title: Effect of glutaraldehyde (Glut) on growth physiology and gene expression of Desulfovibrio vulgaris Hildenborough

status: Public on Mar 06 2010

city: Calgary

first: Phoebe

middle: Meng-Hsin

last: Lee

address: 2500 University Dr NW

department: Biological sciences

country: Canada

institute: University of Calgary

summary:
The effect of glutaraldehyde stress on Desulfovibrio vulgaris Hildenborough (DvH) gene expression was determined by comparing the gene expression profiles of DvH with glutaraldehyde added at mid-log phase against DvH grown without glutaraldehdyde. Low concentration glutaraldehyde had little influence over instantaneous growth rate constant and final cell density of the culture. Changes in gene expression caused by exposure to glutaraldehyde were determined using full-genome DvH microarrays. A lot of gene expressions were altered by glutaraldehyde.

Keywords: Glutaraldehyde Stress

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.

first: Gerrit

last: Voordouw


title: ChIP-chip from mouse male and female adult livers and P12.5 embryos with H3K27me3

status: Public on Mar 05 2010

city: Seattle

first: Fan

last: Yang

state: WA

address: 1959 NE pacific street

country: USA

institute: University of Washington

type: Genome binding/occupancy profiling by genome tiling array

summary:
The H3K27me3 is a repressive histone mark associated with repressive chromatin and is important for X chromosome inactivation.
ChIP-chip of H3K27me3 along the mouse X chromosome in male and female livers and p12.5 embryos demonstrated that H3K27me3 is absent at the genes that escape X inactivation.

overall_design: Comparison of H3K27me3 enrichment along the X chromosome in male and female adult livers and P12.5 embryos

first: Christine

middle: M

last: Disteche


title: MyoD ChIP-chip on Ciona intestinalis embryo (early-mid gastrula)

status: Public on Mar 09 2010

city: Kyoto

first: Atsushi

last: Kubo

state: Kyoto

address: Sakyo-ku

department: Department of zoology, Graduate School of Science

country: Japan

institute: Kyoto University

summary:
A genomic overview of in vivo binding of a transcription factor MyoD in the ascidian gastrula embryo.
MyoD is known to be essential and sufficient for differentiation of the muscle.
Keywords: ChIP-chip

overall_design:
Fertilized eggs were electroporated with a construct encoding GFP-tagged MyoD. After fixation, Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE DNA were amplified by LM-PCR for the Chip analysis.
Two independent experiments were performed to reduce experimental errors.

first: Yutaka

last: Satou


title: Transcriptional response to protease treatments (kallikrein, papain and chymotrypsin) of Bifidobacterium breve 210B

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary: Members of the serpin (serine protease inhibitor) superfamily have been identified in higher, multicellular eukaryotes, as well as in bacteria, although surveillance of available genome sequences indicates that bacterial serpin-encoding (ser) homologs are not widely distributed. In members of the genus Bifidobacterium this gene appears to be present in at least five, and perhaps up to nine, out of 30 species tested. Moreover, phylogenetic analysis using available bacterial and eukaryotic serpin sequences revealed that bifidobacteria specify serpins that form a separate clade. We characterized the ser210B locus of Bifidobacterium breve 210B, which consists of a number of genes, whose deduced protein products display significant similarity to proteins encoded by corresponding loci found in several other bifidobacteria. Northern hybridization, primer extension, micro array analysis, RT-PCR and Quantitative Real Time (qRT) - PCR analysis revealed that a 3.5 kb polycistronic mRNA, encompassing the ser210B operon with a single transcriptional start site, is strongly induced following treatment of B. breve 210B cultures with particular proteases. In contrast, transcription of the ser homolog of other bifidobacteria, such as Bifidobacterium longum subsp. infantis, Bifidobacterium dentium and B. longum subsp. longum, appears to be triggered by a different set of proteases

first: Francesca

last: Turroni

first: Elena

last: Foroni

first: Mary

last: O’Connell Motherway

last: Bottacini

first: Vanessa

last: Giubellini

first: Aldert

last: Zomer

first: Massimo

last: Delledonne

first: Ziding

last: Zhang

first: Douwe

last: van Sinderen

first: Marco

last: Ventura


title: ZicL ChIP-chip on Ciona intestinalis embryo (early gastrula)

summary:
A genomic overview of in vivo binding of a transcription factor ZicL in the ascidian gastrula embryo. ZicL is a key regulator of the early ascidian development, and so called 'master-regulatory genes' for mesodermal and neural tissues are under the control of ZicL.
Keywords: ChIP-chip

overall_design:
Fertilized eggs were electroporated with a construct encoding GFP-tagged ZicL. After fixation, Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE DNA were amplified by LM-PCR for the Chip analysis.
Two independent experiments were performed to reduce experimental errors.


title: S. cerevisiae TAF5 and taf5 temperature conditional mutants grown at permissive and non-permissive temperature

city: Nashville

first: Justin

middle: Harrison

last: Layer

state: TN

address: 21st and Garland Avenue, 746 Robinson Research Building

department: Molecular Physiology and Biophysics

institute: Vanderbilt University

summary:
Expression analysis of Saccharomyces cerevisiae TAF5 and taf5 temperature conditional mutants grown at permissive and non-permissive temperature.

Investigation of whole genome gene expression level changes in Saccharomyces cerevisae taf5-17, taf5-45, taf5-408 and taf5-10.4 mutants, compared to the wild-type strain.  The mutations engineered into the strains confer temperature conditional growth.
The mutants analyzed in this study are further described in Layer et. al., 2010.  Direct Transactivator-Transcription Factor IID (TFIID) Contacts Drive Yeast Ribosomal Protein Gene Transcription.  Journal of Biological Chemistry.

overall_design: A twenty chip study using total RNA recovered from four separate wild-type cultures of Saccharomyces cerevisiae and four separate cultures for each of four taf5 temperature conditional mutants (16 mutant cultures).  Each chip measures the expression level of 5,777 genes from Saccharomyces S288C with eight 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

middle: H

first: P

middle: A

last: Weil


title: microRNA expression in human hepatitis c virus (HCV) liver biopsy samples

status: Public on Mar 08 2010

first: Xinxia

last: Peng

address: Rosen Building, 960 Republican St.

department: Microbiology

summary: In order to infer the inverse expression relationships between microRNAs and mRNAs during HCV infection, we profiled both microRNA and mRNA expressions in HCV positive (HCV+) and HCV negative (HCV-) human liver biopsy tissue samples. This series includes all microRNA profiles.

overall_design: This series includes microRNA profiles of 36 samples, 24 HCV positives and 12 HCV negatives.

first: Yu

last: Li

first: Kathie-Anne

last: Walters

first: Elizabeth

middle: R

last: Rosenzweig

first: Sharon

middle: L

last: Lederer

first: Lauri

middle: D

last: Aicher

first: Sean

last: Proll

first: Michael

middle: G

last: Katze


title: Effect of THPS on growth physiology and gene expression of Desulfovibrio vulgaris Hildenborough

first: Phoebe

last: Lee

summary:
The effect of tetrakis (hydroxymethyl) phosphonium sulfate (THPS) stress on Desulfovibrio vulgaris Hildenborough (DvH) gene expression was determined by comparing the gene expression profiles of DvH with THPS added at mid-log phase against DvH grown without THPS. Low concentration THPS had little influence over instantaneous growth rate constant and final cell density of the culture. Changes in gene expression caused by exposure to THPS were determined using full-genome DvH microarrays. In comparison to Glutaraldehyde and BAC microarray results, not lot of gene expressions were altered by THPS.

Keywords: THPS Stress

platform_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

first: Gerrit

last: Voordouw


title: Molecular Hydrogen Impact on Chalcopyrite Bioleaching by the Extremely Thermoacidophilic Archaeon Metallosphaera sedula

status: Public on Mar 15 2010

city: Raleigh

first: Kathryne

middle: Sherlock

last: Auernik

state: NC

address: Partners II, rm 3309, 849 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: Hydrogen served as a competitive inorganic energy source, impacting the CuFeS2 bioleaching efficiency of the extremely thermoacidophilic archaeon Metallosphaera sedula. Open reading frames encoding key terminal oxidase and electron transport chain components were triggered by CuFeS2. Evidence of heterotrophic metabolism was noted after extended periods of bioleaching, presumably related to cell lysis.

overall_design: One 3 slide loop for Mse cells includes 3 conditions: M. sedula inoculum prior to introduction to chalcopyrite (d0~day 0), M. sedula after 3 days on chalcopyrite (d3~day 3), and M. sedula after 9 days on chalcopyrite (d9~day 9). Half of an RNA sample for one condition (consisting of pools of RNA from multiple cultures) was labeled with Cy3 while the other half was labeled with Cy5. The two differently labeled samples were run on different slides. Each probe is spotted on each slide 5 times (5 spots/slide x 2 slides = 10 technical replicates per condition; spot intensities for all replicates on slide provided in associated raw data file).

middle: S

first: Robert

last: Kelly


title: The functional potential of high Arctic permafrost

city: Montreal

first: Etienne

last: Yergeau

state: Qc

address: 6100 Royalmount Ave

department: Environmental Microbiology

institute: NRC-BRI

summary: The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown. Here, a 2 m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2 m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2 m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries. This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw.

sample_organism:
environmental samples
environmental samples
environmental samples
environmental samples

platform_organism: Bacteria Archaea

overall_design: A 2m deep permafrost sample and it overlying active layer were sampled and their metagenome analysed. For microarray analyses, 8 other soil samples from the same region were used for comparison purposes.

first: Hervé

last: Hogues

first: Lyle

last: Whyte

first: Charles

middle: W

last: Greer


title: EGR1 regulates metastatic potential of v-src transformed chicken sarcoma cell lines

city: Basel

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: A model of tumor metastasis based on v-src transformed immortalized cell lines was developed. The model consists of highly metastatic PR9692 cell line and a derived clone PR9692-E9 which has lost the metastatic abilities. Introduction of exogenous EGR1 gene into the non-metastasizing PR9692-E9 cells completely restores the metastatic potential. Revealed changes in gene expression provide insight into the molecular mechanisms contolling metastatic behavior of sarcoma cells.

