title: Impact of Animal Strain on Gene Expression in a Rat Model of Acute Cardiac Rejection

first: Hao

state: MD

address: 9000 Rockville Pike

department: CC

institute: NIH

summary: The expression levels of many genes show wide natural variation among strains or populations. This study investigated the potential for animal strain-related genotypic differences to confound gene expression profiles in acute cellular rejection (ACR). Additional analysis allowed for selection of 49 candidate genes uniquely associated with ACR, but only after accounting for the unexpectedly large effect of animal strain.  Studies of ACR that examine gene expression in peripheral blood may be confounded by strain differences. These results indicate the need for study designs that eliminate or control for the large effect of genetic background on the transcriptome of immune cells.

overall_design: Using a rat heart transplant model microarrays were performed on native hearts, transplanted hearts, and peripheral blood mononuclear cells (PBMC).  Total RNA was isolated, reverse transcribed, labeled, and hybridized to oligonucleotide microarrays. In heart tissue, strain alone affected the expression of only 33 probesets while rejection affected the expression of 1368 probesets (FDR 10% and FC ï?³ 3).  Only 13 genes were affected by both strain and rejection, which was < 1% (13/1368) of all probesets differentially expressed in ACR.  However, for PBMCs, strain alone affected 265 probesets (FDR 10% and FC ï?³ 3) and the addition of ACR had little further effect. Pathway analysis of strain effect in PBMCs associated gene expression differences with immune response, cell motility and cell death, functional themes that overlap with those related to ACR.

first: Peter

last: Munson

first: Robert

last: Sanner

first: Michael

last: Solomon


title: Fiber and NMJ / synaptic gene expression comparisons in rat extraocular muscle (EOM) and tibialis anterior (TA) muscle.

status: Public on Apr 16 2010

city: Philadelphia

first: Murat

middle: T

last: Budak

state: PA

country: USA

institute: University of Pennsylvania

summary:
Purpose: To examine and characterize the expression profile of genes expressed at the neuromuscular junctions (NMJs) of extraocular muscles (EOMs) in comparison to the NMJs of tibialis anterior muscle (TA).
Methods: Adult rat rectus EOMs and TAs were dissected, flash-frozen, serially sectioned and stained for acetylcholinesterase to identify NMJs. Approximately 6000 NMJs for EOM (EOMsyn) and 6000 NMJs for TA (TAsyn) and equal amounts of NMJ-free fiber regions (EOMfib, TAfib) and underlying myonuclei were captured using laser capture microdissection (LCM). RNA was isolated, processed and used for microarray-based expression profiling. Profiles were generated for genes differentially expressed at synaptic and non-synaptic regions of TA (TAsyn vs TAfib) and EOM (EOMsyn vs EOMfib) using a false discovery rate (FDR) of 5% as well as an “interaction list” revealing the most significantly differentially expressed genes at an FDR of 1%. We validated the profiles by real-time quantitative reverse transcription-polymerase chain reaction (qPCR).
Results: The regional transcriptomes associated with NMJ of EOMs and TAs were identified. We found 275 genes that were preferentially expressed in EOMsyn and 230 known transcripts that were preferentially expressed in TAsyn; 288 of the transcripts were common to both synapses; these included well-known, evolutionarily conserved, synaptic markers (e.g. nicotinic Acetylcholine receptor (ACHR) alpha and epsilon subunits, nestin) as well as a large number of novel genes.

Conclusion: Transcriptome level differences exist between EOM synaptic regions and TA synaptic regions. Our definition of the synaptic transcriptome provides insight into the mechanism of formation and functioning of the unique synapses of EOM and their differential involvement in diseases noted in the EOM allotype.

overall_design:
Tissue preparation:
A total of 4 rats were killed by CO2 inhalation. The bony orbit was removed from the skull and opened at the lamina cribrosa. The globe with the four recti EOMs still attached was carefully dissected from the bony orbit. The eyeball with muscles was placed on cryomolds, covered with OCT tissue embedding medium (Tissue-Tek: Sakura Finetek, Tokyo, Japan) and flash-frozen in isopentane, cooled in liquid nitrogen and stored at -80 °C. The tibialis anterior (TA) muscles of all rats were dissected and frozen in the same way. The EOM’s and TA’s were then cut transversely into 10 μm sections using a Microm HM 500 cryostat (Zeiss, Oberkochen, Germany), mounted on PEN (poly-ethylene-naphthalene) Membrane Slides (Arcturus) and refrozen immediately. Unfixed sections were stored at -80°C until needed.

Section staining:
Sections for LCM were stained for acetylcholinesterase based on the method of Karnowsky and Roots to visualize NMJ.

Palm microdissection:
The PALM MicroBeam System was used for microdissection and for catapulting isolated tissue into a microfuge cap containing 80 μl RLT-Lysis Buffer (Quiagen).
Approximately 1000 NMJ and equal amount of non-synaptic regions were collected for each muscle.

first: Caroline

last: Ketterer

first: Ulrike

last: Zeiger

first: Neal

middle: A

last: Rubinstein

first: Tejvir

middle: S

last: Khurana


title: Neurotrophin NT3 promotes ovarian primordial to primary follicle transition

status: Public on Feb 16 2010

city: Pullman

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary:
Neurotrophins are growth factors that are known to have a role in promoting cell survival and differentiation. The focus of the current study is to examine the role of neurotrophins in regulating ovarian primordial follicle development. Ovaries from 4-day old rats were placed into organ culture and cultured for 10 days in the absence or presence of neurotrophin-3 (NT3), brain-derived neurotrophic factor (BDNF), or nerve growth factor (NGF). Treatment of ovaries with NT3 resulted in a significant (P<0.01) increase in primordial follicle development (i.e. primordial to primary follicle transition). Treatment with BDNF at high doses of 100–250 ng/ml also significantly (P<0.01) increased primordial follicle development, but NGF had no effect. Immunohistochemical studies determined that NT3 was present in granulosa cells, interstitial tissue, and in the oocytes of primordial and primary follicles. The NT3 receptor NTRK3 was present in oocytes at all stages of development. Analysis of ovaries that contain predominantly primordial follicles demonstrated the transcripts for NT3, NTRK3, NGF, and the BDNF/neurotrophin-4 (NT4) receptor NTRK2 are expressed, while BDNF, NT4, and the NGF receptor NTRK1 are not detectable. Inhibition of the NTRK3 receptor with the tyrophostin AG 879 resulted in oocyte death and a significant (P<0.01) reduction in follicle pool size. Inhibition of the NTRK receptors with K252a slowed primordial to primary follicle transition. A microarray analysis demonstrated that a small number of genes were differentially expressed after NT3 treatment. Observations indicate that the neurotrophin NT3, acting through the NTRK3 receptor in oocytes, promotes the primordial to primary follicle transition.  Reproduction (2009) 138, pp. 697-707

We used microarrays to determine genes expressed differentially between control and NT3 (neurotrophin-3) treated P4 ovary.

overall_design: RNA samples from 3 control groups are compared to 3 NT3 treated ovary groups.

first: Eric

middle: E

last: Nilsson

first: Gretchen

last: Dole


title: Temporal dysregulation of cortical gene expresssion in the isolation-reared Wistar rat

status: Public on Jun 04 2010

city: Dublin

first: Keith

middle: J

last: Murphy

address: UCD Conway Institute, Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University College Dublin

summary:
The critical sequence of molecular, neurotransmission and synaptic disruptions that underpin the emergence of psychiatric disorders like schizophrenia remain to be established with progress only likely using animal models that capture key features of such disorders.
Gene expression was assessed in social control and isolation reared rats at 4 increasing postnatal ages to relate gene expression dysregulation to behavioural and endophenotype emergence.

overall_design: We prepared cDNA from brain tissue samples of the medial prefrontal cortex from socially reared Wistar rats (Soc) and matching isolation reared cohorts (Iso) at postnatal day (P) 30, 40, 60 and 80.

first: David

last: von Schack


title: Gene expression underlying the effects of biotin deficiency in rat liver, worms and yeast

status: Public on May 31 2010

city: MEXICO, D.F.

first: Pablo Antonio

last: Velázquez-Arellano

address: Av. IMAN No. 1, 4th floor

department: Molecular Biology and Biotechnology

country: Mexico

institute: Institute for Biomedical Research, UNAM

summary:
Biotin is cofactor of crucial enzymes for intermediary metabolism, and its deficiency affects the transcription of some critical genes of mammalian glucose metabolism. However, the precise mechanisms of biotin starvation on gene expression are unknown. Here we show that metabolic changes ushered by deficiency of this vitamin sets in motion extensive reorganization of carbon metabolism gene expression, consistent across three diverse eukaryotes, that is mediated through a regulatory circuitry at the genome level similar in the three species.

We used affymetrix microarrays to detail the global gene expression underlying the effects of biotin deficiency in Rattus norvegicus liver, Caenorhabditis elegans and Saccharomyces cerevisiae and identified distinct classes of up-regulated genes during this event.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Caenorhabditis elegans
Rattus norvegicus

overall_design:
Five male rats (Wistar strain) aged 21 days and 50g of weight were made biotin-deficient, and another five rats of similar gender, age and weight served as controls.

Nematodes synchronized in L1 stage grown in minimal medium (MM) with 5 and 0.05 nM of biotin (sufficient and deficient, respectively).

Biotin-deficient cultures of yeast were obtained by growing cells overnight in a defined synthetic minimal (SD) media with dextrose as the principal carbon source (2%) and (NH4)2SO4 as nitrogen source with aminoacids, minerals and vitamins as complements but without biotin. Cells were centrifuged, washed, and used to inoculate cultures in MMY with 0.4nM and 8nM of biotin adjusted to an A600 absorbance of 0.04 by triplicate. Cells were harvested when cultures reached an A600 absorbance of 0.6-0.8.

first: Daniel

last: Ortega-Cuellar

first: Armando

last: Hernández-Mendoza

first: Elizabeth

last: Moreno-Arriola

first: Antonio


title: Alterations in the developing testis transcriptome following embryonic vinclozolin exposure

status: Public on Feb 14 2010

summary:
The current study investigates the direct effects of in utero vinclozolin exposure on the developing rat testis transcriptome. Vinclozolin is a commonly used fungicide in agriculture and is an endocrine disruptor with anti-androgenic activity. Previous studies have demonstrated that exposure to vinclozolin during embryonic gonadal sex determination induces epigenetic modifications of the germ line and transgenerational adult onset disease states that include spermatogenic cell defects, prostate disease, kidney disease, and tumor development. An investigation of the molecular actions of vinclozolin was initiated through an analysis of direct actions on the F1 generation embryonic testis development. Microarray analyses were performed to compare control and vinclozolin treated testis transcriptomes at embryonic day 13, 14 and 16. A total of 576 differentially expressed genes were identified and the major cellular functions and pathways associated with these altered transcripts were examined. The sets of regulated genes at the different development periods were found to be transiently altered and distinct. Interestingly, genes previously shown to be regulated during normal male sex determination were not altered by vinclozolin treatment. Categorization by major known functions of all 576 genes altered by in utero vinclozolin exposure demonstrates transcription, signaling, cytoskeletal and extra cellular matrix associated transcripts are highly represented. Specific cellular process and pathway analyses suggest the involvement of Wnt and calcium signaling, vascular development and epigenetic mechanisms as potential mediators of the direct F1 generation actions of vinclozolin.

