title: L. plantarum growth curve experiment sampled a different optical densities

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

summary: Specific Lactobacillus strains are marketed as probiotics i.e. health promoting organisms. As previously shown in vivo, L. plantarum WCFS1 modulates immune responses via nuclear factor (NF)kB in a growth phase dependent manner, likely caused by changed microbial cell surface characteristics. Here, we identified the differential cell-surface proteome composition of L. plantarum WCFS1 cells derived from the mid-logarithmic and late stationary growth phase by surface trypsination of intact bacterial cells, followed by a combined 1D- and 2D-LC-MS shotgun proteomics strategy, and growth phase dependent transcriptome analysis. Overall, these analyses led to the identification of 31 surface proteins differentially present in the logarithmic and stationary phase, whereas additional 17 and 33 proteins appeared solely present in stationary and logarithmic phase of growth, respectively. From 75% of predicted surface related genes displaying relatively high expression levels, the corresponding proteins were detected, demonstrating a high correlation between transcriptome and proteome profiles. The impact of cell-surface peptide fractions on cellular host responses was evaluated using NFkB promoter activation assays in intestinal epithelial cells, revealing that only late stationary phase derived peptides are capable of attenuating flagellin and cell envelope induced NFkB activation. Overall our data mechanistically expand earlier observations that revealed growth-phase dependent immunomodulation by L. plantarum WCFS1, leading to a typical adjuvant- or tolerance-like response after exposure to stationary phase harvested bacterial cells. Sub-fractionation of the late stationary phase peptide fraction revealed a sub-set of strong attenuator peptides able to manipulate NFkB related pathways to hereby attenuate pro-inflammatory signaling.

overall_design: Samples were hybridizedin a loop design linking each timepoint to the next as well as the previous timepoint. Additional hybridizations were introduced linking each sample three timepoints forward and three timepoints back. All samples were hybridized unsing at least each of the two dyes once.

first: Daniela

last: Remus

first: Fabrizia

last: Fusetti

first: Jurgen

last: Karcewski

first: Roger

middle: S

last: Bongers

first: Bert

last: Poolman

first: Paul

last: de vos

first: Jerry

last: Wells

first: Peter

last: Bron

last: Kleerebezem


title: Modulation of Lactobacillus plantarum gastrointestinal robustness by fermentation conditions enables identification of bacterial robustness markers

status: Public on Jan 01 2012

summary: Transcriptome profiles of control Lactobacillus plantarum WCFS1 cells were compared with a lp_1669 deletion mutant in MRS and 2*CDM media.

overall_design: A continuous culture was performed on MRS and 2*CDM media and whole genome transcriptome analysis was perfomred on the WCFS1 and NZ3417CM (harboring a chlooramphenicol resistance marker (cat) replacement mutation in lp_1669) strains.

first: Hermien

middle: v

last: van de Veen

first: I

last: Lee

first: Maria

last: Marco


title: Normal human osteoblasts and MCF7 mono and coculture

status: Public on Jan 06 2012

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

summary: As a model for investigating changes in gene expression in response to epithelial-osteoblast interactions in bone metastases of breast carcinomas, cells that represented malignant epithelial cell compartments (MCF7) and cells that represented skeletal compartments (Normal Human (NH) Osteoblasts) were examined in an in vitro mixed co-culture setting. These two types of cells were co-cultivated for 48 h in a low-serum medium [0.2% fetal bovine serum (FBS)] to allow reciprocal signal exchange with minimal background from undefined molecular signals that are inherent in fetal bovine serum. We examined the effects of co-cultivation on each cell pairing in two independent biological replicates. The gene expression profiles of the co-cultures were compared to the expression profiles of the corresponding cells that were kept in monoculture using HEEBO microarrays. After mono or co-culturing, total RNA was extracted and amplified using a modified Eberwine procedure. The amplified RNA was labeled with the fluorescent dye Cy5 and pooled with Cy3 labeled reference RNA, and then the pooled RNA was hybridized onto HEEBO microarrays. After hybridization and washing, arrays were scanned on a fluorescent microscope scanner.

overall_design: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

first: Tatiparthi

last: Reddy


title: Expression of Stem Cell Pluripotency genes in mASCs and ES, iPS, and mi-iPS cells

city: Suita

first: hideshi

last: ishii

state: Osaka

address: Yamadaoka 2-2

department: Department of Gastroenterological Surgery

country: Japan

institute: Osaka University Graduate School of Medicine

summary: Comparison of TaqMan Gene Signature Arrays (Mouse Stem Cell Pluripotency Array) was represented in mASCs and ES, iPS, and mi-iPS cells.

first: N

last: Miyoshi

first: H

last: Ishii

first: M

last: Mori


title: Normal human osteoblasts and T47D mono and coculture

summary: As a model for investigating changes in gene expression in response to epithelial-osteoblast interactions in bone metastases of breast carcinomas, cells that represented malignant epithelial cell compartments (T47D) and cells that represented skeletal compartments (Normal Human (NH) Osteoblasts) were examined in an in vitro mixed co-culture setting. These two types of cells were co-cultivated for 48 h in a low-serum medium [0.2% fetal bovine serum (FBS)] to allow reciprocal signal exchange with minimal background from undefined molecular signals that are inherent in fetal bovine serum. We examined the effects of co-cultivation on each cell pairing in two independent biological replicates. The gene expression profiles of the co-cultures were compared to the expression profiles of the corresponding cells that were kept in monoculture using HEEBO microarrays. After mono or co-culturing, total RNA was extracted and amplified using a modified Eberwine procedure. The amplified RNA was labeled with the fluorescent dye Cy5 and pooled with Cy3 labeled reference RNA, and then the pooled RNA was hybridized onto HEEBO microarrays. After hybridization and washing, arrays were scanned on a fluorescent microscope scanner.


title: Normal human osteoblasts and Hs578t mono and coculture

summary: As a model for investigating changes in gene expression in response to epithelial-osteoblast interactions in bone metastases of breast carcinomas, cells that represented malignant epithelial cell compartments (Hs578T) and cells that represented skeletal compartments (Normal Human (NH) Osteoblasts) were examined in an in vitro mixed co-culture setting. These two types of cells were co-cultivated for 48 h in a low-serum medium [0.2% fetal bovine serum (FBS)] to allow reciprocal signal exchange with minimal background from undefined molecular signals that are inherent in fetal bovine serum. We examined the effects of co-cultivation on each cell pairing in two independent biological replicates. The gene expression profiles of the co-cultures were compared to the expression profiles of the corresponding cells that were kept in monoculture using HEEBO microarrays. After mono or co-culturing, total RNA was extracted and amplified using a modified Eberwine procedure. The amplified RNA was labeled with the fluorescent dye Cy5 and pooled with Cy3 labeled reference RNA, and then the pooled RNA was hybridized onto HEEBO microarrays. After hybridization and washing, arrays were scanned on a fluorescent microscope scanner.


title: Microarrays analysis of RNA isolated from 7days-Sertoli cell culture of 14 day-old AMH-Cre/WT and WT/WT C57BL/6J mouse testes

city: Giessen

first: Eveline

last: Baumgart-Vogt

state: Hesse

address: Aulweg 123

department: Institute for Anatomy and Cell Biology II

country: Germany

institute: Justus Liebig University Giessen

summary: In order to understand whether sole Cre recombinase expression has an effect on stress signalling pathways and the peroxisomal or other subcellular compartments, we have analyzed total RNA isolated from Sertoli cell cultures of anti-Müllerian-hormone (AMH)-Cre/wild-type and wild-type/wild-type C57BL/6J mouse testes using microarrays.

overall_design: The Sertoli cells were isolated from individual 14 day-old mice and were cultivated for 7 days. Total RNA was isolated from the Sertoli cell culture (for AMH-Cre/WT 5 mice and WT/WT 3 mice) and the same genotypes were pooled together. For the microarray analysis two technical replicates for each genotype were generated.

first: Yu

last: Xiao

first: Srikanth

last: Karnati

first: Guofeng

last: Qian

first: Anca

last: Nenicu

first: Anita

last: Höland

first: Hamid

last: Hossain

first: Svetlin

last: Tchatalbachev

first: Florian

last: Guillou

first: Georg

middle: H

last: Lüers


title: Subcutaneous and omental white adipose tissue biopsies analysed from five obese patients

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

country: United Kingdom

institute: Biomathematics & Statistics Scotland

summary: The objective was to characterize differences in the secretome of human omental compared with subcutaneous adipose tissue using global gene expression profiling. Gene expression was measured using Affymetrix microarrays in subcutaneous and omental adipose tissue (n=5 independent subjects; 10 arrays). Predictive bioinformatic algorithms were employed to identify those differentially expressed genes that code for secreted proteins and to identify common pathways between these proteins. The time course data was not included in the publication and  has yet to be published. Patients undergoing surgery were weight stable one month prior to the operation and were not on any medication. All patients provided informed written consent before inclusion in the study which was approved by the North of Scotland Research Ethics Committee (NOSREC).

overall_design:
The subcutaneous and omental white adipose tissue biopsies were analysed from five obese patients (BMI 44.5 +/-10 kg/m2; age 42.7 +/- 10 years) who had fasted overnight.
Subcutaneous and omental white adipose tissue biopsies were taken at the time of surgery for vertical banded gastroplasty from n=5 independent subjects who had fasted overnight. (10 arrays).

Further subcutaneous adipose tissue samples were taken at approximately four months post vertical banded gastroplasty surgery as the volunteers actively lost weight and at 12 months when the volunteers became weight stable (n=5 independent subjects, three time points 0, 4, and 12 months; 15 arrays). Therefore we report on 20 arrays in total including the arrays used to analyse the omental adipose tissue.

