title: Comparison of yeast (Saccharomyces cerevisiae) strain with histone H4 R45 mutated to H with wild type yeast strain WY139

status: Public on Jun 23 2008

city: Pullman

last: Smerdon

institute: Washington State University

summary:
Total RNA samples from three replicate cultures of wild type and mutant yeast strains was isolated and expression profile done using Affymetrix arrays. Comparsion between the samples indicate how mutation in a single amino acid residue in histone H4 (H4R45H) affects gene expression in yeast. Such a mutation in histone H4 is known to generate a specific class of mutants called SWI/SNF independent (SIN) mutants, and the mutants were identified by their ability to carry out transcription in the absence of yeast chromatin remodeling complex SWI/SNF. SIN mutations are known to affect higher order chromatin structure and the comparative expression profile would help identification  of genes which get affected by such altered chromatin landscape.
Keywords: mutant analysis

overall_design: Comparison of genes whose mRNA levels are affected in histone H4R45H mutant yeast strains compared to wild type yeast strain WY139. This comparison reveals how subtle change in a single amino acid residue in core domain of histone H4 affects gene expression profile in yeast.

first: Ronita

last: Nag


title: Complement activation in the peripheral nervous system following the spinal nerve ligation model of neuropathic pain

status: Public on Mar 31 2008

city: North Brunswick

first: Jason

middle: Gang

last: Jin

address: 675 US Highway

country: USA

institute: MaxyBio

summary:
Neuroinflammatory and neuroimmune mechanisms, as exemplified by infiltrating immune cells and activation of resident endothelial/glial cells, respectively, are known to be involved in the establishment and maintenance of chronic pain. An immune system pathway that may be involved in the activation of both immune and glial cells is complement. The complement pathway is made up of a large number of distinct plasma proteins which react with one another to opsonize pathogens and induce a series of inflammatory responses to help fight infection. Cleaved products and complexes produced by complement activation are responsible for a range of effects including mediation of immune infiltration, activation of phagocytes, opsonization/lysis of pathogens and injured cells, and production of vasoactive amines such as histamine and serotonin.
Gene-expression microarray-analysis was performed on the rat spinal nerve ligation (SNL) model of neuropathic pain
Keywords: organ type comparison, disease state analysis and drug treatment

overall_design: For gene expression analysis, rats from five experimental groups were sacrificed 19–21 days after surgery: (1)Naïve+ vehicle; (2) Naïve + GPN; (3) sham + vehicle; (4) SNL + vehicle; (5) SNL + GPN. Tissue was collected from whole brain, hemisected spinal cord, mid thigh sciatic nerve, and L4, L5 and L6 dorsal root ganglia (DRG), both ipsilateral(ipsi) and contralateral (contra) to the injury. In addition,‘‘organ recital’’ tissues were harvested from naı ¨ve animals: adrenal,aorta, fetal brain, kidney, liver, quadriceps muscle, spleen,submaxillary gland, and testis and 15 other tissues.For each experimental group and tissue, samples rapidly frozen on dry ice were separated into two pools(Pool 1 and Pool 2), consisting of half or 4-6 animals each.Pool 1 total RNA was subjected to standard methods on Affymetrix GeneChip  Arrays using rat U34 A, B, and C.

first: Margaret

middle: E

last: Levin

middle: G

first: Rui-Ru

last: Ji

first: Jeifei

last: Tong

first: James

middle: D

last: Pomonis

first: Daniel

middle: J

last: Lavery

first: Scott

middle: W

last: Miller

first: Lillian

last: Chiang


title: The Oxidative Stress Response of a Lager Brewing Yeast Strain during Industrial Propagation and Fermentation

status: Public on Apr 23 2008

city: Loughborough

first: Katherine

middle: A

last: Smart

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

summary:
Commercial brewing yeast strains are exposed to a number of potential stresses including oxidative stress. The aim of this investigation was to measure the physiological and transcriptional changes of yeast cells during full-scale industrial brewing processes with a view to determining the environmental factors influencing the cell’s oxidative stress response. Cellular antioxidant levels were monitored throughout an industrial propagation and fermentation and microarray analysis was employed to determine transcriptional changes in antioxidant-encoding and other stress response genes. The greatest increase in cellular antioxidants and transcription of antioxidant-encoding genes occurred as the rapidly fermentable sugars glucose and fructose were depleted from the growth medium (wort) and the cell population entered the stationary phase. The data suggest that, contrary to expectation, the oxidative stress response is not influenced by changes in the dissolved oxygen concentration of wort but is initiated as part of a general stress response to growth-limiting conditions, even in the absence of oxygen. A mechanism is proposed to explain the changes in antioxidant response observed in yeast during anaerobic fermentation. The results suggest that the yeast cell does not experience oxidative stress, per se, during industrial brewery handling. This information may be taken into consideration when setting parameters for industrial brewery fermentation.

Experimenter name: Brian Gibson
Experimenter phone: +44 (0)1159516214
Keywords: time_series_design;  fermentation

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: 17 samples were used in this experiment

first: Brian

last: Gibson

first: Stephen

last: Lawrence

first: Chris

last: Boulton

first: Wendy

last: Box

first: Neil

middle: S

last: Graham

first: Robert

last: Linforth


title: Carbohydrate metabolism and the lager yeast transcriptome during brewery fermentation

status: Public on Jun 09 2008

summary:
The fermentable carbohydrate composition of wort and the manner in which it is utilised by yeast during brewery fermentation has a direct influence on fermentation efficiency and quality of the finished product. In this study the response of a brewing yeast strain to changes in wort fermentable carbohydrate concentration and composition during full-scale (3275 hL) brewery fermentation was investigated by measuring transcriptome changes with the aid of oligonucleotide based DNA arrays. Up to 90% of the detectable genes showed a significant (P ≤ 0.05) differential expression pattern during fermentation and the majority of these genes showed either transient or prolonged peaks in expression following the exhaustion of the monosaccharides glucose and fructose from the wort. Those which did not display this apparent carbon catabolite derepression response were mainly those genes involved in cytokinesis and cell budding, which had higher expression values during active growth of cells. Transcriptional activity of many genes was consistent with their known responses to glucose de/repression under laboratory conditions, despite the presence of di- and trisaccharide sugars in the wort.
Experimenter name: Katherine Smart
Experimenter phone: 0044-1159516214
Experimenter address: School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire
Experimenter zip/postal_code: LE12 5RD
Experimenter country: England
Keywords: time series design

overall_design: 14 samples were used in this experiment

middle: R

first: Zoe

last: Emmerson

first: Beatrice

last: Schildknecht


title: Rat expression data after acute FSH suppression

status: Public on Jan 29 2008

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary:
To unravel the genes that underpin the effects of FSH on spermatogenesis, testicular gene expression was compared in juvenile rats after FSH suppression to littermate controls.  Based on existing data, it is apparent that the dominant function of FSH shifts between 9 and 18 day postpartum (dpp) during the first wave of spermatogenesis from driving Sertoli cell proliferation to support of germ cells.  To enable comprehensive analysis of the impact of acute in vivo FSH suppression on Sertoli and germ cell development and to determine the genes that underpin these affects, FSH was selectively suppressed in Sprague Dawley rats by passive immunisation for 4 days prior to testis collection at 18 days postpartum. FSH suppression did not affect Sertoli cell proliferation at 18 dpp, but germ cell numbers were decreased at 18 dpp following FSH suppression, with a corresponding increase in germ cell apoptosis measured. Sixty transcripts were measured as changed at 18 dpp in response to 4 days of FSH suppression, as assessed using Affymetrix™ microarrays.  Some of these are known as Sertoli cell-derived FSH-responsive genes (e.g. StAR, cathepsin L, insulin-like growth factor binding protein-3), while others encode proteins involved in cell cycle and survival regulation (e.g. cyclin D1, scavenger receptor class B 1). These data demonstrate that FSH affects germ cells in vivo, by supporting germ cell viability at day 18. This model enabled identification of candidate genes that contribute to the FSH-mediated pathway by which Sertoli cells support germ cells.
Keywords: time course

overall_design: Sprague Dawley male rats at day 14 postpartum received either a rat FSH antibody raised in sheep or a control sheep immunoglobulin for 4 days. RNA was extracted from the testis and hybridisation on Affymetrix microarrays was conducted.

first: Sarah

last: Meachem

first: Saleela

last: Ruwanpura

first: Jessica

last: Ziolkowski

first: Jacquelyn

last: Ague

first: Mike

first: Kate

last: Loveland


title: Non-alcoholic Steatohepatitis following feeding of high polyunsaturated fat diets

status: Public on May 19 2008

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

summary:
Most commonly used models of non-alcoholic steatohepatitis (NASH) are diets based on specific gene knockouts or represent extreme manipulations of diet. We have examined the effects of modest increased caloric intake and high dietary unsaturated fat content on the development of NASH in male rats using a model in which overfeeding is accomplished via intragastric infusion of liquid diets as a part of total enteral nutrition. Male Sprague dawley rats were fed diets 5% corn oil containing diets at 187 Kcal/kg3/4/d or fed 70% corn oil containing diets at 220 Kcal/kg3/4/d for a period of 3 weeks. Hepatic gene expression were assessed at the end of the study. Our results indicate that overfeeding of high unsaturated fat diets leads to pathological, endocrine and metabolic changes characteristic of NASH patients and is associated with increased oxidative stress and TNF-a.
Keywords: Steatosis and unsaturated fat

overall_design:
Two groups of male sprague dawley rats were fed liquid diets via total enteral nutrition.
Group 1, Control, Rats were fed diets containing 5% Corn oil at 187 Kcal/kg3/4/d for 3 weeks.
Group 2, NASH, Rats were fed diets containing 70% corn oil at 220 Kcal/kg3/4/d for 3 weeks.

first: January

middle: N

last: Baumgardner

first: Leah

last: Hennings

first: Thomas

middle: M

last: Badger

first: Martin

last: Ronis


title: Expt. A; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling

status: Public on Jan 15 2009

city: Bethesda

first: David

middle: C.

last: Klein

state: MD

address: 49 Convent Dr.

department: PDEGEN

institute: NICHD/NIH

summary:
Biological processes are optimized by circadian and circannual biological timing systems.  In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle.
We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression. We have also used these data to characterize the non-rhythmic features of the transcriptome that set the pineal gland apart from other tissues by comparing them to the median expression in other rat tissues as found in the  Genomics Institute of the Novartis Research Foundation (GNF), Entrez Gene Expression Omnibus (GEO) dataset GDS589.

