Life Sciences Commons^™

Transcriptomic Profiles Of Peripheral White Blood Cells In Type Ii Diabetes And Racial Differences In Expression Profiles, Jinghe Mao, Junmei Ai, Xinchun Zhou, Ming Shenwu, Manuel Ong Jr., Marketta Blue, Jasmine T. Washington, Xiaonan Wang, Youping Deng

Faculty Publications

Background: Along with obesity, physical inactivity, and family history of metabolic disorders, African American ethnicity is a risk factor for type 2 diabetes (T2D) in the United States. However, little is known about the differences in gene expression and transcriptomic profiles of blood in T2D between African Americans (AA) and Caucasians (CAU), and microarray analysis of peripheral white blood cells (WBCs) from these two ethnic groups will facilitate our understanding of the underlying molecular mechanism in T2D and identify genetic biomarkers responsible for the disparities.

Results: A whole human genome oligomicroarray of peripheral WBCs was performed on 144 …

State Space Model With Hidden Variables For Reconstruction Of Gene Regulatory Networks, Xi Wu, Peng Li, Nan Wang, Ping Gong, Edward J. Perkins, Youping Deng, Chaoyang Zhang

Faculty Publications

Background: State Space Model (SSM) is a relatively new approach to inferring gene regulatory networks. It requires less computational time than Dynamic Bayesian Networks (DBN). There are two types of variables in the linear SSM, observed variables and hidden variables. SSM uses an iterative method, namely Expectation-Maximization, to infer regulatory relationships from microarray datasets. The hidden variables cannot be directly observed from experiments. How to determine the number of hidden variables has a significant impact on the accuracy of network inference. In this study, we used SSM to infer Gene regulatory networks (GRNs) from synthetic time series datasets, investigated …

A Deep Insight Into The Sialotranscriptome Of The Gulf Coast Tick, Amblyomma Maculatum, Shahid Karim, Parul Singh, José M.C. Ribeiro

Faculty Publications

Background

Saliva of blood sucking arthropods contains compounds that antagonize their hosts' hemostasis, which include platelet aggregation, vasoconstriction and blood clotting; saliva of these organisms also has anti-inflammatory and immunomodullatory properties. Perhaps because hosts mount an active immune response against these compounds, the diversity of these compounds is large even among related blood sucking species. Because of these properties, saliva helps blood feeding as well as help the establishment of pathogens that can be transmitted during blood feeding.

Methodology/Principal Findings

We have obtained 1,626,969 reads by pyrosequencing a salivary gland cDNA library from adult females Amblyomma maculatum ticks at different …

Functional Dissection Of The Glucose Signaling Pathways That Regulate The Yeast Glucose Transporter Gene (Hxt) Repressor Rgt1, David J. Jouandot Ii, Adhiraj Roy, Jeong-Ho Kim

Faculty Publications

The yeast Rgt1 repressor is a bifunctional protein that acts as a transcriptional repressor and activator. Under glucose-limited conditions, Rgt1 induces transcriptional repression by forming a repressive complex with its corepressors Mth1 and Std1. Here, we show that Rgt1 is converted from a transcriptional repressor into an activator under high glucose conditions and this occurs through two independent but consecutive events mediated by two glucose signaling pathways: (1) disruption of the repressive complex by the Rgt2/Snf3 pathway; (2) phosphorylation of Rgt1 by the cAMP-dependent protein kinase (cAMP-PKA) pathway. Rgt1 is phosphorylated by PKA at four serine residues within its amino-terminal …

The Nuclear Pore Complex Mediates Binding Of The Mig1 Repressor To Target Promoters, Nayan J. Sarma, Thomas D. Buford, Terry Haley, Kellie Barbara-Haley, George M. Santangelo, Kristine A. Willis

Faculty Publications

All eukaryotic cells alter their transcriptional program in response to the sugar glucose. In Saccharomyces cerevisiae, the best-studied downstream effector of this response is the glucose-regulated repressor Mig1. We show here that nuclear pore complexes also contribute to glucose-regulated gene expression. NPCs participate in glucose-responsive repression by physically interacting with Mig1 and mediating its function independently of nucleocytoplasmic transport. Surprisingly, despite its abundant presence in the nucleus of glucose-grown nup120Δ or nup133Δ cells, Mig1 has lost its ability to interact with target promoters. The glucose repression defect in the absence of these nuclear pore components therefore appears …

