Life Sciences 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 …

Morphological Deformities As Biomarkers In Fish From Contaminated Rivers In Taiwan, Peter Lin Sun, William E. Hawkins, Robin M. Overstreet, Nancy J. Brown-Peterson

Faculty Publications

Tilapia (Oreochromis spp.) were collected seasonally from four contaminated rivers in southwestern Taiwan for studies of morphological deformities that could be used as biomarkers of contamination. Morphological deformities found in tilapia were separated into 15 categories. Overall, the prevalence of deformities such as split fins, lower lip extension and gill deformities were significantly related to various water quality parameters, including low DO and high ammonium, lead and zinc concentrations. The persistence of tilapia in polluted waters and the development of a suite of morphological deformities suggest that tilapia can be used as sentinels of non-point source pollution in rivers.

Sport As A Vehicle For Socialization And Maintenance Of Cultural Identity: International Students Attending American Universities, James Taylor Allen

Dissertations

Sport can be utilized by immigrants as a vehicle for maintaining cultural identity. Conversely, sport participation provides immigrants with opportunities for adopting an entirely new culture. Previous research also suggests that sport provides individuals with opportunities for attaining social capital. While this can be a beneficial situation for some, sport is also promoting elitism and serving as a powerful mechanism for exclusion. Globalization has led large numbers of foreign nationals to seek educational opportunities in the United States. Due to the increase in the number of international students and the lack of empirical studies, the need to study their participation …

Factors Influencing The Environmental Quality Of The Bay Of Saint Louis, Mississippi And Implications For Evolving Coastal Management Policies, Pradnya Ankush Sawant

Dissertations

The Bay of St. Louis, MS is a small northern Gulf of Mexico estuary that has been identified by the Mississippi Department of Environmental Quality (MDEQ) as an impaired waterbody for its designated uses, mainly due to the presence of pollutant pathogens. A systematic study of this estuary was important to understand the behavior and responses of the bay to several natural and anthropogenic forcing factors. A 14- month long study (bimonthly sampling) to evaluate its environmental quality was undertaken from April 2003 to May 2004. Environmental quality was defined as "the health of an ecosystem characterized in terms of …

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 …

Inferring Gene Regulatory Networks From Time Series Microarray Data, Peng Li

Dissertations

The innovations and improvements in high-throughput genomic technologies, such as DNA microarray, make it possible for biologists to simultaneously measure dependencies and regulations among genes on a genome-wide scale and provide us genetic information. An important objective of the functional genomics is to understand the controlling mechanism of the expression of these genes and encode the knowledge into gene regulatory network (GRN). To achieve this, computational and statistical algorithms are especially needed.

Inference of GRN is a very challenging task for computational biologists because the degree of freedom of the parameters is redundant. Various computational approaches have been proposed for …

The Relationship Between Calcium Intake, Obesity, And Cardiovascular Disease Risk Factors: The Jackson Heart Study, Marjuyua Lartey-Rowser

Dissertations

Cardiovascular disease (CVD) is a major health risk in the United States. Major indicators of CVD risk include obesity, blood lipids, and blood pressure. Modifiable risk factors associated with CVD include body composition (body mass index and waist circumference), serum lipids, and blood pressure. Data suggest calcium intake may play a role in regulation of weight, serum lipids, and blood pressure. The purpose of this study was to assess relationships of dietary calcium intake with weight status, and cardiovascular disease risks in African American population participating in the Jackson Heart Study.

The subjects included 4,267 African American adults ages 21-95 …

Chemical And Isotopic Characterization Of Size-Fractionated Organic Matter From Cryoturbated Tundra Soils, Northern Alaska, Chunhao Xu, Laodong Guo, Chien-Lu Ping, Daniel M. White, Thomas D. Lorenson

Faculty Publications

Recent studies indicate a second layer of organic matter often accumulates in the lower active layer and upper permafrost in arctic tundra soils as a result of cryoturbation. In this study, cryoturbated organic matter was characterized using a combination of physical size fractionation and modern analytical techniques for elemental composition (C and N), stable isotopes (delta(13) C and delta(15)N), radiocarbon content (Delta(14)C), and molecular fingerprinting (pyrolysis-gas chromatography/mass spectrometry, Py-GC/MS). The results indicated that cryoturbated organic matter could be highly bioavailable. Soil organic matter (SOM) associated with fine sand particles was considered to be the organic carbon pool most sensitive to …

