title: A role for nuclear factor interleukin-3 (NFIL3), a critical transcriptional repressor, in down-regulation of periovulatory gene expression

status: Public on Jan 20 2011

summary: The LH surge triggers dramatic transcriptional changes in genes associated with ovulation and luteinization. The present study investigated the spatiotemporal expression of nuclear factor interleukin-3 (NFIL3), a transcriptional regulator of the bZIP transcription factor superfamily, and its potential role in the ovary during the periovulatory period. NFIL3, also known as E4-binding protein 4 or NFIL3/E4BP4, was originally identified as a transcriptional repressor based on its DNA-binding activity at the promoter of the gene encoding the adenovirus E4 protein. Immature female rats were injected with PMSG, treated with hCG, and ovaries or granulosa cells were collected at various times after hCG. Nfil3 mRNA was highly induced both in intact ovaries and granulosa cells after hCG treatment. In situ hybridization demonstrated that Nfil3 mRNA was highly induced in theca-interstitial cells at 4-8 h after hCG, localized to granulosa cells at 12 h, and decreased at 24 h. Over-expression of NFIL3 in granulosa cells inhibited the induction of prostaglandin-endoperoxide synthase 2 (Ptgs2), progesterone receptor (Pgr), epiregulin (Ereg), and amphiregulin (Areg) and down regulated levels of prostaglandin E2. The inhibitory effect on Ptgs2 induction was reversed by NFIL3 siRNA treatment. In theca-interstitial cells the expression of hydroxyprostaglandin dehydrogenase 15-(NAD) (Hpgd) was also inhibited by NFIL3 over-expression. Data from luciferase assays demonstrated that NFIL3 over-expression decreased the induction of the Ptgs2 and Areg promoter activity. EMSA and ChIP analyses indicated that NFIL3 binds to the promoter region containing the DNA binding sites of CREB and C/EBP?. In summary, hCG induction of NFIL3 expression may modulate the process of ovulation and theca-interstitial and granulosa cell differentiation by regulating expression of PTGS2, PGR, AREG, EREG, and HPGD, potentially through interactions with CREB and C/EBP? on their target gene promoters.

overall_design: The granulosa cells were exposed to Ad- NFIL3 or Ad-GFP at a multiplicity of infection (MOI) of 50 pfu/cell.  Two hours later, Medium was replaced with fresh Opti-MEM medium. At 24 h after adenovirus exposure, granulosa cells were treated with FSK + PMA for 6 h before collection for RNA isolation using a RNeasy kit according to the manufacturer’s instructions (Qiagen Inc., Valencia, CA). Five micrograms of total RNA were used as a template for cDNA synthesis by the University of Kentucky Microarray Core facility as described previously (47). The Affymetrix Rat 230-2.0 oligonucleotide array sets were hybridized, washed, and scanned using Affymetrix equipment and protocols (Affymetrix, Santa Clara, CA). The DNA microarray assays were performed on total RNA pooled from granulosa cells obtained from 3 separate experiments. The changes observed by DNA microarray analysis were confirmed by real-time PCR for a select subset of genes. Affymetrix GCS 3000 7G scanner was used.

first: Feixue

first: Jing

last: Liu

first: Misung

last: Jo

first: Thomas

last: Curry


title: Hepatic gene expression profile in persimmon peel extract administrated GK rat

status: Public on Mar 17 2011

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

summary: Persimmon (Diospyros kaki L. f.) is a most popular fruit in Asian countries but its peels are totally wasted despite of containing a plenty of antioxidants such as carotenoids and polyphenols.  We prepared a fat-soluble extract from a persimmon peel (PP) fraction and fed type 2 diabetic Goto-Kakizaki (GK) rats with a PP extract-containing AIN-93G diet (PP diet) for 12 weeks.  Compared with the control AIN-93G diet, the feeding of the PP diet reduced the plasma glutamic-pyruvate transaminase activity significantly, with accumulation of β-cryptoxanthin in the liver.  A DNA microarray analysis revealed that the PP diet altered the hepatic gene expression profiles.  In particular, insulin signaling pathway-related genes were significantly enriched in differentially expressed gene sets.  Moreover, Western blotting analysis actually showed the promotion of IRβ tyrosine phosphorylation.  All these data suggest that the PP extract administration to the GK rats improves their insulin resistance.

overall_design: Male GK rats (90–107 g), aged 5 weeks, were purchased from Japan SLC Co. (Hamamatsu, Japan). The rats were maintained in a room at 22 ± 1°C under a 12-h light-dark cycle (lights on at 0800) and administered a commercial diet (AIN-93G, Research Diets, Inc., New Brunswick, NJ, USA) for a week. The rats were allowed free access to diet and water. After one week, they were divided into two groups with similar average body weights. The control group rats (n = 4) were fed on the commercial diet, and the PP group rats (n = 4) on the same diet containing the PP extract. After the 12-week-feeding the liver was excised and analyzed the effect of PP extract administration on hepatic gene expression.

first: Ryoichi

last: Izuchi

first: Hidehito

last: Takahashi

first: Shota

last: Ushiama

first: Shinji

last: Okada

first: Takumi

last: Misaka

first: Keiko

last: Abe


title: Expression data from normal rat and steroid induced necrosis of femoral head rat

status: Public on Dec 28 2010

city: Hangzhou

first: Qiang

last: Mao

state: Zhejiiang Province

address: Binjiang District

country: China

institute: Zhejiang Chinese Medical University

summary:
The steriod-induced necrosis of femoral head(SINFH) is a serious clinical problem and the underlying mechanism of this disease remains unknown. As its etiology and pathogenesis are not clear, there hasn’t been an effective treatment yet. In-depth studies on its pathogenesis will provide important information for the prevention and treatment of this devastated disease. Animal model researches are helpful to a better understanding of its etiology and pathogenesis, to early diagnosis and treatments and provide the basis for clinical treatment It has been proved that the occurrence of SINFH is related to gene itself and its polymorphism. These studies, in which only one or a few genes were investigated, could not provide a comprehensive understanding to the pathogenesis of SINFH.
We used microarrays to compare the gene expression profile of SINFH rats with that of normal rats and identified gene expression changes between SINFH rats and normal rats.

overall_design: Adult healthy male Wistar rats(body weight 200±10g) were randomly divided into control and experimental groups. All the rats were given injection of E. coli endotoxin at a dose of  20μg/kg body weight into abdominal cavity for two times with a 24 hour interval. 24 hours after the second administration of E. coli endotoxin, methylprednisolone 40mg/kg was administered into the left gluteus muscle of experimental group rats for three times with a 24 hour interval. Rats were then killed 6 weeks after steroid administration. In experiment, immediately after death the left femoral heads were isolated. Femoral heads were used for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the gene expression profile of SINFH rats and that of normal rats in order to identified gene expression changes between SINFH rats and normal rats by comparing the gene expression profile of SINFH rats with that of normal rats. To that end, we have established the gene expression profiles of normal and SINFH disease of rat femoral head and found out differentially expressed genes.

first: Peijian

last: Tong

first: Luwei

last: Xiao


title: Gene expression data from liver of rat fed a high-fat diet without/with mulberry leaves

status: Public on Jan 01 2011

city: Minato-ku

first: Yukihiro

last: Kobayashi

state: Tokyo

department: Department of Marine Biosciences

institute: Tokyo University of Marine Science and Technology

summary:
To investigate effects of intake of mulberry leaves on hyperlipidemia, we performed gene expression profiling on rat liver by microarray analysis.
Microarray analysis revealed that mulberry leaves up-regulated the genes involved in alpha-, beta-, and omega-oxidation of fatty acids, mainly relating to peroxisome proliferator-activated receptor signaling pathway, and down-regulated the gene expression involved in lipogenesis. Furthermore, the genes relating to response to oxidative stress were up-regulated in rats administrated mulberry leaves.

overall_design: Rats were fed a high-fat diet without/with orally administration of mulberry leaves (0 or 500 mg/kg/day) for 7 weeks. Livers were taken for RNA extraction and hybridization on Affymetrix microarrays.

first: Maki

last: Miyazawa

first: Asuka

last: Kamei

first: Takashi

last: Kojima


title: Expression data from rat regenerating livers after autonomic nervous system is disrupted

status: Public on Dec 18 2010

city: Xinxiang

first: Cunshuan

last: Xu

address: No. 46, Construction East Road

institute: Henan Normal University

summary:
Autonomic nervous system is widely distributed in liver, and some reserchers have found that disruppted autonomic nerves will delay liver regeneration.
We used microarrays to further highlight the regulatory role of autonomic nervous system in liver regeneration at gene transcription level.

overall_design: Surgical operations of rat partial hepatectomy (PH) and its operation control (OC), sympathectomy combining partial hepatectomy (SPH), vagotomy combining partial hepatectomy (VPH), and total liver denervation combining partial hepatectomy (TDPH) were performed, and the expression profiles of regenerating liver at 2h were detected using Rat Genome 230 2.0 array. Then the significantly changed genes related to liver regeneration (LR)-, injury-, splanchnic nerve-LR-, vagal nerve-LR-, and autonomic nerve-LR-related genes were identified, respectively. The relevance of gene expression profiles and biological processes was analyzed by bioinformatics and systems biology.

first: Xinsheng

last: Zhang

first: Gaiping

last: Wang


title: Circadian regulation in rat Lung

status: Public on Dec 20 2010

city: Buffalo

first: Siddharth

last: Sukumaran

state: NY

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

department: Dept of Biological Sciences

country: USA

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 lungs 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 lungs, and to identify the role of circadian regulation in coordinating the functioning of this dynamic organ.

