title: Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance

city: Lausanne

first: Johann

last: Weber

state: VD

address: Genopode Building

department: Center for integrative Genomics

country: Switzerland

institute: University of Lausanne

summary:
Expression level polymorphisms (ELPs) often result in cis-acting expression quantitative trait loci (cis-eQTL), which are important QTL and association mapping tools and account significantly for phenotypic variability. Generally, it is assumed that such stably heritable ELP represent regulatory element polymorphisms in the respective genes. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here we analyzed heritability of ELP observed between Arabidopsis thaliana accessions Eil-0 and Lc-0 by comparing genotyped recombinant inbred lines (RIL) to their parents in microarray analyses.

Keywords: expression level polymorphism, Arabidopsis thaliana accessions, recombinant inbred lines

overall_design: In order to analyze expression level polymorphisms between the accessions Eil-0 and Lc-0, three independently grown seedling pools were analyzed by two color co-hybridization of the labeled cDNAs in dyeswap experiments, giving a total of six slides. For the analysis of gene expression in seedlings of 7 different RILs, each RIL sample was co-hybridized with each parent (Eil-0 and Lc-0) in a dyeswap, resulting in two slides per parent vs. RIL comparison. The total number of slides in this study was 34.

first: Stephanie

last: Plantegenet

first: Darlene

middle: R

last: Goldstein

first: Cindy

last: Nussbaumer

first: Jérôme

last: Thomas

first: Keith

last: Harshman

first: Christian

middle: S

last: Hardtke


title: Nucleosome mapping in 20 kb upstream regions of microRNAs

status: Public on Nov 16 2008

city: San Francisco

first: Jun

last: Song

state: CA

address: 513 Parnassus Avenue, Box 0794

department: Institute for Human Genetics

country: USA

institute: UCSF

type: Genome binding/occupancy profiling by genome tiling array

summary:
We mapped the nucleosome locations in upstream regions of all known microRNAs in 3 cell lines using the method described in Nature Biotechnology 2007 Feb;25(2):244-8.
Keywords: Nucleosome Mapping Study

overall_design: 20 kb upstream regions of microRNAs were tiled at 10 bp spacing using mostly 50-mer probes.  Duplicate experiments were performed in MCF7, MALME, and UACC62 cell lines.

first: David

middle: E

last: Fisher


title: Localization of NsrR binding sites in the Escherichia coli genome

status: Public on Nov 19 2008

city: Richardson

first: Stephen

last: Spiro

state: TX

address: 800 W Campbell Road

department: Molecular and Cell Biology

institute: University of Texas at Dallas

summary:
NsrR is a nitric oxide sensitive regulator of transcription. In Escherichia coli, NsrR is a repressor of the hmp gene encoding the flavohemoglobin that detoxifies nitric oxide.  Several other transcription units (including ytfE, ygbA and hcp-hcr) are known to be subject to regulation by NsrR.  In this study, chromatin immunoprecipitation and microarray analysis was used to identify NsrR binding sites in the chromosome of Escherichia coli strain MG1655.
Keywords: ChIP-chip

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: The nsrR gene was modified by the addition of DNA sequences encoding a C-terminal 3X-Flag tag, and the tagged gene was integrated into the chromosome.  Cultures were grown anaerobically in the absence and presence of nitrate, conditions which lead to high and low levels of occupancy of NsrR binding sites, respectively.  Chromatin was extracted from the two cultures, labeled with Cy3 and Cy5 (with no PCR amplification step) and hybridized to high density microarrays fabricated by Oxford Gene Technology.

first: Diane

middle: M

last: Bodenmiller

first: Mike

last: Humphrys

first: Jonathan

middle: D

last: Partridge


status: Public on Nov 20 2008

city: Kgs Lyngby

first: Per

last: Hagglund

address: Soltofts plads

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

summary:
Identification of targets of the protein disulfide reductase thioredoxin using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and thiol specific differential labeling with isotope-coded affinity tags (ICAT). Reduction of specific target disulfides is quantified by measuring ratios of cysteine residues labeled with the heavy (13C) and light (12C) ICAT reagents in peptides derived from tryptic digests of Trx-treated and non-treated samples.

Keywords: protein, LC-MS/MS, ICAT

overall_design:
Biological Material:  Dissected embryos from seeds from the malting barley (Hordeum vulgare) cultivar Barke (2002 harvest) germinated for 48 h as previously described (Bønsager et al., 2007).
Sample preparation:  Sample A. Barley embryo protein extract, treated with iodoacetamide (IAM) during extraction, was incubated ± thioredoxin and after 1 h incubation at RT, IAM was again added (final concentration 10 mM) to irreversibly block cysteines reduced by thioredoxin. Excess IAM was removed and remaining cysteine residues were completely reduced by tris(2-carboxyethyl)phosphine (TCEP) under denaturing conditions and ICAT-labeled (+Trx, ICATL; -Trx, ICATH), essentially as recommended by the manufacturer (Applied Biosystems). The ICATL and ICATH labeled samples were mixed 1:1 and subjected to trypsin digestion followed by isolated of ICAT labeled peptides by avidin affinity chromatography and LC-MS/MS analysis on an Agilent 1100 nanoflow HPLC (Agilent, Palo Alto CA) coupled to a QSTAR quadrupole time-of-flight mass spectrometer (Applied Biosystems). Data were acquired in information dependent mode with a cycle of a survey mass spectrum followed by tandem mass spectra of the three most intense multiply charged ions (1 s each) after which the selected ions were placed on an exclusion list for 45 s.  Sample B (control). Same as for sample A except IAM addition after thioredoxin incubation was omitted.
Data processing and peptide quantification:  The raw data .wiff files were processed with the Mascot script for Analyst (QS 2.0) version 1.6b20 (Matrix Science, London, UK).   The charge state was determined from the survey spectrum with a default charge setting of multiply charged precursors. The MS/MS data was centroided and de-isotoped without MS/MS averaging to generate the Mascot Generic Format (MGF) peak list. Spectra with less than 10 peaks were rejected. Database searches of the centroided data were performed using the Mascot search engine (Matrix Science) against the Viridiplantae (Green Plants) subset of Swiss-Prot 54.6, nrNCBI (downloaded on 20071206) and the Barley EST database (barley gene index [HvGI] release 9.0). The following search criteria were used: MS mass tolerance 0.2 Da; MS/MS tolerance 0.2 Da; no trypsin miss-cleavage allowed. Variable modifications: ICATH (cysteine), ICATL (cysteine), carbamidomethyl (cysteine) and oxidation (methionine). Tentative consensus sequences (TC sequences) identified in HvGI release 9.0 were blasted (http://www.ncbi.nlm.nih.gov/blast) against the nrNCBI database. Quantification of ICAT labeled peptide pairs was performed using the software MS quant version 1.4.3a12 (http://www.msquant.sourceforge.net). Spectra were manually validated and peptides with a sequence tag of at least three amino acids and a Mascot score of 20 were accepted.
References:  Bønsager BC, Finnie C, Roepstorff P, Svensson B (2007) Spatio-temporal changes in germination and radical elongation of barley seeds tracked by proteome analysis of dissected embryo, aleurone layer, and endosperm tissues. Proteomics 7:4528-4540.

last: Hägglund


title: Hard-wiring in the Plasmodium falciparum transcriptome II

status: Public on Nov 15 2008

city: Seattle

first: Pradipsinh

middle: K

last: Rathod

state: WA

address: Campus Box 351700

department: Chemistry

institute: University of Washington

summary:
To help malaria parasites survive unpredictable host immune responses, it is known that genes for surface proteins express stochastically in Plasmodium falciparum. Here, we demonstrate that gene expression for intracellular metabolic functions may be preordained and insensitive to specific metabolic perturbations.  In a tightly-controlled, large microarray study involving over 100 hybridizations to isogenic drug-sensitive and drug-resistant parasites, the lethal antifolate WR99210 failed to over-produce RNA for the biochemically and genetically proven target dihydrofolate reductase-thymidylate synthase (DHFR-TS). Beyond the target, this transcriptional obstinacy carried over to the rest of the parasite genome, including genes for target pathways of folate and pyrimidine metabolism. Even 12 hours after commitment to death, the transcriptome remained faithful to evolutionarily entrained paths.  A system-wide transcriptional disregard for metabolic perturbations in malaria parasites may contribute to selective vulnerabilities of the parasite to lethal antimetabolites. While large protective metabolic responses were not detected, DNA microarrays helped capture small, but reproducible drug-dependent perturbations within hours of drug exposure. In addition, in Plasmodium cells that had adapted to long-term drug exposure, DNA microarrays revealed new, large genome-wide transcriptional adjustments in the hard-wired transcriptional program itself.
Keywords: Plasmodium falciparum treated with pyrimethamine

overall_design: RNA from pyrimethamine-treated parasite vs RNA from untreated control,  Pyr-sensitive TM4/8.2 parasite strain, pyrimethamine concentration at IC50 and treated for 2 h, 4 h, and 8 h, microarray data were obtained from at least four hybridizations using RNA from at least two independent parasite cultures

first: Karthikeyan

last: Ganessan

first: Napawan

last: Ponmee

first: Lei

last: Jiang

first: Joseph

last: Fowble

first: John

last: White

first: Sumalee

last: Kamchonwongpaisan

first: Yongyuth

last: Yuthavong

first: Prapon

last: Wilairat


title: Hard-wiring in the Plasmodium falciparum transcriptome 2

overall_design: RNA from pyrimethamine-treated parasite vs RNA from untreated control,  Pyr-sensitive TM4/8.2 strain, pyrimethamine concentration at IC50 and treated for 0 h and 24 h, microarray data were obtained from at least four hybridizations using RNA from at lease two independent parasite cultures


title: Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole genome tiling arrays

status: Public on Nov 14 2008

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

type: Expression profiling by genome tiling array

summary: Plant responses to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses.

overall_design: After seedlings had been grown for 10 days on solid MS medium at 21°C, they were transferred to liquid MS medium containing no additives (mock control), 200 mM NaCl (salt stress), 300 mM mannitol (osmotic stress) or 100 μM ABA. For cold and heat stress, seedlings were transferred to pre-chilled or pre-warmed liquid MS medium and incubated at 8°C and 30°C, respectively. Samples were taken after 1 h and 12 h of continuous stress treatment. RNA was extracted from whole seedlings and converted into double stranded DNA targets that were hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0R®). All hybridizations were performed with 3 biological replicates.

