title: caArray_geral-00117: Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease

first: Mervi

summary: The identification of genes that contribute to the biological basis for clinical heterogeneity and progression of prostate cancer is critical to accurate classification and appropriate therapy. We performed a comprehensive gene expression analysis of prostate cancer using oligonucleotide arrays with 63,175 probe sets to identify genes and expressed sequences with strong and uniform differential expression between nonrecurrent primary prostate cancers and metastatic prostate cancers. The mean expression value for >3,000 tumor-intrinsic genes differed by at least 3-fold between the two groups. This includes many novel ESTs not previously implicated in prostate cancer progression. Many differentially expressed genes participate in biological processes that may contribute to the clinical phenotype. One example was a strong correlation between high proliferation rates in metastatic cancers and overexpression of genes that participate in cell cycle regulation, DNA replication, and DNA repair. Other functional categories of differentially expressed genes included transcriptional regulation, signaling, signal transduction, cell structure, and motility. These differentially expressed genes reflect critical cellular activities that contribute to clinical heterogeneity and provide diagnostic and therapeutic targets.

overall_design:
geral-00117
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: HG_U95A
Organism: Homo sapiens (ncbitax)
Material Types: synthetic_RNA, organism_part, whole_organism, total_RNA
Disease States: Normal, prostate carcinoma


title: caArray_golub-00299: Chemosensitivity prediction by transcriptional profiling

status: Public on May 16 2015

city: Rockville

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

summary: In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles alone. Using oligonucleotide microarrays, the expression levels of 6,817 genes were measured in a panel of 60 human cancer cell lines (the NCI-60) for which the chemosensitivity profiles of thousands of chemical compounds have been determined. We sought to determine whether the gene expression signatures of untreated cells were sufficient for the prediction of chemosensitivity. Gene expression-based classifiers of sensitivity or resistance for 232 compounds were generated and then evaluated on independent sets of data. The classifiers were designed to be independent of the cells' tissue of origin. The accuracy of chemosensitivity prediction was considerably better than would be expected by chance. Eighty-eight of 232 expression-based classifiers performed accurately (with P < 0.05) on an independent test set, whereas only 12 of the 232 would be expected to do so by chance. These results suggest that at least for a subset of compounds genomic approaches to chemosensitivity prediction are feasible.

overall_design:
golub-00299
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: Hu6800
Organism: Homo sapiens (ncbitax)
Tissue Sites: Kidney, Brain, Blood, Lung, Skin, Colon, Breast, Prostate, Ovary
Material Types: cell, synthetic_RNA, whole_organism, total_RNA
Disease States: Carcinoma, Glioblastoma, Lymphoma, Adenocarcinoma, Melanoma, Amelanotic Melanoma, Large Cell Carcinoma, Precursor Lymphoblastic Leukemia, Carcinosarcoma, Myeloid Leukemia, Plasma Cell Myeloma, Bronchogenic Carcinoma, Chronic Myelogenous Leukemia, Squamous Cell Carcinoma


title: Antivirulence activities of zinc ion and ZnO nanoparticle against Pseudomonas aeruginosa

status: Public on May 25 2015

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

summary: An antivirulence approach targets bacterial virulence rather than cell viability in the antibiotic approach that can readily lead to drug resistance. Opportunistic human pathogen Pseudomonas aeruginosa produces a variety of virulence factors, and biofilm cells of this bacterium are much more resistant to antibiotics than planktonic cells. To identify novel inorganic antivirulence compounds, the dual screenings of thirty-six metal ions were performed to identify that zinc ions and ZnO nanoparticle inhibited the pyocyanin production and biofilm formation in P. aeruginosa without affecting the growth of planktonic cells. Moreover, zinc ion and ZnO nanoparticle markedly reduced the production of 2-heptyl-3-hydroxy-4(1H)-quinolone and siderophore pyochelin, while increased the production of another sideropore pyoverdine and swarming motility. Further, zinc ion and ZnO nanoparticle clearly suppressed hemolytic activity in P. aeruginosa. Transcriptome analyses showed that ZnO nanoparticle induced zinc cation efflux pump czc operon, porin genes (oprD and opdT), and Pseudomonas type III repressor A ptrA, while repressed pyocyanin-related phz operon, which partially explains the phenotypic changes. Overall, ZnO nanoparticle is a potential candidate for use in an antivirulence approach against persistent P. aeruginosa infection.

overall_design: P. aeruginosa Genechip Genome Array (Affymetrix, P/N 900339) was used in order to study the cells after the addition of ZnO nanoparticles. DNA microarray analysis with one biological replicate was performed with an Affymetrix system. P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM). Before sample collection, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 s before centrifugation at 16,000 g for 2 min. The cell pellets were immediately frozen with dry ice and stored at –80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA).

first: Jin-Hyung

first: Moo

middle: H

last: Cho

first: Yong-Guy

last: Kim


title: Conserved nutrient sensor O-GlcNAc transferase is integral to the C. elegans pathogen-specific immune response

status: Public on May 01 2015

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Discriminating pathogenic bacteria from energy-harvesting commensals is key to host immunity. Using mutants defective in the enzymes of O-linked N-acetylglucosamine (O-GlcNAc) cycling, we examined the role of this nutrient-sensing pathway in the Caenorhabidits elegans innate immune response. Using whole genome transcriptional profiling, O-GlcNAc cycling mutants exhibited deregulation of unique stress- and immune-responsive genes as well as genes shared with the p38 MAPK/PMK-1 pathway.  Moreover, genetic analysis showed that deletion of O-GlcNAc transferase (ogt-1) yielded animals hypersensitive to the human pathogen S. aureus but not to P. aeruginosa. Genetic interaction studies further revealed that nutrient-responsive OGT-1 acts through the conserved ß-catenin (BAR-1) pathway and in concert with p38 MAPK/PMK-1 to modulate the immune response to S. aureus.  The participation of the nutrient sensor O-GlcNAc transferase in an immunity module conserved from C. elegans to humans reveals an unexplored nexus between nutrient availability and a pathogen-specific immune response.

overall_design: In C. elegans, three mutant strains(genotypes used: N2 (wild-type), ogt-1 (ok1474), oga-1 (ok1207), and pmk-1 (km25)) were treated with the human pathogen S. aureus (SA) or  P. aeruginosa(PA) and OP50 (E. coli control) with three biological replications.

first: Michelle

middle: R

last: Bond

first: Salil

middle: K

last: Ghosh

first: Peng

last: Wang

first: John

middle: A

last: Hanover


title: caArray_beer-00153: Gene-expression profiles predict survival of patients with lung adenocarcinoma

status: Public on May 06 2015

summary: Histopathology is insufficient to predict disease progression and clinical outcome in lung adenocarcinoma. Here we show that gene-expression profiles based on microarray analysis can be used to predict patient survival in early-stage lung adenocarcinomas. Genes most related to survival were identified with univariate Cox analysis. Using either two equivalent but independent training and testing sets, or 'leave-one-out' cross-validation analysis with all tumors, a risk index based on the top 50 genes identified low-risk and high-risk stage I lung adenocarcinomas, which differed significantly with respect to survival. This risk index was then validated using an independent sample of lung adenocarcinomas that predicted high- and low-risk groups. This index included genes not previously associated with survival. The identification of a set of genes that predict survival in early-stage lung adenocarcinoma allows delineation of a high-risk group that may benefit from adjuvant therapy.

overall_design:
beer-00153
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: Hu6800
Organism: Homo sapiens (ncbitax)
Disease States: lung cancer, normal


title: caArray_cho-00156: Gene Expression in Ovarian Cancer Reflects Both Morphology and Biological Behavior

status: Public on May 07 2015

summary: Biologically and clinically meaningful tumor classification schemes have long been sought. Some malignant epithelial neoplasms, such as those in the thyroid and endometrium, exhibit more than one pattern of differentiation, each associated with distinctive clinical features and treatments. In other tissues, all carcinomas, regardless of morphological type, are treated as though they represent a single disease. To better understand the biological and clinical features seen in the four major histological types of ovarian carcinoma (OvCa), we analyzed gene expression in 113 ovarian epithelial tumors using oligonucleotide microarrays. Global views of the variation in gene expression were obtained using PCA. These analyses show that mucinous and clear cell OvCas can be readily distinguished from serous OvCas based on their gene expression profiles, regardless of tumor stage and grade. In contrast, endometrioid adenocarcinomas show significant overlap with other histological types. Although high-stage/grade tumors are generally separable from low-stage/grade tumors, clear cell OvCa has a molecular signature that distinguishes it from other poor-prognosis OvCas. Indeed, 73 genes, expressed 2- to 29-fold higher in clear cell OvCas compared with each of the other OvCa types, were identified. Collectively, the data indicate that gene expression patterns in ovarian adenocarcinomas reflect both morphological features and biological behavior. Moreover, these studies provide a foundation for the development of new type-specific diagnostic strategies and treatments for ovarian cancer.

overall_design:
cho-00156
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: Hu6800
Organism: Homo sapiens (ncbitax)
Material Types: synthetic_RNA, organism_part, whole_organism, total_RNA
Disease States: Ovary cancer


title: Saccharomyces cerevisiae BY4741 cells treated with n-alkanes

status: Public on Apr 07 2015

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

summary: Transcripitonal profiling of Saccharomyces cerevisiae treated with 2% n-alkanes vs untreatment

overall_design: Multiple condition experiment, S. cerevisiae treated with n-alkanes (n-nonane, n-decane, n-undecane, n-dodecane, respectively) for 24hrs or 48hrs, compared to control (those without treatment)

first: Matthew

middle: W

last: Chang


title: Beta Amyloid toxicity in a Caenorhabditis elegans model of Alzheimer's disease

status: Public on Feb 12 2015

city: Milwaukee

first: Wail

middle: Mostafa

last: Hassan

address: 2400 E. Hartford Ave.

department: Biomedical Sciences

institute: University of Wisconsin

summary:
Transgenic animals were engineered to express human amyloid peptide controlled by a muscle-specific, heat-inducible promoter. At low temperatures (16°C) Abeta expression is minimal, while at higher temperatures (20-25°C) Abeta accummulates in large quantities and causes paralysis.
GFP- and GFP::degron (a toxic aggregating GFP mutant)-expressing animals were used as controls.

overall_design: Animals were grown at 16°C till early 3rd larval stage and then upshifted to 25°C. Animals were harvested at the time of upshift (T0), and every 4 hours later until 20 hours postupshift (T4-T20).

