title: Effect of a High Phosphorus Diet on Renal Gene Expressions in Rat

status: Public on Jan 12 2012

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: The mechanism by which phosphorus levels are maintained in the body was investigated by analyzing changes in gene expression in the rat kidney following administration of a high-phosphorus diet. Male Wistar rats were fed a high phosphorous (HP) diet containing 1.2% phosphorous, or 0.3% HP as a control, for 24 days.  Phosphorous retention was not significantly increased in HP rats, but fractional excretion of phosphorus was significantly increased in the HP group compared to controls, with an excessive amount of the ingested phosphorus being passed through the body. DNA microarray analysis of kidney tissue from both groups revealed changes in gene expression profile induced by a HP diet. Among the genes that were upregulated, gene ontology (GO) terms related to ossification, collagen fibril organization, and inflammation and immune response were significantly enriched. In particular, there was significant upregulation of type IIb sodium-dependent phosphate transporter (NaPi-IIb) in the HP rat kidney compared to control rats. This upregulation was confirmed by in situ hybridization. Discreet signals for NaPi-IIb in both the cortex and medulla of the kidney were apparent in the HP group, while the corresponding signals were much weaker in the control group. Immunohistochemical analysis showed that NaPi-IIb localized to the basolateral side of kidney epithelial cells surrounding the urinary duct in HP rats but not in control animals. These data suggest that NaPi-IIb is upregulated in the kidney in response to the active excretion of phosphate in HP diet-fed rats.

overall_design: Male Wistar rats (4 weeks old) were purchased from Japan SLC Co. (Hamamatsu, Japan) and individually housed in metabolic cages under controlled conditions of 22±1°C and a 12-hour light/dark cycle (lights on from 08:00 to 20:00 daily). Two different diets containing 0.3% phosphorous (control diet) and 1.2% phosphorous (HP diet) were prepared based on the AIN-93G diet (Table 1). All rats were fed the control diet for a 7-day acclimatization period. After acclimatization, rats were divided into two groups of similar mean body weight (n = 5 each) and then fed either the control or the HP diet for 24 days. The animals were allowed to eat ad libitum and had free access to water (MilliQ water).The protocol for the animal experiments was approved by the Animal Use Committee of the Faculty of Agriculture at The University of Tokyo.

first: Tatsuya

last: Suyama

first: Shinji

last: Okada

first: Tomoko

last: Ishijima

first: Kota

last: Iida

first: Keiko

last: Abe


title: Expression data from polycystic kidney disease susceptible and resistant rat strains

status: Public on Jan 01 2012

city: Milwaukee

first: Caitlin

middle: C

last: OMeara

state: WI

address: 8701 Watertown Plank Rd

department: Physiology

country: USA

institute: Medical College of Wisconsin

summary: To facilitate the search for genetic modifiers that modulate ARPKD disease progression and severity, we sought to generate a congenic rat model that carries the PCK Pkhd1 mutation but is resistant to the development of ARPKD. We transferred the Pkhd1 mutation from the PCK rat onto the genetic background of the FHH (Fawn-Hooded Hypertensive) rat. This newly developed strain, called FHH.Pkhd1, showed significant amelioration of renal disease, and delayed onset of biliary abnormalities. To initiate the exploration for genes and pathways that modulate susceptibility to renal cystogenesis, we investigated transcriptional changes in kidneys from PCK, SD, FHH and FHH.Pkhd1 rats by microarray analysis.

overall_design: Both kidneys were harvested from 6 animals for each strain; SD, FHH, PCK, FHH.Pkhd1 (FHH.PCK-(D9Rat35-D9Rat70)/Mcwi, RGD ID 5147594) at 30 days of age.  The kidneys were bisected and stored in RNAlater at 4C for 24hrs. RNA was extracted using the Trizol (Invitrogen) method according to manufacturer’s instructions. RNA from each strain was pooled together, reverse transcribed, and hybridized to three Affymetrix Rat 230 arrays (Affymetrix).

first: Moreno

last: Carol

first: O'Meara

last: Caitlin


title: Skeletal myoblasts protect cardiomyocytes against oxidative stress via c-Met and epidermal growth factor receptor (EGFR)-dependent paracrine pathways

status: Public on Jan 28 2012

city: Helsinki

first: Antti

last: Siltanen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki, Institute of Biomedicine

summary: To study the effect of myoblast-derived paracrine factors on cardiomyocyte gene expression, microarray analysis was performed from isolated rat fetal cardiomyocyte cultures. These cultures were treated for 24 hours with fresh culture medium (control), skeletal myoblast-conditioned medium, or cardiac fibroblast-conditioned medium.

overall_design: In total, 3 samples were analyzed.

first: Kristo

last: Nuutila

first: Hisazumi

last: Uenaka

first: Johanna

last: Mäkelä

first: Tommi

last: Pätilä

last: Vento

first: Yoshiki

last: Sawa

first: Ari

last: Harjula

first: Esko

last: Kankuri


title: Fibrogenic and redox-related but not proinflammatory genes are upregulated in lewis rat model of chronic silicosis

city: Albuquerque

first: Raymond

middle: J

last: Langley

state: New Mexico

address: 2425 Ridgecrest Dr

department: immunology

institute: LRRI

summary: Silicosis, a fibrotic granulomatous lung disease, may occur through accidental high-dose or occupational inhalation of silica, leading to acute/accelerated and chronic silicosis, respectively. While chronic silicosis has a long asymptomatic latency, lung inflammation and apoptosis are hallmarks of acute silicosis. In animal models, histiocytic granulomas develop within days after high-dose intratracheal silica instillation. However, following chronic inhalation of occupationally relevant doses of silica, discrete granulomas resembling human silicosis arise months after the final exposure without significant lung inflammation/apoptosis. To identify molecular events associated with chronic silicosis, lung RNAs from controls or chronically silica-exposed rats were analyzed by Affymetrix at 28 wk after silica exposures. Results suggested a significant upregulation of 144 genes and downregulation of seven genes. The upregulated genes included complement cascade, chemokines/chemokine receptors, G-protein signaling components, metalloproteases, and genes associated with oxidative stress. To examine the kinetics of gene expression relevant to silicosis, qPCR, ELISA, Luminex-bead assays, Western blotting, and/or zymography were performed on lung tissues from 4 d, 28 wk, and intermediate times after chronic silica exposure and compared with 14 d acute silicosis samples. Results indicated that genes regulating fibrosis (secreted phosphoprotein-1, CCL2, and CCL7), redox enzymes (superoxide dismutase-2 and arginase-1), and the enzymatic activities of matrix metalloproteinases 2 and 9 were upregulated in acute and chronic silicosis; however, proinflammatory cytokines were strongly upregulated only in acute silicosis. Thus, inflammatory cytokines are associated with acute but not chronic silicosis; however, genes regulating fibrosis, oxidative stress, and metalloproteases may contribute to both acute and chronic silicosis.

overall_design: 3 rats were chronically exposed to silica by inhalation. Briefly, exposure chambers were maintained with an airflow rate of ~15 cfm and temperature range of 22–26°C. Animals were exposed to 6.2 mg/m3 aerosolized silica (Min-U-Sil 5; U.S. Silica, Mill Creek, OK) with an average particle size of 1.75 ± 0.05 mm (mass median aerodynamic diameter) 6 h/d, 5 d/wk (Monday–Friday) for 6 wk. 3 control animals received filtered air under similar inhalation conditions.

first: Neerad

last: Mishra

first: Juan

last: Peña-Philippides

first: Jean-Clare

last: Seagrave

first: Brandon

last: Rice

first: Shashi

middle: P

last: Singh

first: Mohan

middle: L

last: Sopori


title: Modification of genes expression in the somatolactotrope GH4C1 cell line in presence of the dominant negative mutant POU1F1(R271W)

status: Public on Jan 04 2012

city: Marseille

first: Jean-Louis

last: Franc

address: Bd J. Moulin

country: France

institute: CNRS

summary:
The anterior pituitary-specific transcription factor POU1F1 (also called PIT-1) was initially identified and cloned as a transactivator of PRL, GH and TSHß subunit genes. Different studies indicated that POU1F1 could also have other functions in these cells. The identification of new targets of this factor could be useful to obtain a better understanding of these functions.
Gene expression microarray assays were used to detect genes that have their expression modified in somatolactotrope GH4C1 cells by the expression of a dominant negative form of POU1F1, POU1F1(R271W).

overall_design: Lentiviral vectors containing the transgene of interest under the control of the PGK promoter (pGK-POU1F1(R271W)-IRES-EGFP, or pGK-EGFP used as controls) were generated. After lentiviral transfer in GH4C1 cells were grown in regular medium for 4 days then cells were harvested and total RNA was purified.

first: Jean-Paul

last: Herman

first: Nicolas

last: Jullien

first: Séverine

last: Guillen

first: Alain

last: Enjalbert


title: Transcriptomic analysis of the osmotic and reproductive remodelling of the female rat supraoptic nucleus

status: Public on Dec 29 2011

city: Bristol

first: DAVID

last: MURPHY

state: AVON

address: Whitson Street

department: Medicine and Dentistry

country: United Kingdom

institute: University of Bristol

summary: The supraoptic nucleus (SON) of the hypothalamus is an important integrative brain structure that co-ordinates responses to perturbations in water balance and regulates maternal physiology through the release of the neuropeptide hormones vasopressin and oxytocin into the circulation. Both dehydration and lactation evoke a dramatic morphological remodelling of the SON, a process known as function-related plasticity. We hypothesise that some of the changes seen in SON remodelling are mediated by differential gene expression, and have thus used microarrays to document global changes in transcript abundance that accompany chronic dehydration in female rats, and in lactation. In situ hydridisation analysis has confirmed the differential expression of 3 of these genes, namely Tumour necrosis factor induced protein 6, Gonadotrophin inducible transcription factor 1 and Ornithine decarboxylase antizyme inhibitor 1. Comparison of differential gene expression patterns in male and female rats subjected to dehydration and in lactating rats has enabled the identification of common elements that are significantly enriched in gene classes with particular functions. Two of these are related to the requirement for increased protein synthesis and hormone delivery in the physiologically stimulated SON (translation initiation factor activity and endoplasmic reticulum-Golgi intermediate compartment respectively), whilst others are consistent with concept of SON morphological plasticity (collagen fibril organisation, extracellular matrix organization and biogenesis, extracellular structure organization and biogenesis and homophilic cell adhesion). We suggest that the genes co-ordinately regulated in the SON as a consequence of dehydration and lactation form a network that mediates the plastic processes operational in the physiologically activated SON.

overall_design:
Each independent microarray sample represented the SON from either 5 female euhydrated, 5 dehydrated (water restriction for 72hours with food ad libitum) or 11 days lactating. In total, 5 microarrays were performed for the Dehydrated and the Lactation groups and 4 for the euhydrated controls. Samples within each group may be considered to be both biological and technical replicates.

