title: Gene expression after focal demyelination of the corpus callosum

status: Public on Apr 13 2010

city: Washington

first: Vittorio

last: Gallo

state: DC

address: 111 Michigan Av. NW

department: Center for Neuroscience

institute: CNMC

summary: To determine expression profiles of cytokines and growth factor profiles in the subventricular zone (SVZ) after demyelination we performed gene array analysis. In SVZ after 4 days post lesin (dpl) LPC-injected tissue, demonstrated regulation of BMP pathway elements, including increased chordin, noggin, and ChorR, and decreased BMP4, compared to NaCl-injected tissue.

overall_design: GEArrayTM expression array systems (cat#OMM031 SuperArray, Bethesda, MD) consisted of spotted cDNA fragments encoding 113 mouse genes for neurotrophic signaling molecules involved in neuronal growth and differentiation, as well as regeneration and survival. Control sequences (PUC18, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), peptidylpropyl isomerase A (Ppia), and β-actin) were also included. These microarrays were employed to compare SVZ gene expression 4 days after NaCl or LPC injection in corpus callosum. Total RNA was isolated by Trizol (Invitrogen) and processed for microarray hybridization following the manufacturer’s instructions. Arrays were visualized by autoradiography, and hybridization signals were scanned and analyzed for density in GEArray Expression Analysis Suite 2.0. The normalized value for each gene was calculated by dividing the value of each gene by the average value of the housekeeping genes GAPDH, Ppia, and β-actin.

first: Beata

last: Jablonska

first: Adan

last: Aguirre

first: Matthew

last: Raymond

first: Gabor

last: Szabo

first: Yasuji

last: Kitabatake

first: Kurt

last: Sailor

first: Guo-li

last: Ming

first: Hongjun

last: Song


title: Expression analysis of Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2

status: Public on Apr 15 2010

city: Boston

first: Michael

middle: J

last: Coyne

state: MA

address: 181 Longwood Avenue

department: Medicine

country: USA

institute: Brigham & Women's Hospital

summary:
Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 double mutant compared to the wild-type strain.
Keywords: expression analysis

overall_design: A six chip study using total RNA recovered from three separate wild-type cultures of Bacteroides fragilis NCTC 9343 and three separate cultures of a double mutant strain, Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2, in which ungD1 (BF1706) and ungD2 (BF2848) are deleted.  Each chip measures the expression level of 4,302 genes from Bacteroides fragilis NCTC 9343 and the associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Laurie

middle: E

last: Comstock

first: Maria

last: Chatzidaki-Livanis


title: Gene expression analysis of S. Typhimurium cells residing in the food vacuole (phagosome) of the bacteria grazing ciliate Tetrahymena

city: Albany

first: Marc

middle: Yi Ming

last: Rehfuss

state: CA

address: 800 Buchanan St

department: Produce Safety and Microbiology

institute: USDA

summary: The gene expression of Salmonella enterica Typhimurium MB282 residing in the food vacuole (phagosome) of Tetrahymena was analyzed by microarray.

overall_design: A minimum of three biological replicates were used. Each biological rep was comprised of at least two technical replicate arrays. MB282 incubated in H2O and MB282 grown to mid - log in LB were used as controls.

last: Brandl


title: Intracellular proliferation and virulence gene expression of Salmonella are influenced by pre-invasion growth conditions

status: Public on Apr 19 2010

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary:
Salmonella invasion of non-phagocytic cells is a dynamic process that requires the translocation of effector proteins into host cells by a type III secretion system (T3SS1) encoded on Salmonella pathogenicity island 1 (SPI1). The signals involved in T3SS1 induction in vivo are not known, but SPI1-induced invasive Salmonella can be prepared by growth in synthetic media. Here we compared two different methods of preparing SPI1-induced bacteria by using a combination of transcriptome analysis, a single-cell reporter assay and intracellular gene expression analysis to reveal clear differences between these two bacterial populations that are reflected in their ability to interact with cultured epithelial cells. Invasion efficiency and intracellular replication were greater for bacteria grown with aeration to late-log phase compared to those grown without aeration to stationary phase. No significant differences in SPI1 regulon expression were revealed by transcriptome analysis. By contrast, surface appendage and stress response genes were considerably changed. Single cell analyses of gene expression revealed variation in the frequency of SPI1-induced bacteria and a correlation between SPI1-induction and the presence of flagella. The expression of virulence genes following invasion of cultured epithelial cells was also found to be predetermined by pre-invasion growth conditions.

Key words: epithelial, flagella, invasion, motility, Salmonella-containing vacuole,

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: treatment of shaking versus treatment of static growth conditions for St-SL1344

first: J

middle: A

last: Ibarra

first: Leigh

last: Knodler

first: Daniel

first: Kimmo

last: Virtaneva

first: Aaron

middle: B

last: Carmody

first: Elizabeth

middle: R

last: Fischer

first: Steven

middle: F

last: Porcella

first: Olivia

last: Steele-Mortimer


title: Flux of transcript patterns during soybean seed development

status: Public on May 05 2010

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: Background: To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consisting of up to 27,000 soybean cDNAs. Results: It was discovered that genes related to cell growth and maintenance processes, as well as energy processes like photosynthesis, decreased in expression levels as the cotyledons approached the mature, dry stage. Genes involved with some storage proteins had their highest expression levels at the stage of largest fresh weight. However, genes encoding many transcription factors and DNA binding proteins showed higher expression levels in the desiccating and dry seeds than in most of the green stages. Conclusions: Data on 27,000 cDNAs have been obtained over five stages of soybean development, including the stages of major accumulation of agronomically-important products, using microarrays. Of particular interest are the genes found to peak in expression at the desiccating and dry seed stages, such as those annotated as transcription factors, which may indicate the preparation of pathways that will be needed later in the early stages of imbibition and germination.

overall_design: Five stages of development of soybean cotyledons were studied. The first three, with fresh weights of 25-50mg, 75-100mg, and 400-500mg, were green in color. The last two, yellow-colored cotyledons with a fresh weight of 200-300mg and dry whole seeds approximately 100-200mg in weight, were desiccating and yellow/brown in color. The green stage of 100-200mg fresh weight cotyledons was used as a reference for all other stages. Four replicates, including two dye swaps, were made of each of the first three (green) stages. Two replicates, including one dye swap, were made of each of the last two (yellow/dry) stages. The results from three different platforms (GPL229, GPL1012, and GPL1013) were combined.

first: Sarah

middle: I

last: Jones

first: Delkin

middle: O

last: Gonzalez


title: Loss of tight junction integrity induces loss of epithelial phenotype: case of Claudin11 knock out in testis.

status: Public on Apr 11 2010

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

summary:
Epithelium barrier integrity is assumed at least in part by the presence of junctions between cells. Tight-junction formation may be necessary for Sertoli cells to cease dividing and to support germ cell development. Microarray analysis of P20 Cldn11 +/- and Cldn11-/- testes confirmed the impact od Cldn11 deficiency on cell cytoskeleton and junction-related genes.

Keywords: transcriptomic analysis

overall_design: Two-condition experiment: P20 Cldn11 +/- vs. P20 Cldn11 -/- testes. A pool of RNA from P20 Cldn11 +/- group was used as the reference group. Each P20 Cldn11 -/-  was compared to reference group. Three biological replicates were processed in dye swap.

first: Severine

last: Mazaud-Guittot

first: Emmanuelle

last: Meugnier

first: Sandra

last: Pesenti

first: Brigitte

last: LeMagueresse-Battistoni


title: Adult T-cell leukemia-lymphoma and AZT-IFNa combination therapy

status: Public on Apr 12 2010

city: Stanford

first: Ash

last: Alizadeh

address: 269 Campus Drive, CCSR 1145c

department: Medicine, Divisions of Hematology and of Oncology

institute: Stanford University School of Medicine

summary: Adult T-cell leukemia-lymphoma (ATLL) is an HTLV-1-associated lymphoproliferative malignancy that is frequently fatal. We compared gene expression profiles (GEPs) of leukemic specimens from 9 patients with ATLL at the time of diagnosis and immediately after combination therapy with zidovudine (AZT) and interferon alpha (IFN). GEPs were also related to genetic aberrations determined by comparative genomic hybridization. We identified several genes anomalously over-expressed in the ATLL leukemic cells at the mRNA level, including LYN, CSPG2 and LMO2, with confirmation of LMO2 expression confirmed in ATLL cells at the protein level. In vivo AZT- and IFNa treatment evoked a marked induction of interferon-induced genes accompanied by repression of cell-cycles regulated genes including those encoding ribosomal proteins. Remarkably, patients not responding to IFNa/AZT differed most from responding patients in relative over expression of these same IFN-responsive genes, as well as components of the antigen processing and presentation apparatus.  Demonstration of specific gene expression signatures associated with response to AZT-IFNa therapy may provide novel insights into the mechanisms of action in ATLL.

first: Sean

last: Bohen


title: Quorum Sensing regulation in Brucella melitensis 16M

city: Namur

first: Jean-Jacques

last: Letesson

address: rue de Bruxelles, 61

department: URBM

country: Belgium

institute: University of Namur

summary:
Many pathogenic bacteria use a regulatory process termed Quorum Sensing (QS) to produce and detect small diffusible molecules to synchronize gene expression within a population. In Gram-negative bacteria, the detection and response to these molecules depend on transcriptional regulators belonging to the LuxR family. Such a system have been discovered in the intracellular pathogen Brucella melitensis, a Gram-negative bacteria responsible for brucellosis, a word-wide zoonosis remaining a serious public health concern in endemic countries. Two LuxR-type regulators, VjbR and BabR, have been identified in the genome of this pathogen. The vjbR mutant is highly attenuated in all tested models suggesting a crucial role of QS in the virulence of Brucella. This attenuation is at least due to the involvement of VjbR in the activation of the virB operon coding for a type four secretion system essential for Brucella to reach its intracellular replication compartment. At present, no function has been attributed to BabR. To assess the role of both Brucella QS-regulators, we performed in tandem comparative transcriptomic and proteomic analyses of vjbR and babR mutants. These experiments revealed that 10% of Brucella genome is regulated through those regulators, revealing that QS is a global regulatory system in this intracellular pathogen. The overlapping between BabR and VjbR targets suggest an unexpected cross-talk between these two regulators. Moreover, our results demonstrate that VjbR and BabR regulate many gene and/or proteins involved in stress response, metabolism and virulence. These targets are potentially involved in the adaptation of Brucella to the oxidative, pH and nutritional stresses encountered within the host. These findings highlight the involvement of QS in the virulence of Brucella and led us to suggest that this regulatory system could be implied in the spatial and sequential adaptation of Brucella to the host environment.
Keywords: Quorum Sensing, Comparative gene expression, Brucella melitensis

overall_design: Total RNA were extracted from wt, ∆vjbR and ∆babR, all cultured in triplicate. Triplicate samples of each strain were mixed and one chip was made per strain. Two pairwise comparisons were performed (∆vjbr-wt) and (∆babr-wt). For each comparison, the foldchange was computed as the ratio of intensity averages (mutant/wt).

first: Sophie

last: Uzureau

first: Julien

last: Lemaire

first: Anthoula

last: Gaigneaux

first: Xavier

last: De Bolle


title: Acute effects of different dietary fatty acids on the gene expression profiles of PBMCs of healthy young men

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Acute effects of different dietary fatty acids on the gene expression profiles of peripheral blood mononuclear cells in healthy young men. A randomized cross-over study.