first: Georg

last: Zeller

first: Stefan

last: Henz

first: Christian

last: Widmer

first: Timo

last: Sachsenberg

first: Gunnar

last: Rätsch

first: Detlef

last: Weigel


title: Molecular mechanisms underlying the metabolic changes induced by the Pro12Ala PPARγ2 variant in mice

first: eric

middle: e

last: schadt

address: 401 Terry Ave N

department: Genetics

institute: Merck

summary: The metabolic impact of the common peroxisome proliferator-activated receptor gamma isoform 2 (PPARγ2) variant Pro12Ala in human populations has been widely debated. We demonstrate using a Pro12Ala knock-in model that on chow Ala/Ala mice are leaner, have improved insulin sensitivity and plasma lipid profiles, and longer lifespan. Gene-environment interactions played a key role as high-fat feeding eliminated the beneficial effects of the Pro12Ala variant on adiposity, plasma lipids, and insulin sensitivity. The underlying molecular mechanisms involve changes in cofactor interaction and adiponectin signaling. Altogether, our results establish the Pro12Ala variant of Pparγ2 as an important modulator in metabolic control that strongly depends on the metabolic context.

overall_design: Pparγ Pro12Ala and wild-type littermates were fed regular rodent chow or high-fat diet (D12330, 5560 kcal/kg, Research Diets, New Brunswick, NJ), as indicated. Only males were used to minimize possible effects of variation in estrus status of females. Since the body weight development of Pro/Ala heterozygote mice was intermediate to that of Pro/Pro and Ala/Ala mice, we focused on the two homozygote genotypes in further experimentation. Mice were housed with a 12h light-dark cycle and had free access to water and food. Eight week old male Pro/Pro and Ala/Ala littermate mice were fed either regular rodent chow or high-fat diet (as above) for 15 weeks (n = 8-10 per group), at which time blood and tissue samples were collected. Total RNA extraction, sample amplification, labeling, and microarray (Genechip Mouse Genome 430 2.0 Array, Affymetrix Inc., Santa Clara, CA) processing steps were performed by the Rosetta Inpharmatics Gene Expression Laboratory (Seattle, WA) using custom automated procedures in compliance with manufacturer protocols. Microarray data was processed using Rosetta Resolver (Rosetta Inpharmatics, Seattle, WA) and expressed as relative to the virtual pool of HFD – Pro/Pro group (mlratio). Gene expression signatures were generated from these mlratios for expressed genes (25% of RMA processed intensities above 60% quantile) by T-testing (Pro/Pro vs. Ala/Ala) and correcting for multiple testing (20% cut-off for False Discovery Rate). GSEA was performed according to provider suggestions, Pro/Pro vs. Ala/Ala. Statistical significance was declared if P < 0.05.

first: Sami

last: Heikkinen

first: Carmen

last: Argmann

first: Jérôme

middle: N

last: Feige

first: Hana

last: Koutnikova

first: Marie-France

last: Champy

first: Nassim

last: Dali-Youcef

first: Eric

last: Schadt

first: Markku

last: Laakso

first: Johan

last: Auwerx


title: Nitrogen-regulated genes in Fusarium fujikuroi

status: Public on Nov 21 2008

city: Peoria

first: Robert

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

summary:
Genome-wide search for AreA-dependent and -independent nitrogen-regulated genes in Fusarium fujikuroi by cross-species hybridization with F. verticillioides microarrays.
Keywords: glutamine treatmet

overall_design: Compare expression of genes of Fusarium fujikuroi wild-type and areA mutant strains responding to nitrogen limitation or sufficiency.

first: Birgit

last: Schönig

first: Daren

middle: W

last: Brown

first: Birgitt

last: Oeser

first: Bettina

last: Tudzynski


title: A toolbox for epitope-tagging and genome-wide location analysis in Candida albicans

city: Montreal

first: Hugo

last: Lavoie

state: Quebec

address: 6100 Royalmount

country: Canada

institute: CNRC-IRB

type: Genome binding/occupancy profiling by array

summary:
Background : Candida albicans is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes would lead to further insight into the biology of this common disease-causing microbial agent.
Results: We have developed a toolbox allowing in vivo protein tagging by PCR-mediated homologous recombination with TAP, HA and MYC tags. The transformation cassettes were designed to accommodate a common set of integration primers. The tagged proteins can be used to perform tandem affinity purification (TAP) or chromatin immunoprecipitation coupled with microarray analysis (ChIP-CHIP). Tandem affinity purification of C. albicans Nop1 revealed the high conservation of the small processome composition in yeasts. Data obtained with in vivo TAP-tagged Tbf1, Cbf1 and Mcm1 recapitulates previously published genome-wide location profiling by ChIP-CHIP. We also designed a new reporter system for in vivo analysis of transcriptional activity of gene loci in C. albicans.
Conclusion: This toolbox provides a basic setup to perform purification of protein complexes and increase the number of annotated transcriptional regulators and genetic circuits in C. albicans.

overall_design: Two independent biological replicates of ChIP-CHIP of Mcm1-TAP in yeast and hyphal states. ChIP-CHIP of Cbf1-TAP and Tbf1-TAP.

first: Adnane

last: Sellam

first: Christopher

last: Askew

first: André

last: Nantel

first: Malcolm

last: Whiteway


title: Evidence that cryptic promoters occur extensively throughout the Saccharomyces cerevisiae genome

city: Calgary

first: Gordon

last: Chua

state: Alberta

address: 2500 University Drive, N.W.

department: Biological Sciences

institute: University of Calgary

summary: Microarray analysis was used to identify all cryptic promoters in the S. cerevisiae genome that are activated in spt6 and spt16 mutants.  These experiments showed that cryptic initiation is widespread, occurring in approximately 1,000 genes.

overall_design: We generated 2 microarray profiles from fluor-reversed replicates of wild-type and spt6-1004 or spt16-197 mutants.  See Cheung et al., (2008) in revision.

first: Vanessa

last: Cheung

first: Nizar

last: Batada

first: Christian

last: Landry

first: Steven

last: Michnick

first: Tim

last: Hughes

first: Fred

last: Winston


title: Characterization of an Entamoeba histolytica High-Mobility-Group Box Protein  Induced during Intestinal Infection

city: Charlottesville

first: Carol

middle: A

last: Gilchrist

state: VA

address: Dept. of Medicine/Division of Infectious Diseases, Building MR4, Rm 2126,PO Box 801365

department: Medicine

institute: University of Virginia

summary: The unicellular eukaryote Entamoeba histolytica is a human parasite that causes amebic dysentery and liver abscess. A genome-wide analysis of gene expression modulated by intestinal colonization and invasion identified an up-regulated transcript that encoded a putative high-mobility-group box (HMGB) protein, EhHMGB1. We tested if EhHMGB1 encoded a functional HMGB protein, and determined its role in control of parasite gene expression. Recombinant EhHMGB1 was able to bend DNA in vitro, a characteristic of HMGB proteins. Core conserved residues required for DNA bending activity in other HMGB proteins were demonstrated by mutational analysis to be essential for EhHMGB1 activity. EhHMGB1 was also able to enhance the binding of human p53 to its cognate DNA sequence in vitro, which is expected for an HMGB1 protein. Confocal microscopy, using antibodies against the recombinant protein, confirmed its nuclear localization. Overexpression of EhHMGB1 in HM1: IMSS trophozoites led to modulation of 33 transcripts involved in a variety of cellular functions. Of these, twenty were also modulated at either day one or day 29 in the mouse model of intestinal amebiasis. Notably, four transcripts with known roles in virulence, including two encoding Gal/GalNAc lectin light chains, were modulated in response to EhHMGB1 overexpression. We concluded that EhHMGB1 was a bona fide HMGB protein with the capacity to recapitulate part of the modulation of parasite gene expression seen during adaptation to the host intestine.

overall_design: 6 samples for two groups: 3M and Gir. Each groups contain 3 samples

first: Mayuresh

last: Abhyankar

first: Amelia

last: Hochreiter

first: Jessica

last: Hershey

first: Clive

last: Evans

first: yan

last: Zhang

first: Oswald

last: Crasta

first: Bruno

last: Sobral

first: Barbara

middle: J

last: Mann

first: William

last: Petri


title: Expression profiling of Candida albicans and Candida dubliniensis in reconstituted human oral epithelium 90 min p.i.

city: Rockville

first: Martin

last: Spiering

state: MD

address: 9600 Gudelsky Dr

department: UMBI

institute: University of Maryland

summary: Candida albicans and Candida dubliniensis are closely related species displaying differences in virulence and genome content, therefore providing potential opportunities to identify novel C. albicans virulence genes. C. albicans gene arrays were used for comparative analysis of global gene expression in the two species in reconstituted human oral epithelium (RHE). C. albicans (SC5314) showed upregulation of hypha-specific and virulence genes within 30 min postinoculation, coinciding with rapid induction of filamentation and increased RHE damage. C. dubliniensis (CD36) showed no detectable upregulation of hypha-specific genes, grew as yeast, and caused limited RHE damage. Several genes absent or highly divergent in C. dubliniensis were upregulated in C. albicans. One such gene, SFL2 (orf19.3969), encoding a putative heat shock factor, was deleted in C. albicans. ΔΔsfl2 cells failed to filament under a range of hypha-inducing conditions and exhibited greatly reduced RHE damage, reversed by reintroduction of SFL2 into the ΔΔsfl2 strain. Moreover, SFL2 overexpression in C. albicans triggered hyphal morphogenesis. Although SFL2 deletion had no apparent effect on host survival in the murine model of systemic infection, ΔΔsfl2 strain-infected kidney tissues contained only yeast cells. These results suggest a role for SFL2 in morphogenesis and an indirect role in C. albicans pathogenesis in epithelial tissues.

sample_organism:
Candida albicans
Candida dubliniensis

overall_design: Global gene expression in Candida albicans SC5314 or Candida dubliniensis CD36 on reconstituted human oral epithelium (RHE) 90 min postinoculation. Gene expression on RHE was compared to gene expression on polycarbonate filter (PCF; used as RHE support matrix) 90 min postinoculation. Performed in two biological replicates with reciprocal dye swaps for each biological replicate. Gene expression of Candida cells on RHE was normalized to gene expression in reference control (PCF); log2 ratios were calculated by dividing spot intensity of experimental by that of the reference control.