first: Christopher

middle: D

last: Link

middle: M

middle: E

last: Yerg


title: caArray_golub-00460: Prediction of central nervous system embryonal tumour outcome based on gene expression

summary: Embryonal tumours of the central nervous system (CNS) represent a heterogeneous group of tumours about which little is known biologically, and whose diagnosis, on the basis of morphologic appearance alone, is controversial. Medulloblastomas, for example, are the most common malignant brain tumour of childhood, but their pathogenesis is unknown, their relationship to other embryonal CNS tumours is debated, and patients' response to therapy is difficult to predict. We approached these problems by developing a classification system based on DNA microarray gene expression data derived from 99 patient samples. Here we demonstrate that medulloblastomas are molecularly distinct from other brain tumours including primitive neuroectodermal tumours (PNETs), atypical teratoid/rhabdoid tumours (AT/RTs) and malignant gliomas. Previously unrecognized evidence supporting the derivation of medulloblastomas from cerebellar granule cells through activation of the Sonic Hedgehog (SHH) pathway was also revealed. We show further that the clinical outcome of children with medulloblastomas is highly predictable on the basis of the gene expression profiles of their tumours at diagnosis.

overall_design:
golub-00460
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: Hu6800
Organism: Homo sapiens (ncbitax)
Material Types: synthetic_RNA, organism_part, whole_organism, total_RNA
Disease States: synthetic_RNA, organism_part, whole_orMedulloblastoma, renal rhabdoid tumor, Atypical Teratoid/Rhabdoid Tumor, Supratentorial PNET, Supratentorial PNET (pineoblastoma), Normal, Malignant Glioma, Extrarenal Rhabdoid Tumorganism, total_RNA


title: Genome-wide prediction and analysis of yeast RNase III-dependent snoRNA processing signals

status: Public on Jan 21 2015

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Microbiologie and Infectiologie

country: Canada

institute: Université de Sherbrooke Centre of Excellence in RNA Biology

summary: In Saccharomyces cerevisiae, the maturation of both pre-rRNA and pre-small nucleolar RNAs (pre-snoRNAs) involves common factors, thereby providing a potential mechanism for the coregulation of snoRNA and rRNA synthesis. In this study, we examined the global impact of the double-stranded-RNA-specific RNase Rnt1p, which is required for pre-rRNA processing, on the maturation of all known snoRNAs. In silico searches for Rnt1p cleavage signals, and genome-wide analysis of the Rnt1p-dependent expression profile, identified seven new Rnt1p substrates. Interestingly, two of the newly identified Rnt1p-dependent snoRNAs, snR39 and snR59, are located in the introns of the ribosomal protein genes RPL7A and RPL7B. In vitro and in vivo experiments indicated that snR39 is normally processed from the lariat of RPL7A, suggesting that the expressions of RPL7A and snR39 are linked. In contrast, snR59 is produced by a direct cleavage of the RPL7B pre-mRNA, indicating that a single pre-mRNA transcript cannot be spliced to produce a mature RPL7B mRNA and processed by Rnt1p to produce a mature snR59 simultaneously. The results presented here reveal a new role of yeast RNase III in the processing of intron-encoded snoRNAs that permits independent regulation of the host mRNA and its associated snoRNA.

overall_design: RNA from wild type, rnt1d and rnt1ts grown at 26 C and 37 C on rich media

first: Ghada

last: Ghazal

first: Dongling

last: Ge

first: Julien

last: Gervais-Bird

first: Jules

last: Gagnon


title: Identification of genes involved with P. aeruginosa biofilm antibiotic resistance by microarray analysis

status: Public on May 11 2015

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

institute: Montana State University

summary: Microarray analysis was used to identify changes in the level of transcription of genes in P. aeruginosa drip flow biofilms in response to ciprofloxacin and tobramycin exposure. This data was evaluated and used to select strains that carry transposon mutations in genes that might play a role in antibiotic tolerance of biofilms. The strains were evaluated for defects in biofilm tolerance.

overall_design: Four drip flow biofilm conditions with three replicates each: (1) baseline controls at 72 hours, (2) tobramycin treated for 12 hours past baseline, (3) ciprofloxacin treated for 12 hrs past baseline, and (4) no treatment for 12 hrs past baseline.

first: Philip

last: Stewart

first: Michael

middle: J

last: Franklin

first: James

middle: P

last: Folsom

first: Laura

last: Boegli

first: Garth

last: James


title: Identification of genes induced in P. aeruginosa biofilms by microarray analysis

summary: Transcriptome analysis was applied to characterize the physiological activities of Psuedomonas aeruginosa cells grown for three days in drip flow biofilm reactors when compared to the activities of P. aeruginosa grown planktonically to exponential phase in the same media. Here, rather than examining the effect of an individual gene on biofilm antibiotic tolerance, we used a transcriptomics approach to identify regulons and groups of related genes that are induced during biofilm growth of Pseudomonas aeruginosa. We then tested for statistically significant overlap between the biofilm-induced genes and independently compiled gene lists corresponding to stress responses and other putative antibiotic protective mechanisms. This data was evaluated and used to select strains that carry transposon mutations in genes that might play a role in antibiotic tolerance of biofilms. The strains were evaluated for defects in biofilm tolerance.

overall_design: One planktonic condition with four biological replicates; One drip flow biofilm condition grown for 72 hours with three biological replicates; One drip flow biofilm condition grown for 84 hours with three biological replicates.


title: Pseudomonas aeruginosa LysR PA4203 regulator acts as a repressor of the PA4202 gene encoding a nitronate monooxygenase

status: Public on Jan 23 2015

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

country: Germany

institute: Max Rubner-Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: More than 7% of the Pseudomonas aeruginosa genes are encoding transcriptional regulators, many of  which with unknown functions. Among them, those belonging to the LysR family are the most  represented. The PA4203 gene lies upstream of the previously characterized ppgL gene (PA4204),  which encodes a periplasmic gluconolactonase, which detoxifies gluconolactone by converting it to  gluconate. Upstream of PA4203 and in the opposite orientation are the PA4202 gene coding for a  nitronate monooxygenase and ddlA (PA4201) encoding a D-alanine alanine ligase. This genetic  organization is conserved in all P. aeruginosa genomes, but not in other pseudomonads. The  intergenic regions between PA4203 and ppgL, and PA4202 are very short (79 and 107 nucleotides,  respectively). PA4203 is a repressor of PA4202 and of its own transcription. A chromatin  immunoprecipation analysis confirmed the presence of a single PA4203 binding site between PA4202  and PA4203. Electrophoretic mobility shift assays (EMSAs) with the purified PA4203 protein and in41  gel footprinting with the 1, 10-phenanthroline-copper ion, combined with primer extension analysis to  determine transcriptional startpoints allowed the identification of a LysR binding motive in the  PA4202 and PA4203 intergenic region. Despite this, a transcriptome analysis revealed more genes to  be affected in a PA4203 mutant, likely due to the overexpression of the nitronate monooxygenase  (PA4202). Deletion of the PA4202 gene resulted in an increased sensitivity of the cells to 3-  nitropropionic acid (3-NPA).

platform_organism:
Pseudomonas aeruginosa
Pseudomonas aeruginosa PAO1

overall_design:
[expression]  Two samples of a Delta PA4203 mutant compared to two samples of PAO1 wild type.
[ChIP]  Two samples of PAO1-pUCP4203 compared to one sample of PAO1-wt.

first: Ken

last: Vercammen

first: Qing

last: Wei

first: Daniel

last: Charlier

last: Dötsch

first: Susanne

last: Häussler

first: Sebastian

last: Schulz

first: Francesca

last: Salvi

first: Giovanni

last: Gadda

first: Jim

last: Spain

first: Morten

middle: L

last: Rybtke

first: Tim

last: Tolker-Nielsen

first: Pierre

last: Cornelis


title: The NuA4 complex promotes Translesion Synthesis (TLS) - mediated DNA damage tolerance

status: Public on Feb 21 2015

city: Calgary

first: Jennifer

last: Cobb

state: Alberta

address: 2A18 HRIC 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary: DNA lesions can block a replication fork, leading to its collapse and gross chromosomal rearrangements. To circumvent such outcomes, DNA damage tolerance (DDT) pathways become engaged, allowing the replisome to bypass the lesion and complete S phase in the presence of unrepaired damage. Here we demonstrate a newly identified role for NuA4, including complex components Esa1 and Yng2, on the Translesion Synthesis (TLS) branch of DDT. Moreover, Our data suggest that NuA4 functionality within the tolerance pathway is likely direct as genome-wide transcriptional analysis with esa1-L254P mutants showed little changes in the expression of TLS factors compared to wild type during MMS treatment. When Yng2 expression is restricted to G2/M, cell viability and mutagenesis rates are restored to the levels measured when only the error-free branch of DDT is disrupted, indicating that the critical role of NuA4 in TLS functions in G2, after chromosomal replication is complete. Lastly, disruption of HTZ1, the Saccharomyces cerevisiae histone variant H2A.Z and target of NuA4, exhibits mutagenic rates of reversion that are comparable to the levels measured with NuA4 complex mutants, esa1-L254P and yng2Δ.

overall_design: The esa1-L254P strain was compared to wild type through a series of microarrays utilizing dye swaps with and without treatment of MMS.  These included synchronized cells in G1 and S phase through alpha factor treatment.   Four unique microarrays were performed each with dye swaps, comparing wild type to esa1-L254P in G1 and S phase with and without treatment with MMS.  As a set of controls, four microarrays were performed comparing identical strains with and without MMS in G1 or S phase.

first: Margaret

last: Renaud-Young

first: David

last: Lloyd

first: Katie

last: Chatfeld-Reed

first: Iain

last: George

first: Gordon

last: Chua


title: Inhibitory effects of galacturonic acid on Saccharomyces cerevisiae: involvement of hexose transporters

status: Public on Apr 14 2015

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Aim: Analyse inhibitory effects of galacturonic acid, an important constituent of plant biomass hydrolysates, on growing and starving cultures of Saccharomyces cerevisiae CEN.PK113-7D.   Method & Results: Biomass yields in aerobic and anaerobic glucose-limited chemostat cultures (pH 3.5) were reduced by 25 and 10%, respectively, upon addition of 10 g∙l-1 galacturonic acid.  Genes previously reported to show a transcriptional response to other organic acids were overrepresented in a set of galacturonic-acid responsive genes identified by microarray analysis. These results suggested that galacturonic acid causes weak-acid uncoupling of the yeast plasma membrane pH gradient. Consistent with this hypothesis, galacturonate-accelerated loss of viability in starving cell suspensions was strongly pH dependent. Loss of viability was much slower in a strain in which all HXT (hexose transporter) genes were deleted. Moreover, deletion of HXT genes alleviated growth inhibition on ethanol observed at galacturonic acid concentrations of 10 g∙l-1 and above.  Conclusions: At low pH, galacturonic acid negatively affects the physiology of S. cerevisiae. Reduced sensitivity of hexose-transporter mutants indicated that one or more HXT transporters are involved in transport of galacturonic acid.    Significance and Impact: This study shows that galacturonic acid toxicity should be taken into account in process development for yeast-based fermentative conversion of pectin-rich feedstocks such as sugar beet pulp and citrus peel. Involvement of hexose transporters in galacturonic acid toxicity provides leads for improving tolerance.