On The Mechanisms Of Episodic Salinity Outflow Events In The Strait Of Hormuz, Prasad G. Thoppil, Patrick J. Hogan

Faculty Publications

Observations in the Strait of Hormuz (26.26 degrees N, 56.08 degrees E) during 1997-98 showed substantial velocity fluctuations, accompanied by episodic changes in the salinity outflow events with amplitude varying between 1 and 2 psu on time scales of several days to a few weeks. These events are characterized by a rapid increase in salinity followed by an abrupt decline. The mechanisms behind these strong pulses of salinity events are investigated with a whigh-resolution (similar to 1 km) Hybrid Coordinate Ocean Model (HYCOM) with particular reference to the year 2005. In accordance with the observations, the simulated salinity events are …

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 …

My Two Boots ... A Walk Through The Wetlands. An Annual Outing For 700 Middle School Students, Julie Cwikla, Mark Lasalle, Sybil Wilner

Faculty Publications

No abstract provided.

The Effects Of Dolphin Education Programs On Visitors' Conservation-Related Knowledge, Attitude And Behavior, Lance Joseph Miller

Dissertations

Zoological institutions typically exhibit dolphins in educational programs such as dolphin shows and interaction programs. The goal of these programs is to entertain visitors while increasing their conservation-related knowledge, attitude and behavior towards dolphins and the marine environment. The purpose of the current study was to examine dolphin shows and interaction programs in terms of their effectiveness in meeting these goals. A multi-institutional study was conducted at six different facilities throughout the United States. A repeated measures design was used to examine the knowledge, attitude and behavior of visitors before, immediately after and three months following participation in dolphin shows …

The Effects Of Climate Variability On The Structure Of The Phytoplankton Community In Tumaco Bay, Colombia, Ingrid Garcia-Hansen Honkala

Dissertations

Spatiotemporal variability in the diatom and dinoflagellate community structure and chlorophyll a (chl a) concentrations in Tumaco Bay during the 1993-2005 period was related clearly to seasonal and interannual variability in environmental conditions due to the migration of the Inter-tropical Convergence Zone (ITZC) and the influence of El Nino Southern Oscillation (ENSO) events. A total of 134 species of diatoms that belong to 57 genera, and 78 species of dinoflagellates that belong to 25 genera were identified during the survey. The diatom community was the dominant group in the waters of the bay, being the most abundant with the greatest …

Historical Account Of The Two Family-Group Names In Use For The Single Accepted Family Comprising The "Fish Blood Flukes", Stephen A. Bullard, Kirsten Jensen, Robin M. Overstreet

Faculty Publications

The family-group name for the "fish blood flukes" is unstable, with both "Aporocotylidae Odhner, 1912" and "Sanguinicolidae von Graff, 1907 "in use for the single family. Although "Sanguinicolidae von Graff, 1907" (or "Graff, 1907") has been a widely-accepted family-group name for the fish blood flukes subsequent to Yamaguti's 1954 and 1958 synoptical publications ("Systema Helminthum"), a critical examination of the relevant literature, much of it published in German during 1900 through 1926, reveals that "Aporocotylidae Odhner, 1912" is the earliest available family-group name for these flukes. The name Aporocotylidae, moreover, was in wide usage by alpha taxonomists before 1954 and …

The Influence Of Habitat And Fishing On Reef Fish Assemblages In Cuba, Gaspar Gonzalez-Sanson, Consuelo Aguilar, Ivet Hernandez, Yureidy Cabrera, R. Allen Curry

Gulf and Caribbean Research

The abundance of selected fish species was estimated using the stationary visual census technique in the northwestern region of the Cuban shelf. A total of 26,809 individuals of 32 species were counted in 1,172 stationary point censuses made at 10 reef sites along the coast. We found that the abundance patterns were most probably the consequence of the presence/absence of mangroves and seagrass beds in adjacent lagoon areas. A second factor influencing the spatial variation appeared to be overfishing on an east-west gradient, with lower abundances of commercially targeted species near Havana City in the east.

