Digital Commons Network^™

Response And Transcriptional Regulation Of Rice Sumoylation System During Development And Stress Conditions, Vijay Chaikam

Faculty & Staff Scholarship

Modification of proteins by the reversible covalent addition of the small ubiquitin like modifier (SUMO) protein has important consequences affecting target protein stability, sub-cellular localization, and protein-protein interactions. SUMOylation involves a cascade of enzymatic reactions, which resembles the process of ubiquitination. In this study, we characterized the SUMOylation system from an important crop plant, rice, and show that it responds to cold, salt and ABA stress conditions on a protein level via the accumulation of SUMOylated proteins. We also characterized the transcriptional regulation of individual SUMOylation cascade components during stress and development. During stress conditions, majority of the SUMO cascade …

Hybrid Models Identified A 12-Gene Signature For Lung Cancer Prognosis And Chemoresponse Prediction, Ying-Wooi Wan, Ebrahim Sabbagh, Rebecca Raese, Yong Qian, Dajie Luo, James Denvir, Val Vallyathan, Vincent Castranova

Faculty & Staff Scholarship

Background

Lung cancer remains the leading cause of cancer-related deaths worldwide. The recurrence rate ranges from 35–50% among early stage non-small cell lung cancer patients. To date, there is no fully-validated and clinically applied prognostic gene signature for personalized treatment.

Methodology/Principal Findings

From genome-wide mRNA expression profiles generated on 256 lung adenocarcinoma patients, a 12-gene signature was identified using combinatorial gene selection methods, and a risk score algorithm was developed with Naïve Bayes. The 12-gene model generates significant patient stratification in the training cohort HLM & UM (n = 256; log-rank P = 6.96e-7) and two independent validation sets, MSK …

From 'Omics' To Complex Disease: A Systems Biology Approach To Gene-Environment Interactions In Cancer, Sarah S. Knox

Faculty & Staff Scholarship

Background

Cancer is a complex disease that involves a sequence of gene-environment interactions in a progressive process that cannot occur without dysfunction in multiple systems, including DNA repair, apoptotic and immune functions. Epigenetic mechanisms, responding to numerous internal and external cues in a dynamic ongoing exchange, play a key role in mediating environmental influences on gene expression and tumor development.

Hypothesis

The hypothesis put forth in this paper addresses the limited success of treatment outcomes in clinical oncology. It states that improvement in treatment efficacy requires a new paradigm that focuses on reversing systemic dysfunction and tailoring treatments to specific …

Inferring Predominant Pathways In Cellular Models Of Breast Cancer Using Limited Sample Proteomic Profiling, Yogesh M. Kulkarin, Vivian Suarez, David J. Klinke Ii

Faculty & Staff Scholarship

Background

Molecularly targeted drugs inhibit aberrant signaling within oncogenic pathways. Identifying the predominant pathways at work within a tumor is a key step towards tailoring therapies to the patient. Clinical samples pose significant challenges for proteomic profiling, an attractive approach for identifying predominant pathways. The objective of this study was to determine if information obtained from a limited sample (i.e., a single gel replicate) can provide insight into the predominant pathways in two well-characterized breast cancer models.

Methods

A comparative proteomic analysis of total cell lysates was obtained from two cellular models of breast cancer, BT474 (HER2+/ER+) and SKBR3 (HER2+/ER-), …

Nearest Neighbor Estimates Of Entropy For Multivariate Circular Distributions, Neeraj Misra, Harshinder Singh, Vladimir Hnizdo

Faculty & Staff Scholarship

In molecular sciences, the estimation of entropies of molecules is important for the understanding of many chemical and biological processes. Motivated by these applications, we consider the problem of estimating the entropies of circular random vectors and introduce non-parametric estimators based on circular distances between n sample points and their k th nearest neighbors (NN), where k (≤ n – 1) is a fixed positive integer. The proposed NN estimators are based on two different circular distances, and are proven to be asymptotically unbiased and consistent. The performance of one of the circular-distance estimators is investigated and compared with that …

A Polymorphic Variant Of Afap-110 Enhances Csrc Activity12, David A. Clump, Jing J. Yu, Youngjin Cho, Rui Gao, John Jett, Henry Zot, Jess M. Cunnick, Brandi Snyder, Anne C. Clump, Melissa Dodrill, Peter Gannett, James E. Caod, Robert Shurina, W Douglas Figg, Eddie Reed, Daniel C. Flynn

