Digital Commons Network^™

Pgrmc1: A New Biomarker For The Estrogen Receptor In Breast Cancer, Rolf J. Craven

Pharmacology and Nutritional Sciences Faculty Publications

Estrogen receptor (ER) status is a critical biomarker in breast cancer, in large part because the ER is the target of tamoxifen and similar drugs. In the previous issue of Breast Cancer Research, Neubauer and colleagues used a proteomic approach to identify proteins that are differentially regulated by ER in breast tumors. The authors showed that ER-negative tumors have elevated levels of PGRMC1 (progesterone receptor membrane component-1), a hormone receptor component and binding partner for P450 proteins. In contrast, PGRMC1 was phosphorylated in ER-positive tumors. The staining patterns of ER and PGRMC1 were mutually exclusive in breast tumor sections, and …

Differential Gene Expression Associated With Postnatal Equine Articular Cartilage Maturation, Michael J. Mienaltowski, Liping Huang, Arnold J. Stromberg, James N. Macleod

Veterinary Science Faculty Publications

BACKGROUND: Articular cartilage undergoes an important maturation process from neonate to adult that is reflected by alterations in matrix protein organization and increased heterogeneity of chondrocyte morphology. In the horse, these changes are influenced by exercise during the first five months of postnatal life. Transcriptional profiling was used to evaluate changes in articular chondrocyte gene expression during postnatal growth and development.

METHODS: Total RNA was isolated from the articular cartilage of neonatal (0-10 days) and adult (4-5 years) horses, subjected to one round of linear RNA amplification, and then applied to a 9,367-element equine-specific cDNA microarray. Comparisons were made with …

Crystallization And Structure Of A Plant Peptide Deformylase, Robert L. Houtz, David W. Rodgers, Lynnette M. A. Dirk, Mark A. Williams

Molecular and Cellular Biochemistry Faculty Patents

This invention relates to the crystal structure of a plant peptide deformylase polypeptide and methods of using the structure to design compounds that modulate the activity of the polypeptide.

Childhood Lymphohematopoietic Cancer Incidence And Hazardous Air Pollutants In Southeast Texas, 1995–2004, Kristina W. Whitworth, Elaine Symanski, Ann L. Coker

CRVAW Faculty Journal Articles

BACKGROUND: Cancer is the second leading cause of death among U.S. children with few known risk factors. There is increasing interest in the role of air pollutants, including benzene and 1,3-butadiene, in the etiology of childhood cancers.

OBJECTIVE: Our goal was to assess whether census tracts with the highest benzene or 1,3-butadiene ambient air levels have increased childhood lymphohematopoietic cancer incidence.

METHODS: Our ecologic analysis included 977 cases of childhood lymphohematopoietic cancer diagnosed from 1995–2004. We obtained the U.S. Environmental Protection Agency’s 1999 modeled estimates of benzene and 1,3-butadiene for 886 census tracts surrounding Houston, Texas. We ran Poisson regression …

Endoplasmic Reticulum Stress Markers Are Associated With Obesity In Nondiabetic Subjects, Neeraj K. Sharma, Swapan K. Das, Ashis K. Mondal, Oksana Hackney, Winston S. Chu, Philip A. Kern, Neda Rasouli, Horace J. Spencer, Aiwei Yao-Borengasser, Steven C. Elbein

Clinical and Translational Science Faculty Publications

Objective: Adipocyte and hepatocyte endoplasmic reticulum (ER) stress response is activated in dietary and genetic models of obesity in mice. We hypothesized that ER stress was also activated and associated with reduced insulin sensitivity (S_I) in human obesity.

