title: Transcriptomic profile of mild exercise-enhanced adult hippocampal neurogenesis: Comparison with the effects of intense exercise

status: Public on Apr 05 2014

first: RANDEEP

last: RAKWAL

summary: Mild exercise (ME) with an intensity below the lactate threshold (LT) is sufficient to enhance hippocampal function, while intense exercise (IE) above the LT negates such benefits. However, the question as to why ME more effectively enhances hippocampal function than does IE remains to be clarified. Here, we investigated adult hippocampal neurogenesis (AHN) as a mechanism of ME-induced cognitive improvement, and comprehensively delineated the transcriptomic profile of the hippocampus, using a rat whole-genome microarray approach through comparison with IE. Immunohistochemical results showed that less intense exercise (ME) is better suited to improve AHN, especially in regards to the survival and maturation of newborn neurons. DNA microarray analysis revealed that ME regulated more genes than did IE (ME: 604 genes, IE: 415 genes), and only 44 genes were modified with both exercise intensities. The identified molecular components did not comprise well-known factors related to exercise-induced AHN, such as brain-derived neurotrophic factor (BDNF) and insulin-like growth factor 1 (IGF1), probably due to the timing of hippocampal tissue collection after the last training session and the technical feature of microarray. Rather, network analysis of the microarray data using Ingenuity Pathway Analysis algorithms revealed that the ME-influenced genes were principally related to lipid metabolism, protein synthesis and inflammatory response, which are recognized as associated with hippocampal neuroadaptations including AHN. In contrast, IE-influenced genes linked to immune response, a negative regulatory system of AHN and hippocampal function, were identified. Collectively, these results support our hypothesis that AHN could explain why ME enhances hippocampal function, and provide the ME-specific gene list that contain some potential regulators of this positive regulation. The list will become a foundation to elucidate the molecular pathway involving the ME-induced cognitive gain.

overall_design: Eleven-week-old male Wistar rats (220-270 g; SLC, Saitama, Japan) were housed in polycarbonate steel cages with a 12-h light/dark schedule (lights on at 7:00 a.m.) and given ad libitum access to food and water. A total of 98 rats were used in this study to assess the influence of exercise intensity on physiological states (training effect of skeletal muscle and stress level) (n= 22), MWM (n= 32), AHN (n= 22), and global gene expression profiles of hippocampal by microarray (n= 22). All animal care and experimental procedures were performed in accordance with protocols approved by the University of Tsukuba Animal Experiment Committee, based on the National Institute of Health (NIH) Guidelines for the Care and Use of Laboratory Animals (NIH publication, revised 1996). All efforts were made to minimize animal suffering and to reduce the number of animals used in this study. To adapt the rearing environment and remove any unintended stress effects, animals underwent a week of preliminary rearing to ambient conditions in groups housing conditions (2-3 rats/cage). After the preliminary rearing, the animals were randomized into three groups based on the LT of treadmill running: Sedentary control (CONT, rest on treadmill), Mild Exercise (ME, below LT, 15 m/min) or Intense Exercise (IE, above LT, 40 m/min). Exercise group was habituated to run on a treadmill (KN-73, Natsume Ltd., Tokyo, Japan) for 1 (for ME) or 4 (for IE) weeks. Within a given test period, rats were able to run on the above-mentioned running speeds. After this running habituation, rats were entered into the exercise training session for 6 weeks in total. The running duration was 60 min/day and frequency was 5 times/week. Exercise training was performed between 19:00 and 22:00 (during dark phase). Rat’s body weight and physical condition were monitored until the end of training. If rats could not perform well running on each determined speed and showed poor health, those were eliminated from the study. Based on the criteria, a total of 13 rats were eliminated (bad runner - 4 rats; poor health - 7 rats). Twenty-four or thirty-six hours after the last training, rats were processed to the next step. In the microarray group, the whole brain of each animal was rapidly removed, and hippocampus was separated on ice according to the method of Glowinski and Iversen (1966), with minor modifications. Hippocampi were immediately flash-frozen in liquid nitrogen. The deep-frozen hippocampi were transferred to a pre-chilled (in liquid nitrogen) mortar and pestle, and ground to a very fine powder with liquid nitrogen. The powdered samples were stored in aliquots at -80ºC till used for further analysis. Total RNA was extracted from each sample powder (~50 mg) using the QIAGEN RNeasy Mini Kit (QIAGEN, Maryland, USA). To verify the quality of this RNA, the yield and purity were determined spectrophotometrically (NanoPhotomaterTM, IMPLEN, Munich, Germany) and visually confirmed using formaldehyde gel electrophoresis. We used the sample with a ratio of spectrophotometric absorbance at 260 nm to that at 230 (A260/A230) or 280 nm (A260/A280) above 1.8. An equal amount of RNA (1000 ng) from the five rats, randomly picked up from each exercise group (n = 5), was pooled and used for microarray analysis. In this study, we performed three combinations of comparison analysis of gene expression change. First, we compared the difference between CONT and ME (combination 1) or IE (combination 2) to confirm the exercise-intensity-dependent gene expression change. Subsequently, we made a comparison of ME with IE (combination 3) to elucidate a ME-based difference of IE inducible gene. In all combinations, total RNA (1000 ng) was labeled with either Cy3 or Cy5 dye using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Inc., CA, USA). Fluorescently labeled targets of control as well as treated samples were hybridized to the same microarray slide with 60-mer probes (4 x 44K (41,090 gene probes), rat whole genome, Agilent). A flip labelling (dye-swap or reverse labelling with Cy3 and Cy5 dyes) procedure was followed to nullify the dye bias associated with unequal incorporation of the two Cy dyes into cDNA. Hybridization and wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray scanner. For the detection of significantly differentially expressed genes between control and exercise samples each slide image was processed by Agilent Feature Extraction software (version 9.5.3.1).

first: Koshiro

last: Inoue

first: Masahiro

last: Okamoto

first: Junko

last: Shibato

first: Min

last: Lee

first: Takashi

last: Matsui

first: Randeep

last: Rakwal

first: Hideaki


title: EB-mediated NPY expression and release

status: Public on Aug 02 2014

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

summary: Neuropeptide Y (NPY) is an endogenous modulator of neuronal activity by regulating GABA and glutamate release. Previously, we found that estradiol modulates NPY expression in the hippocampal dentate gyrus. Here we investigated which estrogen receptor type activation is required for the NPY expression. Further, we determined effects of estrogen receptor activation on NPY release. Finally, we determined the contribution of estrogen-mediated remodeling of the GABAergic and glutamatergic network in relation to changes in coupling with NPY in ovariectomized rats. We found that activation of either estrogen receptor type increases NPY expression as well as NPY release in the dentate gyrus. We also found that compared to OVX rats, estrogen replacement increases the likeness of synergistic/antagonistic coupling between the NPY and GABAergic synapse genes while the glutamatergic synapse genes are less likely coupled with NPY. The data together suggest that estrogen plays a critical role in regulation of activity of the NPY system and its coupling to GABAergic and glutamatergic synapses in female rat dentate gyrus.

overall_design: Two-conditions (E = beta-estradiol replacement vs O = oil) experiment. Biological replicates: 4E, 4O.

first: Jana

last: Velíšková

first: Galyna

last: Sidyelyeva

middle: A

first: Sanda

first: Tamar

last: Chachua

first: Libor

last: Velíšek


title: Carbohydrates Regulate Virulence Gene Expression in Streptococcus suis

status: Public on Mar 18 2014

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

summary: Streptococcus suis is a major pig pathogen as well as an emerging zoonotic pathogen. Previous work has demonstrated that the S. suis extracellular amylopullulanase enzyme (ApuA) that degrades {alpha}-glucans also functions as an adhesin for porcine epithelial cells. To identify the mechanisms linking carbohydrate metabolism and virulence, we first compared the transcriptome of S. suis in minimal medium supplemented with glucose to minimal medium containing a complex carbohydrate pullulan as a carbon source. The relative expression of eighteen virulence genes including suilysin and apuA was increased during growth in presence of pullulan, compared to growth in glucose. Increased virulence potential of S. suis grown in pullulan was demonstrated using hemolytic assays and increased adhesion and invasion of porcine epithelial cells in vitro. A metabolic map of S. suis was generated and combined with transcriptome data to visualize the metabolic adaption of S. suis during adhesion and invasion of the porcine epithelial cells representing an in vitro model of infection. The role of carbon catabolite control in virulence gene regulation was investigated and the molecular mechanism of transcriptional regulation was elucidated for apuA. We demonstrate that relief of CcpA repression is a crucial transcriptional control mechanism linking carbohydrate mechanism and virulence. The model for the transcriptional regulation of two important virulence factors apuA and suilysin was verified by qPCR analysis of gene expression in S. suis recovered from the organs and blood of infected pigs.

overall_design: Four-condition experiment (bacteria grown in THB or in CM supplemented with three different carbon sources), at two different timepoints (early exponential or late exponential growth phase). One replicate per array.

first: Maria

middle: L

last: Ferrando

first: Rosaria

last: Piga

first: Roger

last: Bongers

first: Michiel

last: Wels


title: Rat Life Cycle (RLC) Heart Gene Expression Data

status: Public on Sep 30 2014

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research

summary: Cardiovascular disease (CVD) is the leading cause of mortality, with sex and age being strong risk factors. Mitochondria are vital for normal cardiac function, and regulation of mitochondrial structure and function may impact susceptibility to CVD.  We analyzed the basal expression levels of mitochondria-related genes in the hearts of male and female untreated control rats at different ages to identify potential role of mitochondria in differential susceptibility to CVD between the sexes.

overall_design: Hearts from 5 male and 5 female rats at three different ages (young (8-week), adult (21-week), and old (78-week)) were used for investigation of sex-related differences in expression levels of genes.  At each age, rats were humanely euthanized by CO2 asphyxiation and whole hearts were removed quickly, flash frozen in liquid nitrogen, and stored at -80˚C until further investigation.  The frozen hearts were individually ground into powder in liquid nitrogen using a mortar and pestle chilled on dry ice.  Total RNAs were extracted from heart tissue powder and gene expression was measured using Agilent Rat Whole Genome Microarrays (4 x 44k format; Agilent Technologies, Inc.).

first: Tao

last: Han


title: Analyzing the hippocampal gene network to determine the effects of coral calcium hydride on antioxidant ability in rat brain

status: Public on Dec 31 2013

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

summary: In our previous study, we reported that a diet rich in antioxidants such as coral calcium hydride (CCH) increased the endogenous antioxidant ability in the hippocampus of rats. We conducted this study to test the hypothesis that diet supplementation with CCH would change the gene expression in rats and to understand how CCH enhances antioxidant ability. We used a DNA array to compare the expression levels in the hippocampus of rats fed with CCH for 2 weeks with those of rats fed a normal diet. Immune response-related genes were down-regulated, while nuclear respiratory factor 2 and aldehyde dehydrogenase 3A were up-regulated. Our findings about the changes in the mRNA levels of these genes well explain the physiological finding of enhanced antioxidant ability in rat brain.