Faculty & Staff Scholarship

Enhanced expression and activity of cSrc are associated with ovarian cancer progression. Generally, cSrc does not contain acti- vating mutations; rather, its activity is increased in response to signals that affect a conformational change that releases its auto- inhibition. In this report, we analyzed ovarian cancer tissues for the expression of a cSrc-activating protein, AFAP-110. AFAP-110 activates cSrc through a direct interaction that releases it from its autoinhibited conformation. Immunohistochemical analysis re- vealed a concomitant increase of AFAP-110 and cSrc in ovarian cancer tissues. An analysis of the AFAP-110 coding sequence revealed the presence of a nonsynonymous, single-nucleotide polymorphism that …

Distribution And Persistence Of Pleural Penetrations By Multi-Walled Carbon Nanotubes, Robert R. Mercer, Ann F. Hubbs, James F. Scabilloni, Liying Wang, Lori A. Battelli, Diane Schwegler-Berry, Vincent Castranova, Dale W. Porter

Faculty & Staff Scholarship

Background

Multi-walled carbon nanotubes (MWCNT) are new manufactured nanomaterials with a wide spectrum of commercial applications. The durability and fiber-like dimensions (mean length 3.9 μm long × 49 nm diameter) of MWCNT suggest that these fibers may migrate to and have toxicity within the pleural region. To address whether the pleura received a significant and persistent exposure, C57BL/6J mice were exposed by pharyngeal aspiration to 10, 20, 40 and 80 μg MWCNT or vehicle and the distribution of MWCNT penetrations determined at 1, 7, 28 and 56 days after exposure. Following lung fixation and sectioning, morphometric methods were used to …

Self-Reported Dental Hygiene, Obesity, And Systemic Inflammation In A Pediatric Rural Community Cohort, Stephanie J. Frisbee, Christopher B. Chambers, Jefferson C. Frisbee, Adam G. Goodwill, Richard J. Crout

Faculty & Staff Scholarship

Background

A growing body of epidemiologic evidence links oral health, obesity, and cardiovascular health, though few studies have reported on these relationships in children. While underlying mechanisms are unclear, adult studies have suggested sub-acute systemic inflammation, also implicated in the etiology of both obesity and cardiovascular disease. This study investigated associations between self-reported dental hygiene, obesity, and systemic inflammation in children.

Methods

128 children < 19 years of age from rural counties in West Virginia participated in a community-based health screening that included anthropometric assessments, blood collection, and a questionnaire about dental hygiene and self-assessed oral health.

Results

Participants ranged from 3.0-18.7 years. Univariate analysis demonstrated an association between parent-reported dental hygiene, including frequency of preventive dental care and parent-assessed overall dental health, and markers of systemic inflammation but not obesity. In multivariable …

Skeletal Muscle Gene Expression In Response To Resistance Exercise: Sex Specific Regulation, Dongmei Liu, Maureen A. Sartor, Gustavo A. Nader, Laurie Gutmann, Mary K. Treutelaar, Emidio E. Pistilli, Heidi B. Iglayreger, Charles F. Burant, Eric P. Hoffman, Paul M. Gordon

Faculty & Staff Scholarship

Background

The molecular mechanisms underlying the sex differences in human muscle morphology and function remain to be elucidated. The sex differences in the skeletal muscle transcriptome in both the resting state and following anabolic stimuli, such as resistance exercise (RE), might provide insight to the contributors of sexual dimorphism of muscle phenotypes. We used microarrays to profile the transcriptome of the biceps brachii of young men and women who underwent an acute unilateral RE session following 12 weeks of progressive training. Bilateral muscle biopsies were obtained either at an early (4 h post-exercise) or late recovery (24 h post-exercise) time …

Dispersion Of Single-Walled Carbon Nanotubes By A Natural Lung Surfactant For Pulmonary In Vitro And In Vivo Toxicity Studies, Liying Wang, Vincent Castranova, Anurag Mishra, Bean Chen, Robert R. Mercer, Diane Schwegler-Berry, Yon Rojanasakul

Faculty & Staff Scholarship

Background

Accumulating evidence indicate that the degree of dispersion of nanoparticles has a strong influence on their biological activities. The aims of this study were to develop a simple and rapid method of nanoparticle dispersion using a natural lung surfactant and to evaluate the effect of dispersion status of SWCNT on cytotoxicity and fibrogenicity in vitro and in vivo.