Abundance And Distribution Of Two Species Of Squilla (Crustacea: Stomatopoda: Squillidae) In The Northern Gulf Of Mexico, Jennifer L. Wortham

Gulf and Caribbean Research

Stomatopods (mantis shrimps) are predatory benthic crustaceans. Mantis shrimp in the genus Squilla are frequent bycatch animals unintentionally collected in conjunction with the shrimp fishery in the Gulf of Mexico (GOM). Their carcasses are discarded instead of being retained for human consumption, fish meal, or other protein-based food products. The size, depth, salinity, and temperature distributions of these species, as well as their abundance based on gender, were examined to gain biological information that would be necessary if a fishery were to develop in the GOM. I collected samples (n = 2,854) of Squilla empusa and Squilla chydaea in the …

Seagrass Loss In Belize: Studies Of Turtlegrass (Thalassia Testudinum) Habitat Using Remote Sensing And Ground-Truth Data, Gary R. Gaston, Cole Easson, Greg Easson, Justin Janaskie, M.A. Ballas

Gulf and Caribbean Research

Spatial and temporal change in turtlegrass (Thalassia testudinum) habitat of the South Water Caye Marine Reserve (SWCMR) in Belize were analyzed using satellite images backed up with ground-truth data. We had two pri-mary objectives. First, we wanted to determine areal expanse of seagrass across a large area (~12 km by 3 km) of the SWCMR, and address its change over time. We used paired satellite images taken during 2001 and 2005 to determine coverage by seagrass and measure temporal variables. These analyses recorded an overall seagrass loss of 1.8% (52.3 ha) during the 4 yr period. Secondly, we …

Determining Salinity-Tolerance Of Giant Salvinia Using Chlorophyll Fluorescence, Patrick D. Biber

Gulf and Caribbean Research

Salvinia molesta Mitchell, a floating invasive aquatic plant, is one of the top 10 worst invasive aquatic weeds in the world. It was discovered in the lower Pascagoula River in 2005 and evidence suggests that this non-native species is spreading along the northern Gulf of Mexico. These plants exhibit rapid growth and nutrient uptake rates, allowing them to out compete other plants in similar habitats. Distributional observations suggest that non-native S. molesta is able to survive in salinities of up to 7 ppt in the lower Pascagoula River. The response of S. molesta to three salinity levels (0, 5, 10 …

First Records Of The Seagrass Parasite Plasmodiophora Diplantherae From The Northcentral Gulf Of Mexico, Allison K. Walker, Jinx Campbell

Gulf and Caribbean Research

Plasmodiophora diplantherae is known to occur throughout the pantropical distribution of its host, the seagrass genus Halodule. However, records in the subtropical region are limited to Tampa Bay, FL where it was detected once during an examination of herbar-ium specimens of H. beaudettei collected in December 1951 (den Hartog 1965) and to Fort Pierce, FL where it was collected once infecting H. wrightii (Braselton and Short 1985). This communication represents the first report of this parasite from Mississippi and Louisiana in the northcentral Gulf of Mexico (GOM).

A Comparison Of Fish Populations In Shallow Coastal Lagoons With Contrasting Shoalgrass (Halodule Wrightii) Cover In The Northcentral Gulf Of Mexico, Just Cebrian, Glenn A. Miller, Jason P. Stutes, Adrienne L. Stutes, Mairi E. Miller, Kate L. Sheehan

Gulf and Caribbean Research

A number of studies have examined the effects of reduced seagrass cover on local fish populations (e.g., Heck et al. 1989, Ferrell and Bell 1991, Hughes et al. 2002 and more), but few of those studies have focused on shoalgrass (e.g., Tolan et al. 1997, Rydene and Matheson 2003). We present a preliminary comparison of fish populations in three shallow coastal lagoons in the northcentral GOM that have varying levels of shoalgrass cover. Namely, we compare (1) abundances of individual species and the entire fish population, (2) fish population diversity, and (3) length-frequency distributions of the most abundant species.