overall_design: Comparison of expression profiles obtained from highly metastatic PR9692 cell line, derived non-metastatic clone PR9692-E9 and non-metastatic PR9692-E9 cells infected with replication-defective retroviral vector SFCVneo-EGR1 containing full length cDNA of EGR1. For each condition three biological replicates were analyzed.

first: Vladimir

last: Cermak


title: Differential virulence gene expression in the pathogenic dermatophyte Arthroderma benhamiae in vitro versus infection

city: Lausanne

first: Michel

last: Monod

address: Av. de Beaumont 29

department: Dermatology

institute: Centre Hospitalier Universitaire Vaudois

summary:
Although dermatophytes are the most common agents of superficial mycoses in humans and animals, the molecular basis of the pathogenicity of these fungi is largely unknown. In vitro digestion of keratin by dermatophytes is associated with the secretion of multiple proteases, which are assumed to be responsible for their particular specialization to colonize and degrade keratinized host structures during infection. To address this hypothesis a guinea pig infection model was established for the zoophilic dermatophyte Arthroderma benhamiae which causes highly inflammatory cutaneous infections in humans and rodents. Microarray analysis revealed a distinct in vivo protease gene expression profile in the fungal cells, which is surprisingly different from the pattern elicited during in vitro growth on keratin. Instead of the major in vitro expressed proteases others were activated specifically during infection. These enzymes are therefore suggested to fulfill important functions that are not exclusively associated with the degradation of keratin. As the most upregulated in vivo specific A. benhamiae sequence we discovered the gene encoding the serine protease subtilisin 6, which is a known major allergen in the related dermatophyte Trichophyton rubrum and putatively linked to host inflammation. In addition, our approach identified other candidate pathogenicity related factors in A. benhamiae, such as genes encoding key enzymes of the glyoxylate cycle and an opsin-related protein. This first broad transcriptional profiling approach during dermatophyte infection gives new molecular insights into pathogenicity associated mechanisms that make these microorganisms the most successful etiologic agents of superficial mycoses.

Keywords: Two-condition experiment, strong proteolytic activity in the supernatant versus no proteolytic activity or infected tissue versus no proteolytic activity

overall_design: Three independently prepared A. benhamiae replicates grown in each of the three media, Sabouraud, soy and keratin-soy medium (designated SabA/B/C, soyA/B/C and keratin-soyA/B/C) were used. ARN from skin samples and fungus together of Guinea Pig infected with A. benhamieae were prepared. Pairwise transcriptional comparisons, i.e. soy versus Sabouraud, keratin-soy versus Sabouraud and Guinea Pig infected versus Sabouraud were done. The total number of slides in this study was 18.

first: Peter

last: Staib

first: Christophe

last: Zaugg

first: Bernard

last: Mignon

first: Johann

last: Weber

first: Maria

last: Grumbt

first: Sylvain

last: Pradervand

first: Keith

last: Harshman


title: Poly(A)-Specifc Ribonuclease 1 (PARN-1) Overexpression in Procyclic T. brucei

city: Newark

first: Christopher

last: Utter

state: NJ

address: 225 Warren St.

department: Microbiology and Molecular Genetics

institute: University of Medicine and Dentistry of New Jersey-New Jersey Medical School

summary: We sought to determine the effect of TbPARN-1 overexpression on global mRNA steady-state levels in T. brucei.  The mRNA expression profile of tet-induced TbPARN-1 OvEx  procyclic cells was compared to the mRNA profile of control cells (expressing tet-induced TAP tag alone) by microarray analysis.  Since overexpression of TbPARN-1 showed increased deadenylation activity in cytoplasmic extracts, overexpressing PARN-1 in vivo should result in more rapid deadenylation and decay of mRNAs targeted by PARN-1.  Thus, mRNAs with lower steady state levels in PARN-1 OvEx cells can be considered likely targets for PARN-1-dependent deadenylation.

overall_design:
Three different clones of the PARN-1 OvEx and Control cell lines were used for analysis.  Each experiment was run in duplicate, with the dye-labeling reversed between duplicates.  The T. brucei version 3 microarray chip (PFGRC) was used for this experiment.  Each gene on the microarray was represented in duplicate, so for each experiment, mRNA levels were obtained from both points and averaged.

As a control between arrays, we used a control probe set obtained from PFGRC. "The probe set consists of Cy3 and Cy5 end labeled 40-mer probes that are complementary to a set of 500 Arabidopsis thaliana 70-mer targets on PFGRC DNA microarrays. The UMSS is supplied as a ready to use mix of the Cy3 and Cy5 labeled oligonucleotides. A small aliquot is spiked into Cy-dye labeled nucleic acid samples just prior to hybridization on PFGRC microarrays. The UMSS produces a set of reference fluorescent signal intensities and ratios that are generated independent of the user-specific experimental samples. Since PFGRC intentionally targeted a heavy representation of Cy3 and Cy5 signals in the mid-range of detection, the Cy3 and Cy5 signal intensities and ratios generated by the UMSS should be highly reproducible. These signals serve as a reference point to judge the success of microarray experiments, and troubleshoot potential problems."

middle: J

first: Vivian

last: Bellofatto


title: Loss of the actin remodeler Eps8 causes calorie restriction and improved metabolic status in mice

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary: In a variety of organisms, including mammals, caloric restriction improves metabolic status and lowers the incidence of chronic-degenerative diseases, ultimately leading to increased lifespan. Here we show that knockout mice for Eps8, a regulator of actin dynamics, display reduced bodyweight, partial resistance to age- or diet-induced obesity, and overall improved metabolic status. We present evidence that these phenotypes, which are associated to increased lifespan in the Eps8 null mice, are due to caloric restriction. This, in turn, is caused by reduced intestinal fat absorption, due to altered morphogenesis of microvilli in intestinal enterocytes. In the nematode, genetic removal of Eps8, causes a microvillar phenotype, indistinguishable from that observed in mice, which leads to early larval lethality. By exploiting the nematode model system, we demonstrate here that the actin bundling activity of Eps8 is indispensable for viability and proper intestinal morphogenesis. This result links a precise molecular function of Eps8 to proper microvillar morphogenesis, and therefore to the phenotype of Eps8-null mice. Our results implicate actin dynamics in individual variations in bodyweight, metabolic status and longevity.

overall_design: cDNA expression profiling of liver of 4 mutant EPS8 -/- animals versus pool of 4 wt animals. 8 hybridisation including 4 dye swap experiments

first: Marion

last: Horsch

first: Johannes

last: Beckers

first: Nina

last: Offenhäuser


title: Adaptation of group A Streptococcus to human amniotic fluid

city: Warsaw

first: Izabela

last: Sitkiewicz

address: Chełmska 30/34

department: Epidemiology and Clinical Microbiology

country: Poland

institute: National Medicines Institute

summary:
Background. For more than 100 years, group A Streptococcus has been identified as a cause of severe, and in many cases fatal, infections of the female urogenital tract. Due to advances in hospital hygiene and the advent of antibiotics, this type of infection has been virtually eradicated. However, within the last three decades there has been an increase in severe intra- and post-partum infections attributed to GAS.
Principal Findings. The majority of changes in the GAS transcriptome involved down regulation of multiple adhesins and virulence factors and activation of the stress response. We observed significant changes in genes involved in the arginine deiminase pathway and in the nucleotide de novo synthesis pathway.
Conclusions/Significance. Our work provides new insight into how pathogenic bacteria respond to their environment to establish infection and cause disease.

overall_design: To identify genes that were up or down regulated in response to growth in AF, GAS was grown in human AF or standard laboratory media (THY) and samples for expression microarray analysis were collected during mid-logarithmic, late-logarithmic, and stationary growth phases. Microarray analysis was performed using a custom Affymetrix chip and normalized hybridization values derived from three biological replicates were collected at each growth point. Ratios of AF/THY above a 2-fold change and P-value < 0.05 were considered significant.

first: Nicole

last: Green

last: Guo

first: Ann

last: Bongiovanni

first: Steven

last: Witkin

first: James

last: Musser


title: Gene expression in Drosophila montana

status: Public on Mar 04 2010

city: Jyvaskyla

first: Maaria

last: Kankare

address: Survontie 9

country: Finland

institute: University of Jyvaskyla

summary: We created a custom-made microarray for D. montana with 101 genes known to affect traits important in diapause, photoperiodism, reproductive behaviour, circadian clock and stress tolerance in model Drosophila species. This array gave us a chance to filter out genes showing expression changes during photoperiodic reproductive diapause in a species adapted to live in northern latitudes with high seasonal changes.

overall_design: The three samples for the microarray experiments included young females (“young”), 14 days old females cultured under diapause-preventing (“reproducing”) and 14 days old females cultured under diapause-inducing conditions (“diapausing”). Each of these samples had three replicates. The microarray contained 197 unique probe sequences representing 101 candidate genes and seven housekeeping genes. Some of the probes had two copies per array, in which case the averages of their signals were calculated. The Agilent control probes included 77 negative control probes and 200 spike-in probes (10 different probe types, each represented by 20 copies per array).

first: Tiina

last: Salminen

first: Asta

last: Laiho

first: Laura

last: Vesala

first: Anneli

last: Hoikkala


title: Alarm pheromone habituation in Myzus persicae: Fitness consequences and the transcriptome of fear

status: Public on Mar 01 2010

city: Ithaca

first: Georg

last: Jander

state: NY

address: 1 Tower Rd

institute: Boyce Thompson Institute for Plant Research

summary:
In most aphid species, facultative parthenogenetic reproduction allows rapid growth and formation of large single-genotype colonies. Upon predator attack, individual aphids emit an alarm pheromone to warn the colony of this danger. (E)-beta-farnesene (EBF) is the predominant constituent of the alarm pheromone in Myzus persicae (green peach aphid) and many other aphid species. Continuous exposure to alarm pheromone in aphid colonies raised on transgenic Arabidopsis thaliana plants that produce EBF leads to habituation of the aphid population. Whereas naïve aphids are repelled by EBF, habituated aphids show no avoidance response. Individual aphids from the habituated colony can revert back to being EBF-sensitive in three generations, indicating that this behavioral change is not caused by a genetic mutation. Instead, DNA microarray experiments comparing gene expression in naïve and habituated aphids treated with EBF demonstrate an almost complete desensitization in the transcriptional response to EBF. Furthermore, EBF-responsive aphids, but not habituated aphids show significantly lower reproduction in the presence of EBF. Although both naïve and habituated aphids emit EBF upon damage, EBF-responsive aphids display a higher survival rate in the presence of coccinellid predators and thus outperform habituated aphids that do not show an avoidance response. These results provide direct evidence that aphid perception of conspecific alarm pheromone aids in predator avoidance and thereby bestows fitness benefits in survivorship and fecundity. Although habituated M. persicae have equal fecundity on control and EBF-producing plants, such transgenics may have practical applications in agriculture because of increased predation of habituated aphids.
Log fold-changes (LogFC) were computed and contigs with P-values ≤ 0.05 were considered to be differentially expressed  (see Supplementary file at foot of this record).