overall_design: To investigate the impact of galacturonic acid on S. cerevisiae, a DNA microarray-based transcriptome analysis was performed on aerobic, glucose-limited chemostat cultures grown in the presence and absence of 10 g∙l-1 galacturonic acid at pH3.5.

first: Eline

last: Huijses

first: Antonius

last: van Maris

first: Jack

middle: T

last: Pronk


title: Expression data from hsa-mir-125 transfected MCF7 cells

status: Public on Dec 31 2014

city: Ankara

first: Ayse

middle: Elif

last: Erson-Bensan

state: Cankaya

address: Universiteler Mah. No:1

department: Biology

country: Turkey

institute: METU

summary: MicroRNA (miRNA) deregulation has long been associated with various cancers. Among an expanding list of cancer related miRNAs, deregulation of miR-125b has been well documented in various cancers including breast. Based on current knowledge, miR-125b is considered to be a tumor suppressor in breast cancers.  While important mRNA targets have been defined for miR-125b, here, we aimed to further investigate direct/indirect consequences of miR-125b expression in breast cancer cells by using a transcriptome approach. Upon miR-125b expression, a total of 140 cancer related genes were found to be differentially expressed in breast cancer cells.

overall_design: MCF7 cells were stably transfected with pSUPER-mir-125b and pSUPER empty vector controls. Polyclones were selected by G418, molecular confirmation of mir-125b expression was completed by TaqMan RT-qPCR assays.

first: H

middle: B

last: Akman

first: S

last: Selcuklu

first: Mark

last: Donoghue

first: Shiva

last: Akhavantabasi

first: Aysegul

last: Sapmaz

first: Charles

last: Spillane

first: M

middle: C

last: Yakicier

first: A


title: 20% (w/v) Glucose osmotic stress (YP20) vs 1M Sorbitol osmotic stress (YPS)

status: Public on Jan 01 2015

city: Burjassot (Valencia)

first: Marcel·lí

last: del Olmo

address: Dr Moliner, 50

department: Bioquímica i Biologia Molecular

country: Spain

institute: Universitat de València

summary:
Transcriptional profiling of yeast Saccharomyces serevisiae cells exposed to stress (30 min) compared to no stress conditions (YPD)
Two stress condition experiments, YP20 and YPS, each one compared to no-stress conditions (YPD).

overall_design: Two replicates of each condition

last: Gomar-Alba


title: HSD17B14 induction in breast cancer cell lines

status: Public on Mar 01 2015

city: Linköping

first: Agneta

last: Jansson

address: Cell biology floor 9

department: IKE

country: Sweden

institute: Linköping university

summary: The 17beta-hydroxy steroid dehydrogenase family is involved in the fine tuning of conversion of different substances such as steroids, retenoids and fatty acids. The expression of HSD17B14 has been correlated to better prognosis in breast cancer. The function of HSD17B14 is still not known, but it may convert estradiol to estrone. We transfected breast cancer cell lines with a HSD17B14-containing plasmid and compared with mock-transfected samples. The influence on global gene expression was examined with microarrays.

overall_design: The breast cancer cell lines SKBR3 and ZR75-1 were transfected with a HSD17B14-containing plasmid or a plasmid without insertion as control. This was performed in duplicates. The cells were harvested after 48 hours, and RNA was extracted and hybridized on Affymetrix microarrays.

first: Tove

last: Sivik


title: Expression data from patient and primary xenografts esophageal tumour samples

status: Public on Jan 11 2015

city: Toronto

first: Maud

middle: HW

last: Starmans

state: Ontario

address: 661 University Avenue

department: Informatics and Biocomputing Program

institute: Ontario Institute for Cancer Research (OICR)

summary: Microarrays were used to assess differences between 1) human tumours that did and did not engraft, 2) human tumours and their matched primary xenografts, 3) early and late passage primary xenografts and 4) small and large primary xenografts for a series of esophageal patient and primary xenograft tumours

overall_design: Patient esophageal tumour samples were obtained and inplanted in NOD/SCID mice; xenografts that formed were passaged from mouse to mouse. Samples of different passages were selected for profiling.

first: Lorin

last: Dodbiba

first: Jennifer

last: Teichman

first: Andrew

last: Fleet

first: Henry

last: Thai

middle: H

first: Roya

last: Navab

first: Zhuo

last: Chen

first: Hala

last: Girgis

first: Lawson

last: Eng

first: Osvaldo

last: Espin-Garcia

first: Xiaowei

last: Shao

first: Bizhan

last: Bandarchi

first: Joerg

last: Schwock

first: Ming-Sound

last: Tsao

last: El-Zimaity

first: Sandy

last: Der

first: Wei

last: Xu

first: Robert

middle: G

last: Bristow

first: Gail

last: Darling

first: Paul

last: Boutros

first: Laurie

last: Ailles

first: Geoffrey

last: Liu


title: Expression profile for PA14 lasR rhlR double mutant with H2O2 stress

status: Public on Jan 09 2015

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

summary:
Quorum sensing controls the expression of multiple virulence factors.  PA14 genes lasR and rhlR are necessary for quorum sensing via homoserine lactones.
A PA14 lasR rhlR deficient mutant exhibits a reduced oxidative stress response.  Here we conducted a microarray to determine oxidative stress response gene regulation mediated by the homoserine lactone quorum sensing circuits.

overall_design: A PA14 lasR rhlR deficient mutant was compared to the wild-type with and without H2O2 stress.

first: García-Contreras

last: Rodolfo

first: Nuñez-López

last: Leslie

first: Jasso-Chávez

last: Ricardo

first: Belmont

middle: A

last: Javier

first: Rangel-Vega

last: Adrian

first: Maeda

last: Toshinari

first: Kwan

middle: W

last: Brian

first: Wood

middle: K

last: Thomas


title: In vivo gene expression analysis of  C elegans in response to rifampicin

city: New Delhi

first: Arnab

last: Mukhopadhyay

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

summary: We have discovered rifampicin as a glycation inhibitor, which  increases life span in C elegans.  In order to understand the mechanism of rifampicin action, microarray analysis was performed to study the changes in gene expression brought about by the drug.

overall_design: Gene expression profile of wild type N2 worms treated with rifampicin w.r.t to control (DMSO treated) worms.Total RNA was isolated from worms on  8th day of adulthoodin presence of FuDr. Two independent biological replicates for each treatment were analyzed.

first: Sandeep

last: Golegaonkar

first: Mahesh

last: Kulkarni


title: A new global repressor (bvlR) of pathogenicity and tight microcolony formation in P. aeruginosa

status: Public on Dec 10 2014

city: Cork

first: Fergal

last: O'Gara

address: University College Cork

department: Microbiology

country: Ireland

institute: BIOMERIT Research Centre

summary: LysR-type transcriptional regulators (LTTRs) are the most common family of transcriptional regulators found in the opportunistic pathogen Pseudomonas aeruginosa. They are known to regulate a wide variety of virulence determinants and have emerged recently as positive global regulators of pathogenicity in a broad spectrum of serious bacterial pathogens. However, in spite of their key role in modulating expression of key virulence determinants underpinning pathogenic traits associated with the process of infection, surprisingly few were found to be transcriptionally altered in co-culture with host cells. bvlR (PA14_26880) an LTTR of previously unknown function, has been shown to be induced in response to host cells, and was therefore investigated for its potential role in virulence. BvlR expression was found to play a pivotal role in regulation of acute virulence determinants such as type III secretion and exotoxin A production. In contrast, loss of bvlR led to an inability to form tight microcolonies, a key step in biofilm formation in the mucoid lung, although surface attachment was increased. bvlR was also seen to a key role in P.aeruginosa pathogenicity within the acute model of infection, Caenorhabditis elegans. Unusually for LTTRs, BvlR was shown to exert its influence exclusively through the transcriptional repression of 307 genes, including the divergently transcribed gene bvlA. This highlights the importance of BvlR as a previously uncharacterized global virulence regulator in P. aeruginosa with a key role in the transcriptional response underlying the host pathogen interaction.

overall_design: Six samples were analysed in total, three biological replicates of the bvlR mutant and bvlR complemented strains.

first: R

middle: R

last: McCarthy

first: M

last: Mooij

first: F

last: Reen

first: O

last: Lesouhaitier

last: O’Gara


title: BTG1 modulates ATF4 function in response to cellular stress: implications for tumor cell survival

status: Public on Nov 26 2014

city: Nijmegen

first: Laurensia

last: Yuniati

address: Route 412 PO BOX  9101

department: Pediatric Oncology

institute: Radboud university medical center

summary:
Analysis of the effect of glutamine starvation in mouse embryonic fibroblasts (MEFs) with and without Btg1 at gene expression level. The hypothesis tested in the present study was that loss of Btg1 affect the expression of stress-response genes.
Results provide important information of the differentially expressed genes regulated by Btg1 upon glutamine deprivation, explaining the survival advantage of tumor cells harboring Btg1 loss under cellular stress condition.

overall_design: Total RNA was obtained from WT and Btg1-/- MEFs subjected to 16 hours glutamine starvation compared to untreated cells.

first: Laurens

last: van der Meer

first: Esther

last: Tijchon

first: Dorette

last: van Ingen Schenau

first: Liesbeth

last: van Emst

first: Marloes

last: Levers

first: Sander

last: Palit

first: Caroline

last: Rodenbach

first: Geert

last: Poelmans

first: Peter

middle: M

last: Hoogerbrugge

first: Jixiu

last: Shan

first: Michael

last: Kilberg

first: Blanca

last: Scheijen

first: Frank

middle: N

last: van Leeuwen


title: Gene Expression Profiling Reveals Molecular Patterns Underlying the Lifespan-Extending Effect of Tyrosol in Caenorhabditis elegans

status: Public on Nov 01 2014

city: Jaen

first: Francisco

middle: J.

last: Esteban

state: Jaen

address: Campus Las Lagunillas s/n

department: Experimental Biology

institute: University of Jaen

summary: We have previously reported that tyrosol (TYR), one of the main phenols in extra virgin olive oil (EVOO), promotes lifespan extension in the nematode Caenorhabditis elegans, also inducing a stronger resistance to thermal and oxidative stress in this animal model. Although the influence of several longevity-related genes in these effects has been reported by our group, we decided to perform a whole genome DNA-microarray approach in order to identify other genes and molecular pathways further involved in TYR effects on C. elegans longevity. Microarray analysis identified 208 differentially expressed genes (206 overexpressed and 2 underexpressed) when comparing TYR-treated nematodes with non-treated controls. Many of these genes seem linked to processes such as regulation of growth, transcription, reproduction, lipid metabolism and body morphogenesis. Data obtained by microarray was validated by qRT-PCR analysis of selected genes. Our results confirm that several important cellular mechanisms related to longevity are influenced by TYR treatment in this animal model. Moreover, we detected an interesting overlap between the expression pattern elicited by TYR and those induced by other dietary polyphenols known to extend lifespan in C. elegans, such as quercetin and tannic acid.

