Life Sciences Commons^™

Ppar Agonists Down-Regulate The Expression Of Atp10c Mrna During Adipogenesis, A Peretich, Maria Cekanova Ms, Rndr, Phd, S Hurst, Sj Baek, Madhu Dahr

Maria Cekanova MS, RNDr, PhD

No abstract provided.

Multiple Loci Within The Major Histocompatibility Complex Confer Risk Of Psoriasis, Bing-Jian Feng, Liang-Dan Sun, Razieh Soltani-Arabshahi, Anne M. Bowcock, Rajan P. Nair, Philip Stuart, James T. Elder, Steven J. Schrodi, Ann B. Begovich, Goncalo R. Abecasis, Xue-Jun Zhang, Kristina P. Callis Duffin, Gerald G. Krueger, David E. Goldgar

Steven J Schrodi

Psoriasis is a common inflammatory skin disease characterized by thickened scaly red plaques. Previously we have performed a genome-wide association study (GWAS) on psoriasis with 1,359 cases and 1,400 controls, which were genotyped for 447,249 SNPs. The most significant finding was for SNP rs12191877, which is in tight linkage disequilibrium with HLA-Cw*0602, the consensus risk allele for psoriasis. However, it is not known whether there are other psoriasis loci within the MHC in addition to HLA-C. In the present study, we searched for additional susceptibility loci within the human leukocyte antigen (HLA) region through in-depth analyses of the GWAS data; …

E-Science @ Umass: Anticipating And Supporting E-Science Activities At The University Of Massachusetts, Maxine G. Schmidt, Rebecca Reznik-Zellen

Maxine G Schmidt

In March of 2008 an Ad Hoccommittee of Science Librarians from the University of Massachusetts Five Campus System convened to discuss the challenges of e-science and prepare the Libraries for their role in e-science initiatives. Three primary outcomes intended to support e-science activities emerged from the work of the Ad Hoc committee.

Regression When The Predictors Are Images, Philip T. Reiss

Philip T. Reiss

No abstract provided.

Neurosteroid Replacement Therapy For Catamenial Epilepsy, Doodipala S. Reddy, Michael A. Rogawski

Michael A. Rogawski

Perimenstural catamenial epilepsy, the cyclical occurrence of seizure exacerbations near the time of menstruation, affects a high proportion of women of reproductive age with drug refractory epilepsy. Enhanced seizure susceptibility in perimenstrual catamenial epilepsy is believed to be due to the withdrawal of the progesterone-derived GABA-A receptor modulating neurosteroid allopregnanolone as a result of the fall in progesterone at the time of menstruation. Studies in a rat pseudopregnancy model of catamenial epilepsy indicate that following neurosteroid withdrawal there is enhanced susceptibility to chemoconvulsant seizures. There is also a transitory increase in the frequency of spontaneous seizures in epleptic rats that …

30-Month Post-Breast Cancer Treatment Lymphoedema, Jane M. Armer, Bob R. Stewart, Robin Shook

Robin Shook

Background—Quantification of lymphoedema (LE) has been problematic, and the reported incidence of LE varies greatly among women treated with surgery and radiation for breast cancer. Aims—This study aims to describe LE occurrence over time among breast cancer survivors using four diagnostic criteria based on three measurement techniques. Methods—Limb volume and symptom assessment data were followed after surgery every three months for 12 months, then every six months for 30 months. Limb volume changes (LVC) were measured by circumferences and by perometry, and by symptom experience via interview. Standard survival analysis methods identified when the criteria indicating LE were met. Results—Trends …

Nontraditional Epilepsy Treatment Approaches, Michael A. Rogawski, Gregory L. Holmes

Michael A. Rogawski

Overview of articles published in a special issue of Neurotherapeutics (April 2009) on nontraditional (non-drug) epilepsy treatment approaches. From the Fourth Workshop on New Horizons in the Development of Antiepileptic Drugs: Nontraditional Approaches to Treat Epilepsy, which was held at the Clontarf Castle, Dublin, March 5-7, 2008.