Age Estimates Of Two Large Misty Grouper, Epinephelus Mystacinus (Serranidae) From Bermuda With A Comparison Of The Age Of Tropical Groupers In The Western Atlantic, Brian E. Luckhurst, John M. Dean

Gulf and Caribbean Research

Misty grouper are known to attain at least 54 kg and 115 cm total length (TL) (Heemstra and Randall 1993) although a maximum size of 160 cm TL is reported (Appeldoorn et al. 1987, cited in www.FishBase.com). Recently, two specimens (152 and 157 mm TL) were landed by commercial fisherman from the edge of the Bermuda platform, providing documentation of the maximum size which may be attained by this species. There are no age and growth studies on misty grouper (Heemstra and Randall 1993; www.FishBase.com). Therefore, the age data presented here, although not validated, represent the first estimates of maximum …

Macrofauna Associate With Ungrounded Prop Roots Of Rhizophora Mangle In Veracruz And Quintana Roo, Mexico, Kathryn D. Tunnell, Kim Withers

Gulf and Caribbean Research

The prop roots of the red mangrove (Rhizophora mangle) provide a solid substrate for diverse assemblages of marine organisms in areas typically characterized by soft bottoms (Bingham 1992, Farnsworth and Ellison 1996). Macrobenthic communities of mangroves have received little attention compared with other components of the ecosystem, largely due to sampling difficulties (Lee 2008). Mangrove root epifauna are likely used by predatory fish, especially juveniles. Thus, these organisms have the potential of being important links between mangroves and adjacent ecosystems. The fauna associated with red mangrove prop roots along Mexican Gulf of Mexico (GOM) and Caribbean shorelines has …

Morphological Characteristics Of Early Life History Stages Of The Blue Crab, Callinectes Sapidus Rathbun, From The Northern Gulf Of Mexico With A Comparison Of Studies From The Atlantic Seaboard, Kenneth Stuck, Harriet Perry, Darcie Graham, Richard W. Heard

Gulf and Caribbean Research

Zoeae, megalopae, and early crab stages of Callinectes sapidus Rathbun, 1896 were described from the northern Gulf of Mexico (nGOM). Observations during this study were based on larvae reared in the laboratory through the early crab stages and on megalopae and early crab stages collected in the wild. Gulf of Mexico data are compared with similar information for the southeast Atlantic coast of the United States. Size and setation of C. sapidus larvae reared from nGOM stocks were different than those in published descriptions of larvae reared from Atlantic populations. Seasonal differences in size were noted in both reared and …

Note On The Natural And Cultural History Of Hurricane Balls, Joyce M. Shaw

Gulf and Caribbean Research

Hurricane balls are natural phenomena of tropical storms and hurricane winds and waves and are found along the shoreline. Gunter Library at the Gulf Coast Research Laboratory (GCRL) is home to a small collection of hurricane balls which were found along the shore lines of barrier islands and marsh beaches by GCRL staff over the years. Hurricane balls come in many sizes, and large balls can be slightly larger than a standard basketball of 24.8 cm diameter (USA Basketball 2001). Large balls in the Gunter Library collection range from 34.5 cm diameter (from 1969 Hurricane Camille) to 53.5 cm diameter …

Survey Of Blueberry (Vaccinium Spp.) Problems In The Gulf South, Melinda A. Miller-Butler, Kenneth J. Curry, Barbara J. Smith, Jeffrey S. Braswell

Faculty Publications

The blueberry (Vaccinium) industry in Mississippi has been steadily increasing since the early 1980s, but some plants in older fields are now in decline. The root rot pathogen, Phytophthora cinnamomi, is endemic in the southeastern United States and has caused severe losses to blueberries in North Carolina and Arkansas. Because the warm, humid climate of Mississippi, with periods of high precipitation, provides a favorable environment for Phytophthora root rot disease, it was suspected to be the cause of plant decline in older blueberry fields. Members of the Gulf South Blueberry Growers Association were mailed surveys to determine …

Variation Of Morphology And Elemental Concentrations In The California Nickel Hyperaccumulator Streptanthus Polygaloides (Brassicaceae), Robert S. Boyd, Michael A. Wall, Scott R. Santos, Michael A. Davis