Research Design and Methods: We recruited 78 healthy, nondiabetic individuals over a spectrum of body mass index (BMI) who underwent oral and iv glucose tolerance tests, and fasting sc adipose and muscle biopsies. We tested expression of 18 genes and levels of total and phosphorylated eukaryotic initiation factor 2α, c-jun, and c-Jun N-terminal kinase 1 in adipose tissue. We compared …

Technical Variables In High-Throughput Mirna Expression Profiling: Much Work Remains To Be Done, Peter T. Nelson, Wang-Xia Wang, Bernard R. Wilfred, Guiliang Tang

Pathology and Laboratory Medicine Faculty Publications

MicroRNA (miRNA) gene expression profiling has provided important insights into plant and animal biology. However, there has not been ample published work about pitfalls associated with technical parameters in miRNA gene expression profiling. One source of pertinent information about technical variables in gene expression profiling is the separate and more well-established literature regarding mRNA expression profiling. However, many aspects of miRNA biochemistry are unique. For example, the cellular processing and compartmentation of miRNAs, the differential stability of specific miRNAs, and aspects of global miRNA expression regulation require specific consideration. Additional possible sources of systematic bias in miRNA expression studies include …

Focus On Rna Isolation: Obtaining Rna For Microrna (Mirna) Expression Profiling Analyses Of Neural Tissue, Wang-Xia Wang, Bernard R. Wilfred, Donald A. Baldwin, R. Benjamin Isett, Na Ren, Arnold J. Stromberg, Peter T. Nelson

Sanders-Brown Center on Aging Faculty Publications

MicroRNAs (miRNAs) are present in all known plant and animal tissues and appear to be somewhat concentrated in the mammalian nervous system. Many different miRNA expression profiling platforms have been described. However, relatively little research has been published to establish the importance of 'upstream' variables in RNA isolation for neural miRNA expression profiling. We tested whether apparent changes in miRNA expression profiles may be associated with tissue processing, RNA isolation techniques, or different cell types in the sample. RNA isolation was performed on a single brain sample using eight different RNA isolation methods, and results were correlated using a conventional …

Sequiterpene Synthase Gene And Protein, Joe Chappell, Bryan T. Greenhagen

Pharmaceutical Sciences Faculty Patents

The invention relates to sesquiterpene synthases and methods for their production and use. Particularly, the invention provides nucleic acids comprising the nucleotide sequence of citrus valencene synthase (CVS) which codes for at least one CVS. The invention further provides nucleic acids comprising the nucleotide sequence coding for amino acid residues forming the tier 1 and tier 2 domains of CVS. The invention also provides for methods of making and using the nucleic acids and amino acids of the current invention.

Focal Cerebral Ischemia In The Tnfalpha-Transgenic Rat, L. Creed Pettigrew, Mark S. Kindy, Stephen W. Scheff, Joe E. Springer, Richard J. Kryscio, Yizhao Li, David S. Grass

Sanders-Brown Center on Aging Faculty Publications

BACKGROUND: To determine if chronic elevation of the inflammatory cytokine, tumor necrosis factor-alpha (TNFalpha), will affect infarct volume or cortical perfusion after focal cerebral ischemia.

METHODS: Transgenic (TNFalpha-Tg) rats overexpressing the murine TNFalpha gene in brain were prepared by injection of mouse DNA into rat oocytes. Brain levels of TNFalpha mRNA and protein were measured and compared between TNFalpha-Tg and non-transgenic (non-Tg) littermates. Mean infarct volume was calculated 24 hours or 7 days after one hour of reversible middle cerebral artery occlusion (MCAO). Cortical perfusion was monitored by laser-Doppler flowmetry (LDF) during MCAO. Cortical vascular density was quantified by stereology. …

High-Activity Mutants Of Butyrylcholinesterase For Cocaine Hydrolysis And Method Of Generating The Same, Chang-Guo Zhan, Hoon Cho, Hsin-Hsiung Tai