The GeneSpring-derived MAS5 data described in the publication is not included in this submission.

first: Charles

last: Hindmarch

first: Song

middle: T

last: Yao

first: Jing

last: Qiu

first: Jefferey

middle: G

last: Tasker

first: David

last: Murphy


city: Raleigh

last: Dorman

address: 4700 Hillsborough Street

institute: North Carolina State Universisy

summary: Synergism of Iraqi Sand/Cigarette Smoke Co-Exposure in Rats. 24 samples are used.

overall_design: A total of 102 rats will be separated into six exposure groups: each group consisting of 17 male CD Sprague-Dawley rats, 10 to 15 weeks old.  The six exposure groups were each exposed via two routes: 1. nose-only inhalation exposures --- air or cigarette smoke; 2. whole-body inhalation exposures -- air or manufactured silica sand or Iraqi sand.  The nose only exposures were conducted 3 hours per day, 5 days per week for 6 weeks.  During the last two weeks of the nose - only exposures, whole-body exposure were also conducted 18-19 hours per day, 7 days per week.


title: Expression data from  Ad-β-catenin-GFP or Ad-GFP infected cardiomyocytes

status: Public on Dec 30 2011

city: Beijing

first: junjie

last: li

address: #5 Dong Dan San Tiao

country: China

institute: PUMC

summary:
The Wnt pathway is a key regulator of embryonic development, cell growth, differentiation, polarity formation, neural development, carcinogenesis, and stem cell self-renewal, and deregulation of the Wnt signalling is associated with many human disease. The central player in the Wnt pathway is β-catenin, A recent study has shown that β-catenin/Tcf/Lef signaling pathway is an essential growth-regulatory pathway in cardiomyocytes.
We used DNA microarrays to detail the global trends in gene expression underlying β-catenin-overexpressed cardiomyocytes and identified distinct classes of up- or down-regulated genes during this process. Our findings suggest that β-catenin plays a critical role in regulating cardiac dysfunction at transcriptional level and may provide novel insight into how β-catenin modulates heart diseases.

overall_design: Cardiomyocytes were infected with GFP control or β-catenin adenoviruses for RNA extraction and hybridization on Affymetrix microarrays. We sought to define the effects of β-catenin on the global programme of gene expression in primary cardiomyocytes. To that end, neonatal rat cardiomyocytes were infected with GFP control (G) or β-catenin adenovirus (B) for 24 hours.

first: Jun

last: Li

first: Hui

middle: H


title: Patterns of gene Expression during the Spinal cord Injury/Regeneration

first: Li

last: Xiaoguang

address: No.37 of Xueyuan Road, Haidian District

department: School of Biological Science and Medical Engineering

institute: Beihang University

summary:
Spinal cord injury (SCI) induces a sequence of endogenous autodestructive changes known as secondary injury, as well as reactive biochemical changes that are neuroprotective and/or promote recovery. All these responses to SCI are, in part reﬂected in changes in gene expression.
In order to assess changes in gene expression involved in the regeneration process,microarrays were performed as a function of time after SCI for the various treatments.

overall_design: Three groups rats(i.e.NT-3-chitosan tube group, tube alone group and lesion control group) used to interrogate Affymetrix (SantaClara,CA) GeneChips were sacrificed by intraperitoneally over dose injecting 6% chloral hydrate at 1, 3, 10, 20, 30, and 90 d after the operation. The spinal cords were surgically re-exposed and spinal tissue including dura and meninges was dissected into three blocks, i.e. 5 mm long segments in the lesioned area (M), rostral to the lesioned area (R), and caudal to the lesioned areas (C) were sampled under RNAase-free conditions. The samples were quick frozen and kept in liquid nitrogen.

first: Xiaoguang


title: Expression data from hypervitaminosis A rat diaphyseal bone

status: Public on Dec 21 2011

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

summary: Vitamin A is the only known compound that produces spontaneous fractures in rats. In an effort to resolve the molecular mechanism behind this effect, we fed young rats high doses of vitamin A and performed a global transcriptional analysis of diaphyseal bone after one week, i.e. just before the first fractures appeared. Microarray gene expression analysis revealed that 68 transcripts were differentially expressed in hypervitaminotic cortical bone and 118 transcripts were found when the bone marrow was also included. 98% of the differentially expressed genes in the bone marrow sample were up-regulated. In contrast, hypervitaminotic cortical bone without marrow showed reduced expression of 37% of differentially expressed genes. Gene Ontology (GO) analysis revealed that only samples containing bone marrow were associated to a GO term, which principally represented extracellular matrix (ECM). This is consistent with the histological findings of increased endosteal bone formation. Four of the genes in this ECM cluster and four other genes, including Cyp26b1 which is known to be up-regulated by vitamin A, were selected and verified by real-time PCR. In addition, immunohistochemical staining of bone sections confirmed that the bone-specific molecule, osteoadherin (Omd) was up-regulated. Further analysis of the major gene expression changes revealed distinct differences between cortical bone and bone marrow, e.g. there appeared to be augmented Wnt signaling in the bone marrow but reduced Wnt signaling in cortical bone. Moreover, induced expression of hypoxia-associated genes was only found in samples containing bone marrow. Together, these results corroborate our previous observations of compartment-specific effects of vitamin A, with reduced periosteal but increased endosteal bone formation, and suggest important roles for Wnt signaling and hypoxia in the processes leading to spontaneous fractures.

overall_design: Rat diaphyseal bones from hypervitaminosis A and controls (8week old) were extracted for RNA and hybridized on Affymetrix microarrays. Humeri were isolated, and all connective tissue, including periosteum, was completely removed as were both epiphyses, including growth plates. Samples of cortical bone including marrow were snap-frozen in liquid nitrogen and quickly crushed into a fine powder using a mortar and pestle followed by total RNA extraction with TRI Reagent® (Sigma-Aldrich). For cortical bone without marrow, diaphyseal bones were cut into pieces, vortexed in ice-cold PBS three times for 10 s to remove marrow cells followed by snap-freezing in liquid nitrogen, crushing into a fine powder and RNA extraction. Isolated RNA was quantified using spectrophotometry by measuring the absorbance at 260 nm, and the 260/280 nm ratio was calculated. RNA was kept only when this ratio was 1.9-2.0 to ensure the absence of protein contamination and limited RNA degradation. The integrity of sample RNAs was confirmed by capillary electrophoresis separating 18 S and 28 S ribosomal RNA on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Notably, the metaphyses and growth plates were not included in theses samples. Importantly the amount of RNA extracted from cortical bone including marrow was approximately four times the amount of RNA extracted from the pure cortical bone and was therefore considered herein to mainly represent bone marrow cells.

first: Thomas

last: Lind

first: Lijuan

last: Hu

first: P

middle: M

first: Rachael

last: Sugars

first: Göran

last: Andersson

first: Annica

last: Jacobson

first: Håkan

last: Melhus


title: Effect of probiotic Lactobacillus casei Zhang on liver gene expression of hypercholesterolemic rats

status: Public on Dec 31 2011

city: Hohhot

first: Heping

last: Zhang

address: No.306 Zhaowuda road

institute: Inner Mongolia Agricultural University

summary: The hypocholesterolemic effect of probiotics has been observed, but the molecular mechanism of probiotic-host interaction is still obscure. In this study, DNA microarray technology was used to explore the gene expression profile of liver of hypercholesterolemic rats caused by administration of probiotic Lactobacillus casei Zhang, which can decrease the serum triglyceride, low-density lipoprotein cholesterol, hepatic cholesterol and triglyceride of hypercholesterolemic rats.

overall_design: Six liver samples in high fat and probiotic treated group (3 samples in each group) were randomly selected for RNA isolation and microarray hybridization，the 3 samples in high fat group were used as control.

first: Zhi

last: Zhong

first: Wenyi

first: Ruiting

last: Du

first: He

last: Meng


title: Gene expression comparison of wild-type and IL15ko thymic NKT cells

status: Public on Dec 08 2011

city: Nashville

first: Joyce

last: Sebastian

state: TN

address: A-4223 Medical Centre North

department: Department of Microbiology and Immunology

institute: Vanderbilt University School of Medicine

summary: Semi-invariant natural killer T (NKT) cells are thymus-derived innate lymphocytes that  modulate microbial and tumour immunity as well as autoimmune diseases. These  immunoregulatory properties of NKT cells are acquired during their development.  Much has been learnt regarding the molecular and cellular cues that promote NKT cell  development, yet how these cells are maintained in the thymus and the periphery and  how they acquire functional competence are incompletely understood. We found that  IL-15 induced several Bcl-2 family survival factors in thymic and splenic NKT cells in  vitro. Yet, IL15-mediated thymic and peripheral NKT cell survival critically depended  on Bcl-xL expression. Additionally, IL-15 regulated thymic developmental stage 2 (ST2)  to ST3 lineage progression and terminal NKT cell differentiation. Global gene expression  analyses and validation revealed that IL-15 regulated Tbx21 (T-bet) expression in thymic  ST3 NKT cells. The loss of IL15-dependent T-bet expression resulted in poor expression  of IFN-γ and several NK cell receptors in NKT cells. Taken together, our findings reveal  a critical role for IL-15 in NKT cell survival, which is mediated by Bcl-xL, and effector  differentiation, which is regulated by T-bet.

overall_design: Gene expression was measured in NKT cells sorted from pooled thymi of wild-type (3 replicates) or IL-15 deficient (2 replicates) mice.

first: Laura

middle: E

last: Gordy

first: Andrew

middle: I

last: Flyak

first: Sebastian

last: Joyce


title: Cardiovascular gene expression

status: Public on Dec 14 2011

city: Leuven

first: Geofrey

last: De Visscher

address: Minderbroedersstraat 12 Building P

country: Belgium

institute: KULeuven

summary:
Comparison between neonatal and adult heart valve and vascular tissue
Tissue engineering of blood vessels and heart valves aims to create high quality prostheses, with preservation of their growth potential. However, the current markers used to identify the necessary cell phenotypes might not take the developmental properties of such structures into account.

overall_design: 4 x 3 replicates

first: An

last: Lebacq

first: Lindsay

last: Mesure

first: Willem

last: Flameng


title: Differential gene expression of adult rat retinas exposed to light.

status: Public on Oct 30 2011

city: Trieste

first: Diana

middle: Eva

last: Bedolla Orozco

address: Via Bonomea 265

department: Neurobiology

country: Italy

institute: International School for Advanced Studies - SISSA

summary: We performed a microarray screening of adult rat retinas to identify genes that could show and up- or down-regulation due to exposure to light.

overall_design: This study was performed using ex-vivo retinas collected from adult Long Evans rats that were exposed to light (1000 Lux), or were left in dark as control. All experiments were performed at the same hour, so that the contribution from the circadian rhythm would not affect the observations. The hours to which the experiment was performed were at 7am (always in dark), 10am (under 1000 lux) and as control 10am (always kept in dark), 1pm (under 1000 Lux) and 1pm (Always in dark).

