title: Differential pulmonary gene expression in a nonhuman primate model of HIV-related COPD

status: Public on Sep 25 2010

city: Pittsburgh

first: Haiwen

last: Shi

address: 3343 Forbes Ave

department: Genomics and Proteomics Core Laboratories

institute: University of Pittsburgh

summary: HIV-infected persons are at increased risk for developing pulmonary diseases including chronic obstructive pulmonary disease (COPD), and the fungal opportunistic pathogen, Pneumocystis jirovecii (Pc) has been implicated in the pathogenesis of HIV-related COPD.  We previously developed a non-human primate model of HIV-related COPD using simian-human immunodeficiency virus (SHIV) and Pc co-infection in cynomolgus macaques.  In the present study we examined gene expression profiles in lung tissue from SHIV/Pc co-infected monkeys with COPD and compared them to SHIV-infected monkeys infected with normal lung function.  Microarray technology was used to develop gene profiles, and differential gene expression was determined by a comparative evaluation of competing normalization methods applied to our expression data set followed by validation using quantitative real-time polymerase chain reaction analysis for select genes.  Of over 52,000 transcripts representing more than 20,000 genes analyzed, the SHIV/Pc infected macaques with COPD exhibited 243 differentially expressed (DE) genes compared to SHIV-infected monkeys with normal lung function.  DE genes fell into a number of functional categories which may be important in COPD development including: inflammation (pulmonary surfactants A2, B, C, D, upregulated; alternative macrophage activation-associated CC chemokine, upregulated), protease/antiprotease balance (cathepsin H, upregulated; alpha-1-chymotrypsin and secretory leukocyte peptidase inhibitor, downregulated), redox balance (glutathione peroxidase 4 and mitochondrial aldehyde dehydrogenase 2, upregulated) and tissue homeostasis (connective tissue growth factor, downregulated; ornithine decarboxylase antizyme, upregulated). These results identify factors and pathways that may be involved in early development of Pneumocystis and SHIV-associated COPD and reveal several novel, potential therapeutic targets.

overall_design: There are totally 11 samples in the experiment. The sample breakdown is as follows: KN14(group 1) is a true control in that the monkey was not infected with simian-human immunodeficiency virus (SHIV) nor was it colonized with Pneumocystis. KN02, KN03, KN07 and KN08 (group 2) are also controls of a sort. They were infected with SHIV but they did not become colonized with Pneumocystis. The remainder (KN01, KN04, KN06, KN11, KN12, KN13) (group3) were both infected with SHIV and colonized with Pneumocystis. The primary interest is in comparing the two SHIV-infected groups (2 and 3)


title: Rapid SIV Env-specific mucosal and serum antibody induction augments cellular immunity in protecting immunized, elite-controller macaques against high dose heterologous SIV challenge

status: Public on Aug 24 2010

city: Davis

first: William

last: Hu

state: CA

address: 451 Health Science Dr.

department: Medical Microbiology & Immunology

country: USA

institute: UC Davis

summary: Goal of this study was to assess the levels of protection and investigate cellular, humoral, and mucosal immune correlates on the functional and gene transcriptional levels in elite-controller macaques following high dose SIV challenge.

overall_design: Three experimental, post SIV smE660 challenge macaque jejunal samples were individually compared to four pre SIV smE660 challenge baseline samples.

first: Jean

last: Patterson

first: Satya

last: Dandekar

first: Marjorie

last: Guroff


title: Deconvolution of ChIP-chip MBF occupancies reveals the temporal recruitment of Rep2 at the MBF-target genes

status: Public on Nov 26 2010

city: Singapore

first: Majid

last: Eshaghi

state: Singapore

address: Biopolis

department: Bilogical Investigation

country: Singapore

institute: Genome Institute of Singapore

type: Genome binding/occupancy profiling by genome tiling array

summary: Deconvolution analysis using Rpb1 ChIP-chip results distinguishes the Cdc10 bindings at the Rpb1-poor loci (promoters) from those at the Rpb1-rich loci (intragenic sequences). Importantly, Res1 binding at the Rpb1-poor loci, but not at the Rpb1-rich loci, are dependent on the Cdc10 function, suggesting a distinct binding mechanism. Most Cdc10 promoter bindings at the Rpb1-poor loci are associated with the G1/S-phase genes. While Res1 or Res2 is found at both the Cdc10 promoter and intragenic binding sites, Rep2 appears to be absent at the Cdc10 promoter binding sites but present at the intragenic sites. Time-course ChIP-chip analysis demonstrates that Rep2 is temporally accumulated at the coding region of the MBF-target genes, resembling the RNAP-II occupancies.

overall_design: We analyzed MBF binding sites using Nimblegen arrays.

first: Jianhua

last: Liu


title: Biodiversity and functional genomics of endogenous small RNAs induced upon biotic and abiotic stresses in plant (gemsup)

status: Public on Oct 12 2010

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

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

summary:
au07-12_geminiselsup - gemsup - Determine the level of expresison in transgenic plants expressing geminviral gene silencing suppressors. - Transgenic lines of Arabidopsis overexpressing three different geminiviral silencing suppressors: C2, C4 and V2 were grown in adition to a control and their total RNA was extracted in order to study their genetic expressions profiles.

Keywords: gene knock in (transgenic)

overall_design: 9 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Miguel

last: A. botella

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Multiple levels of gene regulation mediate differentiation of the intracellular pathogen Leishmania

status: Public on Aug 15 2010

city: Seattle

first: Dhileep

last: Sivam

state: WA

address: 307 Westlake Ave N

department: Bioinformatics Core

institute: Seattle Biomedical Research Institute

summary: Whole genome high density tiliing array of eight timepoints from the promastitgote to amastigote differentiation process.

overall_design: RNA from two independent biological replicates from eight points in the promastigote to amastigote differentiation process were hybridized to Nimblegen arrays (Madison,WI USA) that contained 10 probes per open reading frame and 3 probes per structural RNA spotted three times per array.  The microarray probes were designed to Leishmania infantum strain JCPM5 and the sample RNA was obtained from Leishmania donovani strain S1.  The two species are thought to be nearly identical at the nucleotide level, however whole-genome sequence was not available from L. donovani.

first: Tami

last: Lahav

first: Hanne

last: Volpin

first: Amanda

last: Anderson-Green

first: Peter

middle: J

last: Myler

first: Dan

last: Zilberstein


title: FnrL regulon in Rhodobacter sphaeroides

status: Public on Jul 01 2010

city: Madison

first: Yann

middle: S

last: Dufour

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

summary: In this study, we performed a ChIP-chip experiment to determine the regulon of FnrL in Rhodobacter sphaeroides. We grew R. sphaeroides under anaerobic photosnthetic conditions, in which FnrL is expected to bind DNA and contol gene expression, and immuno-precipitated FnrL, but also sigma70 and the Beta' subunits of RNA polymerase to determine transcription activity.

overall_design: DNA immunoprecipitated with polyclonal antibodies against FnrL, sigma70, or the Beta' subunit of RNA polymerase was labelled with Cy5 and hybridized on two-color tilling arrays (triplicates for each) with genomic DNA as an input control labelled with Cy3.

first: Timothy

last: Donohue

first: Patricia

last: Kiley


title: Discovery of novel imprinted genes by transcriptional analysis of parthenogenetic embryonic stem cells

status: Public on Jun 21 2010

city: Beaverton

first: Hathaitip

last: Sritanaudomchai

state: OR

institute: OHSU

summary:
Parthenogenetic embryonic stem cells (PESCs) may have future utility in cell replacement therapies. We examined genome-wide mRNA expression profiles of monkey PESCs relative to ESCs derived from fertilized embryos. Several known paternally-imprinted genes were in the highly down-regulated group in PESCs compared to ESCs. Allele specific expression analysis of paternally-imprinted genes, i.e., those genes whose expression is down-regulated in PESCs, led to the identification of one novel candidate that was exclusively expressed from a paternal allele. Our findings suggest that PESCs could be used as a model for studying genomic imprinting and in the discovery of novel imprinted genes.

Keywords: gene expression

overall_design: The transcriptomes of rhesus monkey embryonic stem cell lines derived from IVF-produced embryos (Oregon Rhesus Macaque Embryonic Stem, ORMES-22) were compared with rhesus monkey parthenogenetic embryonic stem cell lines (heterozygous rhesus Parthenogenetic embryonic stem cell lines, rPESC-2) and homozygous rhesus Parthenogenetic embryonic stem cell lines, ORMES-9). Moreover, the transcriptomes of rPESC-2 line were also compared with ORMES-9. Finally, the adult somatic skin fibroblasts were analyzed. Three biological replicates of each cell line (A, B, C) were analyzed.

first: Hong

last: Ma

first: Vikas

last: Dighe

first: Lisa

last: Clepper

first: Sumita

last: Gokhale

first: Randy

last: Bogan

first: Jon

last: Hennebold

first: Don

last: Wolf

first: Shoukhrat

last: Mitalipov


title: Human peripheral blood cells: autoimmune diseases vs. healthy individuals

status: Public on Aug 21 2010

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

country: Japan

institute: Wakayama Medical University

summary: Gene expression profiling of peripheral blood cells from patients with rheumatoid arthritis (RA)/ systemic lupus erythematosus (SLE)/ polyarticular type juvenile idiopathic arthritis (polyJIA)/  systemic-onset JIA (sJIA) vs healthy children (HC) and healthy individual (HI).

overall_design: Peripheral blood was obtained from patients with RA (n=112), SLE (n=22), polyJIA (n=6), sJIA (n=51), HC (n=8), and HI (n=45). Blood samples from 8 HC and 45 HI are used as control.

