title: Assessing the effect of the CLPG mutation on the microRNA catalogue of skeletal muscle using high-throughput sequencing

city: Liege

first: Florian

last: Caiment

address: 1 avenue de l'hopital

department: GIGA

institute: University of Liege

summary: The callipyge phenotype is a monogenic muscular hypertrophy that is only expressed in heterozygous sheep receiving the CLPG mutation from their sire. The wild-type phenotype of CLPG/CLPG animals is thought to result from translational inhibition of paternally expressed DLK1 transcripts by maternally expressed miRNAs. To identify the miRNA responsible for this trans-effect, we used high-throughput sequencing to exhaustively catalogue miRNAs expressed in skeletal muscle of sheep of the four CLPG genotypes. We have identified 747 miRNA species of which 110 map to the DLK1-GTL2 or callipyge domain. We demonstrate that the latter are imprinted and preferentially expressed from the maternal allele. We show that the CLPG mutation affects their level of expression in cis (~3.2-fold increase) as well as in trans (~1.8-fold increase). In CLPG/CLPG animals, miRNAs from the DLK1-GTL2 domain account for ~20% of miRNAs in skeletal muscle.We show that the CLPG genotype affects the levels of A to I editing of at least five pri-miRNAs of the DLK1-GTL2 domain, but that levels of editing of mature miRNA are always minor. We present suggestive evidence that the miRNAs from the domain target the ORF of DLK1 thereby causing the trans-inhibition underlying polar overdominance. We highlight the limitations of high-throughput sequencing for digital gene expression profiling as a result of biased and inconsistent amplification of specific miRNAs.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design:
These data were used to confirm the expression levels found by the high-throughput sequencing analysis.

A total of 8 samples (two animals per callipyge genotype) were analysed using the miRCury LNA microRNA array (Exiqon). On each array, the test sample labelled with Hy3 was hybridized on one channel, and a pool made with the 8 test samples (labelled with Hy5) was used on the other channel as a reference for normalization.

The callipyge mutation (C) is a SNP localised in an imprinted domain. Thus, heterozygous animals will have different phenotypes. The following 4 genotypes were analyzed in this study:

NN: Wild-type (+mat/+pat)
CN: Maternal heterozygous (Cmat/+pat)
NC: Paternal heterozygous (+mat/Cpat)
CC: Homozygous mutant (Cmat/Cpat)

first: Carole

last: Charlier

first: Tracy

last: Hadfield

first: Noelle

last: Cockett

first: Michel

last: Georges

first: Denis

last: Baurain


title: Transcriptome comparison of M1T1 WT, AP and delta CovS strains

status: Public on Sep 22 2010

city: Cincinnati

first: Rita

middle: G

last: Kansal

state: OH

address: 3235 Eden Avenue

country: USA

institute: University Of Cincinnati

summary: Group A streptococci (GAS) may engage different sets of virulence strategies, depending on the site of infection and host context. We previously isolated 2 phenotypic variants of a globally disseminated M1T1 GAS clone: a virulent wild-type (WT) strain, characterized by a SpeB(+)/SpeA(-)/Sda1(low) phenotype, and a hypervirulent animal-passaged (AP) strain, better adapted to survive in vivo, with a SpeB(-)/SpeA(+)/Sda1(high) phenotype. This AP strain arises in vivo due to the selection of bacteria with mutations in covS, the sensor part of a key 2-component regulatory system, CovR/S. To determine whether covS mutations explain the hypervirulence of the AP strain, we deleted covS from WT bacteria (DeltaCovS) and were able to simulate the hypervirulence and gene expression phenotype of naturally selected AP bacteria. Correction of the covS mutation in AP bacteria reverted them back to the WT phenotype. Our data confirm that covS plays a direct role in regulating GAS virulence.

overall_design: A dye-swapped cyclic design was used in this study in order that each strain could be compared across all samples in silico. For each strain treated, 2 biological replicates were each analysed in dye-swapped technical replicates, giving a total of n=10 peplicates for each strain.

first: V

last: Datta

first: Ramy

middle: K

last: Aziz

first: Nourtan

middle: F

last: Abdeltawab

first: Sarah

last: Rowe

first: Malk

last: Kotb


title: Gene expression profiling of aortic media after long-term treatment with an angiotensin II-receptor blocker, Losartan

status: Public on Sep 23 2010

city: Paris

first: Sophie

last: Nadaud

address: 91 Bd de l'hopital

country: France

institute: INSERM

summary: Rats (Wag/Rij, females) were chronically treated with Losartan (20mg/d), an angiotensin II-receptor blocker during 9 months. Gene expression profiling was performed on aortic media to understand the long-term effect of this molecule on the cardiovascular system.

overall_design: Two-conditions experiment, Ctrl vs Losartan-treated animals. Biological replicates: 5 control replicates, 5 Losrtan-treated animals. All the RNA samples were pooled to provide a reference RNA for a two-color experiment.

first: Monique

last: Agrapart

first: Kristell

last: Wanherdrick

first: Florent

last: Soubrier


title: Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica: a reference for comparison with core eudicots and basal angiosperms

status: Public on Sep 21 2010

city: Gainesville

first: Andre

last: Chanderbali

state: FL

address: Museum Road

institute: Univrsity of Florida

summary: Our results provide a foundation for comparative gene expression studies between eudicots and basal angiosperms. We identified whorl-specific gene expression patterns in Eschscholzia, and examined the floral expression of several gene families, such as MADS-box, bHLH and MYB. Interestingly, most homologs of genes important for flower development, except for MADS-box genes, show different expression patterns between Eschscholzia and Arabidopsis. Our comparative transcriptomics study highlights the unique evolutionary position of Eschscholzia compared with basal angiosperms and core eudicots.

overall_design: Custom microarrays targeting 6446 Eschscholzia floral unigenes were used to measure expression levels in eight tissues using an interwoven double-loop design for 16 arrays.


title: BCL6 repression of EP300 provides a basis for rational combinatorial therapy in diffuse large B cell lymphomas.

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

summary: The BCL6 transcriptional repressor is a critical oncogene in diffuse large B-cell lymphomas (DLBCL). The specific BCL6 inhibitor RI-BPI potently kills DLBCL cells. We find that RI-BPI induces a particular gene expression signature in DLBCL. In order to identify classes of drugs that might synergize with RIBPI we examined the connectivity of this signature and found a strong association with HDAC and Hsp90 inhibitors. This was explained by the discovery that BCL6 directly represses the p300 lysine acetyltransferase and its co-factor BAT3. RI-BPI induced expression of p300 and BAT3, and p300 acetyltransferase activity, resulting in acetylation of p300 targets like p53 and Hsp90. As a consequence, RI-BPI could attenuate Hsp90 chaperone function, similar to the effect of Hsp90 and HDAC inhibitors. Induction of p300 and BAT3 was required for the anti-lymphoma effects of RI-BPI since specific blockade of either protein rescued DLBCL cells from the BCL6 inhibitor. RI-BPI synergistically killed DLBCL cells in combination with HDAC inhibitors (SAHA, TSA and VPA) and Hsp90 inhibitors (17-DMAG and PUH71). The combination of RI-BPI and SAHA, or RI-BPI and PU-H71 potently suppressed or even eradicated human DLBCL in mice. BCL6 repression of EP300 thus provides a basis for rational targeted combinatorial therapy for patients with DLBCL.

overall_design: Direct comparison of gene expression levels in DLBCL cell lines after 24hs of treatment with either a Bcl6 inhibitor peptide or control peptide

first: Leandro

last: Cerchietti

first: Ari

last: Melnick

middle: E


title: Mycobacterium tuberulosis H37Rv strains: Control vs. Plumbagin

status: Public on Sep 20 2010

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

country: China

institute: Jilin university

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv strains comparing control DMSO treated strains with Plumbagin treated strains.  Goal was to determine the effects of Plumbagin against Mycobacterium tuberculosis H37Rv strains.

overall_design:
Two-condition experiment,control DMSO vs. Plumbagin. Biological replicates: 2 control replicates, 2 Plumbagin replicates.

The file showing raw and normalized data (~4645 rows) extracted from Agilent Feature Extraction Software is linked below. Samples details are described in PDF file linked below (NOTE: The samples 'Plumbagin' and 'chelerythrine' represent the submissions to GEO).

first: Haiqing

last: Ye


title: TFF3 miRNA expression in mus musculus

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

summary: The aim of the study was to investigate whether the trefoil peptide genes, in concerted action with a miRNA regulatory network, were contributing to nutritional maintrenance. Using a Tff3 knock-out mouse model, 21 specific miRNAs were noted to be significantly deregulated when compared to the wild type strain.

overall_design: n = 6 mus musculus wild type samples and n = 6 knock-down experiments have been screened for a currently known mus musculus miRNAs and validated by TaqMan

first: Aftab

last: Shah


title: PARP-1, H3 and H3K4me3 ChIP-chip from MCF7 cells

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary: We are examining the mechanisms by which the nuclear enzyme PARP-1 regulates gene expression.  We performed ChIP-chip for PARP-1, histone H3 and H3K4me3 (lysine 4 trimethylation on histone H3) in MCF7 breast carcinoma cells, and looked at 23550 RefSeq genes to determine binding patterns of these factors at promoters.  Each experiment was performed in duplicate.

overall_design: ChIP-chip biological replicates for PARP-1, H3 and H3K4me3 (2 replicates each) from MCF7 human breast carcinoma cells are included.

first: Raga

last: Krishnakumar

first: Lee


title: Genome-wide analysis of H3K9me2 in ibm1, kyp, and cmt3 mutants of Arabidopsis thaliana

city: Ikoma

first: Soichi

last: Inagaki

state: Nara

address: 8916-5, Takayama-cho

department: Graduate School of Biological Sciences

country: Japan

institute: Nara Institute of Science and Technology

summary: In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Despites the conservation and importance in the genome integrity, mechanisms to exclude H3K9m from active genes remained largely unexplored. Here we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation); loss-of-function ibm1 mutation caused ectopic H3K9me in thousands of genes, which accompanies genic DNA methylation at non-CG sites. The ibm1-induced genic H3K9me depended on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks – H3K9me and non-CG methylation. Notably, IBM1 enhanced loss of H3K9m in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induced ectopic non-CG methylation, mimicking the loss of IBM1 function. We propose that active chromatin is stabilized by the autocatalytic loop of transcription and H3K9 demethylation. This process counteracts accumulation of silent epigenetic marks, H3K9me and non-CG methylation, which is also autocatalytic.

overall_design: Leaves of 4-week-old plants were fixed as described previously (Saze et al, 2008). Chromatin immunoprecipitation (ChIP) was performed as described previously (Kimura et al, 2008), using antibody against H3K9me2 (CMA307, Kimura et al, 2008, PMID: 18227620). Non-immunoprecipitated DNA (input DNA) and ChIP samples were amplified, labeled, and hybridized to microarray according to the manufacturer’s instruction (Protocols for Chromatin Immunoprecipitation and Amplification, NimbleGen). Input DNA and ChIP DNA were differentially labeled with Cy3 and Cy5, respectively, and competitively hybridized to a microarray chip. We used NimbleGen 2.1M HD2 array covering entire genome of A. thaliana.

first: Asuka

last: Miura

first: Hidetoshi

last: Saze

first: Tetsuji

last: Kakutani


title: Mycobacterium tuberulosis H37Rv strains: Control vs. Chelerythrine

summary: Transcriptional profiling of Mycobacterium tuberculosis H37Rv strains comparing control DMSO treated strains with chelerythrine treated strains. Goal was to determine the effects of chelerythrine against Mycobacterium tuberculosis H37Rv strains.

overall_design:
Two-condition experiment,control DMSO treated strains vs. Chelerythrine treated strains. Biological replicates: 2 control replicates, 2 Chelerythrine replicates.

