title: Time-resolved heat stress response of Saccharomyces cerevisiae

status: Public on Dec 01 2013

city: Amsterdam

first: Femke

last: Mensonides

address: Nieuwe Achtergracht 166

institute: University of Amsterdam

summary:
Whole-genome transcriptional response of S. cerevisiae to an increase in temperature from 28°C to 41°C under well-controlled conditions.
Two subsequent phases of response with very different dynamics: a short term  response for the first hour after the temperature increase and a long term one for up to six hours. The initial response was strongest with almost half of the ORFs being induced or repressed to a statistically significant level (here 1.5 fold). The data was grouped based on the function of the encoded proteins. Analysis showed that the cells overexpressed genes involved in energy conservation processes. Genes encoding molecular chaperones were overexpressed as well, presumably to counteract the effect of the temperature increase on protein denaturation. Furthermore, genes encoding parts of the translation and transcription systems were repressed temporarily, in line with the observed lag in growth. More detailed analysis of certain small groups of genes involved in energy metabolism supported the notion that, although the expression level of genes represent a part of the stress response, they cannot be directly linked to the level of activity of their products.

overall_design: Samples were taken from three replicate control cultures at 28°C at three timepoints and from three replicate stressed cultures at six timepoints

middle: I

first: Klaas

last: Hellingwerf

first: M

last: Teixeira de Mattos

first: Stanley

last: Brul


title: Characterization of the GbdR regulon in Pseudomonas aeruginosa

status: Public on Oct 23 2013

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

country: USA

institute: University of Vermont

summary:
Pseudomonas aeruginosa displays tremendous metabolic diversity, controlled in part by the abundance of transcription regulators in the genome. We have been investigating P. aeruginosa’s response to the host, particularly changes regulated by the host-derived quaternary amines choline and glycine betaine (GB). We previously identified GbdR as an AraC-family transcription factor that directly regulates choline acquisition from host phospholipids (via binding to plcH and pchP promoters), is required for catabolism of the choline metabolite GB, and is an activator that induces transcription in response to GB or dimethylglycine. Our goal was to characterize the GbdR regulon in P. aeruginosa using genetics and chemical biology in combination with transcriptomics and in vitro DNA-binding assays. Here we show that GbdR activation regulates transcription of 26 genes from 12 promoters; 11 of which have measureable binding to GbdR in vitro. The GbdR regulon includes the genes encoding GB, dimethylglycine, sarcosine, glycine, and serine catabolic enzymes, and the BetX and CbcXWV quaternary amine transport proteins. . Additionally, identification of two uncharacterized regulon members suggests roles for these proteins in response to choline metabolites.
The conditions for inclusion in the gbdR regulon were: (i) called present in the array, (ii) changed more than 2.5-fold in signal in a statistically significant manner, (iii) altered in all three 'inducing' conditions (ethylcholine, choline+propargylcholine, and choline in the dgcA mutant), but (iv) not induced in the wild-type choline or diethylcholine treatments.

overall_design: Wild type and dgcA mutant cells were pre-grown in MOPS minimal media and then split and resuspended in MOPS pyruvate, MOPS pyruvate + choline, MOPS pyruvate + ethylcholine, MOPS pyruvate + diethylcholine, or MOPS pyruvate & choline + propargylcholine.

first: Ken

last: Hampel


title: Replacement of the Saccharomyces cerevisiae acetyl-CoA synthetases by alternative pathways for cytosolic acetyl-CoA synthesis

status: Public on Nov 21 2013

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Cytosolic acetyl-coenzyme A is a precursor for many biotechnologically relevant compounds produced by Saccharomyces cerevisiae. In this yeast, cytosolic acetyl-CoA synthesis and growth strictly depend on expression of either the Acs1 or Acs2 isoenzyme of acetyl-CoA synthetase (ACS). Since hydrolysis of ATP to AMP and pyrophosphate in the ACS reaction constrains maximum yields of acetyl-CoA-derived products, this study explores replacement of ACS by two ATP-independent pathways for acetyl-CoA synthesis. After evaluating expression of different bacterial genes encoding acetylating acetaldehyde dehydrogenase (A-ALD) and pyruvate-formate lyase (PFL), acs1Δ acs2Δ S. cerevisiae strains were constructed in which A-ALD or PFL successfully replaced ACS. In A-ALD-dependent strains, aerobic growth rates of up to 0.27 h-1 were observed, while anaerobic growth rates of PFL-dependent S. cerevisiae (0.21 h-1) were stoichiometrically coupled to formate production. In glucose-limited chemostat cultures, intracellular metabolite analysis did not reveal major differences between A-ALD-dependent and reference strains. However, biomass yields on glucose of A-ALD- and PFL-dependent strains were lower than those of the reference strain. Transcriptome analysis suggested that reduced biomass yields were caused by acetaldehyde and formate in A-ALD- and PFL-dependent strains, respectively. Transcript profiles also indicated that a previously proposed role of Acs2 in histone acetylation is probably linked to cytosolic acetyl-CoA levels rather than to direct involvement of Acs2 in histone acetylation. While, for the first time, demonstrating that yeast ACS can be fully replaced by alternative reactions, this study demonstrates that further modifications are needed to achieve optimal in vivo efficiencies of the supply of acetyl-CoA as product precursor.

overall_design: To investigate the impact of introduced changes in native pathway of cytosolic acetyl-CoA formation in S. cerevisiae, a DNA microarray-based transcriptome analysis was performed on aerobic or anaerobic, glucose-limited chemostat cultures.

first: Barbara

middle: U

last: Kozak

first: Harmen

middle: M

last: van Rossum

first: Jean

first: Jack

middle: T

last: Pronk

first: Kirsten

middle: R

last: Benjamin

first: Liang

last: Wu

first: Antonius

last: van Maris


title: Transcriptome-based characterization of the interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat co-cultures

status: Public on Aug 22 2013

summary:
The present study aims to explore chemostat-based transcriptome analysis of mixed cultures by investigating interactions between the yeast S. cerevisiae and the lactic acid bacterium Lb. bulgaricus . S. cerevisiae and Lb. bulgaricus are both frequently encountered in kefir, a fermented dairy product (25). In the context of this study, this binary culture serves as a model for the many traditional food and beverage fermentation processes in which yeasts and lactic acid bacteria occur together (19,26-30). The design of the cultivation conditions was based on the observation that Lb. bulgaricus, but not S. cerevisiae, can use lactose as a carbon source for growth and that S. cerevisiae, but not Lb. bulgaricus, can grow on galactose that is released upon hydrolysis of lactose by the bacterial β-galactosidase.
Mixed populations of yeasts and lactic acid bacteria occur in many dairy, food and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the co-cultures, five mechanisms of interaction were identified. 1. Lb. bulgaricus hydrolyses lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. bulgaricus, is excreted and provides a carbon source for yeast. 2. In pure cultures, Lb. bulgaricus only grows at increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. 3. Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacteria. 4. A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. bulgaricus.  5. Transcriptome analysis of Lb. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipids metabolism suggesting either a competition of the two microorganisms for fatty acids, or a response to the ethanol produced by S. cerevisiae. To our knowledge, this is the first transcriptome study of a cross-kingdom binary mixed culture that analyses responses of both microorganisms. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigated microbial interaction in mixed populations.

overall_design: To investigate the impact of of co-cultivation with Lb. bulgaricus on S. cerevisiae, a DNA microarray-based transcriptome analysis of S. cerevisiae's response was performed on anaerobic, lactose-limited chemostat cultures grown in the presence and absence of L. bulgaricus.

first: Filipa

last: Mendes

first: Sander

last: Sieuwerts

first: Erik

last: de Hulster

first: Marinka

last: Almering

first: Marijke

middle: A

last: Luttik

first: Eddy

last: Smid

first: Peter

last: Bron

first: Pascale

last: Daran-Lapujade


title: Serum-Mediated Responses in Normal and Transformed Oral Keratinocyte Lines

status: Public on Jan 01 2014

first: Roland

last: Grafström

address: Nobelsväg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

summary: Serum-driven responses, many of which are related to wound healing, are potentially deregulated in cancer development and associated genomic alterations might have prognostic value. The current study assessed fetal bovine serum-induced transcriptomic changes for clinical relevance in head and neck squamous cell carcinoma (HNSCC) using oral keratinocyte models otherwise routinely cultured without serum, including normal keratinocytes (NOK) and the transformed keratinocyte lines SVpgC2a, SqCC/Y1 and LK0412. Bioinformatics-driven analysis of gene expression implicated primarily serum-induced terminal differentiation in NOK including alterations in 99 genes, 13 gene ontology-categories and 6 molecular networks and involvement of 7 key regulator genes. Compared to NOK, the transformed lines expressed around 3-fold lower numbers of differently expressed transcripts, unique sets of gene ontologies, molecular networks and key regulator genes for each line, and consistent absence of terminal differentiation markers. Assessment of the complete in vitro/serum exposure-derived set of differentially expressed genes (totally 180 genes) relative a clinical, information-rich HNSCC data set identified 17 survival-associated genes of which only 12 had previous association to HNSCC. Multi-step validation of the survival-associated genes relative to several independent tumor data sets, including in the Human Gene Expression Map and Human Protein Atlas databases, confirmed novel association to HNSCC for genes COTL1 and INSIG1 and novel poor outcome prediction for the genes CUL4B and PDGFRL. The definition of normal and aberrant serum responses in keratinocyte models therefore coupled new genes to HNSCC including with relevance to prognosis.

overall_design: Analysis of gene expression changes in serum-exposed normal and transformed cells relative the respective un-exposed states. Significantly differentially expressed genes were next assessed by bioinformatics processing using Gene Ontology categories and network analyses. Findings were also validated relative independent HNSCC data sets as well as transcriptomics and proteomics databases.

first: Rebecca

last: Ceder

first: Marina

last: Merne

first: Fredrik

last: Jerhammar

first: Matthias

last: Nees

first: Karin

last: Roberg

middle: C


title: SigX ECF sigma factor deletion mutant expression profile in Pseudomonas aeruginosa in M9 minimal medium (M9G)

city: Evreux

first: Sylvie

last: Chevalier

address: 55, rue Saint Germain

country: France

institute: University of Rouen

summary:
Analysis of a SigX knockout mutant of Pseudomonas aeruginosa H103 strain in minimal medium with glucose as carbon source (M9G).
SigX, one of the 19 extra-cytoplasmic function sigma factors of P. aeruginosa, was only known to be involved in transcription of the gene encoding the major outer membrane protein OprF in Pseudomonas aeruginosa. Deletion of the  ECF sigma factor sigX gene provide insights into the SigX role in several virulence and biofilm- related phenotypes in Pseudomonas aeruginosa.