first: Hooi-Ming

last: Lee

first: Chieko

last: Aoki

first: Satoru

last: Ishikawa

first: Hidehiko

last: Sugino

first: Yasuo

last: Adachi

first: Kenichi

last: Matsubara


title: Expression profiling analysis of lung, heart and bone of AGA002 mutant mice

status: Public on Jun 01 2010

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary: Col1a1 is located on mouse distal chromosome 11 (Celera 94607393-94622990bp; 15kb) and encodes type I procollagen that associates stoichiometrically with col1a2 in forming secreted type I mature collagen that self-assembles into a supramolecular fibrillar structure consisting of a protein family. Type I collagens are predominantly enriched in bone, cartilage, skin, tendons, and eye (i.e. in major fibrous tissues) making up the main extracellular matrix (ECM) component for support and scaffolding purposes. Col1a1 is known to be expressed in the embryo (E9.5; Northern dot blot), perioptic mesenchyme (E11), cornea (E11), skeleton (E14.5), brain meninges (E14.5), and cartilage (E14.5) at relatively early stages. Most evidence of type I collagen function is coupled to the latter stages of skeletal development, thus bypassing the major events of axis formation, tissue differentiation, and mesenchlymal-epithial interactions, for example, that are more symbolic of morphogens and growth factors. Members of the integrin cell surface receptor family of molecules mediate cell adhesion to ECM proteins such as collagen (mainly to type IV basement membrane collagen that forms into a polygonal meshwork), fibronectin, and laminin implicated in wound healing and inflammatory responses (e.g. Crohn disease, ulcerative colitis) in connective tissues. There is some evidence for protein-protein interactions between leukocyte-associated integrins and the interstitial matrix in promoting the migration and/or activation of extravasated leukocytes (e.g., T cells and monocytes) within the perivascular compartment, an ECM-rich environment. This region is surmised to be an important location where certain human leukocytes undergo differentiation (e.g. monocytes) and activation (neutrophils, monocytes, lymphocytes) upon extravascular migration. The von Willebrand factor (vWF), type C motif is found in various plasma proteins like complement factors, the integrins, collagen types, and other extracellular proteins. Thus, the majority of vWF-containing proteins are extracellular and a common feature appears to be involvement in multi protein complexes participating in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction).

overall_design: Three organs (lung, heart and bone) of 5 AGA002 mutant mice (age 2x 10 days and 3x 11 days) were analysed by cDNA microarray technology. As reference five mice, 11 days old were used 50% of the chip hybridisations are dye swap experiments.

first: Johannes

last: Beckers

first: Marion

last: Horsch

first: Frank

last: Thiele

first: Gerhard

last: Przemeck


title: Young and aged rhesus hippocampal CA1 and DG

status: Public on Apr 15 2010

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary:
Metabolic, mitochondrial and behavioral correlations with transcriptional profiles from the CA1 and DG hippocampal regions of young and aged rhesus macaque. Increasing evidence indicates that obesity correlates with impaired cognitive performance during normal aging and is a major risk factor for Alzheimer’s disease. However, little is known regarding how peripheral metabolic variables affect cellular pathways in brain regions important for memory. Brain inflammation, mitochondrial dysregulation, and altered transcriptional regulation have all been found to occur with aging, and recent microarray analyses in rodent models have linked these processes and others to age-related memory impairment. However, whether these brain changes are also associated with metabolic variables is not known. Aging monkeys exhibit several metabolic changes similar to those seen in humans. Here, we tested peripheral-brain relationships in six young (7.0 +/- 0.3 years) and six aged (23.5 +/- 0.7 years) female rhesus monkeys. Animal cognition was gauged with a variable delay task; blood constituents were assessed with a serum chemistry panel emphasizing markers of metabolic dysfunction; mitochondrial function was measured from the hippocampus of one hemisphere; and the CA1 and dentate gyrus regions of the other hippocampus were dissected out for gene expression microarray analysis. Aged animals showed reduced performance on the behavioral task, exhibited aspects of metabolic dysregulation including increased insulin, triglyceride, and chylomicron levels (consolidated into a peripheral metabolic index), and showed a significant age-related reduction in State III oxidation, a measure of mitochondrial function. Microarray analyses revealed hundreds of genes that correlated with the peripheral metabolic index. However, DAVID statistical pathway analyses showed that upregulated inflammatory genes in CA1 and downregulated transcriptional regulation genes in dentate gyrus and CA1 were particularly overrepresented among genes correlated with the peripheral index. Thus, the association of metabolic variables with specific neuropathological processes in different regions of the hippocampal formation may have implications for mechanisms through which peripheral metabolism alters the risk for Alzheimer’s disease.

Keywords: Rhesus hippocampal aging

overall_design: Six young (7.0 +/- 0.3 years) and six aged (23.5 +/- 0.7 years) female rhesus monkeys (Macaca Mulatta) were behaviorally assessed on the delayed match to sample task. Briefly, on each trial the subject observed the experimenter place a treat in either the left or right covered food well, the food wells were screened, and after a variable (zero- no delay, short- 10 seconds, long- 30 seconds) delay, the screens were removed. The subject initially selecting the food well containing the treat was rated as a correct response. Each animal received thirty trials (ten of each delay, in random order) per session, and four sessions over the course of one week. Animals were anesthetized with ketamine, venous blood was drawn for peripheral metabolic assays. Metabolic assays included standard blood chemistry and lipoprotein profiles. Animals were fatally dosed with pentobarbital and brains were removed. Hippocampi were dissected: one hippocampus was used for mitochondrial assays and proteomics, and the other was sub-dissected into CA1 and DG sub-regions for micorarrays. Procedures for mitochondrial assays and proteomics are as published previously (Sullivan et al., 2007). Hippocampal sub-region mRNA extraction, labeling and microarray (Affymetrix Rhesus) hybridization proceeded according to standard protocols (Affymetrix; Blalock et al., 2003, 2004; Rowe et al., 2007). Signal intensity and presence call data were derived with the MAS5 (Affymetrix) algorithm. Data were transferred to Excel, Bioconductor, and Multiexperiment Viewer for further analysis. Statistical tests included paired t-tests across region, and unpaired t-tests across age within each region. Post hoc correlation analyses with metabolic, mitochondrial, and behavioral data were used to refine aging related genes and biological pathways. Lists of regulated genes were analyzed for functional overrepresentation using DAVID, Onto-Express, and GenMapp.

first: Richard

last: Grondin

first: Kuey

middle: C

last: Chen

first: Olivier

last: Thibault

first: Veronique

first: Jignesh

last: Pandya

first: An

first: Amy

last: Dowling

first: Zhiming

last: Zhang

first: Patrick

last: Sullivan

first: Joe

middle: E

last: Springer

first: Nada

last: Porter

last: Gash

first: Philip

middle: W

last: Landfield


title: The SaeR/S Gene Regulatory System is Essential for Innate Immune Evasion by Staphylococcus aureus

status: Public on Feb 23 2010

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Methicillin-resistant Staphylococcus aureus (MRSA) is problematic both in hospitals and the community. Currently, we have limited understanding of mechanisms of innate immune evasion used by S. aureus. To that end, we created an isogenic deletion mutant in strain MW2 (USA400) of the saeR/S two-component gene regulatory system and studied its role in mouse models of pathogenesis and during human neutrophil interaction. In this study, we demonstrate saeR/S plays a distinct role in S. aureus pathogenesis and is vital for virulence of MW2 in a mouse model of sepsis. Moreover, deletion of saeR/S significantly impaired survival of MW2 in human blood and after neutrophil phagocytosis. Microarray analysis of genes influenced by saeR/S demonstrated SaeR/S of MW2 influences a wide variety of genes with diverse biological functions. These data shed new insight into how virulence is regulated in S. aureus and associates a specific staphylococcal gene-regulatory system with invasive staphylococcal disease.

platform_organism:
Coxiella burnetii
Rickettsia rickettsii
Chlamydia muridarum
Chlamydia pneumoniae AR39
Staphylococcus epidermidis RP62A
Staphylococcus epidermidis ATCC 12228
Staphylococcus aureus subsp. aureus MW2
Borreliella burgdorferi B31
Coxiella burnetii RSA 493
Chlamydia caviae GPIC
Chlamydia trachomatis D/UW-3/CX
Staphylococcus haemolyticus JCSC1435
Granulibacter bethesdensis

overall_design: Wild type control vs mutant at two different growth phases

first: Jovanka

last: Voyich

first: Cuong

last: Vuong

first: Mark

last: DeWald

first: Tyler

middle: K

last: Nygaard

first: Stanislava

last: Kocianova

first: Shannon

last: Griffith

first: Jennifer

last: Jones

first: Courtney

last: Iverson

first: Daniel

first: Kevin

middle: R

last: Braughton

first: Adeline

last: Whitney

first: Michael

last: Otto

last: DeLeo


title: Infection of MK2 cells with monkeypox virus

status: Public on Mar 25 2010

city: Frederick

first: Abdulnaser

last: Alkhalil

state: MD

address: 1425 Porter st.

institute: USAMRIID

summary: Orthopox viruses, including monkeypox, multiply intracellularly and induce numerous changes in host genes expression.  The virus target mainly humoral host response, and simultaneously, exploits other genes and functions to reproduce effectively.  The goal of this experiment is to identify those host genes and functions that are essential for monkeypox virus replication.

overall_design: Mock infected control cells were treated and incubated identically to time point arms, except for virus exposure.  Two time points of cells infected with monkeypox virus were harvested at 3, 7 hours post infection, and gene expression was assessed using microarray in all arms.  The experiment was done in triplicate.

first: Sofi

last: Ibrahim


title: The Origin Recognition Complex interacts with a subset of metabolic genes tightly linked to origins of replication.