Gene expression profiles of peripheral blood mononuclear cells (PBMCs) have been used to reflect pathological and physiological states of humans. We theorized that these cells could also be used to show fatty acid specific gene expression profiles. Since most individuals are in a postprandial state for the main part of the day, knowledge about acute effects of diet is highly valuable. In a cross over study, 21 healthy male volunteers were given shakes containing mainly polyunsaturated or saturated fatty acids. Before and 6 hours after intake of the shakes blood was taken and PBMCs were isolated to use for whole genome gene expression profiling, using Affymetrix NuGO_Hs1a52018 arrays. PUFA intake showed an decrease in LXR signaling and an increase in cellular stress response, while SFA intake showed an increase in LXR signaling.We conclude that PBMCs can reveal a fatty acid specific gene expression profile and in this study show an adverse effect on cellular stress responses of immune cells upon high PUFA intake. We hypothesize that these cells can therefore be used as biomarkers to reflect the capacity of cells to response to cellular stressors, such as fatty acids.

Keywords: Acute fatty acid shake cross-over intervention study

overall_design: In a cross-over design, fasting venous blood samples were collected at baseline and every 2 hours after intake of shakes containing SFA, MUFA or PUFA, up to eight hours after intake. Bood was collected for PBMC isolation, using BD Vacutainer Cell Preparation Tubes with sodium citrate (BD, Breda, The Netherlands). Immediately after blood collection PBMCs were isolated according to the manufacturer’s manual.  PBMC RNA was isolated from all PBMC samples using Qiagen RNeasy Micro kit (Qiagen, Venlo, the Netherlands). Total RNA from PBMCs from 21 subjects, after intake of the SFA shake and after intake of the PUFA shake, was labeled using a one-cycle cDNA labeling kit (MessageAmpTM II-Biotin Enhanced Kit, Ambion, Inc.) and hybridized to Affymetrix NuGO_Hs1a52018 arrays.

first: Mark

last: Bouwens

first: Mechteld

middle: G

last: Bromhaar

first: Jenny

last: Jansen

first: Michael

last: Müller

first: Lydia

last: Afman


title: Prognostic signature of epithelial-mesenchymal transition in breast cancer

first: Jonathan

last: Pollack

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

summary:
Epithelial-mesenchymal transition (EMT), a switch of polarized epithelial cells to a migratory, fibroblastoid phenotype, is considered a key process driving tumor cell invasiveness and metastasis.  Using breast cancer cell lines as a model system, we sought to discover gene-expression signatures of EMT with clinical and mechanistic relevance.  A supervised comparison of epithelial and mesenchymal breast cancer lines defined a 200-gene EMT signature that was prognostic across multiple breast cancer cohorts.  Immunostaining of LYN, a top-ranked EMT signature gene and Src-family tyrosine kinase, was associated with significantly shorter overall survival (P=0.02), and correlated with the basal-like (“triple-negative”) phenotype.  In mesenchymal breast cancer lines, RNAi-mediated knockdown of LYN inhibited cell migration and invasion, but not proliferation.  Dasatinib, a dual-specificity tyrosine kinase inhibitor, also blocked invasion (but not proliferation) at nanomolar concentrations that inhibit LYN kinase activity, suggesting that LYN is a likely target and invasion a relevant endpoint for dasatinib therapy.  Our findings define a prognostically-relevant EMT signature in breast cancer, and identify LYN as a mediator of invasion and possible new therapeutic target (and theranostic marker for dasatinib response), with particular relevance to clinically-aggressive basal-like breast cancer.

Cell Line: cell line(epithelial-like/fibroblast-like/normal breast fibroblasts)
Keywords: Logical Set

overall_design:
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.

HEEBO oligonucleotide microarrays from the Stanford Functional Genomics Facility were used to perform gene expression profiling of 20 human breast cell lines, in comparison to a universal RNA reference.  Expression data were analyzed by Significance Analysis of Microarrays to identify a 200-gene signature characteristic of EMT.

first: Yoon

last: Choi

first: Jessica

last: Kao


title: Delineation of diverse macrophage activation programs in response to intracellular parasites and cytokines

city: San Francisco

first: Sajeev

last: Batra

institute: UCSF

summary:
To provide a global perspective on the relationships between macrophage activation programs and to understand how certain pathogens circumvent them, we used transcriptional profiling by genome wide microarray analysis to compare the responses of mouse macrophages following exposure to the intracellular parasites Trypanosoma cruzi and Leishmania mexicana, the bacterial product lipopolysaccharide (LPS), and the cytokines IFNG, TNF, IFNB, IL-4, IL-10, and IL-17.  We found that LPS induced a classical activation state that resembled macrophage stimulation by the Th1 cytokines IFNG and TNF.  However, infection by the protozoan pathogen Leishmania mexicana produced so few transcriptional changes that the infected macrophages were almost indistinguishable from uninfected cells.  Trypanosoma cruzi activated macrophages produced a transcriptional signature characterized by the induction of interferon-stimulated genes by 24 h post-infection. Despite this delayed IFN response by T. cruzi, the transcriptional response of macrophages infected by the kinetoplastid pathogens more closely resembled the transcriptional response of macrophages stimulated by the cytokines IL-4, IL-10, and IL-17 than macrophages stimulated by Th1 cytokines.

Keywords: Bone marrow macrophage response to intracellular parasites and cytokines

overall_design: We analyzed a series MEEBO arrays on which were hybed RNA amplified from bone marrow-derived macrophages from C57BL/6 mice.  Macrophages infected with L. mexicana or T. cruzi or stimulated by LPS, IFNG, IL-4, IL-10, TNF, IFNB, or IL-17 were compared to one another as well as to uninfected, unstimulated control macrophages.  All experiments were performed over a 24 h timecourse with timepoints taken at 2 h, 6 h, 12 h, and 24 h.

first: Shuyi

last: Zhang

first: Charles

middle: C

last: Kim

first: James

middle: H

last: McKerrow

first: P’ng

last: Loke


title: Identification of Components Associated with Thermal Acclimation of Photosystem II in Synechocystis sp. PCC6803

status: Public on Apr 09 2010

city: Durham

first: John

last: Rowland

address: South Road

department: Biological & Biomedical Sciences

country: United Kingdom

institute: Durham University

summary:
Photosystem II (PSII) is the most thermally sensitive component of photosynthesis. Thermal acclimation of this complex activity is likely to be critically important to the ability of photosynthetic organisms to tolerate temperature changes in the environment.
We have analysed gene expression using whole-genome microarrays and monitored alterations in physiology during acclimation of PSII to elevated growth temperature in Synechocystis sp. PCC 6803. PSII acclimation is complete within 480 minutes of exposure to elevated temperature and is associated with a highly dynamic transcriptional response. 176 genes were identified and classified into seven distinct response profile groups. Response profiles suggest the existence of an early transient phase and a sustained phase to the acclimation response. The early phase was characterised by induction of general stress response genes, including heat shock proteins, which are likely to influence PSII thermal stability. The sustained phase consisted of acclimation-specific alterations that are involved in other cellular processes. Sustained responses included genes involved in phycobillisome structure and modification, photosynthesis, respiration, lipid metabolism and motility. Approximately 60% of genes with sustained altered expression levels have no known function. The potential role of differentially expressed genes in thermotolerance and acclimation is discussed. We have characterised the acclimation physiology of selected gene ‘knockouts’ to elucidate possible gene function in the response.
All mutants show lower PSII rates under normal growth conditions. Basal PSII thermotolerance was affected by mutations in clpB1, cpcC2, hspA, htpG and slr1674. Final PSII thermotolerance was affected by mutations in cpcC2, hik34, hspA and hypA1, suggesting that these gene products play roles in long-term thermal acclimation of PSII.

overall_design: Gene expression levels were compared during a time-course (up to 8 hours) of thermal acclimation (from 25C to 38C) of a wild-type strain grown under continuous illumination and bubbled with CO2 -enriched air. Up to four independent biological replicates were generated and analysed. Each array: replicate matched time-point vs. 0hr control.

first: Xin

last: Pang

first: Iwane

last: Suzuki

first: Norio

last: Murata

first: William

last: Simon

first: Antoni

last: Slabas


title: Investigation of post-transcriptional gene regulatory networks associated with autism spectrum disorders (ASD) by microRNA expression profiling of lymphoblastoid cell lines

first: Valerie

middle: Wailin

last: Hu

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

summary: Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by abnormalities in reciprocal social interactions and language development and/or usage, and by restricted interests and repetitive behaviors. Differential gene expression of neurologically relevant genes in lymphoblastoid cell lines from monozygotic twins discordant in diagnosis or severity of autism suggested that epigenetic factors such as DNA methylation or microRNAs (miRNAs) may be involved in ASD. The goal of this study was to reveal dysregulation in miRNA levels that are inversely correlated with altered levels of target genes that, in turn, may be associated with the underlying pathophysiology of ASD, and to provide a better understanding of the role of miRNAs as a post-transcriptional gene regulatory mechanism associated with ASD.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Lymphoblastoid cell lines (LCLs) derived from peripheral lymphocytes of 14 male subjects were obtained from the Autism Genetic Resource Exchange (AGRE, Los Angeles, CA). The subjects included three pairs of monozygotic twins discordant for diagnosis of autism, a normal sibling for 2 of the twin pairs, two pairs of autistic and unaffected siblings, and a pair of normal monozygotic twins. Global miRNA expression profiling of these LCLs was performed using high-throughput miRNA microarray analysis. A reference design was used for microarray hybridization in this study. The sample miRNAs were coupled with Cy3, whereas the common reference miRNA was coupled with Cy5, and two-colored miRNA microarray analyses were carried out by cohybridizing an equal amount of both miRNA samples onto one slide. Selected differentially expressed miRNAs were confirmed by quantitative RT-PCR, and the putative target genes of two of the confirmed miRNAs were validated by knockdown and overexpression of the respective miRNAs.

first: Tewarit

last: Sarachana

first: Rulun

last: Zhou

first: Guang

last: Chen

first: Husseini

middle: K

last: Manji

middle: W


title: Differential expression analysis of T. thermophilus HB8 wild-type strain in response to copper.