The file showing raw and normalized data (~4645 rows) extracted from Agilent Feature Extraction Software is linked below. Samples details are described in PDF file linked below (NOTE: The samples 'Plumbagin' and 'chelerythrine' represent the submissions to GEO).

first: Junchao

last: Liang


title: Gene expression in xylem tissue on an Eucalyptus pseudo-testcross population: genotyping subset of discovery array probes

status: Public on Sep 18 2010

middle: Gomide

last: Neves

address: 2033 Mowry Road

department: Plant Molecular and Cell Biology

institute: University of Florida

type:
Expression profiling by array
Other

summary:
Technological advances are progressively increasing the application of genomics to a wider array of economically and ecologically important species. High-density maps enriched for transcribed genes facilitate the discovery of connections between genes and phenotypes. We report the construction of a high-density linkage map of expressed genes for the heterozygous genome of Eucalyptus using Single Feature Polymorphism (SFP) markers.
SFP discovery and mapping was achieved using pseudo-testcross screening and selective mapping to simultaneously optimize linkage mapping and microarray costs. SFP genotyping was carried out by hybridizing complementary RNA prepared from 4.5 year-old trees xylem to an SFP array containing 103,000 25-mer oligonucleotide probes representing 20,726 unigenes derived from a modest size expressed sequence tags collection. An SFP-mapping microarray with 43,777 selected candidate SFP probes representing 15,698 genes was subsequently designed and used to genotype SFPs in a larger subset of the segregating population drawn by selective mapping. A total of 1,845 genes were mapped, with 884 of them ordered with high likelihood support on a framework map anchored to 180 microsatellites with average density of 1.2 cM. Using more probes per unigene increased by two-fold the likelihood of detecting segregating SFPs eventually resulting in more genes mapped. In silico validation showed that 87% of the SFPs map to the expected location on the 4.5X draft sequence of the Eucalyptus grandis genome.
The Eucalyptus 1,845 gene map is the most highly enriched map for transcriptional information for any forest tree species to date. It represents a major improvement on the number of genes previously positioned on Eucalyptus maps and provides an initial glimpse at the gene space for this global tree genome. A general protocol is proposed to build high-density transcript linkage maps in less characterized plant species by SFP genotyping with a concurrent objective of reducing microarray costs. HIgh-density gene-rich maps represent a powerful resource to assist gene discovery endeavors when used in combination with QTL and association mapping and should be especially valuable to assist the assembly of reference genome sequences soon to come for several plant and animal species.

sample_organism: Eucalyptus grandis x Eucalyptus urophylla

overall_design: Two technical replication of 68 individuals were hybridized to the custom microarray, labeled with Cy3 and Cy5. Individuals are fullsib progenies of the cross E. urophylla X E. grandis. A loop design was employed for the hybridization using xylem tissue. In total the microarray comprised 43,803 probes representing  15,698 unigenes. These probes were pre-selected in a screening array based on their mendelian segregation and bimodal signal separation. Twenty-six negative control probes were also included in the microarray.

first: Dario

last: Grattapaglia


title: Regulatory and epistatic networks unravel the complexity of piebald, a pigmentation phenotype in Merino sheep

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

summary: Transcriptional profiling of Ovine skin samples comparing pigmentation samples from piebald and normal Merino sheep

platform_organism:
Bos taurus
Ovis aries

overall_design: All pair comparison of 5 pigmentation samples with dye swaps.   Dye swaps were performed with different biological replicates (labelled 1 or 2)  NOR - White sample from a normal, non-affected wild-type individual sheep  PBB - Black sample from a piebald individual sheep  PBW - White sample from a piebald individual sheep   RSB - Black sample from a recessive black sheep  RSW - White sample from a recissive black sheep taken from the inguinal, non-pigmented area.

first: James

last: Kijas

first: Antonio

last: Reverter


title: Expression profile of contrasting maize genotypes grown on acid and control soil (root tips)

city: Campinas

first: Marcelo

last: Menossi

state: SP

address: Rua Monteiro Lobato, 255, Instituto de Biologia, Departamento de Genetica, Evolucao e Bioagentes

department: Genetica, Evolucao e Bioagentes

country: Brazil

institute: Marcelo Menossi

summary:
Aluminum toxicity is one of the major limiting factors for many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth, leading to poor water and nutrient absorption. The causes of this inhibition are still elusive, with several biochemical pathways being affected and with a significant variation between species. Most of the work done so far to investigate the genes responsible for Al tolerance used hydroponic culture. Here we evaluated plant responses using soil as substrate, which is a condition closer to the field reality.
We used Affymetrix chips to reveal the transcriptional changes of two maize genotypes contrasting for Al tolerance.

overall_design: Root tips from Cat100-6 (Al-tolerant) and S1587-17 (Al-sensitive) maize genotypes were harvested after growing on acid or control soil for 1 or 3 days. Total RNA was extracted and hybridized to Affymetrix GeneChip Maize Genome Array. Three biological replicates were used for each sample.

first: Lucia

last: Mattiello

first: Matias

last: Kirst

first: Renato

middle: A

last: Jorge


title: Gene Expression Analysis for HBx-induced HCC Mouse Model

status: Public on Sep 16 2010

city: Zhunan Town

first: Chiou-Hwa

last: Yuh

state: Miaoli County

address: No. 35 Keyan Road

department: Division of Molecular and Genomic medicine

country: Taiwan

institute: National Health Research Institutes

summary: Hepatoarcinogenesis is a slow and multistep process. We used Hepatitis B virus X antigen (HBx) induced Hepatocellular carcinoma (HCC) as model. We also identify the biomarkers, the pathways and networks underlying HCC formation in this animal model. We analyzed the events from the early, middle, and late stages, in order to predict and prevent the development of cancer. At each specific stage, we analyzed the expression level that differed at least two-fold between HBx transgenic and wild-type mouse liver. Statistical approaches were used to identify genes displaying an increasing or decreasing trend throughout hepatocarcinogenesis.

overall_design: The liver was excised from 6-week-, 8-month-, 12-month-, 14-month-, and 16-month-old HBx transgenic mice (A106 strain) and RNA samples were isolated. In both 14-month- and 16-month-old mice, samples were obtained from both the tumor tissue and the normal.

first: Karthik

last: Prathapachandran


title: Gene expression in xylem tissue on an Eucalyptus pseudo-testcross population: discovery array probes

first: Leandro

overall_design: Two biological replication of 28 genotypes were hybridized to the custom microarray, labeled with Cy3 and Cy5. Genotypes are fullsib progenies of the cross E. urophylla X E. grandis. A loop design was employed for the hybridization using xylem tissue. In total the microarray comprised 103,000 probes representing 20,726 unigenes with an average of five probes per unigene. Twenty-six negative control probes were also included in the microarray.


title: Co-culture stress in Desulfovibrio vulgaris Hildenborough

city: Berkeley

first: Adam

middle: P.

last: Arkin

state: CA

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

summary:
This set of microarray data was used to compare the effects of D. vulgaris grown syntrophically with a hydrogenotrophic methanogen versus D. vulgaris grown in sulfate-limited monoculture.

Keywords: physiological response, one time point (stable continuous culture for both control and treated cells)

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of cells treated with DvH + Mm co-culture + lactate only FC36, FC38, FC44 Co-culture to untreated cells at times of continuous culture at 24 hr retention time min.


title: Sugar utilization in L. plantarum WCFS1

status: Public on Sep 15 2010

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

summary: Lactobacillus plantarum was grown anaerobically on 4 different sugars (Mannose Lactose Fructose and Sucrose) to OD600 = 1.0. Samples were compared with a similar grown culture on glucose. An independnet biological duplicate of tht experimnet was performed (samples 1 and 2).

overall_design: L. plantarum WCFS1 grown in glucose, mannose, fructose, and sucrose

first: Douwe

last: Molenaar

first: Oscar

last: Kuipers

first: Michiel

last: Keerebezem


title: Identification and characteristics of microRNAs in rat abdominal aortic aneurysms

city: Shanghai

first: Liu

last: Guang

address: No. 639 Zhizaoju Rd

institute: Shanghai Jiao Tong University

summary: Abdominal aortic aneurysm (AAA) is a lethal disease, occurring mostly in men more than 65 years of age. Until recently, the pathogenesis of AAA remains poorly understood. MicroRNAs (miRNAs) are a novel class of endogenous small noncoding RNAs that play important roles in diverse biological and pathological processes and was more recently investigated in cardiovascular physiology and pathology. In this study, we employed microarray to detect and compare miRNA expressions of AAAs in rats. Four miRNAs were validated using real time RT-PCR. Functional annotations of putative targets of deregulated miRNAs via bioinformatics approaches revealed that predicted targets were highly enriched and involved in several signaling pathways important for AAA formation. Our results indicate that miRNAs are extensively involved in rat AAA formation and provide a global view of AAA miRNA profiles, which is expected to provide new clues to develop targeted therapies against this calamitous disease.

overall_design: Sprague-Dawley rat AAA model was established by calcium chloride and collagenase co-incubation method. After 28 days, three rats with confirmed AAAs and three normal rats form control(sham operation) group were euthanized and the aortas specimens were used for this experiment.

first: Jiang

last: Mier


title: Budding yeast RNA polymerase II CTD phosphorylation and transcription termination factor localization

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

summary: Whole genome analysis of total RNA pol II, Ser2-, Ser5- and Ser7-phosphorylated RNA pol II, in WT and mutants of the C-terminal domain (CTD) kinases Ctk1 and Kin28, and localization of the termination factors Pcf11, Nrd1 and Rat1.