overall_design: C. elegans were maintained on Nematode Growth Medium (NGM) and E. coli OP50 as described [21]. For microarray experiments, fer15(b26) nematodes were synchronized by hypochlorite treatment and raised at 25°C on NGM plates containing either 250 μM TYR (n=3) or vehicle (control; n=3). At the fourth day of adulthood, nematodes were collected from the plates in M9 buffer, washed 3 times and pelleted by centrifugation for RNA isolation. After centrifugation, worms were resuspended in 350 μl of RLT/BME buffer, flash frozen in liquid nitrogen and thawed at 37 °C three times for disruption and total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer recommended protocol. Final volume of isolated RNA was 50 μl per biological sample. RNA quality was analyzed with the 2100 Bioanalyzer (Agilent Technologies) using the RNA 6000 nano kit. All RNA samples were of sufficient quality for gene array analysis with RIN>7. A total amount of 50 ng of RNA was used as the template for cDNA synthesis and in vitro transcription to synthesized biotin-modified aRNA using the GeneChip® 3’ IVT Express Kit (Affymetrix, 901228). aRNA was purified from unincorporated  nucleotides and other  reaction components using the RNeasy Mini Kit (Qiagen). A total of 15 µg of biotin-labeled aRNA was fragmented following the instructions described  in the Affymetrix  manual (P/N 702646 Rev.8) and  hybridized to C. elegans GeneChip® Genome Arrays (Affymetrix, 900383). They were processed and scanned using Affymetrix instrumentation and with hybridization, washing and scanning parameters provided by the manufacturer. Computational and statistical analyses were carried out using the R software (http://www.r-project.org/) and the appropriate Bioconductor packages (http://www.bioconductor.org/) run under R. In order to remove all the possible sources of variation of a non-biological origin between arrays, densitometry values between arrays were normalized using the RMA (robust multiarray) normalization function implemented in the Bioconductor affylmGUI. Statistically significant differences between groups were identified using the rank product non-parametric test implemented in the Bioconductor Rank-Prod package. Those genes showing a corrected (FDR) p-value < 0.05 were selected as significant.

first: Ana

last: Cañuelo

middle: J

first: Juan

last: Peragón


title: Pathogenic mechanisms of Pseudomonas aeruginosa wound infection in response to murine fascia

status: Public on Oct 01 2014

city: Chicago

first: John

last: Alverdy

state: IL

address: 5841 South Maryland Avenue

department: Surgery

institute: University of Chicago

summary:
Wound infections are traditionally thought to occur when microbial burden exceeds the innate clearance capacity of host immune system. Here we introduce the idea that the wound environment itself plays a significant contributory role to wound infection.
We developed a clinically relevant murine model of soft tissue infection to explore the role of activation of microbial virulence in response to tissue factors as a mechanism by which pathogenic bacteria cause wound infections.
Mice underwent abdominal skin incision and light muscle injury with a crushing forceps versus skin incision alone followed by topical inoculation of Pseudomonas aeruginosa.
Pseudomonas aeruginosa whole genome transcriptional profiling demonstrated that fascia induced the activation of multiple genes responsible for the synthesis of the iron scavenging protein pyochelin.

overall_design:
Ex-vivo murine fascia homogenates were prepared and Pseudomonas aeruginosa MPAO1 was incubated with an inoculum of the fascia homogenate solution.
Pseudomonas aeruginosa MPAO1 incubated under the same condtions without the homogenate was used as the control group. Three biological replicates in each group was used.

first: Moses

last: Kim

first: Scott

last: Christley

first: Nikolai

last: Khodarev

first: Irma

middle: D

last: Fleming

first: Yong

last: Huang

first: Eugene

last: Chang

first: Olga

last: Zaborina


title: DAF-16/FoxO and EGL-27/GATA promote developmental growth in response to persistent somatic DNA damage [N2, daf-2, daf-16, daf-2;daf-16]

status: Public on Nov 18 2014

city: Koeln

first: Bjoern

last: Schumacher

address: Zuelpicher Str. 47

institute: University of Cologne

summary: Genome maintenance defects cause complex disease phenotypes characterized by developmental failure, cancer susceptibility and premature aging. It remains poorly understood how DNA damage responses function during organismal development and maintain tissue functionality when DNA damage accumulates with aging. Here we show that the FoxO transcription factor DAF-16 is activated in response to DNA damage during development while the DNA damage responsiveness of DAF-16 declines with aging. We find that in contrast to its established role in mediating starvation arrest, DAF-16 alleviates DNA damage induced developmental arrest and even in the absence of DNA repair promotes developmental growth and enhances somatic tissue functionality.  We demonstrate that the GATA transcription factor EGL-27 co-regulates DAF-16 target genes in response to DNA damage and together with DAF-16 promotes developmental growth. We propose that EGL-27/GATA activity specifies DAF-16 mediated DNA damage responses to enable developmental progression and to prolong tissue functioning when DNA damage persists.

overall_design: Synchronized L1 and mutant larvae were UV or mock treated, or starved

last: Mueller

first: Laia

last: Castells-Roca

first: Vipin

last: Babu

first: Maria

last: Ermolaeva

first: Roman

middle: U

last: Müller

last: Frommolt

first: Ashley

last: Williams

first: Sebastian

last: Greiss

first: Jennifer

middle: I

last: Schneider

first: Thomas

last: Benzing

first: Bernhard

last: Schermer

first: Björn


title: DAF-16/FoxO and EGL-27/GATA promote developmental growth in response to persistent somatic DNA damage [N2, xpa-1]

overall_design: Synchronized L1 and xpa-1 mutant larvae were UV or mock treated, or starved

first: Michael

first: Peter

middle: B


title: Expression data from Pseudomonas aueruginosa NCTC8626 treated with and without manuka honey

status: Public on Sep 29 2014

city: CARDIFF

last: Giles

address: Heath Park

country: United Kingdom

institute: Cardiff University

summary:
Manuka honey has been shown to inhibit growth in Pseudomonas aueruginosa, the mode of action is currently unclear.
We used microarrays to detail the difference in global gene expresson following treatment of cells with honey. We identified distinct classe of up and down regulated genes

overall_design: Pseudomonas aueruginosa were harvested 4 hours after exposure to treatment for RNA extraction and hybridization on Affymetrix microarrays. Control and honey treated cells were investigates, three biological replicates were used for each sample.

first: Rowena

middle: E

last: Jenkins

first: Rose

last: Cooper


title: mRNAs that co-purify with OMA-1 in the C. elegans germline (microarray)

city: Minneapolis

first: Caroline

last: Spike

state: MN

address: 420 Washington Avenue, SE

department: Genetics, Cell Biology, and Development

institute: University of Minnesota

summary:
The oocytes of most animals arrest at diplotene or diakinesis, but resume meiosis (meiotic maturation) in response to hormones. In C. elegans, maturation of the –1 oocyte requires the presence of sperm, Gas-adenylate cyclase-PKA signaling in the gonadal sheath cells, and germline function of two Tis11-like CCCH zinc-finger proteins, OMA-1 and OMA-2 (OMA proteins).  Prior studies indicate that the OMA proteins redundantly repress the translation of specific mRNAs in oocytes (zif-1, mom-2, nos-2, glp-1) and early embryos (mei-1).
We purified OMA-1-containing ribonucleoprotein particles (RNPs) and identified mRNAs that associate with OMA-1 in oocytes using microarrays. We examined the relative abundances of mRNAs in OMA-1 RNPs using high-throughput RNA sequencing.  Previously identified targets of OMA-dependent translational repression in oocytes were found to be both enriched (>2-fold relative to input RNA) and abundant in purified OMA-1 RNPs.  Furthermore, we verified that some of the newly identified mRNAs that share these characteristics are translationally repressed by OMA-1/2 in oocytes through sequences in their 3’UTRs.  Although meiotic maturation is stimulated by sperm, we found that the mRNAs copurifying with OMA-1 are not significantly different in the presence and absence of sperm, suggesting that sperm-dependent signaling does not modify the suite of mRNAs stably associated with OMA-1.  Further, several tested OMA-1-associated mRNAs were shown to be translationally repressed in both the presence and absence of sperm.

overall_design: RNA co-purifiying with OMA-1 (IP RNA) was isolated and compared to total lysate RNA (input RNA).  Immunopurifications were performed, in triplicate, from lysates made from two different sterile strains.  Sterile fog-1 adults lack sperm.  Sterile spe-9 adults contain fertilization-incompetent sperm that promote meiotic maturation.

first: David

last: Greenstein


title: Expression data from persister and normal cells of Pseudomonas aeruginosa PAO1

status: Public on Nov 25 2014

city: Syracuse

first: Geetika

last: Choudhary

state: NY

address: 329 Link Hall

department: Biomedical and Chemical Engineering

institute: Syracuse University

summary:
Pseudomonas aeruginosa PAO1 persister and normal cells were treated with and without Granulocyte Macrophage Colony-Stimulating Factor (GM-CSF) to understand the effect of GM-CSF on gene expression of PAO1.
We used DNA microarrays to identify the down-regulated and up-regulated genes after GM-CSF treatment.

overall_design: Pseudonmonas aeruginosa PAO1 normal cells were obtained from stationary phase culture and persister cells were isolated by lysing normal cells with ciprofloxacin. The normal cells and isolated persister cells were treated with GM-CSF and selected for RNA extraction and hybridization on Affymetrix microarrays. The experiment was performed in two biological replicates. The samples for the biological replciates were: Control C1, Treatment T1, Control C2, and Treatment T2.

middle: S

first: Dacheng

last: Ren


title: DAF-16/FoxO and EGL-27/GATA promote developmental growth in response to persistent somatic DNA damage

first: Bjoern

last: Schumacher

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptome response to nitric oxide in Pseudomonas aeruginosa

status: Public on Dec 08 2014

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

country: Japan

institute: The University of Tokyo

summary:
DNA microarray analysis was employed to investigate the transcriptome response to nitric oxide in Pseudomonas aeruginosa. We focused on the role played by the nitric oxide-response regulators DNR and FhpR and an oxygen-response regulator ANR in the response.
The transcriptome profiles of the P. aeruginosa strains before and after exposure to nitric oxide under the microaerobic conditions were analyzed. Wild type, its anr, dnr, and fhpR mutants, and the anr mutant that express dnr were used for the analyses.