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 lungs for gene arrays. Time point designations reflect time after lights on in hours.

first: Richard

middle: R

last: Almon


title: Cardiac transcriptome profiles of S.LEW congenic strain compared with the hypertensive Dahl S rat

city: Toledo

first: Bina

last: Joe

state: OH

address: 3000 Arlington avenue

department: Physiology and Pharmacology

institute: University of toledo

summary: Despite inheritance of hypertension in families, identifying genetic mechanisms predisposing individuals to hypertension has remained challenging.  The effects of single genes contributing to the development of hypertension may not be readily detected in individuals whose genomes also contain other genetic factors that resist hypertension. By using a highly permissive rat genome for inherited hypertension, we demonstrate that increased expression of one such gene, Rififylin (Rffl), is a novel inherited risk factor for hypertension and increased mortality. Animals overexpressing Rffl demonstrated delayed endocytic recycling, accumulated polyubiquitinated proteins, increased beats/min of neonatal cardiomyocytes, had shorter QT-intervals and developed salt-insensitive hypertension very early in their life (50-52 days).  Thus, the discovery of a physiological link between overexpression of rififylin and the development of hypertension constitutes a novel mechanism that could be targeted for rectifying normal QT-interval and preventing hypertension.

overall_design: Six male S control and 6 male congenic S.LEW(10)x12x2x3x5 rats born on the same day were selected, weaned at 30 days of age, and caged with 1 congenic and 1 S rat per cage. They were raised on a low-salt (0.3%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley) and sacrificed at 53 days of age and total RNAs were isolated from the heart. The isolated RNA from two animals were pooled together and considered as one biological sample. Three such RNA samples from S and congenic rats were used for the cRNA preparation. cRNA was prepared and fragmented as suggested by Affymetrix technical manual, and simultaneously hybridized (15 µg adjusted cRNA for each chip) to Rat Expression Array 230 2.0 (3' IVT Expression Analysis). Statistical analyses of the microarray data were performed with BH adjustment using R statistical package (version 2.8.1).

first: Kathirvel

last: Gopalakrishnan


title: Testicular lumicrine factors regulate ERK, STAT and NFKB pathways in the initial segment of the rat epididymis to prevent apoptosis

status: Public on Mar 11 2011

city: Research Triangle Park

first: Michael

middle: Bruce

last: Black

address: 6 Davis Dr., P.O. Box 12137

department: Chemical Safety Sciences

institute: The Hamner Institutes for Health Sciences

summary: The initial segment of the epididymis is vital for male fertility, therefore, it is important to understand the mechanisms that regulate this important region. Deprival of testicular luminal fluid factors/lumicrine factors from epididymis, a subset of cells within the initial segment undergo apoptosis. In this study, microarray analyses was used to examine early changes in the downstream signal transduction pathways following the loss of lumicrine factors, and we discovered the following cascade of events leading to loss of protection and eventual apoptosis.  First, mRNA expression of several key components of ERK pathway decreased sharply after 6 hours of loss protection from testicular lumicrine factors.  After 12 hours, the levels of mRNA expression of STAT and NF-кB pathways components increased, mRNA expression of genes encoding cell cycle inhibitors increased. After 18 hours of loss protection from testicular lumicrine factors, apoptosis was observed in the initial segment. In conclusion, testicular lumicrine factors protect the cells of the initial segment by activating ERK pathway, repressing STAT and NF-кB pathways, and preventing a cascade of reactions leading to apoptosis.

overall_design: Unilateral efferent duct ligation (EDL) surgeries were performed to block lumicrine testicular fluid factors from reaching one side of epididymis. For the control, a sham operation was performed on the contra-lateral side within the same animal.  After 6, 12 and 18 hours of EDL, the most proximal region of the initial segment containing zone 1a and 1b of initial segment was dissected out. In this microarray study, sham control and each time point of EDL (sham, 6h EDL, 12h EDL, 18h EDL) all have 4 replicates, a total of 16 arrays were hybridized.

first: Bingfang

first: Rana

last: Abdel-Fattah

first: Ling

last: Yang

first: Sallie

middle: A

last: Crenshaw

middle: B

first: Barry

middle: T

last: Hinton


title: hHGF Overexpression in Myoblast Sheets Enhances Their Angiogenic Potential in Rat Chronic Heart Failure

status: Public on Dec 10 2010

city: Helsinki

first: Antti

last: Siltanen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki, Institute of Biomedicine

summary: Ischemia, fibrosis, and remodeling lead to heart failure after severe myocardial infarction (MI). Myoblast sheet transplantation is a promising therapy to enhance cardiac function and induce therapeutic angiogenesis via a paracrine mechanism in this detrimental disease. We hypothesized that in a rat model of MI-induced chronic heart failure this therapy could further be improved by overexpression of the antiapoptotic, antifibrotic, and proangiogenic hepatocyte growth factor (HGF) in the myoblast sheets. We studied the ability of wild type (L6-WT) and human HGF-expressing (L6-HGF) L6 myoblast sheet-derived paracrine factors to stimulate cardiomyocyte, endothelial cell, or smooth muscle cell migration in culture. Further, we studied the autocrine effect of hHGF-expression on myoblast gene expression using microarray analysis. We induced MI in Wistar rats by left anterior descending coronary artery (LAD) ligation and allowed heart failure to develop for four weeks. Thereafter, we administered L6-WT (n=15) or L6-HGF (n=16) myoblast sheet therapy. Control rats (n=13) underwent LAD ligation and rethoracotomy without therapy and five rats underwent sham-operation in both surgeries. We evaluated cardiac function with echocardiography at 2 and 4 weeks after therapy administration. We analyzed cardiac angiogenesis and left ventricular architecture from histological sections 4 weeks after therapy. Paracrine mediators from L6-HGF myoblast sheets effectively induced migration of cardiac endothelial and smooth muscle cells but not cardiomyocytes. Microarray data revealed that hHGF-expression modulated myoblast gene expression. In vivo, L6-HGF sheet therapy effectively stimulated angiogenesis in the infarcted and non-infarcted areas. Both L6-WT and L6-HGF therapies enhanced cardiac function and inhibited remodeling in a similar fashion. In conclusion, L6-HGF therapy effectively induced angiogenesis in the chronically failing heart. Cardiac function, however, was not further enhanced by hHGF-expression.

overall_design: Analysis of the L6 rat skeletal myoblast cell line and myoblast cell sheets with constitutive human HGF expression.


title: Effect of iodine on early stage thyroid autonomy

status: Public on Dec 01 2010

city: Leipzig

first: Knut

last: Krohn

address: Philipp-Rosenthal-Straße 55

department: Medizinische Fakultät

country: Germany

institute: University Leipzig

summary:
Thyroid autonomy is a frequent cause of thyrotoxicosis in regions with iodine deficiency. Epidemiological data suggest that the prevalence of thyroid autonomy is not only inversely correlated with the ambient iodine supply, but that iodide may also influence the course of pre-existing thyroid autonomy with possibly different effects on thyroid growth and function.
Iodine slows TSH effects on thyroid growth stimulation and this effect is more pronounced in thyrocytes with constitutive cAMP activation i.e. in thyroid autonomy. Iodine induced growth alteration in early stage thyroid autonomy is conferred by induction of apoptosis and G2/M arrest. Transcriptome analysis revealed significant  modulation of gene networks relevant to cell adhesion, cadherin signalling and ion binding with more pronounced effects in constitutively active FRTL-5 cells compared to normal FRTL-5 cells.

overall_design: The aim was to study iodide-induced changes in global gene expression in an in vitro model of thyroid autonomy.  This model makes use of FRTL-5 cells with stable expression of a constitutively activating TSH receptor mutation or wild type TSHR as a control.

first: Kathrin

last: Müller

first: Markus

last: Eszlinger

first: Marian

last: Ludgate

first: Dagmar

last: Führer


title: Effector T cells driving monophasic vs relapse/remitting experimental autoimmune uveitis show unique pathway signatures

city: Neuherberg

first: Christine

last: von Toerne

address: Ingoldstädter Landstraße 1

department: Proteinanalytik

institute: HelmholtzZentrum

summary:
Experimental autoimmune uveitis (EAU) in Lewis rats is a model for the clinical heterogeneity of human uveitis. The autoantigens inducing disease in the rat are also seen in human disease. Depending upon the specific autoantigen used, the experimental disease course can be either monophasic or relapsing/remitting and appears to be dictated by the T cell effector phenotype elicited. We investigated potential differences between monophasic and relapsing/remitting effector T cells using transcriptomic profiling and pathway analysis. RNA samples isolated from three independent T cell lines derived from each specificity where analyzed by microarrays.
Microarray data was used to obtain transcriptomic changes reflecting signal transduction pathway dysregulation.

Keywords: Two group comparison

overall_design: Comparison of two types of cell lines of two different antigen specificities.

first: Gerhild

last: Wildner

first: Peter

last: Nelson


title: Hepatic gene expression profile in hydrogen water administrated SD rat

status: Public on Dec 31 2010

first: Yuji

last: Nakai

summary: The effects of the administration of molecular hydrogen-saturated drinking water (hydrogen water) on hepatic gene expression were investigated in rats. Using DNA microarrays, 548 upregulated and 695 downregulated genes were detected in the liver after a 4-week administration of hydrogen water. Gene Ontology analysis revealed that genes for oxidoreduction-related proteins, including hydroxymethylglutaryl CoA reductase, were significantly enriched in the upregulated genes.

overall_design: 4-week-old male Sprague-Dawley rats were acclimatized for 4 days in a room maintained at 24 ± 3°C with a relative humidity of 55 ± 15% with a 12-h light-dark cycle (lights on at 7:00, off at 19:00) and were fed ad libitum on a commercial diet (MF, Oriental Yeast Co., Yokohama, Japan). After acclimatization, the rats were divided into two groups (n = 8 per group) with similar mean body weights. During a period of 4 weeks, one group (control group) was supplied with sterilized distilled water and the other (HW group) with hydrogen water produced by MiZ Co. Ltd. (Fujisawa, Japan), which contains 0.7 mM dissolved hydrogen (pH 7.4). All the animals drank water ad libitum.  After 4 weeks, each rat was anesthetized with diethyl ether and blood samples were collected from the abdominal aorta.  The liver was then excised and analyzed the effect of hydrogen water extract administration on hepatic gene expression.

first: Bunpei

last: Sato

first: Shota

last: Ushiama

first: Shinji

last: Okada

first: Keiko

last: Abe

first: Soichi

last: Arai


title: Gene expression from primary brain cell cultures and RNA mixtures.

city: Bethesda

first: Alexandre

last: Kuhn

state: MD

address: 35 Convent Dr

department: NIA

institute: NIH

summary:
Gene expression from primary neuronal, astrocytic, oligodendrocytic and microglial cultures, as well as from RNA mixtures thereof.