overall_design: Agilent 8x15K array previously reported by Ramsey et al., 2007 - BMC Genomics 8: 243. Two-condition experiment using Alexa Fluor 555 and 647 dyes. Biological replicates: 4 control replicates, 4 treated replicates.

last: De Vos


title: Ovarian transcriptional profiles of four mouse strains

status: Public on Mar 03 2010

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

summary:
The transcriptional profiles of ovarian tissue from four laboratory mouse-inbred strains were obtained with NIA15K-cDNA microarrays and
then correlated with the divergent spontaneous ovarian tumor rates and reproductive parameters reported for each strain.

overall_design: Four test samples and one reference sample - common reference design- dye swap - 5 to 6 replicates per sample - test samples pooled from 4-6 animals , 23 arrays

first: David

last: Munroe


title: Gene expression of Streptococcus mutans pknB mutant versus wild type strain

city: Zurich

first: Danusia

last: Vanoaica

address: Plattenstr. 11

department: Institute for Oral Biology

institute: University of Zurich

summary:
Bacteria can detect, transmit and react to signals from the outside world by using two-component systems an serine-threonine kinases and phosphatases. Streptococcus mutans contains one serine-threonine kinase, encoded by pknB. A gene encoding a serine-threonine phosphatase, pppL, is located downstream of pknB. In this study, the phenotypes of single mutants in pknB and pppL and a pknBpppL double mutant were characterized. All mutants exhibited a reduction in genetic transformability and biofilm formation, showed abnormal cell shapes, grew slower than the wild type strain in several complex media and had lost acid tolerance. The mutants had reduced cariogenic capacity, but no defects in colonization in a rat caries model. Whole genome transcriptome analysis revealed that pknB mutant showed reduced expression of genes involved in bacteriocin production and genetic competence. Among the genes that were diferentially regulated in the pknB mutant, severeal were likely to be involved in cell wall metabolism.
One such gene, SMU.2146c and two genes encoding bacteriocins, were showed to be also down-regulated in vicK, which encodes a sensor kinase involved in response to oxidative stress. Collectively, the results suggest that PknB can modulate the activity of the two-component signal transduction systems vicKR and comDE. Real-time PCR showed that the genes down-regulated in the pknB mutant were up-regulated in the pppL mutant, indicating that PppL served to counteract PknB.

overall_design: Wild-type strain UA159 and a pknB mutant derivative were grown planktonically until OD600nm was 0.3. RNA was extracted, converted to cDNA, labelled and hybridized on S. mutans microarrays. The experiment was done in triplicate including one dye swap.

last: Banu

first: Jan

last: van der Ploeg


title: Phenotypic plasticity in the pea aphid Acyrthosiphon pisum: miRNA expression

city: Rennes

first: Stephanie

last: Jaubert

address: domaine de la Motte

country: France

institute: INRA

summary: We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 155 miRNAs including 56 conserved and 99 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode.

overall_design: An array including the 155 aphid microRNAs was designed in order to follow the expression of aphid microRNAs during the modification of reproduction mode of the pea aphid

first: Stéphanie

last: Jaubert-Possamai

first: Denis

last: Tagu

first: Fabrice

last: Legeai


title: Responses of S. aureus to stress caused by sublethal concentration of cationic antimicrobial peptides

status: Public on Mar 02 2010

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary: Understanding how pathogens respond to antimicrobial peptides, and how this compares to currently available antibiotics, is crucial to optimizing antibiotic therapy. Staphylococcus aureus has several known resistance mechanisms against human cationic antimicrobial peptides (CAMPs). We aim to determine how S. aureus responds to sheep and frog CAMPs, and whether this response is associated with resistance. Gene expression changes in Staphylococcus aureus Newman cells exposed to linear CAMPs were analyzed by DNA microarray. Three antimicrobial peptides were used in the analysis, two of them are derived from frog, temporin L and dermaseptin K4-S4(1-16), one is from sheep, ovispirin-1. The peptides induced the VraSR cell-wall regulon and several other genes which are also upregulated in cells treated with vancomycin and other cell wall-active antibiotics. In addition to this similarity, three genes/operons were particularly strongly induced by the peptides: vraDE, SA0205 and SAS016, encoding an ABC transporter, a putative membrane-bound lysostaphin-like peptidase and a small functionally unknown protein, respectively. Ovispirin-1 and dermaseptin K4-S4(1-16), which disrupt lipid bilayers by the carpet mechanism, were strong inducers of the vraDE operon. We show that high level induction by ovispirin-1 was dependent on the amide modification of the peptide C-terminus. This suggests that the amide group has a crucial role in the activation of the Aps sensory system, the regulator of vraDE. In contrast, temporin L, which disrupts lipid bilayers by forming pores, was clearly a weaker inducer of vraDE despite the C-terminal amide modification. Sensitivity testing with CAMPs and other antimicrobials suggested that VraDE is a transporter dedicated to resist bacitracin. We also showed that SA0205 belongs to the VraSR regulon. Furthermore, VraSR was shown to be important for resistance against a wide range of cell wall-active antibiotics and other antimicrobial agents including the amide-modified ovispirin-1, bacitracin, teicoplanin, cefotaxime and 10 other β-lactam antibiotics, chlorpromazine, thioridazine and EGTA.

overall_design: The effects of the three different antimicrobial peptides on gene expression of S. aureus Newman were studied by using whole genome oligo-DNA microarrays. Bacteria were grown in BHI medium to the early exponential phase (OD600=0.6) and antimicrobial peptides were added at sublethal concentrations. Samples were taken for RNA isolations after treating the cultures with the peptides for 10 minutes. Control cultures without peptide additions were treated similarly and in parallel.

first: Milla

last: Pietiäinen

first: Patrice

last: Francois

first: Hanne-Leena

last: Hyyryläinen

first: Manuela

last: Tangomo

first: Vera

last: Sass

first: Hans-Georg

last: Sahl

first: Jacques

last: Schrenzel

first: Vesa

middle: P

last: Kontinen


title: Brachyury ChIP-chip on Ciona intestinalis embryo (early-mid gastrula)

first: Atsushi

last: Kubo

address: Sakyo-ku

summary:
A genomic overview of in vivo binding of a transcription factor Brachyury in the ascidian gastrula embryo.
Brachyury is known to be essential and sufficient for differentiation of the notochord.
Keywords: ChIP-chip

overall_design:
Fertilized eggs were electroporated with a construct encoding GFP-tagged Brachyury. After fixation, Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for GFP (Invitrogen). The immunoprecipitated and WCE DNA were amplified by LM-PCR for the Chip analysis.
Two independent experiments were performed to reduce experimental errors.

first: Yutaka

last: Satou


title: Analysis of copy number variations among diverse cattle breeds

city: Beltsville

first: George

last: Liu

state: MD

address: 10300 Baltimore Ave

institute: United States Department of Agriculture

type: Genome variation profiling by genome tiling array

summary: Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.

overall_design: The custom aCGH chips that interrogated the whole genome CNVs were build for 90 cattles from diverse breeds, with Hereford L1 Dominette 01449 as refference sample.

middle: E

first: Yali

last: Hou

first: Bin

last: Zhu

first: Maria

middle: F

last: Cardone

first: Lu

last: Jiang

first: Angelo

last: Cellamare

first: Apratim

last: Mitra

first: Leeson

last: Alexander

first: Luiz

last: Coutinho

last: Dell'Aquila

first: Lou

middle: C

last: Gasbarre

first: Gianni

last: Lacalandra

first: Robert

last: Li

first: Lakshmi

middle: K

last: Matukumalli

first: Dan

last: Nonneman

first: Luciana

last: Regitano

first: Tim

last: Smith

first: Jiuzhou

last: Song

first: Tad

last: Sonstegard

first: Curt

last: VanTassell

first: Mario

last: Ventura

first: Evan

last: Eichler

first: Tara

last: McDaneld

first: John

last: Keele


title: CGH reveals a neo-X chromosome and biased gene movement in stalk-eyed flies (genus Teleopsis)

city: College Park

first: Gerald

last: Wilkinson

address: Bldg 144, 4094 Campus Dr

department: Biology

institute: University of Maryland

summary: In this study, we utilized Comparative Genomic Hybridization (CGH), using probes designed from EST sequence, to identify genes located on the X chromosome of four species in the stalk-eyed fly genus Teleopsis. Analysis of log ratio values from the CGH microarrays for over 3400 genes produces a strongly bimodal distribution that clearly differentiates autosomal from X-linked genes for all four species. Genetic mapping of 35 of these genes in T. dalmanni indicates the CGH results correctly identified chromosomal location in all cases. Syntenic comparison with Drosophila indicates that 90% of the X-linked genes in Teleopsis are homologous to genes located on chromosome 2L in D. melanogaster, suggesting the formation of a nearly complete neo-X chromosome from Muller element B in the Dipteran lineage leading to Teleopsis. Overall, this study demonstrates CGH is a useful technique for identifying chromosomal sex-linkage and should be applicable to other organisms with EST or partial genomic information.