For Samples 1-12: We used microarrays to determine genes expressed differentially between control and in utero Vinclozolin treated E13, E14, and E16 rat testis.
For Samples 13-16: We used microarrays to determine genes expressed differentially between control and in vitro Vinclozolin treated E13 cultured rat testis.
For Samples 17-20: We used microarrays to determine genes expressed differentially between control and in vitro Flutamide treated rat E13 cultured testis.

overall_design:
For Samples 1-12: RNA samples from two control groups are compared to two Vinclozolin treated groups for each E13, E14, E16 testis.
For Samples 13-16: RNA samples from two control groups of E13 cultured testis are compared to two Vinclosolin treated groups of E13 cultured testis.
For Samples 17-20: RNA samples from two control groups of E13 cultured testis are compared to two Flutamide treated groups of E13 cultured testis.

first: Tracy

middle: M

last: Clement

first: Marina

middle: I

last: Savenkova

first: Matthew

last: Settles

middle: D

last: Anway


title: Circadian regulation in rat abdominal adipose tissue

status: Public on Mar 09 2010

city: Buffalo

first: Siddharth

last: Sukumaran

state: NY

address: 109 Cooke Hall, University at Buffalo, North/Amherst Campus

department: Dept of Biological Sciences

institute: State University of New York at Buffalo

summary: Circadian rhythms are oscillations with a periodicity of 24 hours that are controlled by an endogenous clock and are observed in virtually all aspects of mammalian function from expression of genes to complex physiological processes. The master clock is present in the suprachiasmatic nucleus (SCN) in the anterior part of the hypothalamus and controls peripheral clocks present in other parts of the body.  Although much is known about the mechanism of the central clock in the SCN, the regulation of clocks present in peripheral tissues is still unclear.  This study is designed to examine fluctuations in gene expression in abdominal white adipose tissue within the 24 hour circadian cycle in normal animals. The objectives of this study is  to identify and analyze circadian oscillation in gene expression in white adipose tissue, and to identify the role of circadian regulation in coordinating the functioning of this dynamic tissue.

overall_design: Fifty-four male normal Wistar rats (250-350 g body weight) were housed in a strictly controlled stress free environment with light:dark cycles of 12 hr:12hr. Three animals were sacrificed at each of 18 selected time points within the 24 hour cycle. RNA was prepared from abdominal adipose tissue for gene arrays.  Two samples were not used due to RNA degradation: Adipose .25-1 and Adipose 11-2. Time point designations reflect time after lights on in hours.

first: Richard

middle: R

last: Almon


title: Effect of Runx2 Knockdown by siRNA in granulosa cell cultures.

status: Public on Feb 10 2010

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: LH-indced RUNX2 expression is important for luteal gene expression.

overall_design: Granulosa cells were treated with Runx2 siRNA and forskolin to knockdown agonist-induced Runx2 expression. Two separate cultures were performed (n=2) and universal siRNA was used for negative control. Total RNAs were isolated from cultured granulosa cells and used for DNA microarray.

first: Eun-Sil

last: Park

first: Anna-Karin

last: Lind

first: Pernilla

last: Dahm-Kähler

first: Mats

last: Brännström

first: Martha

middle: Z

last: Carletti

first: Lane

last: Christenson

first: Thomas

last: Curry

first: Misung

last: Jo


title: Expression data from the basolateral amygdala of Long-Evans rats with a history of limited intermittent sucrose snacks

status: Public on Feb 17 2010

city: Cincinnati

first: Yvonne

last: Ulrich-Lai

state: OH

address: 2170 E. Galbraith Rd. ML0506

institute: University of Cincinnati

summary: To study the molecular mediators of naturally rewarding effects of palatable food  we used a model of palatable “snacking” (Ulrich-Lai et al., 2007) in which rats are given chronic, brief access to a limited amount of sucrose solution (30%).   Single housed, male Long-Evans rats (250g) (n=12 per group) from Harlan Labs (Indianapolis, IN) received normal rat chow (Harlan Teklad) and water ad libitum for the duration of the experiment.  After a one-week period of acclimation, rats were randomly assigned to drink treatment groups of either 30% sucrose solution or water.  Rats received a 14-day regimen of twice daily (9:30 and 15:30) brief (maximum of 30 minutes) limited (up to 4 mL) access of their assigned drink solution.  Drink solutions were delivered via a graduated sipper placed onto the cage top in addition to the existing water bottle and sippers were immediately removed when the animal had consumed 4mL or after the 30-minute access period, whichever occurred first.  Drink intake, food intake, and body weight were monitored throughout the experiment to verify that the rats learned to drink sucrose, that they adjusted chow intake for calories consumed from sucrose (~10%), and that there was no effect on body weight gain as is normally seen with this model (Ulrich-Lai et al., 2007).  Drink treatment terminated on day 14 and at 8:00 on the morning of day 15, the rats were sacrificed by rapid decapitation. BLA tissue was dissected, RNA extracted, and gene expression changes between water and sucrose groups were accessed by microarray.

overall_design:
We used microarray to assess the changes in gene expression in the BLA of rats that have had a history of sucrose snacks (n=12) vs control (n=12).
Rats received access (up to 4 mL) to extra bottles containing water (control) or 30% sucrose twice daily for 14 days. Rats had ab lib access to chow and water for the duration of the experiment. Rats were sacrificed the morning of day 15 and the BLA was removed for microarray analysis.
Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA).  See supplementary file at the foot of this record.

first: Anne

last: Christiansen

first: Amanda

last: Jones

first: Randy

last: Seeley

first: James

middle: P

last: Herman


title: Phylogenetic & expression analysis of the bHLH transcription factor family: genomic approach to cellular differentiation

status: Public on Feb 11 2010

first: Michael

last: Skinner

summary:
A phylogenetic analysis of seven different species (human, mouse, rat, worm, fly, yeast, and plant) utilizing all (541) basic helix-loop-helix (bHLH) genes identified, including expressed sequence tags (EST), was performed. A super-tree involving six clades and a structural categorization involving the entire coding sequence was established. A nomenclature was developed based on clade distribution to discuss the functional and ancestral relationships of all the genes. The position/location of specific genes on the phylogenetic tree in relation to known bHLH factors allows for predictions of the potential functions of uncharacterized bHLH factors, including EST's. A genomic analysis using microarrays for four different mouse cell types (i.e. Sertoli, Schwann, thymic, and muscle) was performed and considered all known bHLH family members on the microarray for comparison. Cell-specific groups of bHLH genes helped clarify those bHLH genes potentially involved in cell specific differentiation. This phylogenetic and genomic analysis of the bHLH gene family has revealed unique aspects of the evolution and functional relationships of the different genes in the bHLH gene family. PMID: 18557763
We used microarrays to determine bHLH expression in 20d rat Sertoli cells.

overall_design: RNA samples from two control groups (Sertoli cells cultured for 72 h) are compared to two treated groups (Sertoli cells cultured for 72 h with cAMP).

first: Jeffrey

last: Stevens

first: Eric

middle: H

last: Roalson


title: Gene expression in NKR-P1B+ versus Ly49s3+ rat NK cells

status: Public on Mar 18 2010

city: Oslo

first: Marit

last: Inngjerdingen

address: Sognsvannsveien 20

department: Institute of Immunology

country: Norway

institute: Oslo University Hospital, Rikshospitalet and University of Oslo

summary:
Two major subsets of rat natural killer (NK) cells can be distinguished based on their expression of either the Ly49s3 or the NKR-P1B lectin-like receptor. Ly49s3+ NK cells, but not NKR-P1B+ NK cells, express a wide range of Ly49 receptors.
Here, we performed a global gene expression profiling of sorted, single-positive NKR-P1B+ or Ly49s3+ splenic NK cells in order to get an overview of differences in expressed genes between the NKR-P1B+ and Ly49s3+ NK cell subsets.

overall_design: NKR-P1B or Ly49s3 single-positive NK cells were sorted by flow cytometry from NK-enriched mononuclear cells from rat spleens. 9 rats of the PVG.7b strain aged 8-12 weeks were used. Total RNA was harvested by Tri Reagent extraction, and subjected to microarray analysis (Affymetrix Rat Genome 230 2.0 Array).

first: Lise

last: Kveberg


title: Expression data from pure/mixed brain, liver and lung to test feasability and sensitivity of statistical deconvolution

status: Public on Mar 08 2010

city: Stanford

first: Shai

last: Shen-Orr

state: CA

address: 251 Campus Dr. Rm.X-251

institute: Stanford University

summary:
Tissues are often made up of multiple cell-types. Blood, for example, contains many different cell-types, each with its own functional attributes and molecular signature. In humans, because of its accessibility and immune functionality, blood cells have been used as a source for RNA-based biomarkers for many diseases.  Yet, the proportions of any given cell-type in the blood can vary markedly, even between normal individuals. This results in a significant loss of sensitivity in gene expression studies of blood cells and great difficulty in identifying the cellular source of any perturbations.  Ideally, one would like to perform differential expression analysis between patient groups for each of the cell-types within a tissue but this is impractical and prohibitively expensive.
To test the relationship between measured gene expression in mixed samples and the expression of genes in the isolated pure subsets, we begin with a situation in which all factors are known. Tissue samples from the brain, liver and lung of a single rat were analyzed using expression arrays (Affymetrix) in triplicate. Homogenates of those three tissues were then mixed together at the cRNA level. We then measured the gene expression pattern of each mixed sample. Such mixtures mimic the common scenario in which biological samples in a dataset are heterogeneous and vary in the relative frequency of the component subsets from one another.

overall_design: We mixed rat brain, liver and lung biospecimens derived from one animal at the cRNA homogenate level in different proportions. 3 technical replicates each. Snap frozen rat liver and brain was kept frozen while cutting it into pieces. cDNA synthesis and labeling was done with a starting amount of 1 μg, using the Affymetrix Eukaryotic One-Cycle Target Hybridization. Washing, Staining and scanning protocol for Eukaryotic Cartridge Arrays with User-Prepared Buffers and Sloutions according to the technical manuals (Affymetrix GeneChip Expression, Analysis for Cartridge Arrays using the GCAS version 1.4,  Affymetrix GeneChip Expression Analysis (P/N 701021,Rev. 5) , Affymetrix GeneChip Expression Wash, Stain and Scan (P/N 702731, Rev. 3) , following the manufacturer/s instructions. Data was RMA normalized.