last: Bedolla

first: Helena

last: Krmač

first: Vincent

last: Torre


title: Impaired endosomal recycling in proximal tubules is mechanistically linked to proteinuria

status: Public on Dec 17 2011

city: Toledo

first: Bina

last: Joe

state: OH

address: 3000 Arlington avenue

department: Physiology and Pharmacology

institute: University of toledo

summary: Through substitution mapping studies, we previously identified that a <330kb region from a rat strain with no renal pathology (the Lewis rat), which when introgressed onto the genetic background of a rat with renal disease (the Dahl Salt-sensitive (S) rat), caused an increase rather than the expected decrease in proteinuria. The purpose of this study was to prioritize a candidate gene and further delineate the mechanism underlying the observed increased in proteinuria. A higher level of proteinuria independent of dietary salt was observed in the congenic rat at a very young age (50-52 day old). The critical congenic segment was further mapped to <42.5kb containing a single candidate gene, rififylin. Rififylin was expressed 1.59 fold higher in the congenic strain compared with S. Overexpression of rififylin is known to delay recycling of endosomes. Renal transcriptome analysis indicated that Atp1a1 one of the most highly differentially expressed genes. Atp1a1 was 5.33 fold higher in the congenic strain compared with S.  The protein product of Atp1a1, the alpha subunit of Na+K+ATPase, was also significantly higher in the endosomes of proximal tubules from the congenic strain compared with S. To determine whether the higher amounts of this protein in the endosomes is due to a delay in recycling of endosomes caused by the overexpression of rififylin in the congenic strain, recycling of exogenously labeled-transferrin by single cell cultures of proximal tubules was monitored by confocal microscopy. Recycling of transferrin was significantly delayed in the congenic strain compared with S.  These results suggest that impaired endosomal recycling in the proximal tubules from the congenic strain caused by the overexpression of rififylin is a novel molecular mechanism linked to the observed increase in proteinuria of the congenic strain.

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

first: Kathirvel

last: Gopalakrishnan

first: B


title: Genome-wide mRNA expression profiles of FACS-purified rat beta cells freshly isolated from control and 24h-fasted rats

status: Public on Sep 01 2011

city: Brussels

first: Geert

middle: A.

last: Martens

address: Laarbeeklaan 103

department: Diabetes Research Center

institute: Vrije Universiteit Brussel

summary:
The study was designed to capture the in vivo adaptations of nutrient-sensing pancreatic beta cells to fed or fasted (24h) state.
Short periods of fasting are thought to mediate the beta cells’ competence for insulin synthesis and secretion. We examined whether it influenced their typical mRNA expression. After 24h of fasting, a 1.5 fold change was detected in 1.5% of all assayed transcripts (p<0.05), with 95% of altered genes (430 of 452) being down-regulated (Fig.6A). Suppression was more marked for a panel of genes with beta cell-specific expression, of which 12% were 1.5-fold suppressed. Suppressed beta cell marker genes were statistically enriched in gene clusters of endoplasmic reticulum (ER), ER to Golgi transport, protein folding and secretory vesicle-mediated transport, i.e. the pathways of protein synthesis and transport. (See Martens G.A. et al. PLoS One 2011)

overall_design: For both experimental conditions, 3 biological replicates were studied, each representing an independent isolation from n= 5, 10w-old male Wistar rats. Beta cells were snap frozen in liquid nitrogen immediately after the end of the isolation procedure, i.e. within 3 hours after animal killing.

middle: A

first: Daniel

last: Pipeleers

first: Zhidong

last: Ling


title: Expression analysis of astrocytes isolated from the rat forebrain

status: Public on Sep 06 2011

city: Stanford

first: Lynette

last: Foo

state: CA

address: 299 Campus Drive

institute: Stanford University

summary: Comparison of expression data of rat forebrain astrocytes from P1, P7 acutely isolated by immunopanning or cultured with astrocytes prepared by McCarthy and de Vellis' (1980) method. Elucidating the genes induced by serum in immunopannedrat astrocytes.

overall_design:
Three biological replicates for each sample were done.  MD-astrocytes were prepared as described in McCarthy and de Vellis 1980 and harvested for mRNA after 7DIV.  IP-astrocytes were isolated from P1 or P7 Sprague Dawley rats and processed for RNA immediately (IP-astrocytes P1/P7), or cultured for 7 days in HBEGF before harvesting (Cult. IP-astrocytes P1/P7).

For the serum studies, we plated IP-astrocytes P7 in MD-astrocyte media containing 10% fetal calf serum immediately after isolation and cultured them for 7 days.  After 7 days, the cultures were either processed for total RNA or washed 3x with dPBS and astrocyte base media with HBEGF was added.  The cells were cultured for an additional 7 days and then processed for RNA.

We isolated total RNA with the QIAshredder and Qiagen RNeasy Mini Kit.  We used the 3’IVT Express kit for preparation of the RNA and the Rat Genome 230 2.0 Array chip (Affymetrix, Santa Clara).  RT-PCR was used to elucidate the level of contamination in each cell sample.


title: Genomic-Derived Markers for Early Detection of Calcineurin Inhibitor Immunosuppressant–Mediated Nephrotoxicity

status: Public on Nov 23 2011

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The use of calcineurin inhibitor (CI) immunosuppressants has significantly improved the early allograft survival rate in organ transplantation. However, CI therapy has been associated with chronic nephrotoxicity, which limits their long-term utility. In order to understand the mechanisms of the toxicity, we analyzed the gene expression changes that underlie the development of CI immunosuppressant-mediated nephrotoxicity, in male Sprague-Dawley (SD) rats dosed daily with cyclosporine (CsA), FK506 or rapamycin (Rapa) for 1 to 28 days. We identified a group of genes, whose expression in rat kidney is quantitatively correlated with CI-induced kidney injury as observed in changes in blood urea nitrogen (BUN) levels and kidney histopathology. These genes include both up-regulated genes, such as Ren1 and Klks3, and down-regulated genes, such as Calb1, Egf, NCC, and kidney specific Wnk1 (KS-Wnk1). Using the down-regulated genes alone we successfully predicted CI immunosuppressant-mediated kidney injury in rats following 7 days of treatment. Among these genes are two mechanism-related genes, NCC and KS-Wnk1, both of which are involved in the sodium transport in the distal nephrons. The down-regulation of both genes at the mRNA and protein level in rat kidney following CI treatment was confirmed by quantitative RT-PCR and immunohistochemical staining, respectively. We hypothesize that decreased expression of NCC may cause reduced sodium chloride reabsorption in the distal tubules, and contribute to the prolonged activation of the Renin-Angiotensin-System (RAS), a demonstrated contributor to the development of CI-induced nephrotoxicity in both animal models and clinical settings. Therefore, NCC and KS-Wnk1 could potentially be used as biomarkers for early detection and prevention of CI-related nephrotoxicity in clinical practice.

overall_design: Male SD rats approximately 5-7 weeks old were maintained on certified rodent chow and dosed i.p. with olive oil, CsA (CAS # 59865-13-3, 2.5 or 25 mg/kg/day), FK506 (CAS # 104987-11-3, 0.6 or 6 mg/kg/day), or Rapa (CAS # 53123-88-9, 1 or 10 mg/kg/day) (LC Laboratories, Woburn, MA) for 1, 7, 14 or 28 consecutive days. Blood was collected at the terminal necropsy (24 hours after 1, 7, 14 or 28 days of treatment) for clinical chemistry analysis. Each kidney was cut in half (one cross section and the other longitudinal). One half of the left kidney and one half of the right kidney were used for histopathological evaluation and the remaining portions of the kidney were processed for gene expression analysis. Total RNA was isolated from rat kidney using QIAGEN RNeasy kits (QIAGEN Inc., Valencia, CA) following manufacture’s instruction. The rat genome array (RAT 230 2.0) GeneChip (Affymetrix, Santa Clara, CA) was used for gene expression profiling.

first: Yuxia

last: Cui

first: James

last: Auman

first: Qihong

last: Huang

first: Supriya

last: Jayadev

first: Jeff

last: Chou

first: Richard

middle: S

last: Paules


title: Estrogen regulated genes in rat testes and their relationship to recovery of spermatogenesis after irradiation

status: Public on Nov 22 2011

city: Houston

first: Wei

last: Zhou

state: TX

address: 1515 Holcombe Blvd

department: Department of Experimental Radiation Oncology

institute: M.D.Anderson Cancer Center

summary: Despite numerous observations of effects of estrogens on spermatogenesis, identification of estrogen-regulated genes in the testis is limited. We previously showed in rats, in which irradiation had completely blocked spermatogonial differentiation, that testosterone (T) suppression with GnRH-antagonist and antiandrogen stimulated spermatogenic recovery and addition of estradiol (E2) to this regimen accelerated this recovery. We report here the global changes in testicular cell gene expression induced by the E2 treatment. By minimizing the changes in other hormones and also having concurrent data on the regulation of the genes by those hormones, we were able to dissect the effects of estrogen on gene expression, independent of gonadotropin or T changes. Expression of 20 genes, largely in somatic cells, was up- or down-regulated between 2- and 5-fold by E2. There were also early germ cell genes whose expression increased but this was a result of a small increase in spermatogonial numbers. The striking enrichment of transcripts not corresponding to known genes among the E2-downregulated probes led to the identification of one as micro-RNA miR-34a. We propose that genes whose expression levels are altered in one direction by irradiation and in the opposite direction by both T suppression and E2 treatment are candidates for controlling the block in differentiation. Several genes, including insulin-like 3 (Insl3), satisfied those criteria. If they are indeed involved in the inhibition of spermatogonial differentiation, they may be candidate targets for clinical treatments to enhance recovery of spermatogenesis following gonadotoxic exposures, such as those resulting from cancer therapy.

overall_design: 6 sample replicates of hormonal ablation plus estradiol treatment, compared to previous 14 Sample replicates of sham treatment and 11 Sample replicates of hormonal ablation treatment groups in GSE15243

first: Olga

middle: U

last: Bolden-Tiller

first: Shan

last: Shao

first: Connie

last: Weng

first: Gunapala

last: Shetty

first: Mahmoud

last: AbuElhija

first: Pirjo

last: Pakarinen

first: Ilpo

last: Huhtaniemi

first: David

middle: N

last: Stivers

first: Zhilin

last: Liu

first: Marvin

last: Meistrich


title: Mammary Gland Morphological and Gene Expression Changes Underlying Pregnancy Protection of Breast Cancer Tumorigenesis

status: Public on Sep 15 2011

city: Burlington

first: Yogi

last: Misra

state: Vermont

address: 570 Main street

department: Animal Science

institute: UVM

summary:
Pregnancy has been shown to decrease the risk of mammary carcinogenesis in human rretrospective epidemiological studies. In rodents, pregnancy prior to carcinogen administration or after carcinogen challenge has also been shown to reduce the incidence of palpable carcinomas. In this study our objective to determine the underlying genomic signature of the pregnancy and reproductive hormones on the mammary gland that contribute to the protection against mammary gland carcinogenesis.
We used the rat microarray technology to observe total transcriptome changes after the pregnancy and exogenous reproductive hormone stimulation of the mammary gland.