Results

The natural lung surfactant Survanta® was used to disperse single-walled carbon nanotubes (SWCNT) in a biological medium. At physiologically relevant concentrations, Survanta®produced well dispersed SWCNT without causing a cytotoxic or fibrogenic effect. In vitrostudies show that Survanta®-dispersed SWCNT …

Agt M235t Genotype/Anxiety Interaction And Gender In The Hypergen Study, Sarah S. Knox, Xinxin Guo, Yuqing Zhang, G Weidner, Scott Williams, R Curtis Ellison

Faculty & Staff Scholarship

Background

Both anxiety and elevated heart rate (HR) have been implicated in the development of hypertension. The HyperGen cohort, consisting of siblings with severe and mild hypertension, an age-matched random sample of persons from the same base populations, and unmedicated adult offspring of the hypertensive siblings (N = 1,002 men and 987 women), was analyzed for an association of the angiotenisinogen AGTM235T genotype (TT, MT, MM) with an endophenotype, heart rate (HR) in high and low anxious groups.

Methodology

The interaction of AGTM genotype with anxiety, which has been independently associated with hypertension, was investigated adjusting for age, hypertension status, …

The Ww-Hect Protein Smurf2 Interacts With The Docking Protein Nedd9/Hef1 For Aurora A Activation, Finola E. Moore, Evan C. Osmundson, Jennifer Koblinski, Elena Pugacheva, Erica A. Golemis, Sipankar Ray, Hiroaki Kiyokawa

Faculty & Staff Scholarship

The multi-functional adaptor protein NEDD9/HEF1/Cas-L regulates cell motility, invasion and cell cycle progression, and plays key roles in cancer progression and metastasis. NEDD9 is localized to the centrosome and is required for activation of Aurora A kinase in mitosis. Here we demonstrate that the HECT-WW protein Smurf2 physically associ- ates with NEDD9 and is required for the stability of NEDD9 protein. Smurf2 depletion results in a marked decrease in NEDD9 protein levels, by facilitating polyubiquitination and proteasomal degradation of NEDD9. Conversely, forced overexpression of Smurf2 results in upregulation of endogenous NEDD9 protein, confirming the role for Smurf2 in NEDD9 stability. …

Differential Splicing Of The Apoptosis-Associated Speck Like Protein Containing A Caspase Recruitment Domain (Asc) Regulates Inflammasomes, Nicole B. Bryan, Andrea Dorfleutner, Sara J. Kramer, Chawon Yun, Yon Rojanasakul, Christian Stehlik

Faculty & Staff Scholarship

Background

The apoptotic speck-like protein containing a caspase recruitment domain (ASC) is the essential adaptor protein for caspase 1 mediated interleukin (IL)-1β and IL-18 processing in inflammasomes. It bridges activated Nod like receptors (NLRs), which are a family of cytosolic pattern recognition receptors of the innate immune system, with caspase 1, resulting in caspase 1 activation and subsequent processing of caspase 1 substrates. Hence, macrophages from ASC deficient mice are impaired in their ability to produce bioactive IL-1β. Furthermore, we recently showed that ASC translocates from the nucleus to the cytosol in response to inflammatory stimulation in order to promote …

Association Of Perfluorooctanoic Acid (Pfoa) And Perfluorooctane Sulfonate (Pfos) With Uric Acid Among Adults With Elevated Community Exposure To Pfoa, Kyle Steenland, Sarah Tinker, Anoop Shankar, Alan Ducatman

Faculty & Staff Scholarship

Background

Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) are compounds that do not occur in nature, have been widely used since World War II, and persist indefinitely in most environments. Median serum levels in the United States are 4 ng/mL for PFOA and 21 ng/mL for PFOS. PFOA has been associated with elevated uric acid in two studies of chemical workers. Uric acid is a risk factor for hypertension and possibly other cardiovascular outcomes.