first: Frank

last: Staedtler

first: Nicole

last: Hartmann

first: Martin

last: Letzkus

first: Edward

last: Oakeley


title: Identification of a Serum Induced Transcriptional Signature Associated with Type 1 Diabetes in the BioBreeding Rat

status: Public on Dec 17 2009

city: Milwaukee

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary:
Human type 1 diabetes (T1D) arises through autoimmunity towards the insulin-producing pancreatic β cells and is modeled by the BioBreeding (BB) rat.  Factors associated with islet autoimmunity are dilute and difficult to directly measure in the periphery. Therefore, we previously utilized microarray-based bioassay where human T1D sera were used to induce a disease-specific gene expression signature in unrelated, healthy peripheral blood mononuclear cells (PBMC).
Here we report that sera of both spontaneously diabetic BB DRlyp/lyp and diabetes inducible BB DR+/+ rats induce inflammatory signatures in healthy PBMC of non-diabetic Brown Norway (BN) rats, while allogeneic BN sera does not.  Consistent with their common T1D susceptibility, transcriptional signatures of both BB sub-strains share identity, including cytokines, immune receptors and signaling molecules.  However, like the human T1D signature, the DRlyp/lyp signature, which is associated with progression to diabetes, is differentiated from that of the DR+/+ by induction of many IL-1 regulated genes.  Addition of IL-1RA to cultures significantly ablates the DRlyp/lyp signature.  Daily treatment of DRlyp/lyp rats with human recombinant IL-1RA significantly delays onset and sera of treated animals do not induce the characteristic IL-1 signature.  Consistent with the presence of immune regulation in DR+/+ rats is induction of a signature showing negative regulation of the NFκB pathway. This study supports prior human investigations of serum that reflect disease processes associated with progression to T1D and add to a growing body of evidence implicating the balance of IL-1 and IL-1RA as key factors influencing the severity and outcome of inflammatory responses.

overall_design: The induction of gene expression was accomplished by culturing the PBMCs of healthy day180 BN donor rats for 6 h at 37°C in 5% CO2 with a) 20% autologous BN plasma(10 replicates), b) allogeneic BN plasma (15 replicates), c) allogeneic DRlyp/lyp plasma (day 60, 4 replicates), or d) DR+/+ plasma (day 60, 4 replicates). Healthy BN PBMCs were also cultured with d60 DRlyp/lyp serum supplemented with IL-1RA (4 replicates) as well as autologous BN serum supplemented with IL-1B (4 replicates), to respectively block or induce IL-1 mediated gene expression. To determine if IL-1RA-treatment of DRlyp/lyp rats would result in modulation of the DRlyp/lyp signature, additional DRlyp/lyp rats were treated with hIL-1RA (n=6) or PBS (n=6). Rats were treated for 10 days, beginning at d30, then serum was collected at d40 and used to induce gene expression in PBMCs isolated from healthy d180 BN rats. Thus, there are a total of 53 chips being the addition of all the sample conditions mentioned above.

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Rhonda

last: Geoffrey

first: Joel

last: Basken

first: Simon

last: Prosser

first: Ake

last: Lernmark

first: Xujing

last: Wang


title: Gene expression profiling of pancreatic islets in BioBreeding rats

summary:
Like humans, the NOD mouse and other diabetes susceptible rat strains, T1D in BB rats is dependent on the major histocompatibility complex (MHC, insulin dependent diabetes mellitus locus 1, Iddm1) located on chromosome 20. In rats this is the HLA-DQB1 homologue RT1-B, specifically the RT1u haplotype.  Our studies employ congenic derivatives of the BB rat, the DRlyp/lyp and DR+/+ strains, which differ only by the 2 Mb lyp (lymphopenia, Iddm2) region on chromosome 4. TID in the lymphopenic DRlyp/lyp rat is spontaneous and onset occurs in 100% of animals during adolescence (65.3+/-6.3 days) due to a recessive mutation within GIMAP5 (GTPase, IMAP family member 5). Gimap5 is a mitochondrial GTP-binding protein necessary for post-thymic T cell survival. The spontaneously diabetic phenotype observed in DRlyp/lyp rats is thought to be elicited through deficiency in CD4+CD25+ TREG cells as T1D in lymphopenic BB rats can be rescued through adoptive transfer of this population.  Genetic variation in GIMAP5 has been associated with the development of protein-tyrosine phosphatase-2 (IA-2) autoantibodies in human T1D [28] and is significantly associated with systemic lupus erythematosus (SLE). The non-lymphopenic DR+/+ strain possesses wild-type GIMAP5 alleles and does not develop spontaneous T1D, however, T1D is inducible through administration of lymphotoxic anti-RT6 monoclonal antibody and immune activating polyinosinic polycytidylic acid (poly I:C; a ligand of toll-like receptor 3), or through viral depletion of CD4+CD25+ regulatory T (TREG) cells.  Such treatments do not induce T1D in the related Wistar-Furth (WF) rats and suggest the presence of an underlying diabetic predisposition in BB rats that is phenotypically manifested upon loss of immune regulation.
DRlyp/lyp and DR+/+ rats possess characteristics that make them ideal for the identification of pathways relevant to the development of T1D since they possess absolute or conditional susceptibility to T1D.  The Gimap-/- Iddm2 locus conveys upon DRlyp/lyp rats a deficiency in immune regulatory capacity and the spontaneous T1D phenotype. Consistent with the concept that autoimmunity involves both a lack of self-tolerance as well as target organ-specific factors, we have discovered that DRlyp/lyp and DR+/+ (BB) rats share an islet specific stress. This is reflected by the expression of immune mediators, including the chemokine eotaxin that recruits eosinophils, certain T cell subsets, dendritic cells, and mast cells, by islet β cells early in life, before infiltration of immune cells into the islet (insulitis). While BB and WF rats share Iddm1 (RT1u/u MHC), islet eotaxin expression in not observed in WF islets and thus is associated with the T1D susceptibility of BB rats. Further supporting the hypothesis that additional genetic factors, perhaps those working at the level of the pancreatic β cell, are necessary for the development of T1D are the observations that 1) The generation Fischer 344 (F344) rats either homozygous for Gimap5-/-  or homozygous for both RT1u/u and Gimap5-/- fail to develop T1D; and 2) genetic crosses between BB rats and non diabetic strains have identified numerous Iddm loci independent of Iddm1 and Iddm2.

overall_design: In this study, using islet gene expression profiling, direct serum-level measurement, quantitative real-time PCR and targeted histological follow-up, we investigate pancreatic islet gene expression in BB rat at 5 weeks (+/-5 days) which is prior to insulitis in DRlyp/lyp rats. We compare DR+/+, JB++ & JBlyp/lyp islet activity to that of F344 and F344lyp/lyp rats to investigate any potential for reduction in capability to deal with oxidative stress in BB rats compared to non-BB and whether any differences in that capability map to known Iddm regions.

first: Parthav

last: Jailwala

first: Jessica

last: Fuller

first: Ian

last: Sweet

first: Åke

first: Anne

last: Kwitek

first: Marty


status: Public on Feb 01 2010

city: New York

first: steve

last: shen

address: 545 First Ave

department: Biochemistry

institute: New York University

summary:
Full Title: Transition from Compensated Hypertrophy to Systolic Heart Failure in the Spontaneously Hypertensive Rat: Structure, Function, and Transcript Analysis

Gene expression changes and left ventricular remodeling associated with the transition to systolic heart failure (HF) were determined in the spontaneously hypertensive rat (SHR).  By combining transcriptomics of left ventricles from six SHR with HF with changes in function and structure we aimed to better understand the molecular events underlying the onset of systolic HF compared to six age-matched, SHR with compensated hypertrophy.  Left ventricle (LV) ejection fraction was depressed (82±4 to 52±3 %) in compensated vs. failing animals.  Systolic blood pressure decreased and LV end-diastolic and systolic volume increased with HF.  Failing SHR hearts also demonstrated increases in left and right ventricular mass relative to non-failing SHRs.  LV papillary muscle force development and shortening velocity decreased, β-adrenergic responsiveness was depressed, myocardial stiffness and myocardial fibrosis increased with HF relative to non-failing animals.  Initial micro-array analysis revealed that 1,431 transcripts were differentially expressed with HF compared to non-failing SHR (p<0.05).  Of the identified transcripts, lipopolysaccharide binding protein, the most highly expressed transcript with HF, was negatively correlated to myocardial force while elevated expression of the collagen cross-linking enzyme lysyl oxidase correlated positively with muscle stiffness.
Besides these individual transcripts, gene set enrichment analysis (GSEA) identified multiple enriched pathways with HF, most prominent of the altered signaling pathways involved TGF-β and insulin signaling.  GESA analysis additionally identified altered gene sets involving inflammation, oxidative stress, cell degradation and cell death, among others (all p<0.01).  In contrast to diastolic HF where few transcripts are reported to be altered, our data indicate multiple genes and pathways involved in a variety of biological processes characterize the onset of systolic HF, consistent with many functional and structural changes present in the failing hypertensive heart.

overall_design: Comprehensive gene expression profiling of heart failure Rat model vs control.

first: Wesley

last: Brooks

first: Steven

last: Shen


title: Cardiotoxicity of tubulin binders

status: Public on Jan 01 2010

city: Nutley

first: Charu

last: Kanwal

state: NJ

address: 340 Kingsland Street

department: RIGG

institute: Hoffman-La Roche

summary: The use of tubulin binders (TBs) in oncology indications often is associated with cardiotoxicity, the mechanism of which has not been elucidated.  We observed that a single administration of TBs to rats caused an increase in the number of mitotic figures in the myocardial interstitium after 24 hours.  We therefore hypothesized that interstitial cells are the primary target of TBs.  To test this hypothesis, we evaluated the acute effects of a single intravenous administration of 3 reference TBs, colchicine (0.2 and 2 mg/kg), vinblastine (0.5 and 3 mg/kg), and vincristine (0.1 and 1 mg/kg) 6 and 24 hours after dosing.  Mitotic arrest was identified at 24 hours in all high-dose groups based on an increase in the number of mitotic figures in the interstitium coupled with a dramatic decrease in the number of Ki67-positive interstitial cells.  Analysis of the myocardial transcriptomic data further supported G2/M cell cycle arrest 6 hours after dosing with the high-dose groups of all 3 compounds.  Apoptotic figures and an increase in the number of cleaved caspase 3-positive cells were identified at 6 and 24 hours at the highest dose of each compound almost exclusively in interstitial cells; a few cardiomyocytes were affected as well.  Transcriptomic data further suggested that some of the affected interstitial cells were endothelial cells based on the up-regulation of genes typically associated with vascular damage and down-regulation of Endothelial Cell-Specific Molecule 1 and Apelin.  Taken together, these data identify endothelial cells of the myocardium as the primary target of the cardiotoxicity of TBs and identify cell cycle arrest as the mechanism of this toxicity.

overall_design: Gene expression was profiled in the myocardium of rats at 6 and 24 hr after a single dose of colchicine, vinblastine or vincristine.

first: Igor

last: Mikaelian

first: Andreas

last: Buness

first: Cristy

last: de Vera-Mudry

first: Denise

last: Coluccio

first: Erik

last: Rasmussen

first: John

middle: C

last: Downing

first: Hing

middle: W

last: Char

first: Rosemary

last: Nicklaus

first: Holly

last: Hilton

first: Juergen

last: Funk

first: Jean-Christophe

last: Hoflack

first: Mark

last: Fielden

first: Frank

last: Herting

first: Laura

last: Suter-Dick


title: Electric stimulation of neonatal rat ventricular cardiomyocytes

status: Public on Dec 10 2009

city: Maastricht

first: Ruben

last: Martherus

address: Universiteitssingel 50

department: Clinical Genomics

country: Netherlands

institute: Maastricht University

summary:
Study on changes in gene expression in primary cultures of neonatal rat ventricular cardiomyocytes to electric stimulation.
Through comparing non-stimulated, stimulated and blebbistatin supplemented and stimulated cultures we set out to identify the genes that are specifically activated by electric pulsing separate from cardiomyocyte contractions.

