title: Anti-Nogo-A antibody treatment of Rat Hippocampal Slice Cultures

status: Public on Nov 12 2008

first: Laura

last: Montani

address: Winterthurerstrasse 190

department: Neuromorphology

institute: Brain Research Institute - UZH/ETHZ - Zurich

summary:
The neurite outgrowth inhibitory myelin protein Nogo-A has been well studied in the context of central nervous system (CNS) injury and disease. We studied the effects of the application of neutralizing anti-Nogo-A antibodies (11C7 and 7B12) in intact CNS tissue in vitro using rat organotypic hippocampal slice cultures. This study had the purpose of elucidating the role of Nogo-A in the adult intact CNS and determining the consequences of its neutralization through antibody application.
In vitro cultures treated with anti-Nogo-A antibody showed an elicited growth response. The results also gave indications that hippocampal circuitry might be altered due to the regulation at the synaptic and neurotransmission level.

overall_design: Nogo-A function in the intact CNS tissue is not well known, but its neutralization in vivo produced a transitory growth response of Purkinje axons and of the corticospinal tract in intact adult rats (Buffo et al., 2000; Bareyre et al., 2002; Gianola et al., 2003). Nogo-A is relatively highly expressed in oligodendrocytes and some neurons of the hippocampus (Huber et al., 2002; Meier et al., 2003; Gil et al., 2006; Trifunovski et al., 2006). Organotypic hippocampal slice cultures are a good in vitro model to study hippocampal function and structure (Stoppini et al., 1991; 1993; Bahr, 1995; Gahwiler et al., 1997; Hakkoum et al., 2006). They mature in vitro and retain many in vivo features from a structural and functional perspective. We chose this model to study the effects of acute Nogo-A neutralization, using two function blocking monoclonal antibodies, 11C7 and 7B12 (Oertle et al., 2003; Wiessner et al., 2003; Liebscher et al., 2005), exclusively targeted against the Nogo-A specific region. Hippocampal slices from P7 Wistar rats were cultured for 21 DIV. Control untreated cultures where cultured for additional 5days for a total of 26DIV, while control IgG, and 11C7 and 7B12 were added to 21DIV cultures which were then further cultured for 5days, changing medium every 2 days. All the conditions were repeated in triplicates with separate cultures from different animals. For each condition and experimental replicate 24 cultures were pooled together before being processed for RNA extraction. Data analysis was performed by GeneSpring 7.2 (Silicon Genetics, Agilent, CA, US) comparing 11C7 and 7B12 treated samples versus Not treated and IgG treated, as controls. A present call filter (2 out of 3 present calls in at least one out of the 3 experimental replicates) was applied. Normalization was run per chip as well as per gene to the median of the control replicates. Data were statistical restricted through a 1-way Anova (p≤0.05). A final threshold of ≥1.2 fold of increase or decrease in the expression level of each single transcript was applied. Regulated transcripts have been assigned to functional categories according to GeneOntology as well as literature and database mining (Pubmed; Bioinformatics Harvester EMBL Heidelberg; Rat Genome Database).

first: Luis

last: Craveiro

first: Andrea

last: Patrignani

first: Marzanna

last: Kuenzli


title: The Transcriptome of the rat hypothalamo-neurohypophyseal system is highly strain-dependant

status: Public on Sep 22 2008

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

summary:
We have used microarrays to comprehensively describe the transcriptomes of the supraoptic nucleus (SON), the paraventricular nucleus (PVN) and the neurointermediate lobe (NIL) of adult male Sprague-Dawley (SD) and Wistar-Kyoto (WKY) rats, as well as the paraventricular nucleus of Wistar (WIST) rats. Comparison of these gene lists has enabled us to identify surprisingly large differences in hypothalamo-neurohypophyseal system gene expression patterns in these three strains. We have also shown that different transcript populations  are enriched in the PVN and the SON of SD and WKY rats. The transcriptome differences catalogued here may be molecular substrates for the neuro-humoral phenotypic differences exhibited by different strains of rats.
Keywords: Transcriptome, Hypothalamo-neurohypophyseal system, Genetic

overall_design: For each experimental group (SON-WKY, PVN-WKY, NIL-WKY, SON-SD, PVN-SD, NIL-SD, PVN-WISTAR) five chips were hybridised with independantly pooled RNA from a biological n=5.

first: Charles

last: Hindmarch

first: Song

last: Yao

first: Shirley

last: Hesketh

first: David

last: Jessop

first: Michael

last: Harbuz

first: Julian

last: Paton

last: Murphy


title: Coordinated Changes in Xenobiotic Metabolizing Enzyme Gene Expression in Aging Male Rats: Brown Norway and F344

status: Public on Jul 30 2008

city: RTP

first: Hongzu

last: Ren

state: NC

address: 109 TW Alexander Dr

country: USA

institute: US Environmental Protection Agency

summary:
In order to gain insight into the effects of aging on susceptibility to environmental toxins, we characterized the expression of xenobiotic metabolizing enzymes (XMEs) from the livers of male Brown Norway and F344 rats across the adult lifespan. To examine metabolic processes across lifespan after challenge with a xenobiotic compound, Brown Norway rats were exposed to 1.0 g/kg body weight toluene by oral gavage in corn oil (4ml/kg body weight) or corn oil alone.
Keywords: age effect on toxin susceptibility

overall_design:
Brown Norway rats: Analysis of gene expression profiles for XMEs in male Brown Norway rats 4, 12, and 24 months old. Rats were exposed to 1g/kg toluene by oral gavage, and sacrificed after 4 hours. Total RNA was isolated from liver samples and gene expression analyzed using Affymetrix Rat 230 2.0 full-genome GeneChips. Data from 18 samples, with three rats in each of the control age groups and dosed age groups, were analyzed.

F344 rats: Analysis of gene expression profiles for XMEs in male F344 6, 11, 18, and 24 months old. Total RNA was isolated from liver samples and gene expression analyzed using Affymetrix Rat 230 2.0 full-genome GeneChips.  Data from 16 samples, with four rats in each of the 4 age groups, were analyzed.

first: Janice

middle: S

last: Lee

first: William

middle: O

last: Ward

first: Douglas

middle: C

last: Wolf

first: James

last: Allen

first: Camilla

last: Mills

middle: J

last: DeVito

first: J

last: Corton


title: Gene expression profile induced by moderate physical exercise in heart left ventricles in rats

status: Public on Jul 15 2008

city: Florence

first: Betti

last: Giusti

address: viale Morgagni, 85

department: Dpt. of Medical and Surgical Critical Care

country: Italy

institute: University of Florence

summary:
Physical exercise training is a known protective factor against cardiovascular morbidity and mortality. Nevertheless, the underlying specific molecular mechanisms still remain uncompletely explored. To identify molecular mechanisms by which exercise training induces this favorable phenotype a genomic approach was used in an animal model of mild exercise previously demonstrated by our group to induce cardioprotection.
Our data indicate that mild exercise by inducing no or few permanent changes in gene expression profile is able to determine cardioprotection without induction of cardiac hypertrophy.
Keywords: Case-Control: Response to physical exsercise

overall_design: We investigated the gene expression profile by Affymetrix technology (230 2.0 GeneChip rat genome array) induced by mild exercise training (treadmill running: 25 m/min, 10% incline, 1 h/day, 3 days/week, 10 weeks) on left ventricle (LV) of exercise-trained (n=10) and sedentary control (n=10) rats.

first: Luciana

last: Rossi

first: Ilaria

last: Lapini

first: Alberto

last: Magi

first: Arsenio

last: Veicsteinas

first: Marina

last: Marini

first: Michele

last: Samaja

first: Rosanna

last: Abbate


title: Irinotecan-induced gene expression changes in the rat intestine

status: Public on Aug 01 2008

city: Adelaide

first: Joanne

middle: Marie

last: Bowen

state: South Australia

address: North Terrace

department: Medical Oncology

country: Australia

institute: Royal Adelaide Hospital

summary:
The regional specificity and timing of gene activation following chemotherapy, and how this relates to subsequent mucositis development is currently unknown.  The aim of the study was therefore to determine the early time course of gene expression changes along the gastrointestinal tract (GIT) of the DA rat following irinotecan treatment, so as to provide an insight into the genetic component of mucositis.
We have found that changes in gene expression following irinotecan occur by 1 hour, and persist for at least 72 h after treatment.  Overall changes in gene expression are similar along the GIT, however there is temporal variability between regions.

Keywords: Time course and tissue comparison

overall_design: Thirty female DA rats were placed in groups (n = 6) and treated with 200 mg/kg i.p. of irinotecan.  Animals were killed at 0, 1, 6, 24 and 72 h and samples of stomach, jejunum and colon collected. These times were chosen to represent very early responses to treatment, up to the time of peak damage and morphological changes.  The 0 h group did not receive irinotecan and acted as experimental controls. RNA was extracted from whole tissue samples.  RNA was pooled into 2 per group (n = 3) to allow for replication of experiment.  Each sample was then hybridised to Affymetrix GeneChip Arrays (Rat 230 2.0).

middle: M

first: Rachel

last: Gibson

first: Anna

last: Tsykin

first: Andrea

last: Stringer

first: Richard

last: Logan

first: Dorothy

last: Keefe


title: Positional identification of Adamts16 variants linked to inherited hypertension: knockdown of Adamts16 in NRK-52E cells

status: Public on Nov 01 2008

city: Washington, DC

first: Norman

middle: H

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

institute: The George Washington University Medical Center

summary:
We used Affymetrix GeneChips to expression profile rat kidney NRK-52E cells treated with control scrambled siRNA or siRNA specifically targeting Adamts16. The goal of this project was to identify the downstream genes regulated by Adamts16 (the function of Adamts16 has yet to be fully delineated). Gene expression differences resulting from these siRNA-mediated gene knockdown experiments will be compared to the gene expression profiling experiments comparing kidneys from Dahl salt-senstive hypertensive inbred strain versus less hypertensive S.LEW(D1MCO4x1x3Bx1) congenic strain. The S.LEW(D1MCO4x1x3Bx1) congenic animal is an S rat containing the LEWIS allele for Adamts16 instead of the S allele. Gene expression differences in the kidneys of S.LEW(D1MCO4x1x3Bx1) versus S are hypothesized to result from sequence differences between the S and LEWIS alleles for Adamts16. It is further hypothesized that allelic differences in Adamts16 in inbred rats is responsible for blood pressure variance. The downstream genes regulated by Adamts16 may provide insight pertaining to the mechanism of blood pressure differences.