Adipose tissue samples were obtained within 5 minutes of the tissue being extracted from the patients and frozen immediately in liquid nitrogen. Subjects had fasted overnight prior to surgery. Total RNA was extracted using the RNeasy Lipid tissue mini kit followed by incubation with RNase free DNase (Qiagen, Crawley, West Sussex) for DNA-free RNA, following the manufacturer's instructions (Qiagen, Crawley, West Sussex). RNA was quantified on the Agilent 2100 Bioanalyser (Agilent Technologies, South Queensferry, West Lothian). This also shows the quality of the RNA extracted from the tissues. Only RNA showing no degradation (RIN greater than 9.0) was processed further.     The DNA-free RNA from the subcutaneous and omental adipose tissue samples from the patients was then sent to a commercial company for analyses. The RNA from five volunteers (20 arrays ) was fragmented and hybridised to custom Human NuGo (Nutrigenomics; http://www.nugo.org/everyone/35788) Affymetrix (Santa Clara, CA) gene chips HS 1a520180 following the Affymetrix protocol by Service XS (Leiden, The Netherlands). Briefly, the Affymetrix one-cycle target labelling and control reagents were used to synthesize Biotin-labelled cRNA. The concentration of the cRNA was measured using a Nanodrop (Thermoscientific) and Agilent bioanalyser to rule out the possibility that only very short cRNA products were formed. This could have caused a 3’-5’ bias and influenced the data analysis. Approximately 20µg cRNA was used for further fragmentation and finally 10µg was used for the hybridisations. The Affymetrix protocols were followed for the hybridisations, washing, staining and scanning of the chips

first: Nigel

last: Hoggard

first: Morevn

last: Cruickshank

first: Kim

middle: M

last: Moar

first: Shabina

last: Bashir

first: Claus-Dieter


title: Distinct Ldb1/NLI complexes orchestrate γ-globin repression and re-activation through ETO2 in human adult erythroid cells.

status: Public on Jan 05 2012

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

country: USA

institute: National Institutes of Health

type: Genome binding/occupancy profiling by genome tiling array

summary:
The Ldb1/GATA-1/TAL1/LMO2 complex mediates long range interaction between the β-globin locus control region (LCR) and gene in adult mouse erythroid cells but whether this complex mediates chromatin interactions at other developmental stages or in human cells is unknown. We investigated human NLI (Ldb1 homologue) complex occupancy and chromatin conformation of the β-globin locus in human erythroid cells. In addition to the LCR, we find robust NLI complex occupancy at a site downstream of the Aγ-globin gene, within sequences of BGL3, an intergenic RNA transcript. In cells primarily transcribing β-globin, BGL3 is not transcribed and BGL3 sequences are occupied by NLI core complex members together with co-repressor ETO2 and γ-globin repressor BCL11A. The LCR and β-globin gene establish proximity in these cells. In contrast, when γ-globin transcription is re-activated by cytokines in these cells, ETO2 participation in the NLI complex at BGL3 is diminished, as is BCL11A occupancy, and both BGL3 and γ-globin are transcribed. In these cells, proximity between the BGL3/γ-globin region and the LCR is established. Thus, alternative NLI complexes mediate γ-globin transcription or silencing through long range LCR interactions involving an intergenic site of non-coding RNA transcription and ETO2 is critical to this process.
ChIP-chip of GATA-1, NLI, and pol II in cell lines

overall_design: Comparison of GATA-1, NLI, and pol II binding on chromatin. 2 replicates for each protein; ChIP and input DNA for each replicate

first: Chunhui

last: Hou

first: Ann

last: Dean


title: A novel nonsense mutation in DMP1 gene identified by a genome-wide association study is responsible for inherited rickets in Corriedale sheep

city: Ames

first: Dorian

last: Garrick

state: IA

address: 2255 Kildee

institute: Iowa State University

summary: Inherited rickets of Corriedale sheep is characterized by decreased growth rate, thoracic lordosis and angular limb deformities. Previous outcross and backcross studies suggest it is a simple autosomal recessive disorder. A genome wide association study was conducted using the Illumina OvineSNP50 BeadChip on 20 related sheep including 17 affected and 3 carriers. A homozygous region of 199 consecutive single-nucleotide polymorphism (SNP) loci was identified in all the affected sheep, covering a region of 10Mbp on ovine chromosome 6. Among 91 candidate genes in this region, exon 6 of the dentin matrix protein 1 gene (DMP1) was sequenced to reveal 9 SNPs including a nonsense mutation 253T/C which introduced a stop codon (R145X) and could truncate C-terminal amino acids. Genotyping by PCR-RFLP for this mutation showed that, all 17 affected sheep were “T T” genotypes and the 27 phenotypically normal sheep were either “C T” or “C C”. This locus is not in complete linkage disequilibrium with the other 8 SNPs that can all be ruled out as candidates. Previous research has shown that mutations in DMP1 gene are responsible for autosomal recessive hypophosphatemic rickets in humans.  Dmp1_knockout mice also exhibit rickets phenotypes. We believe the R145X mutation to be responsible for the inherited rickets found in Corriedale sheep. A simple diagnostic test can be designed to identify carriers with the defective “T” alleles. Affected sheep could be used as animal models for this form of human rickets, and for further investigation of the role of DMP1 in phosphate homeostasis

overall_design: A genome wide association study was conducted using the Illumina OvineSNP50 BeadChip on 20 related sheep including 17 affected and 3 carriers to define homozygous regions with consecutive single-nucleotide polymorphism (SNP) loci only existing in all the affected sheep. Fine mapping was conducted by screening coding regions and splicing regions on the positional candidate genes within the homozygous regions by using more sheep

first: Xia

last: Zhao

first: Keren

middle: E

last: Dittmer

first: Hugh

middle: T

last: Blair

first: Keith

middle: G

last: Thompson

first: Max

middle: F

last: Rothschild

middle: J


title: Fiorentino 2006-7 dermatomyositis, lupus, control skin

status: Public on Jan 12 2012

city: Stanford

first: David

last: Fiorentino

state: CA

address: 900 Blake Wilbur Drive

department: Dermatology

institute: Stanford University

summary:
Background: Dermatomyositis (DM) is an autoimmune disease that mainly affects the skin, muscle, and lung. The pathogenesis of skin inflammation in DM is not well understood.
Methodology and Findings: We analyzed genome-wide expression data in DM skin and compared them to those from healthy controls. We observed a robust upregulation of interferon (IFN)-inducible genes in DM skin, as well as several other gene modules pertaining to inflammation, complement activation, and epidermal activation and differentiation. The interferon (IFN)-inducible genes within the DM signature were present not only in DM and lupus, but also cutaneous herpes simplex-2 infection and to a lesser degree, psoriasis. This IFN signature was absent or weakly present in atopic dermatitis, allergic contact dermatitis, acne vulgaris, systemic sclerosis, and localized scleroderma/morphea. We observed that the IFN signature in DM skin appears to be more closely related to type I than type II IFN based on in vitro IFN stimulation expression signatures. However, quantitation of IFN mRNAs in DM skin shows that the majority of known type I IFNs, as well as IFN gamma, are overexpressed in DM skin. In addition, both IFN-beta and IFN-gamma (but not other type I IFN) transcript levels were highly correlated with the degree of the in vivo IFN transcriptional response in DM skin.


title: Analysis of deregulated microRNAs in malignant mesothelioma

status: Public on Jan 11 2012

city: Bochum

first: Daniel

middle: Gilbert

last: Weber

address: Bürkle-de-la-Camp Platz 1

department: Molekulare Medizin

institute: IPA

summary: The expression of human microRNAs in the cellular fraction of human peripheral blood of patients with diagnosed malignant mesotheliomas and asbestos-exposed controls. Altered expression of several miRNAs were observed for patients with diagnosed malignant mesotheliomas in comparison with asebstos-expsoed controls.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
The study group consists of 23 patients with diagnosed malignant mesothelioma (mean age 66 years, range 34 – 84 years). Patients were not treated with chemotherapy or radiation therapy before sample collection. The histological subtypes were: one sarcomatoid, seven biphasic, and twelve epithelioid cases. In three cases the histological subtype was unknown. The control group consists of 17 asbestos-exposed age-matched volunteers without any diagnosed cancer (mean age 68 years, range 47 – 80 years).
Oligonucleotide microarrays were purchased from the Norwegican Microarray Consortium (www.microarray.no). The mirVana miRNA Probe Set v2.0 (Ambion) based on the miRBase Sequence Database v8.0. was used.

first: Oleksandr

last: Bryk

first: Thomas

last: Brüning

first: Georg

last: Johnen


title: Gene Expression Changes In potato Tuber Meristems Treated with the Sprout Inhibitor 1,4-dimethylnapthlene

city: Erie

first: Michael

middle: A

last: Campbell

state: PA

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

summary:
The suppression of sprout growth is critical for the long-term storage of potato tubers. 1,4-dimethylenapthlene (DMN) is a new class of sprout control agent but the metabolic mode of action for this compound has yet to be elucidated. Changes in transcriptional profiles of meristems isolated from potato tubers treated with the DMN were investigated using an Agilent 44K 60-mer-oligo microarray. RNA was isolated from nondormant Russet Burbank meristems isolated from tubers treated with DMN for three days or activated charcoal as a control. RNA was used to develop probes that were hybridized against a microarray developed by the Potato Oligo Chip Initiative (POCI). Analysis of the array data was conducted in two stages: total array data was examined using a linear model and the software limma and pathway analysis was conducted by linking the potato sequences to the Arabidopsis thaliana. DMN elicited a change in a number of transcripts associated with cold responses, water regulation, salt stress and osmotic adjustment. Additionally, repression of auxin signaling and transport were observed in DMN-treated tubers, and connections between DMN treatment and repression of FT through mi156 regulation were indicated. DMN also resulted in a repression of cyclin or cyclin-like transcripts. DMN also resulted in a 50% decrease in thymidine incorporation suggesting a repression of the S-phase of the cell cycle.  QT-PCR analysis demonstrated that DMN increased transcripts for the cell cycle inhibitors KRP1 and KRP2. We conclude the DMN results in alteration of genes associated with cold responses and water regulation and maintenance of a G1/S-phase block possibly through the induction of the cell cycle inhibitors KRP1 andKRP2.