Keywords: Primary cell cultures

overall_design: Primary neuronal, astrocytic, oligodendrocytic and microglial cultures (4 biological replicates of each), as well as RNA mixtures thereof (5 different mixing proportions, 2 independent replicates of each mixing proportion).

first: Ruth

last: Luthi-Carter


title: Global transcriptome analysis reveals differences between embryonic and adult dorsal root ganglion axonal mRNAs that are implicated in axonal growth and pain

status: Public on Nov 23 2010

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Local protein synthesis in sensory neuron axons is necessary for axonal regeneration with the efficiency of regeneration decreasing with age.   Because the full repertoire of transcripts in embryonic and adult rat sensory axons is unknown we asked how the pool of mRNAs dynamically changes during ageing. We isolated mRNA from pure axons and growth cones devoid of non-neuronal or cell body contamination. Genome-wide microarray analysis reveals that a previously unappreciated number of transcripts are localised in sensory axons and that this repertoire changes during development toward adulthood. Embryonic sensory axons are enriched in transcripts encoding cytoskeletal-related proteins with a role in axonal outgrowth. Surprisingly, adult axons are highly enriched in mRNAs encoding immune molecules with a role in nociception. To validate our experimental approach we show that Tubulin-beta3 mRNA is present only in embryonic axons where it is locally synthesised. In summary, we show that the population of axonal mRNAs dynamically changes during development, which may partly contribute to the intrinsic capacity of axons at different ages to regenerate after injury and to modulate pain.

overall_design: Pure axonal RNA were extracted from the axons of embryonic and adult dorsal root ganglion neurons, each with 5 biological replicates.  The axonal transcriptomes were analysed using Affymetrix Rat Genome 230 2.0 Arrays.

first: Laura

middle: F

last: Gumy

first: Giles

middle: S

last: Yeo

first: Yi-Chun

middle: L

last: Tung

first: Krishna

last: Zivraj

first: Diana

last: Willis

first: Giovanni

last: Coppola

middle: Y

first: Jeffery

last: Twiss

middle: E

last: Holt

first: James

middle: W

last: Fawcett


title: Pheochromocytoma in rats with multiple endocrine neoplasia (MENX) shares gene expression patterns with human pheochromocytoma

status: Public on Nov 19 2010

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
MENX is a rat multiple endocrine neoplasia syndrome caused by a homozygous mutation of the Cdkn1b gene, encoding p27Kip1. Affected rats develop adrenomedullary hyperplasia which progresses to pheochromocytoma with time (incidence 100%), and to extra-adrenal pheochromocytoma (paraganglioma) (68%).
We here report that hyperplasia and tumor have similar gene expression profiles, suggesting an early determination of the tumorigenic signature. Overexpressed genes in rat adrenal lesions are especially enriched in development/differentiation-associated genes.

overall_design: We performed gene expression microarray analysis of 8 adrenal hyperplasias and 4 pheochromocytomas, each compared with adrenomedullary tissue from wild-type, age-matched littermates.

first: Sara

last: Molatore

first: Martin

last: Irmler

first: Natalia

last: Pellegata


title: The transcriptome of the medullary area postrema: The thirsty rat, the hungry rat and the hypertensive rat

status: Public on Jan 22 2011

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

institute: University of Bristol

summary: The area postrema (AP) is a sensory circumventricular organ characterised by extensive fenestrated vasculature and neurons which are capable of detecting circulating signals of osmotic, cardiovascular, immune and metabolic status. The AP can communicate these messages via efferent projections to brainstem and hypothalamic structures that are able to orchestrate an appropriate response. We have used microarrays to profile the transcriptome of the AP in the Sprague Dawley (SD) and Wistar Kyoto (WKY) rat and present here a comprehensive catalogue of gene expression, focussing specifically on the population of ion channels, receptors and G protein-coupled receptors (GPCRs) expressed in this sensory tissue; of the GPCRs expressed in the rat AP we identified ~36% that are orphans having no established ligand. We have also looked at the ways in which the AP transcriptome responds to the physiological stressors of 72-hours dehydration (DSD) and 48-hours fasting (FSD) and have performed microarrays under these conditions. Comparison between the DSD and SD or between FSD and SD revealed only a modest number of AP genes that are regulated by these homeostatic challenges. The expression levels of a much larger number of genes are altered in the spontaneously hypertensive rat (SHR) AP compared to the normotensive WKY controls however. Finally, analysis of these ‘hypertension-related’ elements revealed genes that are involved in both the regulation of blood pressure and immune function and as such are excellent targets for further study.

overall_design: Using Affymetrix microarrays (Rat 230:2.0) we anaysed the transcriptome of the area postrema. Each microarray in the study represents an independent biological replicate of 5 animals.

first: Charles

middle: C

last: Hindmarch

first: Julian

last: Paton

first: Alastair

middle: V

last: Ferguson

first: Stephen

middle: J

last: Lolait

first: Mark

last: Fry

first: Pauline

middle: M

last: Smith

first: Song

last: Yao

first: Georgina

middle: G

last: Hazell

first: David

last: Murphy


title: Indian Hedgehog Signaling in the Postnatal Growth Plate

city: Stockholm

first: Ola

last: Nilsson

address: Karolinska University Hospital, Q2:08

department: Dept. Woman and Child Health

country: Sweden

institute: Karolinska Institute

summary: In order to characterize mRNA expression in the growth plate, we microdissected postnatal rat growth plates into their constituent zones and used microarray analysis to assess the abundences of individual transcripts. Expression patterns of PTHrP and Ihh-related genes were confirmed using real-time PCR. Using a gli1-lacZ mouse, Gli1 expression, presumably representing Ihh signaling, was visualized during pre- and postnatal development.

overall_design: Microdissection was used to collect individual growth plate zones from proximal tibiae of 1-wk rats and gene expression was analyzed using microarray.

first: Michael

last: Chau

first: Patricia

last: Forcinito

first: Anenisia

last: Andrade

first: Anita

last: Hegde

first: Sohyun

last: Ahn

last: Lui

first: Jeffrey

last: Baron


title: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs COLONY)

status: Public on Nov 14 2010

city: Hyderabad

first: Dr. Gopal

last: Pande

state: Andhra Pradesh

address: Uppal Road

country: India

institute: Centre for Cellular and Molecular Biology

summary:
Cell substrate adhesion plays an important role in cellular transformation of rat fibroblast cell lines, however a few viable non-adherent fibroblast cells when placed in suspension for a time period of 16 h (NA16) showed varied phenotypic characteristics like colony and tumor formation
In order to understand the molecular events associated with adhesion independent cell survival ability of NA16, whole genome profiling was performed using Affymetrix Rat 230_2 GeneChips

Keywords: Expression profiling of a adhesion deprived transformed cell line

overall_design: F111 fibroblast cell lines were grown in adhesion (A16) and suspension (NA16) conditions for 16h. These suspension cells (NA16) were plated on soft agar for colony formation and also injected in nude mice subcutaneously for tumor formation. A16 samples were considered as the control ones. Total RNA isolated from the samples (A16, NA16, Colony and Tumor) was subjected for expression analysis using Affymetrix Rat 230.2 GeneChip System. The experiment was repeated biologically and technically twice.

first: Sivapriya

last: Pavuluri

first: Renu

last: Kapoor

first: Rajeswari

last: Jinka

first: Gopal


title: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs. Tumor)


title: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation (A16 vs NA16)


title: Comparison of Mineralizing Synchronous UMR106-01 cells with UMR106-01 cells treated with Mineralization Inhibitor AEBSF

status: Public on Nov 13 2010

city: Rensselaer

first: Sridar

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: UMR106-01 osteoblastic cells are a model for studying bone mineralization.  We have shown that mineralization is temporally synchronized within cultures grown under defined conditions .  Cells are plated at time zero and differentiate into osteoblastic phenotype by 64 h later.  If an exogenous phosphate source is added to the cultures, the cells form and deposit hydroxyapatite mineral within distinct extracellular supramolecular lipid protein complexes termed biomineralization foci (BMF) starting 12 h later.  Mineralization is largely complete by 24 h later (88 h after plating).  We have also shown that AEBSF, covalent serine protease inhibitor, blocks mineralization within BMF and inhibits the fragmentation of several proteins related to biomineralization.  The present experiment was designed to test whether AEBSF treatment for 12 h has an effect on transcription by UMR106-01 osteoblastic cells.  AEBSF is known to inactivate several serine proteases including SKI-1 (site 1, subtilisin kexin protease-1).SKI-1 functions intracellularly to activate transmembrane bound transcription factor precursors releasing the transcriptionally active N-terminal portions to imported into the nucleus.  Thus, if AEBSF blocks transcription of mineralization related genes, it would support a role for SKI-1 in gene regulation in mineralizing UMR106-01 osteoblastic cells.

overall_design: Comparison of triplicate cultures treated with mineralizing conditions with triplicate cultures treated with AEBSF protease inhibitor for 12 h.

first: Jeff

middle: P

last: Gorski

first: Ronald

last: Midura


title: Comparison of effects of Iodine-deficiency and perchlorate on thyroid

status: Public on Nov 04 2010

city: Athens

first: Ken

last: Jones

state: GA

address: 150 E. Green St.

department: Environmental Health Science

institute: University of Georgia

summary: Perchlorate, which is a ubiquitous and persistent ion, competitively interferes with iodide accumulation in the thyroid, causing iodine deficiency, which may result in reduced thyroid hormone synthesis and secretion. Human studies suggest that perchlorate presents very little risk in healthy individuals; however, the precautionary principle demands that the sensitive populations of iodine deficient adults and mothers require extra consideration. In an attempt to determine if the effects on gene expression were similar, we compared the thyroidal effects of perchlorate (10 mg/kg) treatment for 14 days in drinking water with those caused by 8 weeks of Iodine-deficiency in rats. The thyroids were collected (N=3 each group) and total mRNA was analyzed using the Affymetrix Rat Genome 230 2.0 GeneChip®. Changes in gene expression were compared with appropriate control groups. We compared the 2-fold gene changes due to I-deficiency with changes due to perchlorate treatment. 189 transcripts were changed by the Iodine-deficient diet and 722 transcripts were changed by the perchlorate treatment. 34% of the transcripts changed by the I-deficient diet were also changed by perchlorate and generally in the same direction. three specific transporter genes, AQP1, NIS, & SLC22A3 were changed by both treatments, indicating that the membrane specific changes were similar. Iodine-deficiency primarily caused changes in retinol and calcium signaling pathways and perchlorate primarily caused changes related to the accumulation of extracellular matrix proteins.  This study provides evidence that perchlorate, at least at this dose level, changes more genes and changes different genes compared to iodine deficiency.

overall_design:
Changes in gene expression due to I-deficiency compared to normal diet for 2 months.
Changes in gene expression due to perchlorate in the drinking water compared to normal drinking water for 1 or 14 days.
Feeding study in rats.

first: James

last: McDougal


title: Differential Gene Expression and Clonal Selection during Cellular Transformation Induced by Adhesion Deprivation