Methods

We conducted a cross-sectional study of PFOA and PFOS and uric acid among 54,951 adult community residents in Ohio and West Virginia, who lived or …

Piggybac-Ing On A Primate Genome: Novel Elements, Recent Activity And Horizontal Transfer, Heidi J T Pagan, Jeremy D. Smith, Robert M. Hubley, David A. Ray

Faculty & Staff Scholarship

To better understand the extent of Class II transposable element activity in mammals, we investigated the mouse lemur, Microcebus murinus, whole genome shotgun (2X) draft assembly. Analysis of this strepsirrhine primate extended previous research that targeted anthropoid primates and found no activity within the last 37 Myr. We tested the hypothesis that members of the piggyBac Class II superfamily have been inactive in the strepsirrhine lineage of primates during the same period. Evidence against this hypothesis was discovered in the form of three nonautonomous piggyBac elements with activity periods within the past 40 Myr and possibly into the very recent …

Odors Pulsed At Wing Beat Frequencies Are Tracked By Primary Olfactory Networks And Enhance Odor Detection, Shreejoy J. Tripathy, Oakland J. Peters, Erich M. Staudacher, Faizan R. Kalwar, Mandy N. Hatfield, Kevin C. Daly

Faculty & Staff Scholarship

Each down stroke of an insect’s wings accelerates axial airflow over the antennae. Modeling studies suggest that this can greatly enhance penetration of air and air-born odorants through the antennal sensilla thereby periodically increasing odorant-receptor interactions. Do these periodic changes result in entrainment of neural responses in the antenna and antennal lobe (AL)? Does this entrainment affect olfactory acuity? To address these questions, we monitored antennal and AL responses in the moth Manduca sexta while odorants were pulsed at frequencies from 10–72 Hz, encompassing the natural wingbeat frequency. Power spectral density (PSD) analysis was used to identify entrainment of neural …

Modeling The Aneuploidy Control Of Cancer, Yao Li, Arthur Berg, Louie R. Wu, Zhong Wang, Gang Chen, Rongling Wu

Faculty & Staff Scholarship

Background

Aneuploidy has long been recognized to be associated with cancer. A growing body of evidence suggests that tumorigenesis, the formation of new tumors, can be attributed to some extent to errors occurring at the mitotic checkpoint, a major cell cycle control mechanism that acts to prevent chromosome missegregation. However, so far no statistical model has been available quantify the role aneuploidy plays in determining cancer.

Methods

We develop a statistical model for testing the association between aneuploidy loci and cancer risk in a genome-wide association study. The model incorporates quantitative genetic principles into a mixture-model framework in which various …

A Model For Transgenerational Imprinting Variation In Complex Traits, Chenguang Wang, Zhong Wang, Jiangtao Luo, Qin Li, Yao Li, Kwangmi Ahn, Daniel R. Prows, Rongling Wu

Faculty & Staff Scholarship

Despite the fact that genetic imprinting, i.e., differential expression of the same allele due to its different parental origins, plays a pivotal role in controlling complex traits or diseases, the origin, action and transmission mode of imprinted genes have still remained largely unexplored. We present a new strategy for studying these properties of genetic imprinting with a two-stage reciprocal F mating design, initiated with two contrasting inbred lines. This strategy maps quantitative trait loci that are imprinted (i.e., iQTLs) based on their segregation and transmission across different generations. By incorporating the allelic configuration of an iQTL genotype into a mixture …

History Of The Harte Research Institute For Gulf Of Mexico Studies At Texas A&M University–Corpus Christi, John W. Tunnell Jr.

Gulf of Mexico Science

No abstract provided.

The Dauphin Island Sea Lab – A Tale Of Four Laboratories, George F. Crozier, Michael R. Dardeau

Gulf of Mexico Science

No abstract provided.

Profile Of The Gulf Ecology Division, United States Environmental Protection Agency, Stephen J. Jordan, Raymond G. Wilhour

Gulf of Mexico Science

No abstract provided.

Evolution Of The Florida State University Coastal And Marine Laboratory, Michael J. Greenberg, William F. Herrnkind, Felicia C. Coleman

Gulf of Mexico Science

No abstract provided.

A History Of Florida's Fish And Wildlife Research Institute, Gil Mcrae

Gulf of Mexico Science

No abstract provided.