Keywords: Time course (2 points)

overall_design: Rat pineal glands were obtained at mid-day and mid-night for RNA extraction and hybridization to Affymetrix microarrays. Triplicates of pooled pineal glands were analyzed at each timepoint.

last: Bailey

first: Steven

middle: L

last: Coon

last: Carter

first: Ann

last: Humphries

first: Jong-so

last: Kim

first: Qiong

last: Shi

first: Pascaline

last: Gaildrat

first: Fabrice

last: Morin

first: Surajit

last: Ganguly

first: John

middle: B

last: Hogenesch

first: Joan

last: Weller

middle: F

last: Rath

first: Morten

last: Møller

first: Ruben

last: Baler

last: Sugden

first: Zoila

last: Rangel

first: Peter

last: Munson

middle: C


title: Toxicogenomic Analysis of Gender, Chemical, and Dose Effects in Livers of TCDD- or Aroclor 1254-Exposed Rats

status: Public on Jan 04 2008

city: Niskayuna

first: Erik

last: Carlson

state: NY

address: 1 Research Circle

institute: General Electric

summary:
Chronic exposure of Sprague-Dawley (SD) rats to either 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or Aroclor 1254 results in female-selective induction of hepatic tumors. The relative potency of dioxins and PCB mixtures, such as Aroclor 1254, is often estimated using the internationally endorsed toxic equivalency (TEQ) approach. Comparing the genome wide changes in gene expression in both genders following exposure to toxic equivalent doses of these chemicals should identify critical sets of early response genes while further defining the concept of the TEQ of halogenated aromatic hydrocarbons. Aroclor 1254 at 0.6, 6.0 and 60 mg/kg body weight and TEQ doses of TCDD (0.3 and 3.0 µg/kg), calculated to match the top two Aroclor 1254 doses, were orally administered to SD rats for three consecutive days. Day 4 gene expression in hepatic tissue was determined using microarrays. A linear mixed-effects statistical model was developed to analyze the data in relation to treatment, gender, and gender*treatment (G*T) interactions. The genes most changed included 54 genes with and 51 genes without a significant model G*T term. The known aryl hydrocarbon receptor (AHR) battery genes (Cyp1a1, Cyp1a2, Cyp1b1, Aldh3a1), and novel genes, responded in a TEQ dose-dependent manner in both genders. However, an important observation was the apparent disruption of sexually dimorphic basal gene expression, particularly for female rats. Since many of these genes are involved in steroid metabolism, exposure to either TCDD or Aroclor 1254 could disrupt proliferative signals more in female rats as a possible consequence of altered estrogen metabolism. This study extends the findings of previous rodent bioassays by identifying groups of genes, other than the well-characterized AHR response genes, whose disruption may be important in the tumorigenic mechanism in this rat strain.
Keywords: dose response, Multifactor Linear Model

overall_design: Twenty four female (171-194 g) and 24 male (190-207 g) S-D rats (Crl:CD(SD)IGS BR, Charles River Laboratories, Wilmington, MA) were randomly assigned to 6 groups of four rats per sex. Test chemicals were administered by gastric intubation in corn oil (5 ml/kg) at dose levels of 0.6, 6.0, or 60 Aroclor 1254 mg/kg, or 0.3 or 3.0 TCDD ug/kg for 3 consecutive days. Control groups for each gender received corn oil alone. On Day 4 the animals were euthanized by CO2 overdose and the livers were removed and frozen. Total RNA was isolated from liver tissues and used to hybridize Affymetrix RG-U34A arrays. A total of 68 chips were used in the downstream analyses. These chips include biological and technical replicates (full details are given in the supplementary file Experimental_Design.xls). A probe-level linear mixed-effects statistical model was developed to analyze the data in relation to treatment, gender and gender*treatment interactions.

first: Jay

last: Silkworth

first: Colin

last: McCulloch

first: Kati

last: Illouz

first: Shirlean

last: Goodwin

last: Sutter


title: Comparisons of yeast strains containing the essential histone acetyltransferase, ESA1 or a bypass suppressor of ESA1

status: Public on Dec 12 2007

city: Boston

first: Courtney

last: Sill

state: MA

address: 715 Albany St.

department: Genetics & Genomics

institute: Boston University School of Medicine

summary:
ESA1 (essential SAS-family acetyltransferase) is the only known yeast histone acetyltransferase (HAT) required for cell viability. It is a member of the MYST (MOZ, YBF2/SAS3, SAS2, Tip60) family of HAT proteins and contains a conserved acetyltransferase domain in addition to a chromodomain. While ESA1’s HAT activity is important in processes such as deoxyribonucleic acid (DNA) repair, acetylation is likely not its essential function. Our lab has shown that mutants with a single point mutation in the active site cysteine are still viable even though their acetyltransferase abilities are abolished. Furthermore, chromatin immunoprecipitation assays have shown ESA1 distributed evenly along the length of chromatin, not localized to specific promoters as would be expected from a HAT protein involved in transcriptional regulation. As is the case for other HAT proteins, ESA1’s acetyltransferase activity is significant, but in processes such as DNA replication, DNA repair and cell cycle progression. The aim of this project is to determine the essential function of ESA1 - the catalytic subunit of the yeast HAT complex, NuA4 (nucleosome acetyltransferase of H4) – using a bypass suppression screen to identify suppressors of ESA1. It is proposed that suppressing mutations will alter a gene involved in the process that is the essential function of ESA1. Thus, identifying a suppressor that can bypass the need for ESA1 may provide insight into its essential function. Since ESA1 is an essential gene, a haploid esa1∆ strain in which wild-type ESA1 is provided on a centromeric plasmid was utilized. The bypass suppression screen resulted in suppressors of ESA1 that allowed esa1∆ cells to be viable even in the absence of the essential gene. These second site suppressors (sup-) of ESA1 each show the Mendelian segregation pattern of the suppressing gene and ESA1 in 2:2 ratios, implying they are single genes unlinked to ESA1. Microarray and nuclear morphology studies show abnormal gene expression and morphology of the esa1- sup- cells, further implicating the suppressing mutation in DNA repair and replication processes. Investigating ESA1’s essential role and a probable conservation of function across species can provide a deeper understanding of the capabilities of HAT complexes.
Keywords: Comparison of strains lacking essential ESA1 gene to those containing an ESA1 bypass suppressor.

overall_design: Eight samples were analyzed. The only variables are the ESA1 and SUP2 genes. WT (ESA1 SUP2), 2 replicates. Single mutant (ESA1 sup2-), 3 replicates. Double  mutant (esa1 sup2-), 3 replicates.


title: Effects of ACTH and DEX on gene expression in rat kidneys

status: Public on Nov 01 2007

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

summary:
The left kidneys of 8 Sprague-Dawley rats were removed and the rats were left for 2 weeks to recover. After 4 additional days (during which blood pressure measurements were obtained), they were injected daily subcut. with either saline (1ml/kg), adrenocorticotropic hormone (ACTH, 0.2mg/kg) or dexamethasone (DEX, 0.02mg/kg) for 8 days before the right kidney was removed. ACTH and DEX treatment caused hypertension in the rats as illustrated by increased systolic blood pressure. The gene expression patterns of the kidneys were analysed using Affymetrix arrays.
Keywords: repeat

overall_design: The left kidney of each rat acts as a control for the treated right kidney. Two rats each were treated with either saline, ACTH or DEX.

first: Katja

middle: U

last: McKenzie

first: Frances

last: Shannon

first: Judith

last: Whitworth


title: Alterations in the ovarian transcriptome during primordial follicle assembly and development.

status: Public on Oct 12 2007

first: Michael

last: Skinner

summary:
The assembly of the developmentally arrested primordial follicle and subsequent transition to the primary follicle are poorly understood processes critical to ovarian biology. Abnormal primordial follicle development can lead to pathologies such as premature ovarian failure. The current study used a genome-wide expression profile to investigate primordial follicle assembly and development. Rat ovaries with predominantly unassembled, primordial, or primary follicles were obtained. RNA from these ovaries was hybridized to rat microarray gene chips, and the gene expression (i.e., ovarian transcriptome) was compared between the developmental stages. Analysis of the ovarian transcriptome demonstrated 148 genes up-regulated and 50 genes down-regulated between the unassembled and primordial follicle stages. Observations demonstrate 80 genes up-regulated and 44 genes down-regulated between the primordial and primary follicle stages. The analysis demonstrated 2332 genes common among the three developmental stages, 146 genes specific for the unassembled follicles, 94 genes specific for the primordial follicles, and 151 genes specific for the primary follicles. Steroidogenic genes are up-regulated between unassembled and primordial follicles, and then many are again down-regulated between primordial and primary follicles. The hormones inhibin and Mullerian inhibitory substance (MIS) display a similar pattern of expression with the highest levels of mRNA in the primordial follicles. Several novel unknown genes that had dramatic changes in expression during primordial follicle development were also identified. Gene families/clusters identified that were up-regulated from unassembled to primordial follicles include growth factors and signal transduction gene clusters, whereas a down-regulated gene family was the synaptonemal complex genes associated with meiosis. Gene families/clusters that were up-regulated between primordial and primary follicles included immune response genes, metabolic enzymes, and proteases, whereas down-regulated gene families include the globulin genes and some steroidogenic genes. The expression of several growth factors changed during primordial follicle development, including vascular endothelial growth factor and insulin-like growth factor II. Elucidation of how these changes in gene expression coordinate primordial follicle assembly and the primordial to primary follicle transition provides a better understanding of these critical biological processes and allows selection of candidate regulatory factors for further investigation.
Keywords: expression analysis, developmental time course, follicle assembly, ovary

overall_design: RNA samples from two control groups (pooled untreated cultured ovaries) are compared to two treated groups (pooled cultured ovaries treated with progesterone)

first: Phillip

last: Kezele

first: Jacquelyn

last: Aque

first: Eric

last: Nilsson


title: Development of Progressive Aortic Vasculopathy in a Rat Model of Aging

status: Public on Oct 29 2007

city: Indianapolis

first: Steven

last: Miller

state: IN

address: 1001 West 10th Street

department: Surgery

institute: Indiana University School of Medicine

summary:
This study utilized a standard rat model of aging and global gene expression analyses to attempt to identify the most appropriate time points to study vascular aging and to identify molecules associated with the development of pathology.
Recent studies have established that age is the major risk factor for vascular disease.  Numerous changes occur in vascular structure and function during aging, and animal models, including rodents, are the primary means to determine the underlying mechanisms of age-mediated vascular pathology.  This study utilized a standard rat model of aging and both morphometric and global gene expression analyses to attempt to identify the most appropriate time points to study vascular aging and to identify molecules associated with the development of pathology.  Morphometric analysis of Fischer 344/Brown Norway F1 hybrid (F344xBN) rat thoracic aorta indicated, in contrast to some previous studies, that progressive increases in intimal and medial thickness, as well as smooth muscle cell-containing intimal protrusions, occurred with age.  This structural vascular pathology was associated with a progressive increase in global differential gene expression.  Specific molecules with altered mRNA and protein expression included the adhesion molecules ICAM-1 and VCAM-1, and the bone morphogenic proteins osteopontin and bone sialoprotein-1.  Intimal-associated macrophages were detected with immunohistochemistry in paraffin sections of thoracic aorta and were found to increase significantly in number with age.  Both systemic and tissue markers of oxidant stress, serum 8-isoprostane and 3-nitrotyrosine, respectively, were found to increase during aging.  The results demonstrate that increased inflammation and oxidant stress occur progressively during vascular aging, and suggest therapeutic targets to limit or reverse aging-associated vascular pathology and dysfunction.
Keywords: time course

overall_design: Samples were taken from rats at 4 ages, 3mo, 6mo, 15mo and 28 mo,  with 4 replicates in each age group.