overall_design: To better understand the cellular function of SigX, a deletion mutant of the sigX gene (PAOSX) was generated and its expression profile was compared with parental strain Pseudomonas aeruginosa H103. To this end, H103 and a sigX mutant were cultured in M9G, in which their growth are similar. Three independant biological replicate were taken for the RNA extraction and hybridization on affymetrix array in the middle of the exponential growth phase.

first: Gwendoline

last: Gicquel

first: Emeline

last: Bouffartigues

first: Manjeet

last: Bains

first: Virginie

last: Oxaran

first: Thibaut

last: Rosay

first: Olivier

last: Lesouhaitier

first: Nathalie

last: Connil

first: Alexis

last: Bazire

last: Maillot

first: Magalie

last: Bénard

first: Pierre

last: Cornelis

first: Robert

middle: W

last: Hancock

first: Alain

last: Dufour

first: Marc

last: Feuilloley

first: Nicole

last: Orange

first: Eric

last: Déziel


title: Transcript profiling of normal oral keratinocytes and the tongue squamous cell carcinoma line LK0412

status: Public on Jan 31 2014

first: Roland

last: Grafström

summary: The current study analyzed a unique, serum-free medium derived tongue squamous cell carcinoma (TSCC) line termed LK0412 relative to the normal state to elucidate biomarkers at the protein and transcript level. A bioinformatics approach using Gene Ontology categories, gene networks and signature evaluation was applied to combine the protein and transcript data for identification of various gene signatures. The generated signatures were further assessed in public available data sets from normal and tumor tongue tissues. The analysis identified a novel gene signature that may improve the diagnosis and treatment of TSCC.

overall_design: Analysis of differential gene expression in LK0412 relative to the normal state. Both normal and LK0412 cells were cultured under a standardized serum-free condition.

first: Rebecca

last: Ceder

first: Claudia

last: Staab

first: Karin

last: Roberg

first: Matthias

last: Nees

first: Hans

last: Jörnvall

first: Jan-Olov

last: Höög


title: DRM complex mutant lin-54 vs. H3K36 methyltransferase mutant mes-4 vs. lin-54; mes-4 double mutant vs. wild type C.elegans germline

status: Public on Nov 05 2013

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: Here we uncover antagonistic regulation of transcript levels in the germline of Caenorhabditis elegans hermaphrodites. The histone methyltransferase MES-4 marks genes expressed in the germline with methylated Lys36 on histone H3 (H3K36me) and promotes their transcription; MES-4 also represses genes normally expressed in somatic cells and genes on the X chromosomes. The DRM complex, which includes E2F/DP and Retinoblastoma homologs, affects germline gene expression and prevents excessive repression of X-chromosome genes. Using genome-scale analyses of germline tissue, we show that common germline-expressed genes are activated by MES-4 and repressed by DRM, and that MES-4 and DRM co-bind many germline-expressed genes. Reciprocally, MES-4 represses and DRM activates a set of autosomal soma-expressed genes and overall X-chromosome gene expression. Mutations in mes-4 or the DRM subunit lin-54 oppositely skew target transcript levels and cause sterility; a double mutant restores near wild-type transcript levels and germ cell development. Together, “yin-yang” regulation by MES-4 and DRM ensures transcript levels appropriate for germ cell function, elicits robust but not excessive dampening of X-chromosome-wide transcription, and may poise genes for future expression changes. Our study reveals that conserved transcriptional regulators implicated in development and cancer counteract each other to fine-tune transcript dosage.

overall_design: We compared germline gene expression profile of  wild-type N2 C. elegans, lin-54(n3423) M+Z- mutant, mes-4(ok2326) M+Z- mutant, and lin-54(n3423);mes-4(ok2326) M+Z-mutant grown at 20C.  50~70 Germlines were dissected from young adults (24hours after L4 stage), and region from the tip until late pachytene stage of meiosis were collected. Three biological replicates for each strain were performed.

first: T

last: Tabuchi

first: A

last: Rechsteiner

first: S

first: K

last: Hagstrom


title: Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach perspective of human cancers.

status: Public on Sep 06 2013

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Swiss-Webster B mouse postnatal day 4-5 primary cerebellar culture (pooled from litter mates) treated with sonic hedgehog (Shh), controls (veh), growth arrested (arrest), cycloheximide (cyc) for 1, 3 and 24 hours.

overall_design:
Different treatment conditions with biological replicates.
Mouse cerebellar granule cell neuron precursors under different treatment conditions.

first: Isaac

middle: S

last: Kohane

first: David

middle: H

last: Rowitch


title: Identify genes regulated by zip-2 in absence and presence of P. aeruginosa PA14 infection at 4h

status: Public on Aug 30 2013

city: La Jolla

first: Emily

last: Troemel

department: Cell and Developmental Biology

institute: University of California, San Diego

summary: Very little is known about how animals discriminate pathogens from innocuous microbes. To address this question, we examined infection-response gene induction in the nematode Caenorhabditis elegans. We focused on genes that are induced in C. elegans by infection with the bacterial pathogen Pseudomonas aeruginosa, but are not induced by an isogenic attenuated gacA mutant. Most of these genes are induced independently of known immunity pathways. We generated a GFP reporter for one of these genes, infection response gene 1 (irg-1), which is induced strongly by wild-type P. aeruginosa strain PA14, but not by other C. elegans pathogens or by other wild-type P. aeruginosa strains that are weakly pathogenic to C. elegans. To identify components of the pathway that induces irg-1 in response to infection, we performed an RNA interference screen of C. elegans transcription factors. This screen identified zip-2, a bZIP transcription factor that is required for inducing irg-1, as well as several other genes, and is important for defense against infection by P. aeruginosa. These data indicate that zip-2 is part of a specialized pathogen response pathway that is induced by virulent strains of P. aeruginosa and provides defense against this pathogen.

overall_design: Analysis of differential gene expression in adult N2 C. elegans treated with L4440 control RNAi or zip-2 RNAi, either uninfected (feeding on E. coli) or infected with P. aeruginosa PA14; samples were analyzed after 4 hours of infection

first: Fred

last: Ausubel


title: Multiple DNA repair pathways collectively protect against DNA damage-induced replicative aging.

status: Public on Sep 15 2013

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

institute: SciLifeLab. Stockholm University

summary:
We demonstrate that transcriptomic profiling of the NER mutant ercc-1 offers better understanding of the complex phenotypes of ercc-1 deficiency in C. elegans, as it does in mammalian models. There is a transcriptomic shift in ercc-1 mutants that suggests a stochastic impairment of growth and development, with a shift towards a higher proportion of males in the population. Extensive phenotypic analyses confirm that NER deficiency in C. elegans leads to severe developmental and growth defects and a reduced replicative lifespan, although post-mitotic lifespan is not affected. Results suggest that these defects are caused by an inability to cope with randomly occurring DNA damage, which may interfere with transcription and replication.
The study investigates the developmental and aging phenotypes of different NER deficient C. elegans mutants (xpa-1, ercc-1, xpf-1 and xpg-1), where the transcriptomic profile of ercc-1 mutant is presented. We show that loss of NER function does not affect post-mitotic lifespan, but leads to impaired embryogenesis, germ cell and larval development and causes a reduced replicative lifespan. Phenotypes are most pronounced in ercc-1, xpf-1 and xpg-1 mutant animals. We provide evidence that this more pronounced phenotype is likely caused by the fact that these genes are involved in multiple repair pathways besides NER. Furthermore, transcriptional profiling of ercc-1 mutants confirms these observations, showing that growth and developmental pathways are underrepresented but that insulin signaling is not affected. Our analysis suggests that XPA-1, ERCC-1, XPF-1 and XPG-1 protect animals against replicative aging by preventing the accumulation of randomly acquired DNA damage.

overall_design: Eight mixed stage C. elegans samples were run on  Affymetrix GeneChip C. elegans Genome Arrays. Four samples belong to ercc-1 mutant group and four to the wild-type, N2.

first: Hannes

last: Lans

first: Karen

last: Thijssen

first: Andrea

last: Karambelas

first: Daniel

last: Cupac

first: Ayvind

last: Fensgård

first: Gert

last: Jansen

first: Jan

last: Hoeijmakers

first: Hilde

last: Nilsen

first: Wim

last: Vermeulen


title: GEI-8, a homologue of vertebrate nuclear receptor corepressor NCoR/SMRT, regulates development and neuronal functions in C. elegans.

status: Public on Aug 11 2013

city: Bethesda

first: WeiPing

last: Chen

state: MD

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

department: GCL

institute: NIDDK/NIH

summary: NCoR and SMRT are two paralogous vertebrate proteins that function as corepressors with unliganded nuclear receptors.  Although C. elegans has a large number of nuclear receptors, orthologues of the corepressors NCoR and SMRT have not unambiguously been identified in Drosophila or C. elegans.  Here, we identify GEI-8 as the closest homologue of NCoR and SMRT in C. elegans and demonstrate that GEI-8 is expressed as at least two isoforms throughout development in multiple tissues, including neurons, muscle and intestinal cells.  We demonstrate that a homozygous deletion within the gei-8 coding region, which is predicted to encode a truncated protein lacking the predicted NR domain, results in severe mutant phenotypes with developmental defects, slow movement and growth,  arrested gonadogenesis and defects in cholinergic neurotransmission.  Whole genome expression analysis by microarrays identified sets of de-regulated genes consistent with both the observed mutant phenotypes and a role of GEI-8 in regulating transcription.  Interestingly, the upregulated transcripts included a predicted mitochondrial sulfide:quinine reductase encoded by Y9C9A.16.  This locus also contains  non-coding, 21-U RNAs of the piRNA.  Inhibition of the expression of the region coding for 21-U RNAs leads to irregular gonadogenesis in the homozygous gei-8 mutants, but not in an otherwise wild-type background, suggesting that GEI-8 may function in concert with the 21-U RNAs to regulate gonadogenesis.  Our results confirm that GEI-8 is the orthologue of the vertebrate NCoR/SMRT corepressors and demonstrate important roles for this putative transcriptional corepressor in development and neuronal function.

overall_design: Comparison of Mutant vs. WT control with three replications per treatment group

first: Pavol

last: Mikolas

first: Johana

last: Kollarova

first: Katerina

last: Sebkova

first: Vladimir

last: Saudek

first: Michael

last: Krause

first: Zdenek

last: Kostrouch

first: Marta

last: Kostrouchova


title: Hydrogen sulfide (H2S) modulates lifespan of C.elegans

status: Public on Jul 30 2013

city: London

first: Stephen

last: Sturzenbaum

address: 150 Stamford Street

department: Analytical, Environmental and Forensic Sciences

country: United Kingdom

institute: King's College London

summary: Hydrogen sulfide (H2S) is formed naturally from L-cysteine in a variety of mammalian and non-mammalian cells. To date, numerous biological effects have been ascribed to H2S including control of cardiovascular, immune and nervous function. Over or under production of H2S has been observed in several disease states including hypertension and inflammation. In addition, it has been stipulated that H2S may affect the ageing process. The model nematode Caenorhabditis elegans is ideally suited for assessing drug effects on lifespan since it is relatively short-lived, can be easily exposed to drugs and its genome is fully sequenced and widely annotated.