status: Public on Nov 07 2009

first: Christopher

middle: Lawrence

last: Warren

address: 1400 University Ave

summary: The origin recognition complex (ORC) marks chromosomal sites as replication origins and is essential for replication initiation. In yeast, ORC also binds to DNA elements called silencers, where its primary function is to recruit silent information regulator (SIR) proteins to establish transcriptional silencing. Indeed, silencers function poorly as chromosomal origins. Several genetic, molecular, and biochemical studies of HMR-E have led to a model proposing that when ORC becomes limiting in the cell, such as in the orc2-1 mutant, only sites that bind ORC tightly, such as HMR-E, remain fully occupied by ORC, while lower affinity sites, including most origins, lose ORC occupancy. Since HMR-E possessed a unique non-replication function, we reasoned that other tight sites might reveal novel functions for ORC on chromosomes. Therefore, we comprehensively determined ORC “affinity” genome-wide by performing an ORC ChIP-on-chip in ORC2 and orc2-1 strains. Here we describe a novel group of orc2-1-resistant ORC-interacting chromosomal sites (ORF-ORC sites) that did not function as replication origins or silencers. Instead, ORF-ORC sites were comprised of protein-coding regions of highly transcribed metabolic genes. In contrast to the ORC-silencer paradigm, transcriptional activation promoted ORC association with these genes. Remarkably, ORF-ORC genes were enriched in proximity to origins of replication, and, in several instances, were transcriptionally regulated by these origins. Taken together, these results suggest a surprising connection between ORC, replication origins and cellular metabolism.

overall_design: Two arrays are used, one for WT orc2 and one for mutant orc2-1.  On each array Cy3 was the IP and Cy5 was the input (total sheared genomic DNA).  The arrays were custom designed to tile the S. cerevisiae genome (as of 8/16/2006) with a 51 nt probe every 32 bp.  The probes alternated strands as they tiled the genome.  Microarray synthesis, fluorescent-labeling of ChIP DNA, hybridization of labeled DNA to the microarray, and scanning of the microarray after hybridization were all performed by NimbleGen at a NimbleGen facility.

first: Erika

last: Shor

middle: L

first: Joshua

last: Tietjen

first: Zhonggang

last: Hou

first: Ulrika

last: Muller

first: Ilaria

last: Alborelli

first: Florence

middle: H

last: Gohard

first: Adrian

middle: I

last: Yemm

first: Lev

last: Borisov

first: James

last: Broach

last: Weinreich

first: Conrad

middle: A

last: Nieduszynski

first: Aseem

middle: Z

last: Ansari

first: Catherine

last: Fox


status: Public on Mar 08 2010

city: minneapolis

first: qingsheng

last: li

state: MN

address: Box 196, 420 Delaware ST SE

department: Microbiology

institute: University of Minnesota

summary:
Transcriptional Profiling Reveals Distinguishing Features of Immune Activation in the Lymphatic Tissues of Sooty Mangabeys and Rhesus Macaques in Early SIV Infection
Immune activation in the chronic stages of HIV-1 and SIV infection of rhesus macaques is thought to play a critical role in CD4+ T cell depletion and progression to AIDS. Conversely, the lack of immune activation in the chronic stages of SIV infection of sooty mangabeys is thought to protect this species from a pathogenic outcome. This critical difference in immune activation in rhesus macaques and sooty mangabeys has recently been shown to be established in the early stages of SIV infection where there is immune activation in both species, but in sooty mangabeys immune activation is subsequently resolved. Here we report the results of a microarray analysis of early SIV infection in the lymphatic tissues of rhesus macaques and sooty mangabeys that provides a comprehensive view of the distinguishing features of immune activation and host defenses in the two species. We confirm immune activation in sooty mangabeys, but show that it is less robust than in rhesus macaques, where positive feedback loops involving cytosolic pattern recognition receptors, and chemokines and their ligands amplify the response to early SIV infection. We confirm resolution of immune activation in sooty mangabeys, but show it to be partial and selective, identifying the interferon system and CD38 as key correlates of outcome. We also identify potentially novel immunoregulatory mechanisms that mediate resolution, and defensins as host defenses sooty mangabeys employ as expression of other innate immune system effectors declines.
The studies we report here were undertaken in a collaborative longitudinal analysis of early SIV infection in SMs described in Bosinger et al and previously reported studies (Estes et al.,  J Immunol 1008, 180, 6798-6807.). Briefly, SMs were inoculated i.v. with 1 ml of plasma from an experimentally SIVsmm-infected SM sampled at day 11 post infection, with a viral load 107 copies/ml. In our studies we analyzed axillary or inguinal lymph node biopsies that had been obtained from two SMs prior to infection; two SMs at the peak of viral replication at 14 dpi; and two SMs at 30 dpi as viral loads were decreasing to set point. We analyzed axillary or inguinal LNs from 4 RMs without SIV infection and LNs from four RMs infected intravaginally with 2x105 TCID50 of SIVmac239 and sacrificed at 14 dpi the peak of viral replication from two cross-sectional studies described in (Miller et al., The Journal of Virology 2005, 79, 9217-9227.). For lymph node (LN) biopsies, animals were anesthetized with Ketamine or Telazol; the skin over the axillary or inguinal region was clipped and surgically prepped. An incision was made over the LN, which was exposed by blunt dissection and excised over clamps. A portion of the lymph node biopsy for microarray analysis was snap frozen in liquid N2. All animals were housed and cared for at the Yerkes National Primate Research Center in Atlanta, Georgia in accordance with the regulations of the American Association of Accreditation of Laboratory Animal Care standards. These studies were approved by the Emory University and University of Pennsylvania Institutional Animal Care and Usage Committees (IACUC).
Microarray Analysis
RNA extractions, synthesis of biotin-labeled cRNA probes, microarray hybridization, and data analysis followed previously published procedures (Li et al., The Journal of infectious diseases 2004, 189, 572-582; Li et al., J Immunol 2009, 2009, 183: 1975–1982.). Briefly, snap-frozen lymph node was homogenized in TRIzol. Total RNA was isolated and further purified. Double stranded cDNA and biotin-labeled cRNA probes were synthesized, column purified and fragmented. Fifteen micrograms of fragmented cRNA was hybridized to an Affymetrix GeneChip® Rhesus Macaque Genome Array. After hybridization, chips were washed, stained with streptavidin-phycoerythrin, and scanned with GeneChip Operating Software at the Biomedical Genomics Center at the University of Minnesota. Preparation of cRNA probes and microarray hybridizations were done in duplicate for each RNA sample.
Cel. files were uploaded into the Expressionist program (Genedata, Pro version 5.1) and the expression level for each of the 47,000 transcripts in the arrays were analyzed using the RMA algorithm. The expression levels from duplicate microarrays of the same animal’s RNA were correlated and averaged. Tests for differences between the before and after infection at various time points were conducted using the 2-sample Wilcoxon signed-rank test.  Fold differences in the level of gene expression between after infection and before infection were calculated with the ratio of the means. After statistical analysis, data was sorted based on these transcript cutoffs: p-value of < 0.05 and fold change ≥ 2.0. Significantly changed genes and transcripts were uploaded into NetAffix Analysis Center (http://www.affymetrix.com/analysis/index.affx) to query gene ontology information and into Ingenuity Pathways Analysis (Ingenuity® Systems, www.ingenuity.com) for gene annotation and pathway analysis. Hierarchical clustering analysis was carried out by using Spotfire for DecisionSite for Functional Genomics.

sample_organism:
Cercocebus atys
Macaca mulatta

overall_design: We used affymetrix rhesus microarrays to profile the host transcriptional response to SIV in lymph nodes obtained from SM (Sooty mangabeys, Cercocebus atys)) and RMs ( Rhesus Macaques, Macaca mulatta) in the first two weeks of infection in studies described by Bosinger et al. (GEO accession number GSE16147) of the transcriptional profiles in peripheral blood. We confirm in these genome-wide comparisons that immune activation is a shared feature of early infection in the two species, but show that the breadth of the changes in RMs is much greater than in SMs, with evidence of positive feedback loops that amplify innate and cellular responses in RMs. We also confirm evidence of resolution of immune activation in SMs, but were surprised to find little evidence at the transcriptional level of increased expression of genes that might mediate that resolution. Lastly, we show that as expression of genes involved in host defenses decline in SMs, there is increased expression of defensins that again may represent a species-specific host defense mechanism. Samples: 12 Sooty Mangabeys (uninfected, 14 dpi, and 30 dpi) and 16 Rhesus Macaques (uninfected and 14 dpi).

first: Qingsheng

last: Li

first: Lijie

last: Duan

first: Anthony

last: Smith

first: Ming

last: Zeng

first: John

middle: V

last: Carlis

first: Guido

last: Silvestri

first: Ashley

middle: T

last: Haase


title: CpG island hypermethylation in human astrocytomas

status: Public on Jan 01 2010

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Methylation profiling by genome tiling array

summary: Astrocytomas are common and lethal human brain tumors. Here, we have analyzed the methylation status of over 28,000 CpG islands and 18,000 promoters in normal human brain and in astrocytomas of various grades using the methylated-CpG island recovery assay (MIRA). We identified six to seven thousand methylated CpG islands in normal human brain. ~5% of the promoter-associated CpG islands in normal brain are methylated. Promoter CpG island methylation is inversely and intragenic methylation is directly correlated with gene expression levels in brain tissue. In astrocytomas, several hundred CpG islands undergo specific hypermethylation relative to normal brain with 428 methylation peaks common to more than 25% of the tumors. Genes involved in brain development and neuronal differentiation, such as POU4F3, GDNF, OTX2, NEFM, CNTN4, OTP, SIM1, FYN, EN1, CHAT, GSX2, NKX6-1, RAX, PAX6, DLX2, were strongly enriched among genes frequently methylated in tumors. There was an overrepresentation of homeobox genes and 31% of the most commonly methylated genes represent targets of the Polycomb complex. We identified several chromosomal loci in which many (sometimes more than 20) consecutive CpG islands were hypermethylated in tumors. Seven of such loci were near homeobox genes, including the HOXC and HOXD clusters, and the BARHL2, DLX1, and PITX2 genes. Two other clusters of hypermethylated islands were at sequences of recent gene duplication events. Our analysis offers mechanistic insights into brain neoplasia suggesting that methylation of genes involved in neuronal differentiation, perhaps in cooperation with other oncogenic events, may shift the balance from regulated differentiation towards gliomagenesis.

overall_design: Comparison of methylation patterns of 30 astrocytomas and 6 controls

first: Tibor

last: Rauch

first: Gerd

middle: P

last: Pfeifer


title: Effects of in vitro maturation on oocyte gene expression

status: Public on May 20 2009

city: Philadelphia

first: Young

middle: Shin

last: Lee

state: PA

address: 3307 N. Broad Street AHB 557

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

summary:
In vitro oocyte maturation (IVM) holds great promise as a tool for enhancing clinical treatment of infertility, enhancing availability of non human primates for development of disease models, and facilitating endangered species preservation.  However, IVM outcomes have remained significantly below success rates obtained using in vivo matured (VVM) oocytes from humans and non human primates.  A cDNA array based analysis is presented, comparing the transcriptomes of VVM oocytes with IVM oocytes.  We observe a small set of just 59 mRNAs that are differentially expressed between the two cell types.  These mRNAs are related to cellular homeostasis, cell-cell interactions including growth factor and hormone stimulation and cell adhesion, and other functions such as mRNA stability and translation.  Additionally, we observe in IVM oocytes overexpression of PLAGL1 and MEST, two maternally imprinted genes, indicating a possible interruption or loss of correct epigenetic programming.  These results indicate that, under certain IVM conditions, oocytes that are molecularly highly similar to VVM oocytes can be obtained, however the interruption of normal oocyte-somatic cell interactions during the final hours of oocyte maturation may preclude the establishment of full developmental competence.