Twelve samples, four treatments, three biological replicates

overall_design: Non dormant meristems as control (Control-rep), meristems isolated from tubers treated with water for three days (Control3Days-rep), meristems treated with DMN for three days (DMN3Days-rep), meristems treated with DMN for three days and then vented to the air for two days (DMN3Days-2Out-rep).

first: Alyssa

last: Gleichsner

first: Lindsay

last: Hilldorfer

last: Horvath

first: Jeffrey

last: Suttle


title: Role of Ustilago Nit2 in nitrogen utilization

city: Erlangen

first: Lars

middle: Matthias

last: Voll

address: Staudtstrasse 5

department: Division of Biochemistry

summary: The basidiomycete Ustilago maydis is the causal agent of corn smut disease and induces tumor formation during biotrophic growth in its host plant maize. The Usilago maydis genome harbors a homolog to the GATA transcription factors Nit2 and AreA that act as global regulators of nitrogen catabolite repression in filamentous model fungi Neurospora crassa and Aspergillus nidulans, respectively. We aimed at resolving the role of the Ustilago maydis Nit2 homolog for the utilization of complex nitrogen sources and pathogenicity.

overall_design: Sporidia of the indicated Ustilago maydis strains were grown overnight in ammonium minimal medium (Holliday, 1976) and samples for total RNA extraction were taken 2h after transfer to minimal medium lacking any nitrogen source (-N) during the exponential growth phase to assess those genes that are regulated in response to nitrogen starvation. The solopathogenic strain SG200 (control) and deletion mutants of UmNit2 were studied in two independent experiments. The (Target of Nit2) UmTon1 deletion mutant was examined in one experiment only. All mutants were generated in the SG200 background. Per strain and experiment, three biological replicate samples were analyzed (except for only two biological replicates for the Nit2 mutants in the second experiment).

first: R

last: Horst

first: C

last: Zeh

first: S

last: Sonnewald

first: U

first: L


title: High and low exercise responders

city: TRONDHEIM

first: Anja

last: Bye

address: Olav Kyrres gt 9

country: Norway

institute: NTNU

summary: Aerobic exercise capacity is a strong predictor of disease and survivability but the utility of exercise intervention is largely dependent on how one’s genome interacts with an exercise-training environment. A newly developed rat model selectively bred for inherited differences in response to aerobic exercise training shows to be a useful resource to sort out the networks of genes responsible for signalling exercise-induced changes that benefit cardiac function.

overall_design:
Animals
The study consisted of four groups: 1) HRT trained rats (HRT-T), 2) LRT trained rats (LRT-T) 3) HRT untrained sedentary rats (HRT-S) and 4) LRT untrained sedentary rats (LRT-S) (n=5 in each group).

Experimental protocols were approved by the Institutional Animal Research Ethics Council, Norway.

Sample collection
Left ventricle tissue was snap-frozen in liquid nitrogen and stored at -80oC to time of analysis.

RNA isolation
RNA was isolated from the left ventricle (20 mg) with the mirVana RNA isolation kit (Ambion) according to the manufacturer's instructions.

RNA integrity, purity and quantity were assessed by Bioanalyzer (Agilent Technologies, Santa Clara, US) and Nanodrop (NanoDrop Technologies, Baltimore, US). The concentration of total RNA was measured by Nanodrop with ultraviolet spectrophotometry at 260/280 nm. RNA quality was assessed by electrophoresis on Bioanalyzer chips (Agilent Technologies, Santa Clara, US).

Only samples with a 260/280-ratio of more than 1.8, and RNA integrity number (RIN) value above 8 was analyzed.

Microarray analysis
Samples were hybridized to Applied Biosystems Rat Genome Survey chips v.1.0. All samples were labelled at the same time, and hybridised over two days. The biological groups were balanced between the two hybridisation batches and the samples randomly distributed within this format. Samples were analyzed by the Applied Biosystems 1700 Array Expression System.

The following threes comparisons were done:

A: HRT-S vs. LRT-S
B: HRT-S vs. HRT-T
C: LRT-S vs. LRT-T

Differentially expressed gene analysis
The data files from the AB 1700 Chemiluminescent Microarray Analyzer Software were processed using J-Express Pro v.2.8. The signal intensity values were extracted per spot, and all flagged and control spots were filtered out. Before compiled into an expression profile data matrix, all arrays were quantile normalized to be comparable. Genes with at most 20% missing values were allowed in the final dataset. The signal intensities in the dataset were further log transformed, and missing values were replaced using the method LSimpute Adaptive.

The search for differentially expressed genes was performed both on a single gene and gene set level. Rank Product was used to look for differentially expressed genes on a gene by gene basis, while Gene Set Enrichment Analysis (GSEA) was used to look for sets of genes sharing common characteristics that were differentially expressed between the classes examined.

Gene sets were created using the Panther Biological Processes (241 gene sets) and Panther Molcular Functions (252 gene sets). This information was extracted from the Applied Biosystems Human Annotation File, dated September 30th 2006, with updated information from a Panther search carried out on February 1st 2008. Gene sets smaller than 15 and larger than 500 were excluded from the GSEA.

GSEA
First the genes were ranked according to Golub score, which t is the default method for GSEA. Next an enrichment score (ES) was calculated for each gene set. For instance, when calculating the ES for the gene set “T-cell mediated immunity”, GSEA starts by looking at the gene ranked on top of the genelist. If this gene is a member of T-cell mediated immunity, a positive score is added to the ES, otherwise a negative score is added. Then the next gene on the gene list is evaluated and the ES is updated. This process is repeated for every gene in the entire gene list. The green line in Figure 1 shows how the value of ES changes when evaluating the genes in the ranked list. The maximum value obtained during this “walk” is used as ES for the gene set. Also worth noting is that the positive score that is added to the enrichment score is weigthed, so that a higher score is added when a gene higher on the ranked list is found to be a member of the gene set than when a gene lower on the ranked list is marked with a hit. Therefore, a high ES means that the gene set is overrepresented towards the top of the ranked list.

Gene sets with less than 10 members or more than 500 members were removed from the analysis.


title: TFF2 miRNA expression in Mus musculus

city: Homburg

first: Andreas

last: Keller

address: Building 60

institute: Saarland University

summary: The aim of the study was to investigate whether the trefoil peptide genes, in concerted action with a miRNA regulatory network, were contributing to nutritional maintrenance. Using a Tff2 knock-out mouse model, 48 specific miRNAs were noted to be significantly deregulated when compared to the wild type strain.

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

first: Aftab

last: Shah


title: Differential cardiac gene expression in genetically selected turkeys

city: St. Paul

first: Kent

last: Reed

state: MN

address: 295 ASVM, 1988 Fitch Ave

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

summary: Transcriptional profiling of turkey cardiac muscle at 1d post-hatch and 16wk birds of F (growth-selected) and RBC2 (randombred) lines

overall_design: In this study, we compared 1d post-hatch cardiac muscle to 16wk market weight for both the F and RBC2 lines using the 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray developed for transcriptional profiling of turkey muscle as it relates to growth, development, and downstream meat quality.   The TSKMLO array also includes a number of unique controls probes for each of 30 randomly chosen genes: 1 scrambled sequence control, 3 “distance” controls that included oligos designed within 500, 501-1000, and 1001-1500 bases from the 3’ of the sequence, and 7 “mismatch” controls including 3, 5, 10, 15, 20, or 25 mismatched bases, totaling 300 control probes.  There were 3 biological replicates for each comparison for a total of 12 arrays.  Dye assignments were reversed an equal number of times within each comparison to avoid dye bias.  Birds were randomly assigned to array, and hybridizations were performed randomly.

first: Kristelle

last: Mendoza

first: Kelly

middle: R

last: Sporer

first: Gale

last: Strasburg

first: Robert

last: Tempelman

first: David

last: Frame

first: Sandra

last: Velleman


title: Genome structure of radicicol-induced aneuploids in yeast by array CGH

status: Public on Dec 31 2011

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

type: Genome variation profiling by genome tiling array

summary: Aneuploidy, a state of having uneven numbers of chromosomes, is a form of large-effect mutation able to confer adaptive phenotypes under diverse stress conditions.  Here we investigate whether pleiotropic stresses could in turn induce aneuploidy in budding yeast. Radicicol was shown to induce high level missegregation of an artificial chromosome (CF). This experiment examines possible aneuploidy of other (“natural”) chromosomes induced by radicicol.

overall_design: Red colonies (lost CF) were first screened by FACS. Possible aneuploids were then subjected to hybridization, with WT as the control.

first: Guangbo

last: Chen

first: Brian

last: Fleharty

first: Rong

last: Li


title: Regulation of Energy Metabolism by the Extracytoplasmic Function (ECF) σ factors of Arcobacter butzleri

city: Albany

first: Craig

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

summary: The extracytoplasmic function (ECF) σ factors are fundamental for bacterial adaptation to distinct environments and for survival under different stress conditions. The emerging pathogen Arcobacter butzleri possesses seven putative pairs of σ/anti-σ factors belonging to the ECF family. Here, we report the identification of the genes regulated by five out of the seven A. butzleri ECF σ factors. Three of the ECF σ factors play an apparent role in transport, energy generation and the maintainance of redox balance. Several genes like the nap, sox and tct genes are regulated by more than one ECF σ factor indicating that the A. butzleri ECF σ factors form a network of overlapping regulons. In contrast to other eubacteria, these A. butzleri ECF regulons appear to primarily regulate responses to changing environments in order to meet metabolic needs instead of an obvious role in stress adaptation.

overall_design: Eleven condition experiment, wild-type A. butzleri and 10 mutants.  Three replicates for isolates RM4810, RM4810∆Aσ1::Km, RM4018Δσ1/Aσ1::Km, RM4810∆Aσ2::Km, RM4018∆σ2/Aσ2::Km, RM4018∆Aσ4::Km, RM4018∆σ4/Aσ4::Km, RM4018∆Aσ5::Km, RM4018∆σ5/Aσ5::Km, RM4018∆Aσ7::Km, and RM4018Δσ7/Aσ7::Km independently grown in BHI and incubated at 30°C on a shaking platform set at 150 rpm. RNA was isolated from 5 ml of mid-logarithmic phase cultures (OD550 of approximately 0.5).  A type 2 gene expression experimental design was used, with fluorescently labeled genomic DNA as a reference channel in each experiment as described by Lucchini, S., et al. 2005. Infect Immun 73:88-102.

first: Irati

last: Martinez-Malaxetxebarria

first: Rudy

last: Muts

first: William

last: Miller

first: Steven

last: Huynh

first: Wim

last: Gaastra

first: Jos

middle: P

last: van Putten

first: Aurora

last: Fernandez-Astorga

first: Marc

last: Wösten


title: Karyotype analysis of radicicol-resistant yeast colonies by array CGH (Radr1,2,3)

summary: Aneuploidy, a state of having uneven numbers of chromosomes, is a form of large-effect mutation able to confer adaptive phenotypes under diverse stress conditions. Here we investigate whether pleiotropic stresses could in turn induce aneuploidy in budding yeast.  Cells exposed to radicicol, an Hsp90 inhibitor, exhibit chromosomal instability. To assess the karyotype of cells with an acquired resistance to radicicol, array CGH was used to compare three stably resistant yeast colonies to a WT strain.

overall_design: Single replicates of DNA prepared from radicicol-resistant yeast colonies are compared to a control WT colony.


title: Genotyping of Coxiella burnetii strains collection

city: Marseille

first: LEROY

last: Quentin

address: 27 Boulevard Jean Moulin

country: France

institute: URMITE

summary: Genotyping based on genomic comparative hybridization of different isolates of coxiella burnetii compared to NMI reference strain

overall_design: Two-condition experiment, NMI vs. isolates. One replicate per isolate.