overall_design: The global transcriptome of control nematodes (raised using standardized laboratory conditions) was compared to nematodes exposed to 100 uM GYY4137 (morpholin-4-ium 4 methoxyphenyl(morpholino) phosphinodithioate), a slow releasing H2S donor drug.

first: Ling

last: Li

first: Suresh

last: Swain

first: Philip

middle: K

last: Moore


title: Comparison of gene expression in wild type Drosophila testes with various meiotic arrest mutants (comr and can)

status: Public on Aug 06 2013

city: Cardiff

first: Helen

last: White-Cooper

address: Museum Avenue

department: Biosciences

institute: Cardiff University

summary:
The expression of a very large number of genes changes as male germ cells pass through differentiation into spermatids and then sperm. Much of this transcriptional programme requires the activity of the meiotic arrest genes. There are two principle classes, aly-class (including comr) and can-class, here we compare their effects on gene expression
We extracted RNA from wild type testes, as well as comr mutants and can mutants, and used microarrays to compare gene expression profiles.

overall_design: We dissected testes from 0-1 day old Drosophila males, taking care to remove accessory glands and ejaculatory ducts. The control sample was red e, the background chromosome on which the can mutant was generated, and had normal testes. The comr mutants were  comr[z1340] cn bw. The can mutants were w ; can[3] red e.


title: Regulatory network underlying the adaptive physiology of Pseudomonas aeruginosa under urinary tract-like conditions

status: Public on Jun 30 2013

city: Braunschweig

first: Petra

last: Tielen

address: Spielmannstrasse 7

country: Germany

institute: Technische Universität Braunschweig

summary: Pseudomonas aeruginosa is one of the most frequent pathogen dominant in complicated urinary tract infections (UTI). To unravel the adaptation strategies of P. aeruginosa to the conditions in the urinary tract and to define the underlying regulatory network an artificial growth system mimicking the conditions in the urinary tract was established.  Transcriptome analyses were used to investigate the physiological status of P. aeruginosa under this conditions.

overall_design:
We performed comparisons to identify genes induced under artificial urinary tract conditions to unravel the adaptive strategies and the underlying regulatory network used by Pseudomonas aeruginosa  during urinary tract infections using Affimetrix GeneChips.
Pseudomonas aeruginosa wild type strain PAO1 was grown in an artificial in vitro growth system mimicking the conditions in the urinary tract. Therefore, biofilms were grown on the surface of membrane filters placed on agar plates at 37 °C up to the late logarithmic state under aerobic and anaerobic conditions (incubated in an anaerobic beanch). An artificial urine medium (AUM) simulating the averaged urine of an human adult was used as nutrient souce. 10-fold diluted Luria Bertani (LB)-medium was used as reference medium. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. The biofilms were harveted at this time points and resuspsended in 0.9% (w/v) NaCl. The OD578 of biofilm suspension was 0.8 for all tested conditions.
First comparison: Identification of genes induced or repressed under aerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown aerobically for 18 h to the late logarithmic phase in biofilms on AUM  with the transcriptome profile of the PAO1 strain, which was  grown aerobically for 18 h to the late logarithmic phase in biofilms on 10-fold diluted LB.
Second comparison: Identification of genes induced or repressed under anaerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown anaerobically for 2 days up to the late logarithmic phase in biofilms on AUM supplemented with 50 mM nitrate with the transcriptome profile of the PAO1 strain, which was  grown anaerobically for 2 days up to the late logarithmic phase in biofilms on 10-fold diluted LB supplemented with 50 mM nitrate.

first: Nathalie

last: Rosin

first: Katrin

last: Dohnt

first: Isam

last: Haddad

first: Lothar

last: Jänsch

first: Johannes

last: Klein

first: Ann-Kathrin

last: Meyer

first: Maike

last: Narten

first: Claudia

last: Pommerenke

first: Maurice

last: Scheer

first: Max

last: Schobert

first: Dietmar

last: Schomburg

first: Bernhard

last: Thielen

first: Dieter

last: Jahn


title: Alterations in gene expression in Caenorhabditis elegans associated with organophosphate pesticide intoxication and recovery

status: Public on Oct 05 2013

city: Ft. Detrick

first: John

middle: A.

last: Lewis

address: 568 Doughten Drive

department: Biomarkers Program

institute: U.S. Army Center for Environmental Health Research

summary:
The principal toxicity of acute organophosphate (OP) pesticides poisoning is the disruption of neurotransmission through inhibition of acetylcholinesterase (AChE). However, other mechanisms leading to persistent effects and neurodegeneration remain controversial and difficult to detect. Because Caenorhabditis elegans is relatively resistant to OP lethality—particularly through the inhibition of AChE—studies in this nematode provide an opportunity to observe alterations in global gene expression following OP exposure that cannot be readily observed in less resistant organisms.
We exposed cultures of worms in axenic, defined medium to dichlorvos under three exposure protocols. In the first, worms were exposed continuously throughout the experiment. In the second and third, the worms were exposed for either 2 or 8 h, the dichlorvos was washed out of the culture, and the worms were allowed to recover. We then analyzed gene expression using whole genome microarrays from RNA sampled at multiple time points throughout the exposure. The worms showed a time-dependent response that progressively worsened. Early in the exposure, the predominant effect was on metabolic processes, while at later times, an immune-like response and cellular repair mechanisms dominated the expression pattern. Following removal of dichlorvos, the gene expression in the worms appeared to relatively, rapidly return to steady-state levels. The changes in gene expression observed in the worms following exposure to dichlorvos point towards two potential mechanisms of toxicity: inhibition of AChE and mitochondrial disruption.

overall_design: Synchronized cultures of worms at the L3/L4 molt were treated with dichlorvos (0.6 µM or 15 µM) or maintained as a controls according to one of three protocols. In the first protocol, the set of flasks was incubated without interruption for the duration of the experiment with flasks being harvested at 2, 8, 14, 20, and 26 h. The other two sets were incubated for 2 or 8 h, at which time the worms were centrifuged out of the exposure medium, washed 3 times with a modified CeHR medium (Washout Buffer), resuspended in fresh CeHR medium without dichlorvos, and returned to the incubator. Flasks were harvested at 6 h intervals following the washout through 26 h. Flasks of worms were also harvested prior to beginning the exposure as the 0 h controls. Total RNA was isolated from the frozen harvested worms then analyzed using Affymetrix GeneChips. A total of 148 microarrays were processed (47 per exposure protocol with 4 replicates) however only 146 were included in final analysis as 2 falied to pass QC criteria.

first: Elizabeth

last: Gehman

first: Christine

middle: E

last: Baer

first: David

last: Jackson


title: Genes Required for and Effects of Inducible Alginate Overproduction by Growth of Pseudomonas aeruginosa on PIAAMV

status: Public on Jul 15 2013

city: Aurora

first: Michael

last: Schurr

state: CO

department: Microbiology

institute: University of Colorado School of Medicine

summary: Pseudomonas aeruginosa is an opportunistic pathogen that can adapt to changing environments and can secrete an exopolysaccharide known as alginate as a protection response resulting in a colony morphology and phenotype referred to as mucoid.  However how P. aeruginosa senses its environment and activates alginate overproduction is not fully understood.  Previously, we showed that Pseudomonas isolation agar (PIA) supplemented with ammonium metavanadate (PIAAMV) induces P. aeruginosa to overproduce alginate.  Vanadate is a phosphate mimic and causes protein misfolding by disruption of disulfide bonds.  Here we used PIAAMV to characterize the pathways involved in inducible alginate production and tested the global effects of P. aeruginosa growth on PIAAMV by a mutant library screen, transcriptomics, and in a murine acute virulence model.  The PA14 non-redundant mutant library was screened on PIAAMV to identify new genes that are required for the inducible alginate stress response.  A functionally diverse set of genes encoding products involved in cell envelope biogenesis, peptidoglycan, uptake of phosphate and iron, phenazines biosynthesis, and other processes were identified as positive regulators of the mucoid phenotype on PIAAMV.  Transcriptome analysis of P. aeruginosa growing in the presence of vanadate caused differential expression of genes involved in virulence, envelope biogenesis, and cell stress pathways.  In this study, it was observed that growth on PIAAMV attenuates P. aeruginosa in a mouse pneumonia model.  Induction of alginate overproduction occurs as a stress response to protect P. aeruginosa but it may be possible to modulate and inhibit these pathways based on the new genes identified in this study.

overall_design: Strain PAO1 was cultured on both PIA and PIAAMV for 18 hr.  Three separate plates were used for each media.  The cells from each plate were scraped into 4 ml of RNA Protect (Qiagen) and stored immediately at -80°C.    Cells were treated with RNAprotect (Qiagen) and total RNA was extracted using an RNeasy mini purification kit (Qiagen) per the manufacturer’s instructions.  RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNase treatment.  Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol. RNA isolation, cDNA preparation, labeling and microarray analysis were performed as previously described in reference: Damron, F. H., J. P. Owings, Y. Okkotsu, J. J. Varga, J. R. Schurr, J. B. Goldberg, M. J. Schurr, and H. D. Yu. 2012. Analysis of the Pseudomonas aeruginosa Regulon Controlled by the Sensor Kinase KinB and Sigma Factor RpoN. J Bacteriol 194:1317-30.

first: F

last: Damron

first: Mariette

last: Barbier

last: McKenney

first: Joanna

middle: B

last: Goldberg


title: DNA microarray analysis for HepG2 cells exposed to arsenic trioxide

status: Public on Jul 02 2013

city: Sapporo

first: Hiroe

last: Hara-Yamamura

state: Hokkaido

address: Kita 13-jo, Nishi 8-chome

department: Graduate School of Engineering

country: Japan

institute: Hokkaido University

summary: DNA microarray analysis revealed that the genes related to cell cycle regulation were significantly induced at non- and sub-lethal concentrations (i.e., 0.05-6 µM), while the common feature of heavy metal toxicity such as oxidative damage and following increase in glutathione, heat shock proteins, and metallothionein were confirmed at high concentrations (i.e., 6-40 µM). The concentration dependent modulation of gene expression (induction of cell cycle genes, induction of cell cycle arrest genes and apoptotic genes) following exposure to arsenic was further supported by acceleration of cell proliferation, ROS generation, and cytotoxicity. Furthermore, three cell cycle genes (i.e., CDC25B, UBE2C, and PTTG1) were proposed as marker genes of inorganic arsenic exposure. Those results indicated the potential pro-carcinogenic actions of inorganic arsenic occur in environmentally relevant exposures (as low as 0.07 µM).