Keywords: oocyte maturation

overall_design: Comparison of in vitro matured MII-stage oocytes (4 biological replicates) with in vivo matured MII-stage oocytes (4 biological replicates)

first: Keith

last: Latham

last: VandeVoort


title: Expression Profile of Embryonic Stem Cell Derived Serotonin Neurons

status: Public on May 21 2009

first: Arubala

middle: P.

last: Reddy

address: 505 NW 185th Ave

department: Oregon National Primate Research Center

institute: Oregon Health and Sciences University

summary: The rhesus embryonic stem cell line 366.4 differentiates into serotonin neurons. RNA was extracted from ESC colonies, embryoid body (Ebs), Neurospheres in selection (N1), Proliferating serotonin neurons (N2) and differentiating serotonin neurons (N3). RNA was labeled with Enzo biotin labelling kit and hybridized to Rhesus chip from Affymetrix.

overall_design: single sample represent each stages and total 5 rhesus chip were hybridized

first: Cynthia

last: Bethea


title: Gene expression in unfertilized eggs and the MBT stage of zebrafish embryos

status: Public on Feb 03 2010

city: Oslo

first: Håvard

last: Aanes

state: Oslo

address: Ullevålsveien 72

department: Biochemistry

country: Norway

institute: Norwegian School of Veterinary Science

summary: Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. Culture of embryo-derived cells results in a switch from histone acetylation to K9 and K27 trimethylation on genes transcriptionally inactivated, resulting in a profile similar to that of fibroblasts. All promoters retain H3K4me3, indicating no correlation between H3K4me3 occupancy and gene expression. Our results illustrate a complex chromatin state on the promoter of pluripotency-associated genes in the zebrafish embryo, shortly after the embryonic genome is turned on.

overall_design: We assessed gene expression in unfertilized eggs and the MBT stage of zebrafish embryos (~ 3.5 hpf) using a 44K custom designed chip from Agilent (3 and 4 replicates, respectively). Genes of interest were extracted and evaluated according to expression dynamics and levels.

first: Philippe

last: Collas


title: Glycogen Accumulation in Chlamydia trachomatis is Controlled by its Plasmid Through Regulation of glgA

status: Public on Jan 15 2009

first: Dan

last: Sturdevant

summary:
C. trachomatis possess a cryptic 7.5 kb plasmid of unknown function.  Here we describe a comprehensive molecular and biological characterization of the naturally occurring plasmidless human Chlamydia trachomatis strain L2 (25667R).  We found that despite minimal chromosomal polymorphisms the LGV L2 (25667R) strain was indistinguishable from the L2 (434) plasmid positive strain in its in vitro infectivity characteristics such as growth kinetics, plaquing efficiency, and plaque size. The primary in vitro phenotypic differences between L2 (434) and L2 (25667R) were the accumulation of glycogen granules in the inclusion matrix and the lack of the typical intra-inclusion Brownian-like movement characteristic of C. trachomatis strains.  Conversely, we observed a marked difference between the two strains in their ability to colonize and infect the female mouse genital tract. The ID50 of the L2 (25667R) plasmidless strain was 500 fold greater (1.XX x 10X IFU) than the L2 (434) plasmid bearing strain (1. XX x 10X IFU). Transcriptome analysis of the two strains clearly demonstrated a decrease in transcript levels of a subset of chromosomal genes for the L2 (25667R) strain.  Among those genes was glgA which encodes for glycogen synthase; a finding consistent with the failure of the L2 (25667R) strain to accumulate glycogen granules.  Collectively, these findings support an important role for the plasmid in in vivo infectivity and suggest that this virulence characteristic might be controlled by the plasmids ability to regulate the expression of specific chromosomal genes.   These results also support an important role for the plasmid in the pathogenesis of human infection and disease.
Keywords: strain comparison

overall_design: C. trachomatis strain L2-25667R compared to strain L2-434

last: Carlson

first: William

middle: M

last: Whitmire

first: Luke

last: Wicke

first: Kimmo

last: Virtaneva

first: Daniel

middle: J

last: Kupko III

first: Stephen

middle: F

last: Porcella

first: Neysha

last: Martinez-Orengo

first: Deborah

middle: D

last: Crane

first: Robert

last: Heinzen

first: Laszlo

last: Kari

first: Harlan

last: Caldwell


title: Endometrial profile of low-dose estradiol and tamoxifen combination therapy

status: Public on Feb 03 2009

city: Winston-Salem

first: Charles

last: Wood

state: NC

address: Medical Center Blvd

department: Pathology

institute: Wake Forest University School of Medicine

summary: Combination therapy with estrogen and a selective estrogen receptor modulator (SERM) is a promising approach to safely alleviate important side effects related to estrogen deficiency in women at high risk for breast cancer.  Data related to endometrial safety of estrogen+SERM co-therapies are limited, however.  The primary goal of this study was to evaluate the endometrial profile of low-dose E2 and Tam alone and in combination.

overall_design: In this study 16 postmenopausal female cynomolgus macaques were randomized to receive placebo, low-dose micronized estradiol (E2, 0.25 mg/1800 kcal), the SERM tamoxifen (Tam, 20 mg/1800 kcal), or E2+Tam in a parallel-arm design. Endometrial samples were collected after 4 months of treatment and used for microarray analysis.


title: Pluripotency Genes Overexpressed in Primate Embryonic Stem Cells Are Localized on Homologues of Human 16, 17, 19 and X

status: Public on Oct 21 2009

city: Pittsburgh

first: Thomas

last: Richards

institute: University of Pittsburgh

summary: While human embryonic stem cells (hESCs) are predisposed towards chromosomal aneploidities on 12, 17, 20 and X, rendering them susceptible to transformation, the specific genes expressed are not yet known. Here, by identifying the genes over expressed in pluripotent rhesus ESCs (nhpESCs) and comparing them to both their genetically-identical differentiated progeny (teratoma fibroblasts) as well as genetically-related differentiated parental cells (parental skin fibroblasts from whom gametes were used for ESC derivation), we find that some of those over expressed genes in nhpESCs cluster preferentially on rhesus chromosomes 16, 19, 20 and X, homologues of human chromosomes 17, 19, 16 and X respectively. Differentiated parental skin fibroblasts display gene expression profiles closer to nhpESC profiles than to teratoma cells, which are genetically identical to the pluripotent nhpESCs. Twenty over and under expressed pluripotency modulators, some implicated in neurogenesis, have been identified. The over expression of some of these genes discovered using pedigreed nhpESCs derived from prime embryos generated by fertile primates, which is impossible to perform with the anonymously donated clinically-discarded embryos from which hESCs are derived, independently confirms the importance of chromosome 17 and X regions in pluripotency and suggests specific candidates for targeting differentiation and transformation decisions.

overall_design:
To overcome the genetic background heterogeneity which might mask some aspects of the actual stemness signature, we utilized a newly established bank of pedigreed non-human primate embryonic stem cells (nhpESCs) to generate a unique non-human primate “stemness gene” list generated by the comparison of nhpESC gene expression to two different sources of genetically-identical or genetically-related differentiated fibroblasts. The first were grown out of skin explants taken from the nonhuman primate parents from which gametes were used to generate the stem cell lines. The second were teratoma explants. RNA was isolated from all three types of cells: 1. Skin fibroblasts; these samples are indicated by the letter M (monkey) before the monkey identification number and sample label (a-f). 2. nhpESCs denoted by C (cell line) followed by the cell line and sample. 3. Fibroblast explants from teratomas generated by the injection of nhpESC into immune compromised mice. Since there were a number of teratomas for every stem cell line, we designated the nomenclature as follows: T (teratoma) - number of teratoma from the line - line name - sample. Therefore, TA31b denotes that this is the second sample of the first teratoma from line 3106.   A total of 39 samples were used for this comparison: Pluripotent pedigreed rhesus ESCs (female ESC line C3806; male ESC line C3106) were compared to genetically identical differentiated progeny grown from their resultant teratomas (five male teratomas and three female teratomas: ‘T’, i.e. TA31, TB31, TC31, TD31, TE31 and TA38, TB38, TC38 respectively) as well as to differentiated cells from their macaque parents (‘M’). therefore, 2 cell lines (3106 and 3806) 3 types of skin fibroblasts and 8 teratoma fibroblasts (5 generated from line 3106 and 3 from 3806). All samples were run in biological triplicates for a total of 39 samples.
A total of 39 samples were used for this comparison: Pluripotent pedigreed rhesus ESCs (female ESC line C3806; male ESC line C3106) were compared to genetically identical differentiated progeny grown from their resultant teratomas (five male teratomas and three female teratomas: ‘T’, i.e. TA31, TB31, TC31, TD31, TE31 and TA38, TB38, TC38 respectively) as well as to differentiated cells from their macaque parents (‘M’). therefore, 2 cell lines (3106 and 3806) 3 types of skin fibroblasts and 8 teratoma fibroblasts (5 generated from line 3106 and 3 from 3806). All samples were run in biological triplicates for a total of 39 samples.