overall_design: ChIP-chip using ligation-mediated PCR-amplified material hybridized to NimbleGen 385K arrays (50mers, median probe spacing 32 bp, cat. No. C4214-00-01).

first: Hyunmin

last: Kim


title: Alterations in the Brain Transcriptome in Plasmodium Berghei ANKA Infected Mice

status: Public on Sep 17 2010

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: We have used cDNA microarrays to compare gene expression profiles in brains from normal mice to those infected with the Anka strain of Plasmodium berghei, a model of cerebral malaria.  For each of three brains in each group, we computed ratios of all quantifiable genes with a composite reference sample and then computed ratios of gene expression in infected brains with untreated controls.  Of the almost 12,000 unigenes adequateluy quantified in all arrays, about 3% were significantly downregulated (p<0.05, >50% fold change) and about 7% were upregulated.  Upon inspection of the lists of regulated genes, we identified a high number encoding proteins of importance to normal brain function or associated with neuropathology.  These results emphasize the important impact of malarial infection on gene expression in brain and provide tentative target biomarkers that might provide novel therapeutic targets for neurological sequelae of disease.

overall_design: We have used a previously published protocol (Iacobas et al., Physiol Genomics 2005) and a composite reference RNA sample (R)  prepared in sufficient quantity for the entire experiment from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females). This combination of source tissues provided a high diversity of genes expressed in the midrange of the detection system for the AECOM mouse cDNA microarrays. Briefly, 60μg total RNA, extracted in Trizol® (Invitrogen, Carlsbad, CA) from brains of three infected (I) and three control (C) mice, purified with RNeasy® mini kit (Qiagen, Valencia, CA), were reverse transcribed into cDNA incorporating fluorescent Cy3-dUTP. The composite reference was reverse transcribed to incorporate Cy5-dUTP. Each of the six Cy3-labeled brain extracts was co-hybridized overnight at 50°C against the Cy5-labeled reference with AECOM 32k Mouse oligonucleotide arrays, MO3 printing series (platform described in http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL5371). After hybridization, the slides were washed at room temperature, using solutions containing 0.1% sodium dodecyl sulfate (SDS) and 1% SSC (3M NaCl + 0.3M sodium citrate) to remove the non-hybridized cDNAs.

first: Mahalia

last: Desruisseaux

first: Sanda

first: Shankar

last: Mukherjee

first: Louis

middle: M

last: Weiss

first: Herbert

middle: B

last: Taniwitz

middle: C

last: Spray


title: Developmental decoupling of alternative phenotypes: insights from the transcriptomes of horn-polyphenic beetles

city: Bloomington

first: Emilie

last: Snell-Rood

state: IN

address: 915 E 3rd St MY150

department: Biology

institute: Indiana University

summary: Developmental mechanisms play an important role in determining the costs, limits, and evolutionary consequences of phenotypic plasticity.  One issue central to these claims is the metaphor of developmental “decoupling,” where alternate morphs result from evolutionarily independent developmental pathways.  We test this assumption through a microarray study that explores differences in gene expression between alternate morphs relative to differences between sexes, a classic example of developmental decoupling.  We then examine whether morph-biased genes are less conserved, relative to morph-shared genes, as predicted if developmental decoupling relaxes pleiotropic constraints on divergence.  We focus on the developing horns and brains of two species of horned beetles with spectacular sexual- and morph-dimorphism in the expression of horns and fighting behavior. We find that patterns of gene expression were as divergent between morphs as they were between sexes.  However, overall patterns of gene expression were also highly correlated across morphs and sexes.  Morph-biased genes were more evolutionarily divergent, suggesting a role of relaxed pleiotropic constraints or relaxed selection.  Together these results suggest that alternate morphs are somewhat developmentally decoupled, and that this decoupling has significant evolutionary consequences.  However, alternative morphs may not be as developmentally decoupled as sometimes assumed and such hypotheses of development should be revisited and refined.

sample_organism:
Onthophagus taurus
Onthophagus nigriventris

overall_design: We compared gene expression in three focal epidermal tissues (head, prothorax, legs) relative to a "control" tissue (dorsal abdominal epidermis) without any outgrowths.  We also surveyed gene expression in the brain, relative to ganglionic neural tissue.  We compared such patterns of gene expression between two male morphs (horned, fighter and hornless, sneaker males) and between males and females.  We focused our array analyses (N = 48 arrays) on Onthophagus taurus (the species for which the array was designed), but also ran 19 arrays on thoracic tissue of Onthophagus nigriventris, a species which expresses thoracic horns as adults (O. taurus expresses head horns).  Finally, we included a small subset of arrays (N = 4) directly hybridizing head epidermis tissue of O. taurus male morphs to validate our overall estimates of morph-biased expression.  For more detail, refer to Snell-Rood et al. 2010, Evolution.

first: Amy

last: Cash

first: Mira

middle: V

last: Han

first: Teiya

last: Kijimoto

first: Justen

last: Andrews

first: Armin

middle: P

last: Moczek


title: Acclimation Effects on Acute Thermal Stress in the goby, Gillichthys mirabilis

city: Pacific Grove

first: Cheryl

last: Logan

address: 120 Ocean View Blvd

institute: Stanford University

summary: The goal of this study was to identify transcriptional resonses to acute heat stress following differential acclimation in the highly eurythermal goby fish, Gillichthys mirabilis.  G. mirabilis were acclimated to 3 temperatures (9C, 19C and 28C) for one month and then exposed to an acute heat ramp at 4C/hr and sampled during the timecourse.  Gill tissues were dissected and immediately flash frozen in liquid nitrogen.  Total RNA was extracted, reverse transcribed into cDNA, labeled with cy5 and hybridized against a common reference (cy3) on 2-color cDNA microarray developed for this species. Significant genes were determined by expression differences between groups (one-way ANOVA, FDR<0.05) .

overall_design: Common reference design

first: Geoge

middle: N

last: Somero


title: Effect of clp1 induction on rbf1-dependent gene regulation

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

summary: The clp1 gene is a b-regulated gene that is required for clamp formation during the biotrophic growth phase of U. maydis. Interaction studies demonstrated that Clp1 imnteracts with Rbf1, the central regulator of pathogenciity. To exclude b-dependent effects the experiments were performed in a b-null background to analyze clp1-depndent effects on rbf controlled gene regulation

overall_design: Strains  UKH156 (nitrate inducible Rbf1 expression) and UKH164 (arabinose-inducible Clp1 and and nitrate-inducible Rbf1 expression) were grown for 12h in liquid array medium/nitrate/arabinose.

first: Kai

last: Heimel

first: Joerg

last: Kaemper


title: Prevotella ruminicola 23: Growth on different carbohydrate sources

city: Urbana

first: Carl

middle: James

last: Yeoman

state: IL

address: 1207 W Gregory ave

department: Institute for Genomic Biology

institute: University of Illinois

summary: The transcriptional responses of Prevotella ruminicola were determined during growth on 20 different carbohydrate sources including mono-, di- and tri- saccharides, oligosaccharides, polymeric xylan and complete plant material with the aim of obtaining a more complete understanding of the number of genes and metabolic networks associated with carbohydrate catabolism by this organism

overall_design: All microarray hybridizations and subsequent scanning was undertaken using a two colour system (Cy3 and Cy5): 34 samples

middle: J

first: Jong-Nam

last: Kim

first: Joan

last: Edwards

first: Mirjam

last: Kabel

first: Mark

last: Morrison

first: Issac

last: Cann

first: Roderick

middle: I

last: Mackie


title: Effects of ad libitum feeding on canine subcutaneous adipose tissue gene expression

status: Public on Sep 14 2010

first: Kelly

middle: Scott

last: Swanson

address: 1207 W. Gregory Dr.

summary: Adipose, once considered an inert storage depot, is now known to be an active endocrine tissue involved in total body homeostasis and metabolism, which exerts effects on multiple systems including food intake, immune function, and blood glucose regulation.  During the development of obesity, adipose undergoes major expansion and remodeling, but the biological processes involved in this transition are not well understood.  Thus, we used canine microarrays to analyze gene expression profiles of subcutaneous adipose tissue during the transition from a lean to obese phenotype.

overall_design: Subcutaneous adipose tissue samples were collected from 9 intact female beagles (4 yr-old; 4 control; 5 ad libitum) at baseline, 4, 8, 12 and 24 wk after beginning ad libitum feeding.

middle: S

first: Ryan

middle: W

last: Grant


title: Genome-wide expression analysis of mouse chromosome 2 in gonadal fat and liver tissues reveals a complex architecture of obesity

city: Madrid

first: Gloria

last: Muñoz

address: Crta. Coruña km 7

department: Mejora Genetica Animal

country: Spain

institute: INIA

summary: Transcript abundance in adipose and liver tissues was used to map expression quantitative trait loci (eQTL) underlying fat accretion, weight gain and liver weight. Gonadal fat and liver tissues were used from 48 individuals F2 selected from a cohort (1,200 mice) originated from a cross between M16i and MB2 mice. A complex polygenic architecture within the MB2 locus was observed which was comprised of several locally regulated eQTL (cis-eQTL) with significant correlations to obesity traits.

overall_design: Total RNA obtained from isolated gonadal fat and liver tissues were used to mesured transcript abundance in order to detect expression QTLs.

first: Daniel

last: Pomp


title: Alteration of hepatic gene expression profile in NPC mice correlates with tissue damage and oxidative stress status

city: Santiago

first: Leonardo

middle: Ignacio

last: Pavez

state: Santiago

address: Av Manuel Montt #948

country: Chile

institute: Universidad de Las Américas

summary:
Background: Niemann Pick type C disease (NPC) is a neurovisceral lipid storage disorder, characterized by unesterified cholesterol accumulation in lysosomal/late endosome compartments.  The main tissues affected in the disease are the liver and the cerebellum.  Although the primary defect in this disease occurs in the liver, the pathological mechanisms involved in hepatocyte damage and death have been poorly explored.  Here, we assessed biochemical parameters, liver histology and the mRNA abundance of genes encoding proteins associated to oxidative stress, copper metabolism, fibrosis and inflammation and cholesterol metabolism in livers of WT and NPC mice.
Methodology/Principal Findings: We found that the histology of NPC mice livers show signals of inflammation and fibrosis. This was correlated with an increase of carbonylated proteins and reduced glutathione content in the liver, as well as a significantly increment of total content of copper in liver tissue.  Finally, we analyzed the liver gene expression pattern by qPCR and microarray assays.  We found a correlation between the tissue fibrotic status and a differential hepatic expression of genes related to oxidative stress, fibrosis and inflammation processes in NPC mice.
Conclusions/Significance: Our data show that NPC liver disease is evidenced by an increase in fibrosis as well as in oxidative stress status.  Concomitantly, there is a correlation with an altered gene expression pattern, mainly of oxidative stress and fibrosis related genes, which could be useful as a potential disease progression biomarkers.