The Rice Miniature Inverted Repeat Transposable Element Mping Is An Effective Insertional Mutagen In Soybean, C. Nathan Hancock, Feng Zhang, Kristen Floyd, Aaron O. Richardson, Peter Lafayette, Donna Tucker, Susan R. Wessler, Wayne A. Parrott

Faculty Publications

Insertional mutagenesis of legume genomes such as soybean (Glycine max) should aid in identifying genes responsible for key traits such as nitrogen fixation and seed quality. The relatively low throughput of soybean transformation necessitates the use of a transposon-tagging strategy where a single transformation event will produce many mutations over a number of generations. However, existing transposon-tagging tools being used in legumes are of limited utility because of restricted transposition (Ac/Ds: soybean) or the requirement for tissue culture activation (Tnt1: Medicago truncatula). A recently discovered transposable element from rice (Oryza …

Real-Time Feedback As A Method Of Monitoring Walking Velocity During Gait Analysis, Sarah T. Ridge, James G. Richards

Faculty Publications

When quantifying the mechanics of gait, it is important to ensure that subjects maintain a consistent walking velocity during gait analysis trials. Most methods of measuring walking velocity do not produce data until after the subject has completed the trial. This often results in discarding completed trials from analysis because the subject's velocity was not within an acceptable range. Real-time feedback of position data can be used to help subjects adjust their walking velocity during the trial, when necessary. Results from 14 subjects who participated in gait analysis using real-time feedback to monitor their walking velocity show that they were …

Refnetbuilder: A Platform For Construction Of Integrated Reference Gene Regulatory Networks From Expressed Sequence Tags, Ying Li, Ping Gong, Edward J. Perkins, Chaoyang Zhang, Nan Wang

Faculty Publications

Background: Gene Regulatory Networks (GRNs) provide integrated views of gene interactions that control biological processes. Many public databases contain biological interactions extracted from experimentally validated literature reports, but most furnish only information for a few genetic model organisms. In order to provide a bioinformatic tool for researchers who work with non-model organisms, we developed RefNetBuilder, a new platform that allows construction of putative reference pathways or GRNs from expressed sequence tags (ESTs).

Results: RefNetBuilder was designed to have the flexibility to extract and archive pathway or GRN information from public databases such as the Kyoto Encyclopedia of Genes …

Snapping A Pour Point For Watershed Delineation In Arcgis Hydrologic Analysis, Yanli Zhang, Matthew W. Mcbroom, Jason Grogan, I-Kuai Hung

Faculty Publications

No abstract provided.

Socially Induced Ovulation Synchrony And Its Effect On Seabird Population Dynamics, Shandelle M. Henson, J. M. Cushing, James L. Hayward

Faculty Publications

Spontaneous oscillator synchrony is a form of self-organization in which populations of interacting oscillators ultimately cycle together. This phenomenon occurs in a wide range of physical and biological systems. In rats and humans, oestrous/menstrual cycles synchronize through social stimulation with pheromones acting as synchronizing signals. In previous work, we showed that glaucous-winged gulls (Larus glaucescens) can lay eggs synchronously on an every-other-day schedule, and that synchrony increases with colony density. We posed a discrete-time mathematical model for reproduction during the breeding season based on the hypothesis that pre-ovulatory luteinizing hormone surges synchronize by means of visual, auditory and/or olfactory cues. …

Bioactive Properties And Clinical Safety Of A Novel Milk Protein Peptide, Richard B. Kreider, Mike Iosia, Matt Cooke, Geoffrey M. Hudson, Chris Rasmussen, Helen Chen, Olof Mollstedt, Men-Hwei Tsai

Faculty Publications

Background: Milk protein fractions and peptides have been shown to have bioactive properties. This preliminary study examined the potential mechanisms of action and clinical safety of novel milk protein peptide ( MP).