overall_design: In this study, we examined the gene expression alteration in HepG2 cells exposed to arsenic trioxide (5 nM to 40 µM as As2O3 for 48 hours) by DNA microarray with 8795 human genes. HepG2 cells were also exposed to ε-caprolactam as a reference of non carcinogen since it is the only chemical categorized in IARC’s group 4 (Probably Not Carcinogenic). MQ water was used as control.  For replicate, three dishes were prepared for each sample and individually treated in parallel.

first: Teppei

last: Taga

first: Koji

last: Kawata

first: Satoshi

last: Okabe


title: Effect of chlorination on toxicity of wastewater effluents from different treatment systems to HepG2 human hepatoma cells

status: Public on Jun 21 2013

first: Toshikazu

last: Fukushima

address: Kita13, Nishi8, Kita-ku

summary: Effect of chlorination on the toxicity of wastewater effluents treated by activated sludge (AS) and submerged membrane bioreactor (S-MBRB) systems to HepG2 human hepatoblastoma cells was investigated. In addition to cytotoxicity assay, the DNA microarray-based transcriptome analysis was performed to evaluate the change in modes of toxic actions (MOAs) of effluents by chlorination. Effluent organic matters (EfOM) and disinfection by-products (DBPs) were characterized by using Fourier transform mass spectrometry (FT-MS). The cytotoxicity of AS effluent was elevated by chlorination, while the toxicity of S-MBRB effluent was reduced. The averaged O/C ratio of EfOM in S-MBRB effluent was lower than that in AS effluent. The results of the transcriptome and FT-MS analyses suggested that lower O/C molecules influenced on “response to hormone stimulus” and “acute inflammatory response” but those were decreased by chlorination, which consequently reduced cytotoxicity. On the other hand, larger number of DBPs and other molecules were increased in AS effluents by chlorination. Those molecules might influence on “cellular metabolic process”, which consequently elevated cytotoxicity. Therefore, the combination of the toxicity assays and chemical analysis demonstrated the changes in severity of cytotoxicity and MOAs by chlorination, and the difference of chemical characteristics which relate to those toxicity changes.

overall_design: We examined the gene expression alteration in human hepatoma cell line, HepG2 exposed to the chlorinated wastewater effluents from membrane bioreactor and the activated sludge process. Human Genome Focus Array, which represents 8,795 verified human sequences, was used. All effluent samples were concentrated by using solid phase extraction (SPE).  SPE fraction from MQ water was used as controll. For duplicate, two dishes were prepared for each sample and individually treated in parallel.


title: Microarray analysis of P. aeruginosa PAO1 expression PA5060 (phaF) on pJN105

city: AUSTIN

first: Peter

middle: Allan

last: Jorth

state: TEXAS

address: 2506 Speedway Blvd

department: Molecular Genetics and Microbiology

institute: University of Texas at Austin

summary:
The Pseudomonas aeruginosa PAO1 gene phaF (PA5060) is a transcriptional regulator in the closely related pseudomonad P. putida. phaF is expressed at higher levels in P. aeruginosa clinical isolates from the cystic fibrosis respiratory tract. To determine the role of phaF in regulating P. aeruginosa gene expression, we cloned it under control of the pBAD promoter in expression vector pJN105 and compared expression in this strain relative to an empty vector control strain.
We used microarrays to study overall gene expression in a P. aeruginosa PAO1 phaF  overexpression strain.

overall_design: A P. aeruginosa PAO1 strain over-expressing the transcriptional regulator phaF, PAO1 pJN105-phaF, and the corresponding empty control strain, P. aeruginosa PAO1 pJN105, were grown to exponential phase, RNA was isolated, and gene expression was analyzed via microarray analysis and compared.

first: Holly

last: Huse

first: Marvin

last: Whiteley


title: Histone H3 K4,36,79R 18 hr

status: Public on May 25 2013

city: Pullman

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

summary:
Total RNA from two replicate cultures of the mutant strain were isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the samples and the wild-type control allow the identification of genes regulated by H3 K4,36,79R mutant.  Cells were grown in galactose media and then shifted to glucose media for 18 hours to give the 18 hour time point
Keywords: repeat

overall_design: Histone H3 K4,36,79R time course. Cells were grown in galactose media and then shifted to glucose media, which repressed the expression of wild-type histone H3, leaving the histone H3 K4,36,79R mutant as the sole source of histone H3 protein in the cell. Total RNA was isolated from replicate cultures of wild-type and mutant histone H3 at various time points after the shift to glucose media (0, 6, 9, 12, and 18 hours). Expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by H3 K4,36,79R mutant.

first: Amy

last: Rodrigurez

first: Yi

last: Jin

middle: J


title: PA14-PA2444 vs. PA14-WT biofilm cells

status: Public on Jun 08 2013

city: College Station

first: Mingming

last: Pu

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

summary: Pseudomonas aeruginosa causes many biofilm infections, and the rugose small-colony variants (RSCVs) of this bacterium are important for infection. We found here that mutation in glyA2 (PA2444), which encodes a serine hydroxymethyltransferase, leads to the RSCV phenotype. The phenotype is related to increased c-di-GMP concentrations and depends on an active Wsp chemosensory system, including a diguanylate cyclase WspR.  By characterizing the PA2444 enzyme both in vivo and in vitro, we determined the physiological function of PA2444 and related the enzyme to S-adenosylmethionine concentrations and the methylation of a membrane bound methyl-accepting chemotaxis protein WspA. A transcriptome analysis revealed the possible relationship between PA2444 and the redox state of the cells. Hence, we provide a mechanism for how an enzyme of central metabolism controls the community behavior of the bacterium.

overall_design: The P. aeruginosa genome array (Affymetrix, P/N 510596) was used to investigate differential gene expression in biofilm cells between PA14 and the PA2444 mutant.  Biofilm cells were harvested from 10 g of glass wool after incubation for 7 h in LB with shaking at 250 rpm, and RNA was extracted with the RNeasy Mini Kit (Qiagen, Valencia, CA) using a bead beater (Biospec, Bartlesville, OK ) with RNAlater buffer (Applied Biosystems, Foster City, CA) to stabilize the RNA. For each binary microarray comparison of differential genes expression, if the gene with the larger transcription rate did not have a consistent transcription rate based on the 13 probe pairs (P-value less than 0.05), these genes were discarded. A gene was considered differentially expressed when the P-value for comparing two chips was lower than 0.05 (to assure that the change in gene expression was statistically significant and that false positives arise less than 5%) and when the expression ratio was higher than the standard deviation for the whole microarrays (1.8 for PA14 wild-type and PA2444).

first: Thomas

last: Wood


title: Differential expression analysis of T. thermophilus HB8 wild-type strain in response to addition of silicic acid and removal of iron.

status: Public on May 14 2013

city: Fukuoka

first: Yasuhiro

last: Fujino

address: Higashiku hakozaki 6-10-1

institute: Kyushu-univ.

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 60 min after the addition of silicic acid and removal of iron.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TM medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl and 1% Castenholz' basal salt solution, which was adjusted to pH 7.2 with NaOH. The cells (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70°A600 value being ~0.60). Then the 600 ppm of silicic acid was added into the medium or removal of iron, and continued cultivation. Cells were collected at 60 min time point after the change of medium, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.

first: Y

first: M

last: Iwase

first: K

last: Doi


title: Histone H3 K4,36,79R 12 hr

first: John

summary:
Total RNA from two replicate cultures of the mutant strain were isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the samples and the wild-type control allow the identification of genes regulated by H3 K4,36,79R mutant.  Cells were grown in galactose media and then shifted to glucose media for 12 hours to give the 12 hour time point.
Keywords: repeat

middle: M


title: Genome-wide analysis of gene expression in human pluripotent stem cell-derived melanocyte progenitors, mature melanocytes, and disease-specific melanocytes

status: Public on Jun 01 2013

city: New York

first: Yvonne

last: Mica

state: NY

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

summary: Melanocytes are pigment-producing cells of neural crest origin responsible for protecting the skin against UV-irradiation. Melanocyte dysfunction leads to pigmentation defects including albinism, vitiligo, and piebaldism and is a key feature of systemic pathologies such as Hermansky-Pudlak (HP) and Chediak-Higashi (CH) Syndromes. Pluripotent stem cell technology offers a novel approach for studying human melanocyte development and disease. Here we report that timed exposure to activators of WNT, BMP and EDN3 signaling triggers the sequential induction of neural crest and melanocyte precursor fates under dual-SMAD inhibition conditions. Using a SOX10::GFP hESC reporter line, we demonstrate that the temporal onset of WNT activation is particularly critical for human neural crest induction. Surprisingly, suppression of BMP signaling does reduce neural crest yield. Subsequent differentiation of hESC-derived melanocyte precursors under defined conditions yields pure populations of pigmented cells matching the molecular and functional properties of adult melanocytes. Melanocytes from patient-specific iPSCs faithfully reproduce the ultrastructural features of the HP- and CH-specific pigmentation defects with minimal variability across lines. Our data define a highly specific requirement for WNT signaling during neural crest induction and enable the generation of pure populations of hiPSC-derived melanocytes for faithful modeling of human pigmentation disorders.

overall_design: Total RNA obtained from embryonic stem cells (ESCs), ESC-derived melanocyte progenitors, ESC-derived mature melanocytes, primary melanocytes, and disease-specific induced pluripotent stem cell-derived melanocytes.

first: Gabsang

last: Lee

first: Stuart

last: Chambers

first: Mark

last: Tomishima

first: Lorenz

last: Studer


title: Genome-wide analysis of differential gene expression in human embryonic stem cell-derived central nervous system, neural crest, and progenitor populations over time

overall_design: Total RNA obtained from a timecourse of Dual SMAD Inhibition (DSi), Neural Crest (NC), and Melanocyte (BE) differentiation of human embryonic stem cells in triplicate.


title: D-Glutamate Utilization in Pseudomonas aeruginosa PAO1

status: Public on May 03 2013

city: Atlanta

first: CHun-Kai

last: Yang

state: GA

address: 166 Jesse Hill Jr. Dr.