overall_design:
After initial recovery phase, primary cultures of neonatal rat ventricular cardiomyocytes were cultured for 3 days without pulsing, with electric pulsing or with electric pulsing combined with blebbistatin.
Per treatment: 3 arrays, with samples obtained from 3 separate series of cardiomyocyte isolation and culturing. Per array: sample prepared from pooled (1:1) RNA from duplicate experiments.

first: Sabina

last: Vanherle

first: Erika

last: Timmer

first: Volkert

last: Zeijlemaker

first: Jos

middle: L

last: Broers

first: Hubert

last: Smeets

first: Joep

last: Geraedts

first: Torik

last: Ayoubi


title: Gene expression data from renal preneoplastic lesions

status: Public on Feb 20 2010

city: Konstanz

first: Daniel

middle: R.

last: Dietrich

address: Jakob-Burckhardt-Str. 25

department: Environmental Toxicology

country: Germany

institute: University of Konstanz

summary:
Microarrays were used to analyse gene expression underlying early tumourigenesis in Eker rats. Distinct classes of up- and downregulated genes were identified in different preneoplasic lesion vs. microdissected normal (healthy) renal tubules.
Laser capture microdissected renal basophilic atypical tubule (bAT) and basophilic atypical hyperplasia (bAH) and healthy tissue (HT) of 6-months aristolochic acid (AA)- and ochratoxin A (OTA)-treated and control (C) male Eker rats were isolated for RNA extraction and microarray analysis in order to investigate gene expression profiles induced by AA and OTA as well as to differentiate pathways specific for the bAT to bAH progression.
Keywords: gene expression study, preneoplasic lesion vs. microdissected normal renal tubules

overall_design: For microdissection of preneoplastic lesions from H&E stained renal cryosections, a PALM laser microdissection and pressure catapulting (LMPC) system (PALM Microlaser GmbH) was used. Atypical tubule (bAT), basophilic atypical hyperplasia (bAH) or healthy tissue (HT) were micodissected separately from each of three replicatemale Eker rats per dose group. Lesions of each type or HT from each individual animal were pooled. RNA isolation from pooled samples and subsequent Affymetrix Rat Genome RAE_230A_2.0 chip hybridization was carried out as previously described (Stemmer et al., Toxicology and Applied Pharmacology(2006) Nov 15;217(1):134-42). Time matched controls for microarrays from lesions of OTA and AA treated rats are specified as C(AA) and C(OTA).

first: Hans-Juergen

last: Ahr

first: Heidrun

last: Ellinger-Ziegelbauer

first: Kerstin

last: Stemmer


title: The relationship between brain mRNA levels and behaviour among inbred Lewis rats

status: Public on Nov 24 2009

city: Toronto

first: Paul

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
Behaviour is derived from complex molecular interactions within the brain, in response to specific environmental stimuli. In some rare cases, the direct causes of behaviour have been attributed to the interactions of a single or small group of gene transcripts and proteins. We conducted two experiments with the hope of defining some of the molecular interactors for four separate behaviours: sugar feeding, locomotor activity in a novel field, and acoustic startle reflex, and prepulse inhibition of the acoustic startle reflex, which have been linked to prefrontal cortex dopaminergic function or as predictors of sensorimotor gating in diseases such as schizophrenia. Rats with high and low response phenotypes were selected to determine the differences between these two extremes of behaviour. From our analyses, transcripts of Homer1, a neuronal scaffolding protein which interacts with group1 metabotropic glutamate receptors, were found to be significantly correlated with array data in both experiments, and with behaviour data across three separate tests in the second experiment, indicating that this gene's transcripts and probably downstream protein interactions have a significant correlation with behaviour phenotype in the inbred Lewis rat. Future areas of pursuit for this data should involve modification of the expression of Homer1 in an isolated fashion to determine a pharmacological threshold for differences in behaviour.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

middle: A

last: Feldcamp

first: Susan

last: Rotzinger

first: Mawahib

middle: O

last: Semeralul

first: Franco

last: Vaccarino

first: Arturas

last: Petronis

first: Albert

last: Wong


title: A simple method to integrate different versions of Affymetrix microarrays using duplicate samples

summary: The size and scope of microarray experiments continue to increase. However, datasets generated on different platforms or at different centres contain biases. Improved techniques are needed to remove platform- and batch-specific biases. One experimental control is the replicate hybridization of a subset of samples at each site or on each platform to learn the relationship between the two platforms. To date, no algorithm exists to specifically use this type of control. LTR is a linear-modelling-based algorithm that learns the relationship between different microarray batches from replicate hybridizations. LTR was tested on a new benchmark dataset of 20 samples hybridized to different Affymetrix microarray platforms. Before LTR, the two platforms were significantly different; application of LTR removed this bias. LTR was tested with six separate data pre-processing algorithms, and its effectiveness was independent of the pre-processing algorithm. Sample-size experiments indicate that just three replicate hybridizations can significantly reduce bias. An R library implementing LTR is available.

overall_design: Twenty rats livers were processed, eight on both RAE230-A and RAE230-2 arrays, 8 on only RAE230-A arrays, and 4 on RAE230-2 arrays only.


title: Spatial and Temporal Regulation of Gene Expression in the Mammalian Growth Plate

status: Public on Jan 28 2010

city: Stockholm

first: Ola

last: Nilsson

address: Karolinska University Hospital, Q2:08

department: Dept. Woman and Child Health

country: Sweden

institute: Karolinska Institute

summary: To explore the mechanisms responsible for spatial and temporal regulation of the growth plate, we microdissected postnatal rat growth plates into their constituent zones and then used microarray analysis to characterize the changes in gene expression that occur as chondrocytes undergo spatially-associated differentiation and temporally-associated senescence.

overall_design: Microdissection was used to collect individual growth plate zones from proximal tibiae of 1-wk rats and the proliferative and early hypertrophic zones of growth plates from 3-, 6-, 9-, and 12-wk rats and gene expression was analyzed using microarray.

first: Julian

last: Lui

first: Anenisia

last: Andrade

first: Anita

last: Hegde

first: Wei

last: Chen

first: Jeffrey

last: Baron


title: Candidate genes for alcohol preference in alcohol-preferring and non-preferring reciprocal congenic rats

status: Public on Dec 31 2009

city: Westfield

first: Mark

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

summary:
The goal of this study was to identify candidate genes that may influence alcohol consumption by comparing gene expression in 5 brain regions of alcohol-naïve iP and P.NP rats.

Background: Selectively bred P (alcohol preferring) and NP (alcohol non-preferring) rats differ greatly in alcohol preference, in part due to a highly significant QTL on chromosome 4. Reciprocal congenic strains in which the iP chromosome 4 QTL interval was transferred to the iNP background (NP.P) and the iNP chromosome 4 QTL was transferred to the iP background (P.NP) exhibited alcohol consumption scores that correlated with the introgressed interval. The goal of this study was to identify candidate genes that may influence alcohol consumption by comparing gene expression in 5 brain regions of alcohol-naïve iP and P.NP rats.

Methods: RNA from the amygdala, nucleus accumbens, hippocampus, caudate putamen, and frontal cortex from each of 8 iP and 8 P.NP rats was labeled and analyzed on Affymetrix Rat Genome 230 2.0 microarrays. Expression levels were normalized using robust multi-chip average (RMA), and differential gene expression was measured in individual brain regions and in the average of the five brain regions. Differential gene expression was validated using quantitative real-time PCR. Meta-analysis was applied to compare microarray data from this experiment with data from the reciprocal congenic strains NP.P vs. iNP (Carr et al, 2007).

Results: We detected between 72 (nucleus accumbens) and 89 (hippocampus) cis-regulated probe sets within the QTL that significantly differed between the strains in the five brain regions. There was significant overlap among the regions; 157 cis-regulated probe sets were detected in at least one brain region, of which 104 showed differential expression in more than one region. Fewer trans-regulated probe sets were detected, ranging from 7 in the amygdala to 54 in the caudate putamen, and most of these differed in only one region; only 10 of the 85 trans-regulated probe sets differed in more than one region.  To increase the power to detect differentially expressed genes, data from the five discrete brain regions of each animal were averaged; in this analysis we detected 141 cis-regulated probe sets and 207 trans-regulated probe sets. Meta-analysis comparing the present results from iP vs. P.NP rats with an earlier experiment that used the reciprocal congenic NP.P vs. iP demonstrated that 74 cis-regulated probe sets were differentially expressed in the same direction and with a consistent magnitude of difference in both experiments. No consistent trans-regulated probe sets were identified.

Conclusions: Cis-regulated candidate genes for alcohol consumption that lie within the chromosome 4 QTL were identified and confirmed by meta-analysis with the reciprocal congenic NP.P vs iNP study. These genes are strong candidates for producing the difference in alcohol preference and consumption between the iP and iNP rats. There was little evidence for consistent trans-acting effects.

Keywords: comparison of gene expression profiles for strain1 (P rat) vs. strain2 (P.NP rat)

overall_design: 40 samples each of P and P.NP (8 animals each of P and P.NP. 5 brain regions)

first: Lucinda

middle: G

last: Carr

first: Howard

last: Edenberg

first: Tiebing

last: Liang

first: Jeanette

middle: N

last: McClintick

first: Ashley

last: Clevenger

first: Kevin

last: McCall


title: Effects of moderate ethanol consumption during pregnancy on placental gene expression

status: Public on Jan 29 2010

city: Albuquerque

first: Daniel

last: Savage

state: NM

address: 1University of New Mexico

department: Neurosciences

institute: University of New Mexico

summary: We conducted a preliminary investigation to determine whether ethanol-induced alterations in placental gene expression may have some utility as a diagnostic indicator of maternal drinking during pregnancy as well as a prognostic indicator of risk for adverse neurobehavioral outcomes in affected offspring.

overall_design: Pregnant Long-Evans rats voluntarily consumed either a 0% or 5% ethanol solution four hours each day throughout gestation.  Ethanol consumption produced a mean maternal daily intermittent peak serum ethanol concentration of 84 mg/dL.  Placentas were harvested on Gestational Day 20 for gene expression studies.

first: Martina

middle: J

last: Rosenberg

first: Christina

last: Wolff

first: Ahmed

last: El-Emawy

first: Miranda

last: Staples

first: Nora

last: Perrone-Bizzozero


title: Functional relevance of tetraspanin CD9 in vascular smooth muscle cell injury

status: Public on Nov 12 2009

city: Memphis

first: Celia

last: Longhurst

state: TN

address: 956 Court Avenue Room H300

department: Medicine

institute: UTHSC

summary:
Vascular smooth muscle cell (VSMC) migration and proliferation are critical events in the development of neointima following vascular injury.    Exogenous expression of human CD9 by CD9-adenoviral transduction led to increases in neointima. CD9 expression significantly augmented PI-3 kinase dependent Akt phosphorylation with concurrent adhesion to extracellular matrix protein fibronectin (FN). Furthermore,enhanced Akt phosphorylation was attenuated by anti-CD9 mAb7 binding. As multiple factors contribute to the regulation of VSMC phenotype, our aim was to establish whether increased CD9 expression would induce changes in the expression of other genes associated with VSMC proliferation and motility.  RASM were transduced with either CD9 adenovirus or control and were plated on FN for 6hours. Cells were harvested from 3 replicate plates and total RNA from each was isolated using the TRIzol method and pooled for each CD9 and LacZ transduced RASM.  RNA was sent to Genome Explorations Memphis TN for microarray analysis.  Microarray analyses were done using the U230.2 rat gene chip from Affymetrix using RNA prepared from two RASM transduction experiments. Two independent microarray data sets have been generated and analyzed by comparing the filtered gene lists generated by the Affymetrix GeneChip Operating Software and looking for regulated genes common both sets of data. Analysis of this data showed the regulation of some key genes involved in the modulation of VSMC motility and proliferation.