first: Ahmi

last: Ben-Yehudah

first: Christopher

middle: S

last: Navara

first: Carrie

last: Redinger

first: Jocelyn

last: Mich-Basso

first: Carlos

last: Castro

first: Stacie

last: Oliver

first: Lara

last: Chensny

first: Naftali

last: Kaminski

first: Gerald

last: Schatten


title: Oral mucosal response to SIV infection

status: Public on Jan 13 2009

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary: The objectives of this study were to determine the molecular mechanisms of host response during transition from primary to chronic SIV infection in the oral mucosa of rhesus macaques

overall_design: Transcriptioinal profiles were determined for 2 rhesus macaques infected for 6 wk with SIVmac251 and compared to profiles of 3 uninfected healthy controls

first: Satya

last: Dandekar


title: Effect of Ovarian Hormone on Gene Expression in Rhesus Dorsal Raphe Nucleus with Rhesus Affymetrix Chip

first: Arubala

last: Reddy

summary:
A small block of the midbrain containing the dorsal raphe nucleus was obtained from ovariectomized monkeys treated with placebo, estrogen, progesterone or estrogen plus progesterone
for one month. The RNA was extracted and hybridized to the Rhesus Affymetrix chip. The results were analyzed with GCOS 1.0

overall_design: Each chip represents one monkey. N=3 monkeys per treatment.

first: Cynthia

last: Bethea


title: Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumour

status: Public on Feb 27 2009

city: Bristol

first: Anthony

last: Dallosso

address: University Walk

department: School of Cellular & Molecular Medicine

country: United Kingdom

institute: University of Bristol

overall_design: The data consists of five microarrays hybridized with methylated DNA immunoprecipitated from Wilms' tumours and from a normal foetal kidney control

middle: R

first: Karim

last: Malik


title: mRNA expression data from skeletal muscle of type 2 diabetes

status: Public on Jan 19 2010

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

summary: We used microarray technology to profile mRNA expression in the skeletal muscle of normal (NGT), glucose intolerant (IGT) and type 2 diabetic (DM) subjects. Groups were classified using WHO criteria and, importantly, the DM group were free of anti hypoglycaemic medication for one week prior to biopsy.

overall_design: Total RNA was extracted from the vastus lateralis of normal (NGT), glucose intolerant (IGT) and type 2 diabetic (DM) subjects (n = 118 in total) who had been free of hypoglycemic medication for one week. RNA was hybridized to Affymetric HGU133plus2 platform following manufacturer's directions.

first: James

last: Timmons


title: SIV Encephalitis and Uninfected Control: Hippocampus Expression Profiles

status: Public on Aug 29 2009

city: Omaha

first: Howard

last: Fox

state: NE

address: 985800 Nebraska Medical Center - DRC 3008

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

summary: HIV-associated dementia (HAD) is a syndrome occurring in HIV-infected patients with advanced disease that likely develops as a result of macrophage and microglial activation as well as other immune events triggered by virus in the central nervous system. The most relevant experimental model of HAD, rhesus macaques exhibiting SIV encephalitis (SIVE), closely reproduces the human disease and has been successfully used to advance our understanding of mechanisms underlying HAD.  In this study we integrate gene expression data from uninfected and SIV-infected hippocampus with a human protein interaction network and discover modules of genes whose expression patterns distinguish these two states, to facilitate identification of neuronal genes that may contribute to SIVE/HIV cognitive deficits. Using this approach we identify several downregulated candidate genes and select one, EGR1, a key molecule in hippocampus-related learning and memory, for further study. We show that EGR1 is downregulated in SIV-infected hippocampus and that it can be downregulated in differentiated human neuroblastoma cells by treatment with CCL8, a product of activated microglia.  Integration of expression data with protein interaction data to discover discriminatory modules of interacting proteins can be usefully employed to prioritize differentially expressed genes for further study. Investigation of EGR1, selected in this manner, indicates that its downregulation in SIVE may occur as a consequence of the host response to infection, leading to deficits in cognition.

overall_design: RNA from duplicate hippocampal samples taken from nine control monkeys and nine monkeys with evidence of SIV encephalitis were hybridized to Affymetrix arrays.

first: Steven

last: Head

first: Merril

last: Gersten

first: Cecilia

last: Marcondes

first: Claudia

last: Flynn

first: Mehrdad

last: Alirezaei

first: Tim

last: Ravasi

first: Trey

last: Ideker


title: Differentially expressed genes in subpopulations of monocytes from non infected animals.

status: Public on Jan 31 2009

city: Chestnut Hill

first: K

middle: C

last: Williams

state: MA

address: 140 Commonwealth Avenue

department: Biology

institute: Boston College

summary:
On the basis of the cell-surface molecule expression, CD16+ monocytes are likely comprised of distinct subpopulations of monocytes rather than a continuum of CD14+ monocytes with differing levels of cell activation. To better study this, we used gene array analysis that compared overall gene expression profiles of CD16+ subpopulations (CD14+CD16+ and CD16+) with that of CD14+CD16-. Gene expression in three FACS-sorted monocyte subsets was assessed by Affymetrix rhesus macaque oligonucleotide gene arrays that contain 52,024 probe sets covering 47,000 monkey genes. There were 29,361 probe sets that expressed in at least one subpopulation (raw array signal intensity > 32). Raw data were processed using robust multi-array average. To identify the most strongly, differentially expressed genes in each subpopulation, we only selected transcripts with consistently greater than four-fold difference (P < .05). In comparison to CD14+CD16- monocyte subset, a large number of genes (9098/29361, 30.9%) were differentially expressed in both CD14+CD16+ and CD16+ subsets: 1999 genes down-regulated; and 7099 genes up-regulated. Altogether, we observed large-scale gene expression differences between the CD14+CD16- subset and the two CD16+ subsets (CD14+CD16+ and CD16+), demonstrating transcriptional heterogeneity. The differential gene expression between CD16- and CD16+ monocytes underscore the fundamental differences between these cells.
Comparisons between CD14+CD16+ and CD16+ were made to identify the genes that distinguish between these two CD16+ subpopulations. A relatively small number of genes were specifically associated with each subpopulation. Thirty-one genes were expressed strongly in CD14+CD16+ subset compared to CD16+ subset, and 94 genes were expressed strongly in CD16+ subset compared to CD14+CD16+ subset. A small set of genes that were expressed differentially between the two CD16+ subpopulations highlights similarity between the two cell types, but differentially expressed genes of function observed in each subset suggest different roles that these two subpopulations may play in vivo.

overall_design: To identify differentially expressed genes in subpopulations of monkey monocytes, three monocyte subsets from two normal uninfected rhesus macaques were FACS sorted based on their CD14 and CD16 expression. RNA purification and labeling, hybridization, array scanning, and image quantification were performed according to the manufacturer’s instructions. Briefly, FACS-isolated monocytes were spun down and lysed in Trizol reagents (Invitrogen), and total RNA was prepared using PureLink Micro-to-Midi Total RNA Purification system (Invitrogen). Quality of RNA was determined by 2100 Bioanalyzer RNA LabChip (Agilent Technologies). One hundred ng of high-quality total RNA was subjected to Affymetrix 1-cycle or 2-cycle synthesis amplification, fluorescent labeling, and hybridization to Affymetrix Rhesus Genome Arrays. Expression data was obtained from two aligned replicates using an Affymetrix GSC3000 scanner and processed by GCOS software (Affymetrix). Partek Genomic Suite System was used for downstream analysis of GCOS processed data. Signals from all probe sets were normalized using Rhesus Array Normalization Controls.

first: W

middle: K

last: Kim

first: H

last: Do

first: M

last: McGrath


title: Gene expression data throughout spontaneous functional regression of the rhesus macaque corpus luteum.

status: Public on Oct 27 2008

city: Beaverton

first: Randy

middle: Lloyd

last: Bogan

department: Reproductive Sciences

institute: Oregon National Primate Research Center

summary:
Luteolysis of the corpus luteum (CL) during non-fertile cycles involves a cessation of progesterone (P4) synthesis (functional regression) and subsequent structural remodeling. The molecular processes responsible for initiation of luteal regression in the primate CL are poorly defined. Therefore, a genomic approach was utilized to systematically identify differentially expressed genes in the rhesus macaque CL during spontaneous luteolysis. CL were collected prior to (days 10-11 post-LH surge, mid-late [ML] stage) or during (days 14-16, late stage) functional regression. Based on P4 levels, late stage CL were subdivided into functional late (FL, serum P4 > 1.5 ng/ml) and functionally-regressed late (FRL, serum P4 < 0.5 ng/ml) groups (n=4 CL/group). Total RNA was isolated, labeled and hybridized to Affymetrix genome microarrays that contain elements representing the entire rhesus macaque transcriptome. With the ML stage serving as the baseline, there were 681 differentially expressed transcripts (>2-fold change; p< 0.05) that could be categorized into three primary patterns of expression: 1) increasing from ML through FRL, 2) decreasing from ML through FRL, and 3) increasing ML to FL, followed by a decrease in FRL. Ontology analysis revealed potential mechanisms and pathways associated with functional and/or structural regression of the macaque CL. Quantitative real-time PCR was used to validate microarray expression patterns of 13 genes with the results being consistent between the two methodologies. Protein levels were found to parallel mRNA profiles in 4 of 5 differentially expressed genes analyzed by Western blot. Thus, this database will facilitate the identification of mechanisms involved in primate luteal regression.