first: Gary

middle: P

last: Moran

first: Murielle

last: Chauvel

first: Donna

last: MacCallum

first: Judy

last: Higgins

first: Karsten

last: Hokamp

last: Yeomans

first: Christophe

last: d'Enfert

first: David

middle: C

last: Coleman

first: Derek

last: Sullivan


title: Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense

status: Public on Nov 13 2008

city: Athens

first: Alan

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

summary: Gossypium barbadense is widely cultivated because of its extra-long staple cotton with superior luster, silkiness and high yield. These economically important traits were selected during initial domestication of an agronomically inferior wild ancestor, followed by millennia of human- mediated selection. To reveal the effects of this history on the cotton fiber transcriptome, we conducted comparative expression profiling on mechanically isolated fiber cells at three different stages encompassing early, mid, and late fiber elongation in wild (K101) and domesticated (Pima S-7) accessions, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes across developmental stages was different in the two accessions, with a shift toward greater change earlier in cultivated than in wild G. barbadense. Approximately 4200 genes were differentially expressed between wild and domesticated accessions at one or more of the stages studied. Domestication appears to have led to enhanced modulation of cellular redox levels and the avoidance or delay of stress-like processes. Prolonged fiber growth in cultivated relative to wild G. barbadense is associated with upregulation of signal transduction and hormone signaling genes and down-regulation of cell wall maturation genes. Clues are provided into the processes and genes that may unwittingly have been selected by humans during domestication and development of modern elite lines. Several of the transcriptomic differences between wild and domesticated G. barbadense described here appear to have parallels in a second domesticated cotton species, Gossypium hirsutum, suggesting that replicated domestication of two different species has resulted in overlapping, parallel, metabolic transformations.

overall_design: Two accessions of G. barbadense were studied, the elite cultivar, Pima S-7, and a wild accession from Bolivia, K101. Seeds of both accessions were sown in sterilized potting mix in the Pohl Conservatory at Iowa State University, Ames, IA, and three biological replicates were grown for 3-5 months. Flowers were tagged at anthesis and harvested at three time points, 2, 10, and 20 days postanthesis. For each of three biological replicates, ovules were excised, frozen in liquid nitrogen, and stored at -80C.

first: Bhupendra

last: Chaudhary

first: Ran

last: Hovav

first: Ryan

last: Rapp

first: Neetu

last: Verma

first: Joshua

last: Udall

first: Jonathan

middle: F

last: Wendel


title: S. pombe Sin3 homolog Pst3 is Key in Nucleolar Integrity

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

summary:
The Sin3/HDAC complex is highly conserved from yeast to humans. Sin3 provides the scaffolding needed to coordinate DNA binding proteins with various chromatin modifying enzymes, most often histone deacetylases, to establish chromatin environments important both for correct gene regulation and genome stability  (reviewed in [1]). Three Sin3 homologs are present. Here we explore Pst3, the most ancient of the Sin3 molecules, in Schizosaccharomyces pombe. In contrast to Pst1 [2] and Pst2 [3], Pst3 occupies the entire nuclear space, including the nucleolus. The deletion of pst3+ causes general genome instability including chomosome mis-segregation, gross sporulation defects, rampant anneuploidy, and distended nucleoli. Genome-wide expression analysis indicated a role in both gene repression and gene activation. Interestingly, highly expressed genes encoding ribosomal and nucleolar proteins were positively regulated by Pst3. Genome wide binding analysis for Pst3-GFP indicated that Pst3 is bound both to intergenic and coding regions, and could be correlated with expression data. Proteins previously identified as part of the Clr6/Pst2 complex co-immunopercipitated with Pst3-TAP. Additionally, Snf59, the kinase Ssp1, and the Dead-Box helicase Dbp10 were identified as Pst3 interaction partners. Taken together this data suggests that Pst3 has a direct role in the structure and function of the nucleolus.
Keywords: Expression profiling

overall_design: Expression profiling experiments were performed and quantified according to (Xue et al., 2004).

first: Rebecca

last: Silverstein

first: Julian

last: Walfridsson

first: Carolina

last: Bonilla


title: Expression profiling of Candida albicans and Candida dubliniensis in reconstituted human oral epithelium 30 min p.i.

first: Martin

last: Spiering

overall_design: Global gene expression in Candida albicans SC5314 or Candida dubliniensis CD36 on reconstituted human oral epithelium (RHE) 30 min postinoculation. Gene expression on RHE was compared to gene expression in cells used as inoculum (0 min). Performed in three biological replicates with dye swaps across the biological replicates. Gene expression of Candida cells on RHE was normalized to gene expression in reference control (0 min); log2 ratios were calculated by dividing spot intensity of experimental by that of the reference control.

first: Gary

last: Moran

first: Murielle

last: Chauvel

first: Donna

last: MacCallum

last: Higgins

first: Tim


title: Comparative expression profiling in Candida albicans and Candida dubliniensis in inocula, RHE, and PCF cultures

summary: The opportunistic human pathogens, Candida albicans and Candida dubliniensis, are closely related species displaying large differences in virulence, but the reasons for these differences are elusive. Microarray-based comparative analysis of global gene expression in the two species incubated on reconstituted human oral epithelium (RHE) was used to identify specific and common changes in gene expression and find novel C. albicans virulence genes

overall_design: Comparative analysis of global gene expression in Candida albicans SC5314 and Candida dubliniensis CD36 in reconstituted human oral epithelium (RHE), polycarbonate filter (PCF; used as RHE support matrix) 30 and 90 min postinoculation, and in cultures used as inocula (0 min). Gene expression in  C. albicans and C. dubliniensis was assessed by co-hybridizations matched by treatments. Performed in two or three biological replicates with reciprocal dye swaps for each biological replicate. Gene expression of Candida cells on RHE was normalized to gene expression in reference control (PCF); log2 ratios were calculated by dividing spot intensity of experimental (C. albicans) by that of the reference control (C. dubliniensis).

first: Karsten

last: Hokamp

last: Yeomans

first: David

last: Coleman

first: Derek

last: Sullivan


title: Hard-wiring in the Plasmodium falciparum transcriptome I

first: Pradipsinh

last: Rathod

summary:
To help malaria parasites survive unpredictable host immune responses, it is known that genes for surface proteins express stochastically in Plasmodium falciparum. Here, we demonstrate that gene expression for intracellular metabolic functions may be preordained and insensitive to specific metabolic perturbations.  In a tightly-controlled, large microarray study involving over 100 hybridizations to isogenic drug-sensitive and drug-resistant parasites, the lethal antifolate WR99210 failed to over-produce RNA for the biochemically and genetically proven target dihydrofolate reductase-thymidylate synthase (DHFR-TS). Beyond the target, this transcriptional obstinacy carried over to the rest of the parasite genome, including genes for target pathways of folate and pyrimidine metabolism. Even 12 hours after commitment to death, the transcriptome remained faithful to evolutionarily entrained paths.  A system-wide transcriptional disregard for metabolic perturbations in malaria parasites may contribute to selective vulnerabilities of the parasite to lethal antimetabolites. While large protective metabolic responses were not detected, DNA microarrays helped capture small, but reproducible drug-dependent perturbations within hours of drug exposure. In addition, in Plasmodium cells that had adapted to long-term drug exposure, DNA microarrays revealed new, large genome-wide transcriptional adjustments in the hard-wired transcriptional program itself.
Keywords: Plasmodium falciparum treated with WR99210

overall_design: RNA from P. falciparum Dd2 and B1G9 (WR99210 resistant cell-line) trophozoites that had been treated with 10 nM WR99210 for varying durations (3, 6, 9, 15, 18, 21 and 24h) was hybridized against a common pool of trophozoite RNA from a cognate clone,  a culture containing 0.1% (v/v) DMSO lacking drug was used as untreated control, microarray data were obtained from at least four hybridizations using RNA from two independent parasite cultures

first: Karthikeyan

last: Ganessan

first: Napawan

last: Ponmee

first: Lei

last: Jiang

first: Joseph

last: Fowble

first: John

last: White

first: Sumalee

last: Kamchonwongpaisan

first: Yongyuth

last: Yuthavong

first: Prapon

last: Wilairat


title: Leishmania major promastigote ChIP-chip: TBP, SNAP50, acetylH3

status: Public on Nov 11 2008

first: Sean

last: Thomas

address: WTC East #600, 2211 Elliott Ave

department: Genome Sciences

summary: The goal of this study is to identify likely sites of polycistronic transcription initiation in a kinetoplastid parasite.  Peaks in histone H3 acetylations were found to mark these likely sites, with TBP and SNAP50 enriched upstream of these acetylation peaks.  Acetylation peaks are greater in rapidly dividing cells than in stationary cells.

overall_design: Each ChIP sample was compared to an input chromatin sample that underwent a mock immunoprecipitation (without antiserum), or in the case of acetylH3 ChIPs, used an antiserum that recognized total H3 histones.  Log ratios and raw scores for each probe are provided.

first: Amanda

last: Green

first: Nancy

last: Sturm

last: Campbell

first: Peter

last: Myler


title: EDL933 in human macrophage THP-1 cells at different time point

first: Sébastien

last: Faucher

state: QUEBEC

address: C.P. 6128 Succ. Centre-Ville

department: Microbiology and Immunology

institute: University of Montreal

summary:
Effect of human macrophages phagocytosis on the global transcriptome of EDL933 at different time.
Infection of THP-1 with EDL933. Application of SCOTS technique to have cDNA. Hybridation on microarray.
Reference: EDL933 in RPMI medium
Keywords: stres response, host-bacteria response, time-course

overall_design:
For each time point, 2 microarray are analysed and on each microarray there is 2 replicate
Total of 4 replicate for each time point (including reference medium)


title: Effect of PCN on CAR and PXR regulated genes involved in circadian rhythm, drug metabolism and cholesterol homeostasis

city: Ljubljana

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary: The nuclear receptor PXR (Pregnane X rreceptor) mediates the effects of pregnenolone-16alpha-carbonitrile (PCN) on gene transcription. The relative role of PXR and also CAR to the induction response by PCN was studied on cDNA arrays containing 320 (Steroltalk V2) genes (genes involved in cyrcadian rhythm, drug metabolism, cholesterol biosynthesis, sterol synthesis/transport, heme synthesis). Samples from livers of wild type and CAR-/-, PXR-/- or CAR/PXR-/- knockout mice were tested after treatment with PCN for gene expression within the European Framework V program “Steroltalk” (www.steroltalk.net). Results from these experiments show the complex role of PXR receptor in the expression of genes involved in cyrcadian rhythm, drug metabolism and cholesterol biosynthesis.

overall_design: Animals were injected i.p. 40mg/kg PCN or vehicle (5% DMSO in corn oil). After 12h they were sacrificed and total RNA was isolated from the livers. Pools of untreated samples were mixed in each genetic variant group (wild type and CAR-/-, PXR-/- or CAR/PXR-/-) with the PCN treated ones and hybridized to Steroltalk V2 arrays.