overall_design: CCH was obtained from ICB, Ltd., Sendai, Japan, and coral calcium (CC) was purchased from Coralbio, Okinawa, Japan.  Male Wistar rats were acquired from Kyudo, Co., Ltd. and maintained at the Experimental Animal Center of the University of Miyazaki at a controlled ambient temperature of 23 ± 1 °C and 50 ± 10% relative humidity. The Committee for Ethics on Animal Experiments, Faculty of Medicine, University of Miyazaki, Japan, reviewed and approved the experimental design.   Six-week-old male Wistar rats (n = 8) were assigned to 2 groups: standard diet-fed group (CE-2, Clea Japan, Inc., Tokyo, Japan) and CCH-fed group. The CCH diet was standard CE-2 feed supplemented with 0.1% CCH powder. Inhibition of accelerated aging and an increase in the in vivo antioxidant ability was observed in SAM/P-8 mice fed a diet supplemented with 0.1% CCH. In accordance with these reports, the CCH concentration used in our study was set at 0.1%.The animals were killed by cervical dislocation at the age of 8 weeks. They were decapitated and the hippocampi were removed and rapidly frozen in liquid nitrogen. The hippocampi were then homogenized with a conventional rotor-stator homogenizer. Total RNA was then extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA).

first: Yuto

last: Ueda

first: Taneaki

last: Oikawa


title: Time dependent expression profiles of mRNAs in rat milk

status: Public on Feb 18 2014

city: Zama-City

first: Hirohisa

last: Izumi

state: Kanagawa-Pref.

address: 1-83, 5-Chome, Higashihara

department: Nutrition Research Department

institute: Morinaga Milk Industry Co., Ltd.

summary: We have reported that mRNAs are present in bovine milk. But, it is unknown the roles of milk mRNAs. To clarify the roles of milk mRNAs, experimental animal such as rat study would be needed. However, it is unclear whether rat milk also contains mRNAs. Thus, we have employed microarray to show that rat milk also contains mRNAs.

overall_design: Milk samples were obtained at day 2, 9, and 16 postpartum from 3 rats. And serum samples were obtained from dam rats (n=3) at day 21 postpartum.


title: Hepatic Gene Expression in woodrats on Creosote and Juniper Diets with distinct Plant Secondary Compounds

status: Public on Oct 18 2013

city: Banyuls sur Mer

first: Elodie

last: Magnanou

address: Avenue du Fontaulé

department: BIOM Biologie Intégrative des Organismes Marins CNRS  - UPMC

country: France

institute: Laboratoire Arago

summary: Herbivores are predicted to evolve appropriate mechanisms to process the plant secondary compounds (PSCs) in their diet and these mechanisms are likely specific to particular suites of PSCs. Changes in diet composition over evolutionary time should select for appropriate alterations in metabolism of the more recent dietary components. We investigated differences in gene expression profiles in the liver with respect to prior ecological and evolutionary experience with PSCs in the desert woodrat, Neotoma lepida. This woodrat species has populations in the Mojave Desert that have switched from feeding on juniper to feeding on creosote at the end of the Holocene as well as populations in the Great Basin Desert that still feed on the ancestral diet of juniper and are naïve to creosote. Juniper and creosote have notable differences in secondary chemistry. Woodrats from the Mojave and Great Basin Deserts were subjected to a fully crossed feeding trial on diets of juniper and creosote after which their livers were analyzed for gene expression. Hybridization of hepatic mRNAs to laboratory rat microarrays resulted in a total of 20,031 genes that met quality control standards. We analyzed differences in large-scale patterns of liver gene expression with respect to GO term enrichment. Diet had a larger effect on gene expression than population membership. However, woodrats with no prior evolutionary experience to the diet upregulated relatively far more genes compared to animals with prior exposure to that diet. This pattern may be the result of naive animal’s attempting to mitigate physiological damage caused by novel PSCs.

overall_design: fully crossed design, two by two feeding trial with two populations of the desert woodrat (Great Basin and Mojave) fed the two diets of juniper and creosote bush

middle: D

last: Dearing


title: Intracranial self-stimulation regulates gene expression in rat hippocampus

status: Public on Sep 03 2013

city: Girona

first: Gemma

last: Huguet

address: Campus de Montilivi

country: Spain

institute: Universitat de Girona

summary:
Transcriptional profiling of rat hippocampus 4.5h post intracranial self-stimulation (ICSS) show that this treatment, which improves learning and memory processes in a variety of paradigms of implicit and explicit memory, regulates gene expression of genes related to cAMP-mediated signaling and regulation of synaptic plasticity, among others.

Rats were implanted with a monopolar stainless steel electrode aimed at the lateral hypothalamus in the right hemisphere. Hippocampal gene expression was analyzed 4.5h post treatment comparing rats subjected to acute self-stimulation (2500 stimulation trains; ICSS group) with sham-operated rats (with electrode placement but placed in the ICSS without stimulation during 40 min.; Sham group).

overall_design: Two-condition experiment, ICSS and Sham. Every sample consisted of pooled hippocampi ipsilateral to the electrode from three rats. Slices between Bregma levels -2 and -4 were used for dissections of the hippocampi.  Common reference design, comparing every condition versus a brain pooled tissue consisting of pooled hippocampal tissue ipsilateral to the electrode of sham-operated (n=3) and stimulated (n=3) rats. Biological replicates: 4 DBS and 4 sham.  One replicate per array.

first: Elisabet

last: Kádár

first: Laura

last: Aldavert-Vera

first: Pilar

last: Segura-Torres


title: Global gene expression pattern difference between the high density and the regular density cultured rat bone marrow cells

status: Public on Aug 03 2013

city: Shanghai

first: Yang

last: Lu

address: 639 Zhi Zao Ju Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

summary: In vitro expansion of endothelial progenitor cells (EPCs) remains a challenge in stem cell research and its application. We hypothesize that high density culture is able to expansion EPCs from bone marrow by mimicking cell-cell interactions of the bone marrow niche. To test the hypothesis, rat bone marrow cells were either cultured in high density by seeding or cultured in regular density. Flow cytometric analyses of the cells cultured for 15 days showed that high density cells exhibited smaller cell size and higher levels of marker expression related to EPCs when compared to regular density cultured cells. Global gene expression pattern difference between the high density and the regular density cultured cells was analyzed by a microarray assay.

overall_design: Gene expression in rat bone marrow cells was measured at 15 days after high density culture or regular density cluture.  2 independent experiments were performed using different high density(HD) cultured cells for each experiment and bone marrow cells in regular density(RD) were used as a control.

first: Wen-Jie

last: Zhang


title: Time dependent expression profiles of mRNAs and microRNAs in rat milk

type:
Expression profiling by array
Non-coding RNA profiling by array

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

overall_design: Refer to individual Series


title: A Global Approach to Dissect Palmitate-induced Impairment of Hepatic Glucose Production

status: Public on Nov 08 2013

city: Geelong

first: Bradley

last: Hayward

state: VIC

address: Pigdons Road

country: Australia

institute: Deakin University

summary: Obesity-induced insulin resistance of the liver is characterised by increased gluconeogenesis, which contributes to elevated blood glucose levels in individuals with type 2 diabetes. Research into how fatty acids induce insulin resistance has commonly focused on the induction of insulin resistance. We hypothesise that by shifting focus to the reversal of an insulin resistant phenotype, novel insights can be made into the mechanisms by which insulin resistance can be overcome. Using global gene and lipid expression profiling, we aimed to identify biological pathways altered in parallel with restoration of palmitate-induced deregulation of glucose production using metformin and sodium salicylate.  FAO hepatoma cells were treated with palmitate (0.075mM, 48h) with or without metformin (0.25mM) and sodium salicylate (2mM) in the final 24h of palmitate treatment, and effects on glucose production were determined. Microarray followed by gene set enrichment analysis was performed to investigate pathway regulation. A lipidomic analysis (HPLC-MS/MS) and measurement of secreted bile acids and cholesterol were performed.  Reversal of palmitate-induced impairment of glucose production by metformin and sodium salicylate was characterised by down-regulated expression of metabolic pathways regulating acetyl-CoA to cholesterol and bile acid biosynthesis. Total levels of intracellular and secreted cholesterol and bile acids were not different between impaired and restored glucose production. Total intracellular levels of diacylgycerol, triacylglycerol and cholesterol esters increased with palmitate (impaired glucose production), however, these were not further altered with metformin and sodium salicylate (restored glucose production). Six individual lipid species containing 18:0 and 18:1 side-chains were reduced by metformin and sodium salicylate.  Widespread lipid metabolism changes induced by the reversal of palmitate-induced deregulation of glucose production with metformin and sodium salicylate were identified. While cholesterol and bile acid levels remained unchanged, the flux through these pathways may in part explain these findings. The identification of lipid species containing 18:0 and 18:1 side chains being regulated alongside changes to glucose production may indicate potential mediators of glucose production and insulin resistance.

overall_design: Three-condition experiment, Vehicle, Palmitate (PA) and Palmitate (PA) + Metformin (Met) + Sodium Sailcylate (NaS) with biological replicates: 8 Vehicle, 20 PA and 20 PA+Met+NaS , independently grown and harvested. One replicate per array.

first: Brad

first: Andrew

last: Sanigorski

first: Kelly

last: Windmill

first: Juan-Carlos

last: Molero

first: Nicky

last: Konstantopoulos

first: Carsten

last: Schmitz-Peiffer

first: Peter

last: Meikle

first: Ken

middle: R

last: Walder


title: Balloon injury-induced gene expression in common carotid arteries of wistar rat

status: Public on Jun 29 2013

city: Xuzhou

first: Dong

middle: ye

last: Li

state: Jiangsu

address: No. 84 West Huaihai Road

department: Institute of Cardiovascular Disease Research

institute: Xuzhou Medical College

summary: The whole rat genome microarray expression profiling of carotid artery specimen was emplyed to identify the gene expression profile before and after balloon injury. In our study, the neointimal formation of carotid arteries was apparent at day 7 and markedly increased at day 21 after balloon injury. In order to investigate the underlying mechanism of neointimal formationin in injured carotid arteries, all genes involved in signaling pathways whose expression was altered 2-fold in injured carotid arteries at day 7 and day 21 as compared to uninjured arteries were filtered out. Expression of four genes (TLR4, IRAK1, IκBα, IL-1β) from TLR signaling pathway was quantified in the same RNA samples by quantitative real-time PCR, conforming that TLR signaling pathway participated in neointimal formation of carotid arteries after balloon injury.

overall_design: Balloon injury-induced gene expression in wistar rat was measured at day 7 and day 21 after balloon injury as compared with uninjured arteries. Two independent experiments were performed at each time (uninjured, day 7 or day 21) using different wistar rats for each experiment.