first: William

last: Watson

first: Kimberly

last: Kerr

first: Carlos

last: Barrere

first: Neal

middle: X

last: Chen

first: Mark

last: Deeg

first: Lang

last: Li

first: Joseph

last: Unthank


title: Characterization of zfs1 as an mRNA binding and destabilizing protein in Schizosaccharomyces pombe

status: Public on Nov 28 2007

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Tristetraprolin is a vertebrate CCCH tandem zinc finger protein that can bind to and destabilize certain mRNAs containing AU-rich element binding sites. zfs1 is the single gene in the fission yeast, Schizosaccharomyces pombe, that encodes a protein containing the critical features of the tristetraprolin zinc finger domain. zfs1 has been linked to pheromone signal transduction control and to the coordination of mitosis, but no biological function has been ascribed to the zfs1 protein. Through a functional genomics approach we compared transcript levels in wild-type and zfs1-deficient S. pombe strains; those elevated in the zfs1-deficient strain were examined for the presence of potential tristetraprolin-like binding sites. One such potential target transcript was encoded by arz1, a gene encoding a protein of unknown function that contains armadillo repeats. arz1 mRNA decay was inhibited in the zfs1-deficient strain when it was expressed under the control of a thiamine-repressible promoter. Mutations within one AU-rich element present in the arz1 3’-untranslated region protected this transcript from zfs1-promoted decay, whereas mutating another potential binding site had no effect. Binding assays confirmed a direct interaction between zfs1 and arz1 mRNA-based probes; this interaction was eliminated when key residues were mutated in either zfs1 zinc finger. zfs1 and its targets in S. pombe represent a useful model system for studies of zinc finger protein/AU-rich element interactions that result in mRNA decay.
Keywords: knockout comparison, steady-state analysis

overall_design: S. pombe wild-type and zfs1-deficient strains were grown to 1.0 A600 in EMM+5S at 30°C for steady state analysis.  Total cellular RNA was prepared from four replicate cultures.

first: Brandon

last: Cuthbertson

first: Yanhong

last: Liao

first: Lutz

last: Birnbaumer

first: Perry

last: Blackshear


title: A Phase II Study of Neoadjuvant Gemcitabine Plus Doxorubicin Followed by Gemcitabine Plus Cisplatin in Breast Cancer

status: Public on Jan 12 2008

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
This phase II study examined the pathological complete response (pCR) rate and safety of two gemcitabine-based combinations administered sequentially in breast cancer. We also examined gene expression profiles from tumor biopsies to identify biomarkers predictive of response.
Methods: Indian women with large or locally advanced breast cancer received 4 cycles of gemcitabine 1200 mg/m2 plus doxorubicin 60 mg/m2 (Gem+Dox), then 4 cycles of gemcitabine 1000 mg/m2 plus cisplatin 70 mg/m2 (Gem+Cis), and surgery. To examine dynamic changes in molecular profiles after one dose of therapy, we used three alternate sequences during cycle 1 (Gem d1, 8; Dox d2; Gem d1, 8; Dox d1; or Gem d2, 8; Dox d1).
Results: Of 65 women (median age 46) treated, 13 (24.5% of 53 patients with surgery) had a pCR and 22 (33.8%) had a complete clinical response. Patients who received Gem d1, 8 and Dox d2 in cycle 1 (20/65) reported more toxicities, with G3/4 neutropenic infection/febrile neutropenia (7/20) and vomiting (5/20) as the most common cycle 1 events. Four drug-related deaths occurred. 46/65 patients yielded successful pretreatment gene expression profiles. Ten-fold cross-validated supervised analyses identified gene expression patterns that predicted with >73% accuracy (1) clinical complete response after eight cycles, (2) overall clinical complete response, and (3) pCR.
Conclusions: This neoadjuvant regimen showed strong activity. A subset of patients receiving Gem d1, 8 and Dox d2 experienced unacceptable toxicity, whereas patients on other sequences had more manageable safety profiles. The predictive gene expression patterns may provide a method for selecting patients most likely to benefit from gemcitabine-containing neoadjuvant therapy.
Key words: breast cancer, chemotherapy, gemcitabine, , gene expression, microarrays, neoadjuvant therapy

Keywords: Dose response

first: Pramond

last: Julka


title: Chronic rat exposure to cigarette smoke

status: Public on Dec 11 2007

city: Horsham

first: Christopher

last: Stevenson

address: Wimblehurst Road

department: Respiratory Diseases

institute: Novartis Institutes for BioMedical Research

summary:
Chronic obstructive pulmonary disease is a smoking-related disease that lacks effective therapies due partly to the poor understanding of disease pathogenesis.  The aim of this study was to identify molecular pathways which could be responsible for the damaging consequences of smoking. To do this, we employed recently described bioinformatic methods to analyze differences in global gene expression, which we then related to the pathological changes induced by cigarette smoke (CS).  Sprague-Dawley rats were exposed to whole-body CS for 1 day and for various periods up to 8 months.
Keywords: Timecourse

overall_design: Timecourse with 12 timepoints with 8 replicates at each time point.


title: Effects of maternal vitamin A administration on the transcriptional profile of rat ductus arteriosus

status: Public on Sep 30 2007

city: Setagaya

first: Yoji

last: Sato

state: Tokyo

address: 1-18-1 Kami-yoga

department: Cell. Gene Thpy. Prod.

country: Japan

institute: NIHS

summary:
The effects of retinoic acid/vitamin A signal on the transcriptional profile of the ductus arteriosus during development were examined.
Keywords: time course, development, response to a nutritional agent

overall_design: Total RNA samples were isolated from pooled tissues obtained from Wister rat embryos on embryonic day 19 and 21, and from neonates on the day of birth (n>=120).  The RNA was converted to biotin-labeled cRNA, which was hybridized to Affymetrix RG_U34A microarray.  The hybridization experiments were performed in duplicate.

first: Utako

last: Yokoyama

first: Seiichi

last: Ishida

first: Junichi

last: Sawada

first: Yasuo

last: Ohno

first: Mari

last: Iwamoto

first: Hideaki

last: Hori

first: Shumpei

last: Yokota

first: Yoshihiro

last: Ishikawa

first: Susumu

last: Minamisawa


title: A perturbation in the system leads to period doubling

city: Duarte

first: Robert

last: Klevecz

state: CA

address: 1450 E. Duarte Rd.

department: Biology

institute: Beckman Research Institute of the City of Hope

summary:
Perturbation of the gated-synchrony system in yeast with phenelzine, an antidepressant drug used in the treatment of affective disorders in humans, leads to a rapid lengthening in the period of the genome-wide transcriptional oscillation. The effect is a concerted, genome-scale change in expression that is first seen in genes maximally expressed in the late-reductive phase of the cycle, doubling the length of the reductive phase within two cycles after treatment. Clustering of genes based on their temporal patterns of expression yielded just three super clusters whose trajectories through time could then be mapped into a simple 3D figure. In contrast to transcripts in the late-reductive phase, most transcripts do not show transients in expression relative to others in their temporal cluster but change their period in a concerted fashion. Mapping the trajectories of the transcripts into low-dimensional surfaces that can be represented by simple systems of differential equations provides a readily testable model of the dynamic architecture of phenotype. In this system, period doubling may be a preferred pathway for phenotypic change. As a practical matter, low-amplitude, genome-wide oscillations, a ubiquitous but often unrecognized attribute of phenotype, could be a source of seemingly intractable biological noise in microarray studies.
Keywords: Time Course Experiment

overall_design: Phenelzine was added to the system after the first cycle to induce period doubling

first: Caroline

last: Li


title: Expression data from rat uterine myometrium -effect of estrogen

status: Public on Sep 21 2007

city: Kansas City

first: Dora

last: Agbas

state: KS

address: 3901 Rainbow blvd.

department: Physiology

institute: University of Kansas Medical Center

summary:
Uterine tissue is highly responsive to estrogen, which plays a mayor role in sympathetic innervation remodeling in myometrium
Microarrays were used to investigate which estrogen resposive myometrial proteins can be involved in innervation modulation
Keywords: control vs. treatment, timepoints

overall_design: Mature female rats were ovariectomized, than treated with estradiol benzoate or vechicle, myometrial samples were analyzed 6 or 24 h after treatment

first: Peter

middle: G

last: Smith

first: Tetyana

last: Pedchenko


title: Functional Gene Expression Differences between Inbred Alcohol-Preferring (iP) and  non-preferring (iNP) Rats

status: Public on Jul 28 2007

city: Westfield

first: Mark

middle: William

last: Kimpel

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

summary:
The objective of this study was to test the hypothesis that innate differences in gene expression in the brain could
contribute to the differences in alcohol drinking or response to alcohol between adult male inbred alcohol-preferring (iP) and -non-preferring
(iNP) rats. Gene expression was determined in the nucleus accumbens (ACB), amygdala (AMYG), frontal cortex (FC), caudate-putamen (CPU) and
hippocampus (HIP) of alcohol-naïve adult male iP and iNP rats, using Affymetrix Rat Genome U34A microarrays (n = 6/strain).
Significant differences between the two strains for each region were determined using Statistical Analysis of Microarrays (SAM).
Using a false discovery rate threshold of 0.2, there were 46 genes with higher expression in iP rats and 61 genes with lower expression in
the ACB, 111 genes with higher and 56 genes with lower expression in the AMYG, 61 genes with higher and 25 genes with lower expression in the FC,
39 genes with higher and 42 genes with lower expression in the CPU, and 35 genes with higher and 51 genes with lower expression in the HIP.
In the AMYG, iP rats had higher expression of genes that are involved in neuronal growth and neurogenesis, e.g., brain derived neurotrophic factor,
neuritin, etc. In contrast, in the ACB, iP rats had lower expression of genes involved in neurogenesis or cellular plasticity,
e.g. cyclin E, vascular endothelial growth factor A. Many of the differences were in genes involved in intracellular signaling,
cell membranes, extracellular matrix, and metabolism. These regional gene differences between the iP and iNP rat lines may contribute to
the divergent alcohol drinking phenotypes of these rats.
Keywords: alcohol, inbred, rat, gene expression, brain, nucleus accumbens, amygdala, frontal cortex, hippocampus, caudate-putamen

overall_design: Brain regions (accumbens, amygdala, frontal cortex, hippocampus, and striatum) from 6 biologic replicates of the selected inbred alcohol preferring and non-preferring lines iP5C and iNP1 were dissected and subjected to microarray analysis for comparison.