first: Viola

last: Tamasi

first: Markus

last: Beer

first: Damjana

last: Rozman

first: Urs

last: Meyer


title: Colony Stimulating Factor 1 (CSF-1) responses in human monocyte derived macrophages

city: Brisbane

first: Katharine

last: Irvine

address: 306 Carmody Rd

country: Australia

institute: Institute for Molecular Bioscience

summary:
Although the role of macrophage colony stimulating factor (M-CSF/CSF-1) in homeostasis and disease processes has been studied extensively in mice, little is known of the impact of this cytokine on differentiated human macrophages. Here we show that, in contrast to its effects on mouse bone marrow-derived macrophages (BMM), CSF-1 did not induce expression of urokinase plasminogen activator mRNA, repress expression of apolipoprotein E mRNA, or prime LPS-induced TNF secretion in human monocyte-derived macrophages (HMDM) from several independent donors. Using expression profiling, we show that CSF-1 dynamically regulated the expression of several genes that encode chemokines and chemokine receptors (e.g. CXCL10/IP-10, CXCL2, CCL7, SDF2L1, CXCR4) in HMDM. CSF-1 also upregulated the expression of several genes encoding enzymes of the cholesterol biosynthetic pathway (HMGCR, MVD, IDI1, FDPS, SQLE, CYP51A1, EBP, NSDHL, DHCR7 and DHCR24), while expression of ABCG1, encoding a cholesterol efflux transporter, was repressed. Although the CSF-1/CSF-1R system has been proposed as a target for the treatment of inflammatory and metastatic disease based on studies in rodents, this is the first systematic analysis of the effects of CSF-1 on mature human macrophages. Our data demonstrates that CSF-1 represents a further link between inflammation and cardiovascular disease, inflammtion and immunity.
Keywords: Stimulus response

overall_design: In vitro differentiated (HMDM) from 3 individuals were stimulated with CSF-1 for 6h and compared to unstimulated controls on a single-channel microarray.

first: Matthew

last: Sweet

first: David

last: Hume


title: Duplicate genes increase expression diversity in closely related species and allopolyploids

city: Bethesda

first: Misook

last: Ha

address: NIH

institute: National Heart Lung Blood Institute

type:
Expression profiling by array
Genome variation profiling by array

summary: Polyploidy or whole genome duplication (WGD) provides raw genetic materials for sequence and expression evolution of duplicate genes. However, the mode and tempo of expression divergence between WGD duplicate genes in closely relates species and recurrent allopolyploids are poorly understood. Arabidopsis is a suitable system for testing the hypothesis that duplicate genes increase expression diversity and regulatory networks. In Arabidopsis, WGD occurred more than once prior to the split between Arabidopsis thaliana and Arabidopsis arenosa, and both natural and human-made allotetraploids are available. Comparative genomic hybridization analysis indicated that single-copy and duplicate genes after WGD were well preserved in A. thaliana and A. arenosa. Analysis of gene expression microarrays showed that duplicate genes generally had higher levels of expression divergence between two closely related species than single-copy genes. The proportion of the progenitors' duplicate genes that were nonadditively expressed in the resynthesized and natural allotetraploids was significantly higher than that of single-copy genes. Duplicate genes related to environmental stresses tended to be differentially expressed, and multi-copy duplicate genes were likely to diverge expression between progenitors and in the allotetraploids. Compared to single-copy genes, duplicate genes tend to contain TATA boxes and less DNA methylation in the promoter regions, facilitating transcriptional regulation by binding transcription factors and/or cis-and trans- acting proteins. The data suggest an important role of WGD duplicate genes in modulating diverse and novel gene expression changes in response to external environmental cues as well as internal genetic turmoil such as recurrent polyploidy events.

sample_organism:
Arabidopsis thaliana
Arabidopsis arenosa
Arabidopsis suecica

overall_design:
To analyze expression change of duplicate genes conserved in A.thaliana and A.arenosa, we selected the duplicate genes with the same hybridization intensities in comparative genomic hybridization (CGH) between A. thaliana and A. arenosa.
To test the hypothesis that duplicate genes change expression regulation among different polyploid species, we first compared expression divergences of single-copy and duplicate genes between A. thaliana and A. arenosa. We then examined how duplicate genes affect expression change in new round of polyploidy detecting expression variations of single-copy and duplicate genes between each resynthesized allopolyploid and their progenitors.

first: Jeffrey

last: Chen

first: Jianlin

last: Wang

first: Eun-Deok

last: Kim

first: Lu

last: Tian

first: Hyeon-Se

last: Lee

first: Ning

last: Wei

first: Hongmei

last: Jiang

first: Brain

last: Watson

first: Andreas

last: Madlung

first: Thoman

last: Osrborn

first: R

last: Doerge

first: Luca

last: Comai


title: A global analysis of gene expression in histological layers of the shoot apical meristem of maize

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

summary:
All above ground organs of higher plants are ultimately derived from specialized organogenic structures termed shoot apical meristems (SAMs).  The SAM exhibits distinctive structural organization, marked by cell layering. Maize SAMs are comprised of two cell layers, L1 (single cell layered tunica) and L2 (corpus).  To identify genes required for layer-specific functions intact maize SAMs were fixed, embedded in paraffin and sectioned.  L1 and L2 cells were isolated from these sections via laser capture microdissection (LCM).  RNA was isolated from six biological replications of L1 and L2, amplified and hybridized to microarrays spotted with ~37,000 maize cDNA clones.  This experiment identified ~700 ESTs that are preferentially expressed in the L1 or the L2 (P <0.001). The L1-up-regulated ESTs included ZmOCL1 and ZmOCL4, which are known to exhibit L1-specific expression in the maize SAM. The L2-up-regulated ESTs included KNOTTED1, whose transcripts are known to accumulate in the L2 but not in the L1 of the maize SAM. Differentially expressed ESTs included genes involved in transcription, signal transduction, transport and metabolism, many of which are novel candidates that are required for layer-specific functions in the maize SAM.  Several L1-up-regulated ESTs were annotated as yabby family genes or basic helix-loop-helix transcription factor-like genes, which have not previously been reported as having layer-specific expression in the SAM.  Novel WW domain-containing genes (WW genes) were identified in this study.  The WW domain mediates protein-protein interactions, often with signal transduction components.  These WW genes were substantially up-regulated in the L1 relative to the L2.
Keywords: Cell Type Comparison

overall_design: An experimental aim is to identify genes that are differentially expressed in distinct histological cell layers of maize SAM by comparing the transcript accumulation between L1 (single cell layered tunica) and L2 (corpus) using cDNA microarrays that have over 37,000 informative spots from maize.


title: Colonization, luminescence, and autoinducer effects on host transcription during development of squid-vibrio association

status: Public on Nov 10 2008

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

institute: The University of Iowa

summary: The light-organ symbiosis between the squid Euprymna scolopes and the luminous bacterium Vibrio fischeri offers the opportunity to decipher the hour-by-hour events that occur during the natural colonization of an animal's epithelial surface by its microbial partners. To determine the genetic basis of these events, a glass-slide microarray was used to characterize the light-organ transcriptome of juvenile squid in response to the initiation of symbiosis. Patterns of gene expression were compared between animals not exposed to the symbiont, exposed to the wild-type symbiont, or exposed to a mutant symbiont defective in either of two key characters of this association: bacterial luminescence or autoinducer (AI) production. Hundreds of genes were differentially regulated as a result of symbiosis initiation, and a hierarchy existed in the magnitude of the host's response to three symbiont features: bacterial presence > luminescence > AI production. Putative host receptors for bacterial surface molecules known to induce squid development are up-regulated by symbiont light production, suggesting that bioluminescence plays a key role in preparing the host for bacteria-induced development. Further, because the transcriptional response of tissues exposed to AI in the natural context (i.e., with the symbionts) differed from that to AI alone, the presence of the bacteria potentiates the role of quorum signals in symbiosis. Comparison of these microarray data with those from other symbioses, such as germ-free/conventionalized mice and zebrafish, revealed a set of shared genes that may represent a core set of ancient host responses conserved throughout animal evolution.

overall_design: Six experimental treatments of juvenile animals were performed for the microarray matrix: uncolonized (Apo); uncolonized, but supplemented with AI (Apo + AI); colonized by wild-type V. fischeri (wild type); colonized by a mutant defective in luciferase synthesis (luxA); colonized by a mutant defective in AI synthesis (luxI); and, colonized by the luxI mutant, but supplemented with AI (luxI + AI). At 18 h postinoculation, animals were anesthetized in 2% ethanol in HOSW, and the light organs were removed into RNAlater (Ambion Biosystems).


title: mRNA Sequencing Reveals Altered Synaptic Vesicular Transport in Post-Mortem Cerebellum

status: Public on Nov 12 2008

city: Santa Fe

first: Stephen

last: Kingsmore

state: NM

address: 2935 Rodeo Park Drive East

institute: National Center for Genome Resources

type: Expression profiling by high throughput sequencing

summary: Schizophrenia (SCZ) is a common, disabling mental illness with high heritability but complex, poorly understood genetic etiology.  As the first phase of a genomic convergence analysis of SCZ, we generated 16.7 billion nucleotides of short read, shotgun sequences of cDNA from post-mortem cerebellar cortices of 14 patients and six matched controls.  A rigorous analysis pipeline was developed for analysis of digital gene expression studies.  Sequences aligned to approximately 33,200 transcripts in each sample, with average coverage of 450 reads per gene.  Following adjustments for confounding clinical, sample and experimental sources of variation, 215 genes differed significantly in expression between cases and controls.  Golgi apparatus, vesicular transport, membrane association, Zinc binding and regulation of transcription were over-represented among differentially expressed genes. Twenty three genes with altered expression and involvement in presynaptic vesicular transport, Golgi function and GABAergic neurotransmission define a unifying molecular hypothesis for dysfunction in cerebellar cortex in SCZ.

overall_design: 16.7 billion nucleotides of shotgun, full length cDNA sequence data were generated using Illumina Genome Analyzer platforms with sequencing-by-synthesis (SBS) chemistry from 20 mRNA samples (Lister et al., 2008; Morin et al., 2008)(Mortazvi et al., 2008).  mRNA samples were isolated post-mortem from the lateral hemispheres of the cerebellar cortices of 14 patients with SCZ and 6 control individuals (Paz et al., 2006; Bullock et al., In Press)(Table 1).  Unrelated subjects were chosen to facilitate sampling of genetic heterogeneity (Freimer and Sabatti, 2004; McClellan et al., 2007).  Cases and controls were approximately matched for age (cases, 45.2 + 11.8 years; controls 41.3 + 9.2 years), sex (all male), race, post-mortem interval (cases, 12.2 + 5.0 hours; controls 17.7 + 3.3 hours), cause of death, autopsy brain pH (cases, 6.54 + 0.19; controls 6.46 + 0.10) and RNA integrity number (cases, 8.06 + 0.53; controls, 7.87 + 0.41) (Table 1).  12.5 – 38.7 million, high quality sequences of length 32 – 36 bp were generated per sample (Table 2).  Sequences were aligned to the human genome and RefSeq transcript databases using the algorithm GMAP, which allowed < 2 (< 6%) mismatches (Wu and Watanabe, 2005).  There was little intra-sample variability in the number of sequences aligned to each locus from run-to-run or instrument-to-instrument (Fig. 1A; all source coefficient of variation 3.4%).  43.5 + 6.7% of sequences aligned to a transcript and 69.4 + 9.6% to the genome, evidence that annotation of mRNA isoforms in Homo sapiens is incomplete (Birney et al., 2007) (Table 2).  91% of alignments were unique (Table 2).  Reads aligning to more than one location contained repetitive, paralogous, polymorphic or low complexity sequences and primarily mapped to untranslated regions or highly polymorphic gene families, such as major histocompatibility genes (Sugarbaker et al., 2008).  Unmapped sequences did not align to mitochondrial or 1879 viral genomes, offering negative evidence of chronic viral etiology for SCZ in these patients.