first: Quentin

last: LEROY

first: Fabrice

last: Armougom

first: Pascal

last: Barbry

first: Didier

last: Raoult


title: Suppression of microRNA-125b in response to IPNV infection which lead to TNFα-mediated apoptosis of viral pathogenesis

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary: Infectious pancreatic necrosis virus (IPNV) is an aquatic virus that causes acute infection in freshwater and marine fish. The stage-specific expression of TNFα regulates Bad/Bid-mediated apoptosis and RIP1/ROS-mediated secondary necrosis in IPNV-infected fish cells.  Using microRNA microarray and real-time quantitative PCR assays, the expression patterns of microRNA were characterized in different replication stages of IPNV or stimulation of LPS.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Two-condition experiment, normal vs IPNV-infected cells (at 6, 12 or 24 hr post-infection), or normal vs LPS-stimulated cells (at 6, 12 or 24 h post-treatment).

first: Wei-Lun

last: Wang

first: Gen-Hwa

last: Lin

first: Jen-Leih

last: Wu


title: Developmental underpinnings of differences in rodent novelty-seeking and emotional reactivity

city: Birmingham

first: Sarah

middle: Megan

last: Clinton

state: Alabama

address: 1720 7th Avenue South, SC 745

department: Psychiatry and Behavioral Neurobiology

institute: University of Alabama-Birmigham

summary: Innate differences in human temperament strongly influence how individuals cope with stress and predispose for specific types of psychopathology. The present study examines the developing brain in an animal model of temperamental differences to understand how altered neurodevelopment may engender differences in emotional reactivity that are stable throughout the animal’s life. We utilize selectively-bred High Responder (bHR) and Low Responder (bLR) rats that exhibit dramatic emotional behavior differences, with bHRs exhibiting exaggerated novelty-exploration, aggression, impulsivity and drug self-administration, and bLRs showing marked behavioral inhibition, exaggerated anxiety- and depressive-like behavior. Using Affymetrix microarrays, we assessed bLR/bHR gene expression in the developing brain on postnatal days (P)7, 14, and 21, focusing on the hippocampus and nucleus accumbens, two regions related to emotionality and known to differ in adult bLR/bHR rats. We found dramatic bLR/bHR gene expression differences in the P7 and P14 hippocampus, with minimal differences in the nucleus accumbens. Some of the most profound differences involved genes critical for neurodevelopment and synaptogenesis. Stereological studies evaluated hippocampal structure in developing bHR/bLR pups, revealing enhanced hippocampal volume and cell proliferation in bLR animals. Finally, behavioral studies showed that the bHR/bLR behavioral phenotypes emerge very early in life, with exploratory differences apparent at P16 and anxiety differences present by P25. Together these data point to specific brain regions and critical periods when the bHR/bLR phenotypes begin to diverge, which may eventually allow us to test possible therapeutic interventions to normalize extreme phenotypes (e.g. the anxiety-prone nature of bLRs or drug addiction proclivity of bHRs).

overall_design: 2x2x3 factorial design with N=6 per group. Factors as follows: 1) Two selectively bred strains of rats (derived from an original Sprague Dawley population) termed High Responders (HR) and Low Responders (LR), 2) Two brain regions, Hippocampus (HPC) and Nucleus Accumbens (N.Acc), 3) Three developmental timepoints, specifically postnatal days 7 (P7), 14 (P14) and 21 (P21).

first: John

last: Stead


title: TET2 mutations in acute myeloid leukemia: Results from a comprehensive genetic and clinical analysis of the AML Study Group (AMLSG)

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary:
Purpose: The tet oncogene family member 2 (TET2) gene was recently identified mutated in myeloid disorders including acute myeloid leukemia (AML). To date, there is increasing evidence for a functional role of TET2 mutations (TET2mut) in AML. Thus, we explored frequency, gene expression pattern, and clinical impact of TET2mut in a large cohort of AML patients, in the context of other AML-associated aberrations.

Patients and Methods: Samples from 783 younger adult AML patients were analyzed for the presence of TET2mut (coding exons 3-11), and results were correlated with data from molecular genetic analyses, gene expression profiling, and clinical outcome.

Results: In total, 66 TET2mut were found in 60 (60/783; 7.6%) patients, including missense (n=37), frameshift (n=16), and nonsense (n=13) mutations, which with one exception were all heterozygous. TET2mut were not correlated with distinct clinical features or genetic alterations, except for isocitrate dehydrogenase mutations (IDHmut) that were almost mutually exclusive with TET2mut (p<0.001). TET2mut were characterized by only a weak gene expression pattern, which nevertheless reflected TET2mut-associated biology. TET2mut did not impact response to induction therapy and clinical outcome; combining patients exhibiting TET2mut and/or IDHmut revealed shorter overall survival (p=0.03), although this association was not independent from known risk factors.

Conclusion: TET2mut were identified in 7.6% of younger adult AML patients and did not impact response to therapy and survival. Mutations were mutually exclusive with IDHmut, thereby supporting recent data on a common mechanism of action, which might obscure the impact of TET2mut if compared against all other AML cases.

overall_design: We performed a supervised class comparison analysis comparing 31 TET-mutated AML cases (TET2 mut) vs. 302 TET2-wildtype AML cases (TET wt) to see if a specific gene expression pattern associated with the presence of the identified TET2 mutations could be determined. No technical replicates were performed.


title: Expression data from embryoid body with BRCA1 mutation [miRNA]

city: Frederick

first: Suhwan

last: Chang

address: PO Box B, NCI-Frederick

institute: National Cancer Institute

summary: We examined the functional significance of the R1699Q variant of human BRCA1 gene using a mouse ES cell-based assay.

overall_design: The LMT_miRNA_v2 microarray (NCI-Frederick) was designed by using the Sanger miR9.0 database (http://microrna.sanger.ac.uk) and manufactured by Agilent Technologies as custom-synthesized 8 x 15 K microarrays.

first: Shyam

middle: K

last: Sharan


title: Characterization of Lactobacillus Sigma Factors using a Temperature Sensitive E. coli Sigma70 Mutant

city: College Station

first: James

last: Winkler

state: TX

address: 3122 TAMU

institute: Texas A&M University

summary: Housekeeping sigma factors in the Sigma70 family, as components of the RNA polymerase holoenzyme, are responsible for regulating transcription of genes related to vegetative growth. While these factors are well understood in model organisms such as Escherchia coli and Bacillus subtilis, little experimental work has focused on the sigma factors in members of the Lactobacillus genus such as Lactobacillus brevis and Lactobacillus plantarum. This study evaluates the ability of putative Sigma70 proteins from L. brevis (Sigma70-Lb) and L. plantarum  (Sigma70-Lp) to complement a temperature sensitive mutation in E. coli 285c Sigma70. After finding that the heterologous sigma factors were capable of restoring the viability of E. coli 285c at 42 C through growth kinetics studies, the transcriptional responses of 285c to an extended heat shock in the presence of Sigma70-Lb and Sigma70-Lp were found to be similar to previous studies. These results indicate the Sigma70-Lb and Sigma70-Lp are capable of initiating transcription in a complex with the E. coli 285c RNA polymerase to a sufficient degree to restore viability at elevated temperatures without triggering unusual modifications to the native transcriptional program. These heterologous sigma factors may therefore be useful to improve biochemical knowledge of the sigma factor family or for use in transcriptional engineering.

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

overall_design: 3 biological replicates per sigma factor

middle: D

first: Katy

middle: C

last: Kao


title: Gene expression profile of probiotic Lactobacillus casei Zhang during the late stage of milk fermentation

city: Huhhot

first: Heping

last: Zhang

address: 306 Zhaowuda Road

country: China

institute: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University

summary: Lactobacillus casei Zhang is a probiotic bacterium isolated from koumiss in Inner Mongolia of China that has been commercially used as a starter in the manufacture of dairy products. To study the gene expression profiles of L. casei Zhang during growth in milk, a whole-genome microarray was used. Compared to L. casei Zhang grown to late logarithmic phase in milk, 61 genes were significantly up-regulated (>5 fold) in stationary phase, whereas 26 genes were down-regulated. Collectively, these data showed that the majority of the identified genes was involved in carbohydrate metabolism and energy production, followed by genes involved in nucleotide metabolism, inorganic ion transport, amino acid transport and metabolism, chaperone, etc. This study demonstrates the fundamental effects of cultural conditions on the transcriptome of L. casei Zhang. Moreover, it improves the understanding of the growth and survival mechanism of the bacterium during the late stage of milk fermentation.

overall_design: L. casei Zhang was grown in milk for 14h (late logarithmic phase) or 18h (stationary phase). 2 biological replicates each.

first: Wenyi

first: Jicheng

first: Zhi

last: Zhong

first: Aibing

last: Wei

first: Qiuhua

last: Bao

first: Tiansong

last: Sun

first: He

last: Meng


title: Gene expression profile of Lactobacillus casei Zhang in fermented milk during transit in simulated gastrointestinal tract

summary: The survival of probiotics could be strongly enhanced by delivery vehicles, but the mechanism was unknown. In this study, whole genome microarray technology was used to detect the gene expression profiles of probiotic Lactobacillus casei Zhang in the absence and presence of fermented milk in simulated gastrointestinal tract. The results showed the gene expression profiles were significantly different under these two different conditions. The change of the gene expression profile may be helpful to comprehend the role of delivery vehicles in enhancing the survival of probiotics.

overall_design: Twelve samples of bacterial cells in the absence and presence of fermented milk were collected at 3 h in simulated gastric juice, 4 h and 8 h in intestinal juice, 2 biological replicates were obtained in each time point. The average of the normalized expression values of the 2 biological replicates for each probe was regarded as the expression value of a predicted gene. To identify the expression pattern of each gene across different treatments, n-fold change ratios were calculated for every gene in pure L. casei Zhang versus L. casei Zhang in fermented milk.


title: Transcriptome analysis of probiotic Lactobacillus casei Zhang during fermentation in soymilk

summary: Lactobacillus casei Zhang is a probiotic bacterium isolated from koumiss in Inner Mongolia of China. Gene expression dynamics of L. casei Zhang during growth in soymilk was investigated in attempt to reveal the mechanisms involved in growth stimulation for growing probiotics in. Comparison of different transcripts next to each other revealed 162 and 63 significantly induced genes in late logarithmic phase and stationary phase, of which the expression was at least 3 fold up-regulated and down-regulated, respectively. Approximately, 38.4% of the up-regulated genes were associated with amino acid transport and metabolism notably for histidine and lysine biosynthesis, followed by genes/gene clusters involved in carbohydrate transport and metabolism, lipid transport and metabolism, and inorganic ion transport and metabolism. The analysis results suggest that the stimulatory effect of soymilk-based ecosystem on the L. casei Zhang growth is more complex than amino acids or oligopeptides supply.