Findings: A novel MP mixture inhibits the tyrosine kinase activity of epidermal growth factor receptor ( EGFR), vascular endothelial growth factor receptor 2 (VEGFR2), and insulin receptor (IR) with IC(50) of 9.85 mu M, 7.7 mu M, and 6.18 mu M respectively. In vitro, this multi-kinase inhibitor causes apoptosis in HT-29 colon cancer cells, and in a C. elegans worm study, showed a weak but significant …

Human Pathogen Shown To Cause Disease In The Threatened Elkhorn Coral Acropora Palmata, Kathryn Patterson Sutherland, Sameera Shaban, Jessica L. Joyner, James W. Porter, Erin K. Lipp

Faculty Publications

Coral reefs are in severe decline. Infections by the human pathogen Serratia marcescens have contributed to precipitous losses in the common Caribbean elkhorn coral, Acropora palmata, culminating in its listing under the United States Endangered Species Act. During a 2003 outbreak of this coral disease, called acroporid serratiosis (APS), a unique strain of the pathogen, Serratia marcescens strain PDR60, was identified from diseased A. palmata, human wastewater, the non-host coral Siderastrea siderea and the corallivorous snail Coralliophila abbreviata. In order to examine humans as a source and other marine invertebrates as vectors and/or reservoirs of the APS pathogen, challenge experiments …

Alterations In The Transciptome And Antibiotic Susceptibility Of Staphylococcus Aureus Grown In The Presence Of Diclofenac, James T. Riordan, Joanne M. Dupre, Stephanie A. Cantore-Matyi, Atul Kumar-Singh, Yang Song, Shahrear Zaman, Sonia Horan, Nada S. Helal, Vijayaraj Nagarajan, Mohamed O. Elasri, Brian J. Wilkinson, John E. Gustafson

Faculty Publications

Background

Diclofenac is a non-steroidal anti-inflammatory drug (NSAID) which has been shown to increase the susceptibility of various bacteria to antimicrobials and demonstrated to have broad antimicrobial activity. This study describes transcriptome alterations in S. aureus strain COL grown with diclofenac and characterizes the effects of this NSAID on antibiotic susceptibility in laboratory, clinical and diclofenac reduced-susceptibility (Dc^RS) S. aureus strains.

Methods

Transcriptional alterations in response to growth with diclofenac were measured using S. aureus gene expression microarrays and quantitative real-time PCR. Antimicrobial susceptibility was determined by agar diffusion MICs and gradient plate analysis. Ciprofloxacin accumulation was measured …

A Landscape-Scale Approach For Modeling Habitat Suitability For The Louisiana Black Bear (Ursus Americanus Luteolus) In East Texas, Dan J. Kaminski, Christopher E. Comer

Faculty Publications

No abstract provided.

Emotional Climate, Feeding Practices, And Feeding Styles: An Observational Analysis Of The Dinner Meal In Head Start Families, Sheryl O Hughes, Thomas G Power, Maria A Papaioannou, Matthew B Cross, Theresa A Nicklas, Sharon K Hall, Richard M Shewchuk

Faculty Publications

BACKGROUND: A number of studies conducted with ethnically diverse, low-income samples have found that parents with indulgent feeding styles had children with a higher weight status. Indulgent parents are those who are responsive to their child's emotional states but have problems setting appropriate boundaries with their child. Because the processes through which styles impact child weight are poorly understood, the aim of this study was to observe differences in the emotional climate created by parents (including affect, tone of voice, and gestures) and behavioral feeding practices among those reporting different feeding styles on the Caregiver's Feeding Styles Questionnaire. A secondary …

Bobcats Do Not Exhibit Rub Response Despite Presence At Hair Collection Stations, Chirstopher E. Comer, Symmank M. E., James C. Kroll

Faculty Publications

We evaluated the detection rate for hair snare sampling for bobcats (Lynx rufus) using colocated hair snares and infrared-triggered cameras at 20 locations on private property in eastern Texas. Hair snares and cameras were placed together at survey stations that included both visual and olfactory attractants. In 1,680 trap-nights we photographically documented 15 visits by bobcats but collected only one bobcat hair sample. Our observations suggested limited rubbing behavior by bobcats at hair snares despite presence at hair collection stations. The explanation for this behavior remains unclear but is consistent with observations of low and variable hair trap …

Aintegumenta And Aintegumenta-Like6 Regulate Auxin-Mediated Flower Development In Arabidopsis, Beth A. Krizek

Faculty Publications

Background: Two related genes encoding AP2/ERF-type transcription factors, AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6 (AIL6), are important regulators of floral growth and patterning in Arabidopsis. Evidence suggests that these genes promote several aspects of flower development in response to auxin. To investigate the interplay of ANT, AIL6 and auxin during floral development, I have examined the phenotypic consequences of disrupting polar auxin transport in ant, ail6 and ant ail6 mutants by either genetic or chemical means.