Faculty Publications

The Ni hyperaccumulator Strepthanthus polygaloides (Brassicaceae) is one of a handful of Ni hyperaccumulators known from continental North America. Surveys have revealed four distinctive morphs of this species, relying primarily on floral traits (sepal color and shape): a purple sepal morph (P), a yellow sepal morph (Y), a morph in which sepals start yellow and mature to purple (Y/P), and a morph with light yellow undulate sepals (U). In this study, we raised plants from ten populations (five Y, three P, one Y/P, and one U) under uniform greenhouse conditions to determine if morphs varied in morphology and elemental concentrations …

A Distribution-Free Convolution Model For Background Correction Of Oligonucleotide Microarray Data, Zhongxue Chen, Monnie Mcgee, Qingzhong Liu, Megan Kong, Youping Deng, Richard H. Scheuermann

Faculty Publications

Introduction

Affymetrix GeneChip^® high-density oligonucleotide arrays are widely used in biological and medical research because of production reproducibility, which facilitates the comparison of results between experiment runs. In order to obtain high-level classification and cluster analysis that can be trusted, it is important to perform various pre-processing steps on the probe-level data to control for variability in sample processing and array hybridization. Many proposed preprocessing methods are parametric, in that they assume that the background noise generated by microarray data is a random sample from a statistical distribution, typically a normal distribution. The quality of the final results depends …

High-Throughput Next-Generation Sequencing Technologies Foster New Cutting-Edge Computing Techniques In Bioinformatics, Mary Qu Yang, Brian D. Athey, Hamid R. Arabnia, Andrew H. Sung, Qingzhong Liu, Jack Y. Yang, Jinghe Mao, Youping Deng

Faculty Publications

The advent of high-throughput next generation sequencing technologies have fostered enormous potential applications of supercomputing techniques in genome sequencing, epi-genetics, metagenomics, personalized medicine, discovery of non-coding RNAs and protein-binding sites. To this end, the 2008 International Conference on Bioinformatics and Computational Biology (Biocomp) - 2008 World Congress on Computer Science, Computer Engineering and Applied Computing (Worldcomp) was designed to promote synergistic inter/multidisciplinary research and education in response to the current research trends and advances. The conference attracted more than two thousand scientists, medical doctors, engineers, professors and students gathered at Las Vegas, Nevada, USA during July 14-17 and received great …

An Ensemble Learning Approach To Reverse-Engineering Transcriptional Regulatory Networks From Time-Series Gene Expression Data, Jianhua Ruan, Youping Deng, Edward J. Perkins, Weixiong Zhang

Faculty Publications

Background

One of the most challenging tasks in the post-genomic era is to reconstruct the transcriptional regulatory networks. The goal is to reveal, for each gene that responds to a certain biological event, which transcription factors affect its expression, and how a set of transcription factors coordinate to accomplish temporal and spatial specific regulations.

Results

Here we propose a supervised machine learning approach to address these questions. We focus our study on the gene transcriptional regulation of the cell cycle in the budding yeast, thanks to the large amount of data available and relatively well-understood biology, although the main ideas …

Satellite-Detected Fluorescence Reveals Global Physiology Of Ocean Phytoplankton, Michael J. Behrenfeld, T.K. Westberry, Emmanuel Boss, R.T. O'Malley, D.A. Siegel, Jerry D. Wiggert, B.A. Franz, G.C. Feldman, S.C. Doney, J.K. Moore, G. Dall'olmo, A.J. Milligan, I. Lima, N. Mahowald

Faculty Publications

Phytoplankton photosynthesis links global ocean biology and climate-driven fluctuations in the physical environment. These interactions are largely expressed through changes in phytoplankton physiology, but physiological status has proven extremely challenging to characterize globally. Phytoplankton fluorescence does provide a rich source of physiological information long exploited in laboratory and field studies, and is now observed from space. Here we evaluate the physiological underpinnings of global variations in satellite-based phytoplankton chlorophyll fluorescence. The three dominant factors influencing fluorescence distributions are chlorophyll concentration, pigment packaging effects on light absorption, and light-dependent energy-quenching processes. After accounting for these three factors, resultant global distributions of …