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

overall_design: Refer to individual Series


title: Global gene expression changes in rat retinal ganglion cells after experimental glaucoma

status: Public on Oct 01 2010

city: Boston

first: Danyi

last: Wang

state: MA

address: 243 Charles St

department: Ophthalmology

institute: Harvard Medical School

summary:
Goals of the study:
1. Assess the gene expression profile in rat RGC after experimental IOP elevation to elucidate the molecular mechanisms of RGC death.
2. Identify potentially novel genes and pathways that may contribute to RGC death in glaucoma.
Background: Glaucoma is a neurodegenerative disease characterized by the slow, progressive degeneration of RGC. Elevated IOP is the biggest risk factor for developing glaucoma, loss of RGC and optic nerve atrophy. The pathophysiology of glaucomatous neurodegeneration is not fully understood. It is now clear that RGC die by apoptosis in glaucoma. However, what triggers the apoptosis is still unknown. So far, several gene expression studies have been performed on the retina as a whole. These studies revealed up and downregulation of many genes in response to elevated IOP and optic nerve transection.
However, the retina is a complex tissue composed of neuronal, glial and vascular cell types. The RGCs only comprise 5% or less of retinal cells. The gene expression profiles from whole retina can not represent of RGC gene expression. In the current study, we sought to investigate the whole genome regulation of the RGCs in glaucoma.

overall_design: The study was carried out in 3 adult male Brown Norway rats with experimental glaucoma. An equal number of RGCs were captured from normal eyes and eyes with elevated IOP. Gene expression in the glaucomatous RGC was compared with that in the fellow RGC by using Affymetrix Gene chip.

first: Arjun

last: Ray

first: Kathryn

last: Rodgers

first: Ceren

last: Ergorul

first: Bradley

last: Hyman

first: Wei

last: Huang

first: Cynthia

last: Grosskreutz


title: Role of the Yersinia pestis Virulence Plasmid in Evading a Protective Polymorphonuclear Leukocyte Response During the Early Stages of Bubonic Plague

status: Public on Dec 07 2010

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

summary: A delay in the mammalian inflammatory response is a prominent feature of infection with Yersinia pestis, the agent of bubonic and pneumonic plague. Y. pestis factors have been identified that either do not stimulate a normal inflammatory response, or actively suppress it. Prominent among these are components of the Type III secretion system that is encoded on the Yersinia virulence plasmid (pYV). We used a rat model of bubonic plague to characterize the kinetics and extent of the mammalian transcriptomic response to infection with wild-type or pYV-negative Y. pestis in the draining lymph node. Remarkably, dissemination and multiplication of wild-type Y. pestis during the bubonic stage of disease did not induce any detectable gene expression response by host lymph node cells. This was followed, however, by an extensive transcriptomic response, including upregulation of several cytokine, chemokine, and other immune response genes, after systemic spread during septicemic plague. Matched lymph node samples used for histopathology and extracellular cytokine measurements, combined with the microarray data set, broadly outlined the mammalian immune response to Y. pestis and how it is influenced by pYV-encoded factors. The results indicate that both WT and pYV– Y. pestis induce primarily a Th17 response, and not a Th1 or Th2 response. In the absence of pYV, a sustained recruitment of polymorphonuclear leukocytes, the major Th17 effector cell, to the lymph node resulted in clearance of infection. Thus, the ability to counteract a Th17- driven PMN response in the lymph node appears to be a major function of the Y. pestis virulence plasmid. In contrast, classic markers of the proinflammatory response and macrophage activation, such as TNF-á and IFN-ã, were not induced at all by pYV– Y. pestis, and appeared only late in infection with WT Y. pestis.

overall_design: Rats treated with PBS and Yersinia pestis at various time points.

first: Jason

last: Comer

first: Daniel

first: Aaron

last: Carmody

first: Kimmo

last: Virtaneva

first: Donald

last: Gardner

last: Long

first: Stephen

last: Porcella

first: B

last: Hinnebusch


title: preparative changes in rat intestine and lung for birth

status: Public on Nov 21 2010

first: sarah

middle: louise

last: kempster

state: Cambridgeshire

address: Rosie Hospital, Robinson Way

department: obstetrics and gynaecology

institute: university of cambrige

summary:
To identify genes important in fetal preparation for birth.
Transcript profiling using microarray analysis was performed using lung and intestine RNA from a single animal from each of 10 litters at a given gestational age. Array experiments were performed by the Genomics CoreLab, Cambridge Comprehensive Biomedical Research Centre. Briefly, the Affymetrix Rat Genome 230.2 GeneChip was employed. Total RNA was processed using the standard Affymetrix one-cycle target labeling and hybridization protocols. Data were pre-normalized using robust multiarray averaging and normalization was achieved using the LIMMA software package. Normalized transcript abundance data were compared between E16 and E20 using two independent methods: the Cyber-T algorithm and Rank Product Analysis.  Transcripts that were significantly regulated in both Cyber-T (Bayes p value < 0.001, posterior probability of differential expression, ppde > 0.99) and Rank Product Analysis (p<0.0001) and showed an absolute fold change of over 5 were defined as differentially expressed. Microarray data were annotated using the NetAffx  Analysis Center (Affymetrix). To generate the list of up-or down-regulated genes only Entrez genes or Unigene clusters were considered if at least one probe set gave an unambiguous match.

overall_design: 10 rat embryos 16 days gestation and 10 embryos at 20 days gestation.

first: Sarah

last: Kempster

first: Gusztav

last: Belteki

first: Alison

last: Forhead

first: Abby

last: Fowden

first: Roberto

last: Catalano

first: D

last: Charnock-Jones

first: Gordon

last: Smith


title: Phosphatidylinositol 3-kinase modulation of trophoblast cell differentiation

status: Public on Sep 15 2010

city: Kansas City

first: Lindsey

middle: N

last: Kent

state: KS

address: 3901 Rainbow Blvd.

department: Pathology

institute: The University of Kansas Medical Center

summary:
Rcho-1 trophoblast stem cells can be maintained in a trophoblast stem cell state or induced to differentiate into trophoblast giant cells.  During the differentiation process the PI3K pathway is constitutively activated.
Microarray analysis of  stem, differentiated and differentiated Rcho-1 trophoblast stem cells treated with the PI3K inhibitor LY294002.

overall_design: We used gene profiling to determine changes in gene expression between stem and differentiated Rcho-1 trophoblast stem cells.  We also identified genes regulated by PI3K in Rcho-1 trophoblast stem cells.

first: Toshihro

last: Konno

first: Michael

last: Soares


title: Temporal Gene Expression Profiling during Rat Femoral Marrow Ablation-Induced Intramembranous Bone Regeneration

status: Public on Oct 12 2010

city: Chicago

first: Amarjit

middle: S.

last: Virdi

state: IL

address: 600 South Paulina, Armour Academic Facility, Suite 507

department: Anatomy and Cell Biology

institute: Rush University Medical Center

summary:
Enhanced understanding of differential gene expression and biological pathways associated with distinct phases of intramembranous bone regeneration following femoral marrow ablation surgery will improve future advancements regarding osseointegration of joint replacement implants, biomaterials design, and bone tissue engineering. A rat femoral marrow ablation model was performed and genome-wide microarray data were obtained from samples at 1, 3, 5, 7, 10, 14, 28, and 56 days post-ablation, with intact bones serving as controls at Day 0. Bayesian model-based clustering produced eight distinct groups amongst 9,062 significant gene probe sets based on similar temporal expression profiles, which were further categorized into three major temporal classes of increased, variable, and decreased expression. Differential biological processes and pathways associated with each major temporal group were identified, and significantly expressed genes involved were visually represented by heat maps. It was determined that the increased expression group exclusively contains genes involved in pathways for matrix metalloproteinases (MMPs), Wnt signaling, TGF-β signaling, and inflammatory pathway. Only the variable expression group contains genes associated with glycolysis and gluconeogenesis, Notch Signaling Pathway, natural killer cell mediated cytotoxicity, and B cell receptor signaling pathway, among others. The decreased group exclusively consists of genes involved in heme biosynthesis, p53 signaling pathway, and hematopoietic cell lineage. Significant biological pathways and transcription factors expressed at each time point post-ablation were also identified.
These data present the first temporal gene expression profiling analysis of the rat genome during intramembranous bone regeneration induced by femoral marrow ablation.

overall_design: In an Institutional Animal Care and Use Committee (IACUC) approved study, 27 adult male rats (Sprague Dawley, 400-425 g) were divided into nine groups: intact control (0 day), and 1, 3, 5, 7, 10, 14, 28, and 56 days post marrow ablation. Twenty-four animals received unilateral femoral ablation. At each time point, animals were killed in a carbon dioxide chamber, and whole femurs were harvested and denuded of soft tissue. For three samples per time point, both the distal and proximal ends of the femurs were cut off in order to exclude the epiphyses and growth plate regions. Diaphyseal marrow tissue and cells from the mid-shaft were flushed out using Trizol®. Extracted RNA was homoginized and was prepared for hybridization. For each of the three samples per time point, gene expression was analyzed with GeneChip® Rat Genome 230 2.0 Arrays (Affymetrix, Santa Clara, CA).

first: Joel

middle: K

last: Wise

first: Kotaro

last: Sena

first: Karen

last: Vranizan

first: Jacob

last: Pollock

first: Kevin

middle: H

last: Healy

first: W

last: Hughes

middle: R

last: Sumner


title: MAQC-II Project: NIEHS data set

status: Public on Sep 25 2010

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

summary: The NIEHS data set (endpoint C) was provided by the National Institute of Environmental Health Sciences (NIEHS) of the National Institutes of Health (Research Triangle Park, NC, USA). The study objective was to use microarray gene expression data acquired from the liver of rats exposed to hepatotoxicants to build classifiers for prediction of liver necrosis. The gene expression compendium data set was collected from 418 rats exposed to one of eight compounds (1,2-dichlorobenzene, 1,4-dichlorobenzene, bromobenzene, monocrotaline, N-nitrosomorpholine, thioacetamide, galactosamine, and diquat dibromide). All eight compounds were studied using standardized procedures, i.e. a common array platform (Affymetrix Rat 230 2.0 microarray), experimental procedures and data retrieving and analysis processes.

overall_design: For each compound, four to six male, 12 week old F344 rats were exposed to a low dose, mid dose(s) and a high dose of the toxicant and sacrificed at 6, 24 and 48 hrs later. At necropsy, liver was harvested for RNA extraction, histopathology, and clinical chemistry assessments.


title: Germ-free and anti-biotic treated rats

status: Public on Aug 31 2010

city: Macclesfield

first: James

last: Sidaway

address: Mereside, Alderely Park

department: Safety Assessment

institute: AstraZeneca

summary: The objective of the study was identify hepatic genes with expression by deprivation of gut flora. Two models were used: model 1 (study 1443KR) examined germ-free Sprague Dawley and model 2 (1512KR) examined antibiotic treated Han Wistar rats.

overall_design: Germ-free vs. non-germ-free, antibiotic treated vs. untreated


title: Regression of Cardiac Hypertrophy and Attenuation of Progression to Heart Failure by Paricalcitol Therapy in Rats

status: Public on Sep 14 2010

city: Abbott Park

first: Paul

last: Kroeger

address: 200 Abbott Park Road

department: R4DI, AP52-1N

institute: Abbott Laboratories

summary:
Background: Vitamin D deficiency is associated with cardiac hypertrophy and heart failure, and vitamin D therapy prevents the progression of cardiac hypertrophy in animal models. Here, we examine whether vitamin D therapy regresses pre-existing cardiac hypertrophy, and prevents the progression to heart failure.