Keywords: Gene knockdown with siRNA

overall_design: RNA from 3 independent cultures of NRK-52E cells treated with scrambled control siRNA was extracted for target preparation and hybridization onto Affymetrix GeneChips. We also isolated RNA from NRK-52E cells treated with two different siRNAs targeting Adamts16 (n=2 independent cultures for each siRNA) for target preparation and hybridization onto Affymetrix GeneChips.

first: Bryan

last: Frank

first: Bina

last: Joe


title: TRE-Htt-N853 Huntington's Disease in vitro model

status: Public on Sep 01 2008

city: Bethesda

first: Alexandre

last: Kuhn

state: MD

address: 35 Convent Dr

department: NIA

institute: NIH

summary:
Primary neuron model of Huntington's Disease. 2 treatment groups: A) Infected 4 weeks prior with TRE-Htt-N853-18Q-expressing recombinant lentivirus, B) Infected 4 weeks prior with TRE-Htt-N853-82Q-expressing recombinant lentivirus

Keywords: gene expression study

overall_design: Primary neurons samples infected with TRE-Htt-N853-18Q or -82Q.

first: Heike

last: Runne

first: Ruth

last: Luthi-Carter


title: Identification of Sox10 target genes by comparative expression profiling

status: Public on Jul 08 2008

city: Seoul

first: Sanghyuk

address: 11-1 Daehyun-dong, Seodaemun-gu

department: Division of Life and Pharmaceutical Sciences

country: South Korea

institute: Ewha Womans University

summary: RT4D6 Schwannoma cells were treated with siRNA specific for Sox10 and a mutant siRNA. Total RNA from the cells were used to screen for differentially expressed genes.

overall_design: Specific siRNA and mutant siRNA were used.  Two different sets of paired cells were used.  Biotin labeled probes were generated and separate microarray chips were used to detect expression of genes.

first: Kyung-Eun

first: Seungyoon

last: Nam

first: Eun-ah

last: Cho

first: Ikjoo

last: Seong

first: Jin-Kyung

last: Limb

first: Jaesang

last: Kim


title: Genomic profile of trinitrobencenesulfonic acid (TNBS)-induced colitis model

city: Granada

first: Antonio

last: Suarez

state: Granada

address: Pharmacy Faculty, Campus Cartuja s/n

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Granada

summary:
Trinitrobenzenesulfonic acid (TNBS) rat colitis is one of the most widely used models of inflammatory bowel disease, a condition whose etiology and pathophysiology are incompletely understood. We have characterized the model at the genomic level following a longitudinal approach.
Keywords: Time course and differentially expressed genes analysis

overall_design:
A single enema of 10mg of TNBS in 50% ethanol was administered to rats at day 0. Samples were recovered at days 2, 5, 7 and 14. According to inflammatory markers (myeloperoxidase activity, body weigh loss, colonic weigh/length ratio) we selected three replicates at each time point for the genimoc analysis, and 6 healthy control rats that received a saline enema.
RNA was extracted from homogenized full-thickness colonic tissues in Trizol® reagent (Invitrogen) and purified with RNeasy affinity columns (Qiagen), according to manufacturer´s protocol. The microarray analysis was performed by Progenika Biopharma (Bilbao, Spain) on GeneChip® Rat Genome 230 2.0 Array (Affymetrix). All sample labeling (biotin), hybridization, staining and scanning procedures were carried out using Affimetrix, standard protocols (www.affymetrix.com). Normalization was carried out using Bioconductor sofware (affyPLM package).

first: Fermin

last: Sánchez de Medina

first: Olga

last: Martínez

first: Trinidad

last: Montero

last: Zarzuelo

first: Maria

middle: D

first: Xavier

last: Llor

first: Jose

last: Vieites

first: Miguel

last: Gassull


title: Profiling Single and Repeated Immobilization Stress Responses in Gene Expression

city: Valhalla

first: Xiaoping

last: Liu

state: NY

address: BSB 127, 95 Grassland RD

department: Biochemistry and Molecular biology

institute: New York Medical College

summary:
Microarray profiling single and repeated immobilization stress responses in gene expression in rat adrenal medulla
Keywords: Stress responses

overall_design: Immobilization stress (IMO) was performed with 2-hour once and 2-hour daily for 6 days repeated. Control groups were not exposed to stress (absolute controls). Following the last IMO, rats were euthanized by decapitation and both adrenal medulla tissues were dissected from the animal. Total RNA were isolated and the array experiments were done by Affymetrix. Data analysis will be performed by GeneTraffic program.


title: Gene Expression Changes in Laser Capture Microdissected Nasal Respiratory Epithelium of Rats Exposed to Hydrogen Sulfide

status: Public on Jul 01 2008

city: Greensboro

first: Elizabeth

middle: Sherman

last: Roberts

address: 3200 Northline Ave, Suite 300

institute: Novartis Animal Health US

summary:
Hydrogen sulfide (H2S) is a naturally occurring gas that is also associated with several industries.  The potential for widespread human inhalation exposure to this toxic gas is recognized as a public health concern.  The nasal epithelium is particularly susceptible to H2S-induced pathology.  Injury to and regeneration of the nasal respiratory mucosa occurred in animals with ongoing H2S exposure suggesting that the regenerated respiratory epithelium undergoes an adaptive response and becomes resistant to further H2S induced toxicity.  To better understand this adaptive response, twenty-four naive 10-week old male Sprague-Dawley rats were exposed to air or 200 ppm H2S in a nose-only exposure system for 3h/d for 1 or 5 consecutive days.  Nasal respiratory epithelial cells at the site of injury and regeneration were laser capture microdissected and gene expression profiles were generated at time 3h, 6h, 24h, and 144h post initial exposure using the Affymetrix Rat Genome 430 2.0 microarray. Gene ontology enrichment analysis identified early gene changes in such functional categories as signal transduction, inflammatory/defense response, cell cycle, and response to oxidative stress.  Later gene changes occurred in categories involved in cell cycle, DNA repair, transport, and micro-tubule-based movement.  These data contribute to our understanding of the nasal epithelial cells? response to inhaled environmental toxicants.  A better understanding of the H2S cytotoxicity mechanism will improve human risk assessment.
Keywords: Time course

overall_design: Twenty-four naive 10-week old male Sprague-Dawley rats were exposed to air or 200 ppm H2S in a nose-only exposure system for 3h/d for 1 or 5 consecutive days.  Nasal respiratory epithelial cells at the site of injury and regeneration were laser capture microdissected and gene expression profiles were generated at time 3h, 6h, 24h, and 144h post initial exposure using the Affymetrix Rat Genome 430 2.0 microarray.

first: Marianne

middle: W

last: Marshall

first: Rusty

last: Thomas

first: David

last: Dorman


title: Transgenerational effects of the endocrine disruptor Vinclozolin on the prostate transcriptome and adult onset disease

status: Public on Jun 20 2008

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary:
The ability of an endocrine disruptor exposure during gonadal sex determination to promote a transgenerational prostate disease phenotype was investigated in the current study.

METHODS: Exposure of an F0 gestating female rat to the endocrine disruptor vinclozolin during F1 embryo gonadal sex determination promoted a transgenerational adult onset prostate disease phenotype. The prostate disease phenotype and physiological parameters were determined for males from F1 to F4 generations and the prostate transcriptome was assessed in the F3 generation.

RESULTS: Although the prostate in prepubertal animals develops normally, abnormalities involving epithelial cell atrophy, glandular dysgenesis, prostatitis, and hyperplasia of the ventral prostate develop in older animals. The ventral prostate phenotype was transmitted for four generations (F1-F4). Analysis of the ventral prostate transcriptome demonstrated 954 genes had significantly altered expression between control and vinclozolin F3 generation animals. Analysis of isolated ventral prostate epithelial cells identified 259 genes with significantly altered expression between control and vinclozolin F3 generation animals. Characterization of regulated genes demonstrated several cellular pathways were influenced, including calcium and WNT. A number of genes identified have been shown to be associated with prostate disease and cancer, including beta-microseminoprotein (Msp) and tumor necrosis factor receptor superfamily 6 (Fadd).

CONCLUSIONS: The ability of an endocrine disruptor to promote transgenerational prostate abnormalities appears to involve an epigenetic transgenerational alteration in the prostate transcriptome and male germ-line. Potential epigenetic transgenerational alteration of prostate gene expression by environmental compounds may be important to consider in the etiology of adult onset prostate disease.

Keywords: expression analysis, transgenerational changes due to Vinclozolin

overall_design: RNA samples from ventral prostate or prostate epithelium from F3 generation control rats are compared to corresponding tissues from F3 generation Vinclozolin treated rats

first: Mathew

last: Anway


title: Prg1 is regulated by the basic helix-loop-helix transcription factor Math2

status: Public on Jul 27 2008

city: Tokyo

first: Kou

last: Takahashi

address: 4-1-1 Ogawahigashimachi, Kodaira

country: Japan

institute: NCNP

summary: Math2 (NEX-1/NeuroD6) is a member of the bHLH transcription factor family and is involved in neuronal differentiation and maturation. In the present study, we identified the genes targeted by Math2 using DNA microarrays and cultured rat cortical cells transfected with Math2. Of the genes regulated by Math2, we focused on plasticity-related gene 1 (Prg1). Prg1 expression induced by Math2 was confirmed in cultured rat cortical cells and PC12 cells analyzed by real-time quantitative PCR. Examining the promoter region of rat Prg1, we found four E-boxes designated -E1 to -E4 (CANNTG) which were recognized by the bHLH transcription factor. Using chromatin immunoprecipitation (ChIP) assays, we found that Math2 directly bound to the E-box(es) in the Prg1 promoter. The reporter assay of Prg1 showed that -E1 was critical for the regulation of the Prg1 expression by Math2. Then, the functional role of Math2 and Prg1 was investigated in PC12 cells. Seventy-two hours after transfection of Math2 or Prg1, neurite length and number was significantly induced in PC12 cells. Co-transfection with Prg1-siRNA completely inhibited Math2-mediated morphological changes. Our results suggest that Math2 directly regulates Prg1 expression and Math2-Prg1 cascade plays an important role in neurite outgrowth in PC12 cells.

overall_design: We identified the genes targeted by Math2 using DNA microarrays and cultured rat cortical cells transfected with Math2.Total RNA was used for cDNA synthesis with a Two-Cycle Target Labeling Kit. Gene expression was analyzed by an Affymetrix  GeneChip® Rat Genome 230 2.0 array which was spotted with 31,100 probe sets. Sample preparation for array hybridization was carried out as described in the manufacture’s instructions.

first: Misa

last: Yamada

first: Yoshiko

last: Shida

first: Toshihiro

last: Tanioka

first: Yasuko

last: Nakano

first: Takashi

last: Tobe

first: Mitsuhiko


title: Titin splicing

status: Public on Jun 10 2008

city: Madison

first: wei

last: guo

state: WI

address: 1805 Linden Dr.