first: Shi

last: Bai

middle: Y

first: Zhong

middle: M

last: Zhou

first: Tong

last: Xu

first: Xiao

middle: T

first: Yi

last: Wang

first: Jing

middle: S

last: Guo

first: Tao

first: Yan

middle: B


title: Hippocampal gene expression profiling in a rat model of posttraumatic epilepsy reveals temporal upregulation of lipid metabolism-related genes

status: Public on Dec 31 2012

first: Toshio

last: Kojima

summary: Traumatic brain injury occasionally causes posttraumatic epilepsy. To elucidate the molecular events responsible for posttraumatic epilepsy, we established a rodent model that involved the injection of microliter quantities of FeCl3 solution into the amygdalar nuclear complex. We previously compared hippocampal gene expression profiles in the traumatic epilepsy model and normal rats at 5 days after brain injury (acute phase) and observed the role of inflammation. In this study, we focused on later stages of epileptogenesis. We compared gene expression profiles at 5, 15 (sub-chronic phase), and 30 days (chronic phase) after brain injury to identify temporal changes in molecular networks involved in epileptogenesis. A total of 81 genes was significantly (at least 2-fold) up- or downregulated over the course of disease progression. We found that genes related to lipid metabolism, namely, Apoa1, Gh, Mc4r, Oprk1, and Pdk4, were temporarily upregulated in the sub-chronic phase. Changes in lipid metabolism regulation might be related to seizure propagation during epileptogenesis. This temporal description of hippocampal gene expression profiles throughout epileptogenesis provides clues to potential markers of disease phases and new therapeutic targets.

overall_design: We employed amygdalar FeCl3 injection to induce chronic, recurrent limbic-type partial seizures with spontaneous secondarily generalized seizures in rats . Sixteen male Wistar rats were kept in hanging cages with unlimited access to food and water and 12-h light-dark cycles. Surgical procedures were conducted following anesthesia with intraperitoneal (i.p.) sodium pentobarbital injections (37.5 mg/kg) at 5 weeks of age. Stereotaxic coordinates were determined with the rat brain atlas. The incisor bar was set 3.3 mm below the interaural line. While under anesthesia, a polyethylene tube containing a stylet to serve as an external guide cannula (1.09-mm outer diameter (o.d.), 0.55-mm inner diameter (i.d.), 2.5 cm in length) was stereotaxically implanted and anchored to the skull with miniature screws and dental cement. The cannula was fixed 5.6 mm anterior and 4.8 mm to the right of the lambda and 8.5 mm below the surface of the skull, positioning it at the right amygdaloid body. Randomly selected rats for in vivo microdialysis to estimate redox had guide cannula placed but were prepared without dental cement on the skull where the microdialysis guide cannula was to be placed. Five days later, the stylet was replaced with an internal delivery cannula (0.5 mm o.d., 0.25 mm i.d.). FeCl3 was dissolved in saline solution (100 mM, pH 2.2). FeCl3 solution (1.0 μl) was injected through the inner cannula by means of a microinfusion pump (EP-60; Eicom, Tokyo, Japan) set at a rate of 1.0 μl/min (Fe group; n = 12). The external guide cannula was used for electroencephalogram (EEG) recording with an electroencephalograph (type 1A63; SAN-EI, Tokyo, Japan). Rats in the control group (n = 4) were each injected with 1.0 μl saline (pH 2.2). Both EEG and behavior were observed for at least 6 h after the injection. While we did not measure the rate or frequency of seizures, we did confirm that the animals had recurrent seizures. These observations and the acute recording confirmed the accuracy of the amygdalar injection. No seizure activity was observed in control group rats.  Animals in the control group were sacrificed by cervical dislocation 15 days after amygdalar injection. Animals in the Fe group were subdivided into 3 groups and were sacrificed at 5 (acute phase), 15 (sub-chronic phase of injury), and 30 days (chronic phase of injury) after amygdalar injection. The stages of disease development were categorized according to the EEGs of the model rats; within 5 days after amygdalar injection, epileptiform discharges were recorded in the contralateral and ipsilateral amygdalae; by 15 days after injection, interictal spike discharges were more consistently observed in the contralateral uninjected amygdala; at 30 days after injection bilateral interictal spike discharges continued to be observed. After sacrifice, the right hippocampi were immediately removed and placed in ice-cold phosphate-buffered saline and homogenized (Polytron PT 3000; Brinkmann Instruments, Inc., Westbury, NY, USA) for RNA extraction.

first: Yuto

last: Ueda

first: Aya

last: Kitamoto

first: L

middle: J

last: Willmore


title: Striatal molecular signature of subchronic subthalamic nucleus high frequency stimulation in parkinsonian rat

status: Public on May 01 2013

city: MARSEILLE

first: Sylviane

last: Lortet

address: parc scientifique de Luminy

institute: IBDML

summary:
This study addresses the molecular mechanisms underlying the action of subthalamic nucleus high frequency stimulation (STN-HFS) in the treatment of Parkinson’s disease and its interaction with levoDOPA (L-DOPA), focusing on the striatum. The objectives were 1) to identify the molecular signature of STN-HFS action at striatal level, associated with its efficient antiparkinsonian action, and 2) to investigate the molecular substrates of the interaction between the two treatments in order to evidence possible genes involved in dyskinesia.
Striatal gene expression profile was assessed in rats with nigral DOPAmine neuron lesion, either  treated or not, using agilent microarrays and qPCR verification. The treatments consisted in anti-akinetic STN-HFS (5 days), chronic L-DOPA treatment inducing  dyskinesia (LIDs) or the combination of the two treatments that exacerbated LIDs. STN-HFS modulated 71 genes with functional or biochemical annotation, including  genes sharing the GO terms regulation of growth, regulation of apoptosis, extracellular region. Ttr, Igf2, Sostdc1 and Nr4A3 (Nor-1), are among the 5 genes  showing the highest specific upregulation. Down-regulated genes include Prkcd, Sirt5 and Bbc3. These results show that genes involved in neuroprotection and/or  neurogenesis are key components of STN-HFS action in the striatum. STN-HFS and LDOPA treatment share very few common gene regulation features suggesting that the  molecular substrates underlying their striatal action are mostly different. In addition to genes already reported to be associated with LIDs (Pdyn, Trh, Grm4/mGlu4,  Cnr1/CB1), the comparison between DOPA and DOPA/STN-HFS identifies immunity-related genes: C1s, Rt1-Da and Irf7a, as potential players in L-DOPA side effects.

overall_design: Total RNA was extracted from striatal tissue from four groups of 3 animals bearing 6-hydroxyDOPAmine (6-OHDA)-induced lesion of the nigrostriatal DA pathway: lesion alone without any subsequent treatment (L), L-DOPA treatment for 19 days (D), STN-HFS for 5 days (S) and combination of L-DOPA and STN-HFS (DS).

first: Emilie

last: Lacombe

first: Nicolas

last: Boulanger

first: Pascal

last: Rihet

first: Catherine

last: Nguyen

first: Lydia

last: Kerkerian-Le Goff

last: Salin


title: Profiling of circadian genes expressed in the uterus endometrial stromal cells of pregnant rats as revealed by DNA microarray coupled with RNA interference

status: Public on Jul 23 2013

city: Fukuoka

first: MASA-AKI

last: HATTORI

address: 6-10-1, Hakozaki, Higashi-ku

department: Graduate School of Agriculture

institute: Kyushu University

summary:
The peripheral circadian oscillator plays an essential role in synchronizing local physiology to operate in a circadian manner via regulation of the expression of clock-controlled genes. In the murine uterus, the endometrial stromal cells undergo proliferation and differentiation into decidual cells in response to ovarian steroids and blastocyst implantation at the early stage of pregnancy. The circadian clock genes are attenuated in the decidualizing cells only 2 days after implantation. The present study aimed to evaluate the circadian rhythms of clock genes and clock-controlled genes expressed in the rat uterus endometrial stromal cells (UESCs) during the stage of implantation. The real-time monitoring system of Per2 promoter activity was employed to precisely evaluate the generation of circadian rhythms in the UESCs prepared from transgenic rats constructed with mouse Per2 promoter-destabilized luciferase reporter gene (Per2-dLuc). During monitoring Per2-dLuc oscillation after synchronization with dexamethasone, total RNA was isolated from the cultured UESCs at four-time points (6-h interval) in the first to second phases and cDNA was synthesized. cRNA was synthesized from the double strand cDNA and hybridized on a DNA microarray. RT-qPCR was performed to confirm the expression of core clock genes revealed by DNA microarray analysis. Several clock genes such as Bmal1, Rev-erbα, and Per2 displayed significant rhythms. Of 12,252 genes showing significantly expression, 7,235 genes displayed significant alterations (p < 0.05). These genes were related to growth factors, transcription factors, receptors, channels, and enzymes. Some candidates as clock-controlled genes were evaluated by using RNA interference to Bmal1 mRNA. Down-regulation of Igf1 gene expression was observed by Bmal1 silencing, whereas the expression of Inhβa, Fas, and Caspase3 were significantly increased. These results indicate that clock-controlled genes are up- or down-regulated in rat UESCs during the stage of decidualization. DNA microarray analysis coupled with RNA interference will be helpful to understand the physiological roles of some oscillating genes in blastocyst implantation and placenta formation.
The circadian clock positively or negatively regulates the expression of clock-controlled genes, including growth factors and apoptosis-related factors.

overall_design: To search the clock-controlled genes expressed during the period of implantation, we analyzed the clock genes and clock-controlled genes expressed in cultured uterus endometrial stromal cells prepared from pregnant rats at the stage of implantation using DNA microarray technology. We used transgenic rats constructed with mouse Per2 promoter-destabilized luciferase (Per2-dLuc) reporter gene to precisely adjust the time of gene expression. In addition, several genes of significantly expressed genes including growth factor genes and apoptosis-related genes were analyzed using RNA interference to Bmal1 mRNA whether these were controlled under circadian clockwork.

first: Hirotaka

last: Tasaki

first: Lijia

last: Zhao

first: Keishiro

last: Isayama

first: Huatao

last: Chen

first: Nobuhiko

last: Yamauchi

first: Yasufumi

last: Shigeyoshi

first: Seiichi

last: Hashimoto

first: Masa-aki

last: Hattori


title: In vitro differentiation of rat multipotent adult porgenitor cells to smooth muscle like cells

status: Public on Oct 09 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: The aim of the study was to characterize the molecular mechanism involved in TGF-ß mediated smooth muscle formation in vitro. We employed rat bone marrow derived Oct4 expressing clones of multipotent adult progenitor cells (rMAPC). We subjected these cells to differentiation towards smooth muscle cell as previously reported using TGF-ß1. The differentiation process reuires 6 days with media change every 2 days followed by RNA harvest. RNA was isolated using commercially available kits (Qiagen RNA easy micro kit). RNA integrity and quality was assessed prior to labeling and hybridization. As a control RNA from rat aortic smooth muscle cells was commercially obtained.

overall_design: Two biological replicate clones of rMAPC cells were used for the differentiation to smooth muscle like cells. The RNA was harvested at days 0, 2, 4 and 6 in triplicates. The RNA from primary smooth muscle cells was commercially obtained and was used in duplicates as control.