Methods and Results: When male Dahl salt-sensitive (DSS) rats are fed a high salt (HS) diet, all rats develop cardiac hypertrophy after 5 weeks (H). Thereafter, rats were treated with vehicle (V), paricalcitol (PC, an active vitamin D analog at 200ng, IP 3x/wk), enalapril (EP, 90ug/day), and PC+EP.  All groups were continued on the HS diet and evaluated after 4 weeks of therapy.  The PC and PC+EP, but not the V and EP-only groups, showed significant regression of pre-existing cardiac hypertrophy. The signs of decompensated heart failure were evident in the vehicle-treated group; these heart failure parameters significantly improved with PC, EP or PC+EP therapy. The expression of PKCe, which is regulated by Ca2+ and known to stimulate cardiac hypertrophy, was significantly increased in the vehicle group, and PC, EP or PC+EP effectively decreased PKCe activation. We also observed normalization of genetic alterations during progression to heart failure with PC treatment.

Conclusions: PC treatment resulted in both the regression of pre-existing cardiac hypertrophy, and the attenuation of the progression to heart failure, compared to improvement in progression to heart failure by EP alone.  These beneficial findings in the heart were associated with inhibition of PKCe activation, and reversal of gene alterations.

overall_design: Male Dahl salt-sensitive rats (Harlan Sprague–Dawley, Somerville, NJ) were bred and fed a normal diet until 6 weeks of age. To generate pressure overload cardiac hypertrophy, they were then fed a high salt (6%NaCl) diet for the next 5 weeks. Data for baseline hypertrophic group (H) was obtained at the end of 11 weeks.  Among H group animals, they were divided as follows and treated for an additional 4 weeks: 1) continuation of the HS diet with vehicle injection (H+V); 2) continuation of the HS diet with paricalcitol (19-nor-1,25-(OH)2 D2) (PC) (200ng IP 3x/wk) injection (H+PC); 3) continuation of the HS diet with low dose enalapril (EP), an angiotensin-converting enzyme inhibitor, infusion via osmotic pump and vehicle injection (H+EP+V); and 4) continuation of the HS diet with low dose EP infusion via osmotic pump and PC (200ng IP 3x/wk) injection (H+EP+PC). PC was prepared with 95% propylene glycol and 5% ethyl alcohol solution and administered three times a week on Monday, Wednesday, and Friday for 4 consecutive weeks. Vehicle groups received vehicle injections on the same schedule. Two groups of rats were implanted with pumps to deliver EP for 4 weeks. Since the reduction in blood pressure (BP) from high doses of EP would have effects on cardiac hypertrophy and progression to heart failure, we used low dose EP at 90ug/day, a maximum dose that did not significantly decrease BP in these rats, to study the effects of EP and PC that are independent of BP.

first: Soochan

last: Bae

first: Bhargavi

last: Yalamarti

first: Qingen

last: Ke

first: Sangita

last: Choudhury

first: S

middle: A

last: Karumanchi

first: Ravi

last: Thadhani

first: Peter

last: Kang


title: A small molecule accelerates neuronal differentiation in the adult rat

status: Public on Aug 18 2010

city: San Diego

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary: Adult neurogenesis occurs in mammals and provides a mechanism for continuous neural plasticity in the brain.However, little is known about the molecular mechanisms regulating hippocampal neural progenitor cells (NPCs) and whether their fate can be pharmacologically modulated to improve neural plasticity and regeneration. Here, we report the characterization of a unique small molecule (KHS101) that selectively induces a neuronal differentiation phenotype. Mechanism of action studies revealed a link of KHS101 to cell cycle exit and specific binding to the TACC3 protein, whose knockdown in NPCs recapitulates the KHS101-induced phenotype. Upon systemic administration, KHS101 distributed to the brainandresulted in a significant increase in neuronal differentiation in vivo. Our findings indicate that KHS101 accelerates neuronal differentiation by interaction with TACC3 and may provide a basis for pharmacological intervention.directed at endogenous NPCs.

overall_design: Compare expression profile of KHS101-treated hippocampal progenitor cells (2 concentrations) vs. DMSO (negative control), retinoic acid (positive control)

first: Heiko

last: Wurdak

first: Shoutian

last: Zhu

first: Kyung

last: Min

first: Lindsey

last: Aimone

first: Luke

middle: L

last: Lairson

last: Watson

first: Gregory

last: Chopiuk

last: Demas

first: Bradley

last: Charette

first: Eranthie

last: Weerapana

first: Benjamin

middle: F

last: Cravatt

first: Hollis

middle: T

last: Cline

first: Eric

last: Peters

first: Jay

last: Zhang

first: Chunlei

last: Wu

first: Jonathan

last: Chang

first: Tove

last: Tuntland

first: Charles

last: Cho

last: Schultz


title: DEFINING A RAT BLOOD PRESSURE QUANTITATIVE TRAIT LOCUS TO A <81.8KB CONGENIC SEGMENT: COMPREHENSIVE SEQUENCING AND RENAL TRANSCRIPTOME ANALYSIS.

status: Public on Jul 15 2010

city: Toledo

first: Bina

last: Joe

address: 3000 Arlington avenue

department: Physiology and Pharmacology

institute: University of toledo

summary: Evidence from multiple linkage and genome-wide association studies suggest that human chromosome 2 (HSA2) contains alleles that influence blood pressure (BP). Homologous to a large segment of HSA2 is rat chromosome 9 (RNO9), to which a BP quantitative trait locus (QTL) was previously mapped. The objective of the current study was to further resolve this BP QTL. Eleven congenic strains with introgressed segments spanning <81.8kb to <1.33Mb were developed by introgressing genomic segments of RNO9 from the Dahl salt-resistant (R) rat onto the genome of the Dahl salt-sensitive (S) rat and tested for BP.  The congenic strain with the shortest introgressed segment spanning <81.8kb significantly lowered BP of the hypertensive S rat by 25 mm Hg and significantly increased its mean survival by 45 days. In contrast, two other congenic strains had increased BP compared with the S. We focused on the <81.8kb congenic strain which represents the shortest genomic segment to which a BP QTL has been definitively mapped to date in any species.  Sequencing of this entire region in both S and R rats detected 563 variants. The region did not contain any known or predicted rat protein coding genes. Further, a whole genome renal transcriptome analysis between S and the <81.8kb S.R congenic strain revealed alterations in several critical genes implicated in renal homeostasis. Taken together, our results provide the basis for future studies to examine the relationship between the candidate variants within the QTL region and the renal differentially expressed genes as potential causal mechanisms for BP regulation.

overall_design: Six male S control and 6 male congenic S.R(9)x3x2Bx1x8  rats born on the same day were selected, weaned at 30 days of age, and caged with 1 congenic and 1 S rat per cage. They were raised on a High-salt (2%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley) and sacrificed at 53 days of age and total RNAs were isolated from the kidney. The isolated RNA from two animals were pooled together and considered as one biological sample. Three such RNA samples from S and congenic rats were used for the cRNA preparation. cRNA was prepared and fragmented as suggested by Affymetrix technical manual, and simultaneously hybridized (15 µg adjusted cRNA for each chip) to Rat Expression Array 230 2.0 (3' IVT Expression Analysis). Statistical analyses of the microarray data were performed using R statistical package (version 2.8.1).

first: Kathirvel

last: Gopalakrishnan


title: Expression data from 28 day sham and shunt atrial tissues (set 2)

status: Public on Aug 01 2010

city: Ottawa

first: Adolfo

last: de Bold

state: ON

address: 40 Ruskin St.

department: Cardiovascular Endocrinology

country: Canada

institute: University of Ottawa Heart Institute

summary:
Pharmacological and gene ablation studies have demonstrated a crucial role of the caridac natriuretic peptides (NP) hormones ANF and BNP in the maintenance of cardiovascular homeostasis. Considerable effort has been focused on the elucidation of the mechanistic underlying increased atrial ANF and BNP expression and secretion. These investigations are important because under chronic congestive heart failure, the secretion of NPs although increased and beneficial, is relatively insufficient as demonstrated by the fact that patients  benefit form the unloading of the heart induced by therapeutic administration of either ANF or BNP.
To identify genes involved in the transcriptional response of the endocrine heart under normal and stimulated states, we conducted differential gene expression studies of the rat atria under normal or chronic volume overload, induced by aorto-caval shunt.

overall_design: The left and right atrial appendages were obtained from 28 day sham and shunt operated male Sprague Dawley rats. Total RNA was obtained from three pools (of two tissues) of right atria and left atria under sham and shunt conditions. Three biological replicates for each muscle type and condition were generated.

first: Monica

last: Forero

first: Tsuneo

last: Ogawa


title: Molecular basis for vulnerability to mitochondrial and oxidative stress in an insulinoma cell line

city: San Francisco

first: Natasha

last: Chandiramani

address: 513 Parnassus Av

institute: University of California San Francisco

summary:
BACKGROUND: Many age-associated disorders (including diabetes, cancer, and neurodegenerative diseases) are linked to mitochondrial dysfunction, which leads to impaired cellular bioenergetics and increased oxidative stress. However, it is not known what genetic and molecular pathways underlie differential vulnerability to mitochondrial dysfunction observed among different cell types.

METHODOLOGY/PRINCIPAL FINDINGS: Starting with an insulinoma cell line as a model for a neuronal/endocrine cell type, we isolated a novel subclonal line (named CRI-G1-RS) that was more susceptible to cell death induced by mitochondrial respiratory chain inhibitors than the parental CRI-G1 line (renamed CRI-G1-RR for clarity). Compared to parental RR cells, RS cells were also more vulnerable to direct oxidative stress, but equally vulnerable to mitochondrial uncoupling and less vulnerable to protein kinase inhibition-induced apoptosis. Thus, differential vulnerability to mitochondrial toxins between these two cell types likely reflects differences in their ability to handle metabolically generated reactive oxygen species rather than differences in ATP production/utilization or in downstream apoptotic machinery. Genome-wide gene expression analysis and follow-up biochemical studies revealed that, in this experimental system, increased vulnerability to mitochondrial and oxidative stress was associated with (1) inhibition of ARE/Nrf2/Keap1 antioxidant pathway; (2) decreased expression of antioxidant and phase I/II conjugation enzymes, most of which are Nrf2 transcriptional targets; (3) increased expression of molecular chaperones, many of which are also considered Nrf2 transcriptional targets; (4) increased expression of β cell-specific genes and transcription factors that specify/maintain β cell fate; and (5) reconstitution of glucose-stimulated insulin secretion.