Convection-Enhanced Delivery In The Treatment Of Epilepsy, Michael A. Rogawski

Michael A. Rogawski

Convection-enhanced delivery (CED) is a novel drug-delivery technique that uses positive hydrostatic pressure to deliver a fluid containing a therapeutic substance by bulk flow directly into the interstitial space within a localized region of the brain parenchyma. CED circumvents the blood-brain barrier and provides a wider, more homogenous distribution than bolus deposition (focal injection) or other diffusion-based delivery approaches. A potential use of CED is for the local delivery of antiseizure agents, which would provide an epilepsy treatment approach that avoids the systemic toxicities of orally administered anti-epileptic drugs and bystander effects on nonepileptic brain regions. Recent studies have demonstrated …

E-Science @ The University Of Massachusetts, Maxine G. Schmidt, Rebecca Reznik-Zellen, Raquel Rivera, Cecilia P. Mullen

Maxine G Schmidt

e-Science @ the University of Massachusetts Abstract: What is e-Science and how can libraries and librarians support it? The University of Massachusetts takes a proactive approach to support network-enabled research on its campuses and provides examples where e-Science is already at work. Statement: “e-Science” is a term commonly used to describe research in a networked environment, a growing trend not only in the sciences, but the arts and humanities as well. e-Science creates both opportunities and challenges for academic libraries. The opportunities lie in leveraging the basic skill set that libraries and librarians already possess: the knowledge of and practical …

Uniqueprimer - A Web Utility For Design Of Specific Pcr Primers And Probes, Torstein Tengs

Dr. Torstein Tengs

We have developed a web-based tool for design of specific PCR primers and probes. The program allows you to enter primer sequence information as well as an optional probe, and sequence similarity searches (MegaBLAST) will be performed to see if the sequences match the same sequence entry in the specified database. If primers (and probe) match, this will be reported. The program can handle overlapping amplicons, amplification from a single primer, ambiguous bases and other problematic cases.

Evaluation Of Polymorphism At Codon 192 Of Paraoxonase 1 On Its Kinetic Behavior, Rozaida @ Poh Yuen Ying

Rozaida @ Poh Yuen Ying

Human paraoxonase 1 (PON1), a High-Density Lipoprotein (HDL)-associated esterase has been implicated in slowing down the development of atherosclerosis. In the present study, kinetic and inhibition studies on PON1 were conducted to assess three parameters: the Michaelis constant (KM) and maximal rate of metabolisme (Vmax) of paraoxonase and inhibition constant (Ki) of phenylacetate. Human paraoxonase 1 (PON1) activity was measured spectrophotometrically at 405 nm, using plasma samples in basal (without added NaCl) and salt-stimulated assays with 1 M NaCl. Inhibition studies were performed using phenylacetate as an inhibitor of PON1 in basal assays, pH 8.0. Estimates of KM and Vmax …

Hierarchical Hidden Markov Model With Application To Joint Analysis Of Chip-Chip And Chip-Seq Data, Hyungwon Choi, Debashis Ghosh, Zhaohui S. Qin

Debashis Ghosh

Motivation: Identication of transcription factor binding sites (TFBS) is a fundamental problem in understanding the mechanism of gene regulation. The ChIP-chip technology has accelerated this eort by providing a simultaneous genome-wide map of TFBS in a high-throughput fashion. Recently, a sequencing-based ChIP-seq has appeared as a promising alternative that can identify targets with an improved sensitivity/specicity in high resolution. However, studies have suggested that distinct experimental platforms can be complementary in TFBS identication. The availability of data obtained from multiple platforms motivates a meta-analysis for improved identication of candidate motifs.