first: Wendy

last: Strother

first: Jeanette

last: McClintick

first: Lucinda

last: Carr

first: William

middle: J

last: McBride

first: Howard

last: Edenberg


title: Agreement in Breast Cancer Classification between Microarray and qRT-PCR from Fresh-Frozen and Formalin-Fixed Tissues

status: Public on Apr 20 2007

first: Charles

last: Perou

summary:
Determining agreement in classification between platforms and procurement methods requires a variety of methods. We have shown that centroid-based algorithms are robust classifiers for breast cancer subtype assignment across platforms (microarray and qRT-PCR data) and procurement conditions (fresh frozen and formalin-fixed, paraffin-embedded tissues). On a gene-by-gene basis, we found that the standard deviation, dynamic range, and concordance correlation coefficient are important parameters to assess individual primer set performance across procurement methods. Our strategy for primer set validation and classification have applications in routine clinical practice for stratifying breast cancers and other tumor types
Keywords: reference x sample

overall_design: We used microarray data from 124 breast samples as a training set for classifying tumors into 4 previously defined molecular subtypes: Luminal, HER2(+)/ER(-), basal-like, and normal-like. We used the training set data in 2 different centroid-based algorithms to predict sample class on 35 breast tumors (test set) procured as FF and FFPE tissues (70 samples). We classified samples on the basis of large and minimized gene sets.

first: Michael

last: Mullins


title: Molecular Signatures of Trauma Hemorrhagic Shock-Induced Lung Injury: Hemorrhage- and Injury-Associated Genes

status: Public on Jul 25 2007

city: Newark

first: Virginie

middle: Marie

last: Aris

state: NJ

address: W420M, 225 Warren St

department: Center For Applied Genomics

institute: PHRI-UMNDJ

summary:
The etiology of trauma-hemorrhage shock-induced acute lung injury has been difficult to elucidate due, at least in part, to the inability of in vivo studies to separate the non-injurious pulmonary effects of trauma-hemorrhage from the tissue injurious ones.  To circumvent this in vivo limitation, we utilized a model of trauma-hemorrhagic shock (T/HS) in which T/HS-lung injury was abrogated by dividing the mesenteric lymph duct.  In this way, it was possible to separate the pulmonary injurious response from the non-injurious systemic response to T/HS by comparing the pulmonary molecular response of rats subjected to T/HS which did and did not develop lung injury as well as to non-shocked rats.  Utilizing high-density oligonucleotide arrays and treatment group comparisons of whole lung tissue collected at 3 hours after the end of the shock or sham-shock period, 139 of the 8,799 assessed genes were differentially expressed.
Keywords: Treatment response to shock

overall_design: Four groups of rats (n=3) were studied in order to identify changes in pulmonary gene expression associated with T/HS, both in the presence and absence of lung injury.  These included trauma-sham shock (T/SS) rats which had a laparotomy (trauma) but were not subjected to hemorrhagic shock.  These rats had no lung injury and served as controls for rats which were subjected to T/HS (laparotomy plus 90 min of shock) and had lung injury.  Differences in gene expression between these two groups would represent both the effects of hemorrhagic shock as well as lung injury.  To distinguish the gene response of hemorrhagic shock from the gene response associated with lung injury, gene expression was also compared between T/HS rats (hemorrhage and lung injury) and rats subjected to T/HS plus lymph duct ligation (T/HS-LDL), since the T/HS-LDL rats experienced hemorrhagic shock but had no measurable lung injury.  Lastly, to identify hemorrhagic shock- modified genes, the pulmonary gene response of T/HS-LDL (hemorrhage without lung injury) were compared to rats subjected to T/SS plus LDL (no hemorrhage or lung injury).  Three hours after the end of the 90 min shock or sham-shock period (i.e. 4.5 hrs after the induction of T/HS), the rats were sacrificed and specimens harvested for genechip analysis and histology.

first: Rena

last: Feinman

first: Edwin

middle: A

last: Deitch

first: Hung

last: Chu

first: Billy

last: Abungu

first: DaZhong

last: Xu

first: Qi

last: Lu

first: Frank

last: Caputo

first: Iriana

last: Colorado

first: Deanna

last: Streck

first: James

last: Dermody

first: Patricia

last: Soteropoulos


title: Rat duodenum during immobilization

status: Public on Mar 09 2007

city: Tokushima

first: Tadatoshi

last: Sato

address: 3-18-15, Kuramoto-cho

institute: Department of Clinical Nutrition, Institute of Health Biosciences, The University of Tokushima Graduate School

summary:
In the present study, we examined duodenal gene expression in rats subjected to immobilization, to elucidate the mechanism of the stress response in the duodenum.
Keywords: stress response

overall_design: Total RNA was extracted from the duodenal mucosa with an acid guanidinium thiocyanate-phenol-chloroform mixture. Total RNA was analyzed using the rat genome U34A microarray (Affymetrix). Gene intensity information was converted to a mean intensity for each gene using the manufacturer’s proprietary software (version 4.0; Affymetrix), which includes routines for data filtering and normalization.


title: Hypertensive Rat Kidney Study: Gender-Selective Responses to Salt in Dahl-Iwai & Sprague-Dawley Rats

status: Public on Jul 01 2007

city: West Point

first: David

middle: Lee

last: Gerhold

state: PA

address: Broad St & Sumneytown Pk

department: Mol Invest Toxicol

institute: Merck & Co.

summary:
Dahl-Iwai (DI) salt-sensitive rats were studied using microarrays to identify gender-specific differences in the kidney, both basal differences and responses to a high salt diet. In DI rat kidneys, gene expression profiles demonstrated inflammatory and fibrotic responses selectively in females. Gonadectomy of DI rats abrogated gender differences in gene expression. Gonadectomized female and gonadectomized male DI rats both responded to high salt with the same spectrum of gene expression changes as intact female DI rats. Androgens dominated the gender selective responses to salt. Several androgen-responsive genes were identified with roles potentiating the differential responses to salt including increased male expression of Angiotensin-Vasopressin Receptor and Prolactin Receptor, decreased 5-alpha reductase, and mixed increases and decreases in expression of Cyp4a- genes that can produce eicosanoid hormones. These gender differences potentiate sodium retention by males, and increase kidney function during gestation by females.
Keywords: Disease-State Analysis (Salt-Sensitive Hypertension)

overall_design:
- 68 samples/rats/data tables are represented.
- One microarray was used for each sample.
- 3 rat

first: Daniel

last: Holder

first: Magdalena

last: Alonso-Galicia

last: Figueroa

first: Christopher

last: Austin

first: Ansuman

last: Bagchi

first: Meiqing

first: Brett

last: Connolly

first: Kevin

last: Keenan

first: Hong

last: Jin

first: Yuhong

last: Wang


title: Ethanol induced hepatic gene expression changes during gestation

status: Public on Dec 03 2006

first: Kartik

last: Shankar

summary:
The specific role of nutritional status during gestation in exacerbating or mitigating fetal toxicity of ethanol (EtOH) remains unclear. We used an intragastric infusion model (Total enteral nutrition, TEN) to appropriately control for dietary EtOH consumption and caloric intake. Time impregnated female Sprague Dawley rats (250-300 g) were surgically cannulated with intragastric cannulae (on gestation day 4) and infused either control or EtOH-containing diets. Rats were fed 220 kcal/ kg3/4/d (NRC recommended caloric intake for gestation) or 160 kcal/ kg3/4/d (undernourished to 72% of control) diets containing either 12 g/kg/d EtOH or an isocaloric amount of carbohydrates from gestation days 6-15. Maternal hepatic gene expression profiles were assessed on GD15. The present data dissect specific effects of nutritional status during gestation and EtOH intake and the interaction thereof. The data reveal a highly significant interaction between undernutrition and EtOH consumption.
Keywords: Nutrition-gene interactions

overall_design:
Four groups of time impregnated female Sprague Dawley rats were utilized.
Group 1: Control, TEN-220, control group fed normal (non-EtOH containing) diets at 220 kcal/ kg3/4/d.
Group 2: Ethanol-220, EtOH-220 (EtOH group fed EtOH containing diets) at 12 g EtOH/kg/d diets at 220 kcal/ kg3/4/d.
Group 3: Control-160, TEN-160, (undernourished control group fed normal (non-EtOH containing) diets at 160 kcal/ kg3/4/d.
Group 4: Ethanol-160, EtOH-160, (undernourished rats fed EtOH containing diets) at 12 g EtOH/kg/d diets at 160 kcal/ kg3/4/d

first: Mats

last: Hidestrand

first: Rijin

last: Xiao

first: Charles

last: Skinner

last: Simmen

first: Thomas

last: Badger

first: Martin

last: Ronis


title: IFN-gamma activation of cultured neonatal rat microglia

status: Public on Jan 10 2007

city: London

first: Linda

last: Moran

address: Fulham Palace Road

department: Neuropathology

institute: Imperial College London

summary:
IFN-gamma is a classical microglial stimulant. We used microarrays to investigate the microglial gene regulatory network activated by interferon-gamma.
Keywords: Microglia activation

overall_design: Primary rat microglia cultures were established and maintained for 15 days.  For activation studies, fresh media containing IFN-gamma (100 U/ml) were added and left overnight (16 hours).  Total RNA was extraction and hybridized on Affymetrix microarrays (RG_U34A). Five arrays were run from total RNA derived from unstimulated 5 independent cultures (Mgl_CON1, Mgl_CON2, Mgl_CON3,  Mgl_CON5 and Mgl_CON6).  Three standard microglial cultures were stimulated (Mgl_IFNgamma_2 and Mgl_IFNgamma_3) with one of the samples analysed in triplicate as a technical control (Mgl_IFNgamma_1a, Mgl_IFNgamma_1b and Mgl_IFNgamma_1c).

first: Dawn

last: Duke

first: Manuel

last: Graeber


title: Activity- and mTOR-Dependent Suppression of Kv1.1 Channel mRNA Translation in Dendrites

status: Public on Nov 21 2006

city: San Francisco

first: Kimberly

middle: Frances

last: Raab-Graham

institute: UCSF

summary:
Mammalian target of rapamycin (mTOR) is implicated in synaptic plasticity and local translation in dendrites. Here we found that the mTOR inhibitor, rapamycin, increased the Kv1.1 voltage-gated potassium channel protein in hippocampal neurons and promoted Kv1.1 surface expression on dendrites without altering its axonal expression. Moreover, endogenous Kv1.1 mRNA was detected in dendrites. Using Kv1.1 fused to the photo-convertible fluorescence protein Kaede as a reporter for local synthesis, we observed Kv1.1 synthesis in dendrites upon inhibition of mTOR or the N-methyl-D-aspartate (NMDA) glutamate receptor. Thus, synaptic excitation may cause local suppression of dendritic Kv1 channels by reducing their local synthesis.
Keywords: comparison of synaptosomal mRNA to total hippocampal mRNA

overall_design: mRNA isoloated from the synaptosomes of the hippocampus is compared to mRNA isolated from the total hippocampus to identify mRNAs that are enriched at the synapse

first: Patrick

last: Haddick

first: YuhNung

last: Jan

first: Lily

middle: Y


title: Estrogen response after stroke

status: Public on Jul 18 2006

city: Portland

first: Nabil

middle: J.