sample_organism:
Teleopsis dalmanni
Teleopsis quinqueguttata
Teleopsis whitei
Teleopsis thaii

overall_design: Two-condition experiment, female vs. male DNA, for four species, each with 4 biological replicates

first: Richard

last: Baker


title: Conidia but not yeast cells of the fungal pathogen Histoplasma capsulatum trigger a type I interferon innate immune response in murine macrophages

city: San Francisco

first: Sajeev

last: Batra

state: CA

institute: UCSF

summary:
To identify signaling pathways that are induced by macrophages infected with Histoplasma capsulatum, we examined the whole genome expression profile of murine bone marrow derived macrophages infected with conidia, the natural infectious particle of Histoplasma. Conidia induced the expression of signature Type I interferon response genes. The induction of a Type I interferon response was specific to conidia, yeast cells did not trigger the response. Macrophages that lack the Type I interferon receptor, IFNAR1, were infected and compared to wild-type macrophages. The expression of some Type I IFN response genes are dependent upon

Keywords: Murine bone marrow derived macrophage transcriptional response to infection with Histoplasma capsulatum conidia

overall_design: We analyzed a series of 24 MEEBO arrays on which were hybed RNA amplified from bone marrow derived macrophages from C57BL/6 (WT) or ifnar1-/- mice either mock infected or infected with H. capsulatum conidia or yeast cells.

first: Diane

middle: O

last: Inglis

first: Charlotte

last: Berkes

first: Davina

last: Hocking Murray

first: Anita

last: Sil


title: Comparative Genomic Hybridization: genomic control vs. Multiple sclerosis (MS) patients

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

institute: University of Ferrara

summary: Background: Multiple sclerosis (MS) is a complex disorder thought to result from an interaction between environmental and genetic predisposing factors which have not yet been characterised, although it is known to be associated with the HLA region on 6p21.32. Recently, a picture of chronic cerebrospinal venous insufficiency (CCSVI), consequent to stenosing venous malformation of the main extra-cranial outflow routes (VM), has been described in patients affected with MS, introducing an additional phenotype with possible pathogenic significance.  Methods: In order to explore the presence of copy number variations (CNVs) within the HLA locus, a custom CGH array was designed to cover 7 Mb of the HLA locus region (6,899,999bp; chr6:29,900,001-36,800,000). Genomic DNA of the 15 patients with CCSVI/VM and MS was hybridised in duplicate.   Results: In total, 322 CNVs, of which 225 were extragenic and 97 intragenic, were identified in 15 patients. 234 known polymorphic CNVs were detected, the majority of these being situated  in non-coding or extragenic regions. The overall number of CNVs (both extra- and intragenic) showed a robust and significant correlation with the number of stenosing VMs (Spearman: r=0.6590, p=0.0104; linear regression analysis r=0.6577, p=0.0106).   The region we analysed contains 211 known genes. By using pathway analysis focused on angiogenesis and venous development, MS, and immunity, we tentatively highlight several genes as possible susceptibility factor candidates involved in this peculiar phenotype.   Conclusions: The CNVs contained in the HLA locus region in patients with the novel phenotype of CCSVI/VM and MS were mapped in detail, demonstrating a significant correlation between the number of known CNVs found in the HLA region and the number of CCSVI-VMs identified in patients. Pathway analysis revealed common routes of interaction of several of the genes involved in angiogenesis and immunity contained within this region. Despite the small sample size in this pilot study, it does suggest that the number of multiple polymorphic CNVs in the HLA locus deserves further study, owing to their possible involvement in susceptibility to this novel MS/VM plus phenotype, and perhaps even other types of the disease.

overall_design: 8 female and 7 male MS patients


title: Comparative genomic hybridization of Cronobacter sakazakii BAA-894 with other Cronobacter species

city: Nottingham

first: Eva

last: Kucerova

address: Clifton Lane

country: United Kingdom

institute: Nottingham Trent University

summary:
The genus Cronobacter (formerly called Enterobacter sakazakii) is composed of five species; C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, and C. dublinensis. The genus includes opportunistic human pathogens, and the first three species have been associated with neonatal infections.  The most severe diseases are caused in neonates and include fatal necrotizing enterocolitis and meningitis. The genetic basis of the diversity within the genus is unknown, and few virulence traits have been identified. We report here the first sequence of a member of this genus, C. sakazakii strain BAA-894. The genome of Cronobacter sakazakii strain BAA-894 comprises a 4.4 Mb chromosome (57% GC content) and two plasmids; 31 Kb (51% GC) and 131 Kb (56% GC).  The genome was used to construct a 385,000 probe oligonucleotide tiling DNA microarray covering the whole genome. Comparative genomic hybridization (CGH) was undertaken on five other C. sakazakii strains, and representatives of the four other Cronobacter species. Among 4,382 annotated genes inspected in this study, about 55% of genes were common to all C. sakazakii strains and 43% were common to all Cronobacter strains, with 10 - 17% absence of genes. CGH highlighted 15 clusters of genes in C. sakazakii BAA-894 that were divergent or absent in more than half of the tested strains; six of these are of probable prophage origin. Putative virulence factors were identified in these prophage and in other variable regions. A number of genes unique to Cronobacter species associated with neonatal infections (C. sakazakii, C. malonaticus and C. turicensis) were identified. These included a copper and silver resistance system known to be linked to invasion of the blood-brain barrier by neonatal meningitic strains of Escherichia coli. In addition, genes encoding for multidrug efflux pumps and adhesins were identified that were unique to C. sakazakii strains from outbreaks in neonatal intensive care units.
Comparative genomic hybridization highlighted 15 clusters of genes in C. sakazakii BAA-894 that were divergent or absent in more than half of the tested strains; six of these are of probable prophage origin. Putative virulence factors were identified in these prophage and in other variable regions. A number of genes unique to Cronobacter species associated with neonatal infections (C. sakazakii, C. malonaticus and C. turicensis) were identified. These included a copper and silver resistance system known to be linked to invasion of the blood-brain barrier by neonatal meningitic strains of Escherichia coli. In addition, genes encoding for multidrug efflux pumps and adhesins were identified that were unique to C. sakazakii strains from outbreaks in neonatal intensive care units.

sample_organism:
Cronobacter sakazakii
Cronobacter sakazakii ATCC BAA-894
Cronobacter dublinensis
Cronobacter muytjensii
Cronobacter turicensis
Cronobacter malonaticus

overall_design: Ten Cronobacter samples were analyzed, including total genomic DNA of six C. sakazakii strains, one C. malonaticus strain, one C. muytjensii strain, one C. dublinensis strain and one C. turicensis strain.

first: Xiao-Qin

last: Xia


title: Comparison of the CcpA and CovR Transcriptomes in Group A Streptococcus

city: Houston

first: Samuel

last: Shelburne

state: TX

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

summary: The goal of this study were to compare the transcriptoms of CcpA and CovR in group A Streptococcus.  Isogenic mutant strains were created in which CcpA and CovR were inactivated alone and in combination.  The transcriptomes of the four strains (wild-type, CcpA mutant, CovR mutant, and ccpA-covR double mutant) were then compared.

overall_design: Four biological replicates of each strain were grown to the mid-exponential and stationary phases of growth in THY.  Cells were harvested, RNA isolated, and converted to cDNA.  cDNA was hybridized to a custom-made Affymetrix GeneChip that contains 100% of the ORFs of the wild-type strain MGAS2221.

first: Randall

last: Olsen

first: Bryce

last: Suber

first: Pranoti

last: Saharabhojane

first: Paul

last: Sumby

last: Brennan

first: James

middle: M

last: Musser


title: Global responses of Aliivibrio salmonicida to hydrogen peroxide

city: Tromsø

first: Erik

last: Hjerde

address: Breivika

department: Department of chemistry

country: Norway

institute: University of Tromsø

summary: Aliivibrio salmonicida causes “cold-water vibriosis” (or “Hitra disease”) in fish, including marine-reared Atlantic salmon. During development of the disease the bacterium will encounter macrophages with antibacterial activities such as production of damaging reactive oxygen species (ROS). To defend itself the bacterium will presumably start producing detoxifying enzymes, reducing agents, and proteins involved in DNA and protein repair systems. Even though responses to oxidative stress are well studied for a few model bacteria, little work has been done in general to explain how important groups of pathogens, like members of the Vibrionaceae family, can survive at high levels of ROS. We have used bioinformatic tools and an –omics approach to study how A. salmonicida responds to hydrogen peroxide (H2O2). First, we used the recently published genome sequence to predict potential binding sites for OxyR (H2O2 response regulator). The computer-based search identified OxyR sites associated with 20 single genes and 8 operons, and these predictions were compared to experimental data from Northern blot analysis, microarray analysis and 2D gel electrophoresis. In general, OxyR binding site predictions and experimental results are in agreement. Up- and down-regulated genes are distributed among all functional gene categories, but a striking number of ≥2 fold up-regulated genes encode proteins involved in detoxification or DNA protection and repair, are part of reduction systems, or are involved in carbon metabolism and regeneration of NADH/NADPH. Our predictions and –omics data corroborates well with findings from other model bacteria, but also suggest species-specific gene regulation.

overall_design: Two-condition experiment, cells grown in LB medium (control samples) vs. cells grown under oxidative stress (H2O2) (stimulated samples). Samples collected from three different timepoints (15, 30 and 60 min). Technical replicates for each timepoint: 3 control, 3 stimulated, independently grown and harvested. One replicate per array.

first: Hege

last: Pedersen

first: Steinar

last: Paulsen

first: Hilde

last: Hansen

first: Lotte

first: Sunniva

last: Thode

first: Marcos

middle: T

last: Dos Santos

first: Ruth

middle: H

last: Paulssen

first: Nils

last: Willassen

first: Peik

last: Haugen


title: Expression difference between osteoarthritic chondrocytes and mesenchymal stem cells during chondrogenic differentiation