Keywords: time course plus functional state of corpus luteum

overall_design: The first experimental factor is the stage of the luteal phase when the CL was collected. There were two stages: 1) between days 10-12 post LH-surge (mid-late stage), and 2) days 14-16 (late stage). The mid-late stage is a transitionary period where CL are still functional (i.e., producing significant quantities of P4) but are nearing the time when luteolysis initiates in non-conception cycles, and the late stage corresponds to the normal period when functional regression (cessation of P4 secretion) occurs in non-conception cycles. The second experimental factor is the functional state of the CL which was determined by measuring serum concentrations of P4 at the time of CL collection. Late stage CL with serum P4 levels > 1.5 ng/ml were considered to be functional, and those with serum P4 < 0.5 ng/ml were considered to have completed functional regression. Measuring mRNA levels in CL collected from these groups provides a comprehensive analysis of the primate transcriptome throughout the normal period of functional regression in the macaque CL. There were 12 biological replicates: n = 4 per group, 3 groups in total. The mid-late CL were used as the baseline reference for gene expression.

middle: L

first: Melinda

last: Murphy

first: Jon

last: Hennebold


title: Changes in polysome loading as a consequence of RHA downregulation

status: Public on Dec 20 2008

city: Columbus

first: Kathleen

last: Boris-Lawrie

state: OH

address: 1925 Coffey Rd

department: Department of Veterinary Biosciences

institute: The Ohio State University

summary:
RNA helicase A (RHA) binds its target transcripts at the post-transcriptional control element (PCE) located in the 5’ untranslated region (UTR). This interaction represents an “RNA switch” that regulates protein synthesis. Down regulation of RHA by siRNAs was used to identify transcripts with RHA-dependent translation. Reduced accumulation of RNA in polysomes was monitored with microarrays.
Changes in cytoplasmic RNA steady state abundance was monitored as well. Sixty nine genes exhibit decreased transcript polysome association when subjected to RHA downregulation. A majority of the transcripts that experienced a reduction in the polysome fraction had no significant change in their cytoplasmic abundance (45 genes).

Keywords: gene expression array-based

overall_design: Cytoplasmic lysates of cells treated with RHA targeted or non-silencing control siRNAs were separated by sucrose density gradient centrifugation. Ribosomal RNA profiles were generated, fractions containing polysomes were collected, and RNA was extracted.

first: Julia

last: Hernandez


title: Evolution of virulence control by the staphylococcal agr quorum-sensing regulator

status: Public on Jan 05 2009

first: Dan

last: Sturdevant

summary:
The Staphylococcus aureus accessory gene regulator (agr) is a prototype quorum-sensing system in Gram-positive bacteria and a paradigmatic example of gene regulation by a small regulatory RNA, RNAIII. Using genome-wide transcriptional profiling in the community-associated methicillin-resistant (CA-MRSA) strain MW2, we demonstrate here that in contrast to the current model of target gene regulation by agr, a large subset of agr-regulated genes is controlled independently of RNAIII. This group comprised predominantly metabolism genes, whereas virulence factors were mostly controlled by RNAIII. Remarkably, the phenol-soluble modulin (PSM) leukocidin genes were the only virulence determinants under RNAIII-independent control, emphasizing their exceptional role in S. aureus physiology and pathogenesis. Of note, PSM promoters bound the AgrA response regulator protein, previously believed to interact exclusively with agr promoters, explaining the exceptionally strict control of PSMs by agr. Our results suggest that virulence factor control is a secondary acquisition of the agr regulon, which evolved by development of RNAIII around the mRNA of the PSM d-toxin, exemplifying how gene control via a small regulatory RNA may be linked to a pre-established regulatory circuit. In addition to elucidating agr control in CA-MRSA, which revealed features potentially crucial for CA-MRSA pathogenesis, our study establishes a novel two-level model of cell-density dependent gene regulation in S. aureus and gives important insight into the connection of metabolism and virulence control in this leading opportunistic pathogen.
Keywords: Wild type control vs mutant

overall_design: Wild type in triplicate is compared to mutant in triplicate totalling 27 samples

first: Shu

middle: Y

last: Queck

first: Max

last: Jameson-Lee

first: Amer

middle: E

last: Villaruz

first: Thanh-Huy

last: Bach

first: Burhan

last: Khan

first: Daniel

first: Min

last: Li

first: Michael

last: Otto


title: SarZ is a key regulator of biofilm formation and virulence in Staphylococcus epidermidis

status: Public on Jul 16 2008

summary:
Biofilm-associated infection by the leading nosocomial pathogen Staphylococcus epidermidis is a major problem for the public health system. Here we used an especially discriminatory, two-step screen to discover key biofilm factors. We identified the transcriptional regulator and SarA paralog SarZ as a novel important determinant of biofilm formation and biofilm-associated infection by S. epidermidis. Notably, a sarZ mutant strain exhibited significantly reduced survival in two different models of biofilm-associated infection. Further, in addition to its significant influence on the transcription of the biosynthetic operon for S. epidermidis biofilm exopolysaccharide, sarZ impacted the expression of a series of virulence factors, including lipases and proteases.
As a likely consequence of the regulated proteolytic activity, we observed increased resistance to an important human antimicrobial peptide, indicating a role for sarZ in the regulation of immune evasion. Interestingly, sarZ deficiency led to a hemolytic phenotype, a feature not commonly observed in S. epidermidis. Thus, our study indicates a key role for the SarZ regulator in maintaining the typical S. epidermidis phenotype, which is characterized by pronounced biofilm formation, immune evasion, and suppressed acute virulence, a likely reason for the success of S. epidermidis as a colonizer and pathogen in chronic, biofilm-associated infection.
Keywords: Wild type control vs mutant

overall_design: Wild type untreated in triplicate is compared to SarZ mutant in triplicate

first: Li

last: Wang

first: Dandan

last: Dong

first: Cuong

last: Vuong

first: Qian

last: Gao


title: Co-immunoprecipitation of RNAs with RNA helicase A (RHA)

summary:
Given that RHA regulates translation by binding a PCE located at the 5’ UTR of the target transcripts a genome-wide screen was performed to identify mRNAs that bind RHA in vivo. The results from duplicate experiments with samples obtained in two independent RNA immunoprecipitations identified 407 transcripts that co-immunoprecipitate with FLAG RHA.

Keywords: gene expression array-based

overall_design: Since N-terminal FLAG tagged RHA specifically co-immunoprecipitates PCE-containing mRNAs COS cells were transfected with a CMV-FLAG-RHA construct. Cytoplasmic lysates were pooled and immunoprecipitated with anti-FLAG beads. RNA was extracted from the immunoprecipitate and used to probe rhesus macaque Affimetrix expression arrays. Steady state mRNA levels were monitored on a separate array probed with total RNA.


title: Regulatory NK cells: IL-18-elicited NK cells with immunosuppressive functions

status: Public on Mar 01 2009

city: Bonn

first: Joachim

last: Schultze

address: Carl-Troll-Str. 31

department: LIMES Institute

institute: University of Bonn

summary:
Cancer-induced tolerance mostly involves myeloid suppressor cells, regulatory T cells and immunosuppressive cytokines, which all subvert adaptive immune responses against tumor cells. Here, we show that a subset of innate effectors, c-kit expressing NK cells (Kit+ NK), can participate in tumor-induced tolerance by compromising the NK cell arm of tumor immunosurveillance. IL-18 produced by tumor cells can convert Kit- into Kit+ NK cells that overexpress B7-H1/PD-L1 molecules. Upon tumor inoculation, Kit+ NK cells rapidly develop in lymphoid organs in a IL-18R/MyD88 dependent manner and directly kill Kit- NK cells in a B7-H1/PD-1-dependent manner, thereby promoting the progression of NK-controlled cancers. Our data suggest that, in a tumoral context, IL-18 subverts antitumor NK cell functions. Systemic neutralization of IL-18 by IL-18-binding protein may improve the NK-mediated immunosurveillance.
Keywords: cell type comparison

overall_design:
Treatment Protocol: Two subpopulations of NK cells are sorted from mouse spleens with a FACS Vantage instrument (BD Bioscience). NK kit+ are defined as CD3-NK1.1+CD117+ cells and NK kit- as CD3-NK1.1+CD117- cells. Splenocytes from C57Bl/6 mice were sorted in two steps. First, they were enriched in NK cells (NK1.1+/CD3-) by a magnetic separation using NK cell Isolation Kit (Miltenyi Biotec). Second, enriched NK cells were stained with FITC-conjugated anti-CD117 (c-kit) and PE-conjugated anti-NK1.1 monoclonal antibodies to allow a sorting of NK kit+ and NK kit- cells. Antibodies were purchased from Pharmingen, San Diego, CA or eBioscience, San Diego, CA. The purity of NK cells was around 98% after cell sorting.
Characteristics: CD3-NK1.1+CD117+ NK cells are compared to CD3-NK1.1+CD117- NK cells from spleen. Cell sorts and comparison are performed three times. Strain: C57Bl/6. Gender: female. Age: 7 weeks. C57Bl/6 mice were obtained from C.River Laboratories (L’Arbresle, France) and the Centre d’Elevage Janvier (Le Genest-st-Isle, France).
Biomaterial provided: Material provided from laboratory of Prof. Laurence Zitvogel, Immunology, INSERM U805, Instiut Gustave Roussy, Villejuif, France.