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

country: Japan

institute: RIKEN Harima Institute

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 0 and 30 min after the addition of CuSO4.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70°C for 8 hours (A600 value being ~0.44). Then the 1.25 mM of CuSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of copper ion, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.

first: Yoshihiro

last: Agari

first: Keiko

last: Sakamoto

first: Kazuko

first: Seiki

last: Kuramitsu


title: Xylose utilization timecourse

first: Gavin

last: Sherlock

address: 300 Pasteur Drive

department: Genetics

summary: We have identified a novel xylose-utilization phenotype controlled by a single gene, and we sought to characterize how both the presence and absence of xylose in the presence or absence of the trait affected the S. cerevisiae transcriptional program over time.  To do so, we measured global steady state mRNA levels on three pairs of sister spores from a Simi White strain that was backcrossed twice to S288c.  Each pair of spores was from an independent tetrad, and contained one xylose utilizing ("positive", GSY2465, 2466, 2469) and one xylose non-utilizing spore ("negative", GSY2464, 2467, 2470).  We grew each of the six spores in the presence or absence of xylose for 72 hours with samples taken every 8 hours.  We then assayed relative RNA abundance versus a pooled reference, containing equimolar amounts of each sample, using Agilent yeast catalog arrays.

first: Jared

last: Wenger


title: Proof of principle of novel technique of methylation analysis

city: Pune

first: Ashwin

last: Kelkar

state: Maharashtra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: University of Pune

summary:
In this work we demonstrate a novel method of methylation detection that utilises immunoaffinity to detect the presence of methylated DNA hybridised to a cDNA microarray. We use a monoclonal antibody specific to 5 methylcytosine to detect the presence of 5 methylcytosine in genomic DNA from human fibroblasts bearing the karyotype 45 XO. We report that over 2900 genes show the presence of methylation in this condition. We also report that 165 genes are consistently methylated in all replicates of these experiments. The methylated genes show a uniform distribution over all the chromosomes. The gene ontology of these also indicates no functional correlation between the genes that are methylated. We detect the presence of methylation in IGF2, an imprinted gene and thus known to harbour DNA methylation. The method is extremely specific and offers a quick and efficient way to analyse the methylation landscape on a high throughput scale. This method uses existing technology to assess methylation and thus can integrate very efficiently into any platform used.
A method that detects DNA methylation that is not restricted to specific sequences would provide  a useful platform to analyse methylation distribution among the genes in any given phenotypic condition.Availability of additional approaches to examine DNA methylation would lead to increase in our understanding of the methylome and would help define the intrinsic and extrinsic factors which govern it. Microarray based high throughput methods have been extensively used for gene expression analysis. The method described uses a microarray to analyse DNA methylation levels in a gene/cDNA/oligo specific manner. Here, genomic DNA is fragmented and used for hybridization to microarray slides. The presence of DNA cytosine methylation  in the hybridized DNA is detected by employing Cy3 labelled anti 5mC( 5-methyl cytidine) antibody (monoclonal). The resolution provided by this method is dependent upon the microarray platform used. This method can be adapted to any platform thus enabling seamless integration with existing technology of gene expression analysis

overall_design: The experiment involves the use of genomic DNA from human fibroblasts with the karyotype 45XO and 47XXX. This experiment was performed to analyse the methylation distribution in the human genome in the absence of X chromosome inactivation and this was compared to the methylation distribution in the genome in the background of XCI. 3 technical replicates were used for the XO sample and 2 for XXX. The methylation was estimated by calculating the fold florescence intensity to control spots for the single channel experiments carried out. Each replicate was normalised individually with the background florescence. The normalised florescence values were used for further comparison between and within replicates.

first: Deepti

last: Deobagkar


status: Public on Apr 06 2010

city: Summit-Argo

first: Xiangyu

last: Deng

address: 6502 S. Archer Rd.

department: National Center for Food Safety and Technology

institute: Illinois Insititute of Technology

type: Genome variation profiling by genome tiling array

summary:
Full title: Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes: Implications for its niche adaptation, pathogenesis, and evolution

Listeria monocytogenes is a foodborne bacterial pathogen well known for adaptability to diverse environmental and host niches, and a high fatality rate among infected, immuno-compromised individuals. Three genetic lineages have been identified within this species. Strains of genetic lineages I and II account for more than ninety percent of foodborne disease outbreaks worldwide, whereas strains from genetic lineage III are rarely implicated in human infectious for unknown, yet intriguing, reasons. Here we have probed the genomic diversity of 26 L. monocytogenes strains using both whole-genome sequences and a novel 385,000 probe pan-genome microarray, fully tiling the genomes of 20 representative strains. Using these methods to identify genes highly conserved in lineages I and II but rare in lineage III, we have identified 86 genes and 8 small RNAs that play roles in bacterial stress resistance, pathogenicity, and niche, potentially explaining the predominance of L. monocytogenes lineages I and II in foodborne disease outbreaks. Extending gene content analysis to all lineages revealed a L. monocytogenes core genome of approximately 2,350 genes (80% of each individual genome) and a pan-genomic reservoir of >4,000 unique genes. Combined gene content data from both sequences and arrays was used to reconstruct an informative phylogeny for the L. monocytogenes species that confirms three distinct lineages and describes the relationship of 9 new lineage III genomes. Comparative analysis of 18 fully sequenced L. monocytogenes lineage I and II genomes shows a high level of genomic conservation and synteny, indicative of a closed pan-genome, with moderate domain shuffling and sequence drift associated with bacteriophages is present in all lineages. In contrast with lineages I and II, notable genomic diversity and characteristics of an open pan-genome were observed in the lineage III genomes, including many strain-specific genes and a more complex conservation pattern. This indicates that the L. monocytogenes pan-genome has not yet been fully sampled by genome sequencing, and additional sequencing of lineage III genomes is necessary to survey the full diversity of this intriguing species and reveal its mechanisms for adaptability and virulence.

sample_organism:
Listeria monocytogenes
Listeria monocytogenes EGD-e
Listeria monocytogenes FSL J1-208
Listeria monocytogenes FSL J2-071
Listeria monocytogenes FSL F2-208

platform_organism: Listeria monocytogenes serotype 4b str. F2365

platform_organism: Listeria monocytogenes serotype 1/2a str. F6854

platform_organism: Listeria monocytogenes serotype 4b str. H7858

overall_design: This is a Listeria monocytogenes pan-genome tilling array designed using PanArray algorithm. 9 experimental strains (F2-569, M1-002, F2-208, J2-071, J1-208, W1-111, W1-110, F2-524, F2-501) vs reference (EGD-e) strain.

first: Adam

middle: M

last: Phillippy

first: Zengxin

last: Li

first: Steven

middle: L

last: Salzberg

first: Wei

last: Zhang


title: ChIP-chip from fetal brain tissue with b-Catenin

status: Public on Apr 01 2010

city: Bronx

first: Herb

last: Lachman

state: NY

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

summary:
GSK3b signaling has been implicated in the pathophysiology of bipolar affective disorder based on the inhibitory effect of lithium salts on this pathway. This has been supported by a recent genome wide association study. In addition, GSK3b signaling may also play a role in schizophrenia, an idea that is based on the finding that the protein encoded by the schizophrenia candidate gene DISC1 inhibits GSK3b. Gene expression is affected by GSK3b signaling through the activation of the transcription factor b-catenin, which modulates expression through a protein-protein binding interaction with members of the TCF/LEF family. To identify genes targeted by GSK3b/b-catenin, investigators have used expression profiling in lithium treated cells and animals. Gene knockdown and transfection are other experimental methodologies one can employ. However, these approaches are not possible using human brain tissue. Consequently, we used ChIP-chip to identify promoters bound by b-catenin as an indirect method for identifying genes targeted by GSK3b. Fetal brain was used because schizophrenia is viewed as a neurodevelopmental disorder. In addition, fetal brain tissue is not affected by the confounding factors associated with postmortem tissue (postmortem delay, cause of death, brain pH, use of medication and other environmental factors).

We carried out two complete promoter array hybridizations on different biological isolates using the 385K two-Array Human Promoter Set developed by Nimblegen/Roche. Significant enrichment for b-catenin immunoprecipitates was determined in each experiment if the log2 ratio of signal obtained for the b-catenin antibody compared with control was below an FDR<0.2 using NimbleScan. NimbleScan reports three different levels of enrichment (peaks) based on the FDR score, as described in methods. Since whole brain tissue was used in these experiments, we chose the least conservative FDR (<0.2) to reduce the type II error (false negative) rate, which could be caused by enrichment at some promoters in a subset of cells being diluted by the absence of b-catenin immunoprecipitates at those loci in other cells. A total of 640 gene promoters showed evidence for b-catenin binding on two arrays. We validated enrichment at 9 gene promoters using real time PCR.

The 640 genes are analyzed using SLEP (Sullivan Lab Evidence Project, http://slep.unc.edu). Analysis of the SLEP database was restricted to genome wide association studies (GWAS) and copy number variants (CNVs) in ASD, BD and SZ. In addition, a gene was scored as a potential candidate if it fell within a linkage peak or if multiple positive association studies were found upon a candidate gene analysis. Promoters for 24 genes implicated in these disorders were targeted by b-catenin. Of these, a total of 16 genes are very strong candidates based on unbiased genome-wide surveys (GWAS and CNV screening). The other 8 have been implicated by linkage analysis and candidate gene analysis, which are the least robust genetic methods for targeting specific genes in psychiatric disorders. We carried out a similar analysis on 640 genes that did not show evidence for enrichment in the b-catenin ChIP-chip. Only 5 genes were found, none of which are GWAS or CNV targets. Based on the finding that five candidate genes were found in a group of 640 randomly selected genes, while 24 were identified in the ChIP-chip experiment, the binding of b-catenin to schizophrenia and bipolar disorder candidate gene promoters is highly significant (p = 6.5 x 10-12).