overall_design: Pseudomonas aeruginosa wild type (PAO1ut), anr mutant (RManr), dnr mutant (RMdnr), anr mutant that constitutively expresses DNR (RManrEXdnr), and fhpR mutant (PDM2665) were cultivated microaerobically in LB in 1-liter jar fermenter. When optical density at 600 nm reached 0.3, nitric oxide-saturated water was added to the medium (final nitric oxide concentration was 20 micro-M). RNA was isolated from a 10 ml aliquot of the culture prior to the addition of nitric oxide and at 5 min after the addition. The experiment was performed in duplicate independent cultures.

first: Miho

last: Kuroki


title: Expression data in NK150460 treated breast cancer cell lines

status: Public on Sep 19 2014

city: Kita-ku

first: Kazuteru

last: Fukasawa

address: 31-12, Shimo 3-Chome

department: Pharmaceutical Development Division

institute: Nippon Kayaku Co., Ltd.

summary:
The purpose of this study is to investigate certain genes inuduced/reduced by NK150460, novel compound possessing antitumor activity.
To identify genes, time course samples were prepared from NK150460 sensitive and insensitive breast cancer cell lines. By comparing patterns in both sensitive and resistant cell lines, we tried to identify genes specifically modulated by NK150460 treatment.

overall_design: Four breast cance cell lines (3 sensitive cell lines, 1 insensitive cell line) were treated with NK150460 in vitro. 0, 3, 6, 24 hr after drug addition, total RNA were prepared. In total, 16 samples were prepared and subjected to microarray analysis.

first: Shigehide

last: Kagaya


title: C. Elegans expression: toxic vs. adequate vs. low selenium

status: Public on Jul 03 2014

city: Madison

first: Roger

last: Sunde

state: WI

address: 1415 Linden Dr

department: Nutritional Sciences

institute: University of Wisconsin

summary:
Genome-wide expression analysis in C. Elegans grown in axenic media with low to toxic selenium concentrations
We performed Affymetrix micorarray-based transcriptional profiling on wild-type C. Elegans Bristol N2 grown in low Se axenic media supplemented with five concentrations of selenium, from low to toxic, and harvested at the L4-larva stage.

overall_design: RNA was prepared for hybridization to Affy microarrays from synchronized cultures of wild-type C. elegans seeded in low Se axenic media, supplemented with graded 0, 0.05, 0.1, 0.2, and 0.4 mM Se added as sodium selenite, and harvested at the L4-larva stage (1 culture/sample per Se concentgration).


title: Vastus lateralis biopsies from healthy and COPD patients before and after 3 weeks of endurance training

status: Public on Sep 01 2014

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

institute: University of Birmingham

summary: Study the effects of 3 weeks training exercise in chronic obstructive pulmonary disease (COPD) patients and healthy individuals. Skeletal muscle biopsies of 5 COPD patients (aged 63±2 year) and 3 age-matched healthy individuals were studied before and after 3 weeks of a supervised endurance training program.

overall_design: Samples were collected from open muscle biopsies of the vastus lateralis of 5 COPD patients and 3 age-matched healthy individuals before and after 3 weeks of a supervised endurance training program. Patients and controls underwent an endurance exercise program on a cycloergometer 5 days a week for three consecutive weeks. One 1 h session/day was established in all subjects, with effective exercise periods of at least 30 min in each case.

first: Susana

last: Kalko

first: Francesco

last: Falciani

first: Josep

last: Roca


title: Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles

status: Public on May 12 2014

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

institute: Delft University of Technology

summary: Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and transcriptome has not been studied in detail. In this study, 24-h sinoidal temperature cycles, oscillating between 12 and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. After three diurnal temperature cycles (DTC), concentrations of glucose, and extracellular metabolites, as well as CO2-production rates showed regular, reproducible circadian rhytms. DTC also led to waves of transcriptional activation and repression, which involved one sixth of the yeast genome. A substantial fraction of these DTC-responsive genes appeared to primarily respond to changes in glucose concentration. Elimination of known glucose-responsive genes revealed overrepresentation of previously identified temperature-responsive genes as well as genes involved in cell cycle and de novo purine biosynthesis. Analyses of budding index and flow cytomery demonstrated that DTC led to a partial synchronization of the cell cycle of the yeast populations in the chemostat cultures, which was lost upon release from DTC. Comparison of DTC results with data from steady-state cultures showed that DTC was sufficiently slow to allow S. cerevisiae chemostat cultures to almost completely acclimatize their transcriptome and physiology at the DTC temperature maximum, and to approach acclimation at the DTC temperature minimum.

overall_design: The aim of this study was to investigate the impact of diurnal temperature cycles on the physiology and transcriptome of S. cerevisiae and to assess the extent to which these responses can be predicted from steady-state analyses. To this end, we used a continuous cultivation set-up, in which the yeast was grown under controlled conditions and subjected to 24-h sinoidal temperature cycles. Since the sampling volume was kept within 5% of the reactor volume during 24 h, sampling from two independent duplicate cultures for microarray analysis was spread over the fifth and sixth temperature cycle. Sample points from the fifth and sixth temperature cycle were combined, resulting in six sample points covering one temperature cycle (at temperatures of 30; 21; 14.6; 12; 21 and 27.4°C). For the last time point, one additional analytical duplicate sample was taken. Furthermore, steady-state chemostat cultures at constant temperatures of 12°C and 30°C (independent duplicate cultures at both temperatures) were sampled for microarray analysis. All this resulted in a total array set of 17 arrays.

first: Marit

last: Hebly

first: Dick

last: de Ridder

first: Erik

last: de Hulster

first: Pilar

last: Cortes

first: Jack

middle: T

last: Pronk

first: Pascale

last: Daran-Lapujade


title: Expression data from the starved first larval stage (L1) C. elegans animals that were incubated in S-basal buffer for 30 hours after bleaching

status: Public on May 16 2014

city: Boulder

first: Mingxue

last: Cui

address: Colorado Ave.

department: MDCB

institute: HHMI, University of Colorado at Boulder

summary: How animals coordinate gene expression in response to starvation is an outstanding problem closely linked to aging, obesity, and cancer. Newly hatched Caenorhabditis elegans respond to food deprivation by halting development and promoting long-term survival (L1 diapause), thereby providing an excellent model to study starvation response. Through a genetic search, we have discovered that the tumor suppressor Rb critically promotes survival during L1 diapause and likely does so by regulating the expression of genes in both insulin-IGF-1 signaling (IIS)-dependent and -independent pathways mainly in neurons and the intestine. Global gene expression analyses suggested that Rb maintains the “starvation-induced transcriptome” and represses the “re-feeding induced transcriptome”, including the repression of many pathogen/toxin/oxidative stress-inducible and metabolic genes, as well as the activation of many other stress-resistant genes, mitochondrial respiratory chain genes, and potential IIS receptor antagonists. Notably, the majority of genes dysregulated in starved L1 Rb(-) animals were not found to be dysregulated in fed conditions. Together, these findings identify Rb as a critical regulator of the starvation response and suggest a link between functions of tumor suppressors and starvation survival. These results may provide mechanistic insights into why cancer cells are often hypersensitive to starvation treatment.

overall_design: Gravid C. elegans adult animals were bleached with hypochlorite and sodium hydroxide. The resulting eggs were hatched in 8–10 mL S-basal without cholesterol in 15-mL conical tubes, which were placed on an end-over-end rocker (VWR) at 20 °C. 30 hours later, starved L1s were collected for RNA preparations. Wild type and lin-35/Rb mutant were profiled in triplicate. All replicates were biological replicates.

first: Min

last: Han

first: Cindy

last: Teng


title: Use of an activated beta-catenin to identify Wnt/beta-catenin pathway target genes in C. elegans, including a subset of collagen genes expressed in late larval development

status: Public on May 13 2014

city: Baltimore

first: David

last: Eisenmann

address: 1000 Hilltop Circle

department: Biological Sciences

institute: UMBC

summary: The Wnt signaling pathway plays a fundamental role during the development of metazoans, where it functions in the regulation of diverse processes including cell fate specification, cell migration, and stem cell renewal.  Activation of the beta-catenin dependent or canonical Wnt signaling pathway upregulates expression of Wnt target genes to mediate an appropriate cellular response.  In the nematode C. elegans, a Wnt signaling pathway similar to the canonical pathway regulates several processes during larval development, however few target genes of this pathway have been identified. To address this deficit, we conditionally activated Wnt signaling in living animals during a defined stage of larval life by expressing a dominant, activated beta-catenin protein, then used microarray analysis to identify genes showing altered expression compared to control animals. In this way we identified 166 differentially expressed genes, of which 104 were upregulated.  A subset of the upregulated genes were validated by qPCR and showed altered expression in Wnt pathway mutants with decreased or increased Wnt signaling; we consider these genes to be candidate Wnt pathway targets in the C. elegans hermaphrodite larva.  Amongst these was a group of 6 genes, including the cuticular collagen genes, bli-1 col-38, col-49 and col-71, that show a peak of expression in the mid L4 stage during normal development.  The L4 expression of these genes suggests they may be expressed for use in the adult cuticle, and consistent with this, reduction of function for several of the genes leads to phenotypes suggestive of defects in cuticle function or integrity.  Therefore this work has identified a large number of putative Wnt pathway target genes during larval life, including a small subset of Wnt-regulated collagen genes that may function in synthesis of the adult cuticle.

overall_design: a single pulse heat shock, inducing over-activated signal transduction in the Exp. Three treatment with three control strains of the identical genetical background strains

first: Belinda

last: Jackson

first: Michael

last: Krause

first: Patricia

last: Luzi


title: Expression Data of Reactive Oxygen Species Signalling in C. elegans

status: Public on May 08 2014

city: Montreal

first: Siegfried

last: Hekimi

state: Quebec

address: 1205 ave Docteur Penfield

institute: McGill University

summary:
We have shown that worms that possess mutations in two electron transport chain subunits live longer due to mtROS signalling. Wild type worms can also live longer by treatment with the pro-oxidant paraquat. Paraquat treatment is not additive to the mutations in the ETC subunits. We aimed to determine the underlying changes in gene expression that were common to both paraquat treatment and the two mutations.
We also have shown genetically that the mtROS signal that leads to extended lifespan is dependent on CED-4. We generated double mutants that lack functional CED-4 with the two mutations in the ETC subunits. We have found that a large number of gene expression changes by mtROS signalling are reverted by loss of CED-4.

overall_design: Young adult C. elegans were grown using a 4-hour synchronized lay and harvested by hand picking. At least three biological repeats were obtained for each condition. Worm RNA was extracted and prepared for hybridization to Affymetrix chips. We compared the gene expression patterns of genetic mutants and the wild type treated with paraquat all against a wild type control. We sought to obtain a common pattern of expression between two genetic mutants, isp-1 and nuo-6, and paraquat treatment.