Pharmaceutical Sciences Faculty Patents

A novel computational method and generation of mutant butyrylcholinesterase for cocaine hydrolysis is provided. The method includes molecular modeling a possible BChE mutant and conducting molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations thereby providing a screening method of possible BChE mutants by predicting which mutant will lead to a more stable transition state for a rate determining step. Site-directed mutagenesis, protein expression, and protein activity is conducted for mutants determined computationally as being good candidates for possible BChE mutants, i.e., ones predicted to have higher catalytic efficiency as compared with wild-type BChE. In addition, mutants A199S/A328W/Y332G, A199S/F227A/A328W/Y332G, A199S/S287G/A328W/Y332G, …

Transcriptional Response Of Mexican Axolotls To Ambystoma Tigrinum Virus (Atv) Infection, Jennifer D. Cotter, Andrew Storfer, Robert B. Page, Christopher K. Beachy, S. Randal Voss

Biology Faculty Publications

BACKGROUND: Very little is known about the immunological responses of amphibians to pathogens that are causing global population declines. We used a custom microarray gene chip to characterize gene expression responses of axolotls (Ambystoma mexicanum) to an emerging viral pathogen, Ambystoma tigrinum virus (ATV).

RESULT: At 0, 24, 72, and 144 hours post-infection, spleen and lung samples were removed for estimation of host mRNA abundance and viral load. A total of 158 up-regulated and 105 down-regulated genes were identified across all time points using statistical and fold level criteria. The presumptive functions of these genes suggest a robust innate immune …

The Effects Of Food Stamps On Exiting Welfare And Becoming Employed For Welfare Recipients, Charles Baum

University of Kentucky Center for Poverty Research Discussion Paper Series

Welfare reform’s success encouraging employment may be affected by the federal Food Stamp program because many households receive welfare and Food Stamps. Food Stamp benefits could discourage employment because benefits are reduced proportionally with income; alternatively, it could encourage employment by increasing stability and allowing more resources to be allocated toward employment-related expenses. I examine the effects of Food Stamps on exiting welfare and becoming employed for welfare recipients. Results suggest, if anything, that Food Stamps discourage employment, and such benefits may discourage transitions off welfare, too. If so, then it may be necessary to study the determinants of welfare …

Capturing Hammerhead Ribozyme Structures In Action By Modulating General Base Catalysis, Young-In Chi, Monika Martick, Monica Lares, Rosalind Kim, William G. Scott, Sung-Hou Kim

Center for Structural Biology Faculty Publications

We have obtained precatalytic (enzyme-substrate complex) and postcatalytic (enzyme-product complex) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation …

Missense Mutation In Exon 2 Of Slc36a1 Responsible For Champagne Dilution In Horses, Deborah Cook, Samantha Brooks, Rebecca Bellone, Ernest Bailey

Veterinary Science Faculty Publications

Champagne coat color in horses is controlled by a single, autosomal-dominant gene (CH). The phenotype produced by this gene is valued by many horse breeders, but can be difficult to distinguish from the effect produced by the Cream coat color dilution gene (CR). Three sires and their families segregating for CH were tested by genome scanning with microsatellite markers. The CH gene was mapped within a 6 cM region on horse chromosome 14 (LOD = 11.74 for theta = 0.00). Four candidate genes were identified within the region, namely SPARC [Secreted protein, acidic, cysteine-rich (osteonectin)], SLC36A1 (Solute Carrier 36 family …

Derivatives Of Mithramycin And Methods Of Making And Uses Thereof, Jürgen Rohr, Lily L. Remsing, Mohammad Ner-E-Alam, Jose A. Salas, Carmen Mendez, Alfredo F. Brana, Ana M. Gonzalez

Pharmaceutical Sciences Faculty Patents

The invention, in one aspect, generally relates to mithramycin derivatives from mutated Streptomyces argillaceus and their production. The invention also relates using the derivatives for the treatment of various diseases. Finally, the invention relates to a mutated Streptomyces argillaceus useful in the production of the mithramycin derivatives.