Keywords: vascular smooth muscle cells, vascular injury, tetraspanin, proliferation, neointima, motility, fibronectin (FN), rat aortic smooth muscle (RASM)

first: Lisa

middle: K

last: Jennings


title: Postnatal developmental changes in Sprague-Dawley rats in the model of neuropathic pain 'spare nerve injury'

status: Public on Dec 18 2009

city: Lonndon

first: David

last: Vega-Avelaira

address: Gower street

country: United Kingdom

institute: University College of London

summary:
Neuropathic pain is an apparently spontaneous experience triggered by abnormal physiology of the peripheral or central nervous system, which evolves with time. Neuropathic pain arising from peripheral nerve injury is characterized by a combination of spontaneous pain, hyperalgesia and allodynia. There is no evidence of this type of pain in human infants or rat pups; brachial plexus avulsion, which causes intense neuropathic pain in adults, is not painful when the injury is sustained at birth. Since infants are capable of nociception from before birth and display both acute and chronic inflammatory pain behaviour from an early neonatal age, it appears that the mechanisms underlying neuropathic pain are differentially regulated over a prolonged postnatal period.
We used microarrays to detail the global programme of gene expression underlying the differences in nerve injury between along the postnatal development and identified distinct classes of regulated genes during the injury

overall_design: We have performed a microarray analysis of the rat L4/L5 dorsal root ganglia, 7 days post spared nerve injury, a model of neuropathic pain.  Genes that are regulated in adult rats displaying neuropathic behaviour were compared to those regulated in young rats (10 days old) that did not show the same neuropathic behaviour.

first: Sandrine

middle: M

last: Geranton

first: Maria

last: Fitzgerald


title: Expression data for kidney progenitor tissue from rat embryo  at E13

city: La Jolla

first: Yohan

last: Choi

address: 9500 Gilman Drive, 0693

institute: UCSD

summary:
In this study we compared genes expressed in the unbudded portion of the Wolffian duct with the isolated ureteric bud to find genes novel to early kidney development.  We used the Affymetrix Rat Genome 230 2.0 Array to compare the unbudded tissues with the budded samples.
We used microarrays to find novel genes regulating early kidney formation.

overall_design: Isolated ureteric buds (UB) were separated from the embryonic kidney after a light trypsinization step.  Approximately 100 UBs were pooled together into each replicate.  Approximately 100 isolated Wolffian ducts were dissected from E13 rat embryoes and pooled into each sample.  Approximately 50 Wolffian ducts with attached mesodermal cells were pooled into each replicate.

first: James

middle: B

last: Tee

first: Shinji

last: Kitamura

first: Sanjay

last: Nigam


title: Comparison between the intestinal developmental process in different sucking phases

status: Public on Nov 03 2009

city: Yaan

first: yunzi

last: sun

state: Sichuan

address: No36,Xingkang Road

department: Institute of Animal Nutrition,

country: China

institute: Sichuan Agricultural University

summary: This paper describe the whole genome-wide analysis of differences in postnatal intestinal from 0 day to 21 days of piglets. Using Genome Array，We generated transcriptase profiles of intestine from the Landrace piglets at 0, 3, 8, 14，21 days post natal (dpn). We identified 4014 differentially expressed transcripts during intestinal developing in Landrace piglets. Respectively, the Gene Ontology processes and the time sequence profile analysis of differentially expressed genes were constructed. In the course of growth , the mostly significant enriched GO category of profile  mainly focus on folic acid transport, lipopolysaccharide-mediated signaling pathway, Momolybdopterin cofactor biosynthetic process,The down-regulation genes show the state of malnutritionplay at early growth in pig life.

overall_design: From the Landrace piglets at 0, 3, 8, 14, and 21 days post natal (dpn). Using GeneChip® Porcine Genome Array，we identified differentially expressed transcripts during intestinal developing in Landrace piglets. Respectively, from these, the Gene Ontology processes and the time sequence profile analysis of differentially expressed genes were constructed.


title: Expression profiling in dopaminergic brain structures of rats self-administering cocaine

status: Public on Jan 21 2010

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

summary:
Gene expression profiling in dopaminergic brain structures of rats self-administering cocaine. Effect of histone deacetylase inhibition
We have shown that injection of the HDAC inhibitor trichostatin A (TsA) to rats is sufficient to decrease their motivation to self-administer cocaine. The aim of the present study was to investigate alterations in gene expression patterns in the Anterior Cingulate Cortex and Nucleus Accumbens of rats self-administering cocaine and treated repeatedly with TsA, and compare them with rats taking only cocaine.
We used Affymetrix microarrays to identify genes the expression of which was up-regulated or downregulated during this process.

overall_design:
Drug self-administration was performed in dark operant chambers under a fixed-ratio 1 schedule of reinforcement that was carried out for 4 days during daily 2 h sessions. Each nosepoke into the active hole triggered the i.v. delivery of a 40 μl cocaine solution (0,3 mg/kg/injection) under the control of the computer. Rats were sacrificed 2 h after the 4th self-administration session; the anterior cingulate cortex and the nucleus accumbens  were then dissected.
Two treatments comparison

first: Jean

last: Zwiller

first: Lionel

last: Host

first: Christelle

last: Thibault


title: The Nucleus Accumbens Shell and Central Nucleus of the Amygdala of Alcohol-Preferring Rats Following Binge-Drinking

first: Mark

last: Kimpel

summary: The objective of this study was to determine changes in gene expression within the extended amygdala following binge-like drinking by alcohol-preferring (P) rats. Adult male P rats were given 1-hr access to 15 and 30% ethanol (EtOH) three times daily for 8 weeks. Rats (n = 10/time point for EtOH and n = 6/time point for water) were killed by decapitation 1, 6 and 24 hr after the last drinking episode. Brains were extracted and rapidly frozen in isopentane in dry ice. RNA was prepared from individual micropunch samples of the nucleus accumbens shell (ACB-sh) and central nucleus of the amygada (CeA); microarray analyses were conducted with Affymetrix Rat 230.2 chips. EtOH intakes were 1.5-2 g/kg/session. Because too few genes changed at the individual time points, an overall effect, comparing the water and EtOH groups, was determined. In the ACB-sh and CeA, there were 276 and 402 probe sets for named genes, respectively, that were different between the two groups. There were 1.5- to 3.5- fold more genes up-regulated than down-regulated in both regions, with most differences between 1.1- to 1.2-fold. Although there were several significant Biological Processes categories in common between the 2 regions (e.g., synaptic transmission, neurite development), there were few genes in common between the two regions that differed between the EtOH and water groups. Overall, the results suggest that chronic binge-like alcohol drinking by P rats produces changes in the expression of genes that could alter neuronal function by different mechanisms in the ACB-sh and CeA.

overall_design: 17 samples of control and 31 samples of treatment for each brain region

first: Jonathan

last: Schultz

first: Richard

last: Bell

first: Jeanette

last: McClintick

first: Howard

last: Edenberg

first: William

last: McBride


title: Cadiac GATA-4 overexpression in vivo

status: Public on Dec 01 2009

city: University of OULU

first: Jaana

last: Rysä

address: PO BOX 5000

department: Pharmacology and toxicology

country: Finland

institute: University of Oulu

summary: The objective of the study was to find cardiac GATA-4 target genes by overexpressing GATA-4 transcription factor in the left ventricle by adenoviral gene transfer.

overall_design: Gene expression profiles three days after GATA-4 gene transfer were compared with those of Lac Z –treated animals by screening Affymetrix Rat Expression Set 230_2.0 Arrays (there are 5 samples in both group). Strain:Sprague-Dawley; Gender, Male; Weight 250-300g; tissue, left ventricle.

first: Olli

last: Tenhunen

first: Hanna

last: Leskinen

first: Mona

last: Nemer

first: Heikki

last: Ruskoaho


title: MOLECULAR MECHANISMS ASSOCIATED WITH MARKERS OF HEPATOCARCINOGENICITY DURING A 14 DAY DIETARY STUDY IN MALE FISCHER RAT

status: Public on Oct 28 2009

city: Bracknell

last: Currie

address: Jealott's Hill

institute: Syngenta

summary: To investigate the molecular mechanisms associated with initial dose-related events that are linked to the development of liver tumours: liver growth; cell proliferation; changes in histopathology such as hypertrophy

overall_design: We selected dose levels of phenobarbital to give a carcinogenic (1000ppm) and two non-carcinogenic doses (50 and 500ppm).  This also gave two doses that increased liver weights (500 and 1000ppm) and one that did not (50ppm).  Alterations to liver growth and proliferation are complete after 14 days of dietary treatment and so we chose intermediate time points of 1,3 7 and 14 days of treatement.  Small sections of the left lateral lobe of the liver were processed to give three biological replicates selected from the 5 treated animals in each group, total RNA purified and mRNA levels measured using Affymetrix Rat Genome 230 v2 microarrays.  In addition we also measured a braod range of standard histopathological, clincal chemsitry and metabolomic endpoints.

first: Claire

last: Waterman

first: Julian

last: Griffin

first: Jayne

last: Wright


title: The relationship between brain mRNA levels and behaviour among inbred Lewis rats: Experiment 2

first: Paul

last: Boutros

summary:
Behaviour is derived from complex molecular interactions within the brain, in response to specific environmental stimuli. In some rare cases, the direct causes of behaviour have been attributed to the interactions of a single or small group of gene transcripts and proteins. We conducted two experiments with the hope of defining some of the molecular interactors for four separate behaviours: sugar feeding, locomotor activity in a novel field, and acoustic startle reflex, and prepulse inhibition of the acoustic startle reflex, which have been linked to prefrontal cortex dopaminergic function or as predictors of sensorimotor gating in diseases such as schizophrenia. Rats with high and low response phenotypes were selected to determine the differences between these two extremes of behaviour. From our analyses, transcripts of Homer1, a neuronal scaffolding protein which interacts with group1 metabotropic glutamate receptors, were found to be significantly correlated with array data in both experiments, and with behaviour data across three separate tests in the second experiment, indicating that this gene's transcripts and probably downstream protein interactions have a significant correlation with behaviour phenotype in the inbred Lewis rat. Future areas of pursuit for this data should involve modification of the expression of Homer1 in an isolated fashion to determine a pharmacological threshold for differences in behaviour.