first: Laurence

last: Zitvogel

first: Magali

last: Terme

first: Evelyn

last: Ullrich

first: Svenja

last: Debey-Pascher

first: Daniela

last: Eggle


title: Genomic comparison of virulent Rickettsia rickettsii Sheila Smith and avirulent Rickettsia rickettsii Iowa

status: Public on Jun 04 2008

first: Dan

last: Sturdevant

institute: NIH

summary:
Comparison of gene expression between the virulent Rickettsia rickettsii R strain and
avirulent Rickettsia rickettsii Iowa.
Keywords: virulent vs avirulent

overall_design: Virulent Rickettsia rickettsii R strain in triplicate was compared to avirulent Rickettsia rickettsii Iowa in triplicate

first: Damon

middle: W

last: Ellison

first: Tina

last: Clark

first: Kimmo

last: Virtaneva

first: Stephen

last: Porcella

first: Ted

last: Hackstadt


title: Pedigreed Primate Embryonic Stem Cells Express Homogeneous Familial Gene Profiles

status: Public on Apr 15 2008

city: pittsburgh

first: Naftali

last: Kaminski

address: 3459 5th Avenue

department: Pulmonary, Allergy and Critical Care Medicine

institute: University of Pittsburgh Medical Center

summary:
Pedigreed primate ESCs display homogeneous and reliable expression profiles.
These similarities to mouse ESCs suggest that heterogeneities found among hESCs result from their disparate origins rather than intrinsic biological limitations with primate embryonic stem cells.
Keywords: different nhpESC lines

overall_design:
RNA extraction was performed from 10 nhpESC and hybridization on Affymetrix microarrays. To determine whether primate ESCs have intrinsic biological limitations compared with mouse ESCs [mESCs], we examined expression profiles and pluripotency of newly established pedigreed non-human primate ESC (nhpESCs).  Ten pedigreed nhpESCs, seven full-siblings (fraternal quadruplets and fraternal triplets) and nine half-siblings were derived from 41 rhesus embryos

Information about pedigrees may be found in Pedigree_Attributes.xls.

first: Kaminski

last: Naftali

first: Christopher

last: Navara

first: Jocelyn

last: Mich-Basso

first: Carrie

last: Redinger

first: Ahmi

last: Ben-Yehudah

first: Ethan

last: Jacoby

first: Elizabeta

last: Kovkarova-Naumovski

first: Meena

last: Sukhwahni

first: Kyle

last: Orwig

first: Carlos

middle: A

last: Castro

first: Calvin

last: Simerly

first: Gerald

last: Schatten


title: Expression data from macaque taste buds and lingual epithelium

status: Public on Jul 01 2009

city: San Diego

first: Bryan

last: Moyer

state: CA

address: 4767 Nexus Centre Drive

institute: Senomyx, Inc.

summary: Efforts to unravel the mechanisms underlying taste sensation (gustation) have largely focused on rodents. The first comprehensive database of gene expression in primate (Macaca fascicularis) taste buds is presented. This database provides a foundation for further studies in diverse aspects of taste biology. A taste bud gene expression database was generated using laser capture microdissection (LCM) of tissue freeze medium OTC embedded macaque tongue tissue blocks. We collected fungiform (FG) taste buds at the front of the tongue, circumvallate (CV) taste buds at the back of the tongue, as well as non-gustatory lingual epithelium (LE). Gene expression was also analyzed in the top and bottom portions of CV taste buds collected using LCM. Samples were collected from 10 animals - 7 female, 3 male.

overall_design: This 28 sample dataset is comprised of 6 FG, 4 CV, 10 LE, 4 CV top, and 4 CV bottom samples collected by LCM.

first: Peter

last: Hevezi


title: Rhesus macaque ileal loop study

status: Public on Feb 21 2008

first: Michael

last: George

summary:
Salmonella enterica serotype Typhimurium cause a localized enteric infection in immunocompetent patients while human immunodeficiency virus (HIV)-infected patients develop a life threatening bacteremia. We used a rhesus macaque ileal loop model to study how simian immunodeficiency virus (SIV) infection triggers defects in mucosal barrier function that enhance S. Typhimurium dissemination. SIV infection resulted in significant depletion of CD4+ T cells in the intestinal mucosa. Gene expression profiling revealed a defective TH17 response (with suppression of IL-17 and IL-22 expression) and impaired homeostasis of the intestinal epithelium in SIV-infected animals during NTS infection. These findings correlated with an impaired ability of lamina propria CD4+ T cells from SIV-infected macaques to produce IL-17 upon ex vivo stimulation, while production of IFN-gamma was not affected. This cytokine imbalance in SIV-infected animals was associated with reduced expression of genes required for intestinal epithelial maintenance and repair, increased fluid secretion during NTS infection, epithelial damage and translocation of a non-invasive S. Typhimurium mutant. Although no defects in neutrophil recruitment were noted, the ileum of SIV-infected animals contained lower levels of the enzyme myeloperoxidase, which may indicate defects in neutrophil killing capacity. S. Typhimurium was recovered in markedly increased numbers from the mesenteric lymph nodes of SIV-infected macaques, illustrating the increased potential for systemic dissemination during co-infection. Our data suggest that SIV-infection causes a multi-factorial defect in mucosal barrier function that promotes bacterial dissemination.
Keywords: Disease state analysis

overall_design: Comparison of ileal gene expression profiles in SIV infected rhesus macaques in response to Salmonella challange.

first: Andreas

last: Baumler


title: NIH/NIAID On the resistance of Staphylococcus aureus to neutrophil microbicides

status: Public on Jan 31 2008

city: Hamilton

first: Dan

last: Sturdevant

address: 903 S 4th street

summary:
Staphylococcus aureus strain MW2 was exposed to the following neutrophil microbicides, hydrogen peroxide (H2O2), hypochlorous acid (HOCl) and azurophilic granule proteins.  At the indicated time points, bacterial cultures were centrifuged and bacteria were lysed with RLT buffer (Qiagen) using a FastPrep system.  Purification of MW2 RNA and subsequent preparation of labeled cDNA target was performed as described in Methods.  Labeling of samples, GeneChip hybridization and scanning were performed according to standard Affymetrix protocols.  Experiments were performed in triplicate, using three bacterial cultures from separate days for each treatment.  These analyses provide an enhanced view of the mechanisms used by CA-MRSA to circumvent destruction by the human innate immune system.
Keywords: time course with three treatments

overall_design: 48 samples total:  MW2 with the following treatments, untreated, GP (azurophilic granule proteins), H2O2 (hydrogen peroxide) or HOCl (hypochlorous acid) at 4 time points in triplicate

first: Amy

last: Palazzolo-Ballance

first: Michelle

last: Reniere

first: Kevin

last: Braughton

first: Daniel

first: Barry

last: Kreiswirth

first: Eric

middle: P

last: Skaar

first: Frank

last: DeLeo


title: The antimicrobial peptide-sensing system aps of Staphylococcus aureus

status: Public on Apr 07 2008

summary:
Staphylococcus aureus is a leading cause of hospital-associated infections. In addition, highly virulent strains of methicillin-resistant S. aureus (MRSA) are currently spreading outside health care settings. Survival in the human host is largely defined by the ability of S. aureus to resist mechanisms of innate host defense, of which antimicrobial peptides form a key part especially on epithelia and in neutrophil phagosomes. Here we demonstrate that the antimicrobial-peptide sensing system aps of the standard community-associated MRSA strain MW2 controls resistance to cationic antimicrobial peptides. The core of aps-controlled resistance mechanisms comprised the D-alanylation of teichoic acids (dlt operon), the incorporation of cationic lysyl-phosphatidylglycerol (L-PG) in the bacterial membrane (mprF), and the vraF/vraG putative antimicrobial peptide transporter.
Further, the observed increased production of L-PG under the influence of cationic antimicrobial peptides was accompanied by the up-regulation of lysine biosynthesis. In noticeable difference to the aps system of S. epidermidis, only selected antimicrobial peptides strongly induced the aps response. Heterologous complementation with the S. epidermidis apsS gene indicated that this is likely caused by differences in the short extracellular loop of ApsS that interacts with the inducing antimicrobial peptide. Our study shows that the antimicrobial peptide sensor system aps is functional in the important human pathogen S. aureus, significant interspecies differences exist in the induction of the aps gene regulatory response, and aps inducibility is clearly distinguishable from effectiveness towards a given antimicrobial peptide.
Keywords: Wild type control vs treated vs mutant

overall_design: Wild type untreated in triplicate is compared to wild type treated in triplicate along with three mutants in triplicate with and without treatment of indolicidin, totalling 30 samples

first: Min

last: Li

first: Yuping

last: Lai

first: Amer

last: Villaruz

last: Otto


title: A Gram-positive three-component antimicrobial peptide-sensing system

status: Public on Feb 26 2008

summary:
To survive during colonization or infection of the human body, microorganisms must defeat antimicrobial peptides, which represent a key component of innate host defense in phagocytes and on epithelia. However, is not known how the clinically important group of Gram-positive bacteria sense antimicrobial peptides to coordinate a directed defensive response.
By determining the genome-wide gene regulatory response to human beta defensin 3 in the nosocomial pathogen Staphylococcus epidermidis, we discovered an antimicrobial peptide sensor system that controls major specific resistance mechanisms to antimicrobial peptides and is unrelated to the Gram-negative PhoP/PhoQ system.
Keywords: Wild type control vs treated vs mutant

overall_design: Wild type untreated in triplicate is compared to wild type treated in triplicate along with three mutants in triplicate with and without treatment of human beta defensin 3, totalling 30 samples

first: David

last: Cha


title: Differentially expressed genes among motor and prefrontal areas of macaque monkey neocortex

status: Public on Aug 31 2007

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

summary:
Motor-related areas of neocortex are highly differentiated into several subareas from both functional and cytoarchitectural aspects in the higher primates. To assess the molecular basis of such areal specialization, we investigated the gene expression profiles of primary motor area (M1), premotor area (dorsal and ventral) (PMd and PMv) and prefrontal area (A46) in the rhesus monkey by DNA microarray method. We found that 476 genes were differentially expressed among those areas. More than half of those genes were most abundantly expressed in M1, and most genes were complementarily expressed between M1 and A46. The expression profiles of PMd and PMv were similar to each other compared to those of M1 and A46. The data will give us a fundamental basis for further analysis of structure-function relationship of the primate brain.
Keywords: cerebral neocortex; rhesus monkey; primary motor area; premotor area; prefrontal area

overall_design: Twenty four brain tissues from 4 areas (M1, PMd, PMv and A46) of right and left hemispheres of 3 adolescent rhesus monkeys (Macaca mulatta) aged 2.6-2.7 years which had been bred in group cages without any experimental treatments. Adequate measures were taken to minimize pain and discomfort, in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals (NIH publication no. 80-23).