first: Callista

last: Yee

first: Wen

last: Yang


title: Expression time course of yeast grown in a minimal medium

status: Public on Apr 24 2014

city: Boston

first: Nikolai

last: Slavov

state: MA

address: 360 Huntington Avenue

institute: Northeastern University

summary:
Time course of exponentially growing yeast cells

Fermenting glucose in the presence of enough oxygen to support respiration, known as aerobic glycolysis, is believed to maximize growth rate. We observed increasing aerobic glycolysis during exponential growth, suggesting additional physiological roles for aerobic glycolysis. We investigated such roles in yeast batch cultures by quantifying O2 consumption, CO2 production, amino acids, mRNAs, proteins, posttranslational modifications, and stress sensitivity in the course of nine doublings at constant rate. During this course, the cells support a constant biomass-production rate with decreasing rates of respiration and ATP production but also decrease their stress resistance. As the respiration rate decreases, so do the levels of enzymes catalyzing rate-determining reactions of the tricarboxylic-acid cycle (providing NADH for respiration) and of mitochondrial folate-mediated NADPH production (required for oxidative defense). The findings demonstrate that exponential growth can represent not a single metabolic/physiological state but a continuum of changing states and that aerobic glycolysis can reduce the energy demands associated with respiratory metabolism and stress survival.


title: Expression data from PAO1 and its creBC  derivative mutant (PAOΔcreBC)

status: Public on Jun 25 2014

city: Palma de Mallorca

first: Bartolome

middle: Moya

last: Cañellas

state: Islas Baleares

address: Ctra. Valldemossa

institute: HUSE

summary: We used microarrays to determine the expression profile of the P. aeruginosa creBC mutant regarding its parental wild type strain PAO1.

overall_design: Expression analysis from three independent replicates of PAO1 and its creBC  derivative mutant (PAOΔcreBC) were performed  under basal conditions and with cefoxitin and ceftazidime.  cDNA synthesis, fragmentation, labeling and hybridization were performed according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.

first: Bartolomé

last: Moya

first: J

last: González Rubio

first: Jesús

last: Blazquez


title: Expression data from C. elegans during L3 and L3-lethargus

status: Public on Apr 18 2014

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary:
To identify genes differentially expressed during L3 lethargus, we collected RNA during the third larval stage (L3) lethargus period, 37 hours after feeding developmentally-arrested L1 animals. Animals in lethargus were identified based on quiescence of locomotion and feeding.  Additional time point for RNA collection was in the mid-L3 stage, 32 hours after feeding developmentally-arrested L1 animals.  These samples were interrogated with the Affymetrix C. elegans Genome Array.
A total of 153 gene transcripts were up regulated, and 48 gene transcripts were down regulated, during the L3 lethargus period compared to the L3 stage (false discovery rate (FDR) < 0.05).

overall_design: There were 2 groups and 3x replication for each group, for 6 total samples. The groups were (1) L3 and (2) L3-lethargus. We compared L3-lethargus vs L3 using R/maanova. The permutation based p-values for each test were significant for FDR≤5%.

last: Raizen


title: Expression data from C. elegans during L4, L4-lethargus, and Adult

summary:
To identify genes differentially expressed during the molt, we collected RNA 30-40 minutes after feeding cessation at the start of the fourth larval stage (L4) lethargus.  Additional time points for RNA collection were in the mid-L4 stage, approximately four hours prior to lethargus, and in the young adult stage, four hours after lethargus. These samples were interrogated with the Affymetrix C. elegans Genome Array.
A total of 1,804 gene transcripts were up regulated, and 1,088 gene transcripts were down regulated, during the L4 lethargus period compared to the L4 and Adult stages (false discovery rate (FDR) < 0.05).

overall_design: There were a total of 3 groups and 5x replication for each group, for 15 total samples that were analyzed. The groups were (1) L4, (2) L4-lethargus, (3) Adult. We generated the following pairwise comparisons using R/maanova: L4-lethargus vs L4, L4-lethargus vs Adult. The permutation based p-values for each test were multiplied by 2 and transcripts with an FDR≤5% were selected.


title: C. elegans during lethargus


title: Identiﬁcation of Drosophila TDF/Apt  regulated genes in embryos

status: Public on Apr 01 2014

city: Taian

first: Qing-Xin

last: Liu

state: Shandong

address: No. 61 Daizong Street

country: China

institute: Shandong Agricultural University

summary:
Drosophila tdf, another name apontic (apt), encodes a bZIP transcription factor that is required for the development of trachea, heart, head and neural system. However, little is known about the target of TDF/Apt.
To identify theTDF/ Apt regulated genes, we compared expression profiles of mRNA purified from wild-type and tdf mutant embryos. Summary  file is emtdf-yw.CHP.

overall_design: yw and tdf mutant embryos were selected at later stage of  development for RNA extraction and hybridization on Affymetrix microarrays. We identified tdf mutant embryos using CyOact-GFP balancer chromosome.

first: Xian-Feng

last: Wang

first: Kazuho

last: Ikeo

first: Susumu

last: Hirose

first: Takashi

last: Gojobori


title: Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose

status: Public on Mar 19 2014

first: Jean-Marc

last: Daran

summary: Its characteristic rose-like aroma makes phenylethanol a popular ingredient in foods, beverages and cosmetics. Microbial production of phenylethanol currently relies on whole-cell bioconversion of phenylalanine with yeasts that harbor an Ehrlich pathway for phenylalanine catabolism. Complete biosynthesis of phenylethanol from a cheap carbon source such as glucose provides an economically attractive alternative for phenylalanine bioconversion. In this study, a Synthetic Genetic Array screening was applied to identify genes involved in regulation of phenylethanol synthesis in Saccharomyces cerevisiae. The screen focused on transcriptional regulation of ARO10, which encodes the major decarboxylase involved in conversion of phenylpyruvate to phenylethanol. A deletion in ARO8, which encodes an aromatic amino acid transaminase, was found to cause a transcriptional upregulation of ARO10 during growth with ammonium sulfate as the sole nitrogen source. Physiological characterization revealed that the aro8 mutation led to substantial changes in the absolute and relative intracellular concentrations of amino acids. Moreover, deletion of ARO8 led to de novo production of phenylethanol during growth on a  glucose synthetic medium with ammonium as the sole nitrogen source. The aro8 mutation also stimulated phenylethanol production when combined with other, previously documented mutations that deregulate aromatic amino acid biosynthesis in S. cerevisiae. The resulting engineered S. cerevisiae strain produced over 3 mM of phenylethanol from glucose during growth on a simple synthetic medium. The strong impact of a transaminase deletion on intracellular amino acid concentrations opens new possibilities for yeast-based production of amino acid-derived products.

overall_design: The goal of the present study was to identify genes that influence the transcriptional (de)repression of the Ehrlich pathway during growth with ammonium as the nitrogen source. With the aid of Synthetic Genetic Array technology, we constructed a strain collection in which deletions in the non-essential genes in the S. cerevisiae genome were combined with a reporter plasmid comprising the ARO10 promoter fused to a reporter gene (egfp) encoding a fluorescent reporter protein. After screening by flow cytometry, deletion of ARO8 led to a  deregulated expression from the ARO10 promoter. The impact of this deletion was further studied by transcriptome and intracellular metabolite analyses. Furthermore, phenylethanol production was measured in strains that combined the aro8 mutation with mutations that were previously shown to deregulate aromatic amino acid biosynthesis.

first: Gabriele

last: Romagnoli

first: Pilar

last: de le Torre

first: Jack

last: Pronk


title: Expression profile of hsp31∆, hsp32∆, hsp33∆ during diauxic shift

status: Public on Mar 25 2014

city: Lisboa

first: Leonor

last: Miller-Fleming

state: select a state

address: Avenida Prof. Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

summary:
The yeast Hsp31 mini-family proteins (Hsp31, Hsp32, Hsp33, Hsp34) belong to the highly conserved DJ-1 superfamily. The human DJ-1 protein is associated with cancer and neurodegenerative disorders, such as Parkinson’s disease. However, the precise function of human and yeast DJ-1 proteins is unclear. Here we show that the yeast DJ-1 homologs have a role in diauxic-shift, characterized by metabolic reprogramming due to glucose limitation. We find that the Hsp31 genes are strongly induced in diauxic-shift and in stationary phase (SP), and that deletion of these genes reduces chronological lifespan, impairs transcriptional reprogramming at diauxic-shift, and impairs the acquisition of several typical characteristics of SP, including autophagy induction. In addition, under carbon starvation, the HSP31 family gene deletion strains display impaired autophagy, disrupted TORC1 localization to P-bodies, and caused abnormal TORC1-mediated Atg13 phosphorylation. Repression of TORC1 by rapamycin in the gene deletion strains completely reversed their sensitivity to heat shock. Altogether, our data indicate that Hsp31 mini-family is required for diauxic-shift reprogramming and cell survival in SP, and plays a role upstream of TORC1. The enhanced understanding of the cellular function of these genes sheds light into the biological role of other members of the superfamily, including DJ-1, which is an attractive target for therapeutic intervention in cancer and in Parkinson’s disease.
hsp31∆, hsp32∆, hsp33∆ are compared with its parental strain BY4741. We used One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling from Agilent.

overall_design: Cultures were grown in synthetic complete media until reached diauxic shift. At this time cultures were collected.

first: Joshua

last: Smalley

first: Flaviano

last: Giorgini

first: Tiago

last: Outeiro


title: The Microbial Detection Array for Detection of Emerging Viruses in Clinical Samples - A Useful Panmicrobial Diagnostic Tool--Array Version 2f

status: Public on Mar 05 2014

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

summary: Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travelling, climate changes and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. For many of them, the disease symptoms are similar to each other, as well as to other more common diseases, making them difficult to diagnose. A rapid identification will help to decide about specific treatment and appropriate case management. Real-time PCR is commonly used for specific virus detection in clinical samples. A diagnostic microarray containing probes for all human viruses, could replace hundreds of specific PCR-reactions and identify all viruses by one assay and thereby remove the need for a clear clinical hypothesis. We show that the Microbial Detection Array successfully identifies emerging viruses present in both non-clinical and clinical samples.

sample_organism:
Cowpox virus
Monkeypox virus
Orf virus
Eastern equine encephalitis virus
dengue virus type 1
dengue virus type 2
dengue virus type 3
dengue virus type 4
Japanese encephalitis virus
West Nile virus
Tick-borne encephalitis virus
Yellow fever virus
Rift Valley fever virus
Toscana virus
Dengue virus
sandfly fever Sicilian virus
synthetic construct
Chikungunya virus
Human poliovirus sp.
Usutu virus
Marburgvirus
Zaire ebolavirus
Sandfly fever Naples virus
Hepacivirus hominis
Mammarenavirus lassaense
Orthohantavirus dobravaense
Orthohantavirus hantanense
Orthohantavirus puumalaense
Orthohantavirus seoulense
Orthohantavirus sinnombreense
Orthonairovirus haemorrhagiae

overall_design: Twenty-four clinical samples and 40 non-clinical samples (cell culture supernantants or purified viral DNA or RNA) were analyzed for presence of emerging viruses using the MDA microarray.