Results: In this work, we propose a hierarchical hidden Markov …

A Double-Layered Mixture Model For The Joint Analysis Of Dna Copy Number And Gene Expression Data, Debashis Ghosh

Debashis Ghosh

Copy number aberration is a common form of genomic instability in cancer. Gene expression is closely tied to cytogenetic events by the central dogma of molecular biology, and serves as a mediator of copy number changes in disease phenotypes. Accordingly, it is of interest to develop proper statistical methods for jointly analyzing copy number and gene expression data. This work describes a novel Bayesian inferential approach for a double-layered mixture model (DLMM) which directly models the stochastic nature of copy number data and identifies abnormally expressed genes due to aberrant copy number. Simulation studies were conducted to illustrate the robustness …

Discrete Nonparametric Algorithms For Outlier Detection With Genomic Data, Debashis Ghosh

Debashis Ghosh

In high-throughput studies involving genetic data such as from gene expression microarrays, differential expression analysis between two or more experimental conditions has been a very common analytical task. Much of the resulting literature on multiple comparisons has paid relatively little attention to the choice of test statistic. In this article, we focus on the issue of choice of test statistic based on a special pattern of differential expression. The approach here is based on recasting multiple comparisons procedures for assessing outlying expression values. A major complication is that the resulting p-values are discrete; some theoretical properties of sequential testing procedures …

A Double-Layered Mixture Model For The Joint Analysis Of Dna Copy Number And Gene Expression Data, Debashis Ghosh

Debashis Ghosh

Copy number aberration is a common form of genomic instability in cancer. Gene expression is closely tied to cytogenetic events by the central dogma of molecular biology, and serves as a mediator of copy number changes in disease phenotypes. Accordingly, it is of interest to develop proper statistical methods for jointly analyzing copy number and gene expression data. This work describes a novel Bayesian inferential approach for a double-layered mixture model (DLMM) which directly models the stochastic nature of copy number data and identifies abnormally expressed genes due to aberrant copy number. Simulation studies were conducted to illustrate the robustness …

Discrete Nonparametric Algorithms For Outlier Detection With Genomic Data, Debashis Ghosh

Debashis Ghosh

In high-throughput studies involving genetic data such as from gene expression microarrays, differential expression analysis between two or more experimental conditions has been a very common analytical task. Much of the resulting literature on multiple comparisons has paid relatively little attention to the choice of test statistic. In this article, we focus on the issue of choice of test statistic based on a special pattern of differential expression. The approach here is based on recasting multiple comparisons procedures for assessing outlying expression values. A major complication is that the resulting p-values are discrete; some theoretical properties of sequential testing procedures …

A Quantitative Taqman Mgb Real-Time Polymerase Chain Reaction Based Assay For Detection Of The Causative Agent Of Crayfish Plague Aphanomyces Astaci, Torstein Tengs

Dr. Torstein Tengs

Here we present the development and first validation of a TaqMan minor groove binder (MGB) real-time polymerase chain reaction (RT-PCR) method for quantitative and highly specific detection of Aphanomyces astaci, the causative agent of crayfish plague. The assay specificity was experimentally assessed by testing against DNA representative of closely related oomycetes, and theoretically assessed by additional sequence similarity analyses comparing the primers and probe sequences to available sequences in EMBL/GenBank. The target of the assay is a 59 bp unique sequence motif of A. astaci found in the internal transcribed spacer 1 of the nuclear ribosomal gene cluster. A standard …

Farm Focus - Spring 2009, Brian K. Whitlock, Matt Welborn, Maria Prado, Amy Plummer

Brian K Whitlock, PhD, DVM, DACT

No abstract provided.

Farm Focus - Fall 2009, Brian K. Whitlock, Matt Welborn, Maria Prado, Amy Plummer

Brian K Whitlock, PhD, DVM, DACT

No abstract provided.