overall_design: We compared three liver samples from NPC mice to a common reference sample made from pooled mRNA of three wild type mice

first: Mary

last: Vázquez

first: Talia

last: del Pozo

first: Fermín

last: Robledo

first: Gonzalo

last: Carrasco

first: Mauricio

last: Gonzalez

first: Silvana

last: Zanlungo


title: Development of molecular genetic analysis tools for the domestic ferret (Mustela putorius furo)

status: Public on Sep 13 2010

city: Birmingham

first: Carl

middle: E

last: Bruder

state: AL

address: 2000 9th Ave South

department: Viral Biochemistry

institute: Southern Research Institute

summary: The domestic ferret (Mustela putorius furo) has been used as animal model for decades, largely because its susceptibility to infection with a large number of pathogens such as influenza virus, SARS Corona virus and Canine distemper virus. Despite its importance for biomedical research, little is known about the genome of the M. Furo. The number of reagents for molecular and immunological analysis is thus restricted. To circumvent this, we present here a parallel sequencing effort to produce an extensive EST dataset derived from a normalized ferret cDNA library made from mRNA from ferret blood, liver, lung, spleen and brain. We produced more than 500000 sequence reads that were assembled into over 15000 partial ferret transcripts. These ESTs were combined with the available ferret sequences in the GenBank to develop a ferret specific microarray platform. Using this array, we detected tissue specific expression patterns which were confirmed by quantitative real time PCR assays and comparison to orthologous transcription profiles of mouse and human. We also present a set of 41 ferret transcript with even transcription profile across the tested tissues, indicating their usefulness as housekeeping genes. This study paves way for development of additional reagents for analysis of the ferret model.

overall_design: Three biological replicates of blood, lung, spleen, liver and brain was hybridized to the ferret specific microarray.

first: Suxia

last: Yao

first: Francis

last: Larson

first: Jeremy

last: Camp

first: Ronald

last: Tapp

first: Alexis

last: McBrayer

first: Nicholas

last: Powers

first: Willy

last: Valdivia Granda

first: Colleen

last: B. Jonsson


title: CcpA regulon in L. plantarum

status: Public on Sep 10 2010

first: Marc

last: Stevens

summary: This data set contains samples from Lactobacillus plantarum WCFS1 wild type and its CcpA mutant derivative. Both strains were grown in duplicate (samples L and R) and at four different growth stages samples were taken (early, mid and late log phase, early stationary phase). Samples were compared to each other within one strain and between the two strains. This allows the comparison of the wild type strain to its CcpA derivative in time. Further it allows comparison within one strain during different growth stages.

overall_design: Biological duplicate was performed.

first: Douwe

last: Molenaar

first: Oscar

last: Kuipers

first: Michiel

last: Keerebezem


title: DNA methylation data from non-immortalized lymphocyte samples from participants of the AGES Reykjavik Study

city: Baltimore

first: Peter

last: Murakami

state: MD

address: 855 N Wolfe St, Rangos 580

department: Center for Epigenetics

institute: Johns Hopkins University

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation was studied to identify regions with extreme inter-individual variability, half of which show stability within-person, and some of which show covariation with body mass index consistently and are located in or near genes previously implicated in regulating body weight or diabetes.

overall_design: We isolated genomic DNA from non-immortalized lymphocyte samples from participants of the AGES Reykjavik Study and hybridized it to custom-designed NimbleGen microarrays (CHARM arrays).

first: Rafael

last: Irizarry

first: Andrew

last: Feinberg

first: Delphine

last: Fradin

first: Martin

last: Aryee

first: Thor

last: Aspelund


title: Gene expression profiles of splenocytes of CD22DE12 transgenic mice

city: St. Peter

first: Sanjive

last: Qazi

state: MN

address: 800 west College Av

institute: Gustavus Adolphus College

summary:
Splenocytes from nontransgenic control mice and transgenic mice were isolated and their gene expression profiles were compared to determine if the expression of the transgene results in any changes in regulation of gene expression.
12 differentially expressed genes were classified as the most discriminating genes, including TP53, NF2, MDM2, RAC1, APC, and STATB1 with tumor suppressor gene function as well as cell cycle regulatory genes CDKN1C, CCNG1, and NOTCH4

overall_design: Mice were sacrificed at 6 weeks of age, spleens removed, splenocytes isolated, and RNA extracted from splenocytes.  Mouse ATLAS cDNA expression arrays were used for gene expression profiling.

first: Fatih

last: Uckun

first: Pat

last: Goodman


title: Bacillus subtilis WN715 vs WN716 expression in early stationary phase.

status: Public on Sep 09 2010

city: Merritt Island

first: Wayne

middle: L

last: Nicholson

address: 505 Odyssey Way, Rm. 201-B

department: Microbiology and Cell Science

institute: University of Florida

summary: Five batch cultures of Bacillus subtilis were subjected to laboratory evolution for 6,000 generations under conditions repressing sporulation in complex liquid medium containing glucose. Between 1,000 and 2,000 generations, variants with a distinct small-colony morphology arose and swept through four of the five populations.  To understand the nature of adaptation in these variants, individual strains were isolated from one population before (WN715) and after (WN716) the sweep.  In addition to colony morphology, strains WN715 and WN716 differed in their motility, aerotaxis, and cell morphology.  Competition experiments of WN715 vs. WN716 showed that WN716 had gained a distinct fitness advantage during growth and the transition to stationary phase, which was more pronounced when WN715 was present in co-culture.  Microarray analyses revealed candidate genes in which mutations may have produced some of the observed phenotypes.

overall_design: One condition tested; 1 biological rep; 2 strains

first: Maugan

last: Heather

first: Nicholson

last: Wayne L.


title: The COP9 signalosome mediates transcriptional and metabolic response during fungal development

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: The COP9 signalosome complex (CSN) is a crucial regulator of ubiquitin ligases. Defects in CSN result in embryonic impairment and death in higher eukaryotes, whereas the filamentous fungus Aspergillus nidulans survives without CSN, but is unable to complete sexual development. We investigated overall impact of CSN activity on A. nidulans cells by combined transcriptome, proteome and metabolome analysis. Absence of csn5/csnE affects transcription of at least 15 % of genes during development, including numerous oxidoreductases. csnE deletion leads to changes in the fungal proteome indicating impaired redox regulation and hypersensitivity to oxidative stress. CSN promotes the formation of asexual spores by regulating developmental hormones produced by PpoA and PpoC dioxygenases. We identify more than 100 metabolites, including orsellinic acid derivatives, accumulating preferentially in the csnE mutant. We also show that CSN is required to activate glucanases and other cell wall recycling enzymes during development. These findings suggest a dual role for CSN during development:  it is required early for protection against oxidative stress and hormone regulation and is later essential for control of secondary metabolism and cell wall rearrangement.

overall_design: Two genotypes of A. nidulans (Wildtype and Delta-csnE mutant) were compared in four different growth stages (vegetativ14h, vegetativ20h, asex48h and sex48h). Per growth stage we considered 8 microarrays of 2 biological replicates with direct comparisons including dye swaps between the genotypes.

first: Krystyna

last: Nahlik

last: Dumkow

first: Özgür

last: Bayram

first: Kerstin

last: Helmstaedt

first: Silke

last: Busch

first: Oliver

last: Valerius

first: Jennifer

last: Gerke

first: Michael

last: Hoppert

first: Elke

last: Schwier

first: Lennart

last: Opitz

first: Mieke

last: Westermann

first: Stephanie

last: Grond

first: Kirstin

last: Feussner

first: Cornelia

last: Goebel

first: Alexander

last: Kaever

last: Meinecke

first: Ivo

first: Gerhard

middle: H

last: Braus


title: Saccharomyces cerevisiae response to Octanoic and Decanoic acids

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

institute: INRA

summary: In this study, we present an investigation of the yeast response to the exposure to octanoic and decanoic acids, two major fermentation inhibitors. Aerobically grown cells of  Saccharomyces cerevisiae U13 wine strain have been exposed to 0,05 mM of octanoic and decanoic acid. We have compared the variations of expression induced by the acid challenges in comparison to a reference non trated modality, as well as the two acid responses. The transcriptome analysis is build in a triangular design in which the RNA extracted from three modalities :  reference (non treated cells) , cells exposed to  octanoic acid, and cells exposed to decanoic acid are compared.

overall_design: 12 samples have been analyzed in a triangular design (4 samples per modalité), four references (non treated cells), four samples exposed to octanoic acid, four samples exposed to decanoic acid

first: Claude

last: Erny

first: Christine

last: Le Jeune

first: Marc

last: Lollier

first: Ysabel

last: Adolphe

first: Catherine

last: Demuyter

first: Pierre

last: Delobel

first: Bruno

last: Blondin

first: Francis

last: Karst


title: Embryonic Stem Cell Differentiation LIF vs no LIF

city: Stanford

first: Nesanet

last: Mitiku

address: 300 Pasteur Drive Alway M313

department: Genetics

summary:
Description: The pluripotency of an embryonic stem cell makes it an attractive target for differentiation strategies aimed at producing tissues for therapeutic purposes. Yet, even though we know that ES cells have tremendous capacity for differentiation, we do not fully understand the molecular paths taken by these cells as they differentiate. In addition, it is unclear how important the removal of leukemia inhibitory factor is to ES cell differentiation. Moreover, it is unclear how the path of ES cell differentiation relates to the molecular decisions made by tissues undergoing normal development. The motivation behind this work is to increase our understanding of this relationship and its potential limitations. Dataset is a murine embryonic stem cell differentiation timecourse consisting of 14 timepoints spanning 17 days of differentiation. Samples were harvested at 24 hour intervals on days 0,1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 15, and 17. There two replicates of each sample in this series. Additionally, there are 14 identically stated differentiation samples, where growth was conducted in ES cell media containing LIF. A common reference design was employed.
Groups of assays that are related as part of a time series.
Compound Based Treatment: Treatment or lack of treatment with LIF
Elapsed Time: Samples were harvested at 24 hour intervals on days 0,1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 15, and 17
Keywords: time_series_design

overall_design: Using regression correlation


title: Genome-wide analysis of Embryonic Stem Cell Differentiation

summary:
Description: The pluripotency of an embryonic stem cell makes it an attractive target for differentiation strategies aimed at producing tissues for therapeutic purposes. Yet, even though we know that ES cells have tremendous capacity for differentiation, we do not fully understand the molecular paths taken by these cells as they differentiate. Moreover, it is unclear how the path of ES cell differentiation relates to the molecular decisions made by tissues undergoing normal development. The motivation behind this work is to increase our understanding of this relationship and its potential limitations. Overall Design: Dataset is a murine embryonic stem cell differentiation timecourse consisting of 14 timepoints spanning 17 days of differentiation. Samples were harvested at 24 hour intervals on days 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 15, and 17. There two replicates of each sample. A common reference design was employed.
Groups of assays that are related as part of a time series.
Elapsed Time: amples were harvested on days 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 15, and 17
Keywords: time_series_design


title: Functional redundancy of iron acquisition systems is required for Proteus mirabilis pathogenesis during UTI

city: Ann Arbor

first: Melanie

middle: M

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

summary: Proteus mirabilis is a primary cause of complicated urinary tract infections (UTI).  Surprisingly, iron acquisition systems have been poorly characterized in this uropathogen despite the urinary tract being iron-limited.  In this report the transcriptome of strain HI4320, cultured under iron limitation, was examined using microarray analysis.  Of genes upregulated at least 2-fold, 45 were statistically significant and comprise 21 putative iron-regulated systems.  Two of these systems, PMI0229-0239 and PMI2596-2605, are organized in operons and appear to encode siderophore biosynthesis genes.