overall_design: To study gene expression dynamics of L. casei Zhang during growth in soymilk, a whole genome microarray was used to screen for differentially expressed genes when grown to lag phase, late logarithmic phase, and stationary phase.


title: Arabidopsis: Control- vs. acetic acid treatment

status: Public on Dec 30 2011

city: Valencia

first: Regina

middle: Niñoles

last: Rodenes

address: Ingeniero Fausto Elio, s/n

department: Abiotic stress

country: Spain

institute: IBMCP

summary: Comparing Arabidopsis plants gene expresion in normal conditions (control) with acetic acid treated plants (acetic). Plants were grown on liquid MS media for 13 days, then they were transfered to MS liquid media (control) or MS+3,5 acetic acid (acetic) for two hours.

overall_design: Two-condition experiment, Control vs Acetic. Biological replicates: 4 control, 4 treated with acetic, independently grown. One replicate per array.

first: R

last: Niñoles

first: S

last: Palombieri

last: Serrano


title: Mapping of Polycomb binding in Drosophila larval brain tissue using DamID

city: Amsterdam

first: Maarten

last: van Lohuizen

address: Plesmanlaan 121

department: Molecular Genetics

institute: NKI-AVL

summary:
We made Polycomb (PC) and histone H3 lysine 27 trimethylation (H3K27me3) chromatin binding maps in central brain tissue from 3rd instar larvae, allowing us to make a direct comparison to our 4C data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23166). Our results demonstrate that our PC and H3K27me3 maps are highly similar, and fit with previously identified hallmarks of PcG-bound chromatin, namely: PC and H3K27me3 co-occur in the genome as large contiguous domains that largely repress transcription of the underlying genes, which encode important regulators of development.

Keywords: Genome binding/occupancy profiling by genome tiling array

overall_design: DamID experiments for Polycomb were performed in Drosophila larval brain tissue. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing.

first: Bas

last: Tolhuis

first: Marleen

last: Blom

first: Ron

last: Kerkhoven

first: Ludo

last: Pagie

first: Hans

last: Teunissen

first: Marja

last: Nieuwland

first: Marieke

last: Simonis

first: Wouter

last: de Laat

last: van Steensel


title: EHUA Vibrio alginolyticus EPGS Nimblegen

city: shanghai

first: Yuanxing

last: Zhang

address: 130 meilong road

department: School of Biotechnology

institute: East China University Of Science And Technology

summary: Vibrio alginolyticus is a Gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. In this study, Vibrio alginolyticus wild type strain EPGS is compared with the mutants of Ser-Thr kinase PpkA and phosphatase PppA, after cultured for 7h, in Luria-Bertani containing medium 3 % NaCl at 30 C. Our goal is to determine the ppkA and pppA regulon.

overall_design: Three wild type and five mutant Vibrio alginolyticus samples were compared.

first: Lili

last: Sheng

first: Qiyao

last: Wang

first: Minjun

last: Yang


title: Identification of unique microRNA signature associated with lupus nephritis

city: Oklahoma City

first: Joshua

middle: O.

last: Ojwang

state: OK

address: 825 NE 13th Street

department: Arthritis and Immunology

institute: Oklahoma Medical Research Foundation

summary:
MicroRNAs (miRNA) have emerged as an important new class of modulators of gene expression.  In this sudy we investigated miRNA that are differentially expressed in lupus nephritis.  Microarray technology was used to investigate differentially expressed miRNA in PBMCs and EBV-transformed cell lines obtained from lupus nephritis patients and controls. TaqMan-based stem-loop real-time PCR was used for validation.
Microarray analysis of miRNA expressed in African Americans (AA) derived lupus  nephritis samples revealed 29 differentially expressed miRNA, of 850 tested.
Microarray analysis of miRNA expressed in European American (EA) derived lupus  nephritis samples revealed 50 differentially expressed miRNA, of 850 tested.

overall_design:
In this study 20 EBV-tranformed cell lined derived from AA samples were used (10 affected patients and 10 unaffected controls). All SLE patients fulfilled at least 4 out of 11 ACR criterior for lupus nephritis.
20 EBV-tranformed cell lined derived from European-American samples were used (10 affected patients and 10 unaffected controls). All SLE patients fulfilled at least 4 out of 11 ACR criterior for lupus nephritis.

middle: O

first: John

middle: B

last: Harley


title: Role of the yhcR in the Staphylococcus aureus gene expression

city: Rockville

first: Chun-Hua

last: Wan

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

summary: Staphylococcus aureus is a Gram-positive human pathogen causing a variety of human diseases in both hospital and community settings. This bacterium is so closely associated with prophages that it is rare to find S. aureus isolates without prophages. Two phages are known to be important for staphylococcal virulence: the beta-hemolysin (hlb) converting phage and the Panton-Valentine Leukocidin (PVL) converting phage. The hlb-converting phage is found in more than 90% of clinical isolates of S. aureus. This phage produces exotoxins and immune modulatory molecules, which inhibit human innate immune responses. The PVL-converting phage produces the two-component exotoxin PVL, which can kill human leucocytes. This phage is wide-spread among community-associated methicillin resistant S. aureus (CA-MRSA).  It also shows strong association with soft tissue infections and necrotizing pneumonia. Several lines of evidence suggest that staphylococcal prophages  increase bacterial virulence not only by providing virulence factors but also by altering bacterial gene expression: 1) Transposon insertion into prophage regulatory genes, but not into the genes of virulence factors, reduced S. aureus killing of Caenorhabditis elegans.; 2) Although the toxins and immune modulatory molecules encoded by the hlb- converting phages do not function in the murine system, deletion of NM3, the hlb-converting phage in S. aureus Newman,  reduced staphylococcal virulence in the murine abscess formation model. 3) In a preliminary microarray experiment, prophages in S. aureus Newman altered the expression of more than 300 genes.  In this research proposal, using microarray and high-throughput quantitative RT-PCR (qRT-PCR) technologies, we will identify the effects of the two important staphylococcal phages on the gene expression of S. aureus in both in vitro and in vivo conditions. This project is intended to be completed within one year. All the data – microarray, qRT-PCR and all the primer sequences- will be made available to public 6 month after completion. Data from this project will help us to understand the role of prophages in the S. aureus pathogenesis and can lead to development of a strategy to interfere with the pathogenesis process.

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: Staphylococcus aureus subsp.aureus strain Newman (reference) and Staphylococcus aureus subsp.aureus strain Newman yhcR knockout(query) were grown in TSA broth.Samples were grown under aerobic and anaerobic conditions and RNA samples harvested at mid log, stationary, and log phases.Samples were hybridized on aminosilane coated slides with 70-mer oligos.

first: Marcus

last: Jones

first: Rosslyn

last: Maybank

first: Kenneth

last: Shatzkes

first: Fei

last: Sun

first: Taeok

last: Bae

first: Scott

middle: N

last: Peterson


title: Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes

city: Pittsburgh

first: Lindsay

middle: Renee

last: Dresang

address: 5117 Centre Ave, Hillman Cancer Res. Pav. 1.8

department: Cancer Virology Program

institute: University of Pittsburgh

type: Expression profiling by genome tiling array

summary: Kaposi’s sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are related human tumor viruses that cause primary effusion lymphomas (PEL) and Burkitt’s lymphomas (BL), respectively.  Viral genes expressed in naturally-infected cancer cells contribute to disease pathogenesis; knowing which viral genes are expressed is critical in understanding how these viruses cause cancer.  To evaluate the expression of viral genes, we used high-resolution separation and mass spectrometry coupled with custom tiling arrays to align the viral proteomes and transcriptomes of three PEL and two BL cell lines under latent and lytic culture conditions.  The majority of viral genes were efficiently detected at the transcript and/or protein level on manipulating the viral life cycle.  Overall the correlation of expressed viral proteins and transcripts was highly complementary in both validating and providing orthogonal data with latent/lytic viral gene expression.  Our approach also identified novel viral genes in both KSHV and EBV, and extends viral genome annotation.  The expression of several previously uncharacterized latent genes were validated at both transcript and protein levels.  This systems biology approach coupling proteome and transcriptome measurements provides a comprehensive view of viral gene expression that could not have been attained using each methodology independently.  Detection of viral proteins in combination with viral transcripts is a potentially powerful method for establishing virus-disease relationships.

sample_organism:
Homo sapiens
human gammaherpesvirus 4
Human gammaherpesvirus 8

overall_design: All samples relative to KSHV-negative, EBV-negative reference sample (BJAB).   Experimental samples were chosen based on their natural infection with either KSHV, EBV, both, or neither virus.  Technical replicates of the cell line BC-1 were prepared for both latent (untreated) and lytic (chemically-treated) conditions.

first: Jeremy

last: Teuton

first: Huichen

last: Feng

first: Jon

middle: M

last: Jacobs

first: David

middle: G

last: Camp

first: Samuel

last: Purvine

first: Marina

last: Gritsenko

first: Zhihua

last: Li

first: Richard

last: Smith

first: Bill

last: Sugden

first: Patrick

middle: S

last: Moore

first: Yuan

last: Chang


title: Gene expression profile of murine cutaneous melanoma after systemic treatment with tumor necrosis factor (TNF) associated or not with melphalan (MEL).