last: Alkayed

state: OR

address: 3181 S.W. Sam Jackson Pk. Rd., UHS-2

department: Anesthesiology & Peri-Operative Medicine

institute: Oregon Health & Science University

summary:
Estrogen reduces brain injury after experimental cerebral ischemia in part through a genomic mechanism of action. Using DNA microarrays, we analyzed the genomic response of the brain to estradiol, and we identified a transcript, cocaine- and amphetamine-regulated transcript (CART), that is highly induced in the cerebral cortex by estradiol under ischemic conditions. Using in vitro and in vivo models of neural injury, we confirmed and characterized CART mRNA and protein up-regulation by estradiol in surviving neurons, and we demonstrated that i.v. administration of a rat CART peptide is protective against ischemic brain injury in vivo. We further demonstrated binding of cAMP response element (CRE)-binding protein to a CART promoter CRE site in ischemic brain and rapid activation by CART of ERK in primary cultured cortical neurons. The findings suggest that CART is an important player in estrogen-mediated neuroprotection and a potential therapeutic agent for stroke and other neurodegenerative diseases.
Keywords: treated vs control

overall_design:
affy platform; replicate samples; two treated samples, two placebo.

MIAME compliance: All samples were run in commercial arrays from Affymetrix, using Rat Genome U34A GeneChip arrays as described in the Affymetrix web site. The sample information is described below. Likewise, the Affymetrix protocol is detailed and referenced above. These descriptions include all information currently considered under the MIAME supportive guidelines, with which the JHMI Microarray Core Facility abides in all its procedures.

Methodology. Expression profiling using DNA microarrays (One round amplification):

Experimental Design and Sample Information. Transient focal cerebral ischemia was induced in ovariectomized female rats with and without replacement with 17beta-estradiol by intraluminal middle cerebral artery occlusion (MCAO), as described in the manuscript. At 6 and 24 hours after 2-hour MCAO, total RNA was prepared from the ischemic and contralateral cerebral cortex and striatum between coronal levels 2 and 3 mm relative to Bregma, which represent the core of MCA territory. RNA samples from 3 animals were combined into one pooled sample and hybridized to Affymetrix RG-U34A GeneChip, as described below. Each microarray experiment was performed in duplicate using two independent pooled samples per group (6 animals per group at each time point, 2 pooled samples for each brain region per time point).

Microarray Hybridization Protocol. Total RNA was isolated using the RNeasy Mini Kit (QIAGEN). RNA from control and experimental tissue are processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labeling kit (ENZO Life Sciences Inc., Farmingdale, New York).  15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix U34A GeneChip arrays for 16hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

Quality Control. To ascertain the quality control of the total RNA from the samples, we used the Agilent Bioanalyzer, Lab on a Chip technology, and confirmed the rRNA ratios and clean run patterns of the samples. Likewise, this technology is used to confirm the quality of the RNA in the form of cRNA and fragmented cRNA. To assess the QC of the hybridization, GeneChip image, and comparison between chips, we confirmed the following parameters: scaling factor values within comparable range; low background values (50-95); high percentage of present calls (between 30 and 55%); consistent 3’/5’ ratios of GAPDH as representation of housekeeping genes, and presence or absence of Bio B and C as internal spike controls.


title: Dietary exposure to soy or whey proteins alters colonic global gene expression profiles during rat colon tumorigenesis

status: Public on Oct 26 2006

city: Little Rock

address: 2020 Marshall Street

institute: Nutrition Center, Arkansas Chidren's Hospital

summary:
We previously reported that lifetime consumption of soy proteins or whey proteins reduced the incidence of azoxymethane (AOM)-induced colon tumors in rats. To obtain insights into these effects, global gene expression profiles of colons from rats with lifetime ingestion of casein (CAS, control diet), soy protein isolate (SPI), and whey protein hydrolysate (WPH) diets were determined. We identified 31 induced and 49 repressed genes in the proximal colons of the SPI-fed group and 44 induced and 119 repressed genes in the proximal colons of the WPH-fed group, relative to CAS. Hierarchical clustering identified the co-induction or co-repression of multiple genes by SPI and WPH. The differential expression of I-FABP (2.92-, 3.97-fold down-regulated in SPI and WPH fed rats; P = 0.023, P = 0.01, respectively), cyclin D1 (1.61-, 2.42-fold down-regulated in SPI and WPH fed rats; P = 0.033, P = 0.001, respectively), and the c-neu proto-oncogene (2.46-, 4.10-fold down-regulated in SPI and WPH fed rats; P < 0.001, P < 0.001, respectively) mRNAs were confirmed by real-time quantitative RT-PCR. SPI and WPH affected colonic neuro-endocrine gene expression: peptide YY (PYY) and glucagon mRNAs were down-regulated in WPH fed rats, whereas somatostatin mRNA and corresponding circulating protein levels, were enhanced by SPI and WPH. The identification of transcripts co- or differentially-regulated by SPI and WPH diets suggests common as well as unique anti-tumorigenesis mechanisms of action which may involve growth factor, neuroendocrine and immune system genes. SPI and WPH induction of somatostatin, a known anti-proliferative agent for colon cancer cells, would inhibit tumorigenesis
Keywords: Comarative genomic hybridization

overall_design: Male Sprague Dawley rats, fed one of the three purified diets, were studied at 40 weeks after AOM injection and when tumors had developed in some animals of each group. Total RNA, purified from non-tumor tissue within the proximal half of each colon, was used to prepare biotinylated probes, which were hybridized to Affymetrix RG_U34A rat microarrays.

middle: M

first: Frank


title: Halothane/Isoflurane repetitive exposures

city: Philadelphia

first: Roderic

last: Eckenhoff

institute: University of Pennsylvania

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression data from rat soleus during chronic intermittent physical inactivity

status: Public on Jul 04 2006

city: Columbia

first: Theodore

last: Zderic

state: MO

address: E102 Vet. Med. Bldg. / 1600 E. Rollins Rd.

department: Biomedical Sciences

institute: University of Missouri

summary:
Global gene expression of the rat soleus muscle was assessed with microarrays after 11 days of intermittent physical inactivity (10 hr/day) and compared to normally caged rats with voluntary standing and intermittent cage movements.
Keywords: between group design

overall_design: Rats were prevented from standing on the their hindlimbs for 10 hrs/day for 11 days and compared to caged rats with normal standing/ambulatory activity. RNA was extracted from soleus muscles and each array represents the pooling of the RNA from the soleus of 4-5 different rats.

middle: W

first: Lionel

last: Bey

first: Marc

middle: T

last: Hamilton


title: Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production

status: Public on Nov 30 2006

city: Cambridge

first: Joel

last: Moxley

address: 77 Massachusettes Ave

institute: MIT

summary:
Global transcription machinery engineering (gTME) is an approach for  reprogramming gene transcription to elicit cellular phenotypes important for technological applications. Here we show the application of gTME to Saccharomyces cerevisiae for improved glucose/ethanol tolerance, a key trait for many biofuels programs. Mutagenesis of the transcription factor Spt15p and selection led to dominant mutations that conferred increased tolerance and more efficient glucose conversion to ethanol. The desired phenotype results from the combined effect of three separate mutations in the SPT15 gene [serine substituted for phenylalanine (Phe177Ser) and, similarly, Tyr195His, and Lys218Arg]. Thus, gTME can provide a route to complex phenotypes that are not readily accessible by traditional methods.
Keywords: stress response

overall_design: We measured transcription levels for two strains (wild type control and mutant spt15) under normal (0% ethanol, 20 g/L glucose) and stress (5% ethanol, 60 g/L glucose) in biological triplicate.

first: Hal

last: Alper

first: Elke

last: Nevoigt

first: Gerald

middle: R

last: Fink

first: Gregory

last: Stephanopoulos


title: Expression data from rat soleus during acute physical inactivity and walking

summary:
Global gene expression of the rat soleus muscle was assessed with microarrays after 12 hrs of physical inactivity and also after 12 hours of physical inactivity immediately followed by 2 hrs treadmill walking and compared to normally caged rats with voluntary standing and intermittent cage movements.
Keywords: between group design

overall_design: Rats were either prevented from standing on the their hindlimbs for 12 hrs or were prevented from standing on the their hindlimbs for 12 hrs and then immediately engaged in 2 hours treadmill walking and compared to caged rats with normal standing/ambulatory activity. RNA was extracted from soleus muscles and each array represents the pooling of the RNA from the soleus of 8-10 different rats.


title: Mg++ supplemented and deficient diets

status: Public on Aug 11 2006

city: East Hanover

first: Anthony

last: Masiello

address: One Health Plaza

institute: Novartis

summary:
Left lateral lobe liver samples from rats fed Mg++ supplemented diets, standard diets and Mg++ deficient diets.
Keywords: other

first: Hélène

last: Martin

last: Staedtler

first: Christelle

last: Lamboley

first: Markus

last: Adrian

first: Martin

last: Schumacher

first: Salah-Dine

last: Chibout

first: Pascal

last: Laurant

first: Lysiane

last: Richert

first: Alain

last: Berthelot


title: Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae

status: Public on Feb 01 2007

city: Göteborg

first: Goutham

middle: N

last: Vemuri

address: Kemivagen 10

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary:
When the yeast Saccharomyces cerevisiae is subjected to increasing glycolytic fluxes under aerobic conditions, there is a threshold value of the glucose uptake rate at which the metabolism shifts from being purely respiratory to mixed respiratory and fermentative. This shift is characterized by ethanol production, a phenomenon known as the Crabtree effect due to its analogy with lactate overflow in cancer cells. It is well known that at high glycolytic fluxes there is glucose repression of respiratory pathways resulting in a decrease in the respiratory capacity. Despite many years of detailed studies on this subject, it is not known whether the onset of the Crabtree effect (or overflow metabolism) is due to a limited respiratory capacity or caused by glucose-mediated repression of respiration. We addressed this issue by increasing respiration in S. cerevisiae by introducing a heterologous alternative oxidase, and observed reduced aerobic ethanol formation. In contrast, increasing non-respiratory NADH oxidation by overexpression of a water-forming NADH oxidase reduced aerobic glycerol formation. The metabolic response to elevated alternative oxidase occurred predominantly in the mitochondria, while NADH oxidase affected genes that catalyze cytosolic reactions. Moreover, NADH oxidase restored the deficiency of cytosolic NADH dehydrogenases in S. cerevisiae. These results indicate that NADH oxidase localizes in the cytosol, while alternative oxidase is directed to the mitochondria. The onset of aerobic ethanol formation is demonstrated to be a consequence of an imbalance in mitochondrial redox balancing. In addition to answering fundamental physiological questions, our findings are relevant for all biomass derived applications of S. cerevisiae.
Keywords: Genetic Modification

overall_design: Heterologous gene expression in chemostats using Affymetrix Yeast Genome 2.0 arrays. Total RNA extraction and sample preparation, hybridization was done according to the manufacturer's protocol.

