length Polymorphism (AFLP) molecular markers were used to test …

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 …