first: Nora

last: Perrone-Bizzozero

first: Gary

last: Schroth

first: Joann

last: Mudge

first: Russ

last: Wolfinger

first: Neil

last: Miller

first: Irina

last: Khrebtukova


title: Molecular analysis of photic inhibition of blood-feeding in Anopheles gambiae

city: Baltimore

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary:
Anopheles gambiae mosquitoes exhibit an endophilic, nocturnal blood feeding behavior. Despite the importance of light as a regulator of malaria transmission, our knowledge on the molecular interactions between environmental cues, the circadian oscillators and the host seeking and feeding systems of the Anopheles mosquitoes is limited.
In the present study, we show that the blood feeding behavior of mosquitoes is under circadian control and can be modulated by light pulses, both in a clock dependent and in an independent manner. Short light pulses (~2-5 min) in the dark phase can inhibit the blood-feeding propensity of mosquitoes momentarily in a clock independent manner, while longer durations of light stimulation (~1-2 h) can induce a phase advance in blood-feeding propensity in a clock dependent manner. The temporary feeding inhibition after short light pulses may reflect a masking effect of light, an unknown mechanism which is known to superimpose on the true circadian regulation. Nonetheless, the shorter light pulses resulted in the differential regulation of a variety of genes including those implicated in the circadian control, suggesting that light induced masking effects also involve clock components. Light pulses (both short and longer) also regulated genes implicated in feeding as well as different physiological processes like metabolism, transport, immunity and protease digestions. RNAi-mediated gene silencing assays of the light pulse regulated circadian factors timeless, cryptochrome and three takeout homologues significantly up-regulated the mosquito's blood-feeding propensity. In contrast, gene silencing of light pulse regulated olfactory factors down-regulated the mosquito's propensity to
Our study suggests that the mosquito’s feeding behavior is under circadian control. Long and short light pulses can induce inhibition of blood-feeding through circadian and unknown mechanisms, respectively, that involve chemosensory factors.

overall_design: A series of assays were performed to assess transcriptomic changes in mosquitoes upon light stimulation and blood feeding in order to assess relationships between photic stimulation and modulation of feeding behavior.

first: Suchismita

last: Das


title: Towards an understanding of the mechanism of action of praziquantel

city: Albuquerque

first: Anthony

last: Aragon

address: Castetter Hall Room 214

institute: University of New Mexico

summary:
Although praziquantel (PZQ) has been used to treat schistosomiasis for over 20 years its mechanism of action remains unknown. We have developed an assay based on the transcriptional response of S. mansoni PR-1 to heat shock to confirm that while 6 week post infection (p.i.) schistosomes are sensitive to PZQ, 4 week p.i. schistosomes are not. Further, we have used this assay to demonstrate that this sensitivity develops between days 37 and 40 p.i. PZQ linked to the fluorophore BODIPY appears to easily enter the cells of intact 4 and 6 week p.i. schistosomes as well as mammalian NIH 3T3 cells and together, these data suggest that the differential effects of PZQ is not based on cell exclusion but probably due the differential expression of a target molecule at 6 weeks p.i. A transcriptomal analysis of gene expression between 4 and 6 weeks p.i. revealed 607 candidate genes whose products are potential PZQ targets. A comparison of this gene list with that of genes expressed by PZQ sensitive miracidia reduced this target list to 247 genes, including a number involved in aerobic metabolism and cytosolic calcium regulation. Finally, we also report the effect of an in vitro sub-lethal exposure of PZQ on the transcriptome of S. mansoni PR-1. Annotation of genes differentially regulated by PZQ exposure suggests that schistosomes may undergo a transcriptomic response similar to that observed during oxidative stress.

Keywords: cell type comparison, time course

overall_design:
Cell type comparison: Four biologial replactes of schistosomes harvasted 4 and 6 week post-infection were performed.

Time course: Four samples performed in duplicate for exposure to a sub-lethal dose of PZQ (50 µg/ml) at time points 0, 30, 60, and 240 min over a common reference sample.

first: Charles

last: Cunningham


title: Differential Gene Expression Associated With Postnatal Articular Cartilage Maturation

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

summary:
Chondrocyte gene expression was analyzed to study mechanisms involved in the structural and functional adaptation of articular cartilage during postnatal maturation.  Transcriptional profiling was used to compare articular chondrocytes between four neonatal and four adult horses.  Expressional differences featured matrix proteins and matrix-modifying enzymes reflecting the transition from cartilage growth to cartilage homeostasis.
Keywords: articular cartilage, maturation, horse, cDNA microarray

overall_design: This is a direct comparison between full-thickness neonatal and adult articular cartilage transcriptomes.  Cartilage from four neonatal horses were compared to cartilage from four adults.  For each comparison and its dye-swap, one neonate was randomly compared to one adult.

first: Liping

last: Huang

first: Arnold

last: Stromberg

first: James

last: MacLeod


title: CodY in Staphylococcus aureus: regulatory link between metabolism and virulence gene expression

status: Public on Nov 07 2008

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary: CodY is a conserved regulator in gram-positive organisms described to repress metabolic genes mainly involved in nitrogen metabolism but also to control the expression of virulence genes in pathogens. We constructed codY gene-replacement mutants in three unrelated S. aureus strains (Newman, UAMS-1, RN1HG). codY mutants grew slower in a chemically defined medium compared to the wild type strains. However, only codY mutants were able to grow in medium lacking threonine. Excess of isoleucine resulted in growth inhibition in the wild type but not in the codY mutants indicating a role of isoleucine for CodY dependent repression of metabolic genes. The prototypic CodY-repressed operon ilvDBCleuABCilvA is preceded by a CodY-binding motif and repressed after up-shift with isoleucine and to a lesser extent guanidine. Transcription of the quorum sensing system agr followed a similar expression pattern. The codY dependent repression of agr is in line with the concomitant influence of CodY on typical agr regulated genes such as cap, spa fnbA and coa. However, transcriptional analysis revealed that most of these virulence genes (e.g. cap, fnbA, spa hla) are also regulated by CodY in an agr negative background. Microarray analysis revealed the large majority of codY-repressed genes are involved in amino-acid transport and metabolism, genes showing codY dependent activation were mainly involved in nucleotide transport and metabolism or virulence. In summary, CodY in S. aureus not only acts as repressor for genes involved in nitrogen metabolism but also contributes to virulence gene regulation by supporting as well as substituting agr function.

sample_organism: Staphylococcus aureus subsp. aureus NCTC 8325

sample_organism: Staphylococcus aureus subsp. aureus Mu50

sample_organism: Staphylococcus aureus subsp. aureus N315

sample_organism: Staphylococcus aureus subsp. aureus MRSA252

sample_organism: Staphylococcus aureus subsp. aureus MSSA476

sample_organism: Staphylococcus aureus subsp. aureus USA300

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: The microarray was manufactured by in situ synthesis of 10'807 long oligonucleotide probes , selected as previously described (Charbonnier, 2005). It covers >98% of all ORFs annotated in strains N315 and Mu50 , MW2, COL , NCTC8325, USA300 , MRSA252 an MSSA476 including their respective plasmids.

first: Konstanze

last: Pohl

first: Patrice

last: Francois

first: Ludwig

last: Stenz

first: Frank

last: Schlink

first: Tobias

last: Geiger

first: Silvia

last: Herbert

first: Christiane

last: Goerke

first: Jacques

last: Schrenzel

last: Wolz


title: Chromatin Immunoprecipitation microarray data from antiHA IP in stable LNCaP cells expressing either YFP or HA-SOX4/YFP

city: Atlanta

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

institute: Emory University

summary:
SOX4 is a critical developmental transcription factor in vertebrates and is required for   precise differentiation and proliferation in multiple tissues.  In addition, SOX4 is   overexpressed in many human malignancies, but the precise role of SOX4 in cancer   progression is not well understood.  Here we have identified the direct transcriptional   targets of SOX4 using a genome-wide localization ChIP-chip analysis.

Keywords: ChIP-chip

overall_design: LNCaP prostate cancer cells were stably infected with a lentivirus containing either HA-SOX4-IRES-YFP or IRES-YFP alone.  Cells were sorted for YFP expression and expanded in tissue culture before chromatin immunoprecipitation against the HA epitope tag was performed.

first: Carlos

last: Moreno

first: Christopher


title: Divergent transcription from active promoters

status: Public on Nov 06 2008

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Drive, Room 3114

department: SCRM

institute: UCSD

type: Non-coding RNA profiling by high throughput sequencing

summary: Here we describe a novel class of short RNAs that indicate widespread divergent transcription at mammalian promoters

overall_design: Small RNA cloning and deep sequencing from human embryonic stem cells, derived neural progenitors and neurons


title: Effect of P. gingivalis on human primary gingival epithelial cells

city: Louisville

first: Amar

last: Singh

address: 501 S Preston street

department: Oral Health and Systemic Disease Research Group

institute: University of Louisville

summary:
EXPERIMENT: Microarray expression profiles derived from the human primary gingival epithelial cells 24.0h after exposure to heat inactivated P. gingivalis
ANIMAL MODEL: NON
EXPOSURE: Human primary gingival epithelial cells (at 3rd passage) were exposed to heat inactivated P. gingivalis (MOI:100) at 90% confluence.  Two types of gingival epithelial cells were used.  One with Normal cytokine inducer type (at least 2 fold IL-6/TNF-alpha/IL-1ß when challenged with TLR2/4 agonists) and the other with diminished cytokine inducer type (no change in IL-6/TNF-alpha/IL-1ß when challenged with TLR2/4 agonists).
INTERVAL: NON.
PLATFORM: microRNA expression profile in gingival epithelial cells - miRCURY LNA™ microRNA Arrays (Exiqon). The RNA samples were subjected to microarray on 8/9/2007
Keywords = Human primary gingival epithelial cells
Keywords = P. gingivalis
Keywords = Periodontitis

Keywords: Ordered

overall_design: The effect of heat inactivated P. gingivalison human primary gingival epithelial cells were assayed.

first: Denis

last: Kinane

first: Manjunatha

middle: R

last: Benakanakere

middle: V


title: Transcriptional profiling of Blochmannia floridanus during different host stages

city: Wuerzburg

first: Sascha

last: Stoll

address: Biozentrum am Hubland

department: Dpt. of Microbiology

institute: University of Wuerzburg

summary:
The transcriptome of Blochmannia floridanus, the endosymbiont of the carpenter ant Camponotus floridanus, is presented during eight developmental stages of its holometabolous host by use of a whole genome DNA-macroarray. The detected transcription patterns indicate the presence of local transcription units as well as global regulatory mechanisms. Yet, the overall regulation scale is very modest, rarely exceeding a factor of three which is in line with the low number of transcriptional regulators present in this reduced genome. A large number of genes show differential expression in different life stages and a distinct expression pattern of genes possibly involved in symbiotic function as compared to housekeeping genes is apparent. However, these transcriptional changes are small as compared to the changes in the number of bacteria during host development which is highest in pupae and in young imagines. Control of replication of the bacteria in certain life stages may therefore be the decisive parameter influencing overall gene expression of Blochmannia in the animal. The few highly expressed genes like those encoding molecular chaperones exhibit a significantly higher G+C-content than moderately expressed genes.