first: Mark

last: Eiteman

first: Joan

middle: E

last: McEwen

first: Lisbeth

last: Olsson

first: Jens

last: Nielsen


title: LTM in CA1 Aged versus young rats

status: Public on Jun 30 2006

city: Gainesville

first: Corinna

last: Burger

state: FL

address: 1600 SW Archer Red

institute: University of Florida

summary:
The aim of this study was to investigate whether the differences in memory decline associated with aging are a result of differences in gene expression.  We first categorized age-unimpaired and age-impaired rats based on their performance in the Morris Water Maze and then isolated messenger RNA from the CA1 hippocampal region of each animal to interrogate Affymetrix microarrays.  Microarray analysis (p<0.005) identified a set of 50 genes that were transcribed differently in age-unimpaired animals that had successfully learned a spatial task compared to aged learning-impaired animals and a variety of groups designed to control for all non-learning aspects of exposure to the water maze paradigm.
Keywords: behavior comparison, age comparison

overall_design: a total of 79 samples were analyzed including aged and young rats. One chip was interrogated per animal.  Analysis of aged rat data includes 44 samples.  Controls include cage controls, yoked controls (no platform), visible platform controls.

first: Cecilia

last: Lopez

first: Joyce

last: Feller

first: Henry

middle: H

last: Baker

first: Nicholas

last: Muzyczka

first: Ron

last: Mandel


title: Time course analysis of TSH-stimulated rat thyroid cell lines

status: Public on Oct 01 2006

city: Cusano Milanino

first: Davide

last: Calebiro

address: via Zucchi 18

country: Italy

institute: Istituto Auxologico Italiano

summary:
A time-course analysis of TSH-stimulation in two rat thyroid cell lines (FRTL5 and FRT/TSHR) was performed. The expression levels of 8,784 transcripts were measured at three different time points, i.e. before (0), 30 minutes (30m) and 17 hours (17h) after TSH stimulation, by means of Affymetrix RG-U34A arrays.
Keywords: Time course

overall_design: 2 cell lines, 3 time points and 3 biological replicates per time point were analyzed


title: Effect of 13 weeks of subchronic exposure to TCDD, PeCDF, PCB126, PCB153 and PCB126/PCB153 on hepatic gene expression

status: Public on Sep 08 2006

city: Buffalo

first: Bladimir

middle: Jason

last: Ovando

address: 102 Farber Hall

department: Pharmacology & Toxicology

institute: University at Buffalo

summary:
This study investigates the effects of the aryl hydrocarbon receptor (AhR) ligands TCDD, PCB126 and PeCDF; the non-AhR ligand PCB153 and the binary mixture PCB126/PCB153 on hepatic gene expression in female sprague dawley rats. Rats were treated with toxicological equivalent doses of TCDD (100ng/kg), PeCDF (200ng/kg), PCB126 (1000ng/kg) and PCB153 (1000ug/kg) 5 days a week for 13 weeks.
Keywords: Environmental pollutant toxicity comparison

overall_design: There are 6 control chips and representing animals treated with vehicle control. There are 3 biological replicates (3 chips) for each treatment group (eg. TCDD, PCB126), each biological replicate is derived from 2 individual animals. A total of 21 chips were analyzed. Intensities were normalized using the GC-Robust Multiarray (GCRMA) method through Genetraffic software package.

first: James

last: Olson

first: Chad

last: Vezina


title: Effect of AT1 receptor anatagonist on brain microvessels from hypertensive and normotensive rats

status: Public on Jun 03 2006

city: Bethesda

first: Juan

last: Saavedra

address: 10 Center Drive

department: Section on Pharmacology

institute: NIMH

summary:
In hypertension, abnormal regulation of microcirculation and endothelial dysfunction enhances vulnerability to hypertensive brain damage. In addition to lowering blood pressure, blockade of Angiotensin II AT1 receptors protects against stroke and stress in different animal models and this treatment may be of therapeutic advantage. We studied gene expression using Affymetrix Rat Genome U34A arrays from brain microvessels of spontaneously hypertensive rats (SHR) and their normotensive Wistar Kyoto controls (WKY) rats treated with an AT1 antagonist (candesartan, 0.3 mg/kg/day) or vehicle via osmotic minipumps for 4 weeks.
Keywords: other

overall_design: brain microvessels from hypertensive and normotensive rats treated with candesartan and vehicle were analyzed

first: Jin

last: Zhou

first: Miroslava

last: Macova


title: Microarray analysis of the dynamics of gene expression plasticity in the supraoptic nucleus following dehydration

status: Public on Aug 15 2006

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

institute: University of Bristol

summary:
The hypothalamo-neurohypophyseal system (HNS) is crucial for osmoregulation. The HNS consists of the magnocellular neurons (MCNs) of the hypothalamus that have their axons terminating in the posterior pituitary. The HNS exerts its role in water balance via the release of the anti-diuretic hormone vasopressin (VP). Following dehydration VP is released into the general circulation. By binding to V2-type receptors located in the kidney, VP decrease the amount of water lost in urine. An osmotic stimulus also elicits an increase in VP gene expression and a functional remodelling of the entire HNS. We want to understand this plasticity in terms of the co-ordinated reprogramming of gene expression. We thus used Affymetrix U34a rat GeneChips to examine the dynamics of gene expression plasticity over the duration of a dehydration stimulus. Arrays were probed in triplicate with targets derived from SON of control rats, and rats dehydrated for 1 and for 3 days. Transcripts were thus identified that respond early to dehydration (up- or down-regulated after only 1day of dehydration), or that respond late (up- or down-regulated at 3 days of dehydration).
Keywords: SON, Dehydration, clone

overall_design: 3 chips hybridised with control SON were compared to 3 chips hybridised with  1 day dehydrated SON and 3 chips hybridised with 3 day dehydrated SON

first: Mohamed

last: Ghorbel

first: Charles

middle: C

last: Hindmarch

first: Thomas

last: Thykjaer

first: Torben

last: Orntoft


title: Temperature upshift in E coli gyrBT strain, time series

status: Public on Mar 09 2006

city: Princeton

first: Dipen

last: Sangurdekar

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary:
Responses of Escherichia coli W3110gyrb234 as they are upshifted to 42C
Keywords: time course

overall_design: Escherichia coli W3110gyrb234 cells sampled at several time points (2,5, 10, 40 min) as they are shifted to 42 C in LB, vs 0 min before upshift in LB

first: Friedrich

last: Srienc

first: Arkady

last: Khodursky


title: Yeast Genomic Expression Patterns in Response to Low-Shear Modeled Microgravity

status: Public on Mar 01 2006

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary:
The goal of this study was to assess whether low shear-modeled microgravity (LSMMG) effects yeast
genomic expression patterns using the powerful tool of whole genome microarray hybridization. We determined
changes in the yeast model organism, Saccharomyces cerevisisae, when grown in LSMMG using the rotating High
Aspect Ratio Vessel (HARV). A significant number of genes were up- or down-regulated by at least two fold in cells
that were grown for 5 generations or 25 generations in HARVs. We identified genes in cell wall integrity signaling
pathways containing MAP kinase cascades that may provide clues to novel physiological responses of eukaryotic
cells to the external stress of a low-shear modeled microgravity environment.  A comparison of the microgravity
response to other environmental stress response (ESR) genes showed that 26% of the genes that respond
significantly to LSMMG are involved in a general environmental stress response, while 74% of the genes may
represent a unique transcriptional response to microgravity.  In addition, we found changes in genes involved in
budding, cell polarity establishment, and cell separation that confirm our hypothesis that exposure to LSMMG
causes changes in gene transcription resulting in a phenotypic response. The results of the study provide interesting
clues to potential mechanisms involved in the response to, adaptation to, and survival of eukaryotic cells in a
microgravity environment and our findings may have important health implications for human spaceflight.
Keywords: time course, stress response, budding, microgravity

overall_design: Four conditions are compared with three replicates each:  yeast grown in low-shear modeled microgravity (HARV bioreactor) for 5 and 25 generations; yeast grown in a horizontal (non-LSMMG) HARV bioreactor for 5 and 25 generations.

first: Kathy

middle: B

last: Sheehan

first: Boloroo

middle: L

last: Purevdorj-Gage

first: Linda

last: Hyman


title: Expression data from Rat ventricles 3 days/28 days/42 days after STZ injection

status: Public on May 08 2006

city: Cincinnati

first: Mohammed

middle: Abdul

last: Matlib

state: OH

department: Pharmacology and Cell Biophysics

institute: University of Cincinnati

summary:
Cardiomyopathy in type 1 diabetic patients is characterized by early onset diastolic and late onset systolic dysfunction.  The mechanism underlying development of diastolic and systolic dysfunction in diabetes remains unknown.
We used microarrays to detail the ventricle gene expression changes that underly development of diabetic cardiomyopathy.  We identified distinct classes of up-regulated genes during this process.
Keywords: disease state analysis, time course

overall_design: 150g male Wistar rats (Harlan) we injected with 65 mg/kg streptozotocin to induce Type 1 diabetes.  Four replicates of Control and Diabetic rat ventricles were removed and frozen at Three time points for total RNA isolation and hybridization on the Affymetrix RG-U34A microarray.  The 3 day samples show a baseline for initial diabetic changes in the ventricle.  The 28 day samples show changes associated with diastolic dysfunction in diabetes.  The 42 day samples show changes associated with both diastolic and systolic dysfunction in type 1 diabetic rat ventricles.