overall_design: Fifteen 3 month old post-pubertal virgin Lewis rats were randomly assigned to three groups (5 rats per group): control (C), pregnancy (P) and hormone treatment (H). The P group animals had a full-term pregnancy (21-23 days) and rats in the group H were implanted subcutaneously on the dorsal midline with two silastic capsules [(0.078 inch inner diameter, 0.125 inch outer diameter) x 2 cm long; Dow Corning, Midland, MI) filled separately with 100 μg ethynyl estradiol (Sigma, St. Louis, MO) packed in a cellulose matrix (Sigma) and 30 mg of megesterol acetate (Sigma) for 21 days. The control animals had neither the hormone treatment nor being pregnant. The animals in C and P groups were also implanted with sham capsules filled with cellulose matrix only. The capsules were surgically implanted at the beginning of the experiment and removed from all animals after 21 days except that the capsules were removed from the P group following parturition (21-23 days). The delivered pups in the P group were euthanized within 4-6 hours of delivery to avoid suckling. After the removal of capsules all groups were rested a total of ~49 days before euthanasia. All animals were euthanized during metestrus stage, determined by vaginal cytology and total RNA was extracted from the mammary gland tissues using Trizol reagent.

first: Pamela

last: Bentley

first: Jeffery

last: Bond

first: Scott

last: Tighe

first: Timothy

last: Hunter

first: Feng-Qi

last: Zhao


title: Expression data from PBDE treated rats at PND22 and Week 13

status: Public on Oct 05 2011

first: Keith

last: Shockley

address: 111 TW Alexander Drive

summary:
Liver gene transcripts patterns were used to characterize toxicity from exposure to polybrominated diphenyl ethers (PBDEs), flame retardant components. In this study, Wistar Han dams were exposed by gavage to the PBDE mixture (DE71) starting at gestation day 6 (GD 6) and continuing to weaning on postnatal day 21 (PND 21).  Offspring from the dams began PBDE direct dosing on PND 12 and were dosed daily through PND 21.  After weaning, they were dosed 5 days per week for another 13 weeks.  Liver samples were collected at PND 22 and week 13 for liver gene expression analysis and interrogated with the Affymetrix Rat Genome 230 2.0 Array.
PBDE treatment induced 1,066 liver gene transcript changes in females and 1,200 transcriptional changes in males at PND 22 (false discovery rate (FDR) < 0.01), but only 263 liver transcriptional changes at 13 weeks in male rats (FDR <0.05). No significant differences in dose response were found between male and female pups.

overall_design: There were a total of 6 groups and 5x replication for each group, for 30 total samples that were analyzed. The groups were (1) pup-male-CTL, (2) pup-female-CTL, (3) pup-male-PBDE, (4) pup-female-PBDE, (5) rat-male-CTL, (6) rat-male-PBDE. We generated the following pairwise comparisons using R/maanova: malePups(PBDE vs CTL), femalePups(PBDE vs CTL), maleRats(PBDE vs CTL), CTLpups(male vs female), PBDEpups(male vs female). We also performed ANOVA test for SEX-by-DOSE (pups) and AGE-by-DOSE (males). For pups, genes with an FDR≤1% were selected; for rats, genes with FDR < 5% were selected.

middle: R

first: June

middle: K

last: Dunnick


title: Gene expression in lungs from male HIV transgenic rats

city: Albquerque

first: Amie

last: Lund

state: NM

address: 2425 Ridgecrest Dr. SE

department: Environmental and Cardiopulmonary Toxicology

institute: Lovelace Respiratory Research Institute

summary: HIV Tg rats exhibit pulmonary hypertension and pulmonary artery remodeling.  In an effort to begin to understand cell signaling pathways which are altered in lungs from HIV transgenic rats, we used microarray analysis.

overall_design: n=3 samples of lung tissue from 3 month old male HIV transgenic rat and n=3 samples of lung tissue from 3 month oldmale F344 (control) rat

first: Jay

last: Naik


title: Transcriptional signature of the developing rat testes and ovaries following embryonic exposure to 2,3,7,8-TCDD

status: Public on Oct 12 2011

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

summary: We determined global gene changes in immature ovaries and testes in response to an in utero exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure. Microarray analysis was performed using testes and ovaries of the dioxin-exposed dams’ offspring. One hundred and thirteen genes were differentially expressed in ovaries and 56 genes in testes of 14 and 5 days-old, respectively. Real-time PCR was used to validate and extend data using RNA extracted from 5 to 145-day old rat testes and 3 to 25-day old rat ovaries. A single gene of the classic dioxin battery, i.e., the repressor of the aryl hydrocarbon receptor (Ahrr) was found altered in testes. In contrast, several of them including Cyp1a1, Cyp1b1, Nqo1, and Ahrr were found up-regulated in ovary, pituitary (a different endocrine organ) and liver. In addition to Ahrr, we identified 6 genes targeted by dioxin in both gonads, including the chemokines Cxcl4, Ccl5. Ccl5 gene expression levels were also regulated in pituitary and liver, so as pituitary Cxcl4. Four genes targeted by TCDD in testis and meeting stringent criteria were further surveyed. It included 2 genes with no previous reported function in testis, Art2b, Gzmf, Hpgds and Fgf13. Fgf13 was down-regulated in testis, and pituitary but not in ovary or liver. Interestingly, Art2b and Gzmf were up-regulated in testis, liver and pituitary but not ovary. Finally, Hpgds was unique in that expressed in various tissues it was regulated by TCDD in the gonads but not in the other tissues studied.

overall_design: Transcriptomic analysis on testes at 5 days and in ovaries at 14 days. In both cases, 3 rats treated in utero by TCDD were compared to 3 rats treated with sesame-oil vehicle

first: Solange

last: Magre

first: Diane

last: Rebourcet

first: Muhammad

last: Ishaq

first: Richard

last: Wargnier

first: Cyrille

last: Debard

first: Hubert

last: Vidal

first: Joëlle

last: Cohen-Tannoudji

first: Brigitte

last: Le Magueresse-Battistoni


title: Dietary zinc status reversibly alters both the feeding behaviors of the rats and gene expression patterns in diencephalon

status: Public on Dec 01 2011

city: Bunkyo-ku, Tokyo

first: Shinji

last: Okada

address: 1-1-1 Yayoi

country: Japan

institute: The University of Tokyo

summary: Nutritional status influences feeding behaviors, food preferences and taste sensations. For example, zinc-deficient rats have been reported to show reduced and cyclic food intake patterns with increased preferences for NaCl. Although some impairments of the central nervous and endocrine systems have been speculated to be involved in these phenomena, the effects of short-term zinc deficiency on the brain have not been well examined to date. In this study, we performed a comprehensive analysis of the gene expression patterns in the rat diencephalon, which is a portion of the brain that includes the hypothalamus and thalamus, after short-term zinc deficiency and also during zinc recovery. The rats showed reduced and cyclic food intake patterns with increased salt preferences after a 10-day dietary zinc deficiency. A comparative analysis of their diencephalons using cDNA microarrays revealed that approximately 1% of the genes expressed in the diencephalons showed significantly altered expression levels. On the other hand, a 6-day zinc supplementation following the deprivation allowed for the recovery to initial food intake behaviors and salt preferences. The expression levels of most of the genes that had been altered by exposure to zinc deficient conditions were also recovered. These results show that feeding behaviors, taste preferences and gene expression patterns in the diencephalon respond quickly to changing zinc levels. This suggests that the gene expression changes observed in the diencephalon and the accompanying functional changes may be related to the development of deviations in feeding behaviors and increased preferences for NaCl in zinc-deficient rats.

overall_design:
Four-week-old male Sprague-Dawley rats were purchased from Charles River Japan (Yokohama, Japan). Fifteen rats were individually housed in a stainless steel cage in a room with constant humidity at 22 ± 1 °C under a 12 h light-dark cycle (lights on at 8:00). Zinc-deficient diets (# D19488M, Research Diets, New Brunswick, NJ, USA) were based on the AIN-93G diet and contained 0.6 mg zinc / 1000 g diet (Table 1). For the control zinc-sufficient diets, zinc sulfate supplements were provided with up to 30.0 mg zinc / 1000 g diet. Rats were fed the control diets ad libitum for 1 week for adaptation and then were divided into two groups matched for body weight.
  For the zinc-deficient experiment, rats in the ZD group (n =9) were allowed to eat the zinc-deficient diets ad libitum. The rats in the PF group (n = 6) were pair-fed the control diets to match the intake of the ZD rats. Two fluid bottles with deionized water were attached to each cage for the entire experiment with the exception of the 48 h preference test, in which 300 mM NaCl was provided from days 6 to 8. Zinc was limited for 10 days to reduce the effects of differences in salt intake in the preference test between the two groups.
  For the zinc recovery experiment, the ZR (n = 9) and ZRPF (n = 6) groups were subjected to the same conditions as above. Briefly, after 1 week of adaptation, ZR rats were fed the zinc-deficient diets ad libitum, and ZRPF rats were pair-fed the control diets for 10 days. After that, the rats in both the ZR and ZRPF groups were fed the fixed amount (13 g) of the control diets for the 6 day zinc recovery period to avoid any differences in food intake between the two groups that would be caused by pair-feeding because the previous report showed rapidly increased food intake following the initiation of the zinc-sufficient diets after zinc deficiency [1]. The diet amounts were restricted to the average consumption of the ZR group on the last day of the zinc-deficient period. The 48 h two-bottle preference tests for 300 mM NaCl were performed from days 6 to 8 during the deficient period and from days 14 to 16 during the recovery period. The analysis removed one rat from the ZRPF group showing more than a 0.5 of preference ratio to the 300 mM NaCl solution and three rats from the ZR group showing less than 0.5 preference ratios as assessed by a preference test that was conducted during days 6 to 8.
  At the end of each experiment, the rats were deeply anesthetized with pentobarbital sodium. Blood samples were collected from the carotid arteries and stored at -80 °C. The brains were quickly removed from the bodies after decapitation, and the diencephalons were separated by forceps on ice. The diencephalons were washed in ice-cold phosphate-buffered saline (PBS), treated with RNAlater (Invitrogen, Carlsbad, CA, USA), and stored at -20 °C. The serum zinc concentrations were analyzed with an ICP-AES (SPS 1200 VR, Seiko Instruments, Chiba, Japan). The Animal Care Committee of the University of Tokyo approved all animal experiments.
Four average rats from each group were selected based on body weights, plasma zinc concentrations, and salt preferences.