The findings suggest that many seemingly disparate candidate genes for psychiatric disorders can be grouped into the GSK3b/b-catenin signaling pathway. The results could also have therapeutic implications in helping to identify bipolar patients who respond best to lithium, as well as identify patients with schizophrenia who might benefit from the drug.

overall_design: Immunoprecipitates were generated with an antibody to b-Catenin

first: Erika

last: Pedrosa


title: Class prediction models of thrombocytosis using genetic biomarkers

city: Stony Brook

first: Wadie

last: Bahou

department: Hematology

institute: Stony Brook University

summary: Using custom spotted oligonucelotide platelet-focused arrays, platelet samples were compared. 48 health controls, 23 reactive thrombocytosis (RT) and 24 essential thrombocythemia (ET) samples were compared. An 11-biomarker gene subset was identified that discriminated among the three cohorts with 86.3% accuracy.

overall_design: 70 mer oligonucleotides were spotted in quadruplicate and hybridized versus reference RNA in two color method. Spiked control RNAs were also included.

first: Anil

last: Dhundale


title: Differential expression analysis of T. thermophilus HB8 csoR deficient strain in response to copper.

first: Akeo

last: Shinkai

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 csrR deficient strain at 0 and 30 min after the addition of CuSO4.

overall_design: Three csoR deficient strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70°C for 8 hours (A600 value being ~0.4). Then the 1.25 mM of CuSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of copper ion, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.

first: Yoshihiro


title: Differential expression analysis of Thermus thermophilus HB8 wild-type strain in response to zinc

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 0 and 30 min after the addition of ZnSO4.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70°C for 8 hours (A600 value being ~0.52). Then the 1.0 mM of ZnSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of zinc ion, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.

last: Agari

first: Keiko

first: Miwa

last: Ohmori


title: screen differential expressed microRNAs of RA patients

status: Public on Apr 03 2010

city: Chongqing

first: jingyi

last: li

address: Gao Tan Yan

department: institute of immunology

country: China

institute: the third millitary medical university

overall_design:
We screened the differential expressed microRNA from the rheumatoid arthritis patients and healthy person in their hydrops articuli CD4+ T cells.
1.Isolated the CD4+ T cells from the hydrops articuli cells of 2 rheumatoid arthritis patients.
2.Isolated the CD4+ T cells from healthy person's peripheral blood as control.
3.Isolation of total RNA from CD4+ T cells then sent the samples to KangChen Bio-tech Inc (Shanghai, China) where they were labeled, hybridized, scaned, normalied and transformed to the final data.


title: WT vs KO of lp_2991 comparison

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

summary: A mutant of L. plantarumWCFS1 (deletion of lp_2991) was compared with the wildtype grown in standard MRS broth. Cells were sampled at OD1 for mRNA extraction.

overall_design: Knockout vs wildtype. Technical replicates (same mRNA isolation) used for a dye swap.

first: Marjolein

last: Meijerink

first: Roger

last: Bongers

last: Kleerebezem

first: Jerry

last: Wells


title: Gene expression profiling in Salmonella Typhimurium stimulated heterophils using a chicken 44K Agilent microarray

city: College Station

first: Huaijun

last: Zhou

state: TX

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

summary: To determine the host response to Salmonella Typhimurium (ST) in heterophils, a whole chicken genome array was used to analyze RNA isolated from heterophils stimulated in vitro with ST (30 min, 1 h, 2 h, and 3 h) or medium control (NS). Dual-color, direct comparisons were carried between ST-stimulated and non-stimulated controls (30 min vs. NS (30M/NS), 1 h vs. NS (1HR/NS), 2 h vs. NS (2HR/NS) and 3 h vs. NS (3HR/NS)). Each comparison includes four biological replicates. There were 2791, 3744, 12947 and 12482 genes differentially expressed in the comparisons of 30M/NS, 1HR/NS, 2HR/NS and 3HR/NS, respectively (P < 0.001) , while 50, 82, 153, and 146 genes were related to immune function, respectively. More than 80% of immune-related genes overlapped between the comparisons (30M/NS vs. 1HR/NS, 1HR/NS vs. 2HR/NS, and 2HR/NS vs. 3HR/NS). These candidate genes include cytokines (e.g. Interleukin (IL) 1β, -6, -10B and -12B), chemokines (e.g. IL-8, CCL4, K60 and K203) and cluster of differentiation (CD) markers (e.g. CD44, -47 and -83). A relatively large increase in the number of differentially expressed immune-related genes was observed between 1 h and 2 h post-stimulation. The results of continuous transcriptional change provide important information to elucidate both the cellular and molecular mechanisms of ST stimulation in chickens.

overall_design: Dual-color, common reference comparisons were carried between ST-stimulated (30M, 1HR, 2HR and 3HR) and non-stimulated controls (NS). Four biological replicates, with dye swap labeling, were included in the comparisons of each post-stimulation time point (30M/NS, 1HR/NS, 2HR/NS and 3HR/NS). Background subtracted signal intensity were collected from 16 arrays and normalized before data analysis.

first: Hsin-I

last: Chiang

first: Christina

last: Swaggerty

first: Michael

last: Kogut

first: Scot

middle: E

last: Dowd


title: Promoter proximal pausing and its regulation by c-Myc in embryonic stem cells: ChIP-chip

status: Public on Apr 02 2010

city: Cambridge

first: Charles

last: Lin

address: 9 Cambridge Center

department: Biology

institute: Massachusetts Institute of Technology

type: Genome binding/occupancy profiling by genome tiling array

summary: Recruitment of the RNA Polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA binding transcription factors is well recognized as a key regulatory step in gene expression.  We describe here evidence that promoter-proximal pausing is a general feature of transcription by Pol II in embryonic stem (ES) cells, and thus an additional step where regulation of gene expression may occur.  We report here that c-Myc, which occupies a third of actively transcribed genes in ES cells and is a key regulator of cellular proliferation, binds P-TEFb and contributes to release of promoter-proximal paused Pol II at these genes.

overall_design: ChIP-chip data for Pol II and additional factors controlling pause release in mouse ES cells.

first: Peter

last: Rahl

middle: Y

first: Amy

last: Seila

first: Ryan

last: Flynn

first: Scott

last: McCuine

first: Christopher

last: Burge

first: Philip

last: Sharp

first: Richard

last: Young


title: Tetracycline-treated Litomosoides sigmodontis vs. untreated control Litomosoides sigmodontis

status: Public on Apr 07 2010

city: Bonn

first: Uta

last: Strübing

address: Sigmund-Freud-Str. 25

department: Institute for Medical Microbiology, Immunology and Parasitology

country: Germany

institute: University Hospital Bonn

summary: The filarial nematodes Brugia malayi, Wuchereria bancrofti and Onchocerca volvulus cause elephantiasis, dermatitis and blindness, resulting in severe morbidity in developing countries. 1.3 billion people are at risk of infection. Targeting the essential Wolbachia endobacteria of filarial nematodes with doxycycline has proven to be an effective therapy, resulting in a block in embryogenesis and worm development, and macrofilaricidal effects. However, doxycycline is contraindicated for a large portion of the at-risk population. To identify new targets for anti-wolbachial therapy, understanding the molecular basis of the Wolbachia-filaria symbiosis is required. We performed cross-species hybridization by using the Brugia malayi microarray to identify differentially expressed genes in the rodent filaria Litomosoides sigmodontis after depletion of Wolbachia which therefore might have a role in symbiosis.

platform_organism: Wolbachia endosymbiont strain TRS of Brugia malayi

overall_design: Female adult Litomosoides sigmodontis from patent infections were treated with tetracycline to deplete endosymbiotic Wolbachia bacteria. RNA from tetracycline-treated Litomosoides sigmodontis was compared to untreated age-matched control worms. This experiment was performed for three different timepoints: day 6, 15 and 36 of tetracycline treatment. One biological replicate was performed each with two technical replicates (dye-flip replicates).

first: Achim

last: Hoerauf

first: Kenneth

last: Pfarr


title: Mosquito transcriptome changes and filarial worm susceptibility in Armigeres subalbatus

city: Madison

first: Bruce

last: Christensen

state: WI

address: 1656 Linden Drive

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary: Armigeres subalbatus is a natural vector of the filarial worm Brugia pahangi, but it kills Brugia malayi microfilariae (mf) by melanotic encapsulation.  Because B. malayi and B. pahangi are morphologically and biologically similar, this mosquito-parasite system serves as a valuable model for studying resistance mechanisms in mosquito vectors.  Comparing Ar. subalbatus-B. pahangi susceptibility and Ar. subalbatus-B. malayi refractoriness could provide significant insight into recognition mechanisms required to mount an effective anti-filarial worm immune response in the mosquito, as well as provide considerable detail into the molecular components involved in vector competence.  Accordingly, we initiated transcriptome profiling studies of Ar. subalbatus in relation to filarial worm infection to provide information on the molecular components involved in B. pahangi susceptibility for comparison with our earlier studies on B. malayi refractoriness (Aliota et al., 2007). In addition, these studies also provide information on the infection response of a natural vector, i.e., the overall transcriptional and physiological change that occurs in the mosquito as a result of parasite infection, for comparison with our previous studies that employed a highly susceptible laboratory model, Aedes aegypti (Erickson et al., 2009).  The time course chosen facilitated an examination of key events in the development of the parasite, beginning with the very start of filarial worm infection and spanning to well after infective-stage parasites had completed development in the mosquito.  Herein, we demonstrate that filarial worm susceptibility in Ar. subalbatus is a highly complex process during the first 24 hours of infection.  It is a process that involves many factors of both known and unknown function which are most likely associated with filarial worm penetration through the midgut lumen, invasion into thoracic muscle cells, and maintenance of homeostasis in the hemolymph environment.  The data show that there are distinct and separate transcriptional patterns associated with filarial worm susceptibility as compared to refractoriness, and that an infection response in Ar. subalbatus, a natural vector, can differ significantly from that observed in Ae. aegypti, a common laboratory model.  Finally, the data presented herein provide us with a cadre of information to design wet lab experiments and select candidates for further study to more fully dissect the nature of the anti-filarial worm immune response in this mosquito-parasite system.

overall_design: Nine sample groups were created from thirteen timepoints to study mosquito transcript changes in response to B. pahangi development.  In each sample group, comparisons were made between mosquitoes exposed to an infective bloodmeal containing B. pahangi mf and those exposed to a bloodmeal without parasites.  In addition, a separate set of microarray analyses directly compared transcriptome profiles between mosquitoes in which filarial worms develop to infective stage larvae (B. pahangi) and mosquitoes in which an anti-filarial worm immune response had been initiated (B. malayi).  This direct comparison contained groups of mosquitoes exposed to an infective bloodmeal containing B. pahangi mf or exposed to a bloodmeal containing B. malayi mf.  Samples were collected 1, 6, 12, and 24 h PI and 2-3 d PI.  Three biological replicates, each with two technical replicates done as dye-swapped pairs (Cy5 experimental vs. Cy3 control), were performed for each experimental set in an effort to eliminate bias in the dye coupling.  Each biological replicate consisted of mosquitoes from distinct generations to take into account stochastic variations.  RNA integrity was verified via gel electrophoresis or via Bioanalyzer (Agilent, Santa Clara, CA) and only quality intact RNA was used for cDNA synthesis.

first: Matthew

middle: T

last: Aliota

first: Jeremy

last: Fuchs

first: Thomas

middle: A

last: Rocheleau

first: Amanda

last: Clark

first: Julian

last: Hillyer

first: Cheng-Chen

last: Chen


title: Salt/NaCl stress in Desulfovibrio vulgaris Hildenborough

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

summary:
This set of microarray data was used to investigate the effects of D. vulgaris adaptation to excess NaCl.