overall_design: Five microarrays comparing P. mirabilis HI4320 cultured in LB broth to P. mirabilis cultured in LB broth + 15 uM Desferal (an iron chelator) were analyzed.  All five arrays are biological replicates; arrays #2 and 4 are dye swaps.

middle: D

last: Himpsl

first: Harry

last: Mobley


title: Identification of molecular factors explaining decreased hypocotyl growth at low temperature

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

summary: affy_hypoctemp_medicago - The characterization of several genotypes of the model Legume Medicago truncatula showed a genetic variability for germination and hypocotyl heterotrophic growth at low temperature and optimal temperature. The most important contrast was between the accessions Jemalong A17 and F83005.5. In order to find genes differently expressed between temperatures and genotypes, the present work focuses on transcriptome profiling during hypocotyl heterotrophic growth under low (10°C) and optimal (20°C) temperature conditions for both genotypes. We used Jemalong A17 and F83005.5 seeds coming from the Medicago truncatula Biological Resource Center in Montpellier, produced in 2006. Experiments were performed in the dark to mimic pre-emergence growth. Pots (6.5 cm diameter, 10 cm high) were incubated in growth chambers either at 10°C or 20°C. They were filled with 500g sand and 100ml of a nutrient solution for young seedlings growth (Saglio and Pradet, 1980). Per pot, five scarified seeds were sown at 1.5 cm depth. Seedlings were harvested at three times: 35°Cd (degree day), 50°Cd and 100°Cd. At each timepoint, about 50 seedlings were harvested and hypocotyl lengths was measured. Hypocotyl were cut and immediately frozen in liquid nitrogen for RNA extractions.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Time course of 24 arrays - Medicago

first: Sandrine

last: Balzergue

first: Béatrice

last: Teulat-Merah

first: Johann

last: Pierre

first: Marie-Laure

last: Martin-Magniette


title: Transcriptome analysis of Bifidobacterium animalis subsp. lactis BB12 grown on xylo-oligosaccharides

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

summary: Comparison of the growth of Bifidobacterium animalis subsp. lactis BB12 in MRS (without carbon source) with either 2% XOS (xylo-oligosaccharides) or 2% glucose using whole-genome transcriptome analysis.

overall_design: The sample GSM509238 (glucose against XOS) is a dye-swap of sample GSM509239 (XOS against glucose).

first: Ofir

last: Gilad

first: Susanne

last: Jacobsen

first: Birgitte

last: Stuer-Lauridsen

middle: B

first: Christel

last: Garrigues

first: Birte

last: Svensson


title: Diabetic vs. Menopausal/diabetic kidney cortex

city: Tucson

first: Heddwen

last: Brooks

state: AZ

address: PO Box 245218 1656 E Mabel

institute: University of Arizona

summary: Gene expression in kidney cortex of diabetic mice and menopausal diabetic mice following 6 weeks of diabetes.  Diabetes was induced with low-dose streptozotocin injections and menopause was induced by injection of 4-vinylcyclohexene diepoxide.

overall_design: Samples = 12

first: Maggie

last: Diamond-Stanic

first: Kevin

last: Greer


title: Selective Release of miRNA Species from Normal and Malignant Mammary Epithelial Cells

city: North Chicago

first: Dominik

last: Duelli

address: 3333 Green Bay Road

department: Pathology

institute: Rosalind Franklin University of Medicine and Science

summary: MicroRNAs (miRNAs) in body fluids are candidate diagnostics for a variety of conditions and diseases, including breast cancer. One premise for using extracellular miRNAs to diagnose disease is the notion that the abundance of the miRNAs in body fluids reflects their abundance in the abnormal cells causing the disease. As a result, the search for such diagnostics in body fluids has focused on miRNAs that are abundant in the cells of origin. Here we report that released miRNAs do not necessarily reflect the abundance of miRNA in the cell of origin. We find that release of miRNAs from cells into blood, milk and ductal fluids is selective and that the selection of released miRNAs may correlate with malignancy. In particular, the bulk of miR-451 and miR-1246 produced by malignant mammary epithelial cells was released, but the majority of these miRNAs produced by non-malignant mammary epithelial cells was retained. Our findings suggest the existence of a cellular selection mechanism for miRNA release and indicate that the extracellular and cellular miRNA profiles differ. This selective release of miRNAs is an important consideration for the identification of circulating miRNAs as biomarkers of disease.

overall_design: miRNA microarrays were screened by LC Sciences. One microgram of MCF7 cellular RNA preparation was labeled with Cy3, and one microgram of the extracellular RNA samples was labeled with Cy5. In brief, the RNA was labeled with Cy5 or Cy3 and hybridized to LCSciences standard arrays for mature miRNA of all species available in the Sanger miRBase database (Release 12.0). The data were analyzed including background subtraction, using a LOWESS (locally weighted regression) method on the background-subtracted data. Only transcripts with a signal intensity higher than 3X (background SD) and spot CV<0.5. CV was calculated by (SD)/(signal intensity), and in which repeating probes on the array produced signals from at least 50% of the repeating probes are above detection level.

first: Lucy

last: Pigati

first: Sree

middle: C

last: Yaddanapudi

first: Ravi

last: Iyengar

first: Dong-Ja

last: Kim

first: Steven

last: Hearn

first: David

last: Danforth

first: Michelle

last: Hastings


title: Mucosal responses of healthy humans to three different probiotic Lactobacillus bacteria

status: Public on Sep 08 2010

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

country: Netherlands

institute: Wageningen University

summary:
Probiotic bacteria, specific representatives of bacterial species that are a common part of the human microbiota, are proposed to deliver health benefits to the consumer by modulation of intestinal function via largely unknown molecular mechanisms. To explore in vivo mucosal responses of healthy adults to probiotics, we obtained transcriptomes in an intervention study following a double-blind placebo-controlled cross-over design. In the mucosa of the proximal small intestine of healthy volunteers, probiotic strains from the species Lactobacillus acidophilus, L. casei and L. rhamnosus each induced differential gene regulatory networks and pathways in the human mucosa. Comprehensive analyses revealed that these transcriptional networks regulate major basal mucosal processes, and uncovered remarkable similarity to response profiles obtained for specific bioactive molecules and drugs. This study elucidates how intestinal mucosa of healthy humans perceive different probiotics and provides avenues for rationally designed tests of clinical applications.

Keywords: mucosal response of healthy adult humans to lactic acid bacteria

overall_design: This study was set up according to a randomised double-blind cross-over placebo-controlled design. It contains transcriptional profiles from biopsies from 7 healthy individuals after oral intake of three different Lactobacillus species or placebo control. In total, this study includes data from 7 individuals x 4 treatments=28 arrays.

first: Michiel

last: Kleerebezem

first: Robert-Jan

last: Brummer

first: Cindy

last: van der Meer

first: Guido

last: Hooiveld

first: Fred

last: Troost

first: Mark

last: Boekschoten


title: Genomic diversity of a pneumococcal clonal complex, 199

status: Public on Sep 07 2010

city: New Haven

first: Jonathan

last: Thomas

state: CT

address: 60 College St.

institute: Yale University

summary: Comparative genomic hybridisation of Streptococcus pneumoniae isolates from a single clonal complex, in order to determine genomic diversity. Isolates were selected from a range of tissue types and serotypes in order to cover the full diversity of the clone, and also in order to try and identify tissue-specific genes

overall_design: Biological replicates: 19 clonal complex 199 S. pneumoniae isolates. One clonal complex 180 isolate used as an outgroup. Independently grown and isolated. One isolate per array

first: Marisol

last: Figueira

first: Kristopher

middle: P

last: Fennie

first: Yong

last: Kong

first: Alison

last: Laufer

first: Michael

last: Pichichero

first: Stephen

last: Pelton

first: Melinda

last: Pettigrew


title: WT vs rim101 mutant gene expression under capsule inducing conditions

status: Public on Sep 04 2010

city: Lynchburg

last: Price

state: VA

address: 1971 University Blvd.

department: Biology & Chemistry

institute: Liberty University

summary: Cryptococcus neoformans is a prevalent human fungal pathogen that must survive within various tissues in order to establish a human infection. We have identified the C. neoformans Rim101 transcription factor, a highly conserved pH-response regulator in many fungal species. The rim101- mutant strain displays growth defects similar to other fungal species in the presence of alkaline pH, increased salt concentrations, and iron limitation. However, the rim101- strain is also characterized by a striking defect in capsule, an important virulence-associated phenotype. This capsular defect is likely due to alterations in polysaccharide attachment to the cell surface, not in polysaccharide biosynthesis. In contrast to many other C. neoformans capsule-defective strains, the rim101- mutant is hypervirulent in animal models of cryptococcosis. Whereas Rim101 activation in other fungal species occurs through the conserved Rim pathway, we demonstrate that C. neoformans Rim101 is also activated by the cAMP/PKA pathway. We report here that C. neoformans uses PKA and the Rim pathway to regulate the localization, activation, and processing of the Rim101 transcription factor. We also demonstrate specific host- relevant activating conditions for Rim101 cleavage, showing that C. neoformans has co-opted conserved signaling pathways to respond to the specific niche within the infected host. These results establish a novel mechanism for Rim101 activation and the integration of two conserved signaling cascades in response to host environmental conditions.