first: Moe

last: Abuyama

first: Ryo

last: Yamato

first: Takashi

last: Kondo

first: Masataka

last: Narukawa

first: Takumi

last: Misaka


title: mRNA expression profiling in the spinal nerve ligation model of neuropathic pain in rats

status: Public on Oct 18 2011

city: Cambridge

first: Andrew

last: Hill

state: MA

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

summary: Expression profiling of  L4 and L5 Dorsal Root Ganglion (DRG) in the spinal nerve ligation model of neuropathic pain. The goal of the study was to identify genes involved in neuropathic pain

overall_design: This series of samples comprises of contralateral and ipsilateral L4 and L5 DRG tissue collected 4 weeks after rats underwent a L5 spinal nerve ligation (SNL) or a sham operation with no L5 spinal nerve ligation. This defines 8 groups (i) contralateral L4 DRG from the sham cohort (n=5), (ii) ipsilateral L4 DRG from sham cohort (n=5), (iii) contralateral L4 DRG from SNL cohort (n=5), (iv) ipsilateral L4 DRG from the SNL chort (n=5), (v) contralateral L5 DRG from the sham cohort (n=5), (vi) ipsilateral L5 DRG from sham cohort (n=5), (vii) contralateral L5 DRG from SNL cohort (n=5), (viii) ipsilateral L5 DRG from the SNL cohort (n=5)

first: David

last: vonSchack

first: Michael

last: Agostino

first: Stuart

last: Murray

first: Yizheng

last: Li

first: Padmalatha

last: Reddy

first: Jin

last: Chen

first: Sung

last: Choe

first: Brian

last: Strassle

first: Christine

last: Bates

first: Lynn

last: Zhang

first: Huijuan

last: Hu

first: Smita

last: Kotnis

first: Brendan

last: Bingham

first: Wei

last: Liu

first: Garth

last: Whiteside

first: Tarek

last: Samad

first: Jeffrey

last: Kennedy

first: Seena

last: Ajit


title: Vitamin A nutritional status and retinoic acid as regulators of gene expression in rat liver

city: University Park

first: A.

middle: Catharine

last: Ross

state: PA

address: 110 Chandlee Laboratory

department: Nutritional Sciences

institute: Penn State

summary: Vitamin A (retinol) is an essential precursor for the production of retinoic acid (RA), which in turn is a major regulator of gene expression, affecting cell differentiation throughout the body. Understanding how vitamin A nutritional status, as well as therapeutic retinoid treatment, regulates the expression of retinoid homeostatic genes is important for improving dietary recommendations and therapeutic strategies using retinoids. This study investigated genes central to processes of retinoid uptake and storage, release to plasma, and oxidation in the liver of rats under steady-state conditions after different exposures to dietary vitamin A (deficient, marginal, adequate and supplemented), and acutely after administration of a therapeutic dose of all-trans-RA. Over a very wide range of dietary vitamin A, lecithin:retinol acyltransferase (LRAT) as well as multiple cytochrome P450s (CYP26A1, CYP26B1, and CYP2C22) differed by diet and were highly correlated with one another and with vitamin A status assessed by liver retinol concentration (all correlations, P<0.05). After acute treatment with RA, the same genes were rapidly and concomitantly induced, preceding RARß, a classical direct target of RA. CYP26A1 mRNA exhibited the greatest dynamic range (change of log26 in 3 h). Moreover, CYP26A1 increased more rapidly in the liver of RA-primed rats than naïve rats. By in situ hybridization, CYP26A1 mRNA was strongly regulated within hepatocytes, closely resembling RBP4 in location. Overall, whether RA is produced endogenously from retinol or administered exogenously, changes in retinoid homeostatic gene expression simultaneously favor both retinol esterification and RA oxidation, with CYP26A1 exhibiting the greatest dynamic change.

overall_design: All rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the Steady-State Vitamin A Study (experiment 1) and the Retinoic Acid 16-hour Kinetic Study (experiment 2), lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN-93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. For experiment 1, from weaning, the offspring were fed the same diet modified to contain vitamin A at one of four levels: 0 (vitamin A deficient), 0.4 mg retinol/kg diet (vitamin A marginal), 4 mg retinol/kg diet (vitamin A adequate control), or 100 mg retinol/kg diet (vitamin A supplemented). All rats were studied at 8 weeks of age. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis. In experiment 2, at 8 weeks of age female vitamin A-deficient rats were treated with ~100 ug of All-trans-Retinoic acid (at-RA) for 0 (vehicle only), 3, 6, 10 or 16 h (n=3-4/group). Tissues were collected and RNA was prepared in the same manner as in experiment 1. In the 90-minute "first pass" kinetic study (experiment 3), female rats were purchased at 6 weeks of age and fed a stock rodent diet. When the rats were 8 weeks old they were assigned to a control (naïve) group. Rats in the naive group received an equal amount of vehicle only (vegetable oil/5% ethanol). Food was removed immediately. Sixteen hours after priming, each rat was lightly anesthetized by isoflurane-oxygen inhalation and treated with ~25 ug all-trans-RA bound to albumin [10 ug RA per 100 g bo dy weight], injected into the exposed left common iliac vein. The incision was closed with a surgical staple. The rats were allowed to recover from the anesthesia. Rats were killed at 0 minute (vehicle injection), and 30, 60, and 90 min (n = 3/group) after injection of the RA test dose. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis. For experiment 1, five biological repeats were Vitamin A deficient, seven biological repeats were Vitamin A marginal, six biological repeats were Vitamin A adequate, and two biological repeats were Vitamin A supplemented. In experiment 2, three biological repeats were performed for each of the following treatments: untreated, at-RA for 3 hours, at-RA for 6 hours and at-RA for 16 hours. Four biological repeats were treated with at-RA for 10 hours. For experiment 3, two biological repeats were untreated and three biological repeats were performed for each of the following at-RA treatment times: 30, 60 and 90 minutes. A total of 47 samples were analyzed.


title: MAP Kinase Phosphatase-1 Modulates Regional Effects of Injurious Mechanical Ventilation in Rodent Lungs

status: Public on Aug 27 2011

city: Aurora

first: Michael

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

summary:
Scientific knowledge on the subjects: Injurious mechanical ventilation amplifies acute lung injury in a heterogeneous and regional fashion but the molecular mechanisms underlying regional lung injury and the protective effects of prone positioning are unclear.
Regionally injurious ventilation is associated with discrete differential lung transcriptomic changes. Ventilating in the prone, compared with the supine position abrogates regional injury by depressing MKP-1.

overall_design: Adult rats were ventilated with high (18 mL/Kg, PEEP 0) tidal volume (Vt) in supine or prone position. Non ventilated rats were used as controls. Dorsal-caudal lung mRNA was analyzed by microarray.

first: Moo

last: Park

first: Qianbin

last: He

first: Amen

last: Sergew

first: David

middle: W

last: Riches

first: Richard

last: Albert

first: Ivor

last: Douglas


title: Inhibitory Role of Notch1 in Calcific Aortic Valve Disease

status: Public on Aug 26 2011

city: Columbus

first: Vidu

last: Garg

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

summary:
Aortic valve calcification is the most common form of valvular heart disease, but the mechanisms of calcific aortic valve disease (CAVD) are unknown. NOTCH1 mutations are associated with aortic valve malformations and adult-onset calcification in families with inherited disease. The Notch signaling pathway is critical for multiple cell differentiation processes, but its role in the development of CAVD is not well understood. The aim of this study was to investigate the molecular changes that occur with inhibition of Notch signaling in the aortic valve. Notch signaling pathway members are expressed in adult aortic valve cusps, and examination of diseased human aortic valves revealed decreased expression of NOTCH1 in areas of calcium deposition. To identify downstream mediators of Notch1, we examined gene expression changes that occur with chemical inhibition of Notch signaling in rat aortic valve interstitial cells (AVICs).
We found significant downregulation of Sox9 along with several cartilage-specific genes that were direct targets of the transcription factor, Sox9.  Loss of expression Sox9 has been published to be associated with aortic valve calcification. Utilizing an in vitro porcine aortic valve calcification model system, inhibition of Notch activity resulted in accelerated calcification while stimulation of Notch signaling attenuated the calcific process.  Finally, the addition of Sox9 was able to prevent the calcification of porcine AVICs that occurs with Notch inhibition. In conclusion, loss of Notch signaling contributes to aortic valve calcification via a Sox9-dependent mechanism.

overall_design: 3 samples of aortic valve interstitial cells treated with DAPT were compared with 3 samples of aortic valve interstitial cells treated with DMSO

first: Asha

last: Acharya

first: Sara

last: Koenig

first: Cristi

middle: L

last: Galindo

first: Harold

last: Garner


title: Expression data from rat pluripotent stem (PS) cells

status: Public on Aug 18 2011

city: beijing

first: Yan

last: Shen

address: yiheyuan lu No.5

institute: Laboratory of Stem Cell and Regenerative Biology

summary: Various pluripotent stem (PS) cells can be isolated from early developing embryos in mouse. Among these, two kinds of PS cells were isolated from mouse blastocysts: conventional embryonic stem (ES)  cells with domed morphology that are maintained with LIF and BMP for self-renewal, and FAB-ES cells with flat morphology that need bFGF, activinA and BIO for self-renewal. Here, we report a novel PS cell line from rat blastocysts, which is distinguishable from conventional ES cells but is morphologically similar to mouse epiblast stem cell (EpiSC) lines. We used microarrays to detail the global program of gene expression of rES and rPS.

overall_design: Rat embryonic stem cell (ES) and rat flat pluripotent stem (fPS) cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We analysed each sample for three replications.

first: Hongkui

last: Deng

first: Cheng

last: Shi

first: Wei

last: Wei


title: Exposure to Nickel, Chromium, or Cadmium Causes Distinct Changes in the Gene Expression Patterns of a Rat Liver Derived Cell Line

status: Public on Aug 19 2011

city: Ft. Detrick

first: John

last: Lewis

state: MD

address: 568 Doughten Drive

department: Biomarkers Program

institute: U.S. Army Center for Environmental Health Research

summary:
Many heavy metals, including nickel (Ni), cadmium (Cd), and chromium (Cr) are toxic industrial chemicals with an exposure risk in both occupational and environmental settings that may cause harmful outcomes. While these substances are known to produce adverse health effects leading to disease or health problems, the detailed mechanisms remain unclear. To elucidate the processes involved in the of toxicity of nickel, cadmium, and chromium at the molecular level and to perform a comparative analysis, H4-II-E-C3 rat liver-derived cell lines were treated with soluble salts of each metal using concentrations derived from viability assays, and gene expression patterns were determined with DNA microarrays.
We identified both common and unique biological responses to exposure to the three metals. Nickel, cadmium, chromium all induced oxidative stress with both similar and unique genes and pathways responding to this stress. Although all three metals are known to be genotoxic, evidence for DNA damage in our study only exists in response to chromium. Nickel induced a hypoxic response as well as inducing genes involved in chromatin structure, perhaps by replacing iron in key proteins. Cadmium distinctly perturbed genes related to endoplasmic reticulum stress and invoked the unfolded protein response leading to apoptosis. With these studies, we have completed the first gene expression comparative analysis of nickel, cadmium, and chromium in H4-II-E-C3 cells.