Keywords: Phenotype-Association Study

overall_design: Ten rats with varying behavioural phenotypes were analyzed. 4 behaviour tests: SF, locomotion, ASR, and PPI.

first: Laura

last: Feldcamp

first: Susan

last: Rotzinger

first: Mawahib

last: Semeralul

first: Franco

last: Vaccarino

first: Arturas

last: Petronis

first: Albert

last: Wong


title: Gene expression profiling in differential cognitive outcomes in aging: CA3

status: Public on Nov 01 2009

city: Baltimore

first: Carlo

last: Colantuoni

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

summary: Functional alterations in medial temporal lobe structures, particularly the hippocampus, are central to age-related deficits in episodic memory. Research in aging laboratory animals has characterized physiological and cellular alterations in the hippocampus that occur in association with the presence and severity of such cognitive impairment. The current study compares alterations across hippocampal subregions by gene expression profiling in a rat model that closely mirrors individual differences in neurocognitive features of aging humans across a spectrum of outcomes, including both impaired memory and preserved function. Using mRNA profiling of the CA1, CA3 and dentate gyrus subregions, we have distinguished between gene groups and pathways related to chronological age and those specifically associated with impaired or preserved cognitive ability in aged rats. We confirmed earlier reported changes in gene groups related to inflammation and oxidative stress in multiple subregions and found these to be more associated with chronological age than cognitive function per se. The CA3 profile was best able to segregate aged impaired, aged unimpaired and young subject groups from each other. Characterization of gene changes that distinguished preserved from impaired function among the aged animals found altered expression of synaptic plasticity and neurodegenerative disease-related genes. Together these gene changes suggest recruitment of adaptive mechanisms that mediate synaptic plasticity to maintain function and structural integrity in aged unimpaired rats that does not occur in aged impaired animals.

overall_design: RNA samples from CA3 region of the hippocampi of young animals, aged animals with unimpaired spatial learning, and aged animals with impaired spatial learning were compared to one another using Affymetrix GeneChip Rat Genome 230 2.0 arrays.

first: Rebecca

last: Haberman

first: Alexandra

last: Lunt

first: Jan

middle: T

last: Pedersen

first: Michela

last: Gallagher


title: Hormone effects on gene expression in somatic cells of rat testes (Rattus norvegicus)

status: Public on Sep 30 2009

city: Houston

first: Wei

last: Zhou

address: 1515 Holcombe Blvd

department: Department of Experimental Radiation Oncology

institute: M.D.Anderson Cancer Center

summary: Analysis of hormone effects on irradiated LBNF1 rat testes, which contain only somatic cells except for a few type A spermatgogonia.  Rats were treated for 2 weeks with either sham treatment (group X), hormonal ablation (GnRH antagonist and the androgen receptor antagonist flutamide, group XAF), testosterone supplementation (GnRH antagonist and testosterone, group XAT), and FSH supplementation ((GnRH antagonist, androgen receptor antagonist, and FSH, group XAFF).  Results provide insight into identifying genes in the somatic testis cells regulated by testosterone, LH, or FSH.

overall_design: 14 Sample replicates of sham treatment, 11 Sample replicates of hormonal ablation, 5 Sample replicates of testosterone supplementation, and 5 Sample replicates of FSH supplementation were studied.

first: Olga

middle: U

last: Bolden-Tiller

first: Gunapala

last: Shetty

first: Shan

last: Shao

first: Connie

last: Weng

first: Pirjo

last: Pakarinen

first: Zhilin

last: Liu

first: David

last: Stivers

first: Marvin

last: Meistrich


title: Gene expression profiling in differential cognitive outcomes in aging: Dentate Gyrus

overall_design: RNA samples from DG region of the hippocampi of young animals, aged animals with unimpaired spatial learning, and aged animals with impaired spatial learning were compared to one another using Affymetrix GeneChip Rat Genome 230 2.0 arrays.

middle: P


title: Expression data from PDGF-BB-treated rat aortic smooth muscle cells

status: Public on Nov 20 2009

city: Charlottesville

first: Brian

middle: R

last: Wamhoff

state: VA

address: 409 Lane Road Bldg MR4 Rm6022

department: Cardiology

institute: University of Virginia

summary:
Unlike other terminally differentiated cell types, vascular SMCs display remarkable phenotypic plasticity. The adult, differentiated state is traditionally defined by expression of well-characterized SMC contractile genes. Extracellular cues, however, can induce contractile SMCs to remodel toward a synthetic state characterized by a spectrum of proliferative, migratory, and inflammatory phenotypes.
We used whole-genome expression arrays to to identify genes associated with SMC phenotypic modulation.

overall_design: Rat aortic SMCs were serum-starved for 72 hours and subsequently treated with either PDGF-BB or its respective vehicle (n=2). RNA samples were hybridzed to Affymetrix arrays with the intent to identify early genes associated with SMC phenotypic modulation.


title: Radiation effects on gene expression in rat testes (Rattus norvegicus)

summary: Analysis of LBNF1 rat testes from controls, containing both somatic and all germ cell types and from irradiated rats in which all cells germ cells except type A spermatgogonia are eliminated.  Results provide insight into distinguishing germ and somatic cell genes and identification of somatic cell genes that are upregulated after irradiation.

overall_design: We studied 10 Sample replicates of control rat testes and 5 Sample replicates of irradiated rat testes.

middle: H

middle: C


title: Gene expression profiling in differential cognitive outcomes in aging: CA1

overall_design: RNA samples from CA1 region of the hippocampi of young animals, aged animals with unimpaired spatial learning, and aged animals with impaired spatial learning were compared to one another using Affymetrix GeneChip Rat Genome 230 2.0 arrays.


title: Gene expression profiling in hippocampal subregions in differential cognitive outcomes in aging

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

overall_design: Refer to individual Series


title: Rat response to changes in developmental stage - 3 types of tissue, 3 gravity conditions, 2 developmental conditions

status: Public on Nov 23 2009

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary:
Transcriptional crosstalk between mammary gland, liver and adipose tissue

Keywords: Gene Expression experiment

overall_design: Pregnant and Lactating rats exposed to 3 gravity conditions


title: Expression data from adult rat tail MNs after spinal cord transection

city: stockholm

first: Jesper

last: Ryge

address: retziusvag 8

department: neuroscience

institute: karolinska institutet

summary:
Spinal cord injury leads to impaired motor and sensory functions. After spinal cord injury there is a an initial phase of hypo-reflexia followed by a developing hyper-reflexia, often termed spasticity. Previous studies have suggested a relationship between the reappearence of plateau potentials in motor neurons and the development of spasticity after spinalization. To understand the molecular mechanism behind this phenomenon we examined the transcriptional response of the motor neurons after spinal cord injury.
We used a rat tail injury model where a complete transection of the caudal (S2) rat spinal cord leads to an immidate flaccid paralysis of the tail and a subsequent appearence of spasticity 2-3 weeks post injury that develops into strong spasticity after 2 months.
Gene expression changes were studied in motor neurons 21 and 60 days after complete spinal transection where the tail exhibits clear signs of spasticity.

overall_design: Tail MNs were retorgradely labelled with flourogold injected into the muscle and intra peritoneally. 5-7 days after tracer injections the spinal cord was dissected out, snab frozen in liquid nitrogen, sliced in 10 um thick slices and fluorescent motor neurons were laser dissected into a collector tube to a total of ca. 50-200 cells pr sample. RNA was then extracted, two round amplified and hybridized to Affymetrix rat 230 2.0 arays. 27 samples were hybridized onto chips, 8 Spi-21, 8 Spi-60, 6 ShamC-21 and 5 ShamC-60.

first: Jacob

last: Wienecke

first: Ann-Charlotte

last: Westerdahl

first: Hans

last: Hultborn

first: Ole

last: Kiehn


title: Different gene expression between Contol group, Model group and Drup(7-P) group

city: Beijing

first: yun

last: cheng

address: 100 Xi-Si-Huan-Zhong-Lu

department: Department of immunology

institute: Beijing 302 Hospital

summary:
Aim:
To find the genes that related with the drug's(7-P) function.
Design:
36 Rats were randomly divided into three group:control group(12), model group(12) and drug group(12). At last, randomly choosing 3 Rat from each group to do genechip analysis.
In model group, the  Porcine serum was given intraperitoneally (i.p.)  to rats in a volume of 1.5 mL/kg every 3 days for a total of 20 treatments.  Effect on model animals was confirmed by liver histology and biochemical assays .
In drug group, 7-P was dissolved in balanced saline solution for administration subcutaneously at dosages of 174 μg/kg in a volume of 1 mL/kg.  The doses were given 15 times, one day interval.
In control group, the animals were not treated with porcine serum. but given an equal volume of vehicle alone.
During 7-P and vehicle administration, porcine serum was given intraperitoneally (i.p.) to rats in a volume of 1.5 mL/ kg once weekly.  All animals were fasted for 24 h before porcine serum treatment.

Background:
During investigation of hypervariable region 1 (HVR1) of hepatitis C virus (HCV), a seven amino acids mimic peptide named 7-P was identified within the N-terminal of HVR1 that could induce IFN-γ and IL-10 expression while decreasing the expression of TNF-α in vivo and in vitro. Further studies revealed that 7-P could not only decrease the serum levels of aminotransferases (ALT, AST), alkaline phosphatase (AKP), and billirubin, but were also effective in reversing histopathological evidence of inflammation-mediated hepatic injury in 3 rat models.  The protective mechanism and gene expression profiles were investigated in detail in a rat chronic liver injury model using Affymetrix microarrays .