institute: University of Wisconsin-Madison

summary:
Titin is a striated muscle-specific giant elastic protein and largely responsible for the generation of the diastolic force in the cardiac myocyte. Cardiac titin undergoes developmental changes in isoform expression during the course of cardiac development. At present, at least five size classes of titin isoforms (N2B and N2BA-A1, A2, N1, N2) have been identified using SDS agarose gel electrophoresis. The larger titin isoform N2BAs gradually decreased with ages, in contrast, the smaller titin isoform N2B increased in normal cardiomyocyte, and cardiac myocytes containing a higher proportion of the smaller titin isoform N2B have stronger passive tension than that with a lower proportion of the larger titin isoform N2BAs. Recently we found an autosomal dominant mutation which caused totally opposite cardiac titin isoform expression as compared to developmental stages. The larger total titin isoform N2BA increased in mutant rat cardiac myocytes with ages instead of the smaller cardiac titin isoform N2B. For the moment, mechanism of titin isoform switch is still unknown, therefore, the mutant rats will give us nevol sight to elucidate the titin splicing mechanism.
Keywords: Titin isoforms, autosomal dominant mutation

overall_design: Total RNA was extracted using TRIzol according to manufacturer instruction and further purified by the RNeasy mini kit (Qiagen, Valencia, CA). Double stranded cDNA was synthesized from total RNA (SuperScript II system; Invitrogen). An in vitro transcription reaction was then performed to obtain biotin-labeled cRNA from the double-stranded cDNA (Enzo BioArray High Yield RNA Transcript Labeling kit; Enzo Diagnostics, Farmingdale, NY). The cRNA was fragmented before hybridization, and then mixed in a hybridization mixture containing probe array controls, BSA, and herring sperm DNA. A cleanup procedure was performed on the hybridization cocktail using an RNeasy spin column (Qiagen), after which it was applied to the Affymetrix Rat 230 2.0 probe array. Total eighteen hybridization experiments were performed in which each stage (1-day, 20-day and 49-day) was represented by three normal and three mutant individual ventricular RNA extracts. Hybridization was allowed to continue for 16 h at 45°C in a GeneChip 640 hybridization oven, after which the arrays were washed and stained with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR). Images were scanned using a GeneArray scanner (Agilent Technologies, Palo Alto, CA) and GeneChip cel files were subsequently processed by the log scale robust multi-array analysis (RMA). The log scale robust multi-array analysis (RMA) estimates are based upon a robust average of log2 (B (PM)), where B (PM) are background corrected perfect match intensities. three replicates were available for these conditions: three wild types and three homozygotes for 1-day, three wild types and three homozygotes for 20-day, and three wild types and three homozygotes for 49-day.

first: Wei

last: Guo

first: Marion

middle: L

last: Greaser


title: Expression data from rat mixed tissues samples

status: Public on May 24 2008

city: Thousand Oaks

first: Tiffany

last: Day

state: CA

address: One Amgen Center Drive

institute: Amgen

summary:
To evaluate gene expression changes in mixed tissue samples used as process controls in male Sprague Dawley rats over time.

Keywords: process control

overall_design: This study is designed to evaluate gene expression changes in mixed tissue samples MT1 (Liver:kidney:testes:brain = 3:2:1:4 ) and MT2 (Liver:kidney:testes:brain = 2:2:4:2) over time.  These samples are used as process controls in rat microarray experiments.


title: Genome-wide gene expression in soleus muscle of rats artificially selected for high and low running capacity

status: Public on Jun 01 2008

city: TRONDHEIM

first: Anja

last: Bye

address: Olav Kyrres gt 9

country: Norway

institute: NTNU

summary:
Purpose: Aerobic capacity is a strong predictor of cardiovascular mortality. To determine the relationship between inborn aerobic capacity and soleus gene expression we examined genome-wide gene expression in soleus muscle of rats artificially selected for high and low running capacity (HCR and LCR, respectively) over 16 generations. The artificial selection of LCR caused accumulation of risk factors of cardiovascular disease similar to the metabolic syndrome seen in man, whereas HCR had markedly better cardiac function. We also studied alterations in gene expression in response to exercise training in the two groups, since accumulating evidence indicates that exercise has profound beneficial effects on the metabolic syndrome.

Methods:
Soleus gene expression of both sedentary and exercise trained HCR and LCR was characterized by microarray- and gene ontology analysis.

Results: Although HCR and LCR had an inborn 347% difference in running capacity, only three genes were found differentially expressed in the soleus muscle between the two groups. Up-regulation of the mitochondrial enzyme leucyl-transferRNA synthetase (LARS2) was found in the sedentary LCR. Increased expression of LARS2 has been associated with a mitochondrial DNA mutation linked to maternally inherited diabetes and mitochondrial dysfunction. In line with our findings, a growing body of evidence suggests that LCR have compromised mitochondrial function. After exercise training, 58 genes were altered in the soleus muscle of HCR, in contrast to only one in the LCR group. This suggests that animals born with different levels of fitness respond different to the same type of exercise training. Adaptations to exercise in HCR seemed to be associated with increased lipid metabolism and fatty acid elongation in the mitochondria. Also, genes associated with the peroxisomes, seemed to be central in the adaptation to exercise.

Conclusion: The results indicate that (i) LCR might have mitochondrial dysfunction, which may be a contributing factor of the low inborn aerobic capacity, (ii) animals born with different levels of fitness respond different to the same exercise program.
Keywords: aerobic capacity, metabolic syndrome, soleus muscle, gene expression, metabolism

overall_design: There are 16 samples in this study.

first: Morten

middle: A

last: Høydal

first: Ole

last: Keim

first: Lauren

middle: G

last: Koch

first: Daniele

last: Catalucci

first: Steven

last: Britton

first: Øyvind

last: Ellingsen

first: Ulrik

last: Wisløff


title: Genomic profile of dextran sulphate sodium-induced colitis model in rats

first: Antonio

last: Suarez

summary:
Background & Aims: Dextran sulphate sodium (DSS) induced colitis in rats is one of the most widely used models of inflammatory bowel disease. Animal models can provide new insights into the pathogenesis of intestinal inflammation, which is still unknown. We have performed a genomic analysis of the DSS rat colitis including an acute and a recovery phase. Methods: Expression profile of 6 control rats were compared with colitic rats at day 1 every other day until day 23 after DSS treatment using the GeneChip Rat Genome 230 2.0 Array (Affymetrix). Functional and pathways analysis were made with the differentially expressed genes.
Keywords: Time course and differentially expressed genes analysis

overall_design:
Experimental design: DSS was administered to animals in drinking water as follows:5%DSS from day 1 to 7, 3%DSS from day 8 to 15, 0% DSS from day 16 to 23. Samples were recovered at days 1, 3, 5, 7 (5%DSS), 9, 11, 13, 15 (2%DSS), 17, 19, 21 and 23 (0%DSS). According to inflammatory markers (Myeloperoxidase activity activity, body weight loss, colonic weigth/length ratio), three replicates at each time point were selected for genomic analysis and 6 control healthy rats (42 arrays).
RNA was extracted from homogenized full-thickness colonic tissues in Trizol® reagent (Invitrogen) and purified with RNeasy affinity columns (Qiagen), according to manufacturer´s protocol. The microarray analysis was performed by Progenika Biopharma (Bilbao, Spain) on GeneChip® Rat Genome 230 2.0 Array (Affymetrix). All sample labeling (biotin), hybridization, staining and scanning procedures were carried out using Affimetrix, standard protocols (www.affymetrix.com). Normalization was carried out using Bioconductor sofware (affyPLM package).

first: Trinidad

last: Montero

last: Suárez

first: Xavier

last: Llor

first: Miguel

last: Gassull

first: Fermín

last: Sánchez de Medina

first: Olga

last: Martínez

first: Jose

last: Vieites

first: Angel

last: Gil


title: temporal profiling of retinal transcriptome regulation after IONT and IONC

status: Public on Jun 13 2008

city: MURCIA

first: MARTA

last: AGUDO

address: FACULTAD MEDICINA, CAMPUS ESPINARDO

department: OFTALMOLOGY

institute: MURCIA UNIVERSITY

summary:
retinal ganglion cells die after optic nerve injury, either crush or transection. The molecular causesunderlying this degeneration are largely unkwon
the purpose of this job is to find which  (if any) gene regulation triggers RGC death with the final goal of design neuroprotective protocols
Keywords: time course

overall_design: 3 groups: naive, IONT (intraorbital nerve transection) IONC (intraorbital nerve crush). IONT and IONC lesioned animals were kept the appropriate times postlesion (12h,. 24h, 48h, 3d, 7d, and 15d). For each time point 8-12 animals were used. RNA from 4 animals was pooled and extracted to hybridaze 1 array replica.  All replicas were pooled biological replicas: 5 for naive RNA (each replica 4 retinas, therefore  5 independent RNA extractions were done with a total of 20 retinas), IONT: 12h 3 replicas, 24h 2 replicas, 48h 3replicas, 3d 2 replicas, 7d 3 replicas, 15d 2 replicas. IONC: 3 replicas per time point: 12h, 24h, 48h, 3d and 7d)

first: Marta

last: Agudo

first: Manuel

last: Vida-Sanz

first: Paloma

last: Sobrado


title: Glial derived neurotrophic factor promotes ovarian primordial follicle development during folliculogenesis

status: Public on Apr 11 2008

first: Michael

last: Skinner

summary:
Female fertility is determined in part by the size and development of the primordial follicle pool. The current study investigates the role of glial cell-line derived neurotrophic factor (GDNF) in the regulation of primordial follicle development in the ovary. Ovaries from four-day old female rat pups were maintained in organ culture for ten days in the absence (control) or presence of GDNF or kit ligand/stem cell factor (KL). Ovaries treated with GDNF contained a significant increase in developing follicles, similar to that observed with KL treatment previously shown to promote follicle development. The actions of GDNF on the ovarian transcriptome were investigated with a microarray analysis. Immunohistochemical studies demonstrated that GDNF is localized to oocyte cytoplasm in follicles of all developmental stages, as well as to cumulus granulosa cells and theca cells in antral follicles. GDNF receptor alpha 1 (GFRalpha1) staining was localized to oocyte cytoplasm of primordial and primary follicles, and at reduced levels in oocytes of antral follicles. GFRalpha1 was present in mural granulosa cells of antral follicles, theca cells, and the ovarian surface epithelium. The localization studies were confirmed with molecular analysis. Microarray analysis was used to identify changes in the ovarian transcriptome and further elucidate the signaling network regulating early follicle development. Observations indicate that GDNF promotes primordial follicle development and mediates autocrine and paracrine cell-cell interactions required during folliculogenesis. In contrast to the testis, ovarian GDNF is predominantly produced by germ cells (oocytes) rather than somatic cells.
Keywords: expression analysis, glial derived neurotrophic factor, follicle transition, ovary

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

first: Gretchen

last: Dole

first: Eric

last: Nilsson


title: Rat prostate cancer cells with high Ndrg-1 and vector control - analysis of differentially expressed genes

city: Sydney

first: Zaklina

last: Kovacevic

state: NSW

address: Level 5 Blackburn Building D06, University of Sydney

department: Pathology

institute: University of Sydney

summary:
AT6.1 cells transfected to over-express Ndrg-1 were compared with AT6.1 vector control cells in a microarray analysis. The aim of the study was to identify differentially expressed genes between the two cell lines, as these may be modulated by Ndrg-1.
Keywords: Differential gene expression analysis

overall_design: The sample was AT6.1 cells transfected with Ndrg-1 (# 7 clone) and the control was the same cell line transfected with a vector control (# 9 clone). There are no replicates included.