overall_design: H4-II-E-C3 cells were were exposed to nickel (II) chloride (NiCl2), cadmium chloride (CdCl2), or sodium dichromate (Na2Cr2O7) for 24 hours. The cells were treated with a low, mid, and high concentration of each chemical and shared a control for each biological replicated, and we exposed 4 biologcial replicates for a total of 44 samples.

first: Matthew

last: Permenter

last: Jackson


title: Optimized amplification and single-cell analysis identify GnRH-mediated activation of Rap1b in primary rat gonadotropes.

status: Public on Aug 17 2011

city: New York

first: Tony

last: Yuen

state: NY

address: One Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

summary: Identifying the early gene program induced by GnRH would help understand how GnRH-activated signaling pathways modulate gonadotrope secretory response. We previously analyzed GnRH-induced early genes in LbT2 cells, however these lack GnRH self-potentiation, a physiological attribute of gonadotropes. To minimize cellular heterogeneity, rat primary pituitary cultures were enriched for gonadotropes by 40-60% using a sedimentation gradient. Given the limited number of gonadotropes, RNA was amplified prior to microarray analysis. Thirty-three genes were up-regulated 40 minutes after GnRH stimulation. Real-time PCR confirmed regulation of several transcripts including fosB, c-fos, egr-2 and rap1b, a small GTPase and member of the Ras family. GnRH stimulated rap1b gene expression in gonadotropes, measured by a sensitive single cell assay. Immunocytochemistry revealed increased Rap1 protein in GnRH-stimulated gonadotropes. These data establish rap1b as a novel gene rapidly induced by GnRH and a candidate to modulate gonadotropin secretion in rat gonadotropes.

overall_design: Primary rat gonadotrope cells were exposed to 10 nM GnRH for 40 min, then harvested and processed for RNA extraction using a Qiagen RNeasy mini kit (Qiagen, Valencia, CA). A total of 12 Affymetrix Rat Expression Array 230 v2.0, namely 6 GnRH-treated and 6 vehicle-treated samples, each containing 31,000 gene clusters, were used. Data analysis was performed by Affymetrix GeneChip Operating System (GCOS). A gene was considered to be up-regulated by GnRH if there is at least 50% concordance across multiple pairwise comparisons of GnRH- vs. vehicle-treated microarrays, and if the fold-change was at least 1.50.

first: Hanna

last: Pincas


title: Liver-protecting Effect of Maple Syrup

city: Kanagawa

first: Asuka

last: Kamei

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

department: Project for development of food functionality assessment methods

institute: Kanagawa Academy of Science and technology

summary: Rats fed a 20%-maple syrup diet (maple syrup group) for 11 days showed significantly lower values of the hepatic function markers than those fed a 20%-sugar mix syrup diet (control) likewise. One reasons was suggested by DNA microarray analysis which revealed that the expression of genes for enzymes of ammonia production were down-regulated in the liver of maple syrup group.

overall_design: Rats were quarantined and conditioned by administration of the authentic AIN93G diet for 4 days. Rats had free access to the diet and drinking water during this preliminary feeding. For feeding tests, they were dichotomized (n = 7 and 8) for maple syrup and sugar mix syrup group, respectively, and then fed for 11 days on either the AIN93G diet containing 20% maple syrup or on the 20% sugar mix syrup with a similar sugar composition; the amount of maple syrup or the sugar mix syrup was arranged. Rats in both diet groups were fasted for 16 hours, prior to being anesthetically sacrificed for dissection.

first: Yuki

last: Watanabe

first: Fumika

last: Shinozaki

first: Yuji

last: Nakai

first: Soichi

last: Arai

first: Keiko

last: Abe


title: ssDNA mapping in dmc1 strains

status: Public on Aug 15 2011

first: Andreas

last: Hochwagen

address: 1009 Silver Center 100 Washington Square East

institute: New York University

type: Genome variation profiling by genome tiling array

summary: ssDNA enrichment was used to map and compare DSB hotspots in dmc1, pch2 dmc1, sir2 dmc1, orc1-161 dmc1, dmc1 rdnadelete and dmc1 chr2:12 translocation strains.

overall_design: 6 samples, 2 replicates each.  Averaged data is available as a supplementary file on the Series record (below).

first: Gerben

last: Vader

first: Hannah

last: Blitzblau

first: Mihoko

last: Tame

first: Jill

last: Falk

first: Lisa

last: Curtin


title: Tofu decreases serum lipid levels and modulates hepatic gene expression involved in lipid metabolism in rats

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

summary:
The effects of freeze-dried tofu, a traditional Japanese soy food, were compared with those of major active soy components, protein and isoflavone, by observing physiological differences and global transcriptomes in the liver of male rats.
The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). Significance of expressional change among groups was tested by 2-way ANOVA on the normalized CEL data, which was deposited in a tab-separated ASCII text format. Principal components were identified on the summarized gene data.

overall_design: Rats were randomly divided into 6 groups of 5 samples and assigned experimental diets for 14 days. The experimental diets were as follows: casein diet (C); C containing isoflavone (CI) soy protein diet (S); S containing isoflavone (SI); a diet containing 100 g/kg each of protein derived from casein and freeze-dried tofu (T10); a diet containing 200 g/kg of protein derived from freeze-dried tofu (T20). CI and SI were supplemented with a mixture of isoflavones to match the isoflavone level of T20.

first: Yoko

last: Takahashi


title: Expression data from the hearts of aged Norway Brown rats (18-22 months-old)

status: Public on Jul 23 2011

city: Davis

first: Li

last: Lin

address: 451 Health Sciences Way

department: Department of Medicine

institute: University of California, Davis

summary: Despite an abundance of evidence to the contrary from animal studies, large clinical trials on humans have shown that estrogen administered to post-menopausal women increases the risk of cardiovascular disease.  However, timing may be everything, as estrogen is often administered immediately after ovariectomy (ovx) in animal studies, while estrogen administration in human studies occurred many years post-menopause.  This study investigates the discrepancy by administering 17ß-estradiol (E2) in a slow-release capsule to Norway Brown rats both immediately following ovx and 9 weeks post-ovx (Late), and studying differences in gene expression between these 2 groups as compared to age-matched ovx and sham operated animals.  Two different types of microarray were used to analyze the left ventricles from these groups:  an Affymetrix array (2 samples/group, each sample contained total RNAs pooled from 3 rats) and an Inflammatory Cytokines and Receptors PCR array (N=4 /group).  Key genes were analyzed by western blotting.  Ovx without replacement led to an increase in caspase 3, caspase 9, calpain 2, MMP9, and TNFα.  Caspase 6, STAT3, and CD11b increased in the Late group, while TIMP2, MMP14, and collagen I α1 were decreased.   MADD and fibronectin were increased in both Ovx and Late.  TNFα protein levels increased with Late replacement. Many of these changes were prevented by early E2 replacement.  These findings suggest that increased TNFα may be involved in some of the deleterious effects of delayed E2 administration seen in human studies.

overall_design: The rats were randomly assigned to four groups: Sham, Ovx, Early estrogen group, and Late estrogen group. The Sham rats were anesthetized, had their body cavities opened and then immediately closed with no tissue removal; the Ovx group underwent ovariectomy.  The Early estrogen group after ovariectomy had a 0.5 mg 17-β estradiol 90-day slow release pellet (Innovative Research of America, Sarasota, FL) implanted subcutaneously in the back of the neck at the time of surgery.  The Late estrogen group underwent ovariectomy and had a subcutaneous estrogen pellet placed, as above, at 9 weeks post-ovx. RNA target was prepared according to the instructions of the manufacturer (Affymetrix). For each RNA sample, good-quality total RNA from three rat hearts were pooled together in equal amounts and used to synthesize double-strand cDNA using a one-cycle cDNA synthesis kit (Affymetrix, P/N 900431).  This approach allows repetitive analysis of all groups by the array in a group representative and cost effective manner, and has been used effectively by other investigators. Two pooled RNA samples were prepared for each group, and all the RNA samples were proceeded with Affymetrix expression chip analysis.

first: Anne

last: Knowlton


title: Mouse Macrophage Cells: Control vs. Burkholderia pseudomallei infected cells

status: Public on Jul 15 2011

city: Taoyuan County

first: Ssu Ching

last: Chen

address: 300 Jhongda Rd., Jhongli City

country: Tajikistan

institute: National Central University

summary: Transcriptional profiling of mouse macrophage cells comparing control untreated cells with macrophage cells infected with Burkeholderia pseudomallei.  Goal was to determine the effects of bacterial infection on global macrophage gene expression.

overall_design: Two-condition experiment, macrophage vs. infected macrophage cells.

first: Ssu

middle: C


title: Eukaryotic origin-dependent DNA replication in vitro reveals sequential action of DDK and S-CDK kinases.

status: Public on Jul 22 2011

first: Stephen

middle: P

last: Bell

address: 68-630, 77 Massachusetts Ave.

department: Biology

institute: MIT

type: Genome binding/occupancy profiling by genome tiling array

summary: Initiation of eukaryotic DNA replication requires temporal separation of helicase loading from helicase activation and replisome assembly.  Using an in vitro assay for eukaryotic origin-dependent replication initiation, we investigated the control of these events.  After helicase loading, we found that the Dbf4-dependent Cdc7 kinase (DDK) initially drives origin recruitment of Sld3 and the Cdc45 helicase-activating protein.  Corresponding in vivo studies found that DDK was required for Cdc45 binding at early origins during G1.  Upon activation of S-phase cyclin-dependent kinases (S-CDK), a second helicase-activating protein (GINS) and the remainder of the replisome are recruited to the origin.  Investigation of DNA polymerase recruitment showed that Mcm10 and DNA unwinding both were critical for recruitment of the lagging but not leading strand DNA polymerases.  Our studies identify distinct roles for DDK and S-CDK during helicase activation and support a model in which the leading strand DNA polymerase is recruited prior to DNA unwinding and initial RNA primer synthesis.

overall_design: We performed chromatin immunoprecipitation (ChIP) against Cdc45 in CDC7 and cdc7-4 cells arrested in G1 phase to assess the requirement of the Dbf4-dependent kinase on the recruitment of Cdc45 to origin DNA during G1.

first: Ryan

last: Heller

first: Sukhyun

last: Kang

first: Wendy

last: Lam

first: Shuyan

first: Clara

last: Chan


title: Expression data from junctional zone of placenta in Brown Norway and Holtzman-Sprague Dawley rat strains at gestation day 18.5

status: Public on May 13 2011

city: Bunkyou-ku

first: Toshihiro

last: Konno

state: Tokyo

address: Yayoi 1-1-1

department: Graduate School of Agricultural and Life Sciences

summary: Placentation differs in the BN rat strain when compared to HSD and DSS rat strains. Intrauterine trophoblast invasion is shallow and the junctional zone is underdeveloped in the BN rat. These structural differences are striking but their quantification is not conducive to high throughput analyses. In the rat, the junctional zone can be readily dissected and is more homogenous than other components of the placentation site. HSD and BN rat gestation day 18.5 junctional zone gene expression profiles were determined using DNA microarray analysis to identity placenta-associate quantitate traits.