Topiramate Reduces Excitability In The Basolateral Amygdala By Selectively Inhibiting Gluk1 (Glur5) Kainate Receptors On Interneurons And Positively Modulating Gaba-A Receptors On Principal Neurons, Maria Braga, Vassiliki Aroniadou-Anderjaska, He Li, Michael Rogawski

Michael A. Rogawski

Topiramate [2,3:4,5-bis-O-(1-methylethylidene)-beta-D-fructopyranose sulfamate] is a structurally novel antiepileptic drug that has broad efficacy in epilepsy, but the mechanisms underlying its therapeutic activity are not fully understood. We have found that topiramate selectively inhibits GluK1 (GluR5) kainate receptor-mediated excitatory postsynaptic responses in rat basolateral amygdala (BLA) principal neurons and protects against seizures induced by the GluK1 kainate receptor agonist (R,S)-2-amino-3-(3-hydroxy-5-tert-butylisoxazol-4-yl)propanoic acid (ATPA). Here, we demonstrate that topiramate also modulates inhibitory function in the BLA. Using whole-cell recordings in rat amygdala slices, we found that 0.3 to 10 microM topiramate 1) inhibited ATPA-evoked postsynaptic currents recorded from BLA interneurons; 2) suppressed ATPA-induced …

Nerve, Muscle, Blood, Toil, Tears, And Sweat: England’S Pioneering Biophysicist, Soldier, And Statesman, Arshad M. Khan

Arshad M. Khan, Ph.D.

No abstract provided.

Pathological Alterations In Gabaergic Interneurons And Reduced Tonic Inhibition In The Basolateral Amygdala During Epileptogenesis, Michael A. Rogawski, Brita Fritsch, Felicia Qashu, T. H. Figueiredo, Vicki Aroniadou-Anderjaska, Maria F.M. Braga

Michael A. Rogawski

An acute brain insult such as traumatic head/brain injury, stroke, or an episode of status epilepticus can trigger epileptogenesis, which, after a latent, seizure-free period, leads to epilepsy. The discovery of effective pharmacological interventions that can prevent the development of epilepsy requires knowledge of the alterations that occur during epileptogenesis in brain regions that play a central role in the induction and expression of epilepsy. In the present study, we investigated pathological alterations in GABAergic interneurons in the rat basolateral amygdala (BLA), and the functional impact of these alterations on inhibitory synaptic transmission, on days 7 to 10 after status …

Genome-Wide Scan Reveals Association Of Psoriasis With Il-23 And Nf-B Pathways, Rajan P. Nair, Kristina C. Duffin, Cynthia Helms, Jun Ding, Philip E. Stuart, David Goldgar, Johann E. Gudjonsson, Yun Li, Trilokraj Tejasvi, Bing-Jiag Feng, Andreas Ruether, Stefan Schreiber, Michael Weichenthal, Dafna Gladman, Proton Rahman, Steven J. Schrodi, Sampath Prahalad, Stephen L. Guthery, Judith Fischer, Wilson Liao, Pui-Yan Kwok, Alan Menter, G Mark Lathrop, Carol A. Wise, Ann B. Begovich, John J. Voorhees, James T. Elder, Gerald G. Krueger, Anne M. Bowcock, Goncalo R. Abecasis

Steven J Schrodi

Psoriasis is a common immune-mediated disorder that affects the skin, nails and joints. To identify psoriasis susceptibility loci, we genotyped 438,670 SNPs in 1,409 psoriasis cases and 1,436 controls of European ancestry. We followed up 21 promising SNPs in 5,048 psoriasis cases and 5,041 controls. Our results provide strong support for the association of at least seven genetic loci and psoriasis (each with combined P < 5 10-8). Loci with confirmed association include HLA-C, three genes involved in IL-23 signaling (IL23A, IL23R, IL12B), two genes that act downstream of TNF- and regulate NF-B signaling (TNIP1, TNFAIP3) and two genes involved in the modulation of Th2 immune responses (IL4, IL13). Although the proteins encoded in these loci are known to interact biologically, we found no evidence for epistasis between associated SNPs. Our results expand the catalog of genetic loci implicated in psoriasis susceptibility and suggest priority targets for study in other auto-immune disorders.

Characterization Of Unknown Genetic Modifications Using High Throughput Sequencing And Computational Subtraction, Torstein Tengs

Dr. Torstein Tengs

Background

When generating a genetically modified organism (GMO), the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown.

Results

We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of …