Keywords: stress response, one time point (the mid-log phase for both control and treated cells)

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of cells treated with 250 Salt:NaCl to untreated cells at times of mid-log phase min.


title: 3CB-induced gene expression of Pseudomonas putida KT2440/pSL1 in soil (without RNA amplification)

city: Tsukuba

first: yong

last: wang

state: Ibaraki

address: 3-1-3 Kannondai

department: Environmental Biofunction Division

institute: National Institute for Agro-Environmental Sciences

summary: To know whether the microarray technique could be used to detect bacterial gene expression in soil, large quantity of RNA was extracted from soil cultures of Pseudomonas putida KT2440 containing a chloroaromatic degrading plasmid at the presence or absence of the growth substrate, 3-chlorobenzoate (3CB). The quality and quantity of the extracted RNA were proper for a typical microarray analysis. Gene expression patterns of soil cultures were analyzed by DNA microarray using the extracted RNA. Among 5346 genes on the array, 5% and 4.5% of genes showed up- or down-regulation. Analysis done at the DAVID Bioinformatics Resources server suggested that the benzoate degradation via hydroxylation pathway had the most significant changes after treatment with 3CB. Expression of the 3CB degradation genes located in the genome was confirmed by real-time RT-PCR. In addition, real time RT-PCR analysis revealed that the fluorescent signals from plasmid genes on the microarray were saturated so that the induction ratio of the genes located in the plasmid was underestimated in microarray analysis. To our best knowledge, this report represents the first trial to use microarray technique to detect genome-wide bacterial gene expression in soil.

overall_design: A study using total RNA extracted from soil cultures of Pseudomonas putida KT2440/pSL1.  Each chip measures the expression level of 5,341 genes from Pseudomonas putida KT2440 genome and 5 genes from an introduced plasmid pSL1 with fourteen 60-mer probes per gene which have five-fold technical redundancy.

first: Yong

last: Wang

first: Sho

last: Morimoto

first: Naoto

last: Ogawa

first: Takeshi

last: Fujii


title: Transcriptome analysis reveals a major impact of Tyk2 on the expression of interferon responsive and metabolic genes

city: Vienna

first: Claus

last: Vogl

state: Vienna

address: Veterinaerplatz 1

department: Biomedical Sciences

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: Peritoneal macrophages of Tyk2-/- and wildtype (wt) mice were compared before and after six hours of LPS treatment. Interferon responsive genes are lower expressed in Tyk2-/- macrophages at the basal level, metabolic genes higher before, but even more after LPS treatment.

overall_design: cDNA from macrophages from three replicates of three Tyk2-/- and three wt mice before and after six hours of LPS treatment, respectively, was hybridized to a microarray and analyzed.

last: Flatt

first: Bernd

last: Fuhrmann

first: Elisabeth

last: Hofmann

first: Barbara

last: Wallner

first: Rita

last: Stiefvater

first: Pavel

last: Kovarik

first: Birgit

last: Strobl

first: Mathias

last: Müller


title: Technical variation between RNA isolations from individual embryos

city: Amsterdam

first: Mark

middle: de

last: Jong

address: Kruislaan 318

institute: University of Amsterdam

summary: Transcriptome analysis during embryogenesis usually requires pooling of embryos to obtain sufficient RNA. Hence, the measured levels of gene-expression represent the average mRNA levels of pooled samples and the biological variation among individuals is lost for inclusion into statistical models used to analyze transcriptome data. This can  irreversibly reduce the robustness, resolution and expressiveness of the experiment. Therefore, we developed a robust method to isolate abundant high-quality RNA from individual embryos to perform single embryo transcriptome analyses using the zebrafish as a model.

overall_design: Zebrafish embryos were selected from the germ ring stage. RNA from 4 individual embryos and RNA from 4 pooled embryos and afterwards splitted material was isolated. These 8 samples were hybridized against a common reference made from a pool of 20 embryos.

first: M

last: de Jong

first: H

last: Rauwerda

first: O

last: Bruning

first: J

last: Verkooijen

middle: P

last: Spaink

first: T

last: Breit


title: Transcriptomic characterization of a virulence-deficient phosphatidylcholine-negative Agrobacterium tumefaciens mutant

city: Bochum

first: sonja

last: klüsener

address: Universitätsstrasse 150

institute: Ruhr-Universität Bochum

summary:
To learn more about the global effects of phosphatidylcholine (PC)-deficiency in A. tumefaciens, we performed transcriptomic studies comparing the wild type and a PC-deficient DpmtA Dpcs mutant. We expanded the number of affected virulence genes and showed that the loss of PC was correlated with altered expression of multiple genes encoding membrane or membrane-associated proteins and proteins which fulfil their function at the membrane.
The PC-deficient mutant analyzed in this study is further described in Sonja Klüsener, Stephanie Hacker, Yun-Long Tsai, Julia E. Bandow, Ronald Gust, Erh-Min Lai and Franz Narberhaus. 2010. Proteomic and transcriptomic characterization of a virulence-deficient phosphatidylcholine-negative Agrobacterium tumefaciens mutant.

overall_design: Total RNA was extracted from A. tumefaciens C58 wild-type and PC-deficient mutant cells grown under virulence-induced and non-induced conditions. The 4-plex NimbleGen Gene Expression Array for A. tumefaciens (Design ID 080630) represents 5344 genes and is based on NCBI reference sequences NC_003062, NC_003063, NC_003064 and NC_003065. Each gene is represented by 6 probes (45mer-60mer oligonucleotides), each in two copies on different locations on the array. Three biological replicates for each cultivation condition were analyzed for A. tumefaciens wild-type and PC-deficient mutant strains.

first: Stephanie

last: Hacker

first: Sonja

last: Klüsener

first: Franz

last: Narberhaus


title: Response of Bacillus cereus ATCC 14579 to challenges with sublethal concentrations of enterocin AS-48

status: Public on Apr 08 2010

city: Groningen

first: Anne

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary: Enterocin AS-48 is produced by Enterococcus faecalis S48 to compete with other bacteria in their environment. Due to its activity against various Gram positive and some Gram negative bacteria it has clear potential for use as a food preservative. Here, we studied the effect of enterocin AS-48 challenges on vegetative cells of Bacillus cereus ATCC 14579 by use of transcriptome analysis.

overall_design:
Control: Wild type against Target: Enterocin AS-48 challenge
A supplementary file containing processed data of all samples combined is linked below. Mn column is the lowess normalized LN (Target/Control).

first: Maria-José

middle: J

last: Grande Burgos

first: A

last: Kovács

first: Aleksandra

first: Hikmate

last: Abriouel

first: Antonio

last: Gálvez

first: Oscar

last: Kuipers


title: Identification of Recurrence-Related microRNAs in the Bone Marrow of Breast Cancer Patients

city: Beppu

first: Takehiko

last: Yokobori

state: Oita

address: 4546 Tsurumihara

department: Department of Surgery

institute: Kyushu university

summary: MicroRNA microarray analysis was performed to compare microRNA levels in bone marrow from 4 breast cancer patients with recurrent disease and 4 patients without recurrence.

overall_design: To achieve this goal, we used microRNA microarray analysis to compare microRNA expression in bone marrow from breast cancer patients with and without disease recurrence.

first: Masaki

last: Mori


title: Global transcriptomic response of Leptospira interrogans serovar Copenhageni upon exposure to serum

status: Public on Mar 31 2010

city: Pathumwan

first: Kanitha

last: Patarakul

state: Bangkok

address: 1873 Rama IV Road

department: Microbiology

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

summary: L. interrogans, a causative agent of leptospirosis, can survive in the environment for lengthy periods of time in between infection of mammalian hosts.  In order to identify genes involved in survival in the early spirochetemic phase of infection, we performed a transcriptional analysis of L. interrogans serovar Copenhageni upon exposure to serum in comparison with EMJH medium.

overall_design: Analysis used RNA derived from serum- and EMJH-treated L. interrogans serovar Copenhageni as experimental and control samples, respectively.  The samples were composed of 3 biological replicates with dye swap for each replicate, resulting in 6 arrays.  Direct comparisons were made between arrays of experimental and control samples using raw data pulled from two different channels for data analysis.

first: Miranda

last: Lo

first: Ben

last: Adler


title: Maize tumors caused by Ustilago maydis require organ-specific genes in host and pathogen

city: Stanford

first: John

middle: F

last: Fernandes

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

summary:
Two-organism transcriptome profiling of infected seedling, adult leaf, and tassel demonstrated that both the host and pathogen exhibit organ-specific expression programs.  Phenotypic screening of U. maydis mutants deleted for suites of secreted protein genes and maize growth mutants demonstrated organ-restricted tumorigenesis.  Two-dye, competitive hybridizations were performed on Agilent oligo arrays.