overall_design: Total RNAs from Junctional zone tissues of gestation day18.5 HSD and BN rat strains were subjected to microarray analyses. Three biological replicates of each strains were analyzed.

first: Michael

middle: J

last: Soares


title: Expression data from rat urinary bladder and non-glandular stomach tissue samples

status: Public on Jul 19 2011

city: Thousand Oaks

first: Scott

last: Taylor

address: One Amgen Center Drive

institute: Amgen Inc.

summary: Seven novel and potent Raf small molecule kinase inhibitors were evaluated in 7-day oral repeat-dose rat toxicity studies. All compounds tested induced hyperplasia in multiple tissues. Microarrays were used to investigate transciptional changes associated by treatment with a single compound to gain insight into the cellular changes that may contribute to the tissue hyperplasia.

overall_design: Two groups (25 females/group) received oral daily dosing for 7 days of either Vehicle or compound C1 dosed at 100 mg/kg. Five animals from each group were euthanized on Days 1 (4-5 hrs post first dose; received 1 dose), 2 (received 1 dose), 3 (received 2 doses), 5 (received 4 doses) and 8 (received 7 doses). Bladder tissues were collected and profiled at all five time points. Stomach tissues were collected and profiled at the earliest two time points. A single day 3 animal was not available for genomic profiling; therefore, expression data was collected for a total of 49 bladder and 20 stomach samples.

first: John

last: Wisler

first: Cynthia

last: Afshari

first: Mark

last: Fielden

first: Cameron

last: Zimmermann

first: Josette

last: Carnahan

first: Steven

last: Vonderfecht


title: Expression data from livers of high fat fed rats treated with ACC inhibitor PF-04923503

status: Public on Jun 30 2011

city: Groton

first: William

last: Esler

state: CT

address: Eastern Point Road

summary: Fundamental alterations in lipid metabolism including increased rates of de novo lipogenesis (DNL), reduced fatty acid oxidation (FAOX) and ectopic lipid accumulation in skeletal muscle and liver are characteristic of type 2 diabetes mellitus (T2DM) and have been hypothesized to directly contribute to the molecular pathogenesis of the disease. Acetyl-CoA carboxylase (ACC) catalyzes the formation of malonyl-CoA, the rate limiting substrate for DML and key regulator of FAOX. ACC inhibitors have the potential to pharmacologically rebalance these metabolic alterations. In the present study, PF-04923503, a potent dual ACC1/ACC2 inhibitor with properties optimized for in vivo studies, suppressed levels of malonyl-CoA in primary hepatocytes, rat skeletal muscle ex vivo, as well as rat liver and skeletal muscle in vivo. This impact on malonyl-CoA was directly correlated (r2>0.9) with reduced hepatic DNL and inversely correlated with incresed rates of FAOX (r2>0.9). The pharmacological eccfect of PF-04923503 persisted with chronic treatment. High-fat fed rats treated with PF-04923503 for six weeks showed dose-dependent reductions in skeletal muscle and liver lipid accumulation. These changes correlated directly with markers for improved insulin sensitization. However, liver gene expression indicates that pharmacological inhibition results in compensation by up-regualtion of genes involved with DNL. These results suggest that pharmacological inhibition of ACC may have utility to help rebalance metabolic abnormalities in T2DM and improve insulin sensitivity.

overall_design: Differential gene expression was assessed by Affymetrix microarray experiments for 15 liver samples across 3 pharmacological treatment groups (vehicle control 0.5% methylcellulose had 5 samples, PF-04923503 10mpk had 5 samples, PF-04923503 30mpk had 5 samples)

first: Shaun

last: Grosskurth

first: Max

last: Kuhn

first: Shelley

middle: G

last: des Etages

first: Kirk

last: McPherson

first: Paul

last: Amor


title: Expression data from amoeboid and ramified microglia isolated from the corpus callosum of 5-day and 4-week old rat brain

status: Public on Jun 11 2011

city: Singapore

first: S Thameem

last: Dheen

address: Medical Drive 10

country: Singapore

institute: National University of Singapore

summary:
Microglia, the resident immune cells of the central nervous system (CNS), have two distinct phenotypes in the developing brain: amoeboid form, known to be amoeboid microglial cells (AMC) and ramified form, known to be ramified microglial cells (RMC) alongside several intermediate forms. The AMC are characterized by being proliferative, phagocytic and migratory whereas the RMC are quiescent and exhibit a slow turnover rate. The AMC transform into RMC with advancing age, and this transformation is indicative of the gradual shift in the microglial functions. Both AMC and RMC respond to CNS inflammation, and they become hypertrophic when they are activated by trauma, infection or neurodegenerative stimuli. The molecular mechanisms and functional significance of morphological transformation of microglia during normal development and in disease conditions is not clear. It is hypothesized that AMC and RMC are functionally regulated by a specific set of genes encoding various signaling molecules and transcription factors. To address this, we carried out cDNA microarray analysis using lectin-labeled AMC and RMC isolated from frozen tissue sections of the corpus callosum of 5-day and 4-week old rat brain respectively, by laser capture microdissection (LCM). The global gene expression profiles of both microglial phenotypes were compared and the differentially expressed genes in AMC and RMC were clustered based on their functional annotations. This genome wide comparative analysis helps in identifying genes that are specific to AMC and RMC. The novel and specific molecules identified in both microglial phenotypes can be targeted for therapeutic purposes in developing and adult brain diseases.
We used microarrays to identify the genes specific to amoeboid and ramified microglia.

overall_design: RNA was isolated from the laser-captured amoeboid and ramified microglia from the corpus callosum of 5-day and 4-week old rat brain. The RNA was hybridised onto Affymetrix Rat 230 2.0 array.

first: S

middle: T


title: Discriminant for genotoxic and non-genotoxic carcinogens by differentially expressed gene profiling

status: Public on Aug 11 2011

city: Seoul

first: seulji

last: lee

address: 599 Gwanak-ro, Gwanak-gu

department: collage of pharmacy

country: South Korea

institute: Seoul Nat'l Univ.

summary: The need for an efficient carcinogenicity test prompted this study, in which we used a microarray-based genomics approach, with a short-term in vivo model, in combination with insights from statistical and mechanistic analyses. We performed additional experiments to support the significance of the microarray results. Carcinogens were evaluated based on differences in the mechanisms involved in the response to genotoxic (GTX) carcinogens and non-genotoxic (NGTX) carcinogens. Microarray data were analyzed for 2 time points after treatment with the following 6 carcinogens. The analysis was performed using t-tests to compare the fold changes, and we selected differentially expressed genes (DEGs) and evaluated the reasons for differential expression in terms of cellular pathways and processes. We mapped the DEG-related pathways to analyze cellular processes, and we were able to uncover significant mechanisms that involve critical cellular components, such as CDKN1A (p21) and BAX. In addition, a comparison of the data from two time points showed that the repeated administration model was more effective than a single administration for carcinogen research. The classification analysis of selected DEGs was performed by setting microarray data of 4 carcinogens as test sets; these test sets were evaluated as classifiers. Microarray results were further supported using the Comet and micronucleus assays. It was found that gene expression profiling using microarrays, followed by pathway analysis, was effective in increasing the understanding of the characteristics of different carcinogens, and the efficiency of these methods was exemplified by the short-term (3 day) nature of the animal experiments.

overall_design: The following 10 hepatocarcinogens were used: 2-acetylaminofluorene (53-96-3), diethylnitrosamine (55-18-5), 4-dimethylamino-3'-methyl azobenzene (55-80-1), clofibrate (637-07-0), 1,4-dioxane (123-91-1), DL-ethionine (67-21-0), 1,3-dichloro-2'-propanol (96-23-1), urethane (51-79-6), sodium nitrite (7632-00-0), and methyleugenol (93-15-2). Forty-one data were obtained for the training compounds in this study. We treated rats with one of three compounds or a control for each GTX and NGTX experimental group and measured 2 time points for each group. All experimental procedures were repeated three times. We excluded 1 file that was found to be a failure. Each ‘.CEL’ file obtained as a raw data file was standardized using the RMA (Robust Multi-array Average) algorithm.

first: Seul

last: Lee

first: Woo

first: Young

last: Yum

first: Soojung

last: Sohn

first: Won

first: Sung

last: Kwon

first: Sang-Cheol

last: Kim

first: Sue

last: Park

first: Kyung

middle: H

last: Koo

first: Yuneung

first: Jeong

first: Joo

first: Johan

last: Lim

first: Jeongmi

first: Jee

middle: E


title: ChIP-chip of DSB factors in wild type and pch2 strains

first: Andreas

last: Hochwagen

summary: ChIP-chip was used to compare DSB factor localization in wild type and pch2 strains

overall_design: 10 samples, 2-3 replicates each. Averaged data is available as a supplementary file on the Series record (below).

first: Gerben

last: Vader

first: Hannah

last: Blitzblau

first: Mihoko

last: Tame

first: Jill

last: Falk

first: Lisa

last: Curtin


title: Fetal Rat Testis mRNA Expression after 50 mg/kg Dibutyl Phthalate Exposure

status: Public on Apr 25 2011

city: Wilmington

first: Kamin

last: Johnson

state: DE

address: 1600 Rockland Road

department: Nemours Biomedical Research

institute: Alfred I. duPont Hospital for Children

summary: High dose level dibutyl phthalate (DBP) exposure of fetal rat testes in vivo inhibits testosterone production (i.e. endocrine disruption).  Here, fetal testis mRNA levels were profiled following exposure to a DBP dose level that did not significantly reduce testosterone levels.  The goal was to identify the constellation of gene expression changes that do not correlate with endocrine disruption.

overall_design: Fischer 344 rats were exposed via oral gavage of the dam to vehicle (corn oil) or 50 mg/kg (body weight) DBP daily from gestational day (GD) 12 to 20.  The day after mating was defined as gestational day 0.  Six hours after the final exposure on GD20, fetal testes were dissected and mRNA levels quantified using Affymetrix Rat Expression 230 2.0 microarrays.