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
The recruitment of mesenchymal stem cells in order to reconstruct damaged cartilage of osteoarthritis joints is a challenging tissue engineering task. Vision towards this goal is blurred by a lack of knowledge about the underlying differences between chondrocytes and MSC during the chondrogenic cultivation process. The aim of this study was to shed light on the differences between chondrocytes and MSC occurring during chondral differentiation through tissue engineering.
As a model we used the pellet culture system under chondrogenic conditions for the comparison of chondrocyte and MSC differentiation. Immunohistology was followed by microarray analysis, which was filtered through already published datasets describing different developmental processes. Validation was performed with quantitative RT-PCR.
Results describe inferior chondrogenic ECM-production by MSCs and underline their closer link to the osteogenic lineage. Chondrocytes have an upregulated fatty acid/cholesterol metabolism which might give hints for future modifications of culture conditions.

overall_design: To shed light on the differences between chondrocytes and MSC occurring during chondral differentiation through tissue engineering, a pellet culture system under chondrogenic conditions for the comparison of chondrocyte and MSC differentiation was used after  0, 3, 7 and 14 days

first: Peter

last: Bernstein

first: Angela

last: Jacobi

first: Cornelia

last: Liebers

first: Suzanne

last: Manthey

first: Maik

last: Stiehler


title: Zebrafish (Danio rerio) 72hpf, WT control vs. MO-Prpf31 injected

city: Singapore

first: Jan

last: Brocher

address: 14 Science Drive 4, Block S1A, Level 6

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

summary: Transcriptional profiling performed from total eye RNA extracts of wildtype control fishes versus Prpf31 morpholino injected larvae (at ~72hpf)

overall_design: two-condition experiment: wildtype zebrafish versus MO-Prpf31 injected zebrafish eye RNA; 6 replicates each (extraction from 6 pools (~200 eyes each) of controls and 6 pools MO-Prpf31 (~200 eyes each))

first: Christoph

last: Winkler

first: Sinnakaruppan

last: Mathavan

first: Gek

last: Lee


title: Effects of far-infrared rays on 3 human prostate cancer cell lines

city: Osaka

first: Hiroki

last: Shima

address: 3-7-41 Nakatsu YAMAMOTO  Bild. 4F. Kitaku

institute: SHIMA Institution for Quantum Medicine

summary:
We introduce anticancer effect of the far-infrared rays. The growth of three human prostate cancer cells (DU145, PC-3 and LNCaP) was suppressed in vitro only by far-infrared rays. The far-infrared rays induced the gene activation involved in apoptosis that exert positive effects on cancer control. Shima, H. et al. Far-infrared rays control prostate cancer cells in vitro and in vivo. Nature Precedings, hdl:10101/npre.12008.11980.10101 (2008).

Keywords: cancer control

overall_design: Twelve samples were analyzed. Each sample was cultured quadricate. One replicate per array. The DU145, PC-3 and LNCaP cell lines were obtained from American Type Culture Collection (Manassas, VA, USA). DU145 cells were maintained in minimum essential medium supplemented with 10% heat-inactivated fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin G and 0.1 mM non-essential amino acids in an atmosphere of 5% CO2 at 37°C. PC-3 and LNCaP cells were maintained in F-12K medium and RPMI medium with the same supplements, respectively. All three cancer cells were cultured for 21 and 28 days with or without exposure to far-infrared rays.  The cells without exposure to far-infrared rays were used as the reference samples (Far-infrared rays-treated  vs. non-treated cells). Natural or synthetic rubber/resin (RB) was obtained as far-infrared rays emitter from Yamamoto Corporation (Osaka, Japan). RB consisted of rubber, lime stone and titanium metal powder in a honeycomb structure comprised of micron-sized cells, and had the ability to radiate far-infrared rays (4–25 um). Experimental samples were sandwiched with RBs for 21 and 28 days. Channels 1 were exposed to RB.

first: Jun

last: Qiu

first: Yoshie

last: Yoshikawa


title: Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences

city: Sydney

first: Ian

last: Paulsen

state: NSW

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

country: Australia

institute: Macquarie University

summary: The GacS/GacA signal transduction system is a central regulator in Pseudomonas spp., including the biological control strain P. fluorescens Pf-5, in which GacS/GacA controls the production of secondary metabolites and exoenzymes that suppress plant pathogens. A whole genome oligonucleotide microarray was developed for Pf-5 and used to assess the global transcriptomic consequences of a gacA mutation in P. fluorescens Pf-5. In cultures at the transition from exponential to stationary growth phase, GacA significantly influenced transcript levels of 632 genes, representing more than 10% of the 6147 annotated genes in the Pf-5 genome.  Transcripts of genes involved in the production of hydrogen cyanide, the antibiotic pyoluteorin, and the extracellular protease AprA were at a low level in the gacA mutant, whereas those functioning in siderophore production and other aspects of iron homeostasis were significantly higher in the gacA mutant than in wild-type Pf-5.  Notable effects of gacA inactivation were also observed in the transcription of genes encoding components of a type VI secretion system and cytochrome C oxidase subunits.  Two novel gene clusters expressed under the control of gacA were identified from transcriptome analysis, and we propose global-regulator-based genome mining as an approach to decipher the secondary metabolome of Pseudomonas spp.

overall_design: In this series two conditions have been analyzed.  A gacA mutant of Pseudomonas fluorescens Pf-5 was harvested at early (OD 0.5) and late (OD 2.4) time points and compared to wild-type Pf-5 harvested in parallel.  For each slide, an experimental RNA sample from a gacA mutant was labeled with Cy3 or Cy5 and was hybridized with a reference RNA sample from wild-type Pf-5 labeled with the other Cy dye. There are six slides per condition.  Each condition is represented by three biological replicates. There are two flip-dye replicates for each biological replicate. Each slide contains three replicate spots per gene.

first: Karl

last: Hassan

first: Brenda

last: Shaffer

first: Daniel

middle: A

last: Johnson

first: Katherine

last: Phillippy

first: Joyce

last: Loper


title: Integrative ‘omic’ approaches identify a Ras/PI3K signature sustaining addiction to the MET oncogene

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary: Tumor onset and progression require the accumulation of many genetic and epigenetic lesions. Yet, there are cases in which cancer cells rely on only one of these lesions to maintain their malignant properties, and this dependency results in tumor regression upon oncogene inactivation (‘oncogene addiction’). Determining which nodes of the many networks operative in the transformed phenotype specifically mediate this drastic response to oncogene neutralization is crucial to identify the vulnerabilities of cancer. We combined multiplex phosphoproteomics, genome-wide expression profiling, and functional assays in a variety of cancer cells addicted to tyrosine kinase receptor oncogenes, using the Met receptor as the major model system. Unexpectedly, we found that Met blockade impacts on a limited subset of Met downstream signals: little or no effect was observed for many relevant pathways controlling Met-driven neoplastic growth – such as STATs, NF-kB, JNK, and p38 MAPK – and only a restricted and pathway-specific signature of Ras/PI3K transducers and transcriptional effectors was fully neutralized. An analogous signature was also generated by EGF receptor inhibition in a different cellular context, suggesting a stereotyped response that likely does not depend on receptor type or tissue origin. Biologically, cell-cycle arrest induced by Met de-activation was recapitulated by extinction of Ras/PI3K-dependent signals and was rescued by active forms of the same signals. These findings uncover ‘dominant’ and ‘recessive’ nodes among the numerous oncogenic networks regulated by tyrosine kinase receptors and active in cancer, with the Ras/PI3K pathways being the necessary and sufficient determinants of therapeutic response.

overall_design:
21 samples, of which: (i) Nine samples: biological triplicates of DiFi cells (sensitive to EGFR inhibition) in three different experimental conditions: DMSO-treated (reference), PHA-665752-treated (control, MET inhibition), and Gefitinib-treated (EGFR inhibition). (ii) Twelve samples: biological triplicates of GTL-16 cells (sensitive to MET inhibition) in four different experimental conditions: DMSO-treated (reference), Gefitinib-treated (control, EGFR inhibition), PHA-665752-treated (MET inhibition) and Doxycyclin-treated (MET shRNA induction).

The supplementary file 'GSE19043_non-normalized.txt' contains non-normalized data for Samples GSM471284-GSM471304.

first: Livio

last: Trusolino

first: Andrea

last: Bertotti


title: Functional interaction of chromatin with nucleoporins in Drosophila

city: Amsterdam

first: Maarten

last: Fornerod

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by array

summary: Nuclear pore complexes (NPCs) mediate transport across the nuclear envelope. In yeast, they have also been proposed to interact with active genes, attracting or retaining them at the nuclear periphery. However, some NPC components (nucleoporins) in higher eukaryotes are also found in the nucleoplasm, with so far unknown function. Therefore, we have functionally distinguished between nucleoporin-chromatin interactions at the NPC and within the nucleoplasm in Drosophila. For this we analyzed genomic interactions of full-length nucleoporins Nup98, Nup50 and Nup62 and nucleoplasmic and NPC-tethered forms of Nup98. We found that nucleoporins predominantly interacted with transcriptionally active genes inside the nucleoplasm. A smaller set of non-active genes interacted with the NPC. We identified a direct role for nucleoplasmic Nup98 in stimulating gene expression, as genes downregulated upon Nup98 depletion were activated upon nucleoplasmic Nup98 overexpression and showed strong nucleoplasmic Nup98 interaction. Thus, nucleoporins stimulate gene expression away from the NPC by interacting with genes inside the nucleoplasm.

overall_design: Chromatin nucleoporin (nup) interactions were mapped using DamID. Three full length nups were tested, Nup62, Nup98 and Nup50 on cDNA resolution (GSM478015, GSM478289, GSM478290, GSM478291). Replicate microarrays were used including dye swaps. Nups are located at the nuclear pore complex (NPC) and inside the nucleoplasm. To discriminate between these localizations, two mutants were made: nucleoplasmic Nup98 and NPC-tethered Nup98 (GSM479750, GSM479755). Together with full length Nup98 (GSM479749), Nup50 (GSM479753) and NDC1 (GSM479756), these were mapped on high resolution arrays. Replicate arrays were used including dye swaps. To functionally test the interactions, Nup98 (GSM478903) and Nup50 (GSM478904) were depleted using RNAi and nucleoplasmic Nup98 was overexpressed (GSM478905) and changes in mRNA expression were recorded on oligonucleotide arrays representing the transcribed genome. Replicate experiments were performed including dye swaps. To further investigate Nup/chromatin interactions, the response in chromatin interaction (tested with DamID) was recorded upon ecdysone traetment (GSM478910, GSM478911) or nucleoporin depletion (GSM478906, GSM478907, GSM478908, GSM478909). Replicate experiments were performed including dye swaps. To compare Nup/chromatin interaction with Lamin/chromatin interaction, Lamin/chromatin interaction was recorded using DamID on high resolution on chromosome 2L. Two experiments were performed and hybridized in a dye swap (GSM479757).