Keywords: maize, pathogen, fungus, Ustilago, organ-specificity

sample_organism:
Zea mays
Mycosarcoma maydis

platform_organism:
Zea mays
Mycosarcoma maydis

overall_design: Comparisons were done 1) between mock and infected samples at 1dpi and 3dpi for seedlings and at 3dpi and 9dpi for adult leave and tassels, 2) between the three 3dpi infected samples, 3) between timepoints of infected samples.

first: Gunther

last: Doehlemann

first: David

middle: S

last: Skibbe

first: Virginia

last: Walbot


title: Vibrio cholerae vpsT microarray analysis

city: Santa Cruz

first: Nicholas

middle: Jun

last: Shikuma

address: 1156 High St.

department: Microbiology and Environmental Toxicology

institute: University of California, Santa Cruz

summary: Rugose V. cholerae cells with an in-frame deletion of vpsT (VCA0952) were used in this study.  Cells containing pBAD-Myc/His-B vector, or the vector containing a wild-type copy of vpsT, or vpsT with point mutations M17D, D60A, R134A, or I141E were grown to exponential phase and expression profiles compared.

overall_design: Three biological replicates were performed for each strain and dye swaps were performed for each treatment.  Reference sample consisted of V. cholerae cells with an in-frame deletion of vpsT carrying the pBAD-Myc/His-B vector.

first: Petya

middle: V

last: Krasteva

first: Jiunn

middle: C

last: Fong

first: Sinem

last: Beyhan

first: Marcos

last: Navarro

first: Fitnat

last: Yildiz

first: Holger

last: Sondermann


title: Biological variation between zebrafish development series

first: Mark

last: Jong

overall_design: RNA from 8 individual embryos (16-cell, 128-cell, sphere, dome, germ ring, shield, 75%-epiboly & 8-somite stage) was isolated and hybridized against a common reference (pool of these 8 samples).

first: M

last: de Jong

first: H

last: Rauwerda

first: O

last: Bruning

first: J

last: Verkooijen

last: Spaink

last: Breit


title: Osmotic stress tolerance in Thellungiella halophila

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary:
Suitability of CATMA for the analysis of the transcriptome of Thellungiella halophila - flower/leaf transcriptomic comparison in Arabidopsis and Thellungiella.

adt09-01_thellungiella - thelungiella

sample_organism:
Arabidopsis thaliana
Eutrema halophilum

overall_design: 2 dye-swap - CATMA arrays

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Arnould-

last: Savoure

first: Marie-Laure

last: Martin-Magniette


title: Protein translation as major target for gene expression control of O. tsutsugamushi

city: Seoul

first: Nam-Hyuk

last: Cho

address: 28 Yongon-Dong, Chongno-Gu

department: Microbiology and Immunology

country: South Korea

institute: Seoul National Univ. College of Medicine

summary: Orientia tsutsugamushi, an obligate intracellular bacterium, is the causative agent of Scrub typhus. The bacterium can replicate both in its arthropod host and in mammals, including humans. The control mechanisms for bacterial gene expression within eukaryotic host cells are largely unknown. Previously, we reported that the O. tsutsugamushi genome has the highest repeat density of any sequenced bacterial genome due to the extraordinary proliferation of mobile genetic elements (MGEs), suggesting a unique genomic evolution in intracellular niches. In this study, the global gene expression of O. tsutsugamushi within eukaryotic cells was examined using a microarray and proteomic approaches. These approaches identified 643 genes, corresponding to approximately 30% of genes encoded in the genome. The majority of expressed genes belonged to several functional categories including protein translation, protein processing/secretion, and replication/repair. We also searched the conserved sequence blocks (CSBs) in the genomes of different O. tsutsugamushi strains to identify gene blocks impermeable to proliferating MGEs. Although extensive shuffling of genomic sequences was observed between two different strains, 204 CSBs with sizes ranging from 1 kbp to 29 kbp, covering 48% of the genome, were identified. When combining the data of the CSBs and global gene expression, CSBs in the O. tsutsugamushi genomes correlates well with the location of expressed genes, especially in protein level, suggesting the functional conservation between gene expression and genomic location. Finally, we compared global gene expression of the bacteria infecting fibroblasts and macrophages using microarray analysis. Major changes in the expression of genes with known functions were the downregulation of genes involved in translation, protein processing and secretion, which resulted in significant reduction in bacterial translation rates and growth within macrophages. These results suggest that the replication of O. tsutsgamushi is controlled primarily by the expression of genes involved in bacterial translation and subsequent protein processing/secretion.

sample_organism:
Orientia tsutsugamushi
Mus musculus

overall_design: Microarray analysis using the Combimatrix CustomArrayTM 4X2 microarray (CombiMatrix) was performed according to the standard CombiMatrix protocol described in detail at http://www.combimatrix.com/ products_custom4x2.htm (PTL005). Oligonucleotide probes (27 to 40-mers, 1613 probes) were designed for 1472 CDSs of the O. tsutsugamushi genome (GeneBank accession no. AM494475). 1 to 6 probes per CDS were designed and some probes were duplicated on the microarray (total 2187 spots on an array). As negative controls, 5 and 15 oligonucleotide probes derived from plant and bacteriophage respectively were spotted on the array at 53 sites per array. A local background subtraction method was used and the background-subtracted signal values were imported into the Avadis Prophetic software (ver. 3.3, Strand Genomics) or Expander (ver. 4.1, http://acgt.cs.tau.ac.il/expander/) for data analysis. . Global normalization of gene expression data was performed using the quantile normalization method embedded in the Expander software. The standard deviations of log data and the p-values were calculated using default settings in the Avadis software. Transcriptome analysis was carried out using three biological replicates for uninfected samples (uninfected L929 cells) and five biological replicates for infected samples (L929 cells infected with O. tsutsugamushi for 48 h). For comparison of the O. tsutsugamushi transcriptome from fibroblasts (L929 cells) and macrophages (J774A.1 cells), two biological replicates from each cell line were used.

first: Chan-Ki

last: Min


title: Comparison of gene expression in male and female blastocysts

city: Bunkyo-ku

first: Shin

last: Kobayashi

state: Tokyo

address: 1-5-45 yushima

department: Medical Research Institute

institute: Tokyo Mdical & Dental University

summary:
It is basically understood that male and female development is initiated by gonad differentiation into either testis or ovary.  However, male embryos are reported to develop faster than female during preimplantation, implying sex differences at this stage.  To learn more about when sex differentiation begins, we compared the global gene expression pattern of male and female embryos at the blastocyst stage.

First, Blastocyst samples were sexed, using a novel method for non-invasive sexing of preimplantation stage mouse embryos by tagging the X chromosome with an EGFP transgene,   Next, gene expression patterns of the male and female were compared using DNA microarray.

overall_design: Ｓamples were collected from three independent preparations and the experiments were triplicated. Scanned microarray results were processed with Feature Extraction software (ver. 7.5, Agilent). 　The hybridization experiments were duplicated in a reciprocal labeling manner to reduce dye integration bias, and total of six hybridizations were carried out using each 22K-1 and 22K-2 array.　 Combining plural array results and statistical analyses were carried out by Luminator software (Rosetta).

first: Yoshitaka

last: Fujihara

first: Nathan

last: Mise

first: Kazuhiro

last: Kaseda

first: Kuniya

last: Abe

first: Fumitoshi

last: Ishino

first: Masaru

last: Okabe


title: Comparative analysis of gene expression profiles between whole oocytes and isolated cortices

city: Toba

first: Lixy

last: Yamada

state: Mie

address: 429-63 Sugashima

department: Graduate School of Science,

institute: Nagoya University

summary: Postplasmic/PEM RNAs constitute a large class of cortical maternal RNAs with include at least 2 determinants (Macho1 and PEM1) involved in muscle differentiation, unequal cleavage and posterior patterning of the embryo. Two main classes have been defined - type I (localized in oocytes) and type II (localizing in embryos). Based on the fact that Vasa RNA - the only type II recognized in Ciona - segregates into B8.12 (germ) and sister B8.11 cells, while many others (including Macho1 and PEM1) segregate only into B8.11 (somatic) cells a first attempts at re-classifying these RNAs has been made.  We have analyzed the associations of postplasmic/PEM RNAs with cortical structures in 2 ascidians species Ciona intestinalis and Phallusia mammillata using: - very high resolution fluorescent in situ hybridization localization in eggs and embryos and in their cortical fragments, - comparisons of RNAs extracted from whole oocytes and from isolated cortices using microarray analysis – screening of the Ciona intestinalis genome for the presence in 3’ UTR regions of repeats containing the tri-nucleotide CAC motif (xCACx) followed by localization of xCACx rich RNAs using in situ hybridization.   Based on our combined approaches we observe that: - 1) the vast majority of Ciona intestinalis postplasmic/PEM RNAs (including Ci-Vasa) are cortically localized in the eggs (type I) - 2) postplasmic/PEM RNAs are much more likely to contain xCACx motifs in their 3’UTR than other transcripts. Using this criterion we have found 2 new postplasmic/PEM RNAs: MnK and PSD - 3) some postplasmic/PEM RNAs are anchored to cER while others are located into granules. We therefore come to the conclusion that there are at least 2 distinct categories of postplasmic/PEM RNAs based on their cortical anchorage and cell fate: I) cER sub-domain associated postplasmic/PEM RNAs (Macho1 like) which segregate in the somatic B8.11 cells. II) postplasmic/PEM RNAs associated with (putative germ) granules (Vasa like) which in addition to B8.11 cells segregate into B8.12 germ cells.

overall_design: Two kinds of sample, Dye Swap design with 2 arrays

first: Alexandre

last: Paix

first: Christian

last: Sardet

first: Nori

last: Satoh


title: Response of muscle to stress

status: Public on Mar 26 2010

city: Castanet Tolosan

first: Caroline

last: Molette

address: Avenue de l'Agrobiopole

institute: ENSAT

summary:
As muscle function is relevant for the stress response, and as gene array and proteomics analyses have not been conducted to investigate muscle response in stress paradigm in birds, we developed generic approaches to assess molecular bases of muscle response to stress in chicken. Restraint test was chosen as stress situation because this treatment has previously been shown to be a high stressful situation in birds and mammals.