first: Abhishek

last: Sohni

first: Francesca

last: Mulas

first: Fulvia

last: Ferrazzi

first: Aernout

last: Luttun

first: Riccardo

last: Bellazzi

first: Danny

last: Huylebroeck

first: Stephen

middle: C

last: Ekker

last: Verfaillie


title: PAX8 transcriptional profiling in rat PCCL3 cells

status: Public on Jun 28 2012

city: Madrid

first: Pilar

last: Santisteban

state: Madrid

address: Arturo Duperier 4

department: Physiopathology of the Endocrine and Nervous System

institute: Biomedical Research Institute-CSIC

summary: PAX8 transcriptional profiling of rat PCCL3 cells comparing wild type cells with PAX8 silenced cells and scramble treated with PAX8 silenced cells

overall_design: Three-condition experiment, Wild type vs. PAX silenced cells. Biological replicates: 4 replicates, 4 dye-swap. AND scramble treated vs PAX8 silenced cells. Biological replicates: 4 replicates, 4 dye-swap.

first: Sergio

last: Ruiz-Llorente

first: Enrique

last: Carrillo-de Santa Pau

first: C

last: Montero-Conde

first: Gonzalo

last: Gomez-Lopez

first: J

last: Fagin

first: Alfonso

last: Valencia

first: David

middle: G

last: Pisano


title: Effects of microcystis on Daphnia pulex

status: Public on Jul 27 2012

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

institute: Ghent University

summary: Although cyanobacteria produce a wide range of natural toxins that impact aquatic organisms, food webs and water quality, the mechanisms of toxicity are still insufficiently understood. Here, we implemented a whole-genome expression microarray to identify pathways, gene networks and paralogous gene families responsive to Microcystis stress in Daphnia pulex. Therefore, neonates of a sensitive isolate were given a diet contaminated with Microcystis to contrast with those given a control diet for sixteen days. The microarray revealed 2247 differentially expressed (DE) genes (7.6% of the array) in response to Microcystis, of which 17% are lineage specific and 49% are gene duplicates (paralogs). We identified four pathways/gene networks and eight paralogous gene families affected by Microcystis.  Differential regulation of the ribosome including 3 paralogous gene families encoding 40S, 60S and mitochondrial ribosomal proteins, suggests an impact of Microcystis on protein synthesis of Daphnia. In addition, differential regulation of the oxidative phosphorylation pathway, including the NADH ubquinone oxidoreductase gene family, and trypsin paralogous gene family, major component of the digestive system in Daphnia, could explain why fitness is reduced based on energy budget considerations. For others (.e.g Neurexin IV), a link with fitness remains to be established.

overall_design: RNA was isolated from three independent and concurrently replicated exposures of Daphnia to control and Microcystis conditions. RNA was hybridized to 4 microarrays using a standard, control vs. treated design that included dye swaps.

first: Dieter

middle: I

last: De Coninck

last: Glaholt

first: John

middle: K

last: Colbourne

first: Colin

last: Janssen

first: Joseph

last: Shaw

first: Karel

last: De Schamphelaere


title: Global gene expression profiling in early-stage polycystic kidney disease in the Han:SPRD Cy rat identifies a role for RXR signaling

status: Public on Dec 09 2011

city: Toyoake

first: Kugita

last: Masanori

state: Aichi

address: kutsukake-cho Denngakugakubo 1-98

department: Center of Animal Models for Human Diseases

institute: Fujita Health University

summary: Han:SPRD Cy is a spontaneous rat model of polycystic kidney disease (PKD) caused by a missense mutation in Pkdr1.  Cystogenesis in this model is not clearly understood.  In the current study, we performed global gene expression profiling in early-stage PKD cyst development in Cy/Cy kidneys and normal (+/+) kidneys, at 3 and 7 days of postnatal age.  Expression profiles were determined by microarray analysis, followed by validation with real-time RT-PCR.  Genes were selected with over 1.5 fold expression changes compared with age-matched +/+ kidneys for canonical pathway analysis.  We found 9 pathways in common between 3-day and 7-day Cy/Cy kidneys.  Three significantly changed pathways were designated 'VDR/RXR Activation,' 'LPS/IL-1 Mediated Inhibition of RXR Function,' and 'LXR/RXR Activation'.  These results suggest that RXR mediated signaling is significantly altered in developing kidneys with mutated Pkdr1.  In gene ontology analysis, the functions of these RXR-related genes were found to be involved in regulating cell proliferation and organ morphogenesis.  With real-time RT-PCR analysis, the up-regulation of Ptx2, Alox15b, OSP and PCNA, major markers of cell proliferation associated with the RXR pathway, were confirmed in 3- and 7-day Cy/Cy kidneys compared with 3-day +/+ kidneys.  The increased RXR protein was observed both in nuclei and cytoplasm of cystic epithelial cells in early-stage Cy/Cy kidneys, and the RXR-positive cells were strongly positive for PCNA staining.  Taken together, cell proliferation and organ morphogenesis signals transduced by RXR mediated pathways may have important roles for cystogenesis in early-stage PKD in this Pkdr1-mutated Cy rat.

overall_design: Rats for microarray assay were anesthetized at 3 and 7 days of age with sodium pentobarbital (Schering-Plough Corporation, Kenilworth, NJ, USA), and both kidneys were removed rapidly, causing exsanguination. The left kidney was frozen in liquid nitrogen for RNA extraction. RNA was extracted from kidneys of 3- and 7-day-old rats using a monophasic solution of phenol/guanidine isothiocyanate and TRIzol® reagent (Invitrogen Co., Carlsbad, CA, USA) in accordance with their manual, and the samples were incubated with RNase-free DNase I (Ambion, TX, USA).  The quality and concentration of each sample was confirmed by spectrophotometry (NanoDropTM ND-1000; Asahi glass Co. Ltd., Tokyo, Japan).   Genotypes were determined using polymerase chain reaction-restriction fragment length polymorphism.  200 ng aliquots of total RNA obtained from kidneys of 3- or 7-day-old rats were labeled using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer’s instructions.  The pooled renal RNAs of +/+, Cy/+ or Cy/Cy rats were labeled with the Cy5-fluorescence dye, and the pooled renal RNAs of +/+ rats adopted as the template control were labeled with the Cy3-fluorescence dye.  After determination of labeling efficiency, 1 μg aliquots of Cy3-labeled RNA obtained from age-matched +/+ kidneys and Cy5-labeled RNA from +/+, Cy/+, or Cy/Cy kidneys were mixed and hybridized onto Agilent Rat Oligo Microarrays (product no. G4130A) according to the manufacturer’s hybridization protocol.  After washing, the microarray slides were examined with an Agilent microarray scanner and software (scanner model G2565BA).  Data analysis was performed with Agilent Feature Extraction software (version A.7.1.1) and Excel 2003 (Microsoft).

first: Masanori

last: Kugita

first: Kazuhiro

last: Nishii

first: Miwa

last: Morita

first: Daisuke

last: Yoshihara

first: Hiroe

last: Sugiyama

first: Kouji

last: Yamada

first: Tamio

last: Yamaguchi

first: Darren

middle: P

last: Wallace

first: James

last: Calvet

first: Hiroki

last: Kurahashi

first: Shizuko

last: Nagao


title: bf_vs_f-Comparative Arabidopsis Transcriptome -Sequencing

status: Public on Sep 10 2013

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary: cat-seq - bf_vs_f - A comparative assessment of the Arabidopsis sequencing approach High-throughput sequencing cDNA GAII or HiSeq2000 sequenceur (technology Solexa) and data on CATMA array hybridation (version 6). These different characteristics will be studied through the analysis of control samples but also samples from mutants in genes coding for cytosolic or nuclear PPR proteins - The two selected samples are the flower buds and leaves of Arabidopsis. Two organs known as the transcriptome is very different. This experience will serve as reference

overall_design: 2 dye-swap - organ comparison

first: Sandrine

last: Balzergue

first: Claire

last: Lurin

first: Marie-Laure

last: Martin-Magniette

first: Etienne

last: Delannoy

first: Eddy

last: Blondet


title: Impact of oral compost-extract administration on gene expression in the rat gastrointestinal tract

status: Public on Nov 02 2012

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: Oral administration of an extract of compost fermented with thermophiles to pigs reduces the incidence of stillbirth and promotes piglet growth. However, the mechanism by which compost extract modulates the physiological conditions of the animals remains largely unknown. Here, we investigate the effects of compost extract on the gene expression in the intestine of the rat as a mammalian model. Gene expression analyses of the intestine indicated that several immune-related genes were upregulated following compost exposure. Thus, thermophile-fermented compost can contain microbes and/or substances that activate the gut mucosal immune response in the rat.

overall_design: In Male Wistar rats aged 3 weeks, tap water was supplemented with 1.0% (v/v) compost extract for the experimental rats, whereas water only was given to the control rats. The rats received water ad libitum for 12 weeks. Fresh gut samples were collected from individual rats at the end of the feeding test and stored at -80°C. The intestine were separated from the gut and used as samples for the isolation of total RNA. otal RNA was then subjected to microarray experiments using the Whole Rat Genome (4x44k) Oligo Microarray (Agilent Technologies, Inc.)

first: Hirokuni

last: Miyamoto


title: Genome-wide DNA Microarray Unravels Rapid Changes in the Transcriptome of MK-801 treated Rat Brain

status: Public on Apr 25 2012

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary:
Background: N-Methyl-D-aspartate receptors (NMDAr), widely located around the central nervous system, are known to be involved in behavioral disorders. Dizocilpine (commonly referred to as MK-801) is a well known non-competitive NMDAr antagonist.
Methods: We treated rats with intraperitoneal injection [0.08 (low-dose) and 0.16 (high-dose) mg/kg] of MK-801. In one experiment, 40 min after NaCl (vehicle control) and MK-801 (0.08 mg/kg) injection, electrocorticogram (ECoG) signals were analyzed. In the second experiment, 40 min post-injection, the whole brain of each animal was rapidly removed and separated into amyglada, cerebral cortex, hippocampus, hypothalamus, midbrain and ventral striatum) on ice, followed by analysis using a 4x44K DNA microarray chip.
Results: Spectral analysis revealed that a single subcutaneous injection of MK-801 significantly and selectively augmented the power of spontaneous gamma and higher-frequency oscillations. The results from DNA microarray analysis of 4400 genes showed the largest number (up- and down- regulations) of gene expressions in the cerebral cortex (378), midbrain (376), hippocampus (375), ventral striatum (353), amygdala (301), and hypothalamus (201) under low-dose of MK-801. Under high-dose, ventral striatum (811) showed the largest number of gene expression changes. These genes represented...
Conclusions: Our results reveal that MK-801 triggered i) an increase in the power of gamma oscillations, and ii) simultaneously caused very early changes in gene expressions in the rat brain, representing a first such inventory of gene expression profiles in brain after acute MK-801 treatment.