first: Bernike

last: Kalverda

first: Helen

last: Pickersgill


title: rice whole transcriptome surveyed by high throughput sequencing technology

city: Shenzhen

first: Guangwu

last: Guo

state: Guangdong Province

address: Main Building,Beishan Industrial Zone, Yantian District

department: Bioinformatics center

country: China

institute: Beijing Genomics Institute at Shenzhen

summary: Transcriptome analysis is an important approach to associate genotype with phenotype. The content and dynamics of eukaryotic transcriptome are far more complex than previously anticipated. Here we integrated high-throughput RNA-seq and paired-end method to conduct an unprecedentedly deep survey of transcription profile for cultivated rice, one of the oldest domesticated crops species and has since spread worldwide to become one of the major staple foods. Analysis of reads mapping revealed 4,244 previously uncharacterized transcripts, including a mass of protein-coding genes and putative functional non-coding RNA genes. Alignment of junction reads indicated over 42% of rice multiple-exon genes produce two or more distinct splicing isoforms. It’s intriguing that we identified 1,356 putative gene fusion events, indicating the 234 fusion gene produced by trans-splicing vastly increases the complexity of rice transcriptome, together with the pervasive alternative splicing events. Digital gene expression profiling revealed most rice duplicate genes were maintained by the selection constraint on gene dosages, which would increase the genetic robustness of rice to counteract deleterious mutations

overall_design: 3' SAGE tags of two rice tissues , booting panicle and callus , were sequenced.

first: Guojie

last: Zhang

first: Xueda

last: Hu

first: Qiye

last: Li

first: RuHong

last: Zhuang

first: Wei

last: Tian

first: Quanfei

last: Huang

first: Zengquan

last: He

first: Yong

last: Tao


title: DNMT3B targets in RKO cells by ChIP-on-chip

city: Columbus

first: Samson

middle: T.

last: Jacob

state: OH

address: 420 W. 12th Ave

institute: Ohio State University

summary: Chromatin immunoprecipitation with DNMT3B specific antibody followed by CGI microarray identified genes with or without CGIs, repeat elements and genomic contigs in RKO cells.  ChIP-Chop analysis showed that majority of the target genes including P16, DCC, DISC1, SLIT1, CAVEOLIN1, TBX5, TBX18, HOXB13 and some histone variants, that harbor CGI in their promoters, were methylated in multiple colon cancer cell lines but not in normal colon epithelial cells. Further, these genes were reactivated in RKO cells after treatment with 5-aza-2’-deoxycytidine, a DNA hypomethylating agent. COBRA and bisulfite genomic sequencing showed that the CGIs encompassing the transcription start sites (TSS) of DCC, TBX5, TBX18, SLIT1 were also methylated in primary colorectal tumors compared to matching normal tissues whereas GNA11 was methylated in both. MassARRAY analysis demonstrated that the CGI located ~4.5 kb upstream of HOXB13 +1 site was tumor-specifically hypermethylated in primary colorectal cancers and cancer cell lines. Analysis of tumor suppressor properties of two aberrantly methylated transcription factors, HOXB13 and TBX18, revealed that both inhibited growth and clonogenic survival of colon cancer cells in vitro, but only HOXB13 abolished tumor growth in nude mice.

overall_design: Chromatin immunoprecipitation with DNMT3B specific antibody in RKO cells was compared to control antibody.

first: Kalpana

last: Ghoshal

first: Tasneem

last: Motiwala

first: Pearlly

last: Yan

first: Tim


title: Biallelic and complicated inactivation of Pten in radiation-induced mouse thymic lymphomas

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

institute: National Institute of Radiological Sciences

summary: Inactivation of Pten occurs by multiple mechanisms including epigenetic silencing, point mutations, insertion, and deletion, which are tissue dependent. Although frequent loss of heterozygosity around Pten locus and plausible involvement of epigenetic silencing have been reported in radiation-induced thymic lymphomas, the frequency of Pten inactivation and the spectrum of causal aberrations have not yet been extensively characterized. Here, we assessed the principal mode of inactivation by comprehensively analyzing expression and alterations of Pten gene in 23 radiation-induced thymic lymphomas developed in B6C3F1 mice. We found no evidence for methylation-associated silencing of Pten gene. Instead, we found complex structural abnormalities in 8 lymphomas (35%) that included missense and nonsense mutations, 1- and 3-bp insertions, and focal deletions. Sequencing of deletion breakpoints suggested that illegitimate V(D)J recombination and microhomology-mediated rearrangement were responsible for the focal deletions. Seven out of these 8 lymphomas had biallelic alterations, and 4 of them did not express any Pten protein. These aberrations of Pten were well coincided with downstream Akt phosphorylation on Ser473. In conclusion, Pten inactivation, which is frequently biallelic and is caused by a variety of structural abnormalities but not by epigenetic silencing, is involved in radiation-induced lymphomagenesis.

overall_design: Three thymic lymphomas were analyzed by array-CGH method.

first: Yu

last: Yamaguchi

first: Shizuko

last: Kakinuma

first: Yoshiko

last: Amasaki

first: Mayumi

last: Nishimura

first: Tatsuhiko

last: Imaoka

first: Kazumi

last: Yamauchi

first: Yi

last: Shang

first: Tomoko

last: Miyoshi-Imamura

first: Hiroyuki

last: Nogawa

first: Yoshiro

last: Kobayashi

first: Yoshiya

last: Shimada


title: Oligonucleoteide microarray for the identification of potential mycotoxigenic fungi

city: Pretoria

first: Eugenia

last: Barros

state: Gauteng

address: Meiring Naude Rd

department: Building 20

country: South Africa

institute: CSIR

type:
Expression profiling by array
Other

summary:
Mycotoxins are secondary metabolites which are produced by numerous fungi and pose a continuous challenge to the safety and quality of food commodities in South Africa. These toxins have toxicologically relevant effects on humans and animals that eat contaminated foods. In this study, a diagnostic DNA microarray was developed for the identification of the most common food-borne fungi, as well as the genes leading to toxin production. A total of 40 potentially mycotoxigenic fungi isolated from different food commodities, as well as the genes that are involved in the mycotoxin synthetic pathways, were analyzed. For fungal identification, oligonucleotide probes were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 alpha) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotide probes directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. The probes selected for fungal identification and the probes specific for toxin producing genes were spotted onto microarray slides. The diagnostic microarray developed can be used to identify single pure strains or cultures of potentially mycotoxigenic fungi as well as genes leading to toxin production in both laboratory samples and maize-derived foods offering an interesting potential for microbiological laboratories.

Keywords: Development of a diagnostic microarray for the identification of potentially mycotoxigenic fungi as well as genes leading to toxin production, 40 food-borne fungi, mycotoxins

sample_organism:
Aspergillus amstelodami
Aspergillus clavatus
Aspergillus niger
Aspergillus parasiticus
Claviceps purpurea
Fusarium sambucinum
Curvularia lunata
Fusarium oxysporum
Fusarium sporotrichioides
Fusarium acuminatum
Fusarium graminearum
Alternaria alternata
Penicillium expansum
Talaromyces funiculosus
Talaromyces islandicus
Fusarium sp.
Fusarium avenaceum
Penicillium italicum
Aspergillus carbonarius
Aspergillus multicolor
Fusarium subglutinans
Bipolaris sorokiniana
Aspergillus versicolor
Fusarium anthophilum
Fusarium cerealis
Fusarium decemcellulare
Penicillium viridicatum
Fusarium equiseti
Drechslera sp.
Penicillium fellutanum
Penicillium corylophilum
Fusarium globosum
Fusarium verticillioides
Talaromyces rugulosus
Fusarium solani
Aspergillus chevalieri
Stenocarpella maydis
Fusarium incarnatum
Pseudopithomyces chartarum

platform_organism:
Aspergillus
Aspergillus amstelodami
Aspergillus clavatus
Aspergillus niger
Penicillium
Fusarium
Fusarium oxysporum
Fusarium sporotrichioides
Fusarium acuminatum
Fusarium graminearum
Alternaria alternata
Penicillium expansum
Talaromyces islandicus
Fusarium avenaceum
Aspergillus carbonarius
Fusarium subglutinans
Aspergillus versicolor
Fusarium cerealis
Fusarium equiseti
Penicillium fellutanum
Penicillium corylophilum
Fusarium verticillioides

overall_design: Development of a diagnostic array for the identification of food-borne fungi and their potential mycotoxin-producing genes. Oligonucleotide probes to be printed onto the array were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 α) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotides directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. Analysis was performed with 40 fungal cultures were obtained from the Agricultural Research Council culture collection (ARC), Pretoria, South Africa.an in-house spotted oligonucleotide microarray. The identity of each fungus was confirmed by standard laboratory procedures.  For DNA isolation, the fungal strains were grown on 1.5% malt extract agar at 25°C for 1-2 weeks and total genomic fungal DNA was extracted following the DNA extraction protocol described by Raeder and Broda (1985). The internal transcribed spacer oligonucleotides ITS1, ITS3 and ITS4 were used as a reference for normalization of all spot intensity data.Samples were fluorescently labelled with Cy5 dye by using a Cy™Dye Post-labelling Reactive Dye Pack and wre hybridized to the oligonucleotide microarray overnight. Two biological and one technical replicate (using independent labelling reactions) was performed, each replication consisting of a reverse labelling experiment.