Results: Plants containing mutations in ANT or AIL6 alone or in both genes together exhibit increased sensitivity to disruptions in polar auxin transport. …

Cooperative Red-Cockaded Woodpecker Translocation Strategy Throughout The Southeast, Robert J. Warren, C. Joseph Nairn

Faculty Publications

No abstract provided.

Homoplastic Microinversions And The Avian Tree Of Life, E. L. Braun, R T. Kimball, K. L. Han, N. R. Luhasz-Velez, A. J. Bonilla, Jena L. Chojnowski, J. V. Smith, R. C. Bowie, M. J. Braun, S. J. Hackett, J. Harshman, C. J. Huddleston, B. D. Marks, W. S. Moore, S. Reddy, F. H. Sheldon, C. C. Witt, T. Yuri

Faculty Publications

BACKGROUND:

Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution.

RESULTS:

We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate …

Simulated Reductions In Consumption Of Sugar-Sweetened Beverages Improves Diet Quality In Lower Mississippi Delta Adults, Jessica L. Thomson, Lisa M. Tussing-Humphreys, Stephen J. Onufrak, Carol Connell, Jamie M. Zoellner, Margaret L. Bogle, Kathleen Yadrick

Faculty Publications

Background

Although the effects of replacing sugar-sweetened beverages (SSBs) with water on energy intake and body weight have been reported, little is known about how these replacements affect diet quality.

Objective

To simulate the effects of replacing SSBs with tap water on diet quality and total energy intake of Lower Mississippi Delta (LMD) adults.

Design

Retrospective analysis of cross-sectional dietary intake data using a representative sample of LMD adults (n=1,689). Diet quality was measured using the Healthy Eating Index-2005 (HEI-2005) scores that were computed using the population ratio method. The effects of substituting SSBs with water on diet …

Point-Of-Purchase Nutrition Information Influences Food-Purchasing Behaviors Of College Students: A Pilot Study, Marjorie Freedman, Rachel Conners

Faculty Publications

The goal of point-of-purchase (POP) nutrition information is to help consumers make informed, healthful choices. Despite limited evaluation, these population-based approaches are being advocated to replace traditional, more expensive, individual behavior-change strategies. Few studies have examined the effect of POP information on buying patterns of college students, a group with high obesity rates and poor eating habits. This quasi-experimental pilot project sought to determine whether the “Eat Smart” POP program affected food-purchasing habits of multiethnic college students shopping at an on-campus convenience store. Baseline sales data of foods in the cereal, soup, cracker, and bread categories were collected for 6 …

Redesigning Introductory Biology: A Proposal, Eileen Gregory, Craig Lending, Amanda N. Orenstein, Jane P. Ellis

Faculty Publications

With the increasing complexity and expansion of the biological sciences, there has been a corresponding increase in content in the first-year introductory biology course sequence for majors. In general this has resulted in courses that introduce students to large amounts of material and leave little time for practicing investigative science or skill development. Based on our analysis of data compiled from 742 biology faculty at a variety of institutions across the United States, we verified that there is strong agreement on the content appropriate for introductory biology courses for majors. Therefore, we propose that faculty teaching these courses focus primarily …

A Current Bibliographic Resource For The Red-Cockaded Woodpecker, Federal Wildlife Service

Faculty Publications

No abstract provided.

A ‘Driving Force’ In Developing The Nation’S Forests: The Mcintire-Stennis Cooperative Forestry Research Program., Steven H. Bullard, Perry J. Brown, Catalino A. Blanche, Richard W. Binker, Don H. Thompson

Faculty Publications

The McIntire-Stennis (M-S) Cooperative Forestry Research Program has provided fundamental support for creating and strengthening forestry research and graduate training efforts at colleges and universities across the nation for nearly 50 years. M-S funding has helped produce thousands of forestry scientists and other research professionals, and M-S–supported research has provided critical basic understanding and applied solutions to extend the benefits that flow from forests and related rangelands across the nation over time. The 1962 legislation that created the M-S program authorized funding of up to one-half of the funds appropriated for federal forestry research conducted directly by the USDA. Throughout …

White Potatoes, Including French Fries, Contribute Shortfall Nutrients To Children's And Adolescents' Diets, Marjorie Freedman, Debra Keast