Inhibitors Of Plant Peptide Deformylase For Use As Broad-Spectrum Herbicides And Methods For Identifying The Same, Robert L. Houtz, Lynnette M. A. Dirk, Mark Alan Wiliams

Horticulture Faculty Patents

The invention relates to a method of identifying herbicides and to the use of inhibitors of plant peptide deformylase as broad spectrum herbicides.

Accelerated High Fidelity Prion Amplification Within And Across Prion Species Barriers, Kristi M. Green, Joaquín Castilla, Tanya S. Seward, Dana L. Napier, Jean E. Jewell, Claudio Soto, Glenn C. Telling

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Experimental obstacles have impeded our ability to study prion transmission within and, more particularly, between species. Here, we used cervid prion protein expressed in brain extracts of transgenic mice, referred to as Tg(CerPrP), as a substrate for in vitro generation of chronic wasting disease (CWD) prions by protein misfolding cyclic amplification (PMCA). Characterization of this infectivity in Tg(CerPrP) mice demonstrated that serial PMCA resulted in the high fidelity amplification of CWD prions with apparently unaltered properties. Using similar methods to amplify mouse RML prions and characterize the resulting novel cervid prions, we show that serial PMCA abrogated a transmission barrier …

Alternation Of Tobacco Alkaloid Content Through Modification Of Specific Cytochrome P450 Genes, Ralph E. Dewey, Steven W. Bowen, Balazs Siminszky, Lily Gavilano

Plant and Soil Sciences Faculty Patents

Compositions and methods for reducing the level of nornicotine and N′-nitrosonornicotine (NNN) inNicotiana plants and plant parts thereof are provided. The compositions comprise isolated polynucleotides and polypeptides for cytochrome P450s that are involved in the metabolic conversion of nicotine to nornicotine in these plants. Expression cassettes, vectors, plants, and plant parts thereof comprising inhibitory sequences that target expression or function of the disclosed cytochrome P450 polypeptides are also provided. Methods for the use of these novel sequences to inhibit expression or function of cytochrome P450 polypeptides involved in this metabolic conversion are also provided. The methods find use in …

Biology And Therapy Of Fibromyalgia. Evidence-Based Biomarkers For Fibromyalgia Syndrome, Dina Dadabhoy, Leslie J. Crofford, Michael Spaeth, I. Jon Russell, Daniel J. Clauw

Internal Medicine Faculty Publications

Researchers studying fibromyalgia strive to identify objective, measurable biomarkers that may identify susceptible individuals, may facilitate diagnosis, or that parallel activity of the disease. Candidate objective measures range from sophisticated functional neuroimaging to office-ready measures of the pressure pain threshold. A systematic literature review was completed to assess highly investigated, objective measures used in fibromyalgia studies. To date, only experimental pain testing has been shown to coincide with improvements in clinical status in a longitudinal study. Concerted efforts to systematically evaluate additional objective measures in research trials will be vital for ongoing progress in outcome research and translation into clinical …

Relative Crystallinity Of Plant Biomass: Studies On Assembly, Adaptation And Acclimation, Darby Harris, Seth Debolt

Horticulture Faculty Publications

Plant biomechanical design is central to cell shape, morphogenesis, reproductive performance and protection against environmental and mechanical stress. The cell wall forms the central load bearing support structure for plant design, yet a mechanistic understanding of its synthesis is incomplete. A key tool for studying the structure of cellulose polymorphs has been x-ray diffraction and fourier transform infrared spectroscopy (FTIR). Relative crystallinity index (RCI) is based on the x-ray diffraction characteristics of two signature peaks and we used this technique to probe plant assembly, adaptation and acclimation. Confocal microscopy was used to visualize the dynamics of cellulose synthase in transgenic …

Cytochrome P450 And Uses Of Thereof, Joseph Chappell, Lyle F. Ralston

Pharmaceutical Sciences Faculty Patents

The invention features isolated cytochrome P450 polypeptides and nucleic acid molecules, as well as expression vectors and transgenic plants containing these molecules. In addition, the invention features uses of such molecules in methods of increasing the level of resistance against a disease caused by a plant pathogen in a transgenic plant, in methods for producing altered compounds, for example, hydroxylated compounds, and in methods of producing isoprenoid compounds.