Keywords: comparative genomic expression, skeletal muscle, restraint-transport stress, chicken

overall_design: 5 samples

first: Dominique

last: Hazard

first: Jérémy

last: Pinguet

first: Christophe

last: Chambon

first: Fabien

last: Letisse

first: Ziad

last: Wadih-Moussa

first: Hervé

last: Rémignon

first: Xavier

last: Fernandez


title: Comparative Analyses: Expression Differences for Repair Tissue, Chondrocytes, and Mesenchymal Stromal Cells

status: Public on Mar 30 2010

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

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

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

summary: Previous studies have demonstrated relative deficiencies of repair tissue within articular lesions when compared to articular cartilage.  While cells occupying the lesions might be of mesenchymal origin, they do not recapitulate differentiation to the chondrogenic phenotype of normal articular chondrocytes.  Nevertheless, attributes of repair tissue appear similar to chondrocytes and their precursors at various other different states.  We hypothesized that analyses of gene expression profiles for these other cell phenotypes would elucidate the identity of repair tissue cells. Total RNA was isolated from repair tissue samples, neonatal articular cartilage, primary articular chondrocytes maintained in monolayer culture and passaged weekly over 28 days, and bone marrow stromal cells expanded to 80% confluence in monolayer culture.  Total RNA was linearly amplified and applied to a 9413-probe set equine-specific cDNA microarray.  Four repair tissue samples were compared with a dye-swap experimental design to four samples from each of the three other cell populations for a total of twelve comparisons, or twenty-four slides.  Differential expression of genes of interest was validated by real-time quantitative polymerase chain reaction.  Statistical analysis revealed that a total of 934 (9.9%), 1839 (19.5%), and 940 (10.0%) probe sets were differentially expressed for the bone marrow stromal cells versus repair tissue, de-differentiated chondrocytes versus repair tissue, and neonatal articular chondrocytes versus repair tissue comparisons, respectively.  Transcriptional and translational machinery gene ontological categories were over-represented in transcripts demonstrating stable expression amongst the three comparisons.  Biomarkers typically associated with normal articular cartilage and fibrocartilage repair tissue comprised much of the genes with the greatest levels of differential expression amongst the three comparisons.  Overall, the profiles indicated that repair cells were more chondrogenic than bone marrow stromal cells and de-differentiated chondrocytes.  However, transcript levels of key biomarkers and growth factors for repair tissue cells four months post-operatively fell far short of those of neonatal articular chondrocytes destined to undergo normal cartilage maturation.

overall_design: This is a direct comparison between repair tissue and three cell phenotypes: full-thickness neonatal, de-differentiated chondrocytes, and bone marrow stromal cells.  Each cell type was compared to repair tissue; four replicates representing different horses were used in each comparison (e.g., 4 REP, 4 DDCs, 4 NEO, 4 BMSCs). Thus, each comparison involves one of four repair tissue samples and one of each cell type with a dye-swap.

first: Liping

last: Huang

first: Arne

last: Bathke

first: Arnold

last: Stromberg

first: James

middle: N

last: MacLeod


title: A Comparison of HEEBO Microarray and 3'-end Sequencing for Expression Quantification (3SEQ) (Archival Tumor Samples)

first: Andrew

last: Beck

address: Stanford

summary:
Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3'-end sequencing for expression quantification (3SEQ)) for gene expression profiling from FFPET using next-generation sequencing. We performed gene expression profiling by 3SEQ and microarray on both frozen tissue and FFPET from two soft tissue tumors (desmoid type fibromatosis (DTF) and solitary fibrous tumor (SFT)) (total n = 23).  Analysis of 3SEQ data revealed many genes differentially expressed between the tumor types (FDR < 0.01) on both the frozen tissue (~9.6K genes) and FFPET (~8.1K genes). Analysis of microarray data from frozen tissue revealed fewer differentially expressed genes (~4.64K), and analysis of microarray data on FFPET revealed very few (69) differentially expressed genes. Functional gene set analysis of 3SEQ data from both frozen tissue and FFPET identified biological pathways known to be important in DTF and SFT pathogenesis and suggested several additional candidate oncogenic pathways in these tumors. These findings demonstrate that 3SEQ is an effective technique for gene expression profiling from archival tumor samples and may facilitate significant advances in translational cancer research.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Preservation: either frozen (FROZEN) or formalin fixed paraffin embedded tissue (FFPET)
Disease State: Tumor type: desmoid type fibromatosis (DTF) or solitary fibrous tumor (SFT)

Keywords: Logical Set

overall_design: Computed

first: Matt

last: Van De Rijn


title: delta-arcS versus wild-type

status: Public on Mar 25 2010

city: Marburg an der Lahn

first: Jürgen

last: Lassak

state: Hessen

address: Karl-von-Frisch Strasse

department: Ecophysiology

institute: Max-Planck-Institute for Terrestrial Microbiology

summary: The availability of oxygen is a major environmental factor for many microbes, in particular for bacteria, such as Shewanella species, which thrive in redox-stratified environments. One of the best studied systems involved in mediating the response to changes in environmental oxygen levels is the Arc two-component system of Escherichia coli, consisting of the sensor kinase ArcB and the cognate response regulator ArcA. An ArcA ortholog was previously identified in Shewanella, and as in E. coli, Shewanella ArcA is involved in regulating the response to shifts in oxygen levels. Here, we identified the hybrid sensor kinase SO_0577, now designated ArcS, as the previously elusive cognate sensor kinase of the Arc system in S. oneidensis MR-1. Phenotypic mutant characterization, transcriptomic analysis, protein-protein interaction and phosphotransfer studies revealed that the Shewanella Arc system consists of the sensor kinase ArcS, the single phosphotransfer domain protein HptA, and the response regulator ArcA. Phylogenetic analysis suggests that HptA might be a relict of ArcB. Conversely, ArcS is substantially different with respect to overall sequence homologies and domain organization. Thus, we speculate ArcS might have adopted the role of ArcB after loss of the original sensor kinase, perhaps as a consequence of regulatory adaptation to a redox-stratified environment.

overall_design: In the study presented, expression profiles of  three independent replicates of Shewanella oneidensis MR-1 delta-arcS were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells. All samples were obtained from exponentially aerobically grown cells in LB

middle: M

first: Kai

last: Thormann


title: Multiomics study to identify virulence factors of Rickettsia prowazekii revealed its adaptive mutation capabilities

status: Public on Mar 29 2010

city: Marseille

first: LEROY

last: Quentin

address: 27 Boulevard Jean Moulin

institute: URMITE

summary: We identified four virulence phenotypes of Rickettsia prowazekii (the deadly agent of epidemic typhus) that are associated with the upregulation of antiapoptotic genes (virulent strain) or the Interferon I pathway (avirulent). Transcriptional and proteomic analyses of R. prowazekii linked surface protein expression and methylation with virulence. By sequencing a virulent strain and using comparative genomics, we found hotspots of mutations in homopolymeric tracts of poly(A) and poly(T) that lead to gene split and inactivation and explain the loss of virulence in the vaccine strain. These areas of instability explains adaptive mutations leading to virulence recovery in the vaccine strain.

sample_organism:
Rickettsia prowazekii
Rickettsia prowazekii str. Rp22

overall_design: Transcriptional analysis of two different strains growing in L929 cells. A virulent strain (Rp22) was compared to a avirulent strain (Erus). The experiment was performed with 3 independant biological replicates.

first: Yassina

last: Bechah

first: Khalid

last: El Karkouri

first: Oleg

last: Mediannikov

first: Quentin

last: Leroy

first: Nicolas

last: Pelletier

first: Catherine

last: Robert

first: Claudine

last: Medigue

first: Jean-Louis

last: Mege

first: Didier

last: Raoult


title: Cold acclimation in pea

city: Villeneuve d'Ascq

first: Lucau

last: Anca

address: Cité Scientifique SN2/302

department: Stress Abiotiques et Différenciation des Végétaux Cultivés

institute: UMR  USTL / INRA 1281

summary: To understand physiological mechanisms of cold acclimation in pea, we performed a transcriptomique analysis in order to compare the response to LT treatment in two varieties, one being cold tolerant (Champagne) and the other cold sensitive (Terese).

overall_design: For each genotype, course time d2, d5, d10 and d20 gene expression of each treatment (acclimated and non-acclimated) was compared with gene expression of d0 on slides.

first: Lucau-Danila

first: Toitot

last: Clarisse

first: Blervacq

last: Anne-Sophie

first: Hot

last: David

first: Bahrman

last: Nasser

first: Goulas

last: Estelle

first: Lejeune

last: Isabelle

first: Delbreil

last: Bruno


title: Development and heat stress-induced transcriptomic changes during embryogenesis of the coral Acropora palmata

city: Wilmington

first: Kevin

last: Portune

state: NC

address: 601 S. College Road

institute: University of North Carolina, Wilmington

summary: Projected elevation of seawater temperatures poses a threat to the reproductive success of Caribbean reef-building corals that have planktonic development during the warmest months of the year.  This study examined the transcriptomic changes that occurred during embryonic and larval development of the elkhorn coral,  Acropora palmata, at a non-stressful temperature (28°C) and further assessed the effects of two elevated temperatures (30°C and 31.5°C) on these expression patterns.  Using cDNA microarrays, we compared expression levels of 2,051 genes from early embryos and larvae at multiple developmental stages (including pre-blastula, blastula, gastrula, and planula stages) at each of the three temperatures.  At 12 hours post-fertilization in 28°C treatments, genes involved in cell replication/cell division and transcription were up-regulated in A. palmata embryos, followed by a reduction in expression of these genes during later growth stages.  From 24.5 to 131 hours post-fertilization at 28°C, A. palmata altered its transcriptome by up-regulating genes involved in protein synthesis and metabolism.  Temperatures of 30°C and 31.5°C caused major changes to the A. palmata embryonic transcriptomes, particularly in the samples from 24.5 hpf post-fertilization, characterized by down-regulation of numerous genes involved in cell replication/cell division, metabolism, cytoskeleton, and transcription, while heat shock genes were up-regulated compared to 28°C treatments.  These results suggest that increased temperature may cause a breakdown in proper gene expression during development in A. palmata by down-regulation of genes involved in essential cellular processes, which may lead to the abnormal development and reduced survivorship documented in other studies.

overall_design: Our experimental setup followed a reference design where all samples were hybridized against the same pool made up of equal amounts of RNA from all samples in the experiment.  Biological duplicate samples were used for each temperature at each developmental time period.  Common reference samples were labeled with Cy3 dye, while temperature samples were labeled with Cy5 dye.  Microarrays for A. palmata contained 2,051 coding sequences, of which 54.3% had functional annotations as determined by homology to known genes.

first: Christian

middle: R

last: Voolstra

first: Mónica

last: Medina

first: Alina

last: Szmant


title: Bovine pre-transfer endometrium and embryo transcriptome fingerprints as predictors of pregnancy success after embryo transfer (embryo study)

city: Bonn

first: Dessie

last: Salilew-Wondim

state: NRW

address: Endenicher Allee 15

department: Animal breeding and husbandry group

institute: University of Bonn

summary: The aberrant gene expression in the uterine endometrium and embryo has been the major causes of pregnancy failure in cattle. Therefore, selecting cows having adequate endometrial receptivity and embryos of better developmental competence based on the gene expression could increase the number of calves produced by each cow during its productive life time.