department: Biology

institute: Georgia state University

summary: D-Glutamate (D-Glu), an essential component of peptidoglycans, can be utilized as carbon and nitrogen source by Pseudomonas aeruginosa. DNA microarrays were employed to identify genes involved in D-Glu catabolism. Through gene knockout and growth phenotype analysis, the divergent dguR-dguABC (D-glutamate utilization) gene cluster was shown to participate in D-Glu catabolism and regulation. The dguA gene encodes a FAD-dependent D-amino acid dehydrogenase with D-Glu as its preferred substrate, and its promoter was specifically induced by exogenous D-Glu and D-Gln. The function of DguR as transcriptional activator of the dguABC operon was demonstrated by promoter activity measurements in vivo and by mobility shift assays with purified His-tagged DguR in vitro. Although the DNA-binding activity of DguR did not require D-Glu, the presence of D-Glu in the binding reaction was found to stabilize a preferred nucleoprotein complex. The dguB gene encodes a putative enamine/imine deaminase of the RidA family, but its role in D-Glu catabolism remained to be determined. While a lesion in dguC encoding a periplasmic solute binding protein did not affect growth on D-Glu, the AatJMQP transporter for acidic amino acid uptake was found essential for D-Glu and L-Glu utilization. Expression of this uptake system was subjected to induction by exogenous DL-Glu, most likely via the AauSR two-component system. In summary, DguA was identified in this study as a new member of the FAD-dependent amino acid dehydrogenase family for D-amino acid catabolism. DguR serves as a D-Glu sensor and transcriptional activator of the dguA promoter.

overall_design: Pseudomonas aeruginosa PAO1 was chosen as model to study gene response with different D-amino acids.

first: Weqing

last: He

first: Sonja

last: Young


title: mek-1 and mlk-1 in fed or fasted condition

status: Public on Apr 22 2013

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary: Intermittent fasting is one of the most effective dietary restriction regimens that extend life-span in C. elegans and mammals. Fasting-stimulus responses are key to the longevity response; however, the mechanisms that sense and transduce fasting-stimulus have remained largely unknown. Through a comprehensive transcriptome analysis in C. elegans, we have found that along with the FOXO transcription factor DAF-16, AP-1 (JUN-1/FOS-1) plays a central role in fasting-induced transcriptional changes. KGB-1, one of the C. elegans JNKs, acted as an activator of AP-1, and was activated in response to fasting. KGB-1 and AP-1 were involved in intermittent fasting-induced longevity. Fasting-induced upregulation of the components of the SCF E3 ubiquitin ligase complex via AP-1 and DAF-16 enhanced protein ubiquitination, and reduced protein carbonylation. Our results have thus identified a fasting-responsive KGB-1/AP-1 signaling pathway, which, together with DAF-16, causes transcriptional changes that mediate longevity partly through regulating proteostasis.

overall_design: We synchronized mek-1 and mlk-1 mutants and collected them at 2 day adult, and move them to the new plate with (Fed) or without food (Fasting). Two days later, we collected moved animals and extracted total RNA and subject them to microarray.

first: Masaharu

last: Uno

first: Haruka

last: Hoshikawa

first: Saya

last: Kishimoto


title: Analysis of gene expression changes upon infection of C.elegans with Orsay virus

city: Cambridge

first: Eric

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

institute: University of Cambridge

summary: Analysis of the transcriptional response to viral infection in C.elegans.

overall_design: Comparison of infected and uninfected animals for three strains: N2 (resistant), JU1580 (sensitive), RDE-1 (sensitive)

first: Peter

last: Sarkies

first: Alyson

last: Ashe


title: Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass Samples vs Reference

status: Public on Apr 26 2013

first: Maria

middle: Priscila

last: Almario

state: Texas

summary: Adaptive evolution experiment for enhaced tolerance to hydrolysates of lignocellulosic biomass in S. cerevisiae.  The samples involves a batch culture in YNB and Hydrolysates. Cells were harvested at mid-exponential phase.

overall_design: Three biological replicas of 8 samples vs reference Samples 1-8 are the first replicate, Samples 9-16 are the second replicate, Samples 17-24 are the third replicate.

middle: P

first: Luis

last: Reyes

first: Katy

last: Kao


title: Genome-wide analysis of gene expression in melanocytes derived from human embryonic stem cells and patient specific induced pluripotent stem cells

first: Yvonne

last: Mica

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

overall_design: Refer to individual Series


title: DNA microarray analysis for HepG2 cells exposed to wastewater effluents

status: Public on Mar 29 2013

first: Hiroe

last: Hara-Yamamura

summary: The transcriptome analysis by the human DNA microarray was applied to evaluate the impacts of whole wastewater effluents from the membrane bioreactors (MBRs) and the activated sludge process (AS), on the biological processes of human hepatoma HepG2 cells. The three conventional bioassays (i.e., cytotoxicity tests and bioluminescence inhibition test) and chemical analysis of the domestic effluent standards were conducted in parallel since they are well-established methods with previous applications to wastewater. A significant variation of effluent quality was sdemonstrated among the tested effluents despite that all effluents met the 40 national effluent standards. The three conventional bioassays supported the result of the transcriptome analysis, indicating the comparable or even higher sensitivity of the new assay. The most superior effluent quality was found in the MBR operated at a relatively long sludge retention time (i.e., 40 days) and small membrane pore size (i.e., 0.03 μm). In addition, functional analysis of the differentially expressed genes revealed that the effluents made various impacts on the cellular functions, suggesting the transcriptome analysis by DNA microarray as more comprehensive, rapid and sensitive tool to detect multiple impacts of the whole effluents. Moreover, the potential genetic markers were proposed to quantitatively evaluate the treatability of the wastewater effluents.

overall_design: In this study, we examined the gene expression alteration in human hepatoma cell line, HepG2 exposed to the raw wastewater, effluents from three types of membrane bioreactors (MBRs), and the activated sludge process. Wastewater DNA microarray with 8795 human genes. MQ water was used as control. For duplicate, two dishes were prepared for each sample and individually treated in parallel.

first: Satoshi

last: Okabe


title: Regulation by growth temperature of Pseudomonas aeruginosa quorum-sensing depedent virulence factors production involves two RNA-thermometers.

status: Public on Apr 02 2013

city: México D.F

first: Victoria

last: Grosso

address: Tercer circuito exterior C.U

department: Biología Molecular y Biotecnología

country: Mexico

institute: Instituto de Investigaciones Biomédicas UNAM

summary:
Several bacterial human pathogens regulate the production of virulence factors by temperature, expressing them only at 37 °C. Accordingly we show that the production of all P. aeruginosa virulence factors that are dependent on the QS transcriptional regulator RhlR, but only a fraction that are activated by LasR, are induced at 37 °C compared to 30 °C or 25 °C. The RhlR-dependent induction at 37 °C is a posttranscriptional effect due to an RNA thermometer of the ROSE family that thermoregulates the expression of rhlAB operon involved in rhamnolipids production, a virulence associated trait. This RNA structure also affects the expression of the downstream rhlR gene. A second thermometer is present upstream lasI and causes a reduced expression of this gene at lower temperatures without causing a significant decrease of the autoinducer 3-oxo-dodecanoyl homoserine lactone.
Using transcriptomic analysis and quantitative real time PCR we show that these RNA thermometers are the main mechanism of thermoregulation of P. aeruginosa virulence factor production

overall_design:
For the transcriptome analysis, cells were growth in PPGAS media at 25 °C and 37 °C, respectively. Samples were harvested at O.D600 of 1.5.
Three biological replicates of each growth condition was used for RNA extraction and hybridization on Affimetrix microarrays.


title: Diet specific expression profiles_MA1

status: Public on Mar 28 2013

city: Worcester

first: Lesley

middle: T

last: MacNeil

address: 368 Plantation St

department: Program in Systems Biology

institute: UMass Medical School

summary:
Analysis of wildtype (N2) C. elegans fed different diets: E. coli OP50, E. coli HT115 and Comamonas DA1877
Dietary composition has major effects on physiology. Here we show that developmental rate, reproduction and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard E. coli OP50 diet. We identify a set of genes that change in expression in response to this diet, and use the promoter of one of these (acdh-1) as a dietary sensor. Remarkably, the effects on transcription and development occur even when Comamonas DA1877 is diluted with another diet, suggesting that Comamonas DA1877 generates a signal that is sensed by the nematode. Surprisingly, the developmental effect is independent from TOR and insulin signaling. Rather, Comamonas DA1877 affects cyclic gene expression during molting, likely through the nuclear hormone receptor NHR-23. Altogether, our findings indicate that different bacteria elicit various responses via distinct mechanisms, which has implications for diseases such as obesity and the interactions between the human microbiome and intestinal cells.

overall_design: 3 biological replicates for each condition, OP50 is reference sample

first: Emma

last: Watson

first: H

last: Arda

first: Lihua

last: Zhu

first: A

last: Walhout


title: Expression changes in Caenorhabditis elegans xpa-1 mutant

city: Solna

first: Jessica

last: Lindvall

address: Tomtebodavägen 23A

institute: SciLifeLab. Stockholm University

summary:
Background: The ability of an organism to repair DNA damage is implicated in carcinogenesis and aging. Interestingly expression profiling of Nucleotide Excision Repair (NER) deficient segmental progeroid mice revealed gene expression changes resembling these observed in aged wild type animals. Our previous transcriptional profiling of NER-deficient C. elegans xpa-1 mutant showed overrepresentation of genes involved in lifespan determination and upregulation of several oxidative stress response genes (Fensgard et al. Aging 2010). However, since an independent study performed by Boyd and coworkers (Boyd et al. Mut Res 2010) showed limited number of changes in xpa-1 mutant. Therefore to independently validate that transcriptome modulation does take place in xpa-1 mutants, we performed another global gene expression profiling based on 5 independent biological replicates allowing more stringent statistical analysis.  Results: In agreement with what was observed by Boyd and coworkers (Boyd et al. Mut Res 2010) current transcriptomic analysis detected fewer changes in xpa-1 C. elegans mutant with only a few genes regulated more than 4-fold. Nevertheless, Gene Ontology (GO) enrichment analysis performed on statistically significantly regulated unique protein coding genes revealed overrepresentation of aging gene cluster. Moreover, as before, overexpression of several genes involved in oxidative stress responses was detected.  Conclusion: More stringent statistical analysis predictably resulted in a smaller number of regulated genes and thus overrepresented GOs comparing to the earlier paper. However, major conclusions of the previous study can be still regarded as valid, as the most important aging GO is still overrepresented.
Activation of oxidative stress-responses and downregulation of insulin-like signaling (ILS) is seen in Nucleotide Excision Repair (NER) deficient segmental progeroid mice. Evidence suggests that this is a survival response to persistent transcription-blocking DNA damage, although the relevant lesions have not been identified. Here we provide evidence for transcriptional reprogramming in NER-deficient C. elegans xpa-1 by transcriptomic and proteomic approaches. This reprograming is accompanied by increased intracellular ROS and ATP levels and lifespan shortening in xpa-1 mutant. Moreover we show that Base Excision Repair DNA glycosylase NTH-1 is upstream form the signaling events leading to transcriptomic changes, as its downregulation reverses overexpression of sod-3, gst-4 and aqp-1 genes, reduces intracellular ROS and ATP levels and reverses lifespan shortening observed in xpa-1 mutant. Surprisingly, however, these responses appear to not depend on cyclopurine levels, since these lesions are lower in xpa-1 C. elegans mutant than in the wild type. Finally, we also explore here which other upstream factors are necessary for transcriptional reprograming in xpa-1 mutant.