first: Maiken

last: Rosenstierne

first: Majken

middle: L

last: Olesen

first: Anna

last: Pappa

first: Olivier

last: Engler

first: Sebastien

last: Plumet

first: Ali

last: Mirazimi

first: Manfred

last: Weidmann

first: Matthias

last: Niedrig

first: Anders

last: Fomsgaard

first: Lena

last: Erlandsson


title: Drivers of metallothionein-mediated detoxification of cadmium in C.elegans

status: Public on Jun 01 2014

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

institute: King's College London

summary: Cadmium is toxic and intricate pathways linked to metallothioneins (MT) drive the detoxification process. Whist the mechanisms are well understood in mammalian systems, detailed knowledge is still elusive in invertebrates (which notably differ to mammalian systems).  The model nematode Caenorhabditis elegans is ideally suited for assessing metallothionein mediates detoxification in invertebrates as is relatively short-lived, can be easily exposed and its genome is fully sequenced and widely annotated. The aim of the experiment was to identify new MT mediated target genes involved in Cd toxicosis.

overall_design: The global transcriptome was compared in wild type and a MT double knockout strain raised in the presence or absence of 30 µM Cd.

first: Suresh

middle: C

last: Swain


title: Genomic expression comparison between WT and H2B(K123R)

status: Public on Mar 17 2014

city: Las Vegas

first: Wilson

last: Xu

state: NV

address: One Breakthrough Way

institute: Nevada Cancer Institute

summary: The study aims to elucidate the effect of mono-ubiquitination of histone H2B at K123.

overall_design: The WT and H2B(K123R) yeast in early stationary phase were inoculated in fresh YPD rich media at OD 0.3.  The cells were then grown to OD2.0 and their total RNA was isolated for genomic expression profiling with S98 arrays (Affymetrix).  The experiments were performed in triplicate.


title: Lipopolysaccharide modulates rhinovirus-induced chemokine secretion in monocytes and macrophages.

status: Public on Jan 31 2014

first: Maya

last: Karta

address: 1135 Biochemistry, 420 Henry Mall

department: Biomolecular Chemistry

institute: University Wisconsin-Madison

summary: Rhinovirus (RV) infection has been shown to exacerbate asthma. Understanding of the underlying mechanisms by which RV infections provoke airway inflammation and remodeling in asthma may offer significant insight into asthma pathogenesis and exacerbations as well as offer opportunities for improved disease management. Expression analysis of RV A16-treated primary peripheral blood monocytes from human donors was performed to determine what pattern of gene expression is associated with RV infection of monocytes in vitro.

overall_design: Peripheral blood monocytes were isolated from 5 adults. Following overnight incubation in RPMI supplemented with 10% FBS, the monocytes were stimulated with purified major group RV A16 at multiplicity of infection of 10 plaque forming units (pfu) per cell or with growth media alone (mock). Cells were lysed 4 hours after treatment and isolated total RNAs were pooled per treatment and analyzed using the Affymetrix GeneChip HuGeneFL Array (Hu6800, Affymetrix, Santa Clara, CA).

first: Mary

last: Bates

first: David

last: Hall

first: Paul

last: Bertics


title: The Indispensible and Global Role of NAD Metabolism for the Lifestyle and Virulence of Pseudomonas aeruginosa

status: Public on Feb 01 2014

city: Hannover

first: Sarah

last: Frank

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

institute: Medical School Hannover

summary: A knockout of nrtR gene (PA4916) of Pseudomonas aeruginosa leads to the global changes in metabolic profile of the pathogen to its complete avirulence.

overall_design: Bacterial cells of TBCF10839 and TBCF10839nrtR::Tn5 were grown in LB broth to late exponential phase at 37 oC

first: Elza

last: Okon

first: Anya

last: Pelnikevich


title: Transcriptional profiling of Pseudomonas aeruginosa PAO1161 strain and its parA and parB mutants

status: Public on Feb 12 2014

city: Warsaw

first: Aneta

middle: Agnieszka

last: Bartosik

address: Pawinskiego 5A

department: Institute of Biochemistry and Biophysics

country: Poland

institute: Polish Academy of Sciences

summary: Representatives of two families of bacterial Par proteins, ParA and ParB, are encoded by the majority of bacterial chromosomes in the close vicinity of oriC. ParA(Soj) and ParB(Spo0J) proteins of Pseudomonas aeruginosa are both important for optimal growth, nucleoids segregation, cell division and different types of motility. Comparative transcriptome analysis of parAnull, parBnull mutants versus parental PAO1161 strain of P. aeruginosa demonstrated global changes in genes expression pattern in logarithmic phase of planktonic cultures grown on rich medium. The set of genes that were similarly regulated in both mutant strains as compared to the wild-type strain as well as two sets of genes uniquely affected in the particular mutant were defined suggesting that ParA and ParB may act in common and independently. In general, many genes involved in cell division, DNA and RNA processing and metabolic processes were down-regulated in mutant cells, in contrast genes which products play a role in adaptation, protection, motility, cell-to-cell signaling as well as signal transduction increased their expression in par mutant cells. Besides their role in chromosome segregation, ParA and ParB seem to have the potential to regulate genes transcription. The altered expression of a large number of genes encoding known or predicted transcriptional regulators and genes coding for products involved in c-di-GMP signalling, suggests that the part of observed global changes in genes expression pattern in parAnull and parBnull mutants might be the effect of indirect regulation mediated by regulatory genes under ParA and ParB control. The extended regulatory network provides the mechanism to modulate genes expression in response to the stage of the chromosome segregation process and cell cycle.

overall_design: Pseudomonas aeruginosa PAO1161 (leu, r-, RifR), derivative of PAO1, as a control (reference) strain, Pseudomonas aeruginosa PAO1161 parA1-40::smh (parAnull) and Pseudomonas aeruginosa PAO1161 parB1-18::TcR (parBnull) disruption mutant strains were used in the experiments. Three independent biological replicates of total RNA were isolated for each strain from logarithmic (Log) phase of planktonic culture grown on rich medium (L broth) at 37oC. In total, nine samples of RNA were prepared.

middle: A

first: Grazyna

last: Jagura-Burdzy

first: Anna

last: Fogtman

first: Marta

last: Koblowska


title: Transcriptional response to 2-oxoglutarate (alpha-ketoglutarate) in Pseduomonas aeruginosa PAO1

status: Public on Feb 15 2014

city: Syracuse

first: Christopher

last: Nomura

address: 1 Forestry Dr.

department: Chemistry

institute: SUNY-ESF

summary:
The transcriptome of P. aeruginosa PAO1 in the presence of extracelluar 2-oxoglutarate at a concentration of 20 mM.
We determined the transcriptional response of  P. aeruignosa PAO1 to extracellular 2-oxoglutarate.

overall_design: P. aeruginosa PAO1 was grown in nutrient broth (Oxoid number 2) and induced with 20 mM 2-oxoglutarate.  At 30 min post induction, total RNA was isolated and prepped for Affymetrix GeneChips.

first: Benjamin

middle: R

last: Lundgren


title: Expression data from Caenorhabditis elegans fed with 13L cocoa peptide

status: Public on Dec 31 2013

city: Paterna

first: Patricia

last: Martorell

state: Valencia

address: Catedrático Agustín Escardino Benlloch, 9, Building 2

department: Agrifood Biotechnology

institute: Biópolis SL

summary: Cocoa protein content is a very interesting source for isolation of antioxidant bio-peptides, which can be used for the prevention of age-related diseases. We use microarrays to study the global genome expression of C. elegans fed with a peptide (13L) isolated from cocoa.

overall_design: Wild type strain N2 of C. elegans was fed with 1 µg/mL of 13L peptide or in Nematode Growth medium (MGM, control fed) until reach young adult stage. Worm population were age-synchronized. RNA was isolated from each populations (control and treated) using RNAasy Kit (Qiagen) and hybridizated on Affymetrix microarrays.

first: Salvador

last: Genovés

first: Daniel

last: Ramón

last: Montaner


title: Expression data for Saccharomyces cerevisiae oxidative stress response

status: Public on Dec 17 2013

city: Manchester

first: Pedro

last: Mendes

address: 131 Princess Street

department: Manchester Institute of Biotechnology

institute: University of Manchester

summary:
Oxidative stress is a harmful condition in a cell, tissue, or organ, caused by an imbalnace between reactive oxygen species and other oxidants and the capacity of antioxidant defense systems to remove them. The budding yeast S. cerevisiae has been the major eukaryotic model for studies of response to oxidative stress.
We used microarrays to study the genome-wide temporal response of the yeast S. cerevisiae to oxidative stress induced by cumene hydroperoxide. Keywords: time course

overall_design: The effects of oxidative stress induced by CHP on the transcriptional profile of S. cerevisiae was studied from a dynamical perspective. Yeast cultures were grown in controlled batch conditions, in 1 L fermentors. Three replicate cultures in mid-exponential phase were exposed to 0.19 mM CHP, while three non-treated cultures were used as controls. Samples were collected at t=0 (immediately before adding CHP) and at 3, 6, 12 and 20 min after adding the oxidant. Samples were processed for RNA extraction and profiled using Affymetrix Yeast Genome S98 arrays.

first: D

last: Camacho

first: R

last: Laubenbacher

first: A

last: Martins

first: P

first: W

last: Sha

first: V

last: Shulaev

first: B

last: Stigler


title: High-time-resolution time-series transcriptome data of Pseudomonas aeruginosa PAO1 under two inverted oxygen-availability transitions

status: Public on Dec 10 2013

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary:
We performed high-time-resolution (HTR) transcriptome analyses of Pseudomonas aeruginosa PAO1 (PA) in a continuous cultivation system during the transition from high oxygen tension to low oxygen tension (HLOT) and the reversed transition from low to high oxygen tension (LHOT). From those genes responsive to both transient conditions, we identified 85 essential oxygen-availability responsive genes (EORGs), including the expected ones (arcDABC) encoding enzymes for arginine fermentation. We then predicted a highly accurate regulatory network for the EORGs of PA by integrating information from binding motif searching, literature and inverted HTR datasets.
These results not only reveal stringent EORGs of PA and their transcription regulatory network, but also highlight that achieving a high accuracy of the inferred regulatory network might be only feasible for the apparently affected regulators under the given conditions but not for all the expressed regulators in a genome scale.

overall_design: Pseudomonas aeruginosa PAO1 (PA) from a continuous cultivation system during two inverted oxygen-availability transitions were used for RNA extraction and hybridization on Affymetrix P. aeruginosa Genome Array .  Our aim is to identify essential oxygen-availability responsive genes and to infer an accurate oxygen-responsive regulatory network. In total, 14 samples were harvested at time points 0, 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80 and 90 min after switching from aerobic to microaerobic condition. After reaching a steady state (after about another four bioreactor volume exchange) under these conditions, the culture was shifted from microaerobic back to fully aerobic condition (pO2 set point value from 0.5% to 100%). A similar set of samples were taken during the reversed transition with the same time intervals.