overall_design: Nine male 10-weeks-old Wistar rats (300-350 g BW) were housed in acrylic cages (3/cage) at 24ºC and given access to tap water and laboratory chow ad libitum. The rats were divided into two groups, and each group rats received i.p. injection of 0.08 (low-dose) and 0.16 (high-dose) mg/kg of MK-801, respectively. Three rats were treated with saline as sham (vehicle control group) using the same method. After 40 min post-injection, the whole brain of each animal was rapidly removed and put on ice, and brain regions were separated according to the method of Glowinski and Iversen (1996), with minor modifications (Hirano et al., 2007).  Each brain region was placed in a 2 mL Eppendorf tube, quickly immersed in liquid nitrogen before being stored in -80ºC prior to further analysis. Each sample was immediately weighed, flash-frozen in liquid nitrogen and stored at -80ºC prior to further analysis. A rat 4 x 44K whole genome oligo DNA microarray chip (G4131F, Agilent Technologies, Palo Alto, CA, USA) was used for global gene expression analysis. The effects of MK-801 were examined in the 6 brain reagion, Ventral striatum, Cerebral cortex, Midbrain, Amygdala, Hippocampus, and Hypothalamus.

first: Yuka

last: Kobayashi

first: Sofya

last: Kulikova

first: Junko

last: Shibato

first: Randeep

last: Rakwal

first: Hiroyuki

last: Satoh

first: Didier

last: Pinault

first: Yoshinori

last: Masuo


title: MAPC culture condition supports the derivation of cells with nascent hypoblast features from bone marrow and blastocysts

status: Public on Jul 17 2012

first: Rekin's

last: Janky

summary: Rat Extraembryonic Endoderm Precursor (XEN-P) cells resemble the nascent hypoblast of the blastocyst. Here we show that rat Multipotent Adult Progenitor Cell (rMAPC) lines derived from bone marrow (BM) exhibit salient nascent hypoblast characteristics. We could not identify cells with hypoblast features in rat BM, but they appeared after prolonged in vitro culture under rMAPC conditions. However, rMAPC culture conditions supported the very rapid isolation of new lines with nascent hypoblast features from rat blastocysts that were more homogenous than XEN-P cells isolated on feeders. The gene expression profile, growth factor requirement, Oct4 promoter methylation, and in vitro/vivo differentiation potential of cells isolated using rMAPC culture conditions from BM or blastocysts or XEN-P cells were highly similar. We conclude that the three cell populations have characteristics of hypoblast stem cells (HypoSC) and that rMAPC culture conditions support the isolation of XEN-P/HypoSC from the blastocyst and induction of HypoSC from BM.

overall_design:
Comparison between bone marrow and blastocyst-derived  Hypoblast Stem Cells (hypoSC)
Three cell lines derived from bone marrow, three cell lines derived from blastocyst and one mesenchymal used, as control (for all of them 2 replicates)

first: Antonio

last: Lo Nigro

first: Martine

last: Geraerts

first: Tineke

last: Notelaers

first: Valerie

last: Roobrouck

first: Manja

last: Muijtjens

first: Kristel

last: Eggermont

first: Kartik

last: Subramanian

first: Fernando

last: Ulloa-Montoya

first: Yonsil

last: Park

first: Jason

last: Owens

first: Terry

last: Burns

first: Walter

last: Low

first: Shikha

last: Sharma

first: Abhishek

last: Sohni

first: Annelies

last: Crabbe

first: Karen

last: Pauwelyn

first: Philip

last: Roelandt

first: Xabier

last: Agirre

first: Felipe

last: Prosper

first: Timothy

last: O'Brien

first: An

last: Zwijsen

first: Wei-Shou

last: Hu

first: Bert

last: Binas

first: Catherine

last: Verfaillie


title: Discover preclinical biomarkers of hepatotoxicity: Acetaminophen and Carbon tetrachloride

status: Public on Mar 15 2012

city: Boston

first: Zhenqiang

last: Su

state: MA

address: 22 Thomson Place

department: IP & Science

institute: Thomson Reuters

summary: Preclinical biomarkers useful for identification of idiosyncratic drugs have not been identified.  It is hypothesized that patterns of transcript expression for the hepatotoxicants, including classical and idiosyncratic hepatotoxicants, are similar and the patterns differ from those of non-hepatotoxicants. This experiment is part of the biomarkers study, and focus on two clasical hepatotoxicants: Acetaminophen and Carbon tetrachloride. We have employed whole genome microarray expression profiling to identify liver gene expression changes induced by hepatotoxicants. For the same animal, urinary microRNA profiling were analyzed. APAP and CCl4 both significantly increased the urinary levels of 44 and 28 miRNAs, respectively.  In addition, 10 of the increased miRNAs were in common between APAP and CCl4.  Computational analysis was used to predict target genes of the 10 shared hepatotoxicant-induced miRNAs.  From the same animals, liver gene expression profiling was performed using whole genome microarrays.  Eight putative target genes were found to be significantly altered in the liver of APAP and CCl4 treated animals.

overall_design: Acetaminophen induced liver gene expression changes in rats (Six to seven week-old male Sprague-Dawley rats, provided by the US Food and Drug Administration National Center for Toxicological Research (NCTR) breeding colonies, were used for the study.) were measured at 6 hours, 24 hours, 3 days and 7 days after exposure to doses of 0, 100 and 1250 mg/kg.  Carbon tetrachloride induced liver gene expression changes in rats were measured at 6 hours, 24 hours and 3 days after exposure to doses of 0, 50 and 2000 mg/kg. Each group has at least 4 animals, total of 96 samples.

first: Yang

last: Xi


title: Insulin biosynthesis in neuronal progenitors derived from adult hippocampus and the olfactory bulb

status: Public on Mar 14 2012

first: Makoto

last: Asashima

address: 1-1-1 Higashi

department: Tsukuba Central 4

institute: National Institute of Advanced Industrial Science Technology (AIST)

summary: In this study, we demonstrate that insulin is produced not only in the mammalian pancreas but also in adult neuronal cells derived from hippocampus and olfactory bulb. Paracrine Wnt3 plays an essential role in promoting the active expression of insulin in both hippocampus and olfactory bulb-derived neural stem cells. Our analysis indicates that the balance between Wnt3, which triggers the expression of insulin via NeuroD1 transcription factor, and IGFBP-4, which inhibits the original Wnt3 action, is regulated depending on the diabetic status. We also show that adult neural progenitors derived from diabetic animals retain the ability to give rise to insulin-producing cells and that grafting neuronal progenitors into the pancreas of diabetic animals reduces glucose levels. This study provides an example of a simple and direct use of adult stem cells from one organ to another, without introducing additional inductive genes. In this study, we demonstrate that insulin is produced not only in the mammalian pancreas but also in adult neuronal cells derived from hippocampus and olfactory bulb. Paracrine Wnt3 plays an essential role in promoting the active expression of insulin in both hippocampus and olfactory bulb-derived neural stem cells. Our analysis indicates that the balance between Wnt3, which triggers the expression of insulin via NeuroD1 transcription factor, and IGFBP-4, which inhibits the original Wnt3 action, is regulated depending on the diabetic status. We also show that adult neural progenitors derived from diabetic animals retain the ability to give rise to insulin-producing cells and that grafting neuronal progenitors into the pancreas of diabetic animals reduces glucose levels. This study provides an example of a simple and direct use of adult stem cells from one organ to another, without introducing additional inductive genes.

overall_design: Total four different samples, gene expressions in hippocampal derived neural stem cells (HPC NSC), that in Olfactory bulb-derived neural stem cells (OB NSC), that in neurons derived from the HPC NSCs (HPC Neu) and that in neurons derived from the OB NSCs (OB Neu) were independently analyzed. Three independent experiments were performed to prepare each cell sample, and the extracted total RNAs from each cell source were mixed to apply following microarray analysis (Four independent RNA sample; HPC NSC, OB NSC, HPC Neu and OB Neu).

first: Tomoko

last: Kuwabara

first: Yasuko

last: Onuma

first: Yuzuru

last: Ito


title: Gene expression in the right ventricle of Rattus norvegicus during development of right ventricular heart failure and treatment

status: Public on May 06 2013

city: Richmond

first: Jennifer

middle: I.

last: Drake

state: Virginia

address: 1220 E. Broad Street, Room 6-003

department: Pulmonary and Critical Care Medicine

institute: Virginia Commonwealth University

summary: Right ventricular heart failure (RVF) associated with pulmonary hypertension (PH) is characterized by a distinct gene expression pattern when compared with functional compensatory hypertrophy.  Carvedilol treatment after RVF has been established reduces right ventricle (RV) hypertrophy  and improves the RV function.  In addition, carvedilol treatment has been shown to alter the gene expression of select genes.  We sought to identify, on a genome-wide basis, the effect of carvedilol on gene expression.  RVF was induced in male Sprague-Dawley rats by the combination of VEGF-receptor blockade and chronic hypoxia; thereafter, one group was treated with carvedilol.  RNA was isolated from the RV and subjected to microarray analysis.  A prediction analysis of the carvedilol-treated RVs showed that carvedilol treated RVs most resembled in their expression pattern the RVF pattern. However, an analysis beyond the boundaries of the prediction set revealed a small set of genes associated with carvedilol reversal of RVF.  Pathway analysis of this set of genes revealed expression changes of genes involved in cardiac hypertrophy, mitochondrial dysfunction, protein ubiquitination, and sphingolipid metabolism.  Genes encoding proteins in the cardiac hypertrophy and protein ubiquitination pathways were downregulated in the RV by carvedilol, while genes encoding proteins in the mitochondrial dysfunction and sphingolipid metabolism pathways were upregulated by carvedilol.