Murine Monoclonal Anti-Idiotype Antibody 11d10 And Methods Of Use Thereof, Malaya Chatterjee, Kenneth A. Foon, Sunil K. Chatterjee

Microbiology, Immunology and Molecular Genetics Faculty Patents

The present invention provides a monoclonal anti-Idiotype antibody 11D10 that elicits an immune response against a specific epitope of a high molecular weight mucin of human milk fat globule (HMFG) and a hybridoma that produces 11D10. The hybridoma that produces 11D10 was selected by specific procedures. 11D10 induces an immunological response to HMFG in mice, rabbits, monkeys and patients with advanced HMFG-associated tumors. This invention provides compositions derived from polynucleotide sequences encoding the variable light and/or variable heavy regions of monoclonal anti-idiotype antibody 11D10, as well as polypeptides encoded thereby. The invention also provides compositions which can be used in …

Genomic Analysis Of Gene Regulation Complexity, Brandon Barker, Jim Lund

Biology Presentations

With multiple metazoan genomes in each family being sequenced promoter analysis is becoming a useful tool in genomic analysis. Aligning the promoter regions in the DNA of C. elegans and C. briggsae identifies conserved promoter elements. While not all promoter elements are conserved and not all conserved regions are promoter elements, we find that conservation is a useful method for determining promoter complexity. Promoter complexity identifies which genes have particularly interesting regulation, identifying gene groups with a strong promoter complexity signal and cases where a gene's promoter complexity differs from the group's promoter complexity.

We identify potential promoter sequence by …

Identifying Regulatory Elements And Gene Boundaries With Comparative Genomic Sequence Analysis, Jim Lund

Biology Presentations

For several groups of organisms multiple genomes have been sequenced either completely or to the unfinished shotgun sequencing stage. Comparative sequence analysis can identify functional sequence elements for pairs of organisms that diverged far enough in the past to allow mutational drift of non-conserved sequences. While analysis of a pair of genomes identifies many of these functional elements adding additional genomes allows additional information to be elicited.

Additional conserved sequence elements are identified as additional genomes are analyzed. These conserved sequence elements are often regulatory elements although they are difficult to classify with in silico analysis. For an individual gene, …

Sumoylation Regulates Lamin A Function And Is Lost In Lamin A Mutants Associated With Familial Cardiomyopathies, Yu-Qian Zhang, Kevin D. Sarge

Molecular and Cellular Biochemistry Faculty Publications

Lamin A mutations cause many diseases, including cardiomyopathies and Progeria Syndrome. The covalent attachment of small ubiquitin-like modifier (SUMO) polypeptides regulates the function of many proteins. Until now, no examples of human disease-causing mutations that occur within a sumoylation consensus sequence and alter sumoylation were known. We show that lamin A is sumoylated at lysine 201 and that two lamin A mutants associated with familial dilated cardiomyopathy, E203G and E203K, exhibit decreased sumoylation. E203 occupies the conserved +2 position in the sumoylation consensus Psi KXE. Lamin A mutants E203G, E203K, and K201R all exhibit a similar aberrant subcellular localization and …

A Novel Application Of Quantile Regression For Identification Of Biomarkers Exemplified By Equine Cartilage Microarray Data, Liping Huang, Wenying Zhu, Christopher P. Saunders, James N. Macleod, Mai Zhou, Arnold J. Stromberg, Arne C. Bathke

Veterinary Science Faculty Publications

BACKGROUND: Identification of biomarkers among thousands of genes arrayed for disease classification has been the subject of considerable research in recent years. These studies have focused on disease classification, comparing experimental groups of effected to normal patients. Related experiments can be done to identify tissue-restricted biomarkers, genes with a high level of expression in one tissue compared to other tissue types in the body.