overall_design: Untreated Caenorhabditis elegans mutant deficient in xpa-1 and the wild type N2 strain were subjected to transcriptome analysis using Affymetrix platform.  For each sample group five replicates were analyzed.

first: Katarzyna

middle: D

last: Arczewska

first: Gisele

middle: G

last: Tomazella

first: Henok

last: Kassahun

first: Alfonso

last: Schiavi

first: Bryce

last: Marquis

first: Carina

last: Holmberg-Still

first: Natascia

last: Ventura

first: Bernd

last: Thiede

first: Hilde

last: Nilsen


title: Diet-Induced Developmental Acceleration Independent of TOR and Insulin in C. elegans


title: Integration of Metabolic and Gene Regulatory Networks Modulates The C. elegans Dietary Response

summary:
Analysis of wildtype C. elegans (N2) and pcca-1(ok2282) and metr-1(ok521) mutants fed Comamonas DA1877
Expression profiles are tailored according to dietary input. However, the networks that control dietary responses remain largely uncharacterized. Here, we combine forward and reverse genetic screens to delineate a network of 184 genes that affect the C. elegans dietary response to Comamonas DA1877 bacteria. We find that perturbation of a mitochondrial network comprised of enzymes involved in amino acid metabolism and the TCA cycle affects the dietary response. In humans, mutations in the corresponding genes cause inborn diseases of amino acid metabolism, most of which are treated by dietary intervention. We identify several TFs that mediate the changes in gene expression upon metabolic network perturbations. Altogether, our findings unveil a transcriptional response system that is poised to sense dietary cues and metabolic imbalances, illustrating extensive communication between metabolic networks in the mitochondria and gene regulatory networks in the nucleus.    Expression profiles are tailored according to dietary input. However, the networks that control dietary responses remain largely uncharacterized. Here, we combine forward and reverse genetic screens to delineate a network of 184 genes that affect the C. elegans dietary response to Comamonas DA1877 bacteria. We find that perturbation of a mitochondrial network comprised of enzymes involved in amino acid metabolism and the TCA cycle affects the dietary response. In humans, mutations in the corresponding genes cause inborn diseases of amino acid metabolism, most of which are treated by dietary intervention. We identify several TFs that mediate the changes in gene expression upon metabolic network perturbations. Altogether, our findings unveil a transcriptional response system that is poised to sense dietary cues and metabolic imbalances, illustrating extensive communication between metabolic networks in the mitochondria and gene regulatory networks in the nucleus.

overall_design: 3 biological replicates for each condition, wild type is reference sample


title: Diet specific expression profiles_MA2

summary:
Analysis of wildtype (N2) C. elegans fed different diets: E. coli OP50, Comamonas DA1877, and Diluted Comamonas (1:1000 Comamonas DA1877:E. coli OP50)
Dietary composition has major effects on physiology. Here we show that developmental rate, reproduction and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard E. coli OP50 diet. We identify a set of genes that change in expression in response to this diet, and use the promoter of one of these (acdh-1) as a dietary sensor. Remarkably, the effects on transcription and development occur even when Comamonas DA1877 is diluted with another diet, suggesting that Comamonas DA1877 generates a signal that is sensed by the nematode. Surprisingly, the developmental effect is independent from TOR and insulin signaling. Rather, Comamonas DA1877 affects cyclic gene expression during molting, likely through the nuclear hormone receptor NHR-23. Altogether, our findings indicate that different bacteria elicit various responses via distinct mechanisms, which has implications for diseases such as obesity and the interactions between the human microbiome and intestinal cells.


title: Gene expression analysis of ALS skeletal muscle

status: Public on Feb 28 2013

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

country: Italy

institute: UCSC

summary: Objective: to focus on the molecular mechanisms involved in the ALS related atrophy process that leads to selective wasting  muscles .

overall_design: Design:  gene expression profiling and real time PCR were performed on muscle biopsies

first: C

last: Bernardini

first: E

last: Ricci


title: Milbemycins: more than efflux inhibitors for fungal pathogens

status: Public on Mar 08 2013

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

country: Switzerland

institute: University of Lausanne and University Hospital Center

summary: This study investigated the effect of milbemycons as efflux inhibitors and antifungal agents. Milbemycin oxims can inhibit growth of Candida glabrata and C. albicans. The effect of milbemycins on transcriptomes was inbvestigated.

sample_organism:
Candida albicans
Nakaseomyces glabratus

platform_organism:
Candida albicans
Nakaseomyces glabratus CBS 138

overall_design:
Gene expression was measured in C. glabrata milbemycin-treated cells (1h) and compared to untreated cells in the incubation mediun RPMI.  The one-color system was used. Four biological replicates were used for each condition.
Gene expression was measured in C. albicans milbemycin-treated cells (1h) and compared to untreated cells in the incubation mediun RPMI. The one-color system was used. Three biological replicates were used for each condition.

first: Luis

middle: V

last: Silva

first: Patrick

last: Vandeputte


title: Expression data from Pseudomonas aeruginosa PAO1 treated with phenylacetic acid

status: Public on Feb 21 2013

city: Singapore

first: Yihu

last: Dong

address: 61 Biopolis Drive

country: Singapore

institute: 1Institute of Molecular and Cell Biology

summary:
P. aeruginosa is known to cause acute cytotoxicity against various human and animal cells and tissues. We identified bacterial metabolite - phenylacetic acid (PAA) which acts as an inhibitory molecule counteracting its pathogenic infection.
Microarray and genetic analyses were conducted to investigate the inhibitory mechanism of the identified inhibitor PAA on bacterial virulence. Microarray analysis revealed that treatment of P. aeruginosa with PAA down-regulated the transcriptional expression of type 3 secretion systems (T3SS) genes and related regulatory genes including rsmA and vfr, which were confirmed by transcriptional and translational analysis. Our findings present a new insight to the puzzle of high-cell-density-modulated virulence attenuation in P. aeruginosa and the regulatory mechanisms of T3SS which is associated with bacterial acute infection.

overall_design: Overnight PAO1 culture were diluted 1:200 to fresh LB medium supplemented with nitriloacetic acid (NTA) with or without addition of 1 mM of phenylacetic acid (PAA). The growth was continued with shaking at 37°C for 4 h to allow OD600 reaching about 1.5 and the cells were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Jianhe

last: Wang

first: Yhu

first: Lianhui

last: Zhang


title: A conserved JNK/AP-1 module is a key mediator of intermittent fasting-induced longevity in C. elegans

status: Public on Mar 15 2013

first: Eisuke

last: Nishida

summary:
Dietary restriction extends lifespan and delays the age-related physiological decline in many species. Intermittent fasting (IF) is one of the most effective dietary restriction regimens that extends lifespan in C. elegans and mammals1,2. In C. elegans, the FOXO transcription factor DAF-16 is implicated in fasting-induced gene expression changes and the longevity response to IF3; however, the mechanisms that sense and transduce fasting-stress stimuli have remained largely unknown. Here we show that a KGB-1/AP1 (activator protein 1) module is a key signalling pathway that mediates fasting-induced transcriptional changes and IF-induced longevity. Our promoter analysis coupled to genome-wide microarray results has shown that the AP-1-binding site, together with the FOXO-binding site, is highly over-represented in the promoter regions of fasting-induced genes. We find that JUN-1 (C. elegans c-Jun) and FOS-1 (C. elegans c-Fos), which constitute the AP-1 transcription factor complex, are required for IF-induced longevity. We also find that KGB-1 acts as a direct activator of JUN-1 and FOS-1, is activated in response to fasting, and, among the three C. elegans JNKs, is specifically required for IF-induced longevity. Our results demonstrate that most fasting-induced upregulated genes, including almost all of the DAF-16-dependent genes, require KGB-1 and JUN-1 function for their induction, and that the loss of kgb-1 suppresses the fasting-induced upregulation of DAF-16 target genes without affecting fasting-induced DAF-16 nuclear translocation. These findings identify the evolutionarily conserved JNK/AP-1 module as a key mediator of fasting-stress responses, and suggest a model in which two fasting-induced signalling pathways leading to DAF-16 nuclear translocation and KGB-1/AP-1 activation, respectively, integrate in the nucleus to coordinately mediate fasting-induced transcriptional changes and IF-induced longevity.
To delineate the whole picture of transcriptional changes in response to fasting, we performed genome-wide gene expression analyses during 2 days (48 h) fasting.

overall_design: Two and three independent experiments were performed in the time course and mutants, respectively.

first: Masaharu

last: Uno

first: Tomohito

last: Yamamoto


title: Expression data for developing a GE-HTS signature for neuroblastoma differentiation

status: Public on Apr 08 2013

city: Boston

first: Kimberly

last: Stegmaier

address: Harvard Medical School

department: Department of Pediatric Oncology

institute: Dana-Farber Cancer Institute and Children’s Hospital Boston

summary:
Gene expression data from BE(2)-C cells treated in triplicate with either vehicle (DMSO), 5 μM all-trans retinoic acid (ATRA), 1 mM valproic acid (VPA), or 5 μM ATRA + 1 mM VPA for 6, 24, or 72 hours. Genome-wide expression profiling was performed using Affymetrix U133A microarrays.
While cytotoxic chemotherapy remains the hallmark of cancer treatment, intensive regimens fall short in many malignancies, including high-risk neuroblastoma. One alternative strategy is to therapeutically promote tumor differentiation. We created a gene expression signature to measure neuroblast maturation, adapted it to a high-throughput platform, and screened a diversity oriented synthesis-generated small-molecule library for differentiation inducers. We identified BRD8430, containing a nine-membered lactam, an ortho-amino anilide functionality, and three chiral centers, as a selective Class I histone deacetylase (HDAC) inhibitor (HDAC1 > 2 > 3). Further investigation demonstrated that selective HDAC1/HDAC2 inhibition using compounds or RNA interference induced differentiation and decreased viability in neuroblastoma cell lines. Combined treatment with 13-cis retinoic acid augmented these effects and enhanced activation of retinoic acid signaling. Therefore, by applying a chemical genomic screening approach we identified selective HDAC1/HDAC2 inhibition as a strategy to induce neuroblastoma differentiation.