CONCLUSIONS/SIGNIFICANCE: The molecular profile presented here will enable identification of individual genes or gene clusters that shape vulnerability to mitochondrial dysfunction and thus represent potential therapeutic targets for diabetes and neurodegenerative diseases. In addition, the newly identified CRI-G1-RS cell line represents a new experimental model for investigating how endogenous antioxidants affect glucose sensing and insulin release by pancreatic β cells.

overall_design: Six biological replicates for each of two cell types (12 samples total)

first: Xianhong

last: Wang

first: Marta

last: Margeta


title: Microarray analysis of rat hepatic gene expression identifies new genes associated with postprandial triglyceridemia

status: Public on Aug 28 2010

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

summary: The acute response four hours after a fat load of extra virgin olive oil was investigated using DNA microarrays. Hepatic gene expression was analysed in Wistar Rats.

overall_design:
Male rats, weighing 250- 300 g (purchased from Charles River, Barcelona, Spain), were used for experiments. Rats, housed in sterile filter-top cages (3-4 per cage), were acclimatized in a room maintained at 20ºC with a 12-h light-dark cycle for 10 days, allowed ad libitum access to water and standard chow diet (Pascual S.A., Barcelona, Spain), and fasted for 18 h before experiments.
Two study groups were established: a) The control group did not receive any fat meal. The other  group was fed 5 ml of olive oil (Aceites Toledo, Spain) as a bolus and sacrificed 4 hours after the feeding, respectively. This amount represents the use of a dose of 16 mL olive oil/ kg.

first: Roberto

last: Martínez

first: María

last: Navarro

first: Natalia

last: Guillén

first: Sergio

last: Acín

first: Carmen

last: Arnal

first: Mario

last: Guzman

first: Jesús


title: Temporal changes of gene expression in rat kidney and lung, and the effect of prior growth inhibition on these changes

status: Public on Sep 16 2010

city: Bethesda

first: Julian

middle: CK

last: Lui

address: 10 Center Drive

institute: NICHD, NIH

summary:
Temporal changes of gene expression from 1-wk- to 5-wk-old rat in kidney and lung, and the effect of prior growth inhibition on these genetic changes.
In mammals, body growth is rapid in early life but decelerates with age. Somatic growth deceleration is caused by a gradual decline in cell proliferation that occurs simultaneously in many different organs, but is not caused by a hormonal mechanism. We hypothesize that growth deceleration is driven by a postnatal genetic program that occurs coordinately in multiple organs.
Using microarrays, we investigated the changes of gene expression that occur with age in kidney and lung as growth slows down, and also investigated whether these changes were growth-driven, by asking whether prior delay of postnatal growth caused by malnutrition (tryptophan deficiency) would also delay these genetic changes.

overall_design: To compare gene expression between fast-growing animals and more slowly growing animals, we extracted total mRNA from kidney and lung in 1-wk-old and 5-wk-old mice (5 animals each). Then, to investigate the effect of prior growth on these genetic changes, we also extracted total mRNA from kidney and lung in 5-wk-old mice that received a tryptophan-deficient diet from birth to 4wk of age.

first: Weiping

last: Chen

first: Jeffrey

last: Baron


title: Expression data from 28 day sham and shunt atrial and ventricular tissues

first: Adolfo


title: Microarray analysis of expression of cell death-associated genes in rat spinal cord cells exposed to cyclic tensile stresses in vitro

status: Public on Jul 08 2010

city: Matsuoka

first: Kenzo

last: Uchida

state: Fukui

address: Shimoaizuki 23

department: Department of Orthopaedics and Rehabilitation Medicine

institute: Fukui University Faculty of Medical Sciences

summary:
The application of mechanical insults to the spinal cord results in profound cellular and molecular changes, including the induction of neuronal cell death and altered gene expression profiles. We demonstrated that spinal cord cells undergo cell death in response to cyclic tensile stresses, which were dose- and time- dependent. In addition, we have identified the up regulation of various genes, in particular of the MAPK pathway, which may be involved in this cellular response.
We investigated the effect of cyclic tensile stresses on cultured spinal cord cells from E15 Sprague-Dawley rats, using the FX3000® Flexercell Strain Unit. We examined cell morphology and viability over a 72 hour time course. Microarray analysis of gene expression was performed using the Affymetrix GeneChip System®, where categorization of identified genes was performed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) systems.

overall_design: time course

first: Hideaki

last: Nakajima


title: Global colorectal cancer gene expression in rats

status: Public on Jun 04 2010

city: Sydney

first: Caroline

middle: Audrey

last: Kerr

state: NSW

address: 11 Julius Ave North Ryde

department: Moelcular health Technologies

country: Australia

institute: CSIRO

summary: The rat models of colorectal cancer (CRC), such as the azoxymethane (AOM) cancer-inducing model, are important tools for researching cancer initiation pathways.  However, there is limited understanding of the expression pathways of underlying normal rat colonic epithelium and how this relates to human colonic epithelium. The aim of this study was to study the acute effects of AOM on the gene and pathway expression of the rat's colonic epithelium, whilst contrasting the background normal global expression patterns along the length of the rat as compared to the normal human colonic epithelium.

overall_design: The study used microarrays to investigate global gene expression of the colonic epithelium from proximal and distal sections of AOM- and saline (normal)-treated Sprague Dawley rats.  Rat gene and pathway expression patterns were then compared in-silico with human microarray data (see GSE9254 for files) from normal tissue samples originating from proximal and distal regions of the colon.

first: Barney

last: Hines

first: Janet

last: Shaw

first: Rob

last: Dunne

first: Lauren

last: Bragg

first: Julie

last: Clarke

first: William

last: Wilson

first: Trevor

last: Lockett

first: Richard

last: Head


title: Gene expression changes in response to doxycyline-induced expression of proinsulin (C96Y)-GFP in an INS-1 insulinoma cell line

status: Public on Jun 24 2010

city: Toronto

first: Allen

last: Volchuk

state: Ontario

address: 101 College Street

department: Cellular & Molecular Biology

institute: Toronto General Research Inst.

summary: A doxycyline-inducible INS-1 insulinoma cell line expressing proinsulin (C96Y)-GFP was engineered. Addition of doxycyline causes the production of the proinsulin (C96Y)-GFP, which is retained in the endoplasmic reticulum. This study analyzes the gene expression changes that occur after doxycyline-induced expression of proinsulin (C96Y)-GFP for 24h, 48h and 5 days. Expression changes were compared between control un-induced cells and cells treated with doxycyline. Three replicates (experiments) were performed for each time point.

overall_design: Stable mutant insulin-expressing insulinoma cells were treated or not with doxycyline for 24h, 48h or 5 days and RNA was extracted for expression analysis.


title: Adenosine 5’ monophosphate-activated protein kinase regulates metabolic actions of glucocorticoids by phosphorylating the glucocorticoid receptor through p38 mitogen-activated protein kinase.

status: Public on Jun 30 2010

first: Tomoshige

last: Kino

address: 10 Center Drive MSC 1109

department: Program in Reproductive and Adult Endocrinology

institute: National Institute of Child Health & Human Development

summary: Glucocorticoids play central roles in the regulation of energy metabolism by shifting it toward catabolism, while AMPK is the master regulator of energy homeostasis, sensing energy depletion and stimulating pathways of increasing fuel uptake and saving on peripheral supplies. We showed here that AMPK regulates glucocorticoid actions on carbohydrate metabolism by targeting the glucocorticoid receptor (GR) and modifying transcription of glucocorticoid-responsive genes in a tissue- and promoter-specific fashion. Activation of AMPK in rats reversed glucocorticoid-induced hepatic steatosis and suppressed glucocorticoid-mediated stimulation of glucose metabolism. Transcriptomic analysis in the liver suggested marked overlaps between the AMPK and glucocorticoid signaling pathways directed mostly from AMPK to glucocorticoid actions. AMPK accomplishes this by phosphorylating serine 211 of the human GR indirectly through phosphorylation and consequent activation of p38 MAPK and by altering attraction of transcriptional coregulators to DNA-bound GR. In human peripheral mononuclear cells, AMPK mRNA expression positively correlated with that of glucocorticoid-responsive GILZ, which correlated also positively with the body mass index of subjects. These results indicate that the AMPK-mediated energy control system modulates glucocorticoid action at target tissues. Since increased action of glucocorticoids is associated with development of metabolic disorders, activation of AMPK could be a promising target for developing pharmacologic interventions to these pathologies.

overall_design: We tested the hypothesis by treateing rats with the synthetic glucocorticoid dexamethasone and the AMPK activator 5-aminoimidazole-4-carboxamide-1-β-d-ribonucleoside (AICAR).

first: Nancy

last: Nader

first: Sinnie

middle: S

last: Ng

first: George

middle: I

last: Lambrou

first: Panagiota

last: Pervanidou

first: Yonghong

last: Wang

last: Chrousos


title: Time series gene expression data from adult rat tail MNs following spinal cord transection

status: Public on May 01 2010

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 spinalizaion. To understand the moleclar mechanism behind this pheneomona we examined the transcriptional response of the motor neurons after spinal cord injury as it progress over time.
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 neurones 0, 2, 7, 21 and 60 days after comlete spinal transection.