middle: Q

last: He

first: Wei

last: Wang

first: Ping

last: Zheng

first: Padhmanand

last: Sudhakar

first: Jibin

last: Sun

first: An-Ping

last: Zeng


title: Expression data from  glp-1(e2141) hermaphrodites maintained with or without males for 8 days

status: Public on Oct 25 2013

city: Stanford

first: Travis

middle: Justin

last: Maures

address: 300 Pasteur Drive Alway

department: Genetics

country: USA

institute: Stanford University

summary:
Males induce dramatic physiological changes to hermaphrodites, including a significant shortening of lifespan. We have termed this effect as male-induced demise (MID) of hermaphrodites. This experiment was performed to analyse changes in gene expression due to the presence of males. We have shown that Knock down of utx-1 ameliorates the MID. In this experiment we also examine male-induce gene expression that may be altered when knocking down expression of utx-1 via RNAi.
We used microarrays to detail the global program of gene expression andidentified distinct classes of up-regulated and down-regulated genes upon the addition of males.

overall_design:
There are 12 samples in total. To identify male-induced expression using microarray analysis, 250 glp-1(e2141) L1 hermaphrodites (to avoid production of progeny) were placed in the presence of 250 wild-type males (L4-adult day 1) for 8 days on a 10 cm NGM plate seeded with OP50. As a control for worm number, 500 L1 glp-1(e2141) hermaphrodites were placed on a 10 cm NGM plate seeded with OP50 for 8 days. Both conditions were incubated at 25°C, the restrictive temperature for the glp-1(e2141) worms throughout the experiment. On day 8, male worms were removed from the plate and RNA was extracted from 200 hermaphrodites from each condition. RNA from 3 independent experimentsfor each condition was used for the microarray hybridization with the exception of utx-1 RNAi (with males) of which one condition did not provide sufficient total RNA.
Total RNA was isolated using an RNeasy (Qiagen). Microarray hybridization was performed at the Stanford Protein and Nucleic Acid facility with oligonucleotide arrays (Affymetrix, GeneChipC. elegans Genome Arrays).

first: Bérénice

last: Benayoun


title: Pseudomonas aeruginosa response to lung surfactant

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

summary: The response of bacteria to the conditions at the site of infection is a key part of the transcriptional program that will determine the sucess of the infectious agent. To model the environment of the distal airway, we used bovine pulmonary surfactant (Survanta). P. aeruginosa transcript levels were measured in the presence or absence of Survanta in MOPS minimal medium to identify transcripts altered in response to surfactant. The most highly induced transcript in Survanta was PA5325, renamed sphA based on our findings that the gene was specifically induced by sphingosine derived from the sphingomyelin present in pulmonary surfactant. A divergently transcribed transcription factor, PA5324, was demonstrated to be critical for the sphingosine dependent induction of sphA and was therefore renamed SphR. Microarrays of the sphR mutant cells were compared to wild type to determine the likely SphR regulon.

overall_design: Wild type and sphR mutant cells were pre-grown in MOPS minimal media and then split and resuspended in MOPS pyruvate or MOPS pyruvate + surfactant

first: Annette

last: LaBauve


title: Mechanisms of adaptation to stress and control of virulence in Pseudomonas aeruginosa: the OxyR regulons

status: Public on Dec 13 2013

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary:
Oxidative stress caused by exposure to reactive oxygen species (ROS), is a major challenge for aerobic and especially anaerobic organisms. Bacteria coordinate the response to oxidative stress through the LysR-type transcriptional regulator (LTTR) OxyR. Extensive studies have focused on the classical Escherichia coli system to shed light on the mode of action of defensive weapons against oxidative stress. The underlying mechanism is mediated via the formation of redox-dependent disulfide bond between two conserved cysteines of OxyR, thus activating transcription of members of the OxyR regulon. However, only fragmentary information on the regulation and function of OxyR has been gleaned through genetic and biochemical analyses in the important opportunistic pathogen P. aeruginosa. In this report, we used a comprehensive transcriptional profiling analysis to delineate the OxyR regulon under three conditions (King’s A medium [Pseudomonas medium or PM], Luria Broth (LB), and LB when oxyR is overexpressed), to investigate its roles in different cellular aspects that are independent of the classical oxidative stress response. Interestingly, when grown in LB, OxyR was found to regulating many genes involved in the process of inter-cellular communication known as quorum sensing (QS). In contrast, when grown in PM, OxyR regulate the expression of a newly identified CSS (cell-surface signaling) system in an OxyR-dependent fashion. In addition, the results from oxyR overexpression further confirmed that OxyR was linked to regulation of QS and Type 3 Secretion (T3SS) in addition to the regulation of antioxidative genes.
Taken together, our results show that, apart from its dominant role in defense against oxidative stress in P. aeruginosa, OxyR acts as a global regulator that provides a link between the regulation of oxidative stress response, QS and virulence.

overall_design: 15 samples, representing 5 different biological conditions, including 3 biological replicates for each condition

first: Qing

last: Wei

first: Falk

last: Hildebrand

last: Fletcher

first: Pieter

last: Monsieurs

first: Jean-Pierre

last: Hernalsteens

first: Jeroen

last: Raes

first: Lumeng

last: Ye

first: Natalie

last: Leys

first: Miguel

last: Cámara

first: Daniel

last: Charlier

last: Hassett

first: Pierre

last: Cornelis


title: Expression data from Pseudomonas aeruginosa PAO1 and an isogenic HCN negative mutant (PAO6344), grown under cyanogenic conditions.

status: Public on Sep 16 2013

city: Rome

first: Emanuela

last: Frangipani

address: Viale G. Marconi 446

department: Department of Sciences

country: Italy

institute: University of Roma Tre

summary:
Pseudomonas aeruginosa produces the toxic secondary metabolite hydrogen cyanide (HCN) at high cell population densities and low aeration.
We have used Affimetrix microarrays to investigate the impact of HCN as a signal in cell-cell communication by comparing the transcriptome of the wild-type strain PAO1 to that of an HCN-negative mutant (PAO6344) under cyanogenic conditions.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas aeruginosa PAO1

overall_design: Total RNA was extracted from cultures of the wild-type strain PAO1 as well as from the isogenic HCN negative mutant (PAO6344), when HCN production was maximal (i.e. end of exponential growth phase). Each RNA pool derived from 3 technical replicates. 1 biological replicate per strain was performed on a different day.

first: Isabel

last: Pérez-Martínez

first: Huw

middle: D

last: Williams

first: Gaëtan

last: Cherbuin

first: Dieter

last: Haas


title: To divide or not to divide: a key role of Rim15 in calorie-restricted yeast cultures

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

summary:
The present study aims to explore the role of Rim15 in both physiology and genome wide expression in S. cerevisiae under severe caloric restriction. Non-growing but metabolically active cultures of S. cerevisiae are of major interest for application in industry and as model systems for aging in higher eukaryotes. Using retentostat cultivations, almost non-growing but metabolic active cultures can be obtained resulting from the severe caloric restriction, yet not starvation, yeast experiences. Rim15 plays an important role in several nutrient sensing pathways and is involved in activating stress response and glycogen accumulation upon nutrient shortage. To investigate the role of Rim15 in the extreme robustness and glycogen accumulation of anaerobic retentostat cultures, a rim15 deletion strain is compared with its parental strain under anaerobic calorie restriction on both physiology and transcriptome.
Rim15 is described as essential for G0 entry and glycogen accumulation in yeast during diauxic shift and stationary phase. Anaerobic retentostat cultures display many stationary phase characteristics, including increased expression levels of Rim15 target genes, suggesting an important role for Rim15 under these conditions. Comparing a rim15 deletion strain and its parental strain revealed both on transcriptome level and physiology indeed a major role in the acquired robustness, glycogen accumulation, but also maintenance of viability and cell cycle arrest. The severe caloric restriction, but not starving, conditions applied together with a thorough physiological and transcriptome analysis of the cultures shows that Rim15 is essential in fine-tuning cell cycle progression with glucose availability under extreme growth-limiting conditions.

overall_design: To investigate the impact of rim15 deletion under severe  calorie restricted conditions,  transcriptome of a S. cerevisiae rim15 deletion mutant was monitored during anaerobic retentostat cultivation. Five time points were used, one in the starting point of the retentostat (T0 = chemostat) and four during the course of the retentostat (time points 2, 9, 16 and 20 days). Culture triplicates were performed for T0 in chemostat, while two independent cultures were run for retentostat.

first: Markus

middle: M

last: Bisschops

first: Priscilla

last: Zwartjens

first: Sebastiaan

last: de Keuter

first: Jack

last: Pronk

first: Pascale

last: Daran-Lapujade


title: C. elegans mixed stage embryo total RNA levels by microarray: L4440 RNAi, smo-1 RNAi and sdc-2 (y93)+RNAi

status: Public on Aug 31 2013

city: Berkeley

first: Barbara

last: Meyer

address: 16 Barker Hall

department: Molecular and Cellular Biology

institute: University of California Berkeley

summary: The essential process of dosage compensation equalizes X-chromosome gene expression between C. elegans XO males and XX hermaphrodites through a dosage compensation complex (DCC) that resembles condensin. The DCC binds to both X chromosomes of hermaphrodites to repress transcription by half. Here we show that post-translational modification by the SUMO conjugation pathway is essential for sex-specific assembly of the DCC onto X. Depletion of the SUMO peptide in vivo severely disrupts binding of particular DCC subunits and causes changes in X-linked gene expression similar to those caused by disrupting genes encoding DCC subunits. Three DCC subunits are themselves SUMOylated, and depletion of SUMO preferentially reduces their binding to X, suggesting that SUMOylation of DCC subunits is essential for robust association with X. DCC SUMOylation is triggered by the signal that initiates DCC assembly onto X. The initial step of assembly--binding of X-targeting factors to recruitment sites on X (rex sites)--is independent of SUMOylation, but robust binding of the complete complex requires SUMOylation. SUMOylated DCC subunits are enriched at rex sites, and SUMOylation enhances interactions between X-targeting factors and condensin subunits that facilitate DCC binding beyond the low level achieved without SUMOylation. DCC subunits also participate in condensin complexes essential for chromosome segregation, but their SUMOylation occurs only in the context of the DCC. Our results reinforce a newly emerging theme in which multiple proteins of a complex are SUMOylated in response to a specific stimulus, leading to accelerated complex formation and enhanced function.

overall_design: Total RNA was extracted from mixed stage embryos.

first: Rebecca

last: Pferdehirt