Keywords: Host stage-dependent gene expression

overall_design: C. floridanus laboratory colonies were maintained under constant conditions at 25°C with a 12 h light cycle in artificial nests and fed twice a week with cockroaches (Nauphoeta cinerea), Bhatkar agar (Bhatkar and Whitcomb, 1970), and honey water (50% wt/wt) ad libitum. Developmental stages were defined as L1 (very young larvae, still clustered), L2 (older larvae, approx. 2-4 mm), P1 (pupae before metamorphosis), P2 (pupae after metamorphosis, still uncolored), P3 (pupae shortly before eclosion with dark abdomens), W1 (workers shortly after eclosion, not completely melanized, no aggressive behavior), W2 (fully melanized adult workers from the nest, age not distinguishable), and W3 (adult workers from isolated subcolonies, at least 4 months old). For RNA preparations, midguts of the respective life stage (L2 - W3) were dissected and bacteria were isolated by homogenization and centrifugation. Endosymbionts from small larvae (L1) were isolated from whole animals. RNA for each cDNA array experiment was isolated from individual bacterial preparations; from L1 to W2, each developmental stage was represented by at least three independent experiments and samples from at least three different ant colonies. Two ant colonies (C79 and C118) were represented in every stage from L1 to W2 with additional samples from six other colonies. Old W3 workers were collected from two isolated subcolonies derived from the same mother colony, each sampled in duplicate.

first: Heike

last: Feldhaar

first: Roy

last: Gross


title: ChIP-chip from Ehrlichia chaffeensis-infected THP-1 cells  with ankyrin repeat-containing protein, p200

status: Public on Nov 05 2008

city: Galveston

first: Bing

last: Zhu

address: 301 University Boulevard

institute: utmb

summary:
Host genes interacting with ankyrin repeat-containing protein, p200, in Ehrlichia chaffeensis-infected monocytes.
Chromatin immunoprecipitation (ChIP) together with microarray (chip) analysis demonstrated enrichment of relatively small subset (n=456) of host cell genes associated with molecular and biological processes, many of which are known to be altered during ehrlichial infection.

Keywords: ChIP-chip

overall_design: Detection of genes with high signal enrichment by comparing the ratios of p200/input

first: Jere

last: McBride


title: Iron regulation in P. syringae DC3000

status: Public on Nov 08 2008

city: Ithaca

first: Philip

middle: Alan

last: Bronstein

state: NY

address: Cornell University Plant Science Building RM334

department: Plant Microbe Interaction Research Unit

institute: USDA-ARS

summary:
DC3000 cultures were grown under highly controlled conditions and after the addition of iron citrate or sodium citrate to the media. In the cultures supplemented with iron, we found that cell-associated iron increased rapidly while culture densities were not significantly different over 4 hours when compared to cultures with sodium citrate added. Microarray analysis of samples taken from before and after the addition of either sodium citrate or iron citrate identified 386 differentially regulated genes with high statistical confidence. Differentially regulated genes were clustered based on expression patterns observed between comparison of samples taken at different time points and with different supplements. This analysis grouped genes associated with the same regulatory motifs and/or had similar putative or known function.

Keywords: iron response, environmental signal, time course

sample_organism: Pseudomonas syringae pv. tomato str. DC3000

overall_design: 5 biological replicates, 3 timepoint: 0h, 0.5h, 4h after addition of  iron citrate or sodium citrate to increase final concentration by 50uM

first: Melanie

last: Filialtrault

last: Myers

first: Michael

last: Rutzke

first: David

last: Schneider

first: Samuel

last: Cartinhour


title: Expression profiling of zebrafish sox9 mutants reveals that Sox9 is required for retinal differentiation

city: Eugene

last: Miller

state: OR

address: 1229 University of Oregon

department: Institute of Molecular Biology

institute: University of Oregon

summary: The transcription factor gene Sox9 plays various roles in development, including differentiation of the skeleton, testes, glia, and heart. Other functions of Sox9 remain enigmatic. Because Sox9 protein regulates expression of target genes, the identification of Sox9 targets should facilitate an understanding of the mechanisms of Sox9 action. To help identify Sox9 targets, we used microarray expression profiling to compare wild-type embryos to mutant embryos lacking activity for sox9a and sox9b, the zebrafish co-orthologs of Sox9. Candidate genes were further evaluated by whole mount in situ hybridization in wild-type and sox9 mutant embryos. Results identified genes expressed in cartilage (col2a1a and col11a2), retina (calb2a, calb2b, crx, neurod, rs1, sox4a and vsx1) and pectoral fin bud (klf2b and EST AI722369) as candidate targets for Sox9. Cartilage is a well-characterized Sox9 target, which validates this strategy, whereas retina represents a novel Sox9 function. Analysis of mutant phenotypes confirmed that Sox9 helps regulate the number of Müller glia and photoreceptor cells and helps organize the neural retina. These roles in eye development were previously unrecognized and reinforce the multiple functions that Sox9 plays in vertebrate development.

overall_design: In each experiment, RNA was isolated from 48h wildtype and sox9a, sox9b double mutant embryos and the gene expression profiles were compared using microarrays.  Three biological replicate experiments were performed, and each biological replicate contained a dyeswap.

first: Hayato

last: Yokoi

first: John

middle: H

last: Postlethwait


title: Response of C. elegans immune pathway mutants to P. aeruginosa infection

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Synchronized C. elegans cultures of three geontypes -- wildype N2, daf-2(e1370) and sma-6(wk7) -- were prepared using standard techniques (http://cmgm.stanford.edu/~kimlab/index_methods.html). Live young adult worms were split between NG plates pre-seeded with the non-pathogenic E. coli strain OP50 or the Pseudomonas aeruginosa clinical isolate PA14 and incubated at 25C for 4 or 24 hours before harvesting. This experiment was repeated at least three times on independent occasions. cDNA probes were prepared from experimental samples and from reference mRNA extracted from mixed stage wild type worms grown at 25C, and were labeled with Cy3 or Cy5, as indicated.
A reference experiement design type is where all samples are compared to a common reference.
Elapsed Time: Time
Infection: Exposure to the non-pathogenic E. coli strain OP50 or to the  pathogenic Pseudomonas aeruginosa strain PA14
Strain Name: C. elegans wildtype strain N2 or the immune pathway mutants daf-2(e1370) or sma-6(wk7)

Keywords: reference_design

overall_design: Computed

first: Brigham

last: Hamlin

first: Eric

last: Evans


title: Array-based comparative genomic hybridization study of human embryonic stem cell lines

status: Public on Nov 04 2008

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 101

department: Embryology and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

summary:
G-banding of human embryonic stem cells (hESC) has proved their predisposition to aneuploidy of chromosomes 12, 17 and X. Now, using array-based comparative genomic hybridization, we find that hESC also accumulate other recurrent chromosomal abnormalities, such as duplications of stemness genes, submicroscopic instability of 20q11.21 and the appearance of a derivative chromosome 18.

Keywords: comparative genomic hybridization, genomic integrity of human embryonic stem cells

overall_design: Array-based comparative genomic hybridization was performed on 48 DNA samples from 17 human embryonic stem cell lines, all cultured in our laboratory under the same conditions. All lines were hybridized against DNA obtained from peripheral blood from donors with a known normal karyotype. No replicates were done from the same DNA sample, but, whenever possible the same stem cell line was analysed at later passages. All detected abnormalities were confirmed by FISH and/or G-banding.

first: Ileana

last: Mateizel

first: Mieke

last: Geens

first: Afroditi

last: Mertzanidou

first: Catherine

last: Staessen

first: Vandeskelde

last: Yves

first: Van

last: Josiane

first: Inge

last: Liebaers

first: Karen

last: Sermon


title: Transcriptomic analysis for response of EHEC  to short chain fatty acids

status: Public on Nov 01 2008

city: Suita

first: Toru

last: Tobe

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

country: Japan

institute: Osaka University

summary:
Enterohaemorrhagic Escherichia coli (EHEC) is an emerging pathogen that causes diarrhea and heamolytic uremic syndrome. Expression of genes associated to pathogenicity is strictly regulated by environmental factors. Since short chian fatty acids (SCFAs) are present in intestinal tract which is a target of EHEC infection, we investigated the response of EHEC genes to SCFAs, such as acetate, propionate and butyrate.