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. 31 samples were hybridized onto chips, 4 Spi-0 (Control), 6 Spi-2, 5 Spi-7, 8 Spi-21 and  8 Spi-60.

first: Jacob

last: Wienecke

first: Ann-Charlotte

last: Westerdahl

first: Hans

last: Hultborn

first: Ole

last: Kiehn


title: Effect of odorant inhalation on hypothlamic gene expression profile exposed to restraint stress in rats

status: Public on Jun 26 2010

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: As an attempt to assess physio-psychological effects elicited in odorant-inhaled rats, gene expression profiling in the central nervous system was carried out with rats housed under stressful conditions. (R)-(-)-linalool inhalation to rats during 2 h restraint significantly up-regulated the expression of genes in hypothalamus, which were found to be related to neuron differentiation and regulation of transcription as well as immediate early genes. The expressions of 104 among focused stress-regulated genes were significantly altered by the inhalation. The (R)-(-)-linalool inhalation significantly repressed the restraint-induced changes in the expression levels of 77 of the 104. It also promoted the expression of the remaining 27 genes including those related to anti-apoptotic heat shock proteins. The differences in their hypothalamic gene expressions revealed that the inhaled odorants actually influenced stress responses, based on the restraint-induced hypothalamic gene expressions related to apoptosis. These results indicate that the analysis of gene expression profiles in rats subjected to a stressful condition is  useful to evaluate odorant-induced effects as shown by the particular results that (R)-(-)-linalool inhalation under only 2 h restraint- stressed condition induces neuron differentiation against apoptosis.

overall_design: Male Wistar rats aged 7-8 weeks were housed in a room maintained on a light / dark cycle with lights turned on at 9:00 a.m. and off at 9:00 p.m. They were allowed to get free access to food and water. After acclimatization to the environment and to investigators for 1 week, 16 rats were divided into four groups (n = 4 each); group C (control) exposed to neither stress nor odor, group S exposed to stress only, group SO exposed to both stress and odor, group O exposed to odor only.

first: Akio

last: Nakamura

first: Satoshi

last: Fujiwara

first: Tomoko

last: Ishijima

first: Shinji

last: Okada

first: Ichiro

last: Matsumoto

first: Keiko

last: Abe


title: Gene expression microarray analysis of rat nasal tissue with time and dose following formaldehyde inhalation

status: Public on Jul 28 2010

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

summary: Formaldehyde (FA), an endogenous cellular aldehyde, is a rat nasal carcinogen. In this study, concentration- and exposure-duration transitions in FA mode of action (MOA) were examined with pharmacokinetic (PK) modeling for tissue formaldehyde acetal (FAcetal) and glutathione (GSH) and with histopathology and gene expression studies for tissue responses in nasal epithelium from rats exposed to 0, 0.7, 2, 6, 10 or 15 ppm FA 6 hr/day for 1, 4 or 13 weeks. The study had two goals. The first goal was to develop a basic PK model to estimate various forms of tissue formaldehyde and tissue glutathione (GSH). The second goal was to compare histopathology and gene expression changes in nasal tissues caused by inhalation of FA with changes in tissue FAcetal and free GSH calculated from the PK model.  Patterns of gene expression varied with concentration and with duration. At 0.7 and 2 ppm, sensitive response genes (SRGs) - associated with cellular stress, thiol transport/reduction, inflammation, and cell proliferation - were similarly upregulated at all exposure durations. At 6 ppm and greater, gene expression changes showed enrichment of pathways involved in cell cycle, DNA repair, and apoptosis processes. ERBB, EGFR, WNT, TGF-β, Hedgehog, and Notch signaling were also enriched in differentially expressed genes. Benchmark doses (BMDs) for genes in significantly enriched pathways were lower at 13 weeks than at 1 or 4-week.  The transcriptional and histological changes corresponded to PK model-predicted changes in free GSH at 0.7 and 2 ppm and in FAcetal at 6 ppm. DNA-replication stress, enhanced proliferation, metaplasia, and stem cell-niche activation appear to be associated with FA carcinogenesis at 6 ppm and above. Dose dependencies in MOA, the presence of high physiological FAcetal, and non-linear FAcetal/GSH tissue kinetics indicate that FA concentrations below 150 ppb (and probably any concentrations below irritant levels, i.e., ~ 1 ppm) would not increase cancer risks of inhaled FA in the nose or any other tissue. Closer examination of dose response relationships for endogenous compound toxicity could help guide biologically relevant approaches for chemical risk assessment.

overall_design: Eight week old male F344/CrlBR rats were exposed to formaldehyde through whole body inhalation. Whole-body exposures were performed at doses of 0, 0.7, 2, 6, 10, and 15 ppm (6 hours per day, 5 days per week).  Inhalation animals were sacrified at 1, 4, and 13 weeks following initiation of exposure.  Following sacrifice, tissue from the Level II region of the nose was dissected and digested with a mixture of proteases to remove the epithelial cells.  The epithelial cells acquired from this section of the nose consisted primarily of transitional epithelium with some respiratory epithelium.  Gene expression microarray analysis was performed on the epithelial cells.

first: Melvin

middle: E

last: Andersen

first: Harvey

middle: J

last: Clewell

first: Edilberto

last: Bermudez

first: Darol

last: Dodd

first: Gabrielle

last: Wilson

first: Jerry

last: Campbell

first: Bruce

middle: C

last: Allen


title: Gene expression data from endothelial cells and leukocytes enriched from transplanted rat hearts

status: Public on Jul 06 2010

city: Oslo

first: Bjørg

last: Mikalsen

address: Sognsveien 20

department: Division of Pathology

country: Norway

institute: Oslo University Hospital

summary: Transcriptome analyses of organ transplants have until now usually focused on whole tissue samples containing activation profiles from different cell populations. Here, we enriched endothelial cells from rat cardiac allografts and isografts, establishing their activation profile at baseline and on day 2, 3 and 4 after transplantation. Modulated transcripts were assigned to three categories based on their regulation profile in allografts and isografts. Categories A and B contained the majority of transcripts and showed similar regulation in both graft types, appearing to represent responses to surgical trauma. By contrast, category C contained transcripts that were partly allograft-specific and to a large extent associated with interferon-gamma-responsiveness. Several transcripts were verified by immunohistochemical analysis of graft lesions, among them the matricellular protein periostin which was one of the most highly upregulated transcripts but has not been associated with transplantation previously. In conclusion, the majority of the differentially expressed genes in graft endothelial cells are affected by the transplantation procedure whereas relatively few are associated with allograft rejection.

overall_design: Endothelial cells were enriched from control/non-transplanted hearts and from allografts (DA to Lewis) and isografts (Lewis to Lewis) harvested at day 2, 3 and 4 after transplantation. Three biological replicates from each time point and graft type were analyzed (a total of 24 arrays). Leukocytes were enriched from allografts at day 2 (n=1), day 3 (n=2) and day 4 (n=1) after transplantation.

first: Bjarte

last: Fosby

first: Junbai

last: Wang

first: Clara

last: Hammarström

first: Hilde

last: Bjærke

first: Marlene

last: Lundström

first: Monika

last: Kasprzycka

first: Helge

last: Scott

first: Pål-Dag

last: Line

first: Guttorm

last: Haraldsen


title: Wistar rats with iron deficiency and repletion and Belgrade rats normally fed or fed iron in drinking water: villus

city: Shreveport

first: Kwo-yih

last: Yeh

state: LA

address: 1501 Kings Highway

department: Department of Medicine

institute: LSU Health Science Center

summary:
Gene expression along the crypt-villus (C-V) axis was analyzed using cryostat sectioning to isolate fractions representing the crypts (bottom) and villus tops (top). These fractions were used for analyzing gene expression in iron replete Wistar rats (++), iron deficient Wistar rats (low iron), and in iron deficient Wistar rats fed iron for 3 and 6 days (iron-fed).  Differences were observed between the crypts and villus tops in the expression of genes associated with Wnt and BNP signaling, cell proliferation and apoptosis, lipid and iron transport and metabolism.  Gene expression in villus crypts and tops was also compared between Wistar and Belgrade rats (bb) and Belgrade rats fed iron (iron-fed) particularly as related to iron absorption and metabolism to define the affects of the mutation in DMT1 in the Belgrade rat on the expression of genes related to iron absorption and metabolism and the response to iron feeding.
Keywords: iron stress response

overall_design:
A colony of Wistar strain rats (++) and Belgrade (bb) rats on a Wistar background maintained in our animal quarters was used for this study.  Twelve one-month old ++ rats were separated into 3 groups of four rats each. Group 1 rats (samples 1-8) were fed a normal diet and served as control animals.  Group 2 (samples 9-16) and Group 3 rats (samples 17-22) were fed a low iron diet and bled 2-3 ml every three days for 4 weeks and served as iron deficient rats (low-iron). Group 3 rats, of which one rat died during anesthesia while undergoing phlebotomy, were fed iron supplementation in drinking water (50 µM Ferric ammonium citrate) for the three days before sacrifice (iron-fed).  Rats were fasted overnight, killed by injection of pentobarbital sodium and a 1-cm duodenal segment 1 cm distal from the pylorus was cryostat sectioned at the right angle to the crypt-villus axis and the sections representing the top one-third of villus (top) and the bottom one-third of the villus were pooled for RNA isolation.
For the study of Belgrade rats, eleven bb rats were divided into 3 groups with the 4 rats in Group 1 (samples 23-30) maintained on a normal diet, the 4 rats in Group 2 (samples 31-38) fed iron for 3 days prior to sacrifice, and the 3 rats in Group 3 (samples 39-44) fed iron for 6 days prior to sacrifice.  All procedures for the bb rats were the same as described above for the ++ rats.  An additional ++ rat (samples 45-46) was similarly analyzed in a separate experiment.

first: Mary

first: Paula

last: Polk

first: Jonathan

last: Glass


title: Hepatic gene expression profile of rats fed an iron-deficient diet

status: Public on Apr 22 2010

city: Kanagawa

first: Asuka

last: Kamei

address: LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Project for development of food functionality assessment methods

institute: Kanagawa Academy of Science and technology

summary: Iron is an essential nutritional element; its deficiency in the body causes nutritional problems and a decrease in iron storage that can lead to anemia. The liver not only stores iron but is an important metabolic target as well. Dietary iron deficiency is associated with changes in the metabolism of nutrients such as lipids. However, to the best of our knowledge, a global analysis detailing the consequences of iron deficiency in the body has not yet been reported. We performed a comprehensive transcriptome analysis using DNA microarray technology to reveal the effects of iron deficiency on hepatic gene expression. Four-week-old rats were fed an iron-deficient diet or a control diet for 16 days. On day 17, the rats were sacrificed under anesthesia, and their livers were dissected for DNA microarray analysis. We identified 600 up-regulated and 500 down-regulated probe sets to characterize the iron-deficient diet group. The up-regulated probe sets contained genes for enzymes that are involved in cholesterol, amino acid, and glucose metabolisms, as well as in apoptosis. The down-regulated probe sets included genes for enzymes associated with lipid metabolism. Additionally, the 16-day iron-deficient diet induced anemia. Our gene expression analysis revealed that, as a result, cholesterol biosynthesis, gluconeogenesis, and apoptosis due to endoplasmic reticulum stress were accelerated, while fatty acid biosynthesis was suppressed by dietary iron deficiency. Our analysis also showed that cholesterol metabolism, including bile acid biosynthesis, was accelerated in the initial stages of cholesterol accumulation.