first: Dong

last: Fu

first: Des

middle: R

last: Richardson


title: Transgenerational epigenetic programming of the embryonic testis transcriptome

status: Public on Mar 22 2008

summary:
Embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination appears to promote an epigenetic reprogramming of the male germ line that is associated with transgenerational adult-onset disease states. Transgenerational effects on the embryonic day 16 (E16) testis demonstrated reproducible changes in the testis transcriptome for multiple generations (F1-F3). The expression of 196 genes was found to be influenced, with the majority of gene expression being decreased or silenced. Dramatic changes in the gene expression of methyltransferases during gonadal sex determination were observed in the F1 and F2 vinclozolin generation (E16) embryonic testis, but the majority returned to control-generation levels by the F3 generation. The most dramatic effects were on the germ-line-associated Dnmt3A and Dnmt3L isoforms. Observations demonstrate that an embryonic exposure to vinclozolin appears to promote an epigenetic reprogramming of the male germ line that correlates with transgenerational alterations in the testis transcriptome in subsequent generations.
Keywords: expression analysis, transgenerational changes due to Vinclozolin

overall_design: E16 Testis RNA samples from F1, F2, F3 generation control groups are compared to F1, F2, F3 generation vinclozolin treated groups

first: Mathew

last: Anway

first: Stephen

last: Rekow


title: Microarray Based Analysis of the Developing Sweet Orange Transcriptome

status: Public on Mar 05 2008

city: Davis

first: Abhaya

last: Dandekar

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

summary:
Using a custom microarray platform, we examined expression of 366 genes in leaf, two peel tissues, juice sac, and whole fruit during various developmental stages of Washington Navel orange fruit (Citrus sinensis L. Osbeck). 366 genes were chosen from Citrus EST libraries by in-silico analysis method.
Keywords: time course and tissue comparison

overall_design: Study to compare gene expression between peel layers and over time as fruit matured. Samples taken from leaf tissue, whole fruit at 24 and 38 days after full bloom (DAFB), and from albedo and flavedo layers of the peel at 80 and 165 DAFB, and flavedo from mature fruit at 220 DAFB. In all cases except one, there were three technical replicates hybridized for each Sample simultaneously.

first: Danielle

last: Goudeau

first: Russell

last: Reagan


title: Expression data from ovarian follicles in different developmental stages

status: Public on Mar 15 2008

city: Beijing

first: ning

last: Li

address: Yuanmingyuan West Road 2

country: China

institute: China Agricultural University

summary:
The early (primordial), middle and last stage ovarian follicles gestate important functionally changes during the whole growth phase. The primordial follicles establish the resting pool and keep silent until initiated growth. The middle stage follicles are to be destined for dominance or atresia. And the last stage fllicles develop till ovulation.We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Gene expression profiles of ovarian follicles during their growth phase were revealed in genome wide.
Keywords: time course

overall_design: We sought to obtain general expression profiles of ovarian follicles during their growth phase. Ovarian follicles in successive developmental stages were isolated from ovaries of prepubertal gilts for RNA extraction and hybridization on Affymetrix microarrays. To that end, we isolated follicles according to morphological criteria and diameter sizes at three time-points: primordial follicles (P), middle stage follicleS (M) and the last stage follicles (L).

first: Ning

first: Kerong

last: Shi


title: Expression profile of stages of seminiferous tubules, purifed germ cells and sertoli cells

status: Public on May 19 2008

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

summary:
Mammalian spermatogenesis is a complex biological process that occurs within a highly organized tissue, the seminiferous epithelium.  The coordinated maturation of spermatogonia, spermatocytes and spermatids suggests the existence of precise programs of gene expression in these cells as well as in their neighboring somatic Sertoli cells. The objective of this study was to elucidate genes encoding the proteins that execute these programs.  Rat seminiferous tubules at stages I, II-III, IV-V, VI, VIIa,b, VIIc,d, VIII, IX-XI, XII, XIII-XIV of the cycle were isolated by microdissection and Sertoli cells, spermatogonia plus early spermatocytes, pachytene spermatocytes and spermatids were purified from enzymatically-dispersed testes.  Microarray analysis using Rat Genome 230 2.0 arrays identified a total of 16,971 probe sets that recognized transcripts. A comparison with the transcriptome of other tissues identified 398 testis-specific probe sets, which therefore are potential targets for the development of new contraceptives.  Sequential waves of cell and stage-specific gene expression are associated with progression of germ cells through the stages of the cycle of the seminiferous epithelium and 1612 probe sets recognized transcripts whose expressions varied at least 4-fold across the stages of the cycle. Pathway analyses reveal that entire biological processes are regulated cyclically in testicular cells.  Important among these are cell cycle and DNA repair.  Thus, stage-specific gene expression is a widespread and fundamental characteristic of spermatogenic cells and Sertoli cells.
Keywords: cell-type comparison

overall_design: Seminiferous tubules at the following stages or groups of stages were isolated by transillumination-assisted microdissection: I, II-III, IV-V, VI, VIIa,b,  VIIc,d, VIII, IX-XI, XII, XIII-XIV. Twenty-five segments of tubules, 2 m in length, were collected at each stage or group of stages from each rat.  Tubules from two separate animals were pooled to form one sample from each stage or groups of stages.  A total of 5 independent samples per stage or groups of stages were analyzed. Mature Sertoli cells were isolated to about 85% purity (n=4). Three groups of germ cells were isolated by centrifugal elutriation from enzyme-dispersed testes: round spermatids (n=4), pachytene spermatocytes (n=4) and spermatogonia plus early spermatocytes (n=3) . Purity of these cells has been shown to vary between 85% to 95%

first: Daniel

last: Johston

first: William

last: Wright


title: The effect of the HDAC inhibitor OSU-HDAC42 on gene expression in esophageal tissues and adenocarcinoma cells II

status: Public on Mar 20 2008

city: Columbus

first: Laura

last: Kresty

state: OH

address: CCC Building, Rm 302B

department: Internal Medicine

institute: The Ohio State University

summary:
Title: In vitro and in vivo effects of the orally bioavailable phenylbutyrate-derived histone deacetylase inhibitor OSU-HDAC42 on gene expression in esophageal tissues and in esophageal adenocarcinoma cells.
Histone deacetylases (HDACs) modulate nucleosomal packaging of DNA, thereby influencing gene transcription and multiple cancer-associated processes.
We conducted microarray analysis on esophageal tissue from male Sprague-Dawley rats treated with OSU-HDAC42 or vehicle to assess target effect in an in vivo model utilized for EAC development.
Keywords: esophageal tissue from male Sprague-Dawley rats treated with OSU-HDAC42 or vehicle

overall_design: 5-6 week old male Sprague-Dawley rats were administered OSU-HDAC42 (50 mg/kg/dose thrice weekly for a total dose of 350 mg/kg) or vehicle by gavage.  Twenty-four hours after the final gavage, the esophagi were harvested and total RNA was isolated using the RNA Mini Kit (Qiagen).  Global gene expression analysis was conducted using the 230 2.0 chip (Affymetrix).


title: Analysis of Endoglin function in rat hepatic stellate cells (HSC)

status: Public on Apr 01 2008

city: Aachen

first: Ralf

last: Weiskirchen

state: NRW

address: Pauwelsstr. 30

department: Institute of Clinical Chemistry and Pathobiochemistry

country: Germany

institute: RWTH University Hospital Aachen

summary:
Endoglin is a transmembrane receptor able to bind several members of the transforming growth factor-beta superfamliy. We used a siRNA-mediated knock down approach to analyse the function of Endoglin in hepatic stellate cells (HSC). We found that the targeted disruption is associated with significant changes in gene expression resulting in cellular changes that prolongated cellular activation, morphological maturation, transdifferentiation, expression of basement and fibrillar extracellular matrix proteins. In addition, the lack of Endoglin resulted in rearrangements of cytoskeletal organization.
Keywords: gene function analysis, siRNA, gene knock down

overall_design: We have performed a set of four microarray hybridizations using Agilent Whole Rat Genome Oligo Microarrays. We compartively analysed the gene expression profile in RNAs taken from: (I) untreated HSC taken from one animal vs. HSC that were taken from one animal and transfected with a control siRNA, (II) HSC taken from one animal and transfected with a siRNA targeting endoglin vs. HSC that were taken from one animal and transfected with a control siRNA, (III) untreated HSC that were pooled from three individual animals vs. HSC that were taken from three individual animals and independently transfected with siRNA control, and finally (IV) HSC that were taken from three animals and independently transfected with a siRNA targeting endoglin vs HSC that were taken from three individual animals and independently transfected with a siRNA control.

first: Wanda

middle: N

last: Vreden

first: Steffen

last: Meurer


title: Gene Expression Profile in Rat Adrenal Zona Glomerulosa Cells Stimulated with Aldosterone Secretagogues

status: Public on Jun 29 2008

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

department: Biochemistry

institute: University of Mississippi Medical Center

summary:
The mineralocorticoid aldosterone mainly produced by the adrenal gland is essential for life but an abnormal excessive secretion causes severe pathological effects including hypertension and target organ injury in the heart and kidney. The aim of this study was to determine the gene regulatory network triggered by aldosterone secretagogues in a non transformed cell system. Freshly isolated rat adrenal zona glomerulosa cells were stimulated with the two main aldosterone secretagogues, angiotensin II and potassium, for two hours and subjected to whole genome expression studies using multiple biological and bioinformatics tools. Several genes were differentially expressed by Ang II (n=133) or potassium (n=216). Genes belonging to the nucleic acid binding and transcription factor activity categories were significantly enriched. A subset of the most regulated genes were confirmed by real-time RT-PCR and then their expression analyzed in time curve studies. Differentially expressed genes were grouped according to their time-response expression pattern and their promoter regions analyzed for common regulatory transcription factors binding sites. Finally, data mining with gene promoters, transcription factors and literature databases were performed to generate gene interaction networks for either Ang II or potassium. This study provides for the first time a complete study of the genes that are regulated, and the interaction between them, by aldosterone secretagogues in rat adrenal cells. Increasing our knowledge of adrenal physiology and gene regulation in non transformed cell systems would lead us to a better approach for discovery of candidate genes involved pathological conditions of the adrenal cortex.
Keywords: agent response

overall_design:
Freshly isolated rat adrenal cells were treated with Ang II (100 nM) or potassium (16 mM) for 2 h at 37C.
Total RNA from three independent experiments were isolated, labeled and hybridized to whole genome high-density oligonucleotide microarrays (Affymetrix Rat Genome 230 2.0).