first: Sabine

last: Lezar


title: Biogeography of the human colorectum

city: St Lucia

first: Daniel

last: Aguirre de Carcer

state: QLD

address: 306 Carmody Rd

department: Livestock Industries

institute: CSIRO

summary: We applied numerical ecology methods to data produced with a human intestinal tract-specific phylogenetic microarray (the Aus-HIT Chip) to examine the biogeography of mucosa-associated bacteria along the human colon. The microbial DNA associated with matched biopsy tissue samples taken from the cecum, transverse colon, sigmoid colon and rectum of 10 healthy patients was examined. Consistent with previous studies, the profiles revealed a marked inter-subject variability; however, the numerical ecology methods of analysis allowed the subtraction of the subject effect from the data and revealed, for the first time, evidence of a longitudinal gradient for specific microbes along the colorectum: with Streptococcus, Comamonadaceae, Enterococcus and Lactobacillus in greatest abundance at the cecum, with a gradual decline in their relative abundance through to the rectum. Conversely, the analyses suggest that members of the Enterobacteriaceae increase in relative abundance towards the rectum. These differences were validated by quantitative PCR. We were also able to identify significant differences in the profiles, especially for the Streptococci, on the basis of gender. The results derived by these multivariate analyses are biologically intuitive, and suggestive that the biogeography of the colonic mucosa can be monitored for changes via cross-sectional and/or inception cohort studies.

sample_organism: Bacteria Archaea

overall_design: 10 patients, 5 males and 5 females. Four different locations along the colorectum.


title: Novel genes in Sitka spruce associated with wood density identified from global transcriptomic analysis

city: Southampton

first: Patrick

last: Stephenson

address: Bassett Crescent East

department: School of Biological Sciences

institute: University of Southampton

summary: The current study uses a transcriptomic approach to identify genes associated with differences in wood density, that are likely to be of value as candidate genes in Sitka breeding programmes for improved wood density. Following extensive wood density analysis from a Sitka spruce (Picea sitchensis (Bong) Carr.) field grown clonal trial, three detailed microarray studies were conducted to compare the transcriptome of cambial tissue from contrasting clonal lines with high and low wood density. Twenty five genes exhibited differential expression, reaching as high as 50 fold, in at least two of the three microarray experiments and this was verified using real-time PCR. Identified genes functioned in cell wall synthesis, transcriptional regulation and plant pathogen defence, amongst others. These results confirm the importance of previously-identified density-related genes, and highlight a number of novel genes with a putative role in wood quality. A wide range of processes influence wood density, but this study has allowed the identification of potential regulators in these pathways. Future studies may now use this information to understand the control of natural variation in wood density, and manipulate the expression of these genes to improve timber quality.

overall_design:
The Sitka spruce (Picea sitchensis (Bong) Carr.) ‘Experiment 35’ clonal trial was grown at Newcastleton, Scotland (OS grid reference: NY506881, latitude: 55.1847, longitude: -2.77892) and set up by Forest Research, an agency of the Forestry Commission, which has been described previously (Mboyi and Lee 1999). A total of 750 trees were established from cuttings taken in 1989 of genotypes belonging to 6 unrelated full-sib families with 8 genotypes per family and 15 replicate ramets per genotype.
Cambial cell scrapes were taken in summer 2004 when trees were 15 years old. A 5x2cm section of bark was cut away at a height of 1.3m from the ground for each tree selected for microarray analysis. The exposed xylem was immediately excised using a clean sharp razor blade and snap frozen in liquid Nitrogen. Samples were transported to the laboratory and ground in liquid nitrogen using a chilled mortar and pestle and stored at -80oC prior to RNA extraction.
RNA was extracted and microarray hybridisation performed as described within.

first: Nicole

last: Harris

first: Joan

last: Cottrell

first: Steven

last: Ralph

first: Joerg

last: Bohlmann

first: Gail

last: Taylor


title: Expression data of Vibrio fischeri in response to nitric oxide (NO)

city: Madison

first: Yanling

last: Wang

state: WI

address: 1550 Linden Drive

department: Medical Microbiology and Immunology

institute: University of Wisconsin-Madison

summary: The bioluminescent bacterium Vibrio fischeri initiates a specific, persistent symbiosis in the light organ of the squid Euprymna scolopes. During the early stages of colonization, V. fischeri is exposed to host-derived nitric oxide (NO). While NO can be both an antimicrobial component of innate immunity and a common signaling molecule of eukaryotes, its roles in beneficial host-microbe associations remain undescribed.             V. fischeri encodes HnoX, a member of a family of bacterial NO-binding proteins of unknown function. We hypothesized that HnoX acts as a NO sensor that is involved in regulating symbiosis-related genes during initiation of symbiosis. With an aim to discover the genes whose regulations respond to NO signal, and in an HnoX-mediated fashion in particular, we carried out a whole-genome expression study on the wild-type and an insertional mutant of hnoX.

overall_design: The wild-type parent and an insertional mutant (hnoX-) of the hnoX gene were grown to early log phase in a minimal-salts medium. One half of each culture was treated with 80µM of the NO-generator, DEA-NONOate, and the other half was left untreated as a control. After 30 min, cells from all the cultures were fixed with RNAprotect Bacteria Reagent. Total RNA was isolated, labeled and hybridized to the Custom Vibrio fischeri GeneChip Array (Affymetrix). Three independent experiments were performed on separate days for statistical analysis.

first: Yann

last: Dufour


title: Aquafirst_seabream_pathogen exposure_head kidney

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

country: Ireland

institute: NUI Galway

summary:
To determine the effects of pathogen exposure to Enteromyxum leei on head kidney gene expression.

Keywords: confinement, cortisol, stress response, time course, microarray

overall_design: 30 head kidney samples - Thirty slides were hybridised using a reference design. Three groups (control, infected and non-infected) were compared using five individual fish in each group. Each sample was hybridised twice - the second being a dye-swap of the first.

first: MichaelT

first: Grace

last: Davey

first: Josep

last: Calduch-Giner

first: Jaume

last: Pérez-Sanchez

first: Benoit

last: Houeix

first: Anita

last: Talbot

first: Richard

last: Reinhardt


title: Exon arrays for human embryonic stem cells

city: Turku

first: Elisa

middle: Maarit

last: Närvä

address: Tykistönkatu 6

department: Turku Centre for Biotechnology

institute: University of Turku

summary:
Samples were used to study if genomic copy number variation changes detected with SNP 6.0 array would correlate with the expression level changes in human embryonic stem cells
These samples were used as a portion of the study evaluating the genomic stability and its effects on human embryonic stem cells in prolonged culture.

overall_design: Selected nine human embryonic stem cell samples from different lines having different kind of genomic abnormalities were hybridized to exon arrays.

first: Reija

last: Autio

first: Nelly

last: Rahkonen

first: Neil

last: Harrison

first: Timo

last: Otonkoski

last: Tuuri

first: Harry

middle: D

last: Moore

first: Peter

last: Andrews

first: Olli

last: Yli-Harja

first: Riitta

last: Lahesmaa


title: Identifying the genes involved in CD4+ T cell mediated-acute allograft rejection

city: Jinan

first: guihua

last: hou

state: Shandong

address: 44 wenhua west road

department: Experimental nulclear medicine

institute: School of medicine Shandong university

summary: Acute allograft rejection is a leading cause for the failure of organ allotransplantation. Identifying the genes involved in the rejection process provides clues to study the mechanisms, and to provide specific gene targets for monitoring, predicting and preventing acute allograft rejection. Using a mice model of skin acute allograft rejection and SAGE method, we analyzed gene expression in the CD4+ T cells of the mice, the cell type known to play critical roles in acute allograft rejection. Our study identifies 402 SAGE tags significantly different from these from the control. From these SAGE tags, we identified 91 increasingly and 85 decreasingly expressed genes, and many genes have not been linked with acute allograft rejection before. Functional classification of these genes shows that apoptosis, transcription regulation, cell growth and maintenance and signal transduction are among the most frequently changed functional groups. Our study provides a genome-wide view for the genes involving acute allograft rejection in the CD4+ T cells, and indicates that acute allograft rejection involves multiple genes in different functional categories. The genes identified from the study provide candidates for further studying the mechanisms and for monitoring, predicting and preventing acute allograft rejection.

overall_design:
Female mice of 6-10 week age were used for the study. BALB/c mice (H-2d) and BALB/c severe combined immunodeficient (SCID) mice were from the animal facility of Shandong University (Jinan, China). C57BL/6 (H-2b, B6) were from Vitalriveri Co. ltd (Beijing, China). Mice were maintained in a pathogen-free animal environment during the experimental process. The use of mice for the study was approved by the Institutional Animal Experimental Committee, and animal care and surgical procedures were performed in compliance with the standard animal experimental protocols of Shandong University School of Medicine. The process of generating skin acute allograft rejection followed the established procedure (12). Briefly, dorsal skin of C57BL/6 was transplanted onto the dorsal thorax of BALB/c SCID mice under sterile condition (allotransplant). As a control, dorsal skin of BALB/c mice was transplanted to BALB/c SCID mice (autotransplant). After 28 days of transplantation, CD4+ T cells were harvested from the spleens of BALB/c mice by using the mouse CD4+ T cells enrichment columns (R&D) with the purity >90% as measured by flow cytometry and 8x106 purified CD4+ T cells were adoptively injected into each transplanted mice via the lateral tail vein. The skin graft in each transplanted mice was then monitored daily. The skin graft was considered to fully reject when more than 50% of the skin became necrosis.
SAGE Analysis
Upon 14 days post CD4+ T cell transferring, CD4+ T cells were collected from the spleens of five mice in each group with adaptive CD4 T cell transferring using the same process described above. Total RNA was extracted from the purified cells by using Trizol reagent (Invitrogen) and mRNA was purified from the total RNA using oligo dT beads (Invitrogen). cDNA was synthesized by using MMLV reverse transcriptase and oligo(dT) primers (MBI-add full name). SAGE libraries from 4 allotransplant and autotransplant groups were constructed following the standard procedure (13). For each SAGE library, 1,200 sequences were collected through an ABI 3730 DNA sequencer (Applied BioSystems). SAGE tags were extracted from the sequences by using the SAGE2000 software (Invitrogen).