Conclusion:
We found that IL-1β, tumor necrosis factor receptor superfamily 14 (TNFRSF14), intercellular adhesion molecule 2 (ICAM2), sterol regulatory element-binding protein 1 (SREBP 1), Prohibitin (PHB), and inhibitor of DNA binding 2 (Id2) were the target genes that related with 7-P
Keywords: comparative genomic hybridization

first: Yun

first: Wanzhou

last: Zhao

first: Lifeng

last: Wang

first: Yingqi

last: Zhang

first: Pingyan

last: Chen

first: Jun


title: Gene expression profiles from nandrolone-treated rats with denervation

status: Public on Sep 04 2009

city: Bronx

first: Weiping

last: Qin

address: 130 West Kingsbridge Road, Room 1E-02

department: Center of Excellence for the Medical Consequences of SCI

institute: Bronx Veterans Affairs Medical Center

summary: We showed that nandrolone attenuated subacute, but not acute, denervation atrophy and upregulation of MAFbx. The present study explored the molecular determinants for this time-dependent effect using microarray analysis to identify genes that were differentially regulated by administration of nandrolone for 7 days beginning either concomitantly with denervation (7 days) or 29 days later (35 days)

overall_design: The analysis used gastrocnemius muscle from male Wistar-Hannover rats that had undergone left sciatic nerve transaction followed by the administration of nandrolone or vehicle beginning either on the day of surgery or 29 days thereafter.  Animals had been sacrificed 7 days after starting nandrolone (Nan) or vehicle (Veh) (e.g, at days 7 or 35).

first: Christopher

last: Cardozo

first: William

last: Bauman

first: Jiangping

last: Pan


title: Transitions in infant learning are modulated by dopamine within the amygdala

status: Public on Sep 27 2009

city: Philadelphia

first: Gordon

middle: A.

last: Barr

address: 3615 Civic Center Blvd

department: Anesthesiology and Critical Care Medicine

institute: Children's Hospital of Philadelphia

summary:
Behavioral transitions Young infant rats paradoxically prefer odors paired with shock but older pups learn aversions. This transition is amygdala- and corticosterone-dependent.
Microarray results showed downregulated dopaminergic presynaptic function in the amygdala with preference learning. Corticosterone injected 8-day-old pups and untreated 12-day-old pups learn aversions and had dopaminergic upregulation in the amygdala.

overall_design: 8 day saline or corticosterone treated- or 12 day old untreated  rat pups were trained with odor-shock pairings. Immediately after training pups were sacrificed and the amygdala dissected out. Controls were unpaired shock-odor groups.Paired and unpaired groups were processed together for each experimental condition. Paired and unpaired data were compared by ranked products.


title: Changes in gene expression in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption

status: Public on Sep 01 2009

city: Westfield

first: Mark

last: Kimpel

address: 15032 Hunter Court

institute: Indiana University

summary:
This study investigated changes in gene expression associated with ethanol drinking in adult male P rats under the following conditions for 8 weeks: continuous access (24 hr/day, 7 days/week), multiple scheduled access (three 1-hr sessions during the dark cycle/day, 5 days/week) and ethanol-naive (water).
The objective of this study was to investigate changes in gene expression associated with ethanol drinking. Adult male alcohol-preferring (P) rats were given Ethanol in their home-cages under continuous access (CA; 24 hr/day, 7 days/week) or multiple scheduled access (MSA; three 1-hr sessions during the dark cycle/day, 5 days/week) conditions for 8 weeks. A third group was ethanol-naïve (W group). Average ethanol intakes, across the 8 weeks, for the CA and MSA groups were approximately 9.5 and 6.5 g/kg/day, respectively. Fifteen hr after the last ethanol drinking episode, rats were euthanized, the brains rapidly extracted, and the nucleus accumbens (ACB) dissected. RNA was extracted and purified for microarray analysis. The only significant differences, overall, were between the CA and W groups (p < 0.01; Storey false discovery rate = 0.15); there were 374 significant differences in unique named genes between these 2 groups. There were 20 significant Gene Ontology (GO) biological processes categories, which included ‘negative regulation of protein kinase activity’, ‘anti-apoptosis’, and ‘regulation of G-protein-coupled receptor protein signaling pathway’. Ingenuity® analysis indicated a network of transcription factors, involving oncogenes (Fos, Jun, Junb had higher expression levels in the ACB of the CA than W group), suggesting increased neuronal activity in the CA group. There were 13 genes (Hspa5, Stom, Lcn7, Tceb3, Cdc42, Rap1ga1, Ece1, Dhrs3, Plod1, Kif1b, Nmnat1, Srpr, Esam) significantly different between the CA and W groups located within both mouse and rat ethanol QTLs, suggesting that these genes may contribute to ethanol drinking behavior. In conclusion, the robust differences in gene expression found between the CA and W groups, but not observed between the MSA and W groups, may be a result of the higher daily ethanol intakes of the CA group, and/or its initial ethanol withdrawal.

Keywords: comparison of gene expression profiles for treated vs. control

overall_design: 10 samples each of control, continuous ethanol and limited access ethanol

middle: W

first: Richard

middle: L

last: Bell

first: Jeanette

last: McClintick

first: Wendy

last: Strother

first: Lucinda

last: Carr

first: Tiebing

last: Liang

first: Zachary

last: Rodd

first: R

middle: D

last: Mayfield

first: Howard

last: Edenberg

last: McBride


title: Gene expression data from the LEC rat model with naturally occuring and oxidative stress induced liver tumorigenesis

status: Public on Jul 30 2009

city: Kashiwa

first: Akihito

last: Tsubota

state: Chiba

address: 163-1 Kashiwa-shita

department: Institute of Clinical Medicine and Research

country: Japan

institute: Jikei University School of Medicine

summary:
To elucidate the fundamental molecular mechanisms responsible for multistep hepatotumorigenesis, this study investigated genes that were upregulated in a stepwise manner from the naïve liver condition through to chronic oxidative stress-induced hepatitis and liver tumor by time-series microarray analysis. The time-dependent gene expression profile should reflect the multistep process of hepatotumorigenesis, and might identify genes that function specifically in hepatotumorigenesis.

We reduced several clinicopathological variables by using the Long-Evans Cinnamon rat, a model with naturally occurring and oxidative stress-induced hepatotumorigenesis. Gene expression patterns were analyzed serially by profiling liver tissue from naïve status (4 weeks old) rats through to those with chronic hepatitis (26 and 39 weeks old) to tumor development (67 weeks old).

overall_design: This study represents a normal versus diseased comparison with different time points of spontaneously developed liver tumor and normal liver tissue. In the first series of experiments, equivalent amounts of RNA from 2 pairs randomly selected from 8 paired liver tumor and adjacent nontumor tissue specimens were mixed and analyzed in order to normalize variations among mice. Average gene expression levels for tumor and non-tumor tissue samples were calculated using the 4 Affymetrix microarray datasets, respectively. In the following experiments, a mixture of equivalent amounts of RNA isolated from LEC rats at 4, 26, and 39 weeks of age and controls, respectively, was exploited as an RNA pool for Affymetrix microarray analyses. A total of 12 samples (4 sets of tumor-non-tumor pairs and a normal control, and 3 serial samples) were hybridized to Affymetrix Rat Expression 230 2.0 Arrays.

first: Kenji

last: Matsumoto

first: Kaoru

last: Mogushi

first: Hiroshi

last: Tanaka

first: Hirohisa

last: Saito


title: diabetes mellitus and the progression of post-infarction genetic regulatory expression

city: beijing

first: guangyuan

last: song

address: 167 BeiLiShi Rd, Beijing

department: Center of Coronary Heart Disease

institute: Cardiovascular Institute & Fu-Wai Hospital

summary:
OBJECTIVE: To study the genetic regulatory mechanisms in the remote zone of left ventricular (LV) free wall in order to partly explain the more frequent progression to heart failure after acute myocardial infarction (AMI) in diabetic rats.

METHODS: 10 weeks after diabetes mellitus (DM) induction with Streptozotocin (STZ), the left anterior descending coronary arteries of uncontrolled diabetic Sprague-Dawley (SD) rats and non-diabetic ones were ligated without reperfusion. Then, the remote zone tissues of LV free wall were taken as samples at day 1, 7, 14, 28, and 56 post AMI. Significant different expression genes were filterd from Affymetrix Genechip U230 2.0 array by GCOS software. Genetic changes post myocardial infarction were classified by hierarchical clustering of 10 gene chips. And then, the differential expressions of 10 selected transcripts identified by the microarray were examined in greater detail by Real Time-PCR.

RESULTS: According to hierarchical clustering, we find that the molecular regulatory expression related to cardiac remodeling in the remote zone to myocardial infarction is quite different as time elapses in both diabetic and non-diabetic rats. The gene expression at day 1 and 7 post AMI in both groups is similar, while the genetic changes at day 14 post AMI in diabetic rats and the ones at day 14 and 28 in non-diabetic rats are classified into the same cluster. And then the genetic changes at day 28 and 56 post AMI in diabetic rats and the ones at day 56 in non-diabetic rats are classified into the same cluster. (Figure.1) The patterns of numerous products of genes expression were used in the cluster, including 118 genes, such as leucine-rich PPR-motif containing (IL-6 signaling pathway), procollagen type I, VI, VIII, and XV, fibronectin1, RT1, and TIMP-1, etc.

CONCLUSION: The genetic findings in this study might be the possible mechanism that diabetes mellitus can accerate the progression of post-infarction genetic regulatory expression.

overall_design: All studies were performed with male SD rats (200-220g), aged 8 weeks, which were obtained from laboratorial animal center of Chinese University of Agriculture. DM was induced with a singleintraperitoneal injection of STZ (65 mg/kg in 0.1mmol/L, pH 4.5 sodium citrate buffer) . Age and body weight matched rats that used as non-diabetic controls were injected with the same dose of sodium citrate buffer (0.1mmol/L, pH 4.5). Ultrastructure changes of myocardium were observed 10 weeks after DM induction by TEM. 10 weeks after DM induction,both diabetic and non-diabetic rats were subjected to left anterior descending coronary artery (LADCA) ischemia for 1-56 days without reperfusion. Two-dimensional echocardiography was utilized to obtain LV dimensions and LV percent fractional shortening at baseline, DM 10weeks, and at 1d, 7d, 14d, 28d, 56d after AMI; the remote zone tissues of LV free wall were taken as samples at day 1, 7, 14, 28, and 56 post AMI for gene chip microarray analysis (10 samples from 30 rats); in addition, heart-to-body weight and heart to tibial length ratios and masson's trichrome staining was measured as an index of cardiac hypertrophy and fibrosis at baseline, DM 10weeks, and at 1d, 7d, 14d, 28d, 56d after AMI.

first: yongjian

last: wu

first: yuejin

last: yang

first: rutai

last: hui

first: hanjun

last: pei

first: rui

last: li


title: Modulation of gene expression by rapamycin in hepatic cell lines, WB-F344 and WB311

status: Public on Sep 20 2009

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

summary: Two rat hepatic cell lines, WB-F344 and WB311, were characterized for the effect of rapamycin on gene expression.  The WB311 cell line, which is tumorigenic and resistant to the growth inhibitory effects of rapamycin, was originally derived from the WB-F344 parental hepatic epithelial cell line.  The goal of this experiment was to identify genes that responded to rapamycin in the sensitive cells but not the resistant cells, thereby providing insight into the mechanism of rapamycin resistance.

overall_design: Total RNA for each of four experimental groups was prepared and analyzed in triplicate: WB-F344, vehicle control; WB-F344, rapamycin; WB311, vehicle control; WB311, rapamycin.

first: Rosa

last: Jimenez

first: Joan

last: Boylan

middle: A

first: Philip

last: Gruppuso


title: Kidney-specific Dysfunction of the Organic Anion Transporter MRP2 (ABCC2): Functional Consequences for Renal Grafts

status: Public on Aug 27 2009

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

institute: Universitätsmedizin Greifswald

summary:
Transplanting renal allografts represents the major curative treatment of chronic renal failure. Despite recent advances in immunosuppressive therapy, long-term survival of allografts remains a major clinical problem. Kidney function depends in part on transport proteins such as MRP2 (ABCC2) which facilitates renal secretion of amphiphilic exogenous and endogenous compounds. Inherited variants of genes not related to the immune system have been shown to modify the outcome after renal transplantation. We investigated whether ABCC2 gene variants in the donor kidney affect renal graft function.
A congenic rat model was established carrying a single nucleotide deletion in the ABCC2 gene. Renal cross transplantations were performed with wild type rats. Renal excretion of the MRP2 substrates bilirubin glucuronide and p-aminohippuric acid, but not morphine-6-glucuronide, was affected by the donor genotype. Moreover, proteomic analyses and transcriptional profiling revealed modified expression patterns indicative of increased oxidative stress in renal grafts carrying the mutated gene.
In the clinical part our study, we assessed ABCC2 haplotypes in renal transplant patients and evaluated graft function. The 3563T>A gene polymorphism was significantly associated with delayed graft function. Together, both experimental and clinical data show that the ABCC2 genotype of the donor kidney affects renal graft function.
Keywords: dysfunction of organic anion transporter MRP2 (ABCC2)

overall_design: Performed analyses of (6) wild-type  and (6) MRP2 deficient  kidneys that had been transplanted in wild-type recipients.