3 independent cell preparations.
In each experiement there is one tube control, one Ang II (100 nM) and potassium (16 mM).

first: Maria

last: Plonczynski

first: Bronwyn

last: Welsh

first: Celso

middle: E

last: Gomez-Sanchez

first: Ming

middle: Y

last: Zhou

first: Elise

middle: P


title: Expression data from brain tissue of Rattus norvegicus treated with D-Serine

status: Public on Mar 08 2008

city: WPAFB

first: Molly

last: Davidson

address: 2729 R Street, Bldg 837

institute: AFRL/RHPB

summary:
d-serine is naturally present throughout the human body.  It is also used as add-on therapy for treatment-refractory schizophrenia. d-Serine interacts with the strychnine-insensitive glycine binding site of NMDA receptor, and this interaction could lead to potentially toxic activity (i.e., excitotoxicity) in brain tissue.  The transcriptomic changes that occur in the brain after d-serine exposure have not been fully explored.
Affymetrix microarray technology was used to determine differential gene expression resulting from D-Serine exposure.
Keywords: Dose course

overall_design: Male Fisher 344 rats aged 11-12 weeks were treated with various doses (0, 5, 20, 50, 200 & 500 mg/kg) of d-serine and terminally sacrificed 96 hours post-exposure.  An approximate 30mg-section of the forebrain was processed for total RNA isolation.

first: Victor

middle: T

last: Chan


title: Belgrade +/b and b/b Duodenum and Jejunum

status: Public on Mar 03 2008

city: Buffalo

first: James

middle: F.

last: Collins

address: 3435 Main Street

department: Exercise and Nutrition Sciences

institute: University at Buffalo

summary:
Three groups of male +b and bb rats were obtained (ages between 6 and 14 months) and intestinal scrapes were taken. Tissues was combined from 3 rats per group and processed for gene chip analysis.
Keywords: Belgrade, iron deficiency, intestine, microarray

overall_design: Three groups of each genotype were utilized and samples from each group of rats was reacted with one chip. 6 total experimental groups X 2 tissues (duodenum and jejunum) = 12 total chips used.

first: Michael

last: Garrick


title: Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue

status: Public on Mar 01 2008

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
Acute progressive feed restriction (APFR) represents a specific form of caloric restriction in which feed availability is increasingly curtailed over a period of a few days to a few weeks. It is often used for control animals in toxicological and pharmacological studies on compounds causing body weight loss to equalize weight changes between experimental and control groups and thereby, intuitively, to also set their metabolic states to the same phase. However, scientific justification for this procedure is lacking. In the present study, we analyzed by DNA microarrays the impact on hepatic gene expression in rats of two APFR regimens that caused identical diminution of body weight (19%) but differed slightly in duration (4 vs. 10 days). In addition, white adipose tissue (WAT) was also subjected to the transcriptomic analysis on day-4. The data revealed that the two regimens led to distinct patterns of differentially expressed genes in liver, albeit some major pathways of energy metabolism were similarly affected (particularly fatty acid and amino acid catabolism). The reason for the divergence appeared to be entrainment by the longer APFR protocol of peripheral oscillator genes, which resulted in derailment of circadian rhythms and consequent interaction of altered diurnal fluctuations with metabolic adjustments in gene expression activities. WAT proved to be highly unresponsive to the 4-day APFR as only 17 mRNA levels were influenced by the treatment. This study demonstrates that body weight is a poor proxy of metabolic state and that the customary protocols of feed restriction can lead to rhythm entrainment.
Keywords: physiological state comparison

overall_design: Thirteen feed restricted and thirteen control animals, each hybridized to a single array.  Pre-processing was performed by group: all WAT samples together in one group, all four-day liver samples in a second group, and all ten-day liver samples in a third.

first: Raimo

last: Pohjanvirta

first: Ivy

last: Moffat

first: Jere

last: Linden

first: Dominique

last: Wendelin

first: Allan

middle: B

last: Okey


title: Triazole Antifungal Toxicogenomics: rat_repro_Testis

status: Public on Feb 07 2008

city: Research Triangle Park

first: David

last: Dix

address: 109 TW Alexander Drive

department: ORD/NCCT

institute: US EPA

summary:
The modes of triazole reproductive toxicity have been characterized by an observed increased in serum testosterone and reduced insemination and fertility indices. The key events involved in the disruption in testosterone homeostasis and reduced fertility remain unclear. Gene expression analysis was conducted on liver and testis from Wistar Han IGS rats fed myclobutanil (M: 500, 2000 ppm), propiconazole (P: 500, 2500 ppm), or triadimefon (T: 500, 1800 ppm) from gestation day six to postnatal day 92. Pathway-based analysis highlighted key biological processes affected by all three triazoles in the liver including fatty acid catabolism, steroid metabolism, and xenobiotic metabolism. Triadimefon induced a distinctive expression profile of genes involved in liver sterol biosynthesis. There were no common pathways modulated by all three triazoles in the testis. Within the pathways identified in the liver, specific genes involved in phase I-III metabolism (Aldh1a1, Cyp1a1, Cyp2b2, Cyp3a1, Slco1a4, Udpgtr2), fatty acid metabolism (Cyp4a10, Pc, Ppap2b), and steroid metabolism (Srd5a1, Ugt1a1, Ugt2a1) were affected by all three triazoles. These modulated genes are part of a network of lipid and testosterone homeostasis pathways regulated by the constitutive androstane (CAR) and pregnane X (PXR) receptors. Gene expression profiles from this study indicate triazoles activate CAR and PXR; increase fatty acid catabolism, sterol biosynthesis, and steroid metabolism in the liver; constituting a plausible series of key events contributing to the observed disruption in testosterone homeostasis.
Keywords: dose response, comparative toxicogenomics

overall_design: A total of 34 testis samples were analyzed.  Seven biological replicates for control, 4 biological replicates for mid dose myclobutanil, 5 biological replicates for high dose myclobutanil, 4 biological replicates for mid dose propiconazole, 5 biological replicates for high dose propiconazole, 4 biological replicates for mid dose triadimefon, and 5 biological replicates for high dose triadimefon.

middle: J

first: Amber

last: Goetz


title: Rosiglitazone effects on kidney gene expression

status: Public on Mar 04 2008

city: washington DC

first: swasti

last: Tiwari

address: 4000 reservoir road, NW

institute: Georgetown University

summary:
Thiazolidinediones increase tissue insulin sensitivity and are protective against worsening of nephropathy and hypertension in diabetes. Mechanisms underlying protection at the renal level likely involve a variety of unknown changes in gene expression.   We examined kidney gene expression in obese and lean Zucker rats in response to rosiglitazone (Avandia®), a peroxisome proliferator activated receptor (gamma-subtype) agonist.  Lean and obese Zucker rats were treated with either control chow or chow with added rosiglitazone (3 mg/kg•bw) for 12 weeks (n = 3/group).  Total kidney mRNA expression was evaluated using the Affymetrix Rat Genome 230 2.0 GeneChip. 903 probe sets were significantly (P < 0.05) altered with at least 1.5-fold changes between groups.  In untreated obese rats, 300 probe sets were increased and 244 decreased, relative to lean.  Increased genes included the β-subunit of the epithelial sodium channel (ENaC), the thiazide-sensitive Na-Cl cotransporter, and aquaporin 3.  Decreased genes included angiotensin converting enzyme, type 1 (ACE1).  FatiGO analysis showed that the highest number of altered genes between lean and obese belonged to the categories: ion binding, hydrolase activity, and protein binding.  RGZ increased expression of uncoupling protein 1 (UCP1), CD36, and fatty acid binding protein 4 (FAbp4) in both lean and obese rats.  In obese rats, 33 genes were normalized by RGZ (no longer different from lean) including ACE1, fatty acid synthase (Fasn), and stearoyl-coenzyme A desaturase 2 (Scd2).  Ingenuity Pathways System analysis of genes upregulated by RGZ in obese rats revealed two major nodes affected:  PPAR-gamma and tumor necrosis factor alpha (TNF-alpha).
Keywords: Thiazolidinediones, PPAR-gamma agonists, renal, type II diabetes, obesity

overall_design: Twelve male Zucker rats (6 Lean and 6 Obese) were used in the study. Three rats from each body type were fed either with control diet (ground chow diet) or control diet with rosiglitazone (3 mg/kg body weight). The rats were weighed weekly and fed diets and recieved water ad libitum for 12 weeks.


title: Actions of anti-Mullerian hormone on the ovarian transcriptome to inhibit primordial to primary follicle transition.

status: Public on Feb 20 2008

city: Pullman

last: Skinner

address: Abelson 507

institute: WSU

summary:
The oocytes found within the primordial follicles of mammalian ovaries remain quiescent for months to years until they receive the appropriate signals to undergo the primordial to primary follicle transition and initiate folliculogenesis. The molecular mechanisms and extracellular signaling factors that regulate this process remain to be fully elucidated. The current study investigates the mechanisms utilized by anti-Müllerian hormone (AMH; i.e. Müllerian inhibitory substance) to inhibit the primordial to primary follicle transition. Ovaries from 4-day-old rats were placed into organ culture and incubated in the absence or presence of AMH, either alone or in combination with known stimulators of follicle transition, including basic fibroblast growth factor (bFGF), kit ligand (KITL), or keratinocyte growth factor (KGF). Following 10 days of culture, the ovaries were sectioned, stained, and morphologically evaluated to determine the percentage of primordial versus developing follicles. As previously demonstrated, AMH treatment decreased primordial to primary follicle transition. Interestingly, AMH inhibited the stimulatory actions of KITL, bFGF, and KGF. Therefore, AMH can inhibit the basal and stimulated development of primordial follicles. To investigate the mechanism of AMH actions, the influence AMH has on the ovarian transcriptome was analyzed. AMH treatment when compared with controls was found to alter the expression of 707 genes. The overall effect of AMH exposure is to decrease the expression of stimulatory factors, increase the expression of inhibitory factors, and regulate cellular pathways (e.g. transforming growth factor beta signaling pathway) that result in the inhibition of primordial follicle development. Analysis of the regulatory factors and cellular pathways altered by AMH provides a better understanding of the molecular control of primordial follicle development.
Keywords: expression analysis, follicle assembly, AMH effect, ovary

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

first: Eric

last: Nilsson

first: Natalie

last: Rogers


title: Triazole Antifungal Toxicogenomics: rat_repro_Liver

overall_design: A total of 35 liver samples were analyzed.  Seven biological replicates for the controls, 5 biological replicates for mid dose myclobutanil and 5 biological replicates for high dose mylcobutanil.  There are 5 biological replicates for mid dose propiconazole, 4 biological replicates for high dose propiconazole, 5 biological replicates for mid dose triadimefon, and 4 biological replicates for triadimefon.