History Of The Southeast Fisheries Science Center Miami Laboratory, Alex Chester, Albert C. Jones

Gulf of Mexico Science

No abstract provided.

Utah Adaptive Resources Management Greater Sage-Grouse Local Working Groups 2009-2010 Accomplishment Report, Terry A. Messmer, T. Black, Shandra Nicole Frey, S. Lupis, R. Hart

Wildland Resources Faculty Publications

The Community-based Conservation Program (CBCP) encompasses the historical range of sagegrouse in Utah as identified in the 2002 (2009 revised) Strategic Management Plan for Sagegrouse (Figure 1). The plan, approved by the Utah Wildlife Board on 1 June 2002 (revised 2009), mandated the organization of local sage-grouse working groups (LWGs) to develop and implement sage-grouse conservation plans. The Utah Division of Wildlife Resources (UDWR) in cooperation with Utah State University Extension (USUEXT), private landowners, public and private natural resource, wildlife management, and conservation agencies and organizations have implemented the CBCP.

Empirical Bayes Analysis Of Sequencing-Based Transcriptional Profiling Without Replicates, Zhijin Wu, Bethany D. Jenkins, Tatiana A. Rynearson, Sonya T. Dyhrman, Mak A. Saito, Melissa Mercier, Leann P. Whitney

Cell and Molecular Biology Faculty Publications

Background:

Recent technological advancements have made high throughput sequencing an increasingly popular approach for transcriptome analysis. Advantages of sequencing-based transcriptional profiling over microarrays have been reported, including lower technical variability. However, advances in technology do not remove biological variation between replicates and this variation is often neglected in many analyses.

Results:

We propose an empirical Bayes method, titled Analysis of Sequence Counts (ASC), to detect differential expression based on sequencing technology. ASC borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available. Compared to current …

Algae And Biodiesel: Patenting Energized As Green Goes Commercial, Matthew R. Priess, Stanley P. Kowalski

Law Faculty Scholarship

In the twenty-first century, predominant dependence on fossil fuels as energy resources will not be sustainable. Developing and commercializing green energy innovations will be an essential component of the transition to a more diversified energy economy. Algal biodiesel is one of the most promising green fuels because of its potential as a renewable and sustainable fuel source without displacing food crops. Algal biodiesel research and development are necessary early steps towards a transition to a green energy economy. The strategic use of strong patent portfolios will drive this by attracting investment, incentivizing innovation and accelerating commercialization. Whereas algal biodiesel research …

Intellectual Property, Medicine And Health: Current Debates, Stanley P. Kowalski

Law Faculty Scholarship

Johanna Gibson’ s “Intellectual Property, Medicine and Health: Current Debates” is an ambitious attempt to bridge the gap between IPR (largely patents) and the ethical, moral and philosophical issues which should influence global access to innovations in health. This intent is noteworthy and timely, as the complexities are important to address and there is an urgent need for clear-headed strategy. However, disappointingly, the book largely fails, as it is a rambling polemic that lacks focus, clarity and originality. Wading through the thicket of verbiage becomes so daunting that whatever message might be present is lost. The book also is flawed …

Potential Energy, Edward Bull

Electronic Theses and Dissertations

Potential Energy. (Under the direction of Pat Rushin.) Potential Energy is a collection of sixteen short stories. They range from the fictional to the autofictional to the entirely non-fictional. In all of them, characters both real and imagined struggle to live and define themselves in a world that is outside their control. They cope with the inevitability of loss, dangers both internal and external, and the passing of their own greatness. Some of these characters become lost while others learn to embrace life on its own terms'to accept 'without hope or expectation.' More often, they are not lost or enlightened, …

Production Of Activated Carbon From Fermentation And Pyrolysis Residues, Dan Cheng

Theses

The objective of this study is to produce activated carbon from fermentation and pyrolysis residues. It was found that both fermentation and pyrolysis residues are highly appropriate as precursors for activated carbon production because of their high carbon content and low ash content. The effects of activation temperature, activation time and phosphoric acid concentration on the yield and quality of activated carbon were investigated. Increased activation temperature, activation time and acid concentration have similar effect of decreasing the yield of activated carbon. Increased activation temperature and activation time decreases the BET surface area and pore volume of activated carbon while …