RESULTS: In this study, cartilage was compared with ten other body tissues using a two color array experimental design. Thirty-seven probe sets were identified as cartilage biomarkers. Of these, 13 (35%) have existing annotation associated with …

Medical Students: Abuse Of Psychoactive Substances And Sexuality Aspects, Kepler Alencar Mendes Carvalho, Maria José Carvalho Sant'anna, Verônica Coates, Hatim A. Omar

Pediatrics Faculty Publications

University students aged 17 to 24 years of age are prone to many risk factors.

OBJECTIVES: Identify risk factors related to exploring sexuality and characteristics of consumption of psychoactive substances in students attending medical school.

METHODS: 465 Medical students from Santa Casa of São Paulo Faculty of Medical Sciences (FCMSCSP) were prospectively and transversely evaluated during 2005. An anonymous, semi-structured, self-filling questionnaire was used. The average age of the students was 21.5 years, 43% females. 76.2% preferred alcohol, and 11.1% tobacco consumption; chloroethane (lança-perfume) consumption occurred in 22.6% and 15.3% consumption of other types of illicit drugs, with marijuana as …

Medical Supervision Of Young Female Athletes Training In Complex Coordinational Sports, Irina Schevchenko, Viktor V. Abramov, Paul T Gibson, Hatim A. Omar

Pediatrics Faculty Publications

This article proposes simple medical criteria that can be used by trainers and others for effective medical supervision of young female athletes.

METHODS: The cross-sectional, age-stratified study compared girls 10-17 years of age involved in intensive training in gymnastic floor exercises, trampoline, or badminton. Each sport and/or control group was represented by 40-45 girls. Data included medical history, morphometric variables and observation of biological development.

RESULTS: Gymnasts started training earliest (approximately 5-years-old) and trained most intensely (18-20 h/wk), followed by trampolinists and then badmintonists. Height, weight, body mass index, and % body fat were reduced in athletes, with gymnasts showing …

Nitrite Reduction By Siderite, Sudipta Rakshit, Christopher J. Matocha, Mark S. Coyne

Plant and Soil Sciences Faculty Publications

Nitrate-dependent Fe(II) oxidation is an important process in the inhibition of soil Fe(III) reduction, yet the mechanisms are poorly understood. One proposed pathway includes chemical reoxidation of mineral forms of Fe(II) such as siderite [FeCO3(s)] by NO2 −. Accordingly, the objective of this study was to investigate the reactivity of FeCO3(s) with NO2 −. Stirred-batch reactions were performed in an anoxic chamber across a range of pH values (5.5, 6, 6.5, and 7.9), initial FeCO3(s) concentrations (5, 10, and 15 g L−1) and initial NO2 − concentrations (0.83–9.3 mmol L−1) for kinetic and stoichiometric determinations. Solid-phase products were characterized using …

A Polyadenylation Factor Subunit Implicated In Regulating Oxidative Signaling In Arabidopsis Thaliana, Jingxian Zhang, Bala Subrahmanyam Addepalli, Kil-Young Yun, Arthur G. Hunt, Ruqiang Xu, Suryadevara Rao, Qingshun Q. Li, Deane L. Falcone

Kentucky Tobacco Research and Development Center Faculty Publications

BACKGROUND: Plants respond to many unfavorable environmental conditions via signaling mediated by altered levels of various reactive oxygen species (ROS). To gain additional insight into oxidative signaling responses, Arabidopsis mutants that exhibited tolerance to oxidative stress were isolated. We describe herein the isolation and characterization of one such mutant, oxt6.

METHODOLOGY/PRINCIPAL FINDINGS: The oxt6 mutation is due to the disruption of a complex gene (At1g30460) that encodes the Arabidopsis ortholog of the 30-kD subunit of the cleavage and polyadenylation specificity factor (CPSF30) as well as a larger, related 65-kD protein. Expression of mRNAs encoding Arabidopsis CPSF30 alone was able to …