overall_design: WT and rim101 mutant total RNA isolated from yeast grown under capsule inducing conditions were compared in a dye-swap experiment.  One culture of each representing a population of each strain were incubated in YPD culture medium to mid-logarithmic phase, then washed three times with sterile water before incubation in DMEM culture medium for 3 hours. Cells were washed three times before centrifugation and freezing on dry ice and lyophilizing.

first: Teresa

middle: R

last: O'Meara

first: Diana

last: Norton

first: Christie

last: Hay

first: Meredith

middle: F

last: Clements

first: Connie

last: Nichols

first: James

middle: A

last: Alspaugh


title: MicroRNA profiling of human pancreas development.

status: Public on Sep 06 2010

city: Miami

first: Ricardo

last: Pastori

state: FL

department: Diabetes Research Institute

institute: University of Miami

summary: MicroRNAs (miRNAs) are non-coding RNAs that play a fundamental role in regulation of gene expression affecting differentiation and development. In particular, miRNAs have been described to regulate genes important for pancreatic development and islet function. The aim of this study was to determine the miRNA expression signature during human pancreas development. We identified 212 miRNAs that were expressed throughout different gestational ages. From those, 4 miRNAs increased (group I), 35 miRNAs decreased (group II), during pancreatic development. The expression of the remaining 173 miRNAs was relatively constant throughout all assessed gestational ages. The determination of the specific group of miRNAs expressed in the human developing pancreas may further the understanding of gene expression regulation during this important process.

overall_design: In this study we define expression profiles of a total of 352 miRNAs for different stages of the pancreas development. Each TLDA card contains 2 endogenous controls which are present in 8 replicates each. Analysis of these controls allows calculating the intra- and inter-assay variation. Quantitative values (RQ) were calculated measuring the dCt between the Ct values of each miRNA and the Ct value of the small nucleolar RNU48 RNA.

first: V

last: Bravo-Egana

first: R

first: S

last: Rosero


title: Analysis of the Haloferax volcanii Transcriptome

city: Columbus

first: Chuck

last: Daniels

state: OH

address: 484 West 12th Avenue

department: Microbiology

institute: The Ohio State Uinversity

type: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array

summary: In this study the transcriptome of Haloferax volcanii DS70 (Wendoloski D, Ferrer C, Dyall-Smith ML. Microbiology. 2001, 147: 959-64), grown under of a variety of conditions, was mapped using a custom genome-wide tiled array consisting of 25 nt probes spaced in 35 nt windows. H. volcanii is a facultative aerobe capable of growth on simple carbon and nitrogen sources, it is amenable to genetic manipulations and has become a widely used model organism for studies on haloarchaeal physiology and global gene regulation.  Of particular interest is the identification of genes encoding enzymes needed for growth on simple carbon and nitrogen sources and how these cells respond to limitations in these key nutrients.  To address these questions we have compared the RNA populations of cells undergoing balanced growth in completely defined minimal medium (CDM) with succinate-glycerol, pyruvate or lactate as sole carbon sources with RNA from cells grown in complex rich medium (CX) containing yeast extract and tryptone.   Data from these studies have identified a core group of genes expressing during balanced growth in either condition as well as specific genes associated with the biosynthesis of amino acids, nucleotides and other key building blocks.  The response to nutrient limitation was also investigated.  RNA populations from cells entering stationary phase from growth in CDM and CX media were compared to those undergoing balanced growth, and these RNAs were also compared with RNA populations of cells subjected to nitrogen or carbon starvation.  Growth in the presence of histidine as the sole source of nitrogen in CDM medium also presented a model for growth with a “poor” nitrogen source.  The results of these studies identified specific subpopulations of genes associated with nitrogen limitation and general nutrient limitation associated with the transition to stationary phase.   Many of the responsive protein encoding genes were assigned general functions based on their similarity to known proteins; however, in each comparison, approximately half of the affected genes encode proteins classified as unknown or hypothetical proteins. The haloarchaea are also distinct among the Archaea in having multiple genes encoding the general transcription factor proteins TATA binding protein (TBP) and transcription factor IIB (TFB).  We observed differential expression of these genes, providing further support for the proposal that alternative TBP-TFB pairings are associated with programmed changes in gene expression in the haloarchaea.

overall_design: RNA was prepared from H. volcanii DS70 cells grown under a variety of conditions.  These include: balanced growth in completely defined medium with succinate and glycerol, pyruvate, or lactate as sole carbon source; balanced growth in complex medium with yeast extract and tryptone; starvation for nitrogen or carbon by re-suspending cells, undergoing balanced growth, in media lacking these agents; balanced growth in the presence of low (10% w/v NaCl) and high (20 % or 25% w/v NaCl) salt, and cells entering stationary from growth in CDM or CX media.  Four independent cultures were prepared for each growth variable and RNA was isolated from each culture.  RNA samples were identified as acceptable for use in array analysis if clear 23S rRNA, 16S rRNA and tRNA-sized bands were present in agarose gel and capillary electrophoresis analysis of the samples.  Three RNA samples were chosen for each growth variable and each was used as the source material for a separate chip experiment; these constituted three biological replicates for the growth variable.  Data from 48 chip hybridizations, representing 16 growth conditions, were combined for the quantile scaling (Auer H, Newsom DL, Nowak NJ, McHugh KM, Singh S, Yu CY, Yang Y, Wenger GD, Gastier-Foster JM, Kornacker K. BMC Genomics. 2007, 8:111-124) presented in the data analyses.  Two additional experiments are included where the RNAs of three independent biological samples were pooled into a single RNA population and used as the source material for an array experiment.  These included RNA samples enriched for species less than 500 nt that were isolated from cells undergoing balanced growing, and entry into stationary phase, in CDM or CX media.  A second pooled series were obtained from the H. volcanii DS70 mutant strains ASD40 (∆pyrF) and ASD41 (∆pyrF∆hutR) grown in CDM with ammonium ion or histidine as the sole source of nitrogen.  Pooled samples are presented as quantile normalized values (Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. Bioinformatics. 2003, 19: 185-193). Total genomic DNA from H. volcanii DS70 was also used as probe, in two independent array experiments, to measure the inherent hybridization to the probes.  These data are presented as quantile scaled values (Auer et. al., 2007).

first: Anice

last: Sabag-Daigle

first: Shoko

last: Morimoto

first: Richard

middle: N

last: Nist

first: Charles

middle: J


title: DNA methylation signatures define molecular subtypes of Diffuse Large B Cell Lymphoma

status: Public on Sep 03 2010

city: New York

first: Rita

last: Shaknovich

state: NY

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medical Center

summary:
We performed DNA methylation (HELP) and gene expression profiling in 69 samples of diffuse large B cell lymphoma (DLBCL). First, by gene expression, two molecular subtypes of DLBCL termed as germinal center B cell-like (GCB) and activated B cell-like (ABC) DLBCL were assigned to the 69 DLBCL cases. Then, we performed  supervised analysis using HELP data and defined DNA methylation signature differentiating 2 subgroups of DLBCLs.
Keywords: DNA methylation profiling

overall_design:
The retrospective study included DNA extracted from 69 clinical samples.

[This Series represents the DNA methylation profiling component of the study.]

first: Ari

last: Melnick

first: Randy

last: Gascoyne

first: Olivier

last: Elemento

first: Huimin

last: Geng


title: WT vs gcn5 mutant gene expression under capsule inducing conditions

first: Michael

middle: S

last: Price

summary: Cryptococcus neoformans is an environmental fungus and an opportunistic human pathogen. Previous studies have demonstrated major alterations in its transcriptional profile as this microorganism enters the hostile environment of the human host. To assess the role of chromatin remodeling in host-induced transcriptional responses, we identified the C. neoformans Gcn5 histone acetyltransferase and demonstrated its function by complementation studies of Saccharomyces cerevisiae. The C. neoformans gcn5Δ mutant strain has defects in high-temperature growth and capsule attachment to the cell surface, in addition to increased sensitivity to FK506 and oxidative stress. Treatment of wild-type cells with the histone acetyltransferase inhibitor garcinol mimics cellular effects of the gcn5Δ  mutation. Gcn5 regulates the expression of many genes that are important in responding to the specific environmental conditions encountered by C. neoformans inside the host. Accordingly, the gcn5Δ mutant is avirulent in animal models of cryptococcosis. Our study demonstrates the importance of chromatin remodeling by the conserved histone acetyltransferase Gcn5 in regulating the expression of specific genes that allow C. neoformans to respond appropriately to the human host.

overall_design: WT and gcn5 mutant total RNA isolated from yeast grown under capsule inducing conditions were compared in a dye-swap experiment. One culture of each representing a population of each strain were incubated in YPD culture medium to mid-logarithmic phase, then washed three times with sterile water before incubation in DMEM culture medium for 3 hours. Cells were washed three times before centrifugation and freezing on dry ice and lyophilizing.

first: Teresa

last: O'Meara

first: Christie

first: Steve

last: Giles


title: Polyphenols from Myrothamnus flabellifolia Welw. inhibit in vitro adhesion of Porphyromonas gingivalis and exert anti-inflammatory cytoprotective effects in KB cells

status: Public on Sep 02 2010

city: Rostock

first: Sylvio

last: Redanz

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Institute of microbiology, virology and hygiene

institute: hospital university rostock

summary:
Investigation of whole genome gene expression level changes in Porphyromonas gingivalis ATCC 33277 treated with an anti-adhesive extract from Myrothamnus flabellifolia compared to the untreated strain.
Aim: Identification of anti-adhesive plant extracts against cell surface binding of Porphyromonas gingivalis.
Materials and Methods: Polyphenol-enriched extract from Myrothamnus flabellifolia (MF) traditionally used for periodontitis was tested for inhibition of P. gingivalis adhesion to KB cells by FACS, for influence on gingipain activity, hemagglutination and by microarray analysis for effects on the bacterial transcriptome. P. gingivalis-induced inflammation parameters were monitored by RT-PCR.
Results: MF (100 µg/ml) reduced P. gingivalis adhesion/invasion about 50% by interacting with fimbriae and bacterial OMPs.  Microarray analysis of MF-treated bacteria indicated up-regulation of genes involved in cell adhesion. As confirmed by RT-PCR, fimbrillin- and Arg-gingipain-encoding genes were upregulated by MF. On the protein level, inhibition (70%) of Arg-gingipain activity was observed, while the corresponding Lys-gingipain was hardly influenced. MF also inhibited hemagglutination. While exposure to P. gingivalis resulted in an increased expression of inflammation-related genes in KB cells, pretreatment of KB cells with MF evoked cytoprotective effects concerning IL-1β, IL-6, IL-8 and TNFα gene expression as well as IL-6 release rates.
Conclusions: While being cytoprotective, MF exerts strong anti-adhesive effects against P. gingivalis. Thus, MF may be useful for the prevention of P. gingivalis-associated periodontal diseases.