first: Lamar

middle: K

last: Gerber

first: Bruce

middle: J

last: Aronow


title: Methylation induced by the RAS oncogene

status: Public on Mar 12 2006

city: Berlin

first: Christine

last: Sers

address: Schumannstr. 20/21

department: Institute of Pathology

country: Germany

institute: Charite

summary:
Silencing of gene expression by methylation of CpG islands in regulatory elements is frequently observed in cancer. However, an influence of the most common oncogenic signalling pathways onto DNA methylation has not yet been investigated thoroughly. To address this issue, we identified genes suppressed in HRAS-transformed rat fibroblasts but up-regulated after treatment with the demethylating agent 5-Aza-CdR and with the MEK1,2 inhibitor U0126. Analysis of gene expression by microarray and Northern blot analysis revealed the MEK/ERK target genes clusterin, Mmp2, Ppicap, syndecan 4, Timp2, Thbs1 to be repressed in the HRAS-transformed FE-8 cells in a MEK/ERK- and in a methylation-dependent manner. Hypermethylation of putative regulatory elements in HRAS-transformed cells as compared to immortalized fibroblasts was detected within a CpG island 14.5 kb upstream of clusterin, within the clusterin promoter and within a CpG island of the Mmp2 promoter by bisulphite sequencing. Furthermore, hypermethylation of the clusterin promoter was observed ten days after induction of HRAS in immortalized rat fibroblasts and a clear correlation between reduced clusterin expression and hypermethlyation could also be observed in distinct rat tissues. These results suggest that silencing of individual genes by DNA methylation is controlled by oncogenic signalling pathways, yet the mechanisms responsible for initial target gene suppression are variable.
Keywords: expression analysis

overall_design: Gene expression was analyzed in immortal (208F) and HRAS oncogene-transformed (FE8) rat fibroblasts after demethylation by 5-aza-2'-deoxycytidine. Genes potentially methylated in RAS-transformed cells were identified by bisulphite sequencing


title: Genetic susceptibility to mammary carcinogenesis among rat strains

status: Public on Dec 30 2005

city: Seattle

first: Xuefeng

last: Ren

state: WA

institute: Fred Hutchinson Cancer Research Center

summary:
32 arrays from 6 rat strains
Keywords: other

first: Helmut

last: Zarbl

first: Andrea

last: Kim


title: Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells

status: Public on Feb 07 2006

city: College Station

first: Gus

middle: John

last: Menger

state: TX

department: Anatomy and Neurobiology

institute: Texas A&M Health Science Center


title: normal and diabetic rat muscle treated and untreated with vanadyl sulfate

status: Public on Mar 05 2006

first: Gail

last: Willsky

state: NY

address: 140 Farber Hall

department: Biochemistry

summary:
RNA was obtained from rear leg muscle of normal and diabetic rats in the presence and absence of oral treatment with vandyl sulfate. Diabetes was induced with streptozotocin and expression profiles were determined using Affymetrix Rat Genechip U34A.  The effect of treatment and disease on gene expression was examined.
Keywords: vanadium treatment

overall_design:
4 groups (normal, diabetic, normal treated with vanadyl sulfate and diabetic treated with vanadyl sulfate) with 5 replicates in each group were analyzed.

PMID:16403228 discusses 2 groups (normal, diabetic).
PMID:16684804 discusses all four groups.

first: Lai-Har

last: Chi

first: Yulan

last: Liang

first: Daniel

middle: P

last: Gaile

first: Zihua

last: Hu

first: Debbie

last: Crans


title: Organ - specific expression profiles of rat treated with targretin, 9-cis retinoic acid, and 4-hydroxyphenylretinamide

status: Public on Dec 31 2005

city: st louis

first: Yan

last: Lu

address: 660 s. euclid ave

institute: washington univ.

summary:
A rexinoid, targretin (TRG) and two retinoids, 9-cis retinoic acid (9cRA) and 4-hydroxyphenylretinamide (4HPR) were examined for their effects on gene expression in rat mammary gland, liver, and lung tissues. The chemopreventive effects of these agents have largely been attributed to their ability to interact with retinoic acid receptors (RAR) and/or retinoid X-receptors (RXR). TRG interacts with the RXR receptors. 9cRA interacts with both the RAR and RXR receptors, while 4HPR has a moderate affinity primarily for RAR gamma. Based on previously performed mammary chemoprevention studies, TRG (150mg/Kg diet), 9cRA (100 mg/Kg diet), and 4HPR (792 mg/Kg diet), were administrated to rats continually in their diet for 7 days. Tissue - and agent - specific expression differences were determined by comparing tissues from treated rats with those form rats administered a control diet. There were significantly more changes seen associated with TRG than 9cRA or 4HPR. Only a limited number of expression changes were found with 4HPR treatment. For each organ, TRG and 9cRA treated tissues clustered closely together, whereas 4HPR treated tissues clustered with the tissues from the control diet group. In contrast to 9cRA treatment, TRG treatment altered genes that involved fatty acid metabolism and modulation of various cytochromes P450 in the liver clearly demonstrating the very disparate nature of these two retinoids. These expression signatures could provide useful pharmacodynamic biomarkers for retinoids’ treatment and chemoprevention.
Keywords: parallel sample

overall_design:
Agent : The 3 agents were obtained from NCI Chemical Repository (Bethesda, MD), Targretin, 9-cis retinoic acid, and 4-hydroxyphenylretinamide.
Rat :Female Sprague-Dawley rats were used (Harlan Sprague-Dawley, Inc. Indianapolis, IN)
Treatment: Starting at 100 days of age, the rats received treatment of TRG (60 mg/kg BW, gavage), 9cRA (100 mg/kg diet), or 4HPR (782 mg/kg diet) for 7 days. At the end of the 7-day treatment, normal mammary gland, liver and lung tissues were collected.

first: Yian

last: Wang

first: Ming

last: You


title: Ochratoxin A study on rat liver and kidney gene expression

status: Public on Dec 19 2005

city: Lausanne

first: James

last: Holzwarth

state: Vaud

address: vers chez les blanc

department: Bioanalytical Sciences

country: Switzerland

institute: Nestle Research Center

summary:
Ochratoxin A gene expression profiling in liver and kidney, with time points of exposure from 7 days to 12 motnhs
Keywords: timecourse

overall_design: three replicates for each timepoint measured, control and ochratoxin A treated for both liver and kidney

first: Maricel

last: Marin-Kuan


title: Downstream targets of Pax6 in the early developing rat brains

status: Public on Oct 06 2005

city: Sendai

first: Yoko

last: Arai

state: Miyagi

address: 2-1, Seiryo-machi, Aoba-ku,

department: Div. Devel. Neurosci

institute: Tohoku Univ. Sch. of Med

summary:
Pax6 is a transcription factor that is expressed in neuroepithelial cells from the initial stage of brain development.  Region specific expression of Pax6 plays pivotal roles in the developing CNS, including brain patterning, neuronal specification, neuronal migration, and axonal projection.  Regarding neurogenesis, Pax6 multiply works either as to promote neuronal differentiation or cell proliferation in a highly context-dependent manner.  However, no Pax6 target gene is identified as to promote proliferation and/or inhibit differentiation of neuroepithelial cells.  Here, we performed comparative analysis using the Affymetrix U34A array to identify genes that are differentially expressed in the early stage of wild-type and Pax6 homozygous mutant rat (rSey2/rSey2) brains.
Keywords = Pax6 transcription factor
Keywords = rat
Keywords = forebrain and hindbrain regions of the wild-type or Pax6 homozygous embryos
Keywords = up-or down-regulated genes
Keywords: ordered

first: Nobuo

last: Funatsu

first: Keiko

last: Numayama-Tsuruta

first: Tadashi

last: Nomura

first: Shun

last: Nakamura

first: Noriko

last: Osumi


title: Aging laryngeal muscle: shifts in gene expression patterns and function

status: Public on Sep 17 2005

city: Lexington

first: Colleen

middle: A

last: McMullen

state: KY

address: 800 Rose St MS508

department: Physiology

institute: University of Kentucky

summary:
Sarcopenia is the decreased muscle mass and weakness associated with aging and a major cause of morbidity and mortality in the elderly. To what extent non-locomotive muscles are susceptible to this condition is unclear. For example, age affects laryngeal function (ventilation, airway protective reflexes, swallowing and phonation). Age-related laryngeal dysfunction may be due to effects on its intrinsic muscles that have a unique phenotype: very small, mostly fast oxidative muscle fibers. For this study, we examined how age alters the functional characteristics and gene expression profile of posterior cricoarytenoid (PCA), an intrinsic laryngeal muscle. PCA muscles from Fischer 344-Brown Norway F1 hybrid rats (6 and 30 months of age) were used for cDNA microarrays, light and electron (EM) microscopy, and in vitro contractile function. Histological analyses demonstrated a ~40% increase in mean PCA fiber size and in the number of fibers with low myosin ATPase activity. There was also evidence of ragged-red fibers, a hallmark of mitochondrial dysfunction. In turn, mitochondrial volume density, determined by EM, was significantly higher in PCA muscles at 30 months (43% vs. 21% at 6 months). In vitro function showed a decrease in velocity of unloaded shortening at 30 months. Finally, cDNA microarrays demonstrated a transcriptome shift in PCA muscle with age. Gene classes with the largest changes were: signal transduction, transcription factors, and metabolic enzymes. These data demonstrate that PCA muscles are significantly altered by age. Moreover, the observed changes in muscle fiber size, mitochondrial content and gene expression profile suggest that the PCA response to age diverges from that seen in more typical skeletal muscles.
Keywords: aging, time course

overall_design: Total RNA was obtained with TRIzol (Invitrogen Carlsbad, CA) following the manufacturers recommended protocol. Tissues from 4 animals were combined into each RNA sample to decrease inter-subject variability. Biotinylated cRNA samples were hybridized to Affymetrix Rat Genome U34 gene chips (n=9 chips) described previously [McMullen et al. 2004]. Microarrays were washed and stained with a streptavidin-bound marker and scanned. Data were analyzed with Affymetrix Microarray Suite 5.0 software. Only genes with consistent absent/present calls in all three independent replicates per group were considered for further analysis. Comparisons used the 6-mo transcriptome as the baseline and the one-sided Wilcoxon’s signed rank test to estimate “increase/no change/ decrease” difference calls for each pair-wise comparison. Only difference calls consistent in all pair-wise comparisons and with average changes > 1.70 were considered significant, resulting in a conservative list of genes with changed expression levels. Functional classification of genes was based on an extensive literature review.

first: Francisco

last: Andrade


title: Sugar stress during fermentation (baker's yeast)

status: Public on Feb 23 2007

city: Tsukuba

first: Jun

last: Shima

state: Ibaraki

address: 1-2-12 Kannondai

department: Applied Microbiology

institute: National Food Research Institute

summary:
Functional genomic analysis using different types of baker's yeast.
Keywords: fermentation

overall_design:
Fermentation at different concentrations of sucrose.