first: Qing

last: Xia


title: Mapping of meiotic double-strand break (DSB) sites and DSB factor association near repetitive DNA elements in S. cerevisiae

summary:
DNA double strand breaks (DSBs) in repetitive sequences are a potent source of genomic instability, due to the possibility of non-allelic homologous recombination (NAHR). Repetitive sequences are especially at risk during meiosis, when numerous programmed DSBs are introduced into the genome to initiate meiotic recombination 1. Within the budding yeast repetitive ribosomal (r)DNA array, meiotic DSB formation is prevented in part through Sir2-dependent heterochromatin 2,3. Here, we demonstrate that the edges of the rDNA array are exceptionally susceptible to meiotic DSBs, revealing an inherent heterogeneity within the rDNA array. We find that this localised DSB susceptibility necessitates a border-specific protection system consisting of the meiotic ATPase Pch2 and the origin recognition complex subunit Orc1. Upon disruption of these factors, DSB formation and recombination specifically increased in the outermost rDNA repeats, leading to NAHR and rDNA instability. Strikingly, the Sir2-dependent heterochromatin of the rDNA itself was responsible for the induction of DSBs at the rDNA borders in pch2? cells. Thus, while Sir2 activity globally prevents meiotic DSBs within the rDNA, it creates a highly permissive environment for DSB formation at the heterochromatin/euchromatin junctions. Heterochromatinised repetitive DNA arrays are abundantly present in most eukaryotic genomes. Our data define the borders of such chromatin domains as distinct high-risk regions for meiotic NAHR, whose protection may be a universal requirement to prevent meiotic genome rearrangements associated with genomic diseases and birth defects.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Two types of study were undertaken to understand the regulation of meiotic DSB formation close to repetitive DNA elements in yeast. First, DSBs were mapped using ssDNA enrichment in strains isogenic for a dmc1 mutation, and also including pch2 delete, orc1-161, rdna delete and a reciprocal translocation between chromosomes 2 and 12 (trans2to12). Second, the association of the DSB factors Hop1, Rec114, Mer2, and Mre1, as well as total histone H3 and H3K4-trimethylation were measured by ChIP-chip analysis in wild-type and pch2 delete strains.


title: Gene expression profiles in rat mesenteric lymph nodes upon supplementation with conjugated linoleic acid during gestation and suckling

city: Barcelona

first: Carlos

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Barcelona

summary:
A summary of the work associated to these microarrays is the following:

Diet plays a role in the development of the immune system, and polyunsaturated fatty acids can modulate the expression of a variety of genes. Human milk contains conjugated linoleic acid (CLA), a fatty acid that seems to contribute to immune development. Indeed, recent studies carried out in our group in suckling animals have shown that the immune function is enhanced after feeding 80:20 isomer mix of c9,t11 and t10,c12 CLA, respectively. However, little work has been done on the effects of CLA on gene expression, and even less regarding immune system development in early life. With all these concepts in mind, we determined the expression profile of Mesentheric Lymph Nodes (MLN) from animals supplemented with CLA during gestation and suckling through dam’s milk (Group A) or by oral gavage (Group B), supplemented just during suckling (Group C) and control animals (Group D) with the aid of the specific GeneChip ® Rat Genome 230 2.0 (Affymettrix). Bioinformatic analyses were performed using the GeneSpring GX software package v10.0.2 and lead to the identification of 123 genes differentially expressed in all three dietary approaches. Generation of a Biological Association Network (BAN) evidenced several genes, such as connective tissue growth factor (Ctgf), tissue inhibitor of metalloproteinase 1 (Timp1), galanin (Gal), synaptotagmin 1 (Syt1), growth factor receptor bound protein 2 (Grb2) actin gamma 2 (Actg2) and smooth muscle alpha actin (Acta2), as highly interconnected nodes of the resulting network. Gene underexpression was confirmed by Real-Time RT-PCR. We conclude that Ctgf, Timp1, Gal and Syt1, among others, are genes modulated by CLA supplementation that may have a role on lymphoproliferation and mucosal immune responses in early life.

overall_design: The aim of our study was to evaluate, by using whole genome microarrays, the effects of dietary supplementation with an 80:20 isomer mix of c9,t11 and t10,c12 CLA, respectively, on Mesentheric Lymph Nodes gene expression, during gestation and/or suckling. Three experimental approaches were conducted to assess the effects of CLA supplementation on I) pups from dams fed with 1% CLA diet during the two weeks of gestation and throughout the suckling period (Group A). These pups received CLA through the dam’s milk during suckling (Total Period of CLA Supplementation (TPS) 5 wk); II) pups from dams fed with 1% CLA diet during gestation and standard diet during suckling. These pups were CLA-supplemented daily during suckling by oral gavage (TPS 5 wk) (Group B); III) pups from dams fed standard diet during gestation and suckling and receiving CLA by daily oral gavage throughout the suckling period (TPS 3 wk) (Group C). Group D, pups from dams fed standard diet throughout the study, constituted the reference diet group (TPS 0 wk). Triplicate samples were hybridized for each experimental condition (12 samples in total). The samples provided were analyzed using the specific software GeneSpring GX.

first: Elisabet

last: Selga

first: Veronique

last: Noe


title: Gene expression profiling of vasoregression in the retina

status: Public on Mar 15 2011

city: Mannheim

first: Li

last: Li

address: Theodor-Kutzer-Ufer

country: Germany

institute: University Heidelberg

summary:
Vasoregression is a hallmark of vascular eye diseases but the mechanisms involved are still largely unknown. We have recently characterized a rat ciliopathy model which develops primary photoreceptor degeneration and secondary vasoregression. To improve the understanding of secondary vasoregression in retinal neurodegeneration, we used microarray techniques to compare gene expression profiles in this new model before and after retinal vasoregression. Differential gene expression was validated by quantitative RT-PCR, Western blot and immunofluorescence. Of the 374 genes regulated more than twofold, the MHC class II invariant chain CD74 yielded the strongest upregulation, and was allocated to activated microglial cells close to the vessels undergoing vasoregression. Pathway clustering identified genes of the immune system, inflammatory signaling, and components of the complement cascade upregulated during vasoregression. Furthermore, macroglial cells were markedly activated. Together, our data suggest that glial cells involved in retinal immune response participate in the initiation of vasoregression in the retina.
we used microarray techniques to define gene expression profiles related to vasoregression in a rat ciliopathy model.

overall_design: PKD-2-247 rats (TGR) and male Sprague-Dawley (SD) rats at 1 and 3 months of age were used for the analysis. SD rats served as control in this study. Three individual rat retinae (n=3) in each group were analysed.

first: Hans-Peter

last: Hammes

first: Norbert

last: Gretz

first: Yuxi

last: Feng

first: Yumei

last: Wang

first: Sigrid

last: Hoffmann


title: Deep Sleep and Parietal Cortex Gene Expression Changes are Related to Cognitive Deficits with Age

status: Public on Apr 21 2011

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary:
Background: Age-related cognitive deficits negatively affect quality of life and can presage serious neurodegenerative disorders. Despite sleep disruption’s well-recognized negative influence on cognition, and its prevalence with age, surprisingly few studies have tested sleep’s relationship to cognitive aging.
Methodology: We measured sleep stages in young adult and aged F344 rats during inactive (enhanced sleep) and active (enhanced wake) periods. Animals were behaviorally characterized on the Morris water maze and gene expression profiles of their parietal cortices were taken.
Principal Findings: Water maze performance was impaired, and inactive period deep sleep was decreased with age. However, increased deep sleep during the active period was most strongly correlated to maze performance. Transcriptional profiles were strongly associated with behavior and age, and were validated against prior studies. Bioinformatic analysis revealed increased translation and decreased myelin/ neuronal pathways.
Conclusions: The F344 rat appears to serve as a reasonable model for some common sleep architecture and cognitive changes seen with age in humans, including the cognitively disrupting influence of active period deep sleep. Microarray analysis suggests that the processes engaged by this sleep are consistent with its function. Thus, active period deep sleep appears temporally misaligned but mechanistically intact, leading to the following: first, aged brain tissue appears capable of generating the slow waves necessary for deep sleep, albeit at a weaker intensity than in young. Second, this activity, presented during the active period, seems disruptive rather than beneficial to cognition. Third, this active period deep sleep may be a cognitively pathologic attempt to recover age-related loss of inactive period deep sleep. Finally, therapeutic strategies aimed at reducing active period deep sleep (e.g., by promoting active period wakefulness and/or inactive period deep sleep) may be highly relevant to cognitive function in the aging community.

KEYWORDS: frontal cortex, rat, young or aged

overall_design: We implanted young and aged Fischer 344 rats (n = 6/ group) with wireless EEG, EMG and movement monitoring devices to measure sleep architecture. Animals were trained in the Morris water maze to assess cognitive function, and frontal cortices were removed for microarray analysis.sleep disruption and cognitive decline.

first: Heather

last: Buechel

first: Jelena

last: Popovic

first: Luke

last: Searcy

first: Nada

last: Porter

first: Olivier

last: Thibault


title: Hepatic gene expression changes in aging and R-α-lipoic acid supplementation: Necroinflammatory phenotype, lipid synthesis regulation and circadian rhythms.

status: Public on Mar 03 2011

city: Corvallis

first: Tory

last: Hagen

state: OR

address: 110 Weniger Hall

department: Linus Pauling Institute

institute: Oregon State University

summary: To determine the effects of age and lipoic acid supplementation on hepatic gene expression, we fed young (3 months) and old (24 months) male Fischer 344 rats a diet with or without 0.2% (w/w) R-α-lipoic acid (LA) for two weeks. Total RNA isolated from liver tissue was analyzed by Affymetrix microarray to examine changes in transcriptional profile.  Results showed an increase in pro-inflammatory gene expression in the aging liver, with increased immune cell function and tissue remodeling genes, representing 45% of the age-related transcriptome changes. Increased inflammation was corroborated by increases in soluble ICAM1 levels with age. There were also observed age-related increases in transcription of genes related to lipid and cholesterol synthesis including Acetyl CoA Carboxylase (Acacb) and Fatty acid Synthase (Fasn).  Supplementation of old animals with LA did not reverse this necro-inflammatory phenotype, yet limited age-associated hepatic dyslipidemia.  Dietary LA further affected a small but concerted number of hepatic genes regardless of age.  These included declines in lipid and bile synthesis genes.  Decline in lipid synthesis genes was further corroborated by a decrease in Fasn and Acc protein levels.  Intriguingly, LA also altered the expression of genes governing circadian rhythm, most notably Bmal1, Npas2, and Per2, which changed in a coordinated manner with respect to their rhythmic transcription. Thus, advanced age is associated with a necro-inflammatory phenotype and increased lipid synthesis, while chronic LA supplementation influences hepatic genes associated with energy metabolism and circadian rhythm regardless of age.

overall_design: Young (3 months) and old (24 months) Fischer 344 male rats were fed an AIN-93M diet  ± 0.2% (w/w) R-α-lipoic acid for two weeks prior to sacrifice.  Total RNA was extracted from the median lobe of the liver and analyzed using Affymetrix Rat Genome 230 2.0 Genechips.  There were hybridizations for 8 animals in each of the young control, young LA-supplemented, and old control groups, and 6 animals in the old LA-supplemented group.  There are only 6 animals in the old LA group because two animals died during the two-week feeding period.  This is the reason for nonsequential numbering of animals in this group.

first: Liam

middle: A

last: Finlay