platform_organism:
Streptococcus mutans UA159
Porphyromonas gingivalis W83

overall_design: The chip study used total RNA recovered from two separate MF-treated and two separate untreated Porphyromonas gingivalis ATCC 33277 cultures. Each chip measured the expression level of 1,842 genes from P. gingivalis ATCC 33277 with thirteen 60-mer probes per gene, with three-fold technical redundancy.

first: Gesine

last: Löhr

first: Thomas

last: Beikler

first: Andreas

last: Podbielski

first: Kerstin

last: Standar

last: Hensel


title: Effect of overexpressing E2FB in tomato plants

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

institute: Centro de Biotecnología y Genómica de Plantas

summary: The cell cycle transcription factor E2FB has been overexpressed in tomato plants (Solanum lycopersicum cv. Micro-Tom). This overexpression accelerates plant development and increases fruit yield.

overall_design: Total RNA was purified from true leaves and apical meristem of 14 days-old WT or E2FB-OE seedlings.

first: Zamira

last: Abraham


title: Human PBMNCs: Control vs. Patients with Kawasaki disease

city: Fukuoka

first: Kazuyuki

last: Ikeda

state: Fukuoka

address: Maidashi 3-1-1

department: Pediatrics

institute: Kyushu university

summary: Genes that were consistently up-regulated in KD patients compared with healthy controls, and that showed over 2.0 or 3.0-fold differences by the comparison between the two groups in the mean expression levels were selected.

overall_design: Microarray analysis for PBMNCs of acute-phase KD patients was performed using an AceGene Human Oligo Chip 30K 1 Chip Version (Hitachi Software Engineering) that contains approximately 30,000 genes. In the study presented here, 3 cases of Kawasaki disease at acute phase,and 5 healthy controls,were used. The data with low signal-to-noise ratios (S/N<3) were not used for further analysis.

first: Kenichiro

last: Yamaguchi

first: Tamami

last: Tanaka

first: Yumi

last: Mizuno

first: Atsushi

last: Hijikata

first: Osamu

last: Ohara

first: Hidetoshi

last: Takada

first: Koichi

last: Kusuhara

first: Toshiro

last: Hara


title: Chicken Spleen Tissues: MDV-infected vs non-infected in inbred lines 63, 72 & RCSM

city: Bethesda

first: Apratim

last: Mitra

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

summary: Transcriptional profiling of chicken spleen tissues from Marek's disease virus (MDV) infected and non-infected control individuals from three inbred chicken lines 63, 72, RCSM with varying disease resistance characteristics. Line 63 is highly resistant; line 72 is highly susceptible; and line RCSM has intermediate resistance.  Our goal was to investigate the genetic basis of systemic variation in disease resistance in these genetically similar individuals. Three time points were chosen at different stages of disease progression - 5 days post-infection (dpi) - early cytolytic phase; 10 dpi - latent phase; and 21 dpi - late cytolytic phase with 4 replicates at each stage.

overall_design: Two-condition experiment, MDV infected sample vs non-infected control, 3 chicken lines - 63, 72 and RCSM, 3 time points - 5, 10 & 21 dpi. Biological replicates: 4 non-infected control replicates, 4 infected replicates for each line at each time point.

first: Ying

last: Yu

last: Luo

first: Fei

last: Tian

first: Huanmin

last: Zhang

first: Ping

last: Yuan

first: Jiuzhou

last: Song


title: Diurnal Regulation of Gene Expression in Immature Ear Over a 72-Hour Period

city: Johnston

first: Kevin

middle: Robert

last: Hayes

state: IA

address: 7200 NW 62nd Ave

institute: Pioneer Hi-Bred International

summary: Background: Plant diurnal rhythms are vital environmental adaptations to coordinate internal physiological responses to alternating day-night cycles.   A comprehensive view of diurnal biology has been lacking for maize (Zea mays), a major world crop. Methodology: A photosynthetic tissue, the leaf, and a non-photosynthetic tissue, the developing ear, were sampled under natural field conditions. Genome-wide transcript profiling was conducted on a high-density 105K Agilent microarray to investigate diurnal rhythms.

overall_design: The top-most immature ear, 4-5 cm in length, was collected.  Plants were sampled every 4 hours over 3 days. Our sampling times were: 6 am (dawn), 10 am, 2 pm, 6 pm, 10 pm and 2 am. Tissues were collected from three field reps and within each field rep we collected samples from three individual plants

first: Olga

last: Danilevskaya


title: Diurnal Regulation of Gene Expression in Leaves Over a 72-Hour Period

overall_design: The top-most fully expanded leaf from each plant collected. Plants were sampled every 4 hours over 3 days. Our sampling times were: 6 am (dawn), 10 am, 2 pm, 6 pm, 10 pm and 2 am. Tissues were collected from three field reps and within each field rep we collected samples from three individual plants


title: Control vs. Menopausal kidney cortex

first: Heddwen

last: Brooks

summary: Gene expression in kidney cortex of control mice and menopausal mice 8 weeks after mice entered menopause.  Menopause was induced by injection of 4-vinylcyclohexene diepoxide.

first: Maggie

last: Diamond-Stanic

last: Greer


title: Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase

city: Tallinn

first: Ranno

last: Nahku

address: Akadeemia tee 15b

country: Estonia

institute: TFTAK

summary:
Background: The biotechnology industry has extensively exploited Escherichia coli for producing recombinant proteins, biofuels etc. However, high growth rate aerobic E. coli cultivations are accompanied by acetate excretion i.e. overflow metabolism which is harmful as it inhibits growth, diverts valuable carbon from biomass formation and is detrimental for target product synthesis. Although overflow metabolism has been studied for decades, its regulation mechanisms still remain unclear.
Results: In the current work, growth rate dependent acetate overflow metabolism of E. coli was continuously monitored using advanced continuous cultivation methods (A-stat and D-stat). The first step in acetate overflow switch (at μ = 0.27 ± 0.02 1/h) is the repression of acetyl-CoA synthethase (Acs) activity triggered by carbon catabolite repression resulting in decreased assimilation of acetate produced by phosphotransacetylase (Pta), and disruption of the PTA-ACS node. This was indicated by acetate synthesis pathways PTA-ACKA and POXB component expression down-regulation before the overflow switch at μ = 0.27 ± 0.02 1/h with concurrent 5-fold stronger repression of acetate-consuming Acs. This in turn suggests insufficient Acs activity for consuming all the acetate produced by Pta, leading to disruption of the acetate cycling process in PTA-ACS node where constant acetyl phosphate or acetate regeneration is essential for E. coli chemotaxis, proteolysis, pathogenesis etc. regulation. In addition, two-substrate A-stat and D-stat experiments showed that acetate consumption capability of E. coli decreased drastically, just as Acs expression, before the start of overflow metabolism. The second step in overflow switch is the sharp decline in cAMP production at μ = 0.45 1/h leading to total Acs inhibition and fast accumulation of acetate.
Conclusion: This study is an example of how a systems biology approach allowed to propose a new regulation mechanism for overflow metabolism in E. coli shown by proteomic, transcriptomic and metabolomic levels coupled to two-phase acetate accumulation: acetate overflow metabolism in E. coli is triggered by Acs down-regulation resulting in decreased assimilation of acetic acid produced by Pta, and disruption of the PTA-ACS node.

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

overall_design: Reference samples at specific growth rate (μ) 0.11 1/h were compared to the ones acquired at μ 0.21, 0.26, 0.31, 0.36, 0.40 and 0.48 1/h

first: Kaspar

last: Valgepea

first: Kaarel

last: Adamberg

first: Petri-Jaan

last: Lahtvee

first: Liisa

last: Arike

first: Raivo

last: Vilu


title: Characterization of the oxidative stress regulon of Campylobacter jejuni

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Ottawa

summary:
Background: During gut colonization, the enteric pathogen C. jejuni has to surmount the toxic effects of reactive oxygen species produced by its own metabolism, by the host immune system and by the intestinal microflora.  Elucidation of C. jejuni oxidative stress defense mechanisms is critical for understanding Campylobacter pathophysiology.    Results: The mechanisms of oxidative stress defenses in Campylobacter jejuni were characterized by transcriptional profiling, genes mutagenesis, and phenotypic analysis. The transcriptome changes, in response to H2O2, cumene hydroperoxide, or menadione exposure, were found to be oxidant specific and revealed the differential expression of genes belonging to a variety of biological pathways, from the classical oxidative stress defense systems, to the heat shock response, DNA repair and metabolism, fatty acid and capsule biosynthesis, and multidrug efflux pumps. To define the peroxide sensing regulator PerR, an isogenic mutant was constructed and its transcriptome profile compared to the wild-type strain. Sixty-six genes were found to belong to the PerR regulon. PerR appear to regulate gene expression both dependently and independently of the presence of iron and/or H2O2. The perR mutant was affected in its motility and attenuated in the chick colonization model.  Mutagenic and phenotypic studies of the superoxide disumutase SodB, the alkyl-hydroxyperoxidase AhpC, and the catalase KatA, revealed their role in oxidative stress defenses and chick gut colonization.   Conclusion: This study reveals the interplay between PerR, the iron metabolism and the oxidative stress defenses and highlights their role in the colonization and/or survival of C. jejuni in the chick cecum.

Keywords: Transcriptional response to 3 oxidants (H2O2, menadione and cumene hydroperoxide) and characterization of the perR regulon (comparison of the transciptomes from the wild-type and perR mutant).