overall_design: BE(2)-C cells were treated in triplicate with either vehicle (DMSO), 5 μM all-trans retinoic acid (ATRA), 1 mM valproic acid (VPA), or 5 μM ATRA + 1 mM VPA for 6, 24, or 72 hours. Genome-wide expression profiling was performed using Affymetrix U133A microarrays [HT-HG_U133A Early Access].

first: Stacey

last: Frumm

first: Kenneth

middle: N

last: Ross


title: Identification of Biofilm Inhibitors from Streptomyces Strains for Reducing Pseudomonas aeruginosa Biofilm Formation

status: Public on Mar 21 2013

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

summary: Biofilms are ubiquitous in natural, medical, and engineering environments. While most antibiotics that primarily aim to inhibit cell growth may result in bacterial drug resistance, biofilm inhibitors do not affect cell growth and there is less chance of developing resistance.  This work sought to identify novel, non-toxic and potent biofilm inhibitors from Streptomyces bacteria for reducing the biofilm formation of Pseudomonas aeruginosa PAO1. Out of 4300 Streptomyces strains, one species produced and secreted peptide(s) to inhibit P. aeruginosa biofilm formation by 93% without affecting the growth of planktonic cells. Global transcriptome analyses (DNA microarray) revealed that the supernatant of the Streptomyces 230 strain induced phenazine, pyoverdine, and pyochelin synthesis genes. Electron microscopy showed that the supernatant of Streptomyces 230 strain reduced the production of polymeric matrix in P. aeruginosa biofilm cells, while the Streptomyces species enhanced swarming motility of P. aeruginosa. Therefore, current study suggests that Streptomyces bacteria are an important resource of biofilm inhibitors as well as antibiotics.

overall_design: For the microarray experiments, P. aeruginosa were inoculated in 25 0ml of LB medium in 1000 ml shake flasks with overnight cultures that were diluted 1:100. Streptomyces 230 strain culture media was added in at 1% .  Cells were cultured with 10g of glass wool in LB at 37°C with 100 rpm shaking for 7 hrs.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Valencia, CA, USA).  RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA).

first: Yong-Guy

last: Kim

first: Jin-Hyung

first: Chang-Jin

first: Moo

middle: H

last: Cho


title: Heme utilization in the Caenorhabditis elegans hypodermal cells is facilitated by HRG-2

status: Public on Jan 01 2013

city: Bethesda

first: WeiPing

last: Chen

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

department: GCL

institute: NIDDK/NIH

summary: The roundworm Caenorhabditis elegans is a heme auxotroph that requires the coordinated actions of HRG-1 heme permeases to transport environmental heme into the intestine and HRG-3, a secreted protein, to deliver intestinal heme to other tissues including the embryo.  Here we show that heme homeostasis in the extraintestinal hypodermal tissue is facilitated by the transmembrane protein HRG-2.  Systemic heme deficiency upregulates hrg-2 mRNA expression over 200-fold in the main body hypodermal syncytium hyp 7.  HRG-2 is a type I membrane protein which binds heme and localizes to the endoplasmic reticulum and apical plasma membrane.  Cytochrome heme profiles are aberrant in HRG-2 deficient worms, a phenotype that is partially suppressed by heme supplementation.  Heme-deficient yeast strain, ectopically expressing worm HRG-2, reveal significantly improved growth at submicromolar concentrations of exogenous heme.  Taken together, our results implicate HRG-2 as a facilitator of heme utilization in the C. elegans hypodermis and provide a mechanism for regulation of heme homeostasis in an extraintestinal tissue.

overall_design: Two experimental groups: Group 1: three 4um Controls vs. three 4uM hrg-2 Mutants; Group 2: three 20um Controls vs. three 20uM hrg-2 Mutants

first: Caiyong

first: Tamika

last: Samuel

first: Michael

last: Krause

first: Harry

middle: A

last: Dailey

first: Iqbal

last: Hamza


title: Gene expression analysis of Pseudomonas aeruginosa wild type, delta-gbdR, and delta-plcHR deletion mutants

city: Hanover

first: Thomas

last: Hampton

state: NH

address: North College Street

department: Pharm/Tox

institute: Dartmouth Medical School

summary:
Pseudomonas aeruginosa is a virulent opportunistic pathogen responsible for high morbity in COPD, burns , implanted medical devices and cystic fibrosis.
Pseudomonas aeruginosa is a problematic colonizer of the human lung. P. aeruginosa produces a phospholipase C (PlcH) that degrades choline-containing lipids such as phosphatidylcholine and sphingomylein that are found in lung surfactant and in host membranes. In this study,  we analyzed gene expression in mutants defective in PlcH production (delta-plcH and delta-gbdR) and the wild type when growing in medium with lung surfactant.

overall_design: Pseudomonas aeruginosa was cultured in liquid cultures with aeration in a defined medium with Survanta, a lung surfactant replacement. Cultures were harvested during mid-exponential phase, and RNA was isolated for microarray analysis. The P. aeruginosa strain PAO1 wild type gene expression was compared to expression profiles from delta-gbdR and delta-plcHR deletion mutants, two mutants defective in PlcH production.

first: Angelyca

last: Jackson

first: Deborah

last: Hogan


title: A non-classical LysR type transcriptional regulator PA2206 is required for an effective oxidative stress response in Pseudomonas aeruginosa.

city: Cork

first: Fergal

last: O'Gara

address: University College Cork

country: Ireland

institute: BIOMERIT Research Centre

summary: LysR-type transcriptional regulators (LTTRs) are emerging as key circuit components in regulating microbial stress responses and are implicated in modulating oxidative stress in the human opportunistic pathogen Pseudomonas aeruginosa. The oxidative stress response encapsulates several strategies to overcome the deleterious effects of reactive oxygen species. However, many of the regulatory components and associated molecular mechanisms underpinning this key adaptive response remain to be characterised. Comparative analysis of publically available transcriptomic datasets led to the identification of a novel LTTR, PA2206, whose expression was altered in response to a range of host signals in addition to oxidative stress. PA2206 was found to be required for tolerance to H2O2 in vitro and lethality in vivo in the Zebrafish embryo model of infection. Transcriptomic analysis in the presence of H2O2 showed that PA2206 altered the expression of 58 genes, including a large repertoire of oxidative stress and iron responsive genes, independent of the master regulator of oxidative stress, OxyR. Contrary to the classic mechanism of LysR regulation, PA2206 did not autoregulate its own expression and did not influence expression of adjacent or divergently transcribed genes. The PA2214-15 operon was identified as a direct target of PA2206 with truncated promoter fragments revealing binding to the 5’-ATTGCCTGGGGTTAT-3’ LysR box adjacent to the predicted -35 region. PA2206 also interacted with the pvdS promoter suggesting a global dimension to the PA2206 regulon, and suggests PA2206 is an important regulatory component of P. aeruginosa adaptation during oxidative stress.

overall_design: Six samples were analysed in total, three biological replicates of the PA2206 mutant and PA2206 complemented strains. Each biological replicate included three technical replicates.

first: Jill

last: Haynes

first: F

last: Reen

first: Marlies

last: Mooij

last: O’Gara


title: Gene expression data from C.elegans

status: Public on Dec 31 2012

city: Montevideo

first: Tamara

last: Fernandez-Calero

state: Montevideo

address: Mataojo 2020

department: Bioinfomatics Unit

country: Uruguay

institute: Institut Pasteur de Montevideo

summary: Numerous studies have shown that resistance to oxidative stress is crucial to stay healthy and to reduce the adverse effects of aging. Accordingly, nutritional interventions using antioxidant food-grade compounds or food products are currently an interesting option to help improve health and quality of life in the elderly. Live lactic acid bacteria (LAB) administered in food, such as probiotics, may be good antioxidant candidates. Nevertheless, information about LAB-induced oxidative stress protection is scarce. To identify and characterize new potential antioxidant probiotic strains, we have developed a new functional screening method using the nematode Caenorhabditis elegans as host. C. elegans were fed on different LAB strains (78 in total) and nematode viability was assessed after oxidative stress (3mM and 5mM H2O2). One strain, identified as Lactobacillus rhamnosus CNCM I-3690, protected worms by increasing their viability by 30% and, also, increased average worm lifespan by 20%. We performed a transcriptomic analysis of C. elegans fed with this strain and showed that increased lifespan is correlated with differential expression of the DAF-16/insulin-like pathway, which is highly conserved in humans.

overall_design: Gene expression in C. elegans wild-type strain (N2) was analyzed in worm populations fed with E. coli OP50 (control condition) or the corresponding LAB (Lactobacillus rhamnosus CNCM I-3690 or Lactobacillus rhamnosus CNCM I-4317) . Three days and ten days feeding period was analyzed.

first: Gianfranco

last: Grompone

first: Patricia

last: Martorell

first: Silvia

last: Llopis

first: Núria

last: Gonzalez

first: Salvador

last: Genovés

first: Ana

last: Mulet

last: Fernández-Calero

first: Inés

last: Tiscornia

first: Mariela

last: Bollati-Fogolín

first: Isabelle

last: Chambaud

first: Benoit

last: Foligné

first: Agustín

last: Montserrat

first: Daniel

last: Ramón


title: Expression data from rho+ and rho0 budding yeast celles harvetsed from complete medium with 2% glucose before or after shifting to complete medium without glucose

status: Public on Dec 31 2013

city: Edmonton

first: Michael

middle: C.

last: Schultz

state: Alberta

department: Biochemistry

country: Canada

institute: University of Alberta

summary:
This experiment compares mRNA expression in cells with and without mitochondrial DNA (ρ+ and ρ0 cells respectively). We used global RNA profiling to measure mRNA expression in ρ+ and ρ0 cells harvested at log phase from synthetic medium with glucose (CM + 2% glucose, "CMD"), and at 4 hours after transfer to the same medium without glucose (CM).
This profiling provided new clues about the ways in which nutirent signaling is reprogrammed in cells lacking mitocondrial DNA.

overall_design: mRNA expression was assessed by analyzing the RNA from three biological replicates obtained under four conditions: ρ+ cells in glucose, ρ+ cells no glucose, ρ0 cells in glucose, ρ0 cells no glucose.