Faculty Publications

To test the hypothesis that white potatoes (WP), oven-baked fries (OBF), and french fries (FF) contribute important nutrients within energy needs to children's and adolescents' diets, secondary analysis of 24-hour dietary recall data from the National Health and Nutrition Examination Survey 2003-2006 was conducted. Potato content of survey foods was determined using US Department of Agriculture recipe databases (Standard Reference (SR)-Link files). Nutrient content of potatoes was determined by linking SR codes to US Department of Agriculture food composition data. Daily nutrient intakes from potatoes were determined by applying the composition database to respondent's recall data. Sample-weighted data were analyzed; …

The Proteogenomic Mapping Tool, William S. Sanders, Nan Wang, Susan M. Bridges, Brandon M. Malone, Yoginder S. Dandass, Fiona M. Mccarthy, Bindu Nanduri, Mark L. Lawrence, Shane C. Burgess

Faculty Publications

Background: High-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the high speed of experimental data generation and to aid in structural genome annotation, experimentally observed peptides need to be mapped back to their source genome location quickly and exactly. Previously, the tools to do this have been limited to custom scripts designed by individual research groups to analyze their own data, are generally not widely available, and do not scale well with large eukaryotic genomes.

Results: The Proteogenomic Mapping Tool includes a Java implementation of …

Morphological Convergence During Pregnancy Among Predator And Nonpredator Populations Of The Livebearing Fish Brachyrhaphis Rhabdophora (Teleostei: Poeciliidae), Jeff S. Wesner, Eric J. Billman, Adam Meier, Mark C. Belk

Faculty Publications

Predation can drive morphological divergence in prey populations, although examples of divergent selection are typically limited to nonreproductive individuals. In livebearing females, shape often changes drastically during pregnancy, reducing speed and mobility and enhancing susceptibility to predation. In the present study, we document morphological divergence among populations of nonreproductive female livebearing fish (Brachyrhaphis rhabdophora) in predator and nonpredator environments. We then test the hypothesis that shape differences among nonreproductive females are maintained among reproductive females between predator and nonpredator environments. Nonreproductive females in predator environments had larger caudal regions and more fusiform bodies than females in nonpredator environments; …

Homocysteine And Cardiac Neural Crest Cell Cytoskeletal Proteins In The Chick Embryo, Anthony R. Mwakikunga, Amanda L. Clubine, Darrell J. Wiens

Faculty Publications

Elevated serum homocysteine (Hcys) is correlated with cardiovascular disease and with embryonic malformations related to neural crest cells (NCCs). We predicted Hcys may alter the balance of actin networks, stress fibers and focal adhesions, altering migration. We cultured neural tube explants in control and Hcys-treated medium and visualized actin, α-actinin, vinculin, filamin, and LIM3 protein in NCCs migrating outward. In Hcys, phalloidin-stained actin in stress fibers was brighter, and vinculin was more abundant in focal adhesions and lamellipodia. α-actinin and LIM3 were also enhanced around nuclei and in focal adhesions, and α-actinin also in filopodia. Filamin was unchanged. Hcys caused …

Electrospinning Fabrication, Structural And Mechanical Characterization Of Rod-Like Virus-Based Composite Nanofibers, Laying Wu, Jianfeng Zang, L. Andrew Lee, Zhongwei Niu, Gary C. Horvatha, Vaughn Braxtona, Arief C. Wibowo, Michael A. Bruckman, Soumitra Ghoshroy, Hans-Conrad Zur Loye, Xiaodong Li, Qian Wang

Faculty Publications

Tobacco mosaic virus (TMV) was electrospun with polyvinyl alcohol (PVA) into continuous TMV–PVA composite nanofibers to form a biodegradable nonwoven fibrous mat as an extracellular matrix (ECM) mimetic. Morphological characterizations by electron microscopyshowed that the addition of varying amounts of TMV resulted in homogeneous nanofibers without phase separation and did not change the diameter of the composite nanofibers. The orientation of TMV in as-spun fibers could be readily controlled and post-processing of the nonwoven TMV–PVA mat significantly improved its water resistance. In addition, tensile tests were performed on individual nanofibers, which revealed that the TMV–PVA composite nanofibers achieved a comparable …

Across Bacterial Phyla, Distantly-Related Genomes With Similar Genomic Gc Content Have Similar Patterns Of Amino Acid Usage, John Lightfield, Noah R. Fram, Bert Ely

Faculty Publications

The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. …