Keywords: Culture condition

overall_design: 3 sets of comparison between transcription profiles in EHEC growing in the presence of acetate, propionate or butyrate against EHEC growing in the presence of NaCl. Labelling of cDNA and hybridization were performed twice with independently prepared RNAs.

first: Noriko

last: Nakanishi


title: Zebrafish Zili- and Ziwi-interacting small RNAs

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

summary: Small RNAs exert an effect through diverse RNA interference pathways to transcriptionally or post-transcriptionally silence their targets. The Piwi-interacting RNAs (piRNAs) represent a germline-specific small RNA pathway where Piwi proteins themselves are thought to mediate piRNA biosynthesis. Here, we provide strong evidence for a piRNA amplification loop in zebrafish, in which Ziwi and Zili bind piRNAs of opposite polarity. Furthermore, we describe a function for Zili in transposon defense and germ cell differentiation, as well as a crucial function in meiosis, significantly extending the function of Piwi proteins beyond the control of transposable elements in vertebrates.

overall_design: small RNA from total gonads or Argonaute IPs were cloned and sequenced using 454 GS FLX system.

first: Saskia

last: Houwing

first: Rene

last: Ketting


title: R. conorii transcriptional response within inoculation eschar battlefield

first: FRANCOIS

last: Patrice

summary:
Rickettsia conorii, the causative agent of the MSF is transmitted to humans by the bite of infected ticks Rhipicephalus sanguineus. The skin thus constitutes an important barrier for the entry and propagation of R. conorii. Given this, analysis of the survival strategies used by the bacterium within infected skin is critical for our understanding of rickettsiosis. Here, we report the first genome-wide analysis of R. conorii gene expression from infected human skin biopsies. Our data showed that R. conorii exhibit a striking transcript signature that was remarkably conserved across patients, regardless of genotype. The expression profiles obtained using custom Agilent microarrays were validated by quantitative RT-PCR. Within eschars, approximately 15% (n = 211) of the total predicted R. conorii ORFs appeared differentially expressed. These genes are mostly down-regulated and encode proteins essential for bacterial replication. Some of the strategies displayed by rickettsiae to overcome the host defense barriers, thus avoiding killing, were also pointed out. The observed up-regulation of rickettsial genes associated with DNA repair is likely to correspond to a DNA-damaging agent enriched environment generated by the host cells to eradicate the pathogens. Survival of R. conorii within eschars also involves adaptation to osmotic stress, changes in cell surface proteins and up-regulation of some virulence factors. Interestingly, in contrast to down-regulated transcripts, we noticed that up-regulated ones rather exhibit a small nucleotide size, most of them being exclusive for the spotted fever group rickettsiae.
On the overall, this work provides some insights on how R. conorii counteracts the host cell attack at the site of inoculation which corresponds to the front line of human host defense against rickettsia diffusion and that resembles to battlefield.

sample_organism:
Rickettsia conorii
Rickettsia conorii str. Malish 7

overall_design: 9 R.conorii clinical isolates from eschars co-hybridized with reference strain R.conorii Strain Malish 7

first: Patricia

last: Renesto

first: Clarisse

last: Rovery

first: Patrice

last: François

first: Quentin

last: Leroy

first: Antoine

last: Huyghe

first: Wenjun

last: Li

first: Hubert

last: Lepidi

first: Jacques

last: Schrenzel

first: Didier

last: Raoult


title: An array based analysis of miRNA expression comparing matched frozen and FFPE human tissue samples

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

institute: Queen's University

summary:
MicroRNAs (miRNAs) are small non-coding RNAs that repress gene expression at the post transcriptional level via an antisense RNA-RNA interaction. Generally, miRNAs derived from snap frozen or fresh samples are used for array based profiling. Since tissues in most pathology departments are available only in formalin fixed and paraffin embedded state, we sought to evaluate the miRNA derived from formalin fixed and paraffin embedded (FFPE) samples for microarray analysis.  In this study, miRNAs extracted from matched snap frozen and FFPE samples were profiled using the Agilent miRNA array platform. Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. A total of seven cases were compared in either duplicate or triplicate.  Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results, as technical replicates showed high correlations (Kendall tau=0.722-0.853, Spearman rank correlation coefficient=0.891-0.954). Our results showed consistent high correlation between matched frozen and FFPE samples (Kendall tau=0.669-0.815, Spearman rank correlation coefficient=0.847-0.948), supporting the use of FFPE-derived miRNAs for profiling.

Keywords: formalin-fixed and paraffin-embedded (FFPE) miRNA profiling

overall_design: 7 matched frozen and FFPE lymphoid hyperplasia tissues were profiled and compared. Triplicate arrays were performed for two pairs of hyperplasia samples and duplicate arrays for three pairs of hyperplasia samples.

first: Victor

last: Tron


title: The Detection and Subtyping of Seasonal Influenza A H1N1 Isolates Using a Microarray

city: Mukilteo

first: Michael

last: Lodes

address: 6500 Harbour Heights Pkwy, Suite 303

department: Assay Development

institute: CombiMatrix Corp

summary:
An influenza A microarray was used to type influenza A H1N1 specimens collected in Washington State and the results compared with identification by both culture and real time RT PCR. The microarray was more sensitive than conventional influenza testing. Cluster analysis of the microarray data discriminated specimens into distinct clades. Specimens from two pediatric decedents formed a unique clade upon H1 analysis.

Keywords: Comparative genome study; Influenza A strains; Subtype H1N1

overall_design: 23 influenza A H1N1 specimens collected in Washington State were subtyped by microarray and data was compared with identification by both culture and real time RT PCR.

first: David

middle: S

last: Boyle

first: Brandon

middle: T

last: Leader

first: Elizabeth

last: Wieman

first: Paul

last: Swenson

first: Dominic

last: Sucuiu

first: Robin

last: Liu

first: Jinxin

last: Hu


title: Comparative transcriptome analysis between original and evolved recombinant lactose-consuming S. cerevisiae strains

city: Braga

first: Pedro

middle: M. R.

last: Guimaraes

address: Campus de Gualtar

department: Department of Biological Engineering

country: Portugal

institute: University of Minho - CEB

summary: The engineering of Saccharomyces cerevisiae strains for lactose utilization has been attempted with the intent of developing high productivity processes for alcoholic fermentation of cheese whey. A recombinant S. cerevisiae flocculent strain that efficiently ferments lactose to ethanol was previously obtained by evolutionary engineering of an original recombinant that displayed poor lactose fermentation performance. In this study, we compared the transcriptomes of the original and the evolved recombinant strains (T1 and T1-E, respectively) growing in lactose, using cDNA microarrays. Microarray data revealed 173 genes whose expression levels differed more than 1.5-fold. About half of these genes were related to RNA mediated transposition. We also found genes involved in DNA repair and recombination mechanisms, response to stress, chromatin remodelling, cell cycle control, mitosis regulation, glycolysis and alcoholic fermentation. These transcriptomic data are in agreement with some of the previously identified physiological and molecular differences between the recombinants, and point to further hypotheses to explain those differences.

overall_design:
Four samples, each corresponding to independent biological cultivations of the two strains (T1 and T1-E), were analysed.
To reduce the bias due to unequal incorporation or differences in quantum efficiency of the two dyes, RNA samples from a second independent experiment were labeled by opposite dye to the first experiment (method called dye switch), and this procedure was repeated 4 times, leading to 4 independent intensity values for each gene (spots) on the microarray. This experimental design minimizes the intrinsic biological noise between identical culture conditions and the technical variations inherent to the DNA microarray technology.

first: Veronique

last: Le Berre

first: Serguei

last: Sokol

first: Jean

last: Francois

first: Jose

last: Teixeira

first: Lucilia

last: Domingues


title: Mutation in Transcription Factor Upc2p Causes Upregulation of Ergosterol Biosynthesis Genes and Fluconazole Resistance

city: Memphis

first: Katherine

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

summary:
In the pathogenic yeast Candida albicans, the zinc cluster transcription factor Upc2p has been shown to regulate expression of ERG11 and other genes involved in ergosterol biosynthesis upon exposure to azole antifungals.  ERG11 encodes lanosterol demethylase, the target enzyme of this antifungal class.  Over-expression of UPC2 reduces azole susceptibility, whereas its disruption results in hypersusceptibility to azoles and reduced accumulation of exogenous sterols.  Constitutive up-regulation of ERG11 is a major cause of resistance to fluconazole in clinical isolates of C. albicans, yet the mechanism for this has yet to be determined.  Using genome-wide gene expression profiling, we found UPC2 and other genes involved in ergosterol biosynthesis to be coordinately up-regulated with ERG11 in a fluconazole resistant clinical isolate as compared with a matched susceptible isolate from the same patient.  Sequence analysis of the UPC2 alleles of these isolates revealed that the resistant isolate contained a single nucleotide substitution in one UPC2 allele that resulted in a G648D exchange in the encoded protein.  Introduction of the mutated allele into a drug susceptible strain resulted in constitutive up-regulation of ERG11 and increased resistance to fluconazole.  By comparing the gene expression profiles of the fluconazole resistant isolate and of strains carrying wild-type and mutated UPC2 alleles, we identified target genes that are controlled by Upc2p.  Here we show for the first time that a gain-of-function mutation in UPC2 leads to increased expression of ERG11 and imparts resistance to fluconazole in clinical isolates of C. albicans.
Keywords: genome-wide expression profiling

overall_design: Clinical isolates S1 (susceptible) and S2 (resistant), genome strain SC5314, UPC2 disruption strains (UPC2M4A and UPC2M4B), UPC2 re-integrant strains of non-mutated UPC2 allele (UPC2M2K21A and UPC2M2K21B), and UPC2 re-integrant strains of mutated UPC2 allele (UPC2M2K31A and UPC2M2K31B) were grown for 3 hours until log phase.  RNA was extracted for each isolate/strain.  Experiments were performed in duplicate.

first: Nico

last: Dunkel

first: Teresa

first: Ramin

last: Homayouni

first: Joachim

last: Morschhauser

last: Rogers


title: ING4 ChIP-chip in HT1080 cells

first: Tiffany

last: Hung

state: CA

address: 371 SERRA MALL

institute: Stanford University

summary: Aberrations in chromatin dynamics play a fundamental role in tumorigenesis, yet relatively little is known of the molecular mechanisms linking histone lysine methylation to neoplastic disease. ING4 (Inhibitor of Growth 4) is a native subunit of an HBO1 histone acetyltransferase (HAT) complex and a tumor suppressor protein.  Here we show a critical role for the specific read-out of histone H3 trimethylated at lysine 4 (H3K4me3) by the ING4 PHD finger in mediating ING4 gene expression and tumor suppressor functions.  The interaction between ING4 and H3K4me3 augments the acetylation activity of HBO1 on H3 tails, and drives H3 acetylation at ING4 target promoters to effect a DNA damage-dependent gene expression program.  Further, ING4 facilitates apoptosis in response to genotoxic stress and inhibits anchorage-independent cell growth, and these functions are dependent on ING4 interactions with H3K4me3.  Together, our results demonstrate a mechanism for brokering crosstalk between H3K4 methylation and histone H3 acetylation, and reveal a new molecular link between chromatin modulation and tumor suppressor mechanisms.

overall_design:
ING4 ChIP-chip +/- Doxorubicin treatment in HT1080 cells on Nimblegen whole genome promoter array