overall_design: Male Sprague-Dawley rats (Harlan Laboratories Inc., Indianapolis, IN) weighing 200g were injected subcutaneously with SU5416 suspended in 0.5% (w/v) carboxymethylcellulose sodium, 0.9% (w/v) sodium chloride, 0.4% (w/v) polysorbate 80, and 0.9% (v/v) benzyl alcohol in deionized water.  Rats were given a single injection of SU5416 (20 mg/kg) at the beginning of the 6-week experiment.  The animals were then exposed to chronic hypoxia (simulated altitude of 5,000 m in a nitrogen dilution chamber) for four weeks; thereafter the animals were kept at the altitude of Richmond, VA (sea level) for another two weeks. Hypoxia-only rats were exposed to chronic hypoxia for four weeks. Carvedilol (15 mg/kg; Sigma-Aldrich, St. Louis, MO) was dissolved in 20% dimethyl sulfoxide and water and administered once daily per oral gavage for 4 weeks, beginning after return to room air breathing.  Six rats per treatment group were randomly assigned.  Rats were euthanized with Euthanasia-III Solution (390 mg/ml pentobarbital sodium, 50 mg/ml phenytoin sodium; Med-Pharmex, Inc., Pomona, CA) and hearts were removed.  The RV was dissected from the LV and both ventricles were snap-frozen in liquid nitrogen.  Total RNA was isolated from approximately 30 mg of snap-frozen rat heart tissue using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA).  Hearts were homogenized with Buffer RLT and beta-mercaptoethanol in an MP FastPrep®-24 Lysing Matrix D tube (MP Biomedicals LLC, Solon, OH), and then RNA was isolated and purified following the manufacturer’s protocol.  RNA concentration was determined using a NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).  All samples had an A260/A280 ratio between 1.9 and 2.1.  The amplification and hybridization process is as follows.  500 ng of total RNA was amplified and labeled with Cyanine-5 and 500 ng of universal rat reference RNA (Stratagene, Santa Clara, CA) was amplified and labeled with Cyanine-3 using the Agilent QuickAmp Labeling kit (Agilent Technologies Inc., Santa Clara, CA) to produce labeled cRNA following the manufacturer’s protocol.  After amplification and labeling, the dye incorporation was determined using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE).  All ratios were greater than 8.0 pmole dye per mg cRNA per the manufacturer’s recommendation.  825 ng of sample and 825 ng of reference RNA were combined and incubated with an Agilent Whole Rat Genome 4x44k microarray slide (Agilent Technologies Inc., Wilmington, DE) for 17 hours at 65°C.  Following hybridization, slides were washed following the manufacturer’s protocol and scanned using an Axon GenePix 4200A scanner (Axon Instruments, Union City, CA) at a resolution of 5 mM.  The raw data were generated using GenePix Pro 5.0 software (Axon Instruments, Union City, CA).  Raw expression data files were uploaded into R and normalized using the Bioconductor marray package by the Lowess normalization algorithm, then exported to BRB Array Tools for analysis.

first: Jose

last: Gomez-Arroyo

last: Dumur

first: Donatas

last: Kraskauskas

first: Ramesh

last: Natarajan

first: Harm

last: Bogaard

first: Paul

last: Fawcett

first: Norbert

middle: F

last: Voelkel


title: Effects of corn oil gavage on gene expression profiles of thymus in Wistar Rats

status: Public on Nov 11 2011

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

summary: To investigate the effects of corn oil (CO), common drug vehicle, on the gene expression profiles in rat thymus with microarray technique. Female Wistar Rats were administered daily with normal saline (NS), CO 2, 5, 10 ml/kg for 14 days, respectively. Then, the thymus samples of rats were collected for microarray test and histopathology examination. The microarray data showed that 0, 40, 458 differentially expressed genes (DEGs) in 2, 5, 10 ml/kg CO group compared to NS group, respectively. The altered genes were associated with   immune response, cellular response to organic cyclic substance, regulation of fatty acid beta-oxidation, et al. However, no obvious histopathologic change was observed in the three CO dosage groups. These data show that 10 ml/kg CO , that dosage has been determined as the vehicle in drug safety assessment , can cause obvious influence on gene expression in rat thymus. Our study suggest that the dosage of CO gavage as the vehicle for water-in-soluble agents in drug development should be no more than 5 ml/kg if agents’ molecular effects in thymus want to be assessed.

overall_design: Gene expression in thymus from female Wistar rats daily administered with 2, 5, 10 ml/kg of corn oil or 10 ml/kg of saline by gavage for 14 consecutive days were measured using Agilent Rat Whole Genome 8×*60K array.

first: Xingchao

last: Geng

first: Liang

last: Zhang

first: Ying

last: Song

first: Zhi

last: Lin

first: Yingqi

first: Bo

last: Li

first: Junzhi

last: Wang


title: Effect of telmisartan on prostate carcinogenesis in TRAP rats

status: Public on Jul 31 2011

city: Nagoya

first: Satoru

last: Takahashi

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Pathology

institute: Nagoya City University

summary: We investigate the direct effects of ARBs on prostate cancer growth and progression.

overall_design: A total of 36 heterozygous male TRAP rats of 3 weeks of age were randomly divided into three groups. Rats in group 1 as a control received basal diet and tap water. The rats in groups 2 and 3 continuously received 2 or 10 mg/kg/day telmisartan in drinking water for 12 weeks, respectively. Total RNAs of both control and telmisartan (10 mg/kg/day) were applied to microarray analysis.

first: Hiroji

last: Uemura

first: Seeni

last: Azman

first: Masami

last: Komiya

first: Ne

last: Long

first: Koji

last: Hoshino

first: Hitoshi

last: Ishiguro

first: Yoshinobu

last: Kubota

first: Tomoyuki

last: Shirai


title: Olfactory Enshealting Cells : p75 High vs p75 Low cells population

status: Public on Jul 20 2011

city: Rouen

first: nicolas

last: guerout

state: Normandy

address: 22 Bd Gambetta

institute: Faculty of medecine of Rouen

summary: Comparative gene expression profiling of olfactory enshealting cells : p75 High vs p75 Low cells population

overall_design: Two-color experiment, p75 high(Cy5)/p75Low (Cy3). Biological replicates: 4 . Paired samples.

first: Nicolas

last: Guerout

first: Celine

last: Derambure

first: Axel

last: Honore


title: Neurotoxin tetrodotoxin TTX withdrawal induced neuronal activity: RNA Pol II is poised for rapid induction of arc and other neuronal VF-IEGs

status: Public on Apr 15 2011

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Transcription of immediate early genes (IEGs) in neurons is exquisitely sensitive to neuronal activity, but the mechanism underlying the earliest of these transcription events is largely unknown. Here we demonstrate that very fast IEGs (VF-IEGs) such as arc/arg3.1 are poised for rapid transcription by the stalling of RNA Polymerase II (Pol II) just downstream of the transcription start site. RNAi-depletion of two subunits of a mediator of Pol II stalling, Negative Elongation Factor, reduces Pol II occupancy of the arc promoter and compromises rapid induction of arc and other VF-IEGs. In contrast, reduction of Pol II stalling did not prevent expression of other fast IEGs (F-IEGs). These F-IEGs are expressed with comparatively slower kinetics and largely lack promoter proximal Pol II stalling. Taken together, our data strongly indicate that very fast kinetics of neuronal IEG expression require poised Pol II and suggest a role for this mechanism in transcription-dependent learning and memory.

overall_design: TTX withdrawal induced neuronal activity. To study activity-induced gene expression, neurons were treated with TTX for 48 hours and then TTX was washed out either for 15 minutes (W15) or for 45 minutes (W45). Gene expression was measured in these two groups in comparison to TTX treated neurons.

first: Ramendra

middle: N

last: Saha

first: Emma

last: Bailey


title: Spalax gene expression profiling of muscle and brain under hypoxia

status: Public on Dec 31 2012

city: Urbana

first: Mark

middle: Robert

last: Band

state: IL

address: 1201 W. Gregory Dr

department: Biotechnology

institute: University of Illinois

summary: Spalax, an underground fossoral rodant is exposed to chronic hypoxic environments. Measurements of Spalax burrows indicated 7% oxygen and up to 15% CO2. In the laboratory Spalax can survive 3% oxygen up to 14 hours as compared to rats that survive less than 4 hours at these oxygen levels. we have proposed Spalax as a model species for the investigation of hypoxia tolerance. this research has implications for many biomedical phenomena involving ischemic disease, notably heart disease and cancer. In this work we have subjected Spalax to 3%, 6% and 10% O2 levels for varying lengths of time and have profiled expression patterns and differential expression in muscle and brain, two tissues with high energy requirements. For comparison with a terrestrial mammal we have profiled RNA from rats exposed to either 21% or 6% oxygen.

sample_organism:
Rattus norvegicus
Nannospalax galili

platform_organism:
Rattus norvegicus
Nannospalax galili

overall_design: Spalax animals, captured in the field and held in captivity were subjected to 3 different levels of hypoxia. (1) 3% O2 for 6 hrs (2) 6% O2 for 6 hrs (3) 10% O2 for 44hrs (4) 21% O2 (normoxia). For comparison, Rats were subjected to 21% and 6% oxygen. Animals were euthanized according to approved protocols and RNA extracted from muscle and brain. Samples were labeled using the Agilent low input 2-color labeling kit and hybridized to a custom Spalax microarray (8x15K format). Results were normalized and analyzed using Limma from the R bioconductor package. Differentially expressed gens were identified as well as over-represented gene onotolgy defined functions.

first: Assaf

last: Malik

first: Aaron

last: Avivi

first: Avraham

last: Korol


title: Differential expression of microRNAs in the placentae of Chinese patients with severe pre-eclampsia

status: Public on Apr 14 2011

first: Jianqing

last: Zhao

address: 18 Life Science Parkway

institute: Capitalbio. Crop

summary: To determine differential expression of microRNAs in placentae with severe pre-eclampsia and normal placenta. Differential expression of microRNAs in placentae (4 severe pre-eclampsia and 4 normal control) was screened by microarray platform, then some differential microRNAs were selected and validated with real-time quantitative reverse transcription polymerase chain reaction in placentae of severe pre-eclampsia (n=24) and normal control group (n=26). Results: We validated the expression of some microRNAs altered in the microarray, and found the following microRNAs were significantly increased in severe pre-eclampsia placentae: miR-16, miR-29b, miR-195, miR-26b, miR-181a, miR-335 and miR-222. Conclusion: These differential microRNAs may play an important role in pathogenesis of pre-eclampsia.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We analyzed the microRNA expression in the placentae of Chinese patients with severe pre-eclampsia.

first: Yali

last: Hu


title: Gene expression data from liver of rat fed a high-fat diet and high-fructose water without/with Eucommia ulmoides leaves

status: Public on Aug 22 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 Eucommia ulmoides leaves on hyperlipidemia, we performed gene expression profiling on rat liver by microarray analysis.
Microarray analysis revealed that Eucommia ulmoides leaves up-regulated the gene expression involved in alpha-, beta-, and omega-oxidation of fatty acids, mainly relating to peroxisome proliferator-activated receptor signaling pathway.

overall_design: Rats were fed a high-fat diet and high-fructose water without/with orally administration of Eucommia ulmoides leaves for 5 weeks. Livers were taken for RNA extraction and hybridization on Agilent microarrays.

first: Testuya

last: Hiroi

first: Mayumi

last: Araki

first: Takahiko

last: Hirokawa

first: Maki

last: Miyazawa

first: Nobuyoshi

last: Aoki

first: Takashi

last: Kojima

first: Toshiyuki

last: Ohsawa


title: Evolutionary Diversification of Duplicated Genes; Experiment L, K

status: Public on Feb 01 2011

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

summary: This study measured the rates at which duplicated genes in the Daphnia pulex genome diverge in function, based on significant differences in their gene expression when paralogs of various ages were tested across 8 to 12 contrasting conditions. The conditions were designated A to L.  The number and diversity of experiments were designed to uncover condition specific expression. The age of duplicated genes was measured as the level of silent-site nucleotide substitution (Ks) between paralogs. Two methods were used to evaluate the degree to which expression pattern of paralogs differ. (1) The first method investigated variation in the differential expression patterns among duplicates of individual gene families by calculating the M values (log2 treatment – log2 reference) from eight experiments, then calculating Pearson correlations. (2) The second method is a global investigation which defined a distinguishable expression pattern by a significance criterion (p < 0.05) using ANOVA for the simple statistical model of aov( Yab ~ Xab ), for matrices Yab differential expression M values and Xab gene factors, with replicates. We used pr(M) < 0.05 as criterion that expression differs between paralog genes, for zero to twelve treatments. The hypothesis that is tested is one of how many paralog pairs in each Ks category reach the criterion of a distinguishable expression pattern, which is tested for significance with Fisher's exact test for count data. This method is reliable for as few as two probes for one gene and one probe for the other, although a greater number of replicate probes produced more significant results.