first: Olaf

last: Grisk

first: Antje

last: Steinbach

last: Ciecholewski

first: Torsten

last: Schlüter

first: Ingrid

last: Klöting

first: Helmut

last: Schmidt

first: Eike

last: Dazert

first: Elke

last: Schaeffeler

first: Leif

last: Steil

first: Stefan

last: Gauer

first: Gabriele

last: Jedlitschky

first: Matthias

last: Schwab

first: Gerd

last: Geisslinger

first: Ingeborg

last: Hauser

first: Uwe

last: Völker

first: Heyo

last: Kroemer

first: Rainer

last: Rettig


title: Expression data in polysomal and total RNA from perinatal rat lung

status: Public on Jul 07 2009

city: Toronto

first: Gail

last: Otulakowski

state: ON

address: 555 University Ave

department: Physiology & Experimental Medicine

institute: Hospital for Sick Children Research Institute

summary:
During the peri-partum period, the lung must respond to many factors with potential to impact protein synthesis via regulation of translation initiation.  Microarray analysis of polysomal versus total RNA from fetal day (FD) 19, FD22 and postnatal day 1 (P1) rat lungs was used to identify genes whose association with large polysomes changed either pre- or postnatally.

Keywords: development

overall_design: Using three independent litters at each developmental time point, we prepared lysates from FD19, FD22 and P1 (5 h after birth) rat lungs (total 9 lysates).  An aliquot of each lysate was used to prepare total RNA.  Remaining lysate was subjected to sucrose density gradient centrifugation to isolate large polysomes ( n>7 ribosomes/mRNA) from which we isolated polysomal RNA.  Matched total and polysomal RNAs were hybridized to Affymetrix expression arrays (total 18 chips).

first: Wenming

last: Duan

first: Hugh

last: O'Brodovich


title: Effects of testosterone on dexamethasone-induced changes in gene expression in gastrocnemius muscles from male rats

status: Public on Jul 01 2009

first: christopher

middle: p

last: cardozo

address: 130 West Kingsbridge Road

department: CMSCI

institute: Bronx VA Medical Center

summary:
Glucocorticoids are a well recognized and common cause of muscle atrophy.  Glucocorticoid-induced atrophy can be prevented by testosterone, but the molecular mechanisms underlying such protection have not been described. Thus, the global effects of testosterone on dexamethasone-induced changes in gene expression were evaluated in rat gastrocnemius muscle using Affymetrix 230_2 DNA microarrays.  Gene expression was analyzed after 7 days administration of dexamethasone, dexamethasone plus testosterone, or vehicle.  Effects of these agents on weights of gastrocnemius muscles from these animals has been reported (1. Zhao W, Pan J, Zhao Z, Wu Y, Bauman WA, and Cardozo CP. Testosterone protects against dexamethasone-induced muscle atrophy, protein degradation and MAFbx upregulation. J Steroid Biochem Mol Biol 110: 125-129, 2008.)  Dexamethasone changed expression of 876 probe sets by at least 2-fold, of which 474 probe sets were changed by at least two fold in the opposite direction in the dexamethasone plus testosterone group (genes  in opposition).  Major biological themes represented by genes in opposition included IGF-1 signaling, protein synthesis, myogenesis and muscle development, and ubiquitin conjugases and ligases.  Testosterone blocked increased expression of DDIT4 and eIF4EBP1, FOXO1 and of the p85 regulatory subunit of the IGF-1 receptor, while preventing decreased expression of IRS-1.  Testosterone blocked decreased expression of LXR and suppressed upregulation of C/EBP beta and delta.  Testosterone prevented increase expression of Cdkn1A (p21) and decrease expression of cyclins B and D, as well as many other changes that would be expected to reduce cell cycle progression.  Testosterone prevented increased expression of muscle development factors Csrp3 and Mbn1 and blocked reduced expression of Wnt4. These data suggest that testosterone blocks multiple changes in gene expression that, collectively, would otherwise downregulate molecular signals that promote protein synthesis and muscle hypertrophy and that stimulate muscle protein catabolism.

Keywords: Evaluate drug effects at a single time point

overall_design: Rats (250 g males) were administered dexamethasone (0.7 mg/kg/day) alone or with testosterone (20 mg/kg/day) dissolved in vehicle (propylene glycol) by continuous infusion (Alzet pumps) for 7 days.  Control animals were administered vehicle only.  Gene expression was compared among the 3 groups at 7 days using one chip per animal, 3 animals per group.

first: Christopher

last: Cardozo

first: Yong

last: Wu


title: Expression data from lungs of rats with pulmonary hypertension

status: Public on Jun 16 2009

city: Turku

first: Ilana

last: Saarikko

address: Linnankatu 55

institute: Genolyze Ltd

summary: Pulmonary hypertension is a frequent consequence of left heart disease and congestive heart failure (CHF) and causes extensive lung vascular remodelling which leads to right ventricular failure. Functional genomics underlying this structural remodelling are unknown but present potential targets for novel therapeutic strategies. We used microarrays to detail the gene expression underlying vascular remodeling in the pathogenesis of pulmonary hypertension and identified distinct classes of up-regulated genes during this process.

overall_design: Control rat lung samples were compared to samples of aortic banding rat lungs which exhibit pulmonary hypertension

first: Wolfgang

last: Kuebler

first: Julia

last: Hoffmann


title: Segregation of genes influencing skeletal phenotypes in congenic P/NP rats

city: Indianapolis

first: Charles

last: Turner

address: 723 W. Michigan St. SL 220C

department: Biomedical Engineering

institute: Indiana University Purdue University Indiapanolis

summary:
Bone mineral density and structure candidate gene analysis in alcohol-non-preferring (NP), alcohol-preferring (P), congenic NP (NP.P) and congenic P (P.NP) rats
Genetic mapping in alcohol-preferring (P) and alcohol-non-preferring (NP) rats has identified a major quantitative trait locus (QTL) in the region between q22 – q34 on chromosome (Chr) 4 for alcohol preference. In a separate genome-wide linkage study, using inbred Fischer 344 (F344) and Lewis (LEW) rats, several QTL linked to bone density and structure were identified at the same location suggesting that bone mass and strength genes might co-segregate with genes that regulate the alcohol preference trait. The aim of this study is to identify the genes segregating for skeletal phenotypes and alcohol trait in congenic P/NP rats. We compared bone mineral content (BMC), areal/volumetric bone mineral density (aBMD/vBMD) and biomechanical strength at different skeletal sites from 6-month-old inbred and congenic P/NP rats. Transfer of the NP Chr 4 QTL into P background significantly increased body weight but decreased BMC, aBMD/vBMD in whole body, cranium, femur, and lumbar vertebrae. On the other hand, transfer of P Chr 4 QTL into NP background significantly decreased body weight but increased BMC and aBMD in the same skeletal sites. Microarray analysis was performed from the femurs of 4-week-old rats (n = 5 per strain) using Affymetrix Rat Genome 230 2.0 arrays.   A total of 53 genes, including 41 candidate genes and 12 predicted genes, were differentially expressed among all strains of rats with a false discovery rate (FDR) less than 10%. Several candidate genes from microarray analysis were found to be were strongly correlated (r2>0.50) with different skeletal phenotypes. Gene expression of top 3 candidate genes from microarray profiling was validated by quantitative real-time PCR (qRT-PCR). Ingenuity pathway analysis revealed relationships among the candidate genes related to bone metabolism including pathways related to beta-estradiol, tumor necrosis factor and androgen receptor.

Keywords: Comparison of gene expression profiles between NP, P, NP.P and P.NP rats

overall_design: Comparison of differentially expressed genes between 4q22-4q34 on chromosome 4 in NP, P, NP.P and P.NP rats.

first: Imranul

last: Alam

first: Lucinda

middle: G

last: Carr

first: Yunlong

last: Liu

first: Jeanette

middle: N

last: McClintick

first: Ron

last: Jerome

first: Howard

middle: J

last: Edenberg

first: Michael

last: Econs


title: Gene expression profile in a DMBA-induced rat breast tumor: biopsy vs total tumor

status: Public on Jun 01 2009

city: Granada

first: Sergio

last: Granados

address: Avenida del Conocimiento

country: Spain

institute: University of Granada

summary: The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors from an initial stage to the moment of sacrifice. To this end, a cDNA microarray was performed (Affymetrix’s Rat Genome 230 2.0 array). This gene expression study was carried out on the umor biopsy samples and compared with matched tumor biopsy samples once the study ended (7 weeks after initial biopsy).

overall_design: Breast tumors were induced with a single oral dosage of 7,12-dimethylbenz(alpha)anthracene (100 mg/kg body weight) in female Sprague-Dawley rats. Gene expression analysis was performed in paired samples as follows: DMBA final trucut tumor vs initial trucut tumor (DMBA final vs basal). For this assay, 5 samples were chosen according to histopathologic criteria (Bloom-Richardson grade II). Gene expression profiling was carried out using Affymetrix’s GeneChip technology, using the Rat Genome 230 2.0 array from this provider. All the protocols and apparatus were recommended by Affymetrix. Total RNA from frozen mammary tumors was extracted by RNeasy Mini kit and homogenized by QIAshredder columns according to manufacturer’s instructions. The quality and quantity of the obtained RNA was checked out through agarose electrophoresis and later spectrophotometry at 260/280 nm. Biotinylated cRNA was synthesized following the IVT labeling kit from Affymetrix and purified by the GeneChip Sample Cleanup Module from Affymetrix. The quality and quantity of the obtained cRNA was again checked out through agarose electrophoresis and posterior spectrophotometry at 260/280 nm. After hybridization, slides were washed and scanned following the manufacturer’s standard protocol. Intensity values were normalized by Robust Multichip Average method and subsequently these were filtered to remove the control sequences and those with a hybridization signal close to background. The spike controls were: BioB, BioC, BioD and Cre; because BioB was the least abundant in the samples, it was used to estimate the sensitivity of the experiment. The housekeeping control was GAPDH. After non-supervised clustering using Pearson correlation coefficient, statistical significance of gene expression was estimated by Student’s T test for paired samples, using GeneSpring GX 7.3 software (Agilent).

last: Granados Principal

first: María

last: Ramírez Tortosa

first: Jose

last: Quiles

first: Cesar

first: P

last: Sanchez Rovira

last: Camacho Corencia