4 samples: HT1080 cell lines stably expressing Flag-ING4 or Flag-ING4-D213A,  +/- doxorubicin

first: Olivier

last: Binda

first: Or

last: Gozani


title: Wild type H37Rv vs HtpX mutant. Heat shocked samples

city: Boston

first: Kevin

last: Conlon

state: MA

address: 300 Longwood avenue

department: Infectious Disease

institute: Childrens Hospital Boston

summary: This experiment examines the differences in global gene expression in a wild type and mutant strain grown under standard shaking conditions to mid log phase (OD600 0.5) followed by heat shock at 50C for 15 minutes.

overall_design: 3 repeats were performed. Trizol was used to prep the RNA. TIGR protocols were closely followed.

middle: M

first: Robert

middle: N

last: Husson


title: Comparison of genomic DNA amplification methods

city: Toronto

first: Paul

last: Boutros

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
Hybridization of amplified genomic DNA against unamplified genomic DNA using three different amplification methods to assess the bias introduced by amplification alone.
Keywords: genomic DNA

overall_design: Three different amplification methods were assessed and total genomic DNA hybridized against equal amounts of amplified genomic DNA for each method.

first: Romina

last: Ponzielli

first: Sigal

last: Katz

first: Adam

last: Hanley

first: Angelina

last: Stojanova

first: Fereshteh

last: Khosravi

first: Igor

last: Jurisica

first: Linda

middle: Z

last: Penn


title: Transcriptomic regulation during meiosis (Clb5Delta-Clb6Delta mutant)

city: New York

first: Nicolas

last: Robine

address: 101 Avenue of the Americas

department: Bioinformatics

institute: New York Genome Center

summary:
We studied the meiotic regulation of transcription in the mutant Clb5Delta-Clb6Delta (deficient for the meiotic replication), by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h.
Keywords: yeast meiotic time course, transcriptome

overall_design: For each time point, we measured the level of mRNA extracted at the time point to a mRNA meiotic mix composed of mRNA extracted at each time point. We normalize this ratio to the ratio measured at time t=0h and transform into log2ratios.

first: Valérie

last: Borde

first: Waka

last: Lin

first: Sandrine

last: Bonfils

first: Vincent

last: Géli

first: Alain

last: Nicolas


title: Transcriptome in yeast by exposure of 7 transition metals

city: RTP

first: Yohan

last: Jin

state: NC

address: 111 TW Alexander Dr.

institute: NIEHS

summary:
7 transition metals (silver, arsenic, cadmium, chromium, copper, mercury and zinc) were treated (2hr) on diploid yeast BY4743.
Keywords: Response to metals

overall_design:
Condition for RNA preparation
7 metals
3 independent isolates
two concentrations (EC10 and EC50)
every metal has 6 total RNA samples * 2 technical replicates (dye-swap)

Labeling and hybridization (Paradigm Array Labs)
total RNA
Low-input labeling method (Agilent)
10,807 60-mer oligo microarray representing 6,256 ORF (Agilent)

first: YongHwan

first: Hanan

last: Alrefai

first: Edward

last: Lobenhofer

first: Jonathan

last: Freedman


title: Characterization of technical variation in ChIP-on-chip studies

first: Paul

last: Boutros

summary:
Analysis of technical variance of ChIP-on-Chip studies by characterization of Myc-binding in HL60 cells.
Keywords: Chip-on-chip

overall_design: Fully-blocked study of technical variance in Myc-binding in HL60 cells. Two different antibodies were used to generate 6 biologically independent replicates each. Each replicate was hybridized to arrays from two different batches in both dye-swap orientations, leading to 48 total arrays.

first: Romina

last: Ponzielli


title: Wild type H37Rv vs htpX deletion mutant

first: Kevin

last: Conlon

summary: We compared global transcription in the wild type strain and a htpX (Rv0563) mutant strain. 3 seperate experiments (replicates) were performed.

overall_design: Cultures were grown in 7H9 media until mid log phase (OD600 0.5). RNA was harvested using the Trizol method. TIGR protocols for cDNA synthesis, cy dye labeling and hybridisation were followed closely.

first: Robert

last: Husson


title: c-Myc binding in HL60 cells

overall_design: Characterization of c-Myc binding in HL60 cells.  Thirteen biologically independent replicates of growing HL60 cells were subjected to ChIP with an N-terminal c-Myc antibody and hybridized to CpG island microarrays

first: Igor


title: Transcriptomic regulation during meiosis

summary:
We studied the meiotic regulation of transcription, by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h.
Keywords: yeast meiotic time course, transcriptome

overall_design:
For each time point, we measured the level of mRNA extracted at the time point to a mRNA meiotic mix composed of mRNA extracted at each time point. We normalize this ratio to the ratio measured at time t=0h and transform into log2ratios.
The experiment is carried out in triplicates, from three independant cultures.


title: Effect of amino acid availability on vitamin B12 production in Lactobacillus reuteri

status: Public on Oct 31 2008

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

institute: Vrije Universiteit Amsterdam

summary:
Recent functional genomics and genome-scale modeling approaches indicated that B12 production in Lactobacillus reuteri could be improved by medium optimization. Here we show that a series of systematic single amino acid omissions could significantly modulate the production of B12 from nearly undetectable levels (by isoleucine omission) to 20-fold higher than previously reported through omission of cysteine. We analyzed by cDNA microarray experiments the transcriptional response of L. reuteri to the medium lacking cysteine. These results supported the observed high B12 production and provided new avenues for future improvement of production of vitamin B12.

Keywords: cell type comparison

sample_organism: Limosilactobacillus reuteri subsp. reuteri F275

overall_design: loop design

first: F

last: Santos

first: B

last: Teusink

first: J

last: Hugenholtz

first: D


title: Transcriptomic regulation during meiosis (Spo11Y135F mutant)

first: Nicolas

last: Robine

summary:
We studied the meiotic regulation of transcription in the mutant Spo11Y135F (deficient for the formation of meiotic double-strand breaks), by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h.
Keywords: yeast meiotic time course, transcriptome

overall_design:
For each time point, we measured the level of mRNA extracted at the time point to a mRNA meiotic mix composed of mRNA extracted at each time point. We normalize this ratio to the ratio measured at time t=0h and transform into log2ratios.
The experiment is carried out in duplicates, from two independant cultures.

first: Valérie

last: Borde

first: Waka

first: Sandrine

first: Vincent


title: Differential roles of promoters, enhancers, and insulators in cell-type specific gene expression

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

summary:
Chromatin immunoprecipitation was performed using antibodies against CTCF and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.
Keywords: ChIP-chip

overall_design: 3 ChIP-chip Samples

first: Gary

last: Hon

first: R

middle: D

last: Hawkins

first: Lindsey

last: Harp

first: Zhen

last: Ye

first: Jessica

middle: E

last: Antosiewicz

first: Ron

last: Stewart

first: James

middle: A

last: Thomson


title: Antibody microarrays of plasma from bone marrow transplant patients to find markers of graft versus host disease

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary:
A non-invasive diagnostic test does not exist for acute graft versus host disease (aGVHD). We therefore sought to identify biomarkers for aGVHD using antibody microarrays (Schleicher and Schuell Serum Biomarker Chips, Whatman) that simultaneously assayed 120 plasma proteins. We measured these proteins in a set of 42 patient plasma samples following an allogeneic bone marrow transplant (BMT): 21 patients with a diagnosis of aGVHD grade II-IV (+GVHD) and 21 patients without aGVHD (–GVHD) at similar times after transplant.  We excluded data from 2 hybridizations that had very bright dots and appeared as outliers in preliminary principal components analysis, so that we finally compared 20 +GVHD to 20 -GVHD samples.
Keywords: disease state analysis, antibody microarray

overall_design: The arrays are printed on nitrocellulose-coated glass slides, with two identical arrays on each slide, so that two hybridizations can be preformed per slide. We formed a reference pool by combining equal amounts plasma from the 21 +GVHD and 21 -GVHD samples, which was labled with biotin-ULS.  Each individual sample was labled with flourescein-ULS, combined with an aliqout of the reference pool and hybridized to a single array (no replicates).  One +GVHD sample and one -GVHD sample were assayed on the two arrays of each glass slides, with the placement of the two samples alternating so that +GVHD samples used the top array on approximately half of the slides.  We performed the assays in 3 batches, each batch having 7 +GVHD and 7 -GVHD samples.  In the second batch we used an additional slide for control experiments in which one or both of the reference pool aliquots hybridized to the arrays were unlabeled.

first: Sophie

last: Paczesny

first: Oleg

last: Krijanovski

first: Tom

last: Braun

first: Sung

last: Choi

first: Shawn

middle: G

last: Clouthier

first: David

last: Misek

first: Angela

last: Weyand

first: Daniel

last: Bickley

first: Dawn

last: Jones

first: Joel

last: Whitfield

first: John

last: Levine

first: Samir

last: Hanash

first: Jamie

middle: L

last: Ferrara


title: Induction of adaptive changes in the Streptococcus agalactiae transcriptome by human blood

city: Warsaw

first: Izabela

last: Sitkiewicz

address: Chełmska 30/34

department: Epidemiology and Clinical Microbiology

country: Poland

institute: National Medicines Institute

summary: In the present investigation, we conducted a bacterial transcriptome dynamics analysis during GBS incubation with human blood. We observed a large modification in the expression of genes involved in transcriptional regulation and in the metabolism of carbohydrates, purins/pyrimidins and inorganic ions, and an up-regulation of genes involved in attachment and plasminogen contact. We also observed differences in the expression of GBS genes in blood at 40° relative to 37°C.

overall_design:
The serotype III GBS reference strain NEM316 was cultivated in Todd Hewitt broth supplemented with 0.2% yeast extract (THY) in 5% CO2 at 37°C until OD reached 0.7. Culture was harvested by centrifugation 8 minutes at 4000 x g at 37°C, then suspended in phosphate-buffered saline (PBS).
Fresh heparinized human blood was obtained from seven healthy voluntary donors (four males and three females) in accordance with a protocol approved by the Institutional Review Board of the Methodist Hospital Research Institute. The blood was maintained at 37°C no more than one hour prior to use. Bacterial suspension was then incubated with the blood of each donor at 37°C and 40°C under slight rotation to avoid sedimentation of blood and bacterial cells (the volume of blood was equivalent to the volume of bacterial culture prior to centrifugation). Samples were removed for microarrays analysis immediately after adding bacteria, and after 30 and 90 minutes of incubation.
Thus, for each of the seven blood donors, we obtained results for five time points: immediately after mixing the bacterium with the blood (time 0), after 30 minutes of contact with blood (time 1) at 37°C and 40°C, and after 90 minutes of contact with blood (time 2) at 37°C and 40°C.

first: Laurent

last: Mereghetti

first: Nicole

last: Green

last: Musser