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary: Cutaneous melanomas are malignant radio and chemoresistant neoplasias presenting high morbidity and elevated mortality rates. Isolated Limb Perfusion (ILP) with Melphalan (Mel) is used in the treatment of non-resectable locally advanced melanomas of extremity sparing the limb from amputation in 40-50% of the cases. Adding the Tumor Necrosis Factor alpha (Tnfa) improves total complete response to 70-90%. The cellular and molecular mechanisms underlying the changes promoted by Mel and Tnfa are not completely understood. In this study we evaluated the impact of systemic Mel and Tnfa administration on tumor growth, analyzed the morphological changes promoted by each treatment, and searched for early molecular targets of Mel and Tnfa, alone or in combination, in a murine melanoma model. Morphological changes were analyzed by histological analysis, while microarray gene expression followed by quantitative RT-PCR were used to search for early molecular targets.  We found that Mel systemic administration accounted for the impairment of tumor-growth (p<0.001) and improvement of survival. Tnfa co-administration augmented necrosis (p<0.024) and decreased mitotic rates (p=0.001). We identified a set of 118 potential molecular markers that might be correlated with the observed biologic response to treatment with Melphalan and Tnfa and which could represent potential therapeutic targets in melanoma.

overall_design:
We used amplified RNA (aRNA) from 18 tumor samples (Control – 5 samples; Mel – 4 samples; Tnfa – 4 samples; and Mel+Tnfa – 5 samples). For replica hybridization with dye swap, aRNA from the tumors and from a pool composed of equal amounts of RNA extracted from the K1735M2, M2R, B16F10, and B16F1 melanoma cells were labeled with Alexa555 or Alexa647. Labeled aRNA samples were hybridized against a glass platform containing 16,128 immobilized sense oligonucleotides (Fox Chase Cancer Center, USA) corresponding to murine genes.
Slides were pre-hybridized at 42ºC for approximately 6 hours in a solution containing Denhardt’s 5X (Ficoll 400 0.05g/mL, poli-vynil-pyrrolidone 0.05g/mL, bovine serum albumin 0.05g/mL), SSC (sodium saline citrate) 5X, 0.2% SDS (Sigma), and 1% BSA.
For hybridization, we used a mix of 3.5µg of each labeled sample aRNA and reference aRNA. The hybridization solution contained Denhardt’s 5X, formamide 25% (Sigma), SSC 5X, SDS 0.1%, salmon sperm DNA 0.1mg/mL (GE Healthcare), Poly-A 0.1mg/mL (GE Healthcare), and Cot-1 0.1mg/mL (GE Healthcare), to a final volume of 100µL. Hybridizations were carried out on a Gene Tac hybridization station (Genomic Solutions) at 42ºC for about 16h.
The slides were removed from the hybridization cassettes directly to a recipient containing a washing solution (SSC 2X, SDS 0.1%) at 42ºC, put in a slide rack, transferred to another recipient containing fresh solution, and washed under constant agitation at 42ºC for 5 min. After that, they were washed twice for 5min in a second wash solution (SSC 0.1X, SDS 0.1%) at room temperature and rinsed five times for 1min at room temperature with a SSC 0.1X solution. The slides were dried upside down in a centrifuge at 1500rpm for 5min.
The slides were scanned with a confocal laser scanner (ScanArrayTM Express, Perkin-Elmer Life Sciences, USA), and the spot intensities processed with the help of the ScanArray Express program (Packard BioScience), with a 10µm resolution and a PMT of 60% for Alexa 555 and of 70% for Alexa 647. Each slide generated a data set for each channel corresponding to the dyes Alexa 555 and Alexa 647.
The slides were scanned with a confocal laser scanner (ScanArrayTM Express, Perkin-Elmer Life Sciences, USA) with a 10µm resolution and a PMT of 60% for Alexa 555 and of 70% for Alexa 647, and data were extracted with ScanArray Express software (Packard BioScience) using the histogram method. Each slide generated a data set for each channel corresponding to the dyes Alexa 555 and Alexa 647. The Locally Weighted Scatter-plot Smoothing method (LOWESS), adjusted for linear and non-linear systematic variations, both of the intensity dependent type, mainly for low intensity spots, was employed for data normalization.

first: Vladmir

last: de Lima

first: Alex

last: Carvalho

first: Sarah

last: Marques

first: Cesar

last: Torres

first: Luiz

middle: F

last: Reis

first: Adriana

middle: A

last: Dias


title: Early gene expression changes in peripheral blood leukocytes with rush immunotherapy

city: Dallas

first: Laurie

last: Davis

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern Medical Center

summary: Peripheral blood mononuclear cells (PBMC) were collected from ficoll gradients of whole blood and immediately processed for total RNA and stored at -80oC until use. Blood was from allergic patients at different timepoints pre or post immunotherapy (RIT). Gene expression was compared for the different timepoints.

overall_design: Blood samples were collected from allergic patients before or after rush immunotherapy (RIT), total RNA was prepared and gene expression assessed by Illumina. Samples were collected pre-rush or at 1 week, 7 weeks, 4 months (and for one patient 5 months) after beginning rush immunotherapy. Blood was taken at each timepoint prior to the patient receiving immunotherapy at each timepoint.


title: Light versus Dark gene expression in SAR11

city: Madison

first: Michael

last: Schwalbach

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin-Madison

summary: We investigated the transcriptional response of cand. Pelagibacter ubique cultures to light and dark when grown under carbon replete and deplete conditions. Results: During exponential phase, few genes were differentially transcribed between light:dark growth conditions. In stationary phase, a high proportion (9.7%) of coding sequences were found differentially expressed between treatments; 4.7% being up-regulated in the light (n=64) and 4.9% being up-regulated in the dark (n=67). Several components of the oxidative phosphorylation pathway were up-regulated in the dark, supporting physiological data showing higher respiration rates in darkness than in the light under starvation conditions. We also observed up-regulation of a proton translocating pyrophosphate synthase (SAR11_1040), which may be an additional energy production mechanism utilized by SAR11 cells in the dark. Finally, we noted the up-regulation of pili formation genes in the array data, consistent with the observation of pili in dark grown cells via electron microscopy.

platform_organism:
Candidatus Pelagibacter ubique HTCC1002
Candidatus Pelagibacter ubique HTCC1062
Candidatus Pelagibacter sp. HTCC7211

overall_design:
Triplicate biological replicates were collected from five growth conditions (n=15 total):
1) exponential phase, 24 hour light (n=3)
2) exponential phase, 24 hour dark (n=3)
3) stationary phase, 12:12 hour light:dark cycles (n=3)
4) stationary phase, 24 hour dark (n=3)
5) stationary phase, 6 hours after transfer to darkness (n=3)

first: Laura

last: Steindler

first: Francis

last: Chan

first: Stephen

middle: J

last: Giovannoni


title: Enhanced salt stress tolerance of rice plants expressing a vacuolar H+-ATPase subunit c1 (SaVHAc1) gene from the halophyte grass Spartina alterniflora Löisel

status: Public on Dec 27 2011

city: Baton Rouge

first: Niranjan

last: Baisakh

state: LA

address: 104 Madison B Sturgis Hall

department: School of Plant, Environmental, and Soil Sciences

institute: Louisiana State University Agricultural Center

summary: From the microarray experiment, many of the 43,311 probes were significantly different: 4,287 (9.9 %) between genotypes (WT and SaVHAc1-rice), 6,761 (15.6 %) between environments (saline or non-saline conditions), and 705 (1.6 %) responded differently to the environment depending upon the genotype.  Although a large number of genes showed upregulation in SaVHAc1-rice relative to WT, eighteen genes that showed more than two-fold increase or decrease in transcription in SaVHAc1-rice were considered significantly up- or down-regulated, respectively.  Fourteen genes encoding proteins with either ion transport or metal binding function were significantly upregulated.  The four genes that showed significant down-regulation in SaVHAc1-rice did not have any functional annotation (hypothetical or expressed proteins). Interestingly, none of the other subunits of vATPase was observed as being affected by SaVHAc1.

overall_design: Two genotypes (transgenic and wildtype), both exposed to two environments (saline and control) for up to 72 hours. Four biological replicates per genotype/environment combination. One sample per array.

first: Cheryl

last: Vanier


title: A conserved RRM domain of B. napus FCA improves cotton fiber quality and yield by regulating cell size

city: Shanghai

first: Fan

last: Sun

address: 220 Handan Road

institute: Fudan University

summary: Cotton fiber is actually unicellular trichome, therefor its length is really hard to be modified but very meaningful to fiber quality and yield. We have reported the function of the second RRM domain of Oryza sativa FCA in rice cell size regulation. Data shows it is highly conserved across dicotyledonous and monocotyledonous plants. Here we provide evidence showing that the second RRM domain of Brassica napus FCA worked in Gossypium hirsutum, leading to the enlargement of multiple types of cells, such as pollen, cotyledon petiole and cotton fiber. In the transgenic cotton, the length of unicellular cotton fiber increased by about 10% and fiber yield per plant also showed a dramatic increase, ranging from 35% to 66%, over the control. Thus, this RRM domain may be an ancient and common cell size regulator and has great economic value on cotton industry.

overall_design:
FCA encodes a strong promoter of the transition to flowering in Arabidopsis thaliana, which contains two RRM (RNA recognition motif) domain and a WW protein interaction domain (Macknight et al., 1997). We have previously found that cell size and yield of rice (Oryza sativa) can be increased by ectopic expression of the first RRM domain of OsFCA (Hong et al., 2007). The second RRM domain of OsFCA can also increase cell size (Attia et al., 2005), suggesting OsFCA-RRMs each play a role in homeostatic cell size regulation. We designate them as Oryza sativa cell size RRM 1 (Os-csRRM1) and Oryza sativa cell size RRM 2 (Os-csRRM2), respectively. Both of them exhibit a high degree of evolutionary conservation in plant. For Os-csRRM2, significant homology was observed in Triticum aestivum (90% identity), Hordeum vulgare (90% identity), Lolium perenne (82% identity), Zea mays (81% identity),Ricinus communis (76% identity), Vitis vinifera (68% identity), Arabidopsis thaliana (68% identity) and Brassica napus (64% identity) (Fig. 1). The high degree of conservation suggests that this RRM domain might have similar function in different plants. Indeed, we observed that overexpression of Bn-csRRM2 also increased the cell size of B. napus (unpublished data). As cotton fiber length is a key factor in cotton yield and quality, we investigated whether this attribute could be enhanced by constitutive expression of Bn-csRRM2.
Transgenic and wild-type cotton were grown in same condition. The leaves of 25 day and 45 day plants were harvested for microarray analysis. RNA samples were isolated from 3 biological replications using TRIzol (Invitrogen) as described by the manufacturer. Microarray analyses were carried out using Agilent Cotton Gene Expression Microarray (G2519F-022523). Microarrays were scanned on Agilent Technologies Scanner G2505C and data points were extracted using Agilent Feature Extraction software (Version 10.7.1.1). Comparisons were made between transgenic samples and their corresponding wild-type samples.

first: Chuanliang

last: Liu

first: Chaojun

last: Zhang

first: Weiwei

last: Qi

first: Xueyan

first: Zhixia

last: Wu

first: Depei

last: Kong

first: Qianhua

last: Wang

first: Haihong

last: Shang

first: Xiaoyin

last: Qian

first: Fuguang

last: Li

first: Jinshui

last: Yang


title: Microarray analysis of human bone metastases samples

status: Public on Dec 29 2011

city: L'Aquila

first: Mattia

last: Capulli

address: Via Vetoio Coppito 2

country: Italy

institute: University of L'Aquila

summary: We performed microarray analysis with two different chip platforms, Affymetrix and Agilent, on bone metastasis samples from breast cancer patients with only bone metastases and metastases in bone and visceral organs.