PerChip normalization using only positive (exclude pombe) genes and PerGene normalization were applied using GeneSpring (v7.0).


title: JNK-dependent genes_rVSMC

status: Public on Nov 09 2005

city: Ube

first: Hiroki

last: Aoki

state: Yamaguchi

address: 1-1-1 Minami Kogushi

department: Molecular Cardiovascular Biology

institute: Yamaguchi University School of Medicine

summary:
Oxidative stress-dependent genes are defined as those induced or suppressed by H2O2 treatement in rat vascular smooth muscle cells.
JNK-induced genes in rat vascular smooth muscle cells are defined as those induced by adenoviruses encoding constitutively active MKK7 (caMKK7) + wild type JNK1 (wtJNK1) and suppressed by adenovirus encoding dominant negative JNK1 (APF).
JNK-suppressed genes in rat vascular smooth muscle cells are defined as those suppressed by adenoviruses encoding constitutively active MKK7 (caMKK7) + wild type JNK1 (wtJNK1) and induced by adenovirus encoding dominant negative JNK1 (APF).
Adenovirus encoding nuclear localizing GFP was used as a control.
Keywords = vascular smooth muscle
Keywords = hydrogen peroxide
Keywords = c-Jun N-terminal kinase
Keywords = JNK
Keywords = adenovirus
Keywords = oxidative stress
Keywords: repeat sample

first: Koichi

last: Yoshimura

first: Yasuhiro

last: Ikeda

first: Kozo

last: Fujii

first: Masunori

last: Matsuzaki


title: Biological Classification of Breast Cancer by Real-Time Quantitative RTPCR: Comparisons to Microarray and Histopathology

status: Public on Jan 31 2006

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
Microarrays have shown that gene expression patterns can be used to molecularly classify breast cancers into distinct and clinically significant groups. In order to translate these profiles into routine diagnostics, we have recapitulated a microarray breast cancer classification using real-time quantitative (q)RT-PCR. We performed statistical analyses on multiple independent microarray datasets to select an “intrinsic” gene set that can classify breast tumors into four different subtypes designated as Luminal, Normal-like, HER2+/ER-, and Basal-like. A minimal gene set from the microarray “intrinsic” list, and additional genes important for outcome (e.g., proliferation genes), were used to develop a real-time qRT-PCR assay comprised of 53 classifiers and 3 housekeepers.  We prospectively compared the expression data and classifications from microarray and real-time qRT-PCR using 123 unique breast samples (117 invasive carcinomas, 1 fibroadenoma and 5 normal tissues) and 3 cells lines.  The overall correlation for the 50 genes in common between microarray and qRT-PCR was 0.76. There was 91%  (114/126) concordance in the hierarchical clustering classification of the real-time qRT-PCR minimal “intrinsic” gene set (37 genes) and the larger (402 genes) microarray gene set from which the PCR list was derived. As expected, the Luminal tumors (ER+) had a significantly better outcome than the HER2+/ER- (p=0.043) and Basal-like tumors (p=0.001). High expression of the proliferation genes GTBP4 (p=0.011), HSPA14 (p=0.023), and STK6 (p=0.027) were significant predictors of relapse free survival (RFS) independent of grade and stage. Our study shows that genomic microarray data can be translated into a qRT-PCR diagnostic assay that enhances the ability to predict outcome and may therefore improve the standard of care in breast cancer.
Keywords: other

first: Laurent

last: Perreard

first: Cheng

last: Fan

first: John

middle: F

last: Quackenbush

middle: M

first: Philip

middle: S

last: Bernard

first: Zhiyuan

last: Hu


title: Expression profiling of DRG from L5 spinal nerve ligation model of neuropathic pain in the rat

status: Public on Jul 07 2005

city: London

first: Jakir

last: Ullah

institute: Novartis

summary:
DRG samples were extracted at 28 and 50 days from L5 spinal nerve ligated rats and sham operated rats.  Samples were pooled for each time point per group and hybridised to duplicate to RG_u34 genchips (A, B and C chips).
Keywords: Disease state analysis

overall_design: Samples were pooled and therefore no biological replication was possible on the arrays


title: Identification of novel transcriptional networks in response to the treatment D3T (3H-1, 2-dithiole-3-thione)

status: Public on Aug 24 2005

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary:
3H-1, 2-dithiole-3-thione (D3T), an inducer of antioxidant and phase 2 genes, is known to enhance the detoxification of environmental carcinogens, prevent neoplasia, and to elicit other protective effects. However, a comprehensive view of the regulatory pathways induced by this compound has not yet been elaborated. Fischer F344 rats were gavaged daily for 5 days with vehicle or D3T (0.3 mmol/kg). The global changes of gene expression in liver were measured with Affymetrix RG-U34A chips. Using functional class scoring, a semi-supervised method exploring both the expression pattern and the functional annotation of the genes, the Gene Ontology classes were ranked according to the significance of the impact of D3T treatment. Two unexpected functional classes were identified for the D3T treatment, cytosolic ribosome constituents with 90% of those genes increased, and cholesterol biosynthesis with 91% of the genes repressed. In another novel approach, the differentially expressed genes were evaluated by the Ingenuity computational pathway analysis tool to identify specific regulatory networks and canonical pathways responsive to D3T treatment. In addition to the known glutathione metabolism pathway (ρ = 0.0011), several other significant pathways were also revealed, including antigen presentation (ρ = 0.000476), androgen/estrogen biosynthesis (ρ = 0.000551), fatty acid (ρ = 0.000216) and tryptophan metabolism (ρ = 0.000331) pathways. These findings showed a profound impact of D3T on lipid metabolism and anti-inflammatory/immune-suppressive response, indicating broader cytoprotective effect of this compound than previously expected.
Keywords: Response to antioxidant compound

overall_design: Total RNA were isolated from either vehicle or D3T (0.3mmol/kg body weight) treated rat liver, 4 rats for each group, hybridized on 8 Affymetrix RG-U34A chips

first: Jian

last: Yan

first: Ronald

last: Lubet

first: Thomas

middle: W

last: Kensler

middle: R

last: Sutter


title: Temporal analysis of P15 and P30 hippocampi in kainate-induced seizures

status: Public on Feb 14 2006

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Tosini-1R01NS043459-01A1

status: Public on Jul 06 2005

summary:
It is well known that many genes are expressed in the retina where they show a clear daily pattern of expression.  Although several studies have investigated gene expression in the retina, no study – so far - has investigated the daily and the circadian pattern of gene expression using microarray. In the present study we propose to investigate the daily and circadian pattern of expression in the retina.
To determine gene expression in the retina in Light:Dark cycles and in constant condition (constant dim light) in the rat.
We hypothesize that (a) different genes are expressed in different retinal layers and (b) the pattern of expression of the same genes can differ among the different layers.
Wistar rats (3 for each time point) will be killed in the middle of the day (ZT6) and in the middle of the night (ZT18). Eyeballs will be collected and the retina will be removed and immediately frozen and then stored at -80 oC. The same experiment will be repeated on animals that have been maintained in constant dim light for 3. Retinas (3 for each time point) will be obtained from animal killed at CT6 (middle subjective day) and CT 18 (middle subjectice night) and stored at – 80 oC. The samples will be then shipped to NINDS-NIMH array facility for analysis.
Keywords: time-course

overall_design: as above

first: G

last: Tosini


title: giza-affy-rat-84719

summary:
Traumatic brain injury (TBI) induces a complex cascade of molecular and physiological effects.  This study proposes to investigate the gene expression profile in cortex and hippocampus over early time points, following two different injury severities.  These results will complement prior knowledge of both metabolic and neuroplastic changes after TBI, as well as serve as a starting point to investigate additional gene families whose expression is altered after TBI.
To characterize the profile of gene expression following a diffuse traumatic brain injury of varying severity in adult rats.
Distinct patterns of gene expression following traumatic brain injury will occur in a time- and injury-dependent fashion.  In particular, changes in expression of enzymes involved in energy metabolism and neuroplasticity will be detected.
Adult rats will be subjected to mild and severe lateral fluid percussion injury OR sham surgery without injury.  At various post-injury timepoints (0.5, 4 and 24 hours), animals will be sacrificed, brain regions (parietal cortex and hippocampus, ipsilateral and contralateral to injury) will be dissected and RNA isolated.  RNA will be used to synthesize cRNA probes for microarray hybridization.  RNA from 2 matched animals will be pooled onto a single chip (U34A rat, Affymetrix).  Comparisons will be made between sham and injured animals, with brain region, injury severity, and post-injury time point as the experimental variables.
Keywords: time-course

first: C

last: Giza


title: Aging extraocular muscles: shifts in gene expression patterns

first: Colleen

last: McMullen

summary:
The fast and constant activity of the extraocular muscles (EOMs) impose mechanical and metabolic stresses not typically seen in limb skeletal muscles.  These functional properties may explain why EOMs seem to age at a faster rate than other skeletal muscles.  Using high-density cDNA microarrays, this study investigated the gene expression profile of EOMs and extensor digitorum longus muscles (EDL) of Fischer 344/Brown Norway F1 hybrid rats at 6-, 18- and 30-months of age.  At 6-mo, 705 genes and expressed sequence tags (ESTs) were differentially expressed in EOMs (436 up, 269 down).  Overall, the EOM profile at this age was mostly consistent with the increased expression of fetal, developmental and EOM-specific myosin isoforms, enzymes involved in glycolysis and TCA cycle, and ion transporters and pumps, confirming the notion that EOM may represent a distinct muscle group (PNAS 98:12062, 2001).  Interestingly, at 18-mo only 36 probes were significantly different in EOM (15 up, 21 down), most of them ESTs.  However, at 30-mo EOMs had 655 differentially expressed genes and ESTs (480 up, 175 down).  In this age group, the EOM expression profile reverted to a pattern similar to that found at 6-mo, with evidence of ongoing tissue remodeling and increased expression of antioxidant enzymes.  These results indicate that the gene expression profile of EOM and EDL evolve differently throughout the lifespan.
Keywords: aging, muscle type comparison

overall_design: Total RNA was obtained with TRIzol (Invitrogen Carlsbad, CA) following the manufacturers recommended protocol. Tissues from 4 animals were combined into each RNA sample to decrease inter-subject variability. Biotinylated cRNA samples were hybridized to Affymetrix Rat Genome U34 gene chips (n=24 chips) described previously [McMullen et al. 2004]. Microarrays were washed and stained with a streptavidin-bound marker and scanned. Data were analyzed with Affymetrix Microarray Suite 5.0 software. Only genes with consistent absent/present calls in all four independent replicates per group were considered for further analysis. Comparisons the one-sided Wilcoxon’s signed rank test to estimate “increase/no change/ decrease” difference calls for each pair-wise comparison. Only difference calls consistent in all pair-wise comparisons and with average changes > 2.00 were considered significant, resulting in a conservative list of genes with changed expression levels. Functional classification of genes was based on an extensive literature review.

first: Francisco

middle: H

last: Andrade


title: SHR-WKY

status: Public on Jul 01 2005

city: University of OULU

first: Jaana

last: Rysä

address: PO BOX 5000

department: Pharmacology and toxicology

country: Finland

institute: University of Oulu

summary:
Left ventricular gene expression profiles from 12-, 16- and 20-months old spontaneously hypertensive rats (SHRs) were compared with left ventricular profiles seen in age-matched Wistar-Kyoto (WKY) rats by screening Affymetrix U34A arrays (there are 4 samples in each timepoint except 3 samples of 20-months old WKYs).
Keywords: time-course

first: Heikki

last: Ruskoaho