overall_design: We compared the gene expression patterns for condition 1 versus condition 2 using four to six biological replicates, including balanced dye-swaps. All probes including random probes were quantile-normalized across chips, subarrays, samples and replicates.

first: John

last: Colbourne

first: Jeong-Hyeon

last: Choi


title: Evolutionary Diversification of Duplicated Genes; Experiment A

summary: This study measured the rates at which duplicated genes in the Daphnia pulex genome diverge in function, based on significant differences in their gene expression when paralogs of various ages were tested across 8 to 12 contrasting conditions. The conditions were designated A to L.  The number and diversity of experiments were designed to uncover condition-specific expression. The age of duplicated genes was measured as the level of silent-site nucleotide substitution (Ks) between paralogs. Two methods were used to evaluate the degree to which expression pattern of paralogs differ. (1) The first method investigated variation in the differential expression patterns among duplicates of individual gene families by calculating the M values (log2 treatment – log2 reference) from eight experiments, then calculating Pearson correlations. (2) The second method is a global investigation which defined a distinguishable expression pattern by a significance criterion (p < 0.05) using ANOVA for the simple statistical model of aov( Yab ~ Xab ), for matrices Yab differential expression M values and Xab gene factors, with replicates. We used pr(M) < 0.05 as criterion that expression differs between paralog genes, for zero to twelve treatments. The hypothesis that is tested is one of how many paralog pairs in each Ks category reach the criterion of a distinguishable expression pattern, which is tested for significance with Fisher's exact test for count data. This method is reliable for as few as two probes for one gene and one probe for the other, although a greater number of replicate probes produced more significant results.


title: Evolutionary Diversification of Duplicated Genes; Experiment J


title: Evolutionary Diversification of Duplicated Genes; Experiments B-I, M-P


title: Evaluation of phenoxybenzamine in the CFA model of pain following gene expression studies and connectivity mapping

status: Public on Oct 07 2010

city: St. Louis

first: Meiping

last: Chang

state: MO

address: 700 Chesterfield Parkway West

department: PGRD

institute: Pfizer Inc.

summary: Background:  We have previously used the rat 4 day Complete Freund's Adjuvant (CFA) model to screen compounds with potential to reduce osteoarthritic pain. The aim of this study was to identify genes altered in this model of osteoarthritic pain and use this information to infer analgesic potential of compounds based on their own gene expression profiles using the Connectivity Map approach. Results:  Using microarrays, we identified differentially expressed genes in L4 and L5 dorsal root ganglia (DRG) from rats that had received intraplantar CFA for 4 days compared to matched, untreated control animals. Analysis of these data indicated that the two groups were distinguishable by differences in genes important in immune responses, nerve growth and regeneration. This list of differentially expressed genes defined a “CFA signature”.  We used the Connectivity Map approach to identify pharmacologic agents in the Broad Institute Build02 database that had gene expression signatures that were inversely related (‘negatively connected’) with our CFA signature. To test the predictive nature of the Connectivity Map methodology, we tested phenoxybenzamine (an alpha adrenergic receptor antagonist) – one of the most negatively connected compounds identified in this database - for analgesic activity in the CFA model. Our results indicate that at 10mg/kg, phenoxybenzamine demonstrated analgesia comparable to that of Naproxen in this model. Conclusion:  Evaluation of phenoxybenzamine-induced analgesia in the current study lends support to the utility of the Connectivity Map approach for identifying compounds with analgesic properties in the CFA model.

overall_design: A naive (control) group of rats (n = 6) and a group of rats injected with CFA (n = 6) were used for gene expression profiling experiments. One animal from the control group did not yield sufficient amount of RNA for microarray and thus was omitted from further processing. In total, 5 microarrays each from the 5 animals in the control group, and 6 microarrays each from the 6 animals in the CFA group were analyzed.

first: Sarah

last: Smith

first: Andrew

last: Thorpe

first: Michael

last: Barratt

first: Farzana

last: Karim


title: Wide-genome analysis of hepatocytes isolated from male and female rats treated with glucocorticoid.

status: Public on Oct 31 2010

first: NIEHS

last: Microarray Core

summary: Glucocorticoids are widely used therapeutically to suppress inflammatory/immune responses and most of their effects are produced either by altering transcription of specific genes directly, or by altering the expression of transcription factors that subsequently alter the expression of downstream genes. Relevant data from previous studies indicate that the number of genes regulated by glucocorticoid receptor exceeds 4000 in cells  and that 358 different genes are regulated in the liver of adrenalectomized males rats treated with a chronic infusion of methylprednisolone for up to 1 week  . However, differences in gene expression between males and females in response to glucocorticoid treatment in isolated hepatocytes are not known.

overall_design: Livers were isolated from adult male and female Sprague-Dawley rats and digested with the collagenase perfusion method developed by Berry and Friend (J Cell Biol 43, 506-520;1969). After collagenase treatment, the liver was excised, minced in balanced salt solution, and centrifuged at 50 g for 3 min. Immediately after isolation, hepatocytes were resuspended in Williams E Medium containing penicillin (100 units/ml), streptomycin (100 μg/ml), 2 mM glutamine pH 7.4, and 10% fetal bovine serum and plated on collagen-coated 94 x 16 mm cell culture dishes and maintained for 24 hours in a 95% air–5% CO2, 37°C incubator. The medium was then changed to free serum Williams E Medium and maintained in culture for an additional 24 hours. Hepatocytes isolated from male and rats were treated with vehicle (0.01% ethanol) or dexamethasone (100 nm) for 6 hours. Total RNA from cells were extracted by using the RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. All samples were treated with the RNase-free DNase set (Qiagen) and were kept at -80°C until labeling and hybridization.

first: Danielle

last: Duma

first: Kevin

last: Gerrish


title: Using Oligo Array Analysis to Determine Genes of Importance in the Meninges and Associated Vasculature Function and their Sensitivity to Amphetamine Toxicity

status: Public on Aug 24 2010

city: Jefferson

middle: Francis

last: Bowyer

address: 3900 NCTR Drive

department: Neurotoxicology

institute: National Center for Toxicological Research FDA

summary: Oligo array analysis with bioinformatics tools identified genes with very high expression levels in the meninges, arachnoid and pial membranes, and associated vasculatures (MAV) which are potentially important and unique to these tissues functional capabilities in rat.  It was also determined if these genes were more sensitive to expression changes after a neurotoxic exposure to environmentally induced hyperthermia (EIH) or amphetamine (AMPH).   Gene expression in the MAV was compared to the neuronal rich tissues of the striatum and parietal cortex.  In controls, 1,116 genes differed by more than 5-fold when comparing MAV to both striatum and parietal cortex.  Genes specifically identified with the blood-brain barrier (BBB) were also expressed at high levels indicating they may help form tight junctions in MAV.  The more than 300 genes having a 15-fold or greater expression in MAV compared to striatum and cortex were deemed of potential uniqueness and importance to MAV function.  Many of these genes are abundant in different types of epithelial tissue and function in binding, transport or metabolism of ions and solute, and may help MAV regulate cerebrospinal fluid. Many others with high expressions are involved in immune system function possibly serving to facilitate lymphocyte and macrophage trafficking in vasculature and cerebrospinal fluid.  Genes in MAV with a higher expression (relative to striatum and cortex) were affected in greater numbers than expected by EIH and AMPH.  Many expression increases evoked by AMPH and EIH in MAV relate to reactive oxidative stress and inflammation.  However, AMPH induced more robust alterations in the expression of genes related to ion/solute transport (Slc15a1), lipid metabolism (Fst), bacterial infection (Lbp) and oddly pancreatitis (Reg3a, Reg3b).  Expression of the BBB-related genes Sox18 and Cldn5 decreased in all regions with AMPH and EIH but even more so in MAV.  Esam increased with AMPH in all regions while Angpt2 was only affected in striatum and parietal cortex.  It is not known how these changes affect MAV, striatum or parietal cortex tight junction function/BBB and integrity.

overall_design: Gene expression patterns in MAV were compared to two regions of brain (striatum and parietal cortex) to identify genes important to MAV function and determine whether their expressions were sensitive to a neurotoxic exposure to amphetamine.

first: Nysia

last: George

first: Tucker

middle: A

last: Patterson

first: Upasana

last: Saini

first: Joseph

last: Hanig

first: Monzy

last: Thomas

first: James

last: Chen


title: Identification of cathepsin L as a potential sex-specific biomarker for renal damage

status: Public on Jan 25 2011

city: Allschwil

first: Axel

last: Klenk

address: Hegenheimermattweg 91

department: Research Informatics

country: Switzerland

institute: Idorsia Pharmaceuticals Ltd.

summary: The renin-angiotensin system is a well-known regulator of blood pressure and plays an important role in the pathogenesis of cardiovascular disease and renal damage. Genetic factors, including single nucleotide polymorphisms and sex, are increasingly recognized as potential risk factors for the development of cardiovascular disease. Double transgenic rats (dTGR), harboring human renin and angiotensinogen genes, were used in this study to investigate potential sex differences influencing renal function and renal gene expression. dTGR males and females had comparable increases in blood pressure, whereas body weight, albuminuria/proteinuria and urine flow rate were higher in males. At eight weeks of age renal plasma flow and glomerular filtration rate were proportionally lower in males, and renal vascular resistance tended to be higher. Males developed more severe tubulointerstitial and vascular lesions. By the end of week eight, 40% of the males, but none of the females had died. Genome expression studies were performed with RNA from kidneys of 7-week-old male and female dTGR and control rats to further investigate the sex-related differences on a molecular level. Forty-five genes showed sex-dependent expression patterns in dTGR that were significantly different compared to controls. Cathepsin L, one of the genes differentially expressed between the sexes, was shown to be also strongly associated with the degree of renal injury. In dTGR, urinary CTSL at week 7 was higher in males (ng/24 hours: M 512 +/- 163, F 132 +/- 70). These results reveal a potential new biomarker for the personalized diagnosis and management of chronic kidney disease.