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: To investigate the transcriptional responses of C. jejuni to oxidant exposure, hydrogen peroxide (H2O2), cumene hydroperoxide (CHP), or menadione sodium bisulfite (MND) was added to the 50 ml broth at a final concentration of 1 mM. The same amount of water or DMSO was added to the bacterial culture that served as reference samples for the transcriptional profile study in response to H2O2, MND or CHP. Furthermore, to investigate the transcriptional response of C. jejuni to H2O2 exposure in the presence of excess iron, ferrous sulfate was added to the bacterial culture at a final concentration of 40 µM, 15 min prior to H2O2 exposure. Ten minutes after the addition of the oxidant, total RNA was extracted and processed for microarray hybridization. To identify the PerR regulon, the wild-type strain C. jejuni NCTC 11168 and the perR mutant were grown in 500 ml flasks containing 250 ml of MEMα medium. At mid-log phase, 50 ml of the cultures were transferred to 100 ml flasks and ferrous sulfate and/or H2O2 were added . Ten minutes following the addition of H2O2 the cells were collected and the total RNA extracted.

first: Kiran

last: Palyada

first: Yi-Qian

last: Sun

first: Annika

last: Flint

first: James

last: Butcher

first: Hemant

last: Naikare


title: Expression data from indole deficient E.coli (MG1655∆tnaA) exposed to indole and norfloxacin during continuous culture

city: Boston

first: Henry

last: Lee

state: MA

address: 36 Cummington St

department: Biomedical Engineering

institute: Boston University

summary: We sought to determine the effect of indole on cells under antibiotic stress.

overall_design: To determine the effects of indole during norfloxacin treatment, we continuously cultured MG1655_delta_tnaA and exposed the culture to three conditions: 1. initial exposure to norfloxacin, 2. exposure to indole and norfloxacin, and 3. reexposure to norfloxacin

first: Michael

last: Molla


title: Identification of new genomic areas within the genomes of Yersinia pestis and Yersinia  pseudotuberculosis strains through targeted genome sequencing

city: Rockville

first: John

last: Braisted

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary:
Yersinia pestis (Y. pestis) is the etiologic agent of the plague, an endemic zoonotic disease of critical clinical and historic importance. The species belongs to a genus comprising eleven members, three of which are human pathogens. Y. pestis and its closest extant relative, Yersinia pseudotuberculosis, are very similar in many respects, yet there is a distinct dichotomy between these species in terms of pathogenicity. Y. pseudotuberculosis produces a relatively benign food- or water-borne gastroenteritis with rare cases of potentially fatal bacteremia. In contrast, the characteristics of high infectivity and high mortality have made Y. pestis a pathogen of historic importance with devastating effects on the human populace over the course of three major pandemics. These qualities coupled with the emergence of multi-drug resistant variants make Y. pestis an ideal candidate for use as a bioterrorism agent. Consequentially, evolutionary biology of this organism has become a priority in the counter-terrorism research effort.

The flow of genetic information within the Y. pseudotuberculosis/Y. pestis group motivated us to identify novel genes for the purpose of creating a pan-genome species DNA microarray to better understand the phylogenomic relationships among its members.

Based on the sequence information be generated from the novel gene discovery project conducted at the PFGRC as well as other publicly available sources regarding Yersinia spp. genome sequences, we designed a species microarray which represents the hitherto known genetic repertoire of this taxonomic group.

In order to create a species microarray that represents novel genes or genes with significant sequence variation, the ArrayOligoSelector software (http://arrayoligosel.sourceforge.net/) was used to design a 70-mer oligonucleotide for each of the annotated ORFs or partial ORFs. A detailed description of the 70-mer oligo design process and filters developed by the PFGRC can be found on the PFGRC web site at (http://pfgrc.tigr.org/presentations/seminars/oligo_design_final.pdf).

sample_organism:
Yersinia pestis
Yersinia pseudotuberculosis

overall_design: One hundred fifty six query strains were investigated in this study, with each query strain hybridized against the reference strain, CO92.  Each strain has a single dye experiment.  Each oligo is spotted on the Y. pestis species microarray once.  Positive controls on the array consist of oligos designed from the sequenced reference genome, CO92, and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.

first: Leka

last: Papazisi

first: Qiang

first: Shashikala

last: Ratnayake

first: Sarah

last: Akkoush

first: Eric

last: Wester

first: A’Drian

last: Pineda

first: Shaohua

last: Jin

first: Erik

last: Snesrud

first: Fatma

last: Onmus

first: Lakshmi

last: Appalla

first: Timothy

last: Minogue

first: Xiaozhe

last: Huang

first: Dana

last: Cash

first: Luther

last: Lindler

first: Mikeljon

last: Nikolich

first: Robert

last: Fleischmann

first: Scott

last: Peterson


title: The Nuclear-retained non-coding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation

status: Public on Sep 01 2010

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

summary: Alternative splicing (AS) of pre-mRNA is utilized by higher eukaryotes to achieve increased transcriptome and proteomic complexity. The serine/arginine (SR) splicing factors regulate tissue- or cell type-specific AS in a concentration and phosphorylation dependent manner. However, the mechanisms that modulate the cellular levels of active SR proteins remain to be elucidated. In the present study, we provide evidence for a role for the long nuclear-retained regulatory RNA (nrRNA), MALAT1 in AS regulation. MALAT1 interacts with SR proteins and influences the distribution of these and other splicing factors in nuclear speckle domains. Depletion of MALAT1 changes AS of endogenous pre-mRNAs, similar to what was observed upon overexpression of SR proteins. Furthermore, MALAT1 regulates cellular levels of phosphorylated forms of SR proteins. Taken together, our results suggest that MALAT1 regulates AS by modulating the levels of active SR proteins. Our results further highlight a novel role for a nrRNA in the regulation of gene expression.

overall_design: Malat1 Antisense and control knockdowns evaluated on a microarray platform to profile alternative splicing levels for 5782 cassette-type alternative exons.

first: Vidisha

last: Tripathi

first: Jonathan

last: Ellis

first: Zhen

last: Shen

first: David

middle: Y

last: Song

first: Andrew

middle: T

last: Watt

first: Susan

last: Freier

first: C.

last: Frank Bennett

first: Alok

last: Sharma

first: Paula

last: Bubulya

first: Benjamin

last: Blencowe

first: Supriya

middle: G

last: Prasanth

first: Kannanganattu

middle: V


title: Discriminating reprotoxic and non-reprotoxic phthalates by transcriptomics analysis of rat testis

city: Amsterdam

first: Xiaolian

last: Yuan

state: North Holland

address: Science Park 904

department: Microarray department

institute: Amsterdam University

summary:
REACH, the EU regulation on chemicals and their safe use, stipulates that about 30,000 chemical substances are to be assessed on their possible risks. Toxicological evaluation of these compounds will at least partly be based on animal testing. Especially reproductive toxicity is one of the most complicated, time-consuming and expensive in vivo endpoints. Introducing microarray-based endpoints can potentially refine in vivo toxicity testing. If compounds from a distinct chemical class induce reproducible gene-expression responses with a recognizable overlap, these gene-expression signatures may indicate intrinsic features of certain compounds, including toxicity. In the present study, we investigated this theory for the reproductive toxicity of phthalates.
Male rats were treated with a single dose of either reprotoxic or non-reprotoxic phthalates and sacrificed 24h thereafter. Subsequently, histopathological and gene-expression profiling analyses were performed. Despite ambiguous histopathological observations, we were able to distinguish the reprotoxic from the non-reprotoxic phthalates based on differential gene expression. This shows that differences in gene expression indicative for the type of exposure can be detected earlier, or at lower doses, than phenotypic tissue damage. These findings are promising for ’early warning’ biomarker analyses and for using toxicogenomics in a category approach.

overall_design: Male rats were treated with a single dose of either reprotoxic (DMP, DEP, DPrP, DOP) or non-reprotoxic phthalates (DBP, DPeP, DHP, DEHP, MEHP), positive control (2-ME) or negative control (vehicle) and killed 24 h thereafter. Rat testes  were preserved for RNA extraction and hybridization on Affymetrix microarrays.

first: Martijs

last: Jonker

first: Jillian

last: de Wilde

first: Aart

last: Verhoef

first: Floyd

last: Wittink

first: Jan

last: van Benthem

first: Jos

last: Bessems

first: Betty

last: Hakkert

first: Raoul

last: Kuiper

first: Harry

last: van Steeg

first: Timo

middle: M

last: Breit

first: Mirjam

last: Luijten


title: The miRNA expression signature of human MALT lymphoma

status: Public on Aug 31 2010

city: Zürich

first: Vanessa

middle: Jane

last: Craig

address: Winterthurerstrasse 190

institute: Institute of molecular cancer research

summary:
To identify key tumour supressor miRNAs involed in MALT lymphoma pathogenesis
Gastric mucosa-associated lymphoid tissue lymphoma develops in the chronically inflamed mucosa of Helicobacter pylori-infected patients. MicroRNA expression profiling of human MALT lymphoma revealed a 10-fold down-regulation of miR-203, which resulted from promoter hypermethylation and coincided with the dysregulation of the miR-203 target ABL1. Demethylating treatment of lymphoma B-cells led to an increase in miR-203 expression and concomitant ABL1 down-regulation. The lentiviral delivery of miR-203, as well as treatment with various ABL inhibitors, prevented primary MALT lymphoma cell proliferation in vitro. Finally, the treatment of tumor-bearing mice with imatinib induced MALT lymphoma regression in vivo. Our results show that MALT lymphomagenesis is epigenetically induced by miR-203 promoter methylation and identify ABL1 as a novel target for the treatment of this malignancy.

overall_design: 5 human fresh frozen MALT lymphoma samples were analysed and 4 human tonsil tissue samples were used as the non-tumour control


title: Expression analysis of Naegleria gruberi (strain NEG) during differentiation from the amoeba to the flagellate form

city: Berkeley

first: Lillian

last: Fritz-Laylin

state: CA

address: 345 LSA, UC Berkeley MCB

department: MCB

institute: UC Berkeley

summary:
Naegleria gruberi is a single-celled eukaryote best known for its remarkable ability to form an entire microtubule cytoskeleton de novo during its metamorphosis from an amoeba into a flagellate, including two basal bodies (equivalent to centrioles), two flagella (equivalent to cilia), and a cytoplasmic microtubule array.  This full-genome transcriptional analysis, performed at 20-minute intervals throughout Naegleria differentiation, reveals vast transcriptional changes, including the differential expression of cytoskeletal, metabolism, signaling and stress response genes.

Naegleria gruberi (strain NEG) was grown in association with Kleibsiella pneumoniae on solid media.  Cells were prepared and differentiated using standard protocols, and harvested at 0, 20, 40, 60 and 80 minutes after initiation of differentiation.

overall_design: Three independent biological replicates were obtained from differentiating N. gruberi.  Each replicate series included the following timepoints: 0, 20, 40, 60 and 80 minutes after initiation of differentiation.

middle: K

first: W

middle: Z

last: Cande


title: MicroRNA expression profile in Dgcr8-homozygous mutant mouse embryonic stem cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: We investigated the effect of Dgcr8-homozygous mutation on microRNA expression profile in mouse embryonic stem cells. MicroRNA expression was substantially impaired, indicating a pivotal role of DGCR8 in microRNA biogenesis.

overall_design: MicroRNA expression profile was compared between Dgcr8-homozygous mutant ES cells and wild-type ES cells

first: Kyoji

last: Horie

first: Junji

last: Takeda