overall_design:
We collected bone metastases biopsies from breast cancer patients with only bone metastases and metastases in bone and visceral organs. RNA was extracted from these samples and subjected to microarray analysis with the Agilent platform. Data were compared with a signsture obtained with the Affymetrix platform, to obtain a signature of differentially regulated genes between the two groups of patients
This Series represents the Agilent data only. The Affymetrix data are provided in GEO Series GSE11078.

first: Nadia

last: Rucci

first: Adriano

last: Angelucci

first: Anna

last: Teti


title: Folsomia candida exposed to different 2-phenylethyl isothiocyanate concentrations in soil

first: Elaine

last: van Ommen Kloeke

address: De Boelelaan 1085

department: Animal Ecology

institute: VU University

summary: Natural toxins, such as isothiocyanate (ITC), are harmful secondary metabolites produced by plants. Many natural toxins occur in commercial crops, yet their possible negative repercussions on especially non-target soil organisms are largely unknown. This study examined molecular effects of 2-phenylethyl ITC on the soil arthropod species: Folsomia candida. Complementing ecotoxicological experiments with gene expression profiling allows the study of the underlying modes of action of toxins. For this the standardized ISO guideline for ecotoxicological experiments and a microarray for F. candida (GPL7150) were used. Toxic effects on reproduction were shown for F. candida, with EC50 values of around 11.5 nmol/g soil, illustrating the toxic character of this compound. A total of 130 genes were significantly differentially expressed between C and AC. The compounds were spiked in with acetone and due to the substantial difference between the two controls, only AC was chosen for further contrast analysis, comparing AC to EC10 and EC50 gene expressions. At EC10 level, 75 genes and at the EC50 level 107 genes were differentially expressed compared to AC. Approximately 36% of all significant genes could be annotated using Blast2GO. Gene expression profiles revealed the importance of lipid metabolism at low exposure concentrations (EC10), which is associated with the lipophilic nature of 2-phenylethyl ITC. At higher dosages (EC50) a wider array of genes was over-expressed, which included genes related to stress and sugar metabolism.   Our study provides new insights in the molecular mode of action of a natural toxin soil animals. This study is the first step towards an understanding of these potential risks by studying the effects of a natural toxin at a life-history trait and molecular level.

overall_design: Four-exposure experiment; Control vs. Acetone control vs.EC10 vs.EC50 exposed animals. Biological replicates: 4 replicates for each exposure.

first: A

middle: E

first: Cornelis

last: van Gestel

first: Bjarne

last: Styrishave

first: Martin

last: Hansen

first: Jacintha

last: Ellers

first: Dick

last: Roelofs


title: Ferulic Acid Challenge of Lactobacillus brevis

first: James

last: Winkler

summary: The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates poses significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Currently, these inhibitory compounds must be removed through additional downstream processing to create feedstock suitable for most industrially important microbial strains. This study explores the high ferulic acid tolerance in Lactobacillus brevis (L. brevis), a lactic acid bacteria often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis under ferulic acid stress reveals that the presence of ferulic acid primarily triggers the expression of membrane proteins to counteract ferulic acid induced changes in membrane fluidity and ion leakage, in the midst of a generalized stress response. Several promising routes for understanding phenolic acid tolerance have been identified based upon these findings. These insights may be used to guide further engineering of model industrial organisms to better tolerate phenolic compounds in processed biomass.

overall_design: Three biological replicates were utilized for each time point. Total RNA was extracted using the Zymo Research Bacterial/Fungal RNA extraction kit Microarrays were indirectly labeled, hybridized, and washed according to the Fairplay III Kit protocol. Slides were scanned using the Axon GenePix 4200A scanner. Data normalization (LOWESS) was carried out on each array separately. The arithmetic average of probe signals was used to compute Log2 values.

first: Katy

last: Kao


title: Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis (CGH)

city: Boston

first: Charles

last: Lee

state: MA

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

summary: Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information.  We further analyzed zebrafish CNVs using pooled samples of 10 zebrafish each from three laboratory strains (AB, Tubingen, and WIK) to identify strain specific CNVs between groups.

overall_design: 10 zebrafish from 3 laboratory strains were pooled and run against the other pooled samples resulting in three array combinations.

first: Kim

middle: H

last: Brown

first: Kimberly

middle: P

last: Dobrinski

first: Arthur

first: Omer

last: Gokcumen

first: Ryan

last: Mills

first: Xinghua

last: Shi

first: Wilson

middle: W

last: Chong

first: J

last: Chen

first: Sthuthie

last: David

first: Paulo

last: Yoo

first: Samuel

last: Peterson

first: Towfique

last: Raj

first: Kwong

last: Choy

first: Barbara

last: Stranger

first: Robin

last: Williamson

first: Leonard

middle: I

last: Zon

first: Jennifer

middle: L

last: Freeman


title: Mapping of H3K27me3 enrichment in Drosophila larval brain tissue using ChIP-chip

first: Maarten

last: van Lohuizen

overall_design: ChIP-chip experiments for H3K27me3 were performed in Drosophila larval brain tissue. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing.

first: Bas

last: Tolhuis

first: Marleen

last: Blom

first: Ron

last: Kerkhoven

first: Ludo

last: Pagie

first: Hans

last: Teunissen

first: Marja

last: Nieuwland

first: Marieke

last: Simonis

first: Wouter

last: de Laat

last: van Steensel


title: Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (CGH ZV81M)

first: Charles

last: Lee

summary: Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates, but the zebrafish reference genome has no annotated CNV information.  We developed a zebrafish CNV map using 80 zebrafish genomes from laboratory strains (AB, Tubingen, and WIK) and one native population, identifying 6,080 CNV elements. Overlapping or adjacent CNVs account for 14.6% of the genome, representing four times the CNV levels from other vertebrates including humans. Highest intra-specific CNV levels were observed for Tubingen, a common laboratory strain due to high fecundity. Tubingen variation likely represents higher initial population size and composite population founders initiating the laboratory strain. Extensive zebrafish CNVs, along with associated phenotypic impacts, advocates for increased usage of isogenic strains for genetic studies intended for human disease translation.

overall_design: 7 full sib adult hybrid fish used for expression Quantatitive Trait Loci (eQLT) analysis to support CNV affects on gene expresion in zebrafish.

first: Kim

last: Brown

first: Kimberly

last: Dobrinski

first: Arthur

first: Omer

last: Gokcumen

first: Ryan

last: Mills

first: Xinghua

last: Shi

first: Wilson

last: Chong

first: Sthuthie

last: David

first: Paulo

last: Yoo

last: Peterson


title: Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (CGH ZV81M 2)

overall_design: 19 zebrafish from 3 laboratory strains and one native population were analyzed using a strain specific reference for each group

first: Samuel

first: Towfique

last: Raj

first: Kwong

last: Choy

first: Barbara

last: Stranger

first: Jennifer

last: Freeman


title: Tissue-specific transcriptome analysis in nodules of Lotus japonicus

city: Uji

first: Kojiro

last: Takanashi

address: Gokasho

department: Research Institute for Sustainable Humanosphere

institute: Kyoto University

summary: Legume plants can establish symbiotic nitrogen fixation (SNF) with rhizobia mostly in root nodules, where rhizobia-infected cells are accompanied with uninfected cells in a mosaic pattern. Inside the mature nodules of legume, carbon and nitrogen nutrients between host plant cells and their resident bacteria are actively exchanged. To elucidate the metabolite dynamics relevant for SNF in nodules, three cell-types from nodule tissues of a model legume, Lotus japonicus, were isolated using laser microdissesction, and transcriptome analysis was done by an oligoarray with 60-mer length representing 21,495 genes. In our cell-type-specific profiling, many genes were identified as being expressed in nodules with spatial-specific manners. Among them, genes coding for metabolic enzymes were classified according to their function, and detailed data analysis figured out that secondary metabolic pathway was highly activated in nodule cortex. In particular, a number of metabolic genes for phenyl propanoid pathway were found as highly expressed genes accompanied with those encoding putative transporters of secondary metabolites. These data suggest the involvement of novel physiological function of phenylpropanoids in SNF.

overall_design: Gene expression in three different cell-types of Lotus japonicus nodule was measured.  Three independent experiments were performed at each cell-types.

first: Hirokazu

last: Takahashi

first: Mikio

last: Nakazono

first: Kazufumi

last: Yazaki


title: Methyl DIP-chip from self-pollinated ddm1 mutant and ddm1 kyp double mutant

status: Public on Dec 25 2011

city: Vienna

first: Taku

last: Sasaki

address: Dr. Bohr-gasse 3

country: Austria

institute: Gregor Mendel Institute

type: Methylation profiling by genome tiling array

summary: Methylation of histone H3 lysine 9 (H3K9me) and small RNA are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. The transposon-specific non-CpG methylation in plants is controlled by small RNA and H3K9me. Although it is often assumed that small RNA directs H3K9me,　interaction between small RNA and H3K9me has not been directly shown in plants. We have previously shown that a mutation in a chromatin remodeling gene DDM1 (decrease in DNA methylation) induces a global decrease as well as local increase of cytosine methylation and accumulation of small RNA in a locus called BONSAI. Here we show that the de novo BONSAI methylation does not depend on RNAi but depends on H3K9me. Notably, in mutant of H3K9 methylase gene KRYPTONITE or H3K9me-dependent DNA methylase gene CHROMOMETHYALSE3, the ddm1-induced de novo cytosine methylation was abolished for all three contexts, CpG, CpHpG, and CpHpH. Furthermore, RNAi mutants showed strong developmental defects when combined with ddm1 mutation. Our results revealed unexpected interactions of epigenetic modifications, which could be conserved among diverse eukaryotes.

overall_design: comparison of DNA methylation between WT, 2G ddm1 (2 replications), 8G ddm1 (2 replications), and 8G ddm1 kyp


title: Ceratitis capitata gene expression related to mating status in mature females (mated vs virgin)

city: Pavia

first: Ludvik

middle: Marcus

last: Gomulski

state: PV

address: Piazza Botta 9

department: Biologia Animale

institute: University of Pavia

overall_design: This analysis compares gene expression between 4 day old mated and 4 day old virgin medfly, Ceratitis capitata females. Samples where made from the heads of the females.