first: Akira

last: Sato

first: Yukio

last: Nishimura

first: Takao

last: Oishi

first: Noriyuki

last: Higo

first: Yumi

last: Murata

first: Hirotaka

last: Onoe

first: Kimika

last: Saito

first: Fumiharu

last: Tsuboi

first: Masahito

last: Takahashi

first: Tadashi

last: Isa


title: Infection of Macaques with SIVmac251 in vivo

status: Public on Mar 02 2007

city: Rockville

first: Maryanne

last: Vahey

address: 1600 East Gude Drive

institute: Walter Reed Army Institute of Research

summary:
Viral infection results in an overall downregulation of gene expression that is greatest by the viral set point. Of the 3647 genes downregulated at the viral set point, 1033 are upregulated as the result of successful ARV treatment
Keywords: time course

overall_design: Affymetrix Rhesus Genome array were used to assay gene expression profiles at baseline, and 2-, 20- and 26- weeks after infection. Drug therapy started at week24


title: Microarray Expression Analysis of SIV infection of Sooty Mangabeys

status: Public on Mar 08 2010

city: Philadelphia

first: Steven

last: Bosinger

address: room 702 Stellar-Chance Laboratories, 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

summary: Natural SIV infection of sooty mangabeys (SMs) does not progress to disease despite chronic virus replication. In contrast to pathogenic SIV infection of rhesus macaques (RMs), chronic SIV infection of SMs is characterized by low immune activation. To elucidate the mechanisms underlying this phenotype, we longitudinally assessed host gene expression in SIV-infected SMs and RMs. We found that acute SIV infection of SMs is consistently associated with a robust innate immune response, including widespread up-regulation of interferon-stimulated genes (ISGs). Our findings indicate that active immune regulatory mechanisms, rather than intrinsically attenuated innate immune responses, underlie the low immuneactivation of chronically SIV-infected SMs.

overall_design: We infected 5 SMs with SIVsmm and assessed their gene expression in RNA derived from whole blood at 3,7,10,14,30 and 180 days post-infection using Rhesus Affymetrix GeneChips. As a comparison, we also analyzed gene expression in 4 RMs infected with SIVsmm, and 8 RMs infected with SIVmac239, a classical pathogenic SIV.

first: Shari

middle: N

last: Gordon

first: Nichole

last: Klatt

first: Luoling

last: Xu

first: Abubaker

last: Sidahmed

first: Longsi

last: Ran

first: Thomas

middle: H

last: Vanderford

first: Mirko

last: Paiardini

first: R

middle: B

last: Isett

first: Don

last: Baldwin

first: James

middle: G

last: Else

first: Silvija

middle: I

last: Staprans

first: Guido

last: Silvestri

last: Kelvin


title: Expression profiling of primate CL following PGF2alpha treatment

status: Public on Jun 02 2007

city: Bangalore

first: priyanka

last: samji

state: Karnataka

address: Malleswaram

department: Molecular Reproduction Development and Genetics

country: India

institute: Indian Institute of Science

summary:
Corpus luteum (CL) is an ephemeral gland whose main function is to secrete progesterone required for the establishment and maintenance of pregnancy. In non-fertile cycles, primate CL has a finite life span of 14-16 days, following which it undergoes regression. Although it has been suggested long time back that PGF2alpha of intra-ovarian or intra-luteal origin acts as a physiological luteolysin in primates, the mechanisms by which PGF2alpha mediates its luteolytic actions are poorly understood. Earlier, we standardized an induced luteolysis model, where 3 injections of PGF2alpha to female bonnet monkeys on day 10 of luteal phase led to luteolysis. To delineate the mechanism of this PGF2alpha-induced luteolysis, we tried to study the global changes in gene expression following PGF2alpha treatment using Affymetrix microarray analysis of PGF2alpha and VEH treated CL and results suggested that PGF2alpha exerts its luteolytic effects by altering gene expression.
Keywords: CL, PGF2alpha, VEH, gene expression

overall_design: For the purpose of microarray analysis, PGF2alpha (3 injections) at a dose of 59 µg/kg BW and PBS as VEH (control) was administered i.m. to female monkeys on day 10 of luteal phase (n=3). At 24 h following either PGF2alpha or VEH administration, CL was collected and immediately cut into 4-5 pieces and snap frozen in liquid nitrogen.

first: Priyanka

last: Samji

first: Jayaram

last: Puttaiah

first: Medhaurthy

last: Rudraiah


title: Transcriptional profiling of rhesus monkey embryonic stem cells

status: Public on Aug 17 2006

middle: Anthony

last: Byrne

address: 505 NW 185th Ave

institute: ONPRC

summary:
Embryonic stem cells (ESCs) may be able to cure or alleviate the symptoms of various degenerative diseases.  However, unresolved issues regarding apoptosis, maintaining function and tumor formation mean a prudent approach should be taken towards advancing ESCs into human clinical trials.   The rhesus monkey provides the ideal model organism for developing strategies to prevent immune rejection and test the feasibility, safety and efficacy of ESC-based medical treatments.  Transcriptional profiling of rhesus ESCs provides a foundation for future pre-clinical ESC research using non-human primates as the model organism.  In this research we use microarray, immunocytochemistry, real-time and standard RT-PCR to characterize and transcriptionally profile rhesus monkey embryonic stem cells.  We identify 367 rhesus monkey stemness genes, we demonstrate the high level (>85%) of conservation of rhesus monkey stemness gene expression across five different rhesus monkey embryonic stem cell lines, we demonstrate that rhesus monkey ESC lines maintain a pluripotent undifferentiated state over a wide range of Pou5f1 (Oct-4) expression levels and we compare rhesus monkey, human and murine stemness genes to identify the key mammalian stemness genes.

The supplementary tables list the genes that have been upregulated in each undifferentiated rhesus monkey embryonic stem cell line (GSM99998, GSM99999,GSM100000, GSM100001, GSM100002, GSM99965, GSM99966) in comparison analysis with the pooled differentiated embryonic stem cells (GSM99840).  Supplemental Table 1 contains the comparison analysis for all 52,865 probe sets on the rhesus monkey gene chip, Supplemental Table  2 contains the rhesus monkey genes that were significantly upregulated (FC>3) in the ORMES-6 biological replicates, Supplemental Table 3 contains the rhesus monkey genes that were significantly upregulated (FC>3) in the pooled differentiated EBs and Supplemental Tables  4-8 represent genes that were significantly upregulated in ORMES 6A, 7, 9, 10 and 13 respectively.  Supplemental Table 9 contains the RT-PCR primers used in this project.
Keywords: Rhesus monkey embryonic stem cell microarray

overall_design: We compare the transcriptomes of three biological replicates of ORMES6 (A, B and C) with pooled differentiated EBs to identify 367 rhesus monkey putative stemness genes.  We demonstrate the high level (>85%) of conservation of rhesus monkey stemness gene expression across five different rhesus monkey embryonic stem cell lines (ORMES 6, 7, 9, 10, 13).

first: Shoukhrat

middle: M

last: Mitalipov

first: Lisa

last: Clepper

last: Wolf


title: AI-2-dependent gene regulation in Staphylococcus epidermidis

status: Public on Oct 10 2008

first: Dan

last: Sturdevant

department: NIAID

summary:
Autoinducer 2 (AI-2), a widespread by-product of the LuxS-catalyzed S-ribosylhomocysteine cleavage reaction in the activated methyl cycle, has been suggested to serve as an intra- and interspecies signaling molecule, but in many bacteria AI-2 control of gene expression is not completely understood. Particularly, we have a lack of knowledge about AI-2 signaling in the important human pathogens Staphylococcus aureus and S. epidermidis. Here, to determine the role of LuxS and AI-2 in S. epidermidis, we analyzed genome-wide changes in gene expression in an S. epidermidis luxS mutant and after addition of AI-2 synthesized by over-expressed S. epidermidis Pfs and LuxS enzymes. Genes under AI-2 control included mostly genes involved in sugar, nucleotide, amino acid, and nitrogen metabolism, but also virulence-associated genes coding for lipase and bacterial apoptosis proteins. In addition, we demonstrate by liquid chromatography/mass-spectrometry of culture filtrates that the pro-inflammatory phenol-soluble modulin (PSM) peptides, key virulence factors of S. epidermidis, are under luxS/AI-2 control. Our results provide a detailed molecular basis for the role of LuxS in S. epidermidis virulence and suggest a signaling function for AI-2 in this bacterium.
Keywords: wild type without glucose control vs luxS mutant vs luxS mutant with auto-inducer II

first: Min

last: Li

first: Amer

last: Villaruz

first: Viveka

last: Vadyvaloo

first: Daniel

first: Michael

last: Otto


title: Expression data from 5 rhesus tissues at 3 centers

status: Public on Feb 23 2007

city: Providence

first: Fenghai

last: Duan

state: RI

address: 121 S. Main Street

department: Biostatistics

institute: Brown University

summary:
Novel approaches were used to generate the DNA sequence information for the rhesus GeneChip (2005). The purpose of this experiment was to test its reliability and validity of the rhesus macaque GeneChip across different tissues and centers.
Keywords: reliability

overall_design: To test the reliability of the rhesus GeneChip across different centers, RNA was isolated from five sources:  cerebral cortex, pancreas, thymus, testis, and an immortalized fibroblast cell line.  Aliquots of this RNA were sent to each of three centers:  Yerkes National Primate Research Center, Oregon National Primate Research Center and the University of Nebraska Medical Center.  Each center labeled the samples and hybridized them to two rhesus macaque GeneChips.

first: Eliot

middle: R

last: Spindel

first: Yuhua

first: Robert

last: Norgren