overall_design: Four condition experiment, dTGR male vs Control male and dTGR female vs Control female. Biological replicates: 8 rats per condition

first: Yasmina

last: Bauer

first: Patrick

last: Hess

first: Changbin

last: Qiu

first: Bérengère

last: Renault

first: Daniel

last: Wanner

first: Rolf

last: Studer

first: Nina

last: Killer

first: Anna

last: Stalder

first: Manuel

last: Stritt

last: Strasser

first: Hervé

last: Farine

first: Katalin

last: Kauser

first: Martine

last: Clozel

first: Walter

last: Fischli

first: Oliver

last: Nayler


title: The Ecoresponsive Genome of Daphnia pulex: Empirical annotation of the Daphnia pulex genome

first: Jacqueline

last: Lopez

type: Expression profiling by genome tiling array

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

overall_design: Refer to individual Series

first: John

last: Colbourne

first: Jeong-Hyeon

last: Choi


title: Tracheal Occlusion Modulates the Gene Expression Profile of the Medial Thalamus in Anesthetized Rats

status: Public on Nov 05 2010

city: Gainesville

first: Vipa

last: Bernhardt

state: FL

address: 1600 Archer Rd

institute: University of Florida

summary: Conscious awareness of breathing requires the activation of higher brain centers. The sensation of breathing is believed to be a neural gating process. The thalamus provides the brain structure that could be responsible for the gating of respiratory sensory information to the cortex. It was reasoned that if the thalamus is the neural gate, then tracheal obstructions will modulate the gene expression profile of the thalamus. Anesthetized rats were instrumented with an inflatable cuff sutured around the trachea. The cuff was inflated to obstruct 2-4 breaths, then deflated for a minimum of 15 breaths. The obstructions were repeated for 10 min followed by immediate brain removal, and the medial thalamus was dissected and prepared for microarray analysis. Gene expression profiles were measured using Agilent Technology Oligo Microarrays. Following the occlusion protocol, 588 genes were found to be altered (p < 0.05, log2 fold change ≥ 0.4), with 327 down-regulated and 261 genes up-regulated. A significant up-regulation of the serotonin HTR2A receptor and significant down-regulation of the dopamine DRD1 receptor genes were found. A pathway analysis was performed targeting serotonin and dopamine receptor pathways. The mitogen activated protein kinase 1 (MAPK1) gene was significantly down-regulated. MAPK1 is an inhibitory regulator of the serotonin HTR2A receptor and facilitatory regulator for the dopamine DRD1 receptor. Down-regulation of MAPK1 may be related to the 2-fold up-regulation of HTR2A and 2-fold down-regulation of DRD1 suggesting an interaction in the medial thalamus serotonin-dopamine pathway elicited by airway obstruction. These results demonstrate an immediate change in gene expression in thalamic arousal-fear-anxiety-motivation related serotonin and dopamine receptors in response to airway obstruction. The results support the hypothesis that the thalamus is a component in the respiratory mechanosensory neural pathway.

overall_design: Four experimental animals that received tracheal occlusions and four surgical control animals were used. A reference design was used to compare all samples.

first: Kathryn

last: Pate

first: Natalia

last: Garcia-Reyero

first: Nancy

last: Denslow

first: Andrea

last: Vovk

first: Paul

last: Davenport


title: Transcriptional profiling of lung tissue of rat pretreated with cobalt in normoxic and hypoxic conditions and comapring with saline treated normoxic and hypoxic lung tissue in different time interval

status: Public on May 01 2010

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: The goal of the study was to examine the effect of hypoxic preconditioning with cobalt on global gene profiling in lung tissues.

overall_design:
Agilent two-color experiment,Organism: Rat ,Slides, Agilent’s Whole Rat Genome Microarray 4x44k GPL4135 with 44000 features, Labeling kit: Agilents Low input RNA linear amplification Kit Cat # 5184-3523, Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA
Rat lung tissue: cobalt + Hypoxia (0h, 6h, 12h, 24h, 48h) vs. Hypoxia (0h, 6h, 12h, 24, 48h)

first: Dhananjay

last: Shukla

first: Anju

last: Bansal


title: Diet and feeding condition induced gene expression in rat peripheral blood mononuclear cells

status: Public on Dec 31 2009

city: Wageningen

first: Jaap

last: Keijer

state: gld

address: Marijkeweg 40

department: Human and Animal Physiology

institute: Wageningen University

summary:
This study analyzed gene expression of rat peripheral blood mononuclear cells by microarray analysis following different feeding conditions (ad libitum feeding, fasting and refeeding) in normoweight (control) and in diet-induced obese rats (cafeteria rats). The aim of this study was to identify genes and biological pathways that were altered by feeding conditions in normoweight and diet-induced obese rats.

Keywords: Dietary treatment, analysis of feeding conditions

overall_design: Gene expression of Peripheral blood mononuclear cells (PBMC) was assesed by whole genome microarray analysis. Normoweight and diet-induced obese (cafeteria-fed) Wistar rats were submitted to ad libitum feeding, fasting and re-feeding feed conditions. Two-month-old male Wistar rats (n=29) were assigned into two dietary groups for 4 months: the control group (n=14) was fed with a standard chow diet, whereas the second group (cafeteria group, n=15) was fed with a fat-rich hypercaloric cafeteria diet in addition to the standard chow. At 6 months of age each group of rats was distributed in three subgroups submitted to different feeding conditions (n=4 or 5 for each condition): feeding (animals provided with ad libitum access to diet), fasting (animals deprived of food for 14 h) and re-feeding (fasted animals with a posterior free access to diet for 6 h). For PBMC isolation, blood samples were collected from the safena vein, using heparine in NaCl (0.9%) as anticoagulant; immediately after the blood collection, PBMC were isolated by Ficoll gradient separation, and RNA was extracted. One sample in the control group was excluded because of low amount of RNA. Gene expression changes were assessed using the Agilent rat whole genome microarray (G4131F Agilent Technologies).

first: A

last: Caimari

first: P

last: Oliver

first: W

last: Rodenburg

first: J

last: Palou


title: Comparative Gene Expression Profiling of Olfactory Ensheathing Cells from Olfactory Bulb and Olfactory Mucosa

status: Public on Dec 02 2009

first: nicolas

last: guerout

summary: The aim of this study was to use global gene expression profiling to define intrinsic molecular differences that distinguish olfactory ensheathing cells from mucosa (OM-OECs) from olfactory ensheathing cells from olfactory bulb (OB-OECs). 10,000 OECs from olfactory mucosa (OM) or olfactory bulb (OB) were isolated from 4 rats.

overall_design: Two-color experiment, OM (Cy5) vs. OB (Cy3) OECs. Biological replicates: 4. Paired samples.

first: Nicolas

last: Guerout

first: Celine

last: Derambure


title: Three Major salivary glands

status: Public on May 15 2010

city: Niigata-city, Chuo-ku

first: Tomoko

last: Nashida

address: 1-8 Hamaura-cho

department: Life Dentistry at Niigata

institute: The Nippon Dental University

summary: The aim of this study is characterize the gene expression of rat parotid, submandibular and sublingual glands, providing basic information for the salivary marker proteins.

overall_design: Three Wistar rats were used to compare gene expression of the parotid, submandibular and sublingual glands.


title: Liver toxicity induced by munitions compounds TNT, 2,6-DNT, 2,4-DNT, 4A-DNT, and 2A-DNT

status: Public on Dec 25 2009

city: Vicksburg

first: Xin

last: Guan

address: 3909 Halls Ferry Rd

department: EPP

institute: USACE-ERDC

summary:
The use of a systems biology approach to analyze common and specific mechanisms of liver toxicity induced by munitions compounds TNT, 2,6-DNT, 2,4-DNT, 4A-DNT, and 2A-DNT
The munitions compound 2,4,6-trinitrotoluene (TNT), its environmental degradation products 2-amino-4,6-dinitrotoluene (2A-DNT) and 4-amino-2,6-dinitrotoulene (4A-DNT), and two other munitions, 2,4-dinitrotoluene (2,4-DNT) and 2,4-dinitrotoluene (2,6-DNT) contaminate contaminate land, water and retired ammunitions plants.  The release of these compounds to the environment is due to military activities and a series of manufacturing processes.  Although toxicity has been characterized for these compounds, little is known of their mechanism of action.
Here we describe to use an integrative systems biology approach including toxicology, pathology, transcriptomics, metabolomics, gene function classification, pathway analysis and gene network modeling to try to understand the mechanisms of toxicity of these compounds.

overall_design: Changes in gene expression were tested using Agilent commercial whole rat genome microarrays (4 X 44K). Experiments were designed for both purposes of temporal and dose response analysis. For temporal analysis, only two time points for each compound were used, 24h and 48h. For dose response analysis, four doses plus a vehicle control were employed for each compound at each time point. A separate control was used for different compounds even at the same time point. The dose selection was based on the LD 50 data for each compound. Except controls, the lowest dose, the second lowest dose, the second highest dose and the highest dose were equivalent to   respectively for each compound (Table 1). Four biological replicates of this design were conducted, each using different animals, and four biological replicates were applied, which resulted in a total of 200 microarrays. ( one array was deleted from the set, 199 arrays used)

first: Youping

last: Deng

first: Sharon

last: Meyer

first: Barbara

middle: L

last: Escalon

first: Katherine

last: Ai

first: Mitchell

last: Wilbanks

first: Ruth

last: Welti

last: Reyero

first: Edward

last: Perkins


title: Evolutionary Diversification of Duplicated Genes; Experiments B-I

first: Jacqueline

last: Lopez

summary: This study measured the rates at which duplicated genes in the Daphnia pulex genome diverge in function, based on significant differences in their gene expression when paralogs of various ages were tested across 8 to 12 contrasting conditions. The conditions were designated A to L.  The number and diversity of experiments were designed to uncover condition specific expression. The age of duplicated genes was measured as the level of silent-site nucleotide substitution (Ks) between paralogs. Two methods were used to evaluate the degree to which expression pattern of paralogs differ. (1) The first method investigated variation in the differential expression patterns among duplicates of individual gene families by calculating the M values (log2 treatment – log2 reference) from eight experiments, then calculating Pearson correlations. (2) The second method is a global investigation which defined a distinguishable expression pattern by a significance criterion (p < 0.05) using ANOVA for the simple statistical model of "aov( Yab ~ Xab )", for matrices Yab differential expression M values and Xab gene factors, with replicates. We used pr(M) < 0.05 as criterion that expression differs between paralog genes, for zero to twelve treatments. The hypothesis that is tested is one of how many paralog pairs in each Ks category reach the criterion of a distinguishable expression pattern, which is tested for significance with Fisher's exact test for count data. This method is reliable for as few as two probes for one gene and one probe for the other, although a greater number of replicate probes produced more significant results.

first: John

last: Colbourne

first: Jeong-Hyeon

last: Choi


title: RNA profiles of rat olfactory epithelia : individual and age related variations

status: Public on Nov 01 2009

city: RENNES

first: Francis

last: Galibert

address: 2 av du Pr Léon Bernard

department: Génétique et Developpement

institute: CNRS UMR6061/Université Rennes1

first: Maud

last: Rimbault

first: Stephanie

last: Robin

first: Amaury

last: Vaysse