overall_design: We used endometrial and embryo biopsy technology in conjunction with the pregnancy outcome information to establish a direct link between the pre-transfer endometrial or in vivo derived embryo gene expression and pregnancy outcome after embryo transfer. Endometrial samples were collected  from Simmental heifers at day 7 and 14 of the estrous cycle, one cycle prior to embryo transfer.  In the next cycle, embryo biopsies consisting of 60-70% of inner cell mass and trophectoderm were transferred to the recipients at day 7 of the estrous cycle. The remaining 30-40% parts of the embryos were retained for analysis.Pregnancy diagnosis was performed at days 28 and 42 by ultrasonography and at day 56 by rectal palpation. Those heifers returned to heat at day 21 were considered as non pregnant or non receptive endometrium (NP) while those heifers ended up with successful pregnancy and calf delivery was considered as the calf delivery group or receptive endometrium (CD). Following this, the endometrial samples collected during the pre-transfer period and the embryo biopsies retained during embryo transfer were categorized based on the pregnancy outcome. Those endometrial biopsies collected at days 7 and 14 of the estrous cycle from heifers resulted in successful calf delivery were designated as CDd7 and CDd14, respectively and endometrial biopsies taken at days 7 and 14 of the estrous cycle from those subsequently resulted in no pregnancy were designated as NPd7 and NPd14, respectively. Similarly, the embryo biopsies were classified as those embryo biopsies resulted in successful calf delivery and those resulted in no pregnancy

first: Michael

last: Hölker

first: Franca

last: Rings

first: Mehmet

last: Ulas-Cinar

first: Jaana

last: Peippo

first: Ernst

last: Tholen

last: Looft

first: Karl

last: Schellander

first: Dawit

last: Tesfaye


title: Bifidobacterium longum mutant

city: Zurich

first: Valeria

last: Mozzetti

address: Schmelzbergstrasse 7

department: D-AGRL

country: Switzerland

institute: ETH

summary:
Transcriptional profiling of Bifidobacterium longum mutant versus wt strain in exponentional phase

Keywords: Characterization of natural mutant

overall_design: One B. longum mutant (HPR2) was analysed versus the wt strain NCC2705 in: exponential phase 37°,pH 6.0, MRS, headspace flushing with CO2. Three biological replicates.

first: Deborah

last: Moine

first: Bernard

last: Berger


title: FBLN1 and FABP4 are drivers of resistance to fleece rot in Australian Merino sheep

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

summary: Transcriptional profiling of Ovine skin samples comparing resistant (RES) to susceptible (SUS) animals following fleece rot induction.

platform_organism:
Bos taurus
Ovis aries

overall_design:
Two condition experiment, RES vs SUS biopsies, over 3 time points. 31 RES 31 SUS
T0: Prior to commencment of treatment
T1: 2-3 days post commencment
T2: 11 days post commencment

The first skin biopsies were taken on the first day (T0) prior to commencement of the five day regime of simulated rainfall. Subsequent skin biopsies were taken 2-3 days into the wetting regime (T1) and following a recovery period of 11 days from the time that the wetting regime had begun (T2).

first: Wendy

last: Smith

first: Antonio

last: Reverter


title: Functional Variomics Library testing for drug resistance in yeast

city: Houston

first: Richard

last: Sucgang

address: 1 Baylor Plaza

department: Biochemistry and Molecular Biology

institute: Baylor College of Medicine

summary: Variants of the essential genes in budding yeast S. cerevisae were cloned into a variomics library, and tested for their ability to confer resistance to three different drugs. Genes were tagged with molecular barcodes, and the relative change in abundance of the molecular barcodes are detected using a spotted Agilent synthesized microarray.

overall_design: Three condition experiment (3 drugs, rapamycin, tunicamycin and cycloheximide).

first: Huang

last: Zhiwei

first: Shi

last: Xiaomin

first: Cui

last: Dandan

first: Sucgang

last: Richard

first: Pan

last: Xuewen


title: Early CCL2 and CXCL10 chemokine expression correlates with lung pathology in Pandemic H1N1 Influenza A infection

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

summary:
Background: Pandemic H1N1 influenza A is a newly emerging strain of human influenza that is easily transmitted between people and has spread globally to over 116 countries. Human infection leads to symptoms ranging from mild to severe with lower respiratory complications observed in a small but significant number of infected individuals. Little is currently known about host immunity and Pandemic H1N1 influenza infections.
Methods: We examined the pathogenic potential of the pandemic influenza A vaccine strain, A/California/07/2009 (H1N1), in ferrets, and characterized the host immune responses using microarray analysis. Gene expression profiles in lung tissue were compared with those from ferrets infected with A/Brisbane/59/2007.
Results: Chemokines CCL2, CCL8, CXCL7 and CXCL10 along with the majority of ISGs were expressed early, correlated to lung pathology, and abruptly decreased expression in 5 days. Interestingly, the drop in innate immune gene expression was replaced by a significant increase in the expression of the adaptive immune genes for granzymes and immunoglobulins. Serum anti-pandemic influenza H1N1 antibodies were also observed on day 7, commensurate with the elimination of viral load.
Conclusions: We propose that the innate phase of host immunity causes lung pathology and a delay or failure to effectively switch to the adaptive phase contributes to morbidity and mortality during severe human pandemic H1N1 influenza A infections.
Keywords: influenza, immune response, cytokines, chemokines, lung infection, time course

overall_design: In the experiment with influenza A/California/07/2009 (H1N1),15 ferrets were randomly allocated to 5 groups: Day 0 (before infection), and Day 3, 5, 7 and 14 (post infection) with 3 biological replicates for each group. Likewise, a second experiment with A/Brisbane/59/2007 (H1N1) was carried out using the same experimental groups, except for a group in Day 2, instead Day 3.  Ferrets were euthanized and lung tissue was excised for RNA purification on the scheduled date. The subsequent gene expression analysis was performed with Affymetrix GeneChip Canine Genome 2.0 Array. Day 0 groups were used as control.

first: David

last: Kelvin


title: Japanese human fibroblasts: Healthy vs. Pachydermoperiostosis (PDP)

city: Yahata-nishi, kitakyushu

first: Junichi

last: Sakabe

state: Fukuoka

address: 1-1 Iseiga-oka

department: Graduate School of Medicine

institute: University of Occupational and Environmental Health

summary:
Human fibroblasts comparison between healthy and PDP.

Keywords: genetic disease

overall_design: Two-condition experiment, Control vs. PDP fibroblasts.

first: Kenji

last: Kabashima

first: Jun-ichi


title: Diurnal expression data from developing barley caryopses

city: Tuebingen

first: Joachim

last: Kilian

address: Auf der Morgenstelle 1

department: ZMBP Plant Physiology

institute: University of Tuebingen

summary:
Caryopses of barley (Hordeum vulgare), like all other cereal seeds, are complex sink organs optimized for storage starch accumulation and embryo development. Their development from early stages after pollination to late stages of seed ripening has been studied in great detail. However, information on the caryopses’ diurnal adaptation to changes in light, temperature and alterations in phloem-supplied carbon and nitrogen remained unknown.
In this study, we applied the 22K Barley1 GeneChip microarray to investigate diurnal gene regulation events of barley caryopses at 11 to 12 days post anthesis.

overall_design: Developing barley caryopses were harvested at different time-points of a day (at 7:00 AM, 2:00 PM, 5:00 PM and 8:00 PM) including dark samples (6:00 AM and 10:00 PM). Pooled caryopses (form 3 Plants) from the respective time points were used for RNA extraction and hybridization on Affymetrix microarrays (Barley1 GeneChip; GEO accsession GPL1340). Biological replicates were performed.

first: Elke

last: Mangelsen

first: Dierk

last: Wanke

first: Christer

middle: G

last: Jansson


title: SEA BREAM PATH_INTEST

city: Galway

first: Michael

middle: Taylor

last: Cairns

address: University Road

department: MRI

country: Ireland

institute: NUI Galway

summary:
To determine the effects on the intestine gene expression of pathogen exposure to Enteromyxum leei. One fish group was exposed to E. leei-contaminated effluent (recipient group = R) . R fish (n= 66, average weight = 134 g) were placed in two replicated 200L fibre-glass tanks which were set to receive exclusively the effluent water from another tank containing 24 infected (donors = D; average weight = 127.3 g; prevalence of infection = 54%) gilthead sea bream. The D to R fish ratio was 0.8. Other 66 naïve fish were allocated in two replicated tanks (control group = CTRL) under the same conditions, but without receiving contaminated effluent. Over the course of the study, day length followed natural changes and water was heated in order to keep temperature always above 18ºC, the range was 18-23 ºC. Water was 5 µm-filtered and UV irradiated, and salinity was 37.5‰. Water flow was 10L/min and oxygen content of outlet water remained higher than 85%saturation. All fish were fed daily a commercial dry pellet diet at about 1% of body weight. Disease signs and daily mortalities were recorded throughout the experiments. The parasitic status of dead fish was checked by microscopic examination of fresh intestinal scrapings.   Fish were sampled after 113 days post exposure (p.e.). Feeding was stopped one day prior to the sampling to ensure that the digestive tract was empty. Head kidney and posterior intestine were rapidly excised, frozen in liquid nitrogen, and stored at -80 °C until RNA extraction and analysis.

Keywords: Treated/Untreated, confinement, cortisol, stress response, time course, microarray

sample_organism:
Sparus aurata
Enteromyxum leei

overall_design: 28 intestine samples - Twenty eight 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: Grace

last: Davey

first: Josep

last: Calduch-Giner

first: Jaume

last: Pérez-Sánchez

first: Benoit

last: Houeix

first: Anita

last: Talbot

last: Reinhardt


title: Transciptional profile of a M. smegmatis mc2155 ΔsigF strain under standard growth conditions

city: Dunedin

first: Anja

last: Huempel

address: 720 Cumberland St

department: Microbiology & Immunology

country: New Zealand

institute: University of Otago

summary: Comparing transciptional profile of a M. smegmatis mc2155 ΔsigF strain and wild type (control) in in vitro culture at two time points (exponential phase and stationary phase) for identification of SigF-dependent genes.

overall_design: Analysis of 2 time points: exponential and stationary phase. 4 biological replicates comparing expression of wild type (control) and ΔsigF strain incl. dye swaps for each time point. 3 technical replicates per array

first: Susanne

last: Gebhard

first: Greg

last: Cook

last: Berney