first: L


title: Normal human osteoblasts and MDA-MB-231 mono and coculture

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

institute: University of Zurich

summary: As a model for investigating changes in gene expression in response to epithelial-osteoblast interactions in bone metastases of breast carcinomas, cells that represented malignant epithelial cell compartments (MDA-MB-231) and cells that represented skeletal compartments (Normal Human (NH) Osteoblasts) were examined in an in vitro mixed co-culture setting. These two types of cells were co-cultivated for 48 h in a low-serum medium [0.2% fetal bovine serum (FBS)] to allow reciprocal signal exchange with minimal background from undefined molecular signals that are inherent in fetal bovine serum. We examined the effects of co-cultivation on each cell pairing in two independent biological replicates. The gene expression profiles of the co-cultures were compared to the expression profiles of the corresponding cells that were kept in monoculture using HEEBO microarrays. After mono or co-culturing, total RNA was extracted and amplified using a modified Eberwine procedure. The amplified RNA was labeled with the fluorescent dye Cy5 and pooled with Cy3 labeled reference RNA, and then the pooled RNA was hybridized onto HEEBO microarrays. After hybridization and washing, arrays were scanned on a fluorescent microscope scanner.

overall_design: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

first: Tatiparthi

last: Reddy


title: Ceratitis capitata gene expression related to mating status in mature males (mated vs virgin)

overall_design: This analysis compares gene expression between 4 day old mated and 4 day old virgin medfly, Ceratitis capitata, males. Samples where made from the heads of the males.


title: MicroRNA expression profiling of Ewing sarcoma cell lines

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

institute: University of Turin

summary: Ewing’s sarcoma family tumors (ESFT) are the second most common bone malignancy in children and young adults, characterized by the expression of a unique chromosomal translocation, that in 85% of cases lead to the expression of the EWS-FLI-1 fusion protein. ESW-FLI-1 functions as an aberrant transcription factor that can both induce and suppress its target genes. We have recently demonstrated that microRNA (miRNA) 145 is a direct EWS-FLI-1 target implicated in ESFT development. Here, we use global miRNA array profiling to show that ESFT display a distinct miRNA signature characterized by the induction or repression of a limited number of miRNAs, including the oncogenic and tumor suppressor miRNA 17-92 and let-7 families, respectively. We demonstrate that repression of the let-7 family member let-7a may be due to direct binding of EWS-FLI-1 to the let-7a promoter and that it participates in the tumorigenic potential of ESFT cells in vivo. The mechanism whereby let-7a repression enhances ESFT growth is shown to be the induction of its target gene HMGA2, as overexpression of let-7a or repression of HMGA2 blocked ESFT cell tumorigenicity. Consistent with these observations, systemic delivery of synthetic let-7a that restored its expression in tumor cells and decreased HMGA2 expression inhibited ESFT growth in vivo. Our observations provide evidence that deregulation of let-7a target gene expression participates in ESFT development and identify let-7a as a promising new therapeutic target for one of the most aggressive pediatric malignancies.

sample_organism:
Homo sapiens
synthetic construct

overall_design: Two Ewing sarcoma cell lines and two samples of human pediatric mesenchymal stem cells are compared to the miRXplore Universal Reference (UR), a defined pool of synthetic microRNAs.

first: Claudio

last: De Vito

first: Nicolo

last: Riggi

first: Mario-Luca

last: Suva

first: Michalina

last: Janiszewska

first: Janine

last: Horlbeck

first: Karine

last: Baumer

first: Ivan

last: Stamenkovic


title: Differential gene expression in mice infected with distinct Toxoplasma gondii strains

status: Public on Dec 22 2011

city: Knoxville

first: Rachel

last: Hill

state: TN

address: 1401 W. Cumberland Ave

department: Microbiology

institute: University of Tennessee Knoxville

summary:
Transcriptome analysis of peritoneal lavage of mice infected with T. gondii
Toxoplasma gondii is the causative agent of toxoplasmosis in human and animals. In mouse model, T. gondii strains can be divided into three groups, including the virulent, intermediately virulent and non-virulent. The clonal Type I, II and III T. gondii strains belong to these three groups respectively. To better understand the basis of virulence phenotypes, we investigated mouse gene expression responses to the infection of different T. gondii strains at day 5 post intraperitoneal inoculation with 500 tachyzoites. The transcriptomes of mouse peritoneal cells  showed that 1927, 1573, and 1009 transcripts were altered more than 2 fold by Type I, II and III infections, respectively, and majority of altered transcripts were shared. Overall transcription patterns were similar in Type I and Type II infections and both had greater changes than that of  Type III. Quantification of parasite burden in mouse spleens showed that Type I was 1000 times higher than Type II, and Type II was 20 times higher than Type III. Fluorescence activated cell sorting revealed that Type I and II infections had comparable macrophage populations and both were higher than Type III infection. In addition, Type I infection had higher percentage of neutrophils than that of Type II and III. Taken together, these results suggested that there is a common gene expression response to T. gondii infection in mice. This response is further modified by parasite strain specific factors that determine their distinct virulence phenotypes.

overall_design: We analyzed mRNA from female CD1 outbred mice, 6-8 weeks old infected with Type I, II and III T. gondii strains.  We used the Affymetrix Mouse Gene 1.0 ST platform. Raw array data was processed by Partek® Genomics SuiteTM software. Three replicates were performed for Type I-GT1 and Type III-CTG and two replicates for Type II- PTG.

middle: D

first: Julia

last: Gouffon

first: Arnold

last: Saxton

first: Chunlei

last: Su


title: Expression microarray with 5-aza-2'-deoxycytidine-treated Caco-2 cells

city: Daejeon

first: sunwoo

last: Lee

address: 829 tamnip-dong, yuseong-gu

country: South Korea

institute: Genomictree,Inc.

summary: 5-aza-2'-deoxycytidine (DAC) treated and untreated Caco-2 cells were compared using an expression microarray.

overall_design: Total RNA from untreated Caco-2 cells was labeled with Cy3, and total RNA from DAC-treated Caco-2 cells was labeled with Cy5.

first: Sunwoo

first: Taejeong

last: Oh


title: Ceratitis capitata gene expression related to sexual maturation in males

first: Ludvik

last: Gomulski

summary: This analysis compares gene expression between 1 day old and 4 day old virgin medfly, Ceratitis capitata, males

overall_design: This analysis compares gene expression between 1 day old and 4 day old virgin medfly, Ceratitis capitata males. Samples where made from the heads of the males.

first: L


title: Elucidation and validation of new targets of the global regulator PdhR in Escherichia coli

status: Public on Dec 21 2011

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: The pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon has not yet been uncovered. To achieve an extended understanding of its gene regulation network, we combined large-scale network inference and experimental verification of results obtained by a systems biology approach.

overall_design: We determined the gene expression of four different strains of E. coli on three different media. The four strains corresponded to the wild-type E. coli (LJ110), a PdhR knockout mutant (LJ110deltapdhR), a  strain carrying an empty plasmid (LJ110/pTM30) and a PdhR overexpression strain (LJ110/pTM30PdhRhis). These strains were cultivated on Luria-Bertani broth (LBo), standard phosphate minimal medium supplemented with acetate and standard phosphate minimal medium supplemented with pyruvate. We obtained an overall 24 microarray experiments from two replicates of each of these cultivations.

first: R

first: A

last: Goehler

last: Kökpinar

first: W

last: Schmidt-Heck

last: Guthke

first: U

last: Rinas

first: S

last: Schuster

first: K

last: Jahreis

first: C

last: Kaleta


title: 5q21 tiling array on prostate tumors

status: Public on Dec 19 2011

city: Stanford

first: Stephanie

last: Huang

address: 269 Campus Drive, CCSR 3240

institute: Stanford University

summary: CGH profiles of prostate tumors on custom designed high resolution arrays tiling chromosome 5q21

overall_design: A custom high-density Agilent 15k CGH array tiling 5q21 was designed to narrow down the region of deletion at 5q21 to a few genes that could be followed up with functional studies.  8 critical prostate tumors samples with the most focal regions of deletion were chosen to be profiled on the 5q21 tiling array.

first: Jonathan

middle: R

last: Pollack


title: Identification of novel markers of the mesothelial lineage and mesothelioma

status: Public on Dec 18 2011

city: Yokohama

first: Alistair

last: Forrest

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN OMICS science centre

institute: RIKEN

summary: Microarray expression arrays on mesothelium and other tissues dissected from mice were used to identify candidate mesothelial lineage markers. These were then tested by qRTPCR across a panel of human mesothelioma cells lines, other cancers, and normal primary cells includidng mesothelial cells.

overall_design: Twenty four samples were analysed, composed of 8 tissues in triplicate

first: Mutsumi

last: Kanamori-Katayama


title: microRNA microarray profiling in the livers of control db/+ and diabetic db/db mice

city: Delhi

first: Malabika

last: Datta

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

summary: Analysis revealed a set of 13 microRNAs to be significantly altered between livers of control db/+ and diabetic db/db mice. Of these, miR-34a, miR-107, miR-378, miR-378*, miR-31, miR-31*, miR-151-5p, miR-676, miR-22, miR-93, let-7b were up-regulated and let-7e and miR-227 were down-regulated. A total of 670 predicted targets for these altered miRNAs were extracted from PicTar and TargetScan and functional characterisation mapped these targets to several biological processess related to varied metabolic pathways. The Wnt signaling pathway that has been shown to be linked to diabetes emerged as the most prominent pathway from these sets of target genes.

overall_design:
Four animals each from control db/+ and diabetic db/db mice were taken for the experiment. There was a significant increase in the body weight and plasma glucose levels in the diabetic group as compared to the control group. The livers were excised and total RNA was isolated, labelled and hybridized to mouse miRNA Microarray (V1) microarrays from Agilent. After hybridization, the slides were washed and scanned on an Agilent microarray scanner (model G2565BA) at 100 and 5% XDR settings. Agilent Feature Extraction software version 9.3.5 was used to extract the raw data.
Microarray Data Analysis:
The raw data were global median normalized and log transformed and analyzed by Significance Analysis of Microarray (SAM). SAM calculates a score for each gene as a change of expression relative to the standard deviation of all measurements and therefore identifies genes that are significantly associated with an outcome variable such as the disease stage. In SAM tests, a false Discovery Rate (FDR) of less than 5% was selected and parameters were set as default.

first: Amit

middle: K

last: Pandey

first: Kirandeep

last: Kaur


title: Multiorgan effects of IUGR caused by maternal protein depletion in rats (Placenta, Kidney, Heart, Lung, Liver)

status: Public on Dec 23 2011

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

institute: INSERM

summary:
All genome expression changes investigated on pools of growth restricted rats (at term) compared to control rats.
The protocol of growth restriction (length, duration) has been extensively described in Buffat et al (Journal of Pathology 2007a and Endocrinology, 2007b)

overall_design: Ten hybridizations, two technical replicates, were carried out using RNAs prepared from pooled organs from 4 to 6 pups.

first: Christophe

last: Buffat