title: Mammary gland gene expression timecourse with or without NMU treatment between Cop and F344 rat

status: Public on Feb 27 2008

city: Seattle

first: Xuefeng

last: Ren

institute: Fred Hutchinson Cancer Research Center

summary:
Gene expression profiles in mammary glands of different rat strains are genetically defined.
Keywords: Different rat strains and Timecourse

overall_design: 18 Cop rats with or without N-nitrosomethylurea (NMU) treatment at 6h, 1d, and 30 d compared to 18 F344 rats with or without NMU treatment at 6h, 1d, and 30 day

first: Helmut

last: Zarbl


title: Triazole Antifungal Toxicogenomics: Iconix3_Triazoles

summary:
The modes of triazole reproductive toxicity have been characterized by an observed increased in serum testosterone and reduced insemination and fertility indices. The key events involved in the disruption in testosterone homeostasis and reduced fertility remain unclear. Gene expression analysis was conducted on liver from Sprague Dawley rats dosed with myclobutanil (300 mg/kg/day), propiconazole (300 mg/kg/day), or triadimefon (175 mg/kg/day) for 72 hours. Pathway-based analysis highlighted key biological processes affected by all three triazoles in the liver including fatty acid catabolism, steroid metabolism, and xenobiotic metabolism. Within the pathways identified in the liver, specific genes involved in phase I-III metabolism and fatty acid metabolism were affected by all three triazoles. These modulated genes are part of a network of lipid and testosterone homeostasis pathways regulated by the constitutive androstane (CAR) and pregnane X (PXR) receptors. Gene expression profiles from this study indicate triazoles activate CAR and PXR; increase fatty acid catabolism and steroid metabolism in the liver; constituting a plausible series of key events contributing to the observed disruption in testosterone homeostasis.
Keywords: comparative toxicogenomics

overall_design: A total of 12 liver samples were analyzed.  Three biological replicates each for the controls, 300 mg/kg/day myclobutanil, 300 mg/kg/day propiconazole, and 175 mg/kg/day triadimefon.


title: Triazole Antifungal Toxicogenomics: GeneLogic_Triazoles

summary:
The modes of triazole reproductive toxicity have been characterized by an observed increased in serum testosterone and reduced insemination and fertility indices. The key events involved in the disruption in testosterone homeostasis and reduced fertility remain unclear. Gene expression analysis was conducted on liver from Sprague Dawley rats dosed with myclobutanil (300 mg/kg/day) or triadimefon (175 mg/kg/day) for 6, 24 or 336 hours. Pathway-based analysis highlighted key biological processes affected by all three triazoles in the liver including fatty acid catabolism, steroid metabolism, and xenobiotic metabolism. Within the pathways identified in the liver, specific genes involved in phase I-III metabolism and fatty acid metabolism were affected by all three triazoles. These modulated genes are part of a network of lipid and testosterone homeostasis pathways regulated by the constitutive androstane (CAR) and pregnane X (PXR) receptors. Gene expression profiles from this study indicate triazoles activate CAR and PXR; increase fatty acid catabolism and steroid metabolism in the liver; constituting a plausible series of key events contributing to the observed disruption in testosterone homeostasis.
Keywords: time course, comparative toxicogenomics

overall_design: A total of 15 liver samples were analyzed.  Five biological replicates each for the controls, 225 mg/kg/day myclobutanil, and 175 mg/kg/day triadimefon.


title: Expression profiling of mammalian Schwann cells in response to NF1 RNAi treatment and the MEK inhibitor U0126

status: Public on Feb 08 2008

city: London

first: Luke

middle: Adam

last: Noon

address: Gower Street

department: LMCB

institute: MRC

summary:
Comparison of the changes in the gene expression profile of cells in which NF1 has been knocked down by RNAi in the presence/absence of the MEK inhibitor UO126
Keywords: RNAi knock-down of NF1 gene

overall_design: Primary Rat Schwann cells were transiently transfected with either scrambled (control) or NF1 RNAi oligonucleotides in the presence/absence of the MEK inhibitor UO126. Total RNA was then harvested 48 hours post-transfection. Three independent biological replicates were analysed.

first: Simona

last: Parrinello

first: Pedro

last: Echave

first: Alison

last: Lloyd

first: Marie

last: Harrisingh

first: Patrick

last: Wingfield-Digby

first: Catherine

last: Cremona

first: Laura

last: Rosenberg

first: Adrienne

last: Flanagan

first: Luis

middle: F

last: Parada


title: Identification of Candidate Genes for Alcohol Preference by Expression Profiling of Congenic Strains

status: Public on Feb 01 2008

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

summary:
A highly significant quantitative trait locus (QTL) that influenced alcohol preference was identified in the iP/iNP rats on chromosome 4.
Congenic strains in which the iP chromosome 4 QTL interval was transferred to the iNP (NP.P) exhibited the expected increase in alcohol
consumption compared to the iNP background strain. This study was undertaken to identify genes in the chromosome 4 QTL interval that might
contribute to the differences in alcohol consumption between the alcohol-naïve congenic and background strains. RNA from five brain regions
from each of 6 NP.P and 6 iNP rats was labeled and analyzed separately on an Affymetrix Rat Genome 230 2.0 microarray. Expression levels
were normalized using robust multi-chip average (RMA). Differential gene expression was validated using quantitative real-time PCR. An analysis
combining five brain regions, including nucleus accumbens, frontal cortex, amygdala, hippocampus, and striatum, identified twenty three
transcripts and nine ESTs that were differentially expressed between the NP.P and iNP. Of the twenty three observed transcripts, thirteen
were known genes, 9 were predicted genes and all but one were located in the chromosome 4 QTL interval. Very interesting cis-regulated
candidate genes for alcohol consumption were identified using microarray profiling of gene expression differences in congenic animals carrying
a QTL for alcohol preference.
Keywords: alcohol, congenic, rat, gene expression, brain, nucleus accumbens, amygdala, frontal cortex, hippocampus, striatum

overall_design: Brain regions (accumbens, amygdala, frontal cortex, hippocampus, and striatum) from 6 biologic replicates of the selected non-preferring line NP and from a NP.P congenic line were dissected and subjected to microarray analysis for comparison.

first: Lucinda

last: Carr

middle: W

first: Tiebing

last: Liang

first: Jeanette

middle: K

last: McClintick

first: Kevin

last: McCall

first: Melissa

last: Grote

first: Howard

last: Edenberg


title: Expression profiling of mammalian Schwann cells in response to treatment with NRG and/or IGF

status: Public on Mar 18 2008

department: MRC LMCB

institute: University College London

summary:
Comparison of the changes in mitochondrial gene expression  of cells in which extracellular growth factors and/or mitogens have been added.
Keywords: Input of growth and mitogenic pathways in mitochondria biogenesis

overall_design: Primary Rat Schwann cells were arrested and synchronized with aphidicolin for 24 hours in 3% FCS containing medium. Cells where then transferred to defined conditions (no factors) with aphidocolin for another 24 hours before appropriate factors were applied for 15 hours prior to cell collection.


title: In vivo administration of Gamendazole and Lonidamine

status: Public on Jan 24 2008

city: Kansas City

first: Joseph

middle: S

last: Tash

state: KS

address: 3901 Rainbow Blvd.

department: Center for Male Contraceptive Research and Drug Development

institute: University of Kansas Medical Center

summary:
rat testis time changes
Experimental details are found at Tash et al, Gamendazole, an orally active indazole carboxylic acid male contraceptive agent, targets HSP-90, eEF1A, and stimulates IL-1 transcription in Sertoli cells, Biol. Reprod. (2007) under review
Keywords: time course

overall_design: Adult male rats administered single ip dose of 6mg/kg Gamendazole or 25 mg/kg lonidamine or vehicle control (buffered DMSO) - testes harvested at 0 4 12 and 24 hr - 3 chips used for each time point


title: Low and High Capacity Runners - Sedentary and Trained: Left Ventricle

status: Public on Jan 04 2008

city: TRONDHEIM

first: Anja

last: Bye

address: Olav Kyrres gt 9

institute: NTNU

summary:
Aerobic capacity is a strong predictor of cardiovascular mortality. To determine the relationship between aerobic capacity and cardiac gene expression we examined genome-wide gene expression in hearts of rats artificially selected for high- and low running capacity (HCR and LCR, respectively) over 16 generations. HCR were born with an athletic phenotype, whereas LCR exhibited features of the metabolic syndrome.

Left ventricle gene expression of both sedentary and exercise trained HCR and LCR was characterized by microarray- and gene ontology analysis. Western immunoblots and immunohistochemistry were used to validate the results at protein level.

Out of 28.0000 screened genes, 1540 were differentially expressed between HCR and LCR. HCR expressed higher amounts of genes involved in lipid metabolism, whereas LCR expressed higher amounts of the genes involved in glucose metabolism and transport. By simply selecting for running capacity, we created a difference in cardiac energy substrate utilisation from normal mitochondrial fatty acid betaoxidation in HCR to carbohydrate metabolism in LCR. This event often occurs in diseased hearts. Differential expression of genes involved in cardiomyocyte growth was also found. LCR rats were associated with fetal gene expression, indicating the presence of pathological remodelling signaling. In addition, different expression of genes associated with cardiac contractility and cellular stress were detected. Also, hypoxia triggered transcription seemed to be involved in several of the functional differences between HCR and LCR.

In conclusion, high- versus low aerobic capacity was associated with differences in genes regulating cardiac energy substrate, growth signalling, contractility and cellular stress.
Keywords: metabolic syndrome analysis

overall_design:
Animals
The experimental rats in this study are the result of artificial selection for high and low aerobic capacity, starting from the N: NIH stock obtained from the National Institutes of Health (USA). The generation of the model has been previously described. Briefly, the rats in each generation were tested for exercise capacity by treadmill running at about 11 weeks of age. The individuals with the highest and lowest aerobic capacity were selected and each group served as the mating population for the next generation of high- and low-capacity runners; HCR and LCR, respectively. Rats from generation 16 were used in this study. The study includes four groups; LCR trained (n=4), LCR sedentary (n=4), HCR trained (n=4) and HCR sedentary (n=4).

Endurance training
The animals in the training groups were submitted to an aerobic interval training program previously described by Hoydal et al. Briefly, after 10 minutes of warm-up, rats ran uphill (25°) on a treadmill for 1.5 hours, alternating between 8 minutes at an exercise intensity corresponding to 85-90% of maximal oxygen uptake (VO2max), and 2 minutes active recovery at 50 - 60%. Exercise was performed 5 days per week over 8 week; controls were age-matched rats that remained sedentary. In the exercising animals VO2max was measured every week to adjust band speed in order to maintain the intended intensity throughout the experimental period. The VO2max-measurements consisted of a 20 minutes warm-up at 50-60% of VO2max, whereupon treadmill velocity was increased by 0.03 m/s every 2 minute until VO2 plateau despite of increased workload. The apparatus and method were previously described and validated.