overall_design: Male 3-week-old Sprague Dawley rats were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room conditioned at 24 ± 1°C and 40 ± 5% humidity with a 12-h light-dark cycle (lights on at 08:00). The rats were given a control diet and water for 24 h ad libitum. Diets for rats were obtained from Research Diets, Inc. (New Brunswick, NJ, USA). The composition of the control diet was based on the AIN93G diet , except that cellulose was replaced by Avicel, since cellulose is an ingredient of variable iron content. The iron-deficient diet was prepared by removal of iron (ferric citrate) from the control diet. At day 8, rats were divided into two groups comprising animals of similar body weights. One group (n = 6) was fed the control diet and the other group (n = 7) was fed the iron-deficient diet (iron-deficient diet group). After iron-deficient diet feeding was started, blood hemoglobin levels were measured every two days. Blood samples for hemoglobin measurements were collected from the tail vein, and hemoglobin levels were measured by using the Wako Hemoglobin B test (Wako Pure Chemical Industries, Osaka, Japan). On day 12 of the iron-deficient diet treatment, diets were removed at 17:00, and feeding was conducted between 09:00 and 17:00 for another 4 days. This protocol was intended to synchronize the rats’ feeding behavior. On day 17 of the iron-deficient diet treatment, rats were fed for 1.5 h prior to sacrifice under anesthesia. Livers were then excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan). Blood hemoglobin level of rats fed an iron-deficient diet decreased significantly over the course of the feeding. On day 17, the hemoglobin level in the iron-deficient diet group was 42% of that of the control diet group (P < 0.01).

first: Yuki

last: Watanabe

first: Tomoko

last: Ishijima

first: Mariko

last: Uehara

first: Soichi

last: Arai

first: Hisanori

last: Kato

first: Yuji

last: Nakai

first: Keiko

last: Abe


title: Gene Profiling Male Fetal Rat Gubernaculum After Insulin-like 3 (Insl3) Exposure

status: Public on Jul 02 2010

city: Wilmington

first: Julia

last: Barthold

state: DE

address: 1600 Rockland Road

department: Urology

institute: Nemours/AI duPonst Hospital for Children

summary: Insl3 is a testis-derived hormone that induces growth and differentiation of the fetal gubernaculum.  The goal of this study was to identify genes showing altered expression in fetal gubernaculum following Insl3 exposure.

overall_design: The number of biological replicates processed initially were six controls, five 10 nM Insl3, and six 100 nM Insl3.  Following data collection, two 10 nM Insl3 samples (biological replicates 4 and 5) were deemed to be outliers based upon Principal Component Analysis and a relatively low yield of biotin-labeled cRNA.  The two outlier samples were not included in the statistical analysis.

first: Kamin

last: Johnson

first: Suzanne

middle: M

last: McCahan


status: Public on Apr 01 2010

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

summary:
Tissue Factor Pathway Inhibitor-2 is Induced by Fluid Shear Stress in Vascular Smooth Muscle Cells and Affects Cell Proliferation and Survival

Introduction: Vascular smooth muscle cells (SMCs) are exposed to fluid shear stress  (FSS) after interventional procedures such as balloon-angioplasty. Whereas the effects  of hemodynamic forces on endothelial cells are explored in detail, the influence of  FSS on smooth muscle cell function is poorly characterized. Here, we investigated the  effect of FSS on SMC gene expression and function.  Methods: Laminar FSS of arterial level (14 dynes/cm2) was applied to SMC cultures  for 24 h in a parallel-plate flow chamber. The effect of FSS on gene expression was  first screened with microarray technology and the results further verified by real time  (RT) PCR and immunoblotting. Protein expression was also studied in the rat carotid  artery after balloon-injury and DNA synthesis and apoptosis was examined in SMCs  in vitro.

Results: Microarrays identified tissue-pathway inhibitor-2 (TFPI-2) as the most  differentially expressed gene by FSS in cultured SMCs. The regulatory effect of FSS  on the expression of TFPI-2 was confirmed by RT-PCR and immunobloting  demonstrating a more than 400-fold increase in TFPI-2 expression in SMCs exposed  to FSS compared to static controls and a consistent upregulation at the protein level.  Functionally, SMC proliferation was decreased by FSS and recombinant TFPI-2 was  found to inhibit SMC proliferation and induce SMC apoptosis as indicated by  activation of caspase-3. In vivo, TFPI-2 expression was found to be up-regulated 5, 10  and 20 h after rat carotid balloon-injury and immunohistochemistry demonstrated  TFPI-2 protein in luminal SMCs exposed to FSS in rat carotid intimal hyperplasia 10  days after balloon-injury.  Conclusion: FSS strongly influence gene expression in cultured SMCs and induce  TFPI-2 expression, which is also expressed after rat carotid balloon injury in luminal  SMCs exposed to FSS. Functionally, TFPI-2 may play an important role in vessel wall  repair by regulating SMC proliferation and survival. Further studies are needed to  elucidate the mechanisms by which TFPI-2 control SMC function.

overall_design: 3 x 2 samples from a paired fluid shear stress experiment on smooth muscle cells.

first: Johan

last: Ekstrand

first: Anton

last: Razuvaev

first: Joy

last: Roy

first: Ulf

last: Hedin


title: Gene expression profiling in Chinese mininature pig liver tissue following clenbuterol administration

status: Public on Jul 01 2010

city: Beijing

first: qiuyue

last: liu

address: Yuanmingyuan, West Road 2, Beijing 100193, China.

department: Biochemistry and Molecular Biology

institute: China Agricultural University

summary: Clenbuterol-HCL can greatly reduce fat deposition and increase skeletal muscle growth at high dosages. In order to advance our understanding of the fundamental molecular mechanisms, Genechips were used to study the differential gene expression profiles of liver tissues among the pigs with/without Clenbuterol-HCL. Differentially expressed genes identified will be the candidates for further investigations on the molecular mechanisms involved in Clenbuterol-HCL of exerting repartition effects on adipose and skeletal muscle tissue.

overall_design:
4 Chinese mininature pigs were broken into 2 groups with each group having two full sib pigs with the same gender. For the following 8 weeks, test pigs were fed 25 mg/kg clenbuterol twice daily in their diets for 4 weeks and 50 mg/kg clenbuterol for another 4 weeks. The vehicle control
pigs were administered in the same manner except that no clenbuterol was added in their diets. The liver expression profiles of 4 pigs were analyzed using Porcine Genome GeneChip. After hybridization, genechips were washed and stained in the Affymetrix Fluidics Station 400 and
scanned by using Hewlett-Packard GeneArray Scanner G2500A.

first: jin

last: zhang

first: wei

last: guo

first: yan

first: yiqiang

last: zhao

first: xiaoxiang

last: hu

first: ning

last: li


title: Effects of Long-term Pioglitazone Treatment on Peripheral and Central Markers of Aging

status: Public on May 05 2010

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary:
Background: Thiazolidinediones (TZDs) activate peroxisome proliferator-activated receptor gamma (PPARgamma) and are used clinically to help restore peripheral insulin sensitivity in Type 2 diabetes (T2DM). Interestingly, long-term treatment of mouse models of Alzheimer’s disease (AD) with TZDs also has been shown to reduce several well-established brain biomarkers of AD including inflammation, oxidative stress and Abeta accumulation. While some of the TZD actions are becoming clear in AD models and may mediate their reported beneficial impact in AD patients, little is known about the functional consequences of TZDs in animal models of normal aging. Because aging is a common risk factor for both AD and T2DM, we investigated whether the TZD, pioglitazone could alter brain aging under non-pathological conditions.  Findings: The TZD pioglitazone (PIO) was incorporated into the diet to yield a final dose of approximately 2.3 mg/kg body weight/day. PIO reduced insulin levels irrespective of age. Interestingly, a significant reduction in the Ca2+-dependent afterhyperpolarization was seen in the aged animals with no significant change in LTP maintenance or learning and memory performance. Finally, a combination of microarray analyses on hippocampal tissue and serum-based multiplex cytokine assays revealed that age-dependent inflammatory changes in brain and periphery were not reversed by PIO.
Conclusions:  While current research efforts continue to address the underlying processes responsible for the progressive decline in cognitive function seen during aging, available medical treatments are still very limited. Our study, therefore, was aimed at elucidating potentially novel actions of TZDs in the aging brain. Using a clinically-relevant dose and delivery method, PIO had no detectable impact on several indices of brain aging and failed to alter both peripheral and central age-related increases in inflammatory signaling.

Keywords: hippocampus, rat, young or aged, control or pioglitazone-treated

overall_design: We used the F344 rat model of aging, and monitored behavioral, electrophysiological, and molecular variables to assess the effects of pioglitazone (PIO-Actos(R) a TZD) on several hippocampal biomarkers of aging associated with learning deficits. Starting at 3 months or 17 months of age, male rats were treated for 4-5 months with either a control or a PIO-containing diet. PIO was incorporated into the diet to yield a final dose of approximately 2.3 mg/kg body weight/day.

first: Jeremiah

last: Phelps

first: Tristano

last: Pancani

first: James

last: Searcy

first: Katie

last: Anderson

last: Gant

first: Jelena

last: Popovic

first: Margarita

last: Avdiushko

first: Donald

last: Cohen

first: Kuey-Chu

last: Chen

first: Nada

last: Porter

first: Olivier

last: Thibault


title: Cardiac Effects of Rosiglitazone in Male Wistar Rats

status: Public on Jun 25 2010

city: Watertown

first: Mary

last: Simcox

address: 500 Arsenal St

institute: Forma Therapeutics

summary: Rosiglitazone, a peroxisome proliferator-activated receptor g (PPARg) agonist of the thiazolidinedione class, is a major insulin-sensitizing drug widely used to treat type-2 diabetes.  Rosiglitazone causes myocardial hypertrophy in rodents and increases the risk of cardiac events in man.  To better characterize its cardiac effects, male Wistar rats were orally administered 0, 10 or 80 mg/kg/day rosiglitazone.

overall_design: Male Wistar rats were orally administered 0, 10 or 80 mg/kg/day rosiglitazone once per day for 14 days.  Samples were obtained 6, 24, 168 or 336 hours after the final treatment.

first: Igor

last: Mikaelian

first: Charu

last: Kanwal


title: Expression data from aged, calorically restricted rat hippocampal regions CA1, CA3, and DG

status: Public on May 25 2010

city: Jupiter

first: Zane

last: Zeier

state: FL

address: 130 Scripps Way

department: Neuroscience

institute: Scripps

summary: Aging is associated with a decline in hippocampal mediated learning and memory, a process wich can be ameliorated by dietary (caloric) restriction. We used Affymetrix gene expression analysis to monitor changes in three regions of the hippocampus (CA1, CA3, DG) of middle aged (18 months) and old (28 month) rats that were exposed to dietary restriction. Old rats were determined to be good performers (GP) or poor performers (PP) in behavioral tests to assess thier hippocampal function.

first: Thomas

last: Foster