first: Jia

last: Xu

first: Dan

last: Wang

first: Chao

last: Zhang

first: Jing

last: Song

first: Ting

last: Liang

first: Yeong

last: Kim

first: Wei

middle: R

last: Jin

first: San

first: Gui

last: Hou


title: Global identification of transcription start sites in the genome of Apis mellifera by using 5’ LongSAGE

status: Public on Feb 28 2010

city: Shanghai

first: Huajun

last: Zheng

address: No.250, Bibo Road

department: Genomic Sequencing Department

institute: Chinese National Human Genome Center at Shanghai

summary: The 5’ LongSAGE (5’LS) approach provides a powerful genomic tool for identifying Transcription start sites (TSSs) in sequenced genome. The main purpose of this study is to identify the actual TSSs of expressed genes as well as the usage of different TSSs in Apis mellifera. We also wish to provide expression evidence for the in silico predicted genes and reveal some previously undiscovered genes.

overall_design: The transcriptome of adult drone head was fathomed through 5’LS analysis, and TSSs of the expressed genes were determined by mapping the 5’LS tag sequences to the honeybee genome sequences.

first: Liangxian

last: Sun

first: Wenjun

last: peng

first: Yan

last: Shen

first: Yuezhu

first: Baohua

first: Wenyi

last: Gu

first: Shengyue


title: Transcriptome changes in Emericella nidulans due to oxidative stress - normalized experimental data (flip-flop)

city: Debrecen

first: Istvan

last: Pocsi

address: Egyetem tér 1.

department: Dept.of Microbiology and Biotechnology

country: Hungary

institute: University of Debrecen

summary:
We examined the transcriptional changes observable under oxidative stress caused by menadione in Emericella nidulans.
Keywords: time-course

overall_design: Late exponential growth phase (18 h) Emericella nidulans mycelia were transferred to minimal media also supplemented with 0.8 mM menadione (sodium bisulfite addition compound) and transcriptome profiles were recorded at 6 h incubation time. Double printed EST-based (3533 unique sequences) DNA chips were used to monitor changes in cDNA populations prepared from mRNA pools isolated from oxidative stress exposed and untreated control cultures. Gene expression ratios were estimated according to the protocol adapted from Biotechniques 29(3) Sept 2000, 548-562. Expression data were read with a GenePix 4000B microarray scanner (Axon Instruments). Intensity ratios were calculated with GenePix Pro 3.0 software. Gene expression ratios were subjected to LOESS-type block-by-block normalization using SAS for Windows, version 8. (SAS Institute Inc., Cary, NC, USA.) software.

first: Marton

last: Miskei

first: Zsolt

last: Karanyi

first: Tamas

last: Emri

first: Patricia

last: Ayoubi

first: Tunde

last: Pusztahelyi

first: Gyorgy

last: Balla

first: Rolf

last: Prade


title: Temporal development of necrotizing enterocolitis in the preterm pig

city: Frederiksberg

first: Jayda

last: Siggers

state: C

address: Roligehdsvej 30

department: Human Nutrition

country: Denmark

institute: University of Copenhagen

summary:
Necrotizing enterocolitis (NEC), a serious gastrointestinal disease that afflicts 5-10% of preterm infants, often progresses rapidly from mild food intolerance into extensive haemorrhage, inflammation and necrosis. Events leading to NEC have remained poorly defined. Similar disease characteristics are observed in preterm pigs 24-48 h after feeding formula. Using this model, we aimed to characterize the temporal development of NEC, and describe the functional and immunological response of the preterm intestine preceding NEC.

Keywords: time course

overall_design: Pigs from treatment groups TPN (n=5), and 8 h (n=5) and 24 h (n=5-6) FORM and COLOS were randomly selected for microarray analysis. Equal amounts of total distal small intestinal RNA from all pigs was pooled to make the reference sample. Samples and reference pool were labelled with Oyster 550 and 650, respectively. The in-house spotted porcine oligonucleotide microarray version 4 (POM4) is a low density microarray consisting of 384 different oligonucleotide probes representing more than 200 different immune related genes and eight different array control oligonucleotides (ArrayControl; Ambion, Nærum, Denmark). The immunologically relevant 60-70mer oligonucleotide probes represent interferons and interleukins (and receptors), chemokines (and receptors), acute phase proteins, apoptosis-related factors and sequences with relevance to Toll-like receptors and their intracellular signalling pathways.

first: Mette

last: Boye

first: Per

last: Sangild

first: Kerstin

last: Skovgaard

first: Richard


title: Is Increased Sinusoidal Flow in the Liver Remnant the primary Stimulus to Regeneration after partial Hepatectomy

city: Aarhus

first: Lene

middle: Nagstrup

last: Conley

state: Denmark

address: Langelandsgade 140

department: Department of Chemistry

institute: University of Aarhus

summary:
The impact of portal arterialization on the liver parenchyma was studied in a series of six pigs with aortoportal shunting of liver segments II, III and IV (and 6 sham animals). Gene expression in the arterialized segments was compared to expression in sham animals. Primary endpoints were gene expression profiles in the hyperperfused segments at sampling time points 1, 5, 10, 30, 60, 90 minutes and 2, 3, 4 and 6 hours after shunt opening.

Keywords: time course, treatment comparison

overall_design: Six pigs were treated with aortoportal shunting of segments II, III and IV and six animals were subject to sham surgery.  Expression profiling was conducted by hybridizing each sample against a common reference, consisting of liver RNA from an unrelated animal..

first: Kim

last: Mortensen

middle: N

first: Ingvild

last: Nygaard

first: Peter

last: Sørensen

first: E

first: Christian

last: Bendixen

first: Arthur

last: Revhaug


title: Expression array for Trichoderma atroviride in mycoparasitic interaction with Rhizoctonia solani

status: Public on Feb 25 2010

city: Salamanca

first: Enrique

last: Monte

state: Salamanca

address: Rio Duero

department: Spanish-Portuguese Centre for Agricultural Research

country: Spain

institute: University of Salamanca

summary:
A self-designed Trichoderma high density oligonuclotide (HDO) microarray  (Roche-NimbleGen, Inc., Madison, WI, USA) was constructed in a similar way  than a previous Trichoderma HDO microarray (Samolski et al., 2009). The  microarray was composed of 392,779 60-mer probes designed against 13,443  EST-derived transcripts (Trichochip-1) and the genomes of T. atroviride (11,100 genes) and T.  virens (11,643 genes). The Trichochip-1 ESTs were obtained from 28 cDNA libraries from eight different species (representing the biodiversity of this genus: T. harzianum, T. atroviride, T. asperellum, T. viride, T. longibrachiatum, T. virens, T. stromaticum and T. aggresivum)  under a wide range of growth conditions, including biocontrol-related conditions and different nutritional situations (Vizcaíno et al., 2006).
The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032)

sample_organism:
Trichoderma atroviride
Rhizoctonia solani

platform_organism:
Trichoderma virens
Trichoderma atroviride

overall_design: T. atroviride P1 mycelium grown (approximately for 24h) at 25ºC on a cellophane sheet on PDA (Difco) plates before contact (at a distance of 5 mm) a R. solani colony grown under identical conditions in the same plate was compared with T. atroviride P1 mycelium after contact (5 mm) the above R. solani colony (mycoparasitic interaction). RNAs from both conditions were extracted and the corresponding cDNAs were use to hybridize by triplicate the Trichoderma HDO microarray.

first: Rosa

last: Hermosa

first: Fran

last: González


title: Ash1 ChIP-chip data from murine Embyonic Stem cells

city: Cambridge

first: Mike

last: Kagey

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute

summary: Ash1 is a Trithorax Group (TrxG) protein with histone methyl transferase activity that  is associated with gene activation.  Here we use ChIP-chip to determine the occupancy of Ash1 at promoters in murine embryonic stem cells.

overall_design: This dataset includes singlet ChIP-chip data targeting Ash1 in murine Embryonic stem cells.


title: Daoy gene expression

city: san antonio

first: raquel

last: abreu

address: 8403 Floyd Curl Drive

institute: CCRI

summary: Using measurements of absolute protein and mRNA concentrations in cellular lysate from a Daoy medulloblastoma cell line, we quantitatively evaluate the influence of absolute transcript levels and a large number of sequence-encoded regulatory elements on steady-state human protein expression levels.

overall_design: mRNA profiling: We prepared two biological replicates, each one was used in a 4-plex format array.

first: Suzanne

last: Burns

first: Raquel

last: Abreu

first: Daijin

last: Ko

first: Luiz

last: Penalva


title: Analysis of DNA strand-specific differential expression with high density tiling microarrays

status: Public on Feb 23 2010

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

institute: Instituto de Biología Funcional y Genómica (IBFG)

type: Expression profiling by genome tiling array

summary:
DNA microarray technology allows the analysis of genome structure and dynamics at genome-wide scale. Expression microarrays (EMA) contain probes for annotated open reading frames (ORF) and are widely used for the analysis of differential gene expression. By contrast, tiling microarrays (TMA) have a much higher probe density and provide unbiased genome-wide coverage. The purpose of this study was to develop a protocol that would take advantage of the high resolution of TMAs for quantitative measurement of DNA strand-specific differential expression of annotated and non-annotated transcripts.
We extensively filtered probes present in Affymetrix Genechip Yeast Genome 2.0 expression and GeneChip S. pombe 1.0FR tiling microarrays to generate custom Chip Description Files (CDF) in order to compare the efficiency of both platforms. We experimentally tested the potential of our approach by measuring the differential expression of 4904 genes in the yeast Schizosaccharomyces pombe growing under conditions of oxidative stress. The results afforded a Pearson correlation coefficient of 0.943, indicating that TMAs are as reliable as EMAs for quantitative expression analysis. A significant advantage of TMAs over EMAs is the possibility of detecting non-annotated transcripts generated only under specific physiological conditions. We combined this property with a target-labelling protocol that preserves the original polarity of the transcripts with a view to determining the differential expression of non-annotated transcriptionally active regions.

overall_design: We have generated custom Chip Description Files (CDF) from Affymetrix Genechip Yeast Genome 2.0 expression and GeneChip S. pombe 1.0FR tiling microarrays to compare the efficiency of both platforms. We have experimentally tested the potential of our approach by measuring differential expression of the yeast Schizosaccharomyces pombe growing under conditions of oxidative stress.

first: Mar

last: Sánchez

first: Francisco

last: Antequera