Tissue collection
At approximately 7 months of age the animals were sacrificed. A section of the left ventricle was formalin fixated for immunohistochemistry and morphological studies, whereas the rest was snap frozen in liquid nitrogen and stored at -80C for later genetic screening and protein analysis. Experimental protocols were approved by the respective Institutional Animal Research Ethics Councils.

Ribonuclease (RNA) isolation
Tissue samples (20 mg) were homogenized in 100 uL TRIzol (Life Technologies, Gaithersburg, MD) using a Mixer Mill MM301 at 20-25 Hz. RNA clean-up was performed using RNA Mini kit (Qiagen, Germantown, MD). Total RNA was isolated and RNA clean-up was performed according to the manufacturer's instructions.

RNA integrity, purity and quantity were assessed by Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Nanodrop (NanoDrop Technologies, Baltimore, MD). The concentration of total RNA was measured by Nanodrop with ultraviolet spectrophotometry at 260/280 nm. RNA quality was assessed by electrophoresis on Bioanalyzer chips (Agilent Technologies).

High quality RNA was classified as a 260/280 ratio above 1.8. Only samples with a 260/280 ratio between 1.8-2.2 and no signs of degradation were used for analysis.

Processing of Affymetrix data
Gene expression were analyzed on whole-genome RAE 230 2.0 chip from Affymetrix GeneChip (Affymetrix, Santa Clara, CA) comprised of 31,042 probe sets, analyzing over 30,000 transcripts and variants from over 28,000 substantiated rat genes. On the Affymetrix GeneChip arrays, each gene is represented by a set of 11-20 probe pairs consisting of a perfect match (PM) and a mismatch (MM) probe. The statistical analysis is based on summary expression measures for each probe set.

Computing summary measures (RMA)
The summary measure for each probeset is computed based on a linear statistical model for background-corrected, normalized and log-transformed PM values for each probe pair by use of the robust multiarray average (RMA) method. The PM values are normalized using the quantile normalization method, normalizing the arrays such that the empirical distribution of the expression measures is equal across arrays.

Statistical analysis for finding differentially expressed genes
For each gene (probeset), a linear regression model, including parameters representing the effect of aerobe capacity is specified. Based on the estimated effects, tests for significant differential expression are performed using  moderated T-tests.

To account for multiple testing, we calculate adjusted p-values controlling the False Discovery Rate (FDR), with the use of the Benjamini-Hochberg step-up procedure. Consequently, selecting differentially expressed genes based on a threshold of 0.05 on the adjusted FDR p-values means that the expected proportion of genes falsely classified as differential expressed should be below 0.05.

All statistical analyses on the gene expression data are performed using the R language (R Development Core Team, 2004) and packages affy, affyPLM and limma from the Bioconductor project.


title: Expression data from rat tissues dosed with AMG A or AMG B

status: Public on Dec 23 2007

city: Thousand Oaks

first: Tiffany

last: Day

address: One Amgen Center Drive

institute: Amgen

summary:
To evaluate and characterize gene expression changes and toxicity following oral gavage administration of AMG A & AMG B in male Sprague Dawley rats.
Keywords: dose response

overall_design: This toxicogenomics study is designed to determine the toxicity and gene expression of AMG A and AMG B dosed orally daily (AMG A at 0mg/kg, 3mg/kg and 30 mg/kg and AMG B at 0mg/kg, 3mg/kg and 60mg/kg) for 1, 4 and 14 days. These doses are expected to produce mild and moderate changes in clinical pathology and histology associated with the pharmacologic antiangiogenic effect.


title: Trancriptome profiling of rat inner medullary collecting duct

status: Public on Dec 21 2007

city: Bethesda

first: Panapat

last: Uawithya

address: 9000 Rockville pike Bldg 10 Rm 6N306

department: NHLBI

institute: NIH

summary:
Identification of gene expressed in the enriched inner medullary collecting duct cells in rat.
Keywords: gene expression comparision between cell type

overall_design:
Rat inner medullary collecting duct (IMCD) cells were isolated from 7 male Sprage-Dawley rats by collagenase and hyaluronidase digestion and follow by low speed centrifugation. The non-IMCD cells were collected by centrifugation of supernatant of enriched IMCD samples.
Total RNA about 3 ug were used per microarray (Rat 230 2.0 Genechip array).
The experiments were repeat 3 times (3 pairs of IMCD VS non-IMCD)

middle: A

last: Knepper


title: Mapping of meiotic single-stranded DNA reveals double-strand break hotspots near centromeres and telomeres.

status: Public on Nov 15 2007

city: New York

first: Andreas

last: Hochwagen

address: 1009 Silver Center 100 Washington Square East

institute: New York University

type: Genome variation profiling by genome tiling array

summary:
Every chromosome requires at least one crossover to be faithfully segregated during meiosis. At least two levels of regulation govern crossover distribution; where the initiating DNA double-strand breaks (DSBs) occur and whether those DSBs are repaired as crossovers. We mapped meiotic DSBs in budding yeast by identifying sites of DSB-associated single-stranded DNA (ssDNA) accumulation. These analyses revealed substantial DSB activity in regions close to centromeres, where crossover formation is largely absent. Our data suggest that centromeric suppression of recombination occurs at the level of break repair rather than DSB formation. Additionally, we found an enrichment of DSBs within a ~100-kb region near the ends of all chromosomes. Introduction of new telomeres was sufficient to induce large ectopic regions of increased DSB formation, revealing a remarkable long-range effect of telomeres on DSB formation. The concentration of DSBs close to chromosome ends increases the relative DSB density on small chromosomes, providing an interference-independent mechanism to ensure that all chromosomes receive at least one crossover per homolog pair. Together, our results indicate that selective DSB repair accounts for crossover suppression near centromeres, and suggest a simple telomere-guided mechanism to ensure sufficient DSB activity on all chromosomes.
Keywords: ssDNA analysis, comparative genomic hybridization, ChIP-chip

overall_design:
We mapped DSB sites by detecting DSB-associated ssDNA enrichment on microarrays. We used the following strains to test determinants of DSB site selection: wild-type, dmc1Δ, spo11Y135F, dmc1Δ ndj1Δ, dmc1Δ zip1Δ and dmc1Δ with bisected chromosome XV. ssDNA was isolated from cells after either 3 hours (WT and spo11Y135F) or 5 hours (all other strains) in sporulation medium. As a reference, ssDNA isolated from cells at 0 hrs in sporulation medium was differentially labeled and co-hybridized to the same array.

For each experiment, we have submitted biological replicates that were hybridized to separate arrays. For each experiment a dye swap was performed and shown to have no effect on the data observed, although not all experiments in this series include the dye swap sample (we have included only two representative experiments for each strain).

We also mapped DSB sites by performing Spo11-18myc ChIP in a rad50S strain incubated for 5 hours in sporulation medium. Immunoprecipitated and input DNA samples were differentially labeled and cohybridized to a single microarray. We have included 3 biological replicates of this experiment, including one dye swap experiment.

first: Hannah

middle: G

last: Blitzblau

first: George

last: Bell

last: Rodriguez

first: Stephen


title: 24 h-fasting effects on the brown and white adipose tissue and liver

status: Public on Jan 09 2008

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary:
The functional balance between brown adipose tissue (BAT) and white adipose tissue (WAT) is important for metabolic homeostasis.  We compared the effects of fasting on the gene expression profiles in BAT, WAT and liver, using DNA microarray analysis.  Tissues were obtained from rats that had been fed or fasted for 24 h.  Taking the false discovery rate (FDR) into account, we extracted the top 1,000 genes that were expressed differentially between fed and fasted rats.  In all three tissues, Gene Ontology analysis revealed marked changes in the expression of ‘metabolism’ category genes and a hypergeometric test demonstrated that within this category, lipid and protein biosynthesis-related genes were down-regulated.  These findings indicate simultaneous down-regulation of genes involved in energy-consuming pathways in the BAT, WAT and liver of fasted rats.  In the BAT of fasted rats, there was marked up-regulation of genes in the ‘protein ubiquitination’ category, suggesting that the ubiquitin-proteasome system is involved in saving energy as an adaptation to food shortage.
Keywords: treatment comparison

overall_design: Rats (7-week-old) were given a commercial diet between 10:00 and 16:00 for 7 days.  At 10:00 on day 8, they were divided into two groups that comprised animals of similar body weights.  One group continued to be fed as described above (fed group, n=4 for array analysis), whereas the other group were not fed (fasted group, n=4 for array analysis).  Both groups received water ad libitum.  At 16:00 on day 8, the liver, interscapular BAT and perinephrial WAT were excised, and analyzed for fasting effect.

first: Hiroko

last: Hashida

first: Koji

last: Kadota

first: Michiko

last: Minami

first: Kentaro

last: Shimizu

first: Ichiro

last: Matsumoto

first: Hisanori

last: Kato

first: Keiko

last: Abe


title: Gene Expression Changes in Response to Baculoviral Vector Transduction of the Rat Brain In Vivo

status: Public on Dec 13 2007

city: Singapore

first: Jerome

last: Boulaire

address: 31 Biopolis Way

department: Gene Delivery

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

summary:
Recombinant baculoviral vectors efficiently transduce several types of cells in the brain. To characterize host responses to viral challenge, thus verifying the suitability of using the virus for the development of gene therapy strategies in the central nervous system, we used cDNA microarray technology to examine in vitro and in vivo global cellular gene expression profiles after viral transduction. We demonstrated that the transduction induced host antiviral responses as a major reaction in all three types of samples profiled, including the rat brain, cultured human astrocytes and human neuronal cells. The related genes were mainly those associated with innate immunity. Several genes of the major histocompatibility complex molecules, an important component of the host adaptive immunity to exogenous pathogens, were up-regulated in the rat brain and human astrocytes, but not in neuronal cells. We also observed that genes related to cell death and apoptosis were up-regulated and genes related cell cycle regulation were down-regulated in neuronal cells, but not obviously affected in astrocytes. These findings should be useful in understating the molecular basis for neural cell response to baculoviral transduction and guiding rational applications of baculoviral vectors in the central nervous systems
Keywords: Baculovirus, brain, astrocytes, neurons, transduction, Infection, gene expression analysis, DNA microarray

overall_design:
For in vivo viral inoculation, adult male Wistar rats (weighing 250–300 g) were used. Five μl of baculovirus vectors (5 x 107 viral particles) was injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis. Five μl of PBS was injection into the contralateral striatum and the tissues were collected and used as controls.
Seven rats were used for the study.
Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer. One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands). Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the human GeneChip Human Genome U133 Plus 2.0 or GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions. Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software.

Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 5 out of 7 brain samples or 2 out of 3 cell replicates had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition. The volcano plot was sometime used to filter the data further with the following cut-off (2-fold difference in expression level and t-test p-value of less than 0.05). Further data manipulation for comparison purposes are described in the text.

middle: L

first: Shu

last: Wang


title: Orc6 is Required for Dynamic Recruitment of Cdt1 During Repeated Mcm2-7 Loading

status: Public on Nov 14 2007

city: Cambridge

address: 68-630, 77 Massachusetts Ave.

department: Biology

institute: MIT

type: Genome binding/occupancy profiling by genome tiling array

summary:
The origin recognition complex (ORC) nucleates DNA replication initiation in eukaryotic cells.  This six-protein complex binds replication origin DNA, recruits other initiation factors and facilitates loading of the DNA helicase.  Studying the function of individual ORC subunits during pre-RC formation has been hampered by the requirement of most subunits for DNA binding.  In this study, we investigate the function of the S. cerevisiae Orc6 subunit, the only subunit not required for DNA binding.  In vivo, depletion of Orc6 inhibits pre-replicative complex (pre-RC) assembly and maintenance.  In vitro, ORC lacking Orc6 fails to interact with Cdt1 and to load the Mcm2-7 helicase onto origin DNA.  We demonstrate that two regions of Orc6 bind Cdt1 directly and that the extreme C-terminus of Orc6 (Orc6-CTD) interacts tightly with the remaining five ORC subunits.  Replacing Orc6 with a fusion protein linking Cdt1 to the Orc6-CTD results in an ORC complex that loads Mcm2-7 onto DNA.  Interestingly, this complex can only perform a single round of Mcm2-7 loading, suggesting that a dynamic association of Cdt1 with ORC is required for multiple rounds of pre-RC assembly.
Keywords: ChIP-chip

overall_design: We used ChIP against MCM and ORC proteins to assess the effect of removal of Orc6 on both the establishment and maintenance of pre-RCs in yeast.

first: Shuyan

last: Chen

first: Milan

last: de Vries


title: Transcriptomics and proteomics in colon mucosa from rats fed quercetin

status: Public on Jan 01 2008

city: Zeist

first: Ashwin

last: Dihal

address: Utrechtseweg 48

department: Business Unit Physiologival Sciences

country: Netherlands

institute: TNO Quality of Life

summary:
Quercetin has been shown to act as an anti-carcinogen in experimental colorectal cancer (CRC). The aim of the present study was to characterise transcriptome and proteome changes occurring in the distal colon mucosa of rats supplemented with 10 g quercetin/kg diet for 11 weeks. Transcriptome data analysed with Gene Set Enrichment Analysis showed that quercetin significantly downregulated the potentially oncogenic mitogen-activated protein kinase (Mapk) pathway. In addition, quercetin enhanced expression of tumor suppressor genes, including Pten, Tp53 and Msh2, and of cell cycle inhibitors, including Mutyh. Furthermore, dietary quercetin enhanced genes involved in phase I and II metabolism, including Fmo5, Ephx1, Ephx2 and Gpx2. Quercetin increased PPARα target genes, and concomitantly enhanced expression genes in volved in of mitochondrial fatty acid degradation. Proteomics performed in the same samples revealed 33 affected proteins, of which 4 glycolysis enzymes and 3 heatshock proteins were decreased. A proteome-transcriptome comparison showed a low correlation, but both pointed out towards altered energy metabolism.

In conclusion, transcriptomics combined with proteomics showed that dietary quercetin evoked changes contrary to those found in colorectal carcinogenesis. These tumor-protective mechanisms were associated with a shift in energy production pathways, pointing at decreased glycolysis in the cytoplasm towards increased fatty acid degradation in the mitochondria.
Keywords: Transscriptomics, proteomics, quercetin-exposed and control rats

overall_design: After an 11-week diet, rats fed quercetin or the control diet were sacrificed and fold changes in gene expression were detemined as quercetin (n=4) vs. control (n=4)

first: Hester

last: van der Woude

first: Peter

last: Hendriksen

first: Halima

last: Charif

first: Lennard

last: Dekker

first: Linda

last: IJsselstein

first: Vincent

last: de Boer

first: Gerrit

middle: M

last: Alink

last: Burgers

first: Ivonne

last: Rietjens

first: Ruud

last: Woutersen

first: Rob

middle: H

last: Stierum


title: Gene expression analysis of brain cortex

status: Public on Dec 12 2007

city: Leioa

first: Leyre

last: Uriguen

state: Vizcaya

address: Barrio Sarriena s/n

department: Pharmacology

institute: University of the Basque Country

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

overall_design: Refer to individual Series


title: Gene expression analysis of brain cortex of corticosterone-treated rats

summary:
Animal models represent a very useful tool for the study of depressive-like behaviour and for the evaluation of the therapeutic efficacy of antidepressants.   Nevertheless, gene expression patterns of these different animal models and whether genes classically associated to human major depression are present in these genetic profiles remain unknown. Gene expression was evaluated in an animal model of depression: corticosterone-treated rats. Gene expression analyses were carried out using the Affymetrix® GeneChip® technology.
Keywords: Treatment vs control comparative genomics study

overall_design: In total, 19 animals were studied, 10 corticosterone-treated rats and 9 control rats

first: David

last: Arteta

first: Rebeca

last: Diez-Alarcia

first: Marcel

last: Ferrer-Alcon

first: Alvaro

last: Diaz

first: Angel

last: Pazos

first: Javier

last: Meana


title: Gene expression analysis of brain cortex of olfactory-bulbectomized rats

summary:
Animal models represent a very useful tool for the study of depressive-like behaviour and for the evaluation of the therapeutic efficacy of antidepressants.   Nevertheless, gene expression patterns of these different animal models and whether genes classically associated to human major depression are present in these genetic profiles remain unknown. Gene expression was evaluated in an animal model of depression: olfactory-bulbectomized rats. Gene expression analyses were carried out using the Affymetrix® GeneChip® technology.
Keywords: Bulbectomized vs sham-operated comparative genomics study

overall_design: In total, 11 animals were studied, five bulbectomized rats and six sham-operated rats


title: Gene expression analysis of brain cortex of reserpine-treated rats

summary:
Animal models represent a very useful tool for the study of depressive-like behaviour and for the evaluation of the therapeutic efficacy of antidepressants.   Nevertheless, gene expression patterns of these different animal models and whether genes classically associated to human major depression are present in these genetic profiles remain unknown. Gene expression was evaluated in an animal model of depression: acute treatment with reserpine. Gene expression analyses were carried out using the Affymetrix® GeneChip® technology.
Keywords: Treatment vs control comparative genomics study

overall_design: In total, 12 animals were studied, six treated samples and six control samples


title: Transcriptome analysis of an oxidative stress-induced rat renal carcinogenesis model

status: Public on Oct 01 2007

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

summary:
An iron chelate, ferric nitrilotriacetate (Fe-NTA), induces oxidative renal tubular damage that subsequently leads to renal cell carcinoma in rodents.  Here we used gene expression microarrays to find target oncogenes in this model.  Network analysis of the gene expression microarray data revealed the involvement of beta-catenin pathway in the induced cancers.
Keywords: dose response, disease state analysis

overall_design: Carcinogenesis protocol was performed using specific pathogen-free male Wistar rats or male F1 hybrid rats between Fischer344 and Brown-Norway strains.  A total of 10 microarrays (Rat Genome 230 2.0; 31,999 genes; Affymetrix Inc., Santa Clara, CA) were used for the screening purpose; two for each group of untreated control, Fe-NTA treatment for 1 week, Fe-NTA treatment for 3 weeks, Fe-NTA-induced RCCs with neither peritoneal invasion nor metastasis and Fe-NTA-induced RCCs with pulmonarymetastasis.

first: Yu-Ting

last: Liu

last: Akatsuka

first: Noriko

last: Noguchi

first: Tatsuhiko

last: Kodama


title: Angiogenesis inhibitors ameliorates inflammatory infiltrate, fibrosis and portal pressure in cirrhotic rats

status: Public on Oct 18 2007

city: Barcelona

first: Manuel

last: Morales-Ruiz

address: Villarroel 170

department: Biochemistry and Molecular Genetics

institute: Hospital Clinic

summary:
Background and aims: There are considerable evidences demonstrating that angiogenesis and chronic inflammation are mutually dependent. However, although cirrhosis progression is characterized with a chronic hepatic inflammatory process, this connection is not sufficiently explored as a therapeutic strategy. Therefore, this study was aimed to assess the potential benefits of targeting angiogenesis in cirrhotic livers to modulate inflammation and fibrosis. For this purpose, we evaluate the therapeutic utility of angiogenesis inhibitors. Methods: The in vivo effects of angiogenesis inhibitors were monitored in liver of cirrhotic rats by measuring angiogenesis, inflammatory infiltrate, fibrosis, a-smooth muscle actin (a-SMA) accumulation, differential gene expression (by microarrays), and portal pressure. Results: Cirrhosis progression was associated with a significant enhancement of vascular density and expression of vascular endothelial growth factor-A (VEGF-A), angiopoietin-1, angiopoietin-2 and placental growth factor (PlGF) in cirrhotic livers. The newly formed hepatic vasculature expressed vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1). Interestingly, the expression of these adhesion molecules correlated well with local inflammatory infiltrate. Livers of cirrhotic rats treated with angiogenesis inhibitors presented a significant decrease in hepatic vascular density, inflammatory infiltrate, a-SMA abundance, collagen expression and portal pressure. Conclusion: Angiogenesis inhibitors may offer a potential novel therapy for cirrhosis due to its multiple mechanisms of action against angiogenesis, inflammation and fibrosis in cirrhotic livers.
Keywords: angiogenesis, cirrhosis, liver, Affymetrix, fibrosis

overall_design: RNA from liver of 4 non-treated cirrhotic rats or 4 rats treated with angiogenesis inhibitors was hybridized to 8 high-density oligonucleotide microarray (Rat2302, Affymetrix, Santa Clara, CA)

first: Sonia

last: Tugues

first: Wladimiro

last: Jimenez


title: Expression data from adult rat testes treated with 3 mg/kg b.w. cadmium chloride via i.p.

status: Public on Nov 07 2007

city: NEW YORK

first: C YAN

last: CHENG

address: 1230 YORK AVENUE

institute: POPULATION COUNCIL

summary:
This is a study to explore the transcriptional changes after cadmium treatment in adult rat testes at three time points (control--0 hour,  8 hour and 4 day). Cadmium is an environmental toxicant that is known to affect the male reproductive system. It disrupts the blood-testis barrier irreversibly,  and affects the Sertoli-germ cells adhesion, causing germ cell depletion from the seminiferous epithelium.
Keywords: Cadmium effect in rat testes

overall_design: Adult Sprague-Dawley rats treated with a single dose of cadmium chloride at 3 mg/kg b.w. by i.p. and terminated after 8 hours (n=2) and 20 hours (n=2). Testes from cadmium-treated rats and untreated (control, 0 hour, n=3) rats were harvested and total RNA were prepared. Standard Affymetrix genechip procedures were followed for the subsequent experiments. Data were analysed in MAS 5.0 and GeneSpring 7.2.

first: Weiliang

last: Xia

first: C

middle: Y

last: Cheng