first: R

last: Friis

middle: C


title: A Dicistrovirus-specific inducible antiviral response in Drosophila

status: Public on Feb 06 2013

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

institute: CNRS

summary: The fruit fly Drosophila melanogaster is a good model to unravel the molecular mechanisms of innate immunity, and has led to some important discoveries on the sensing and signalling of microbial infections. The response of drosophila to virus infections remains poorly characterized, and appears to involve two facets. On one hand RNA interference (RNAi) involves the recognition and processing of dsRNA into small interfering (si) RNAs by the host ribonuclease Dicer-2 (Dcr-2), whereas on the other hand an inducible response controlled by the evolutionarily conserved JAK/STAT pathway contributes to the antiviral host defence. In order to clarify the contribution of the siRNA and JAK/STAT pathways to the control of viral infections, we have compared the resistance of flies wild-type or mutant for Dcr-2 or the JAK kinase Hopscotch (Hop) to infections by seven RNA or DNA viruses belonging to different families. Our results reveal a unique susceptibility of hop mutant flies to infection by DCV and CrPV, two members of the Dicistroviridae family. Genome-wide microarray analysis confirmed that different sets of genes were induced following infection by DCV (GSE2828) or two unrelated RNA viruses, FHV and SINV. Overall, our data reveal that RNAi is an efficient antiviral mechanism, operating against a large range of viruses, including a DNA virus. By contrast, the antiviral contribution of the JAK/STAT pathway appears to be virus-specific.

overall_design: For each experimental challenge (FHV, 48 or 72 hours after infection; SINV, 4 or 8 days after infection), three biologically independent samples composed of 45 male Oregon R flies were used. Infection has been performed by injecting viral stocks prepared in Tris solution. Injection of the same volume of Tris has been used as control. Infected flies were then incubated for 48 or 72 hours in the case of FHV and 4 days or 8 days in the case of SINV.

first: C

last: Kemp

first: S

last: Mueller

first: A

last: Goto

first: V

last: Barbier

last: Dostert

first: L

last: Troxler

last: Hetru

first: J

last: Hoffmann

middle: L


title: Expression data from C. elegans in the presence or absence of copper sulfate

status: Public on Dec 05 2012

city: Nagoya

first: Ayuna

last: Hattori

state: Aichi

address: Chikusa

department: Department of Molecular Biology

institute: Nagoya University

summary:
MAP kinases are integral to the mechanisms by which cells respond to a wide variety of environmental stresses. In Caenorhabditis elegans, the KGB-1 JNK signaling pathway regulates the response to heavy metal stress. The deletion mutants of this cascade show hypersensitivity to heavy metals like copper or cadmium. However, factors that function downstream of KGB-1 pathway are not well characterized.
To understand how the KGB-1 pathway modulates gene activity and to define the physiological processes in which the heavy metal stress response may be involved, we used microarray to examine gene expression changes in wild-type and kgb-1 mutant animals subjected to heavy metal stress.

overall_design: Adult worms of WT or kgb-1 mutant were incubated with H2O or 1 mM copper sulfate for 1 hour. Total RNA was then prepared using Trizol reagent (Invitrogen), followed by DNase I treatment, phenol/chloroform extraction and ethanol precipitation. (WT_Cu-), (WT_Cu+), (kgb-1_Cu-) and (kgb-1_Cu+) RNAs extraction were hybridized on Affymetrix microarrays.

first: Kunihiro

last: Matsumoto


title: Expression data from Caenorhabditis elegans exposed to single-walled carbon nanotubes

status: Public on Oct 11 2012

city: Chiayi

first: Cheng

middle: Chung

last: Chou

state: International

address: 168 University Road, Minhsiung Township

country: Taiwan

institute: ChungCheng university

summary:
The potential environmental risk of single-walled carbon nanotubes (SWCNTs) is evaluated using Caenorhabditis elegans (C. elegans) as an ecotoxicological animal model. Highly soluble amide-modified SWCNTs (a-SWCNTs) are used in the present study so that the dose-response impact of SWCNTs could be studied. mechanisms.
a-SWCNTs are efficiently taken up by worms during feeding and cause significant toxicity in worms, including retarded growth, shortened lifespan and defective embryogenesis. Genome-wide gene expression analysis is performed to investigate the toxic molecular

overall_design: We examined the effect of different concentrations of a-SWCNTs (0, 100, 250 and 500 μg/mL) on the growth of C. elegans. We measured the body length of worms reaching the L4 stage after a-SWCNT exposure for 48 hr at 22°C. Compared to the untreated worms, we found that the average length of worms exposed to a-SWCNTs (500 μg mL-1) was significantly  shorter than the untreated groups. In addition, the dose of a-SWCNTs also caused retarded growth, reduced lifespan and defective embryogenesis in worms. Genome-wide gene expression analysis using an Affymetrix GeneChip was performed to further investigate the molecular basis of these defects.

first: Cheng-Chung

first: Kuang-Ming

last: Hsiao

first: Po-Hsuan

last: Chen


title: Regulon of transcriptional regulator PA2449 in Pseduomonas aeruginosa PAO1

status: Public on Oct 15 2012

city: Syracuse

first: Christopher

last: Nomura

address: 1 Forestry Dr.

department: Chemistry

institute: SUNY-ESF

summary:
The putative trancriptional regulator PA2449 was found to be essential for both glycine/serine metabolism and the production of phenazines in P. aeruignosa PAO1.
We examined the regulon controlled by PA2449 via microarray analysis between wild-type P. aeruignosa PAO1 and the PA2449-null mutant P. aeruginosa PW5126.  Both strains were obtained from the PA-two allele library (Univ. of Washington, Ref. Jacobs et al. 2003. PNAS 100, 14339).

sample_organism:
Pseudomonas aeruginosa
Pseudomonas aeruginosa PAO1

overall_design: Strains were grown under conditions known to induce phenazine biosynthesis (peptone broth), and their resulting transcriptomes were compared.  Total RNA was isolated and prepped for Affymetrix GeneChips.

first: Benjamin

middle: R

last: Lundgren


title: Yeast_FLO8_MSS11_Deletions_LowN

status: Public on Sep 04 2012

city: Ann Arbor

first: Anuj

last: Kumar

state: Michigan

address: 4063 Kraus Natural Sciences Building 830 N. University Avenue

department: Molecular, Cellular, and Developmental Biology (MCDB)

institute: University of Michigan

summary: In filamentous strains of S. cerevisiae, nitrogen stress elicits a complex morphogenetic program resulting in the transition to a filamentous form of growth.  The transcription factors Flo8p and Mss11p are both required for this filamentous growth transition, in that homozygous diploid flo8(delta/delta) and mss11(delta/delta) strains do not undergo filamentation under conditions of nitrogen stress.  To identify genes that are regulated either directly or indirectly by the Flo8p and Mss11p transcription factors, we have implemented DNA microarray analysis to profile changes in mRNA levels in homozygous diploid strains of the filamentous (Sigma)1278b genetic background deleted for FLO8 and MSS11, respectively, under conditions of nitrogen stress.  The transcriptional profiles will identify genes with altered transcriptional levels in the deletion mutants, serving as a means to identify cellular processes and signaling pathways regulated by Flo8p and Mss11p function.

overall_design: Deletion mutants were constructed using a one-step polymerase chain reaction (PCR)-based gene disruption strategy with the G418 resistance cassette from plasmid pFA6a-KanMX6.  After the haploid mutants were confirmed via PCR, the strains were allowed to mate on YPD+G418 plates for approximately 20 hours at 30 degrees Celsius.  Mated cells were then streaked on SC-Trp-Leu plates to select for Y825 x HLY337 diploids.  Yeast transformations were performed according to standard lithium acetate-mediated protocols with modifications.  Yeast strains (wild-type and deletion mutants) were cultured under conditions of nitrogen stress (low ammonium media), and RNA was prepared using the Poly(A) Purist kit (Ambion, Austin, TX).  RNA concentration and purity were determined spectrophotometrically and by gel electrophoresis.  Microarray hybridization was performed with the Yeast Genome S98 Array using standard protocols (Affymetrix, Inc, Santa Clara, CA).  Differentially expressed genes were identified by significance analysis of microarrays (SAM).  SAM computed a nonparametric score for each gene by dividing the between-group difference of (normalized log) gene expression levels and the within-group difference of gene expression levels.  The score was then compared with random permutation scores.  The random permutation scores for a gene were computed in the same manner as the original score, but based on randomly sampled gene expressions.  If the difference between the original score and the random permutation score was larger than a chosen threshold value, the corresponding change in gene expression was claimed to be significant.  Each threshold value corresponded to a false discovery rate (the percentage of genes identified as being significant by chance alone).  For all deletion comparisons in this study, we used SAM’s two-class unpaired analysis function, with significance thresholds selected so that the corresponding false discovery rate was 0.

first: Craig

last: Dobry

first: Jun

last: Ma

first: Thair

last: Judeh

first: Dongxiao

last: Zhu


title: Alterations in gene expression in Caenorhabditis elegans associated with exposure to several classes of toxic industrial chemicals/materials.

status: Public on Nov 28 2012

city: Ft. Detrick

first: John

middle: A.

last: Lewis

address: 568 Doughten Drive

department: Biomarkers Program

institute: U.S. Army Center for Environmental Health Research

summary:
Effective toxicological testing of the vast number of new and existing chemicals currently in use will require efficient and cost effective methods. We evaluated the utility of a simple, low cost toxicity testing system employing the nematode Caenorhabditis elegans to identify toxicologically relevant changes in gene expression.
The objective of this research is to determine genomic and proteomic responses in the model nematode C. elegans to exposures to representatives of several classes of toxic industrial chemicals/materials (TICs/TIMs). A total of 3 chemicals (acrylamide, cadmium chloride, and mercuric chloride) were used in these experiments. Affymetrix GeneChip for C. elegans was used to examine genome-wide responses in the 19,000+ genes of this model organism.

overall_design: Mid-vulval L4 worms were exposed to one of four concentrations of acrylamide, cadmium or mercury for 4h and 8h. Exposures were performed in triplicate.

first: David

last: Jackson

first: Eric

last: Clegg

first: Maria

last: Szilagyi

first: Elizabeth

last: Gehman


title: Expression data from Caenorhabditis elegans L1-stage larvae exposed to ethidium bromide and/or serial ultraviolet C radiation

status: Public on Oct 01 2012

city: Durham

first: Joel

last: Meyer

state: NC

address: Box 90328 LSRC A354

institute: Duke University

summary:
Ultraviolet C radiation (UVC) damages the nuclear and mitochondrial genomes; this damage is repaired in the nuclear but not mitochondrial genome. Ethidium bromide (EtBr) inhibits mitochondrial DNA replication.
We were interested in the transcriptomic response to exposure to UVC, EtBr, and the combination. The UVC exposure protocol results in a high level of mitochondrial DNA damage, and a low level of nuclear DNA damage (because of repair).

overall_design: We exposed age-matched L1-stage Caenorhabditis elegans to ultraviolet C radiation (UVC ) three times, separated in time by 24 h, in the absence of food. After the third exposure, larvae were placed on K agar plates with OP50 bacterial food. In some cases ethidium bromide was also used. Nematodes were sampled for RNA isolation several times.