title: Yeast (Saccharomyces cerevisiae) Overexpression suppression study

city: Claremont

first: Biranchi

last: Patra

address: 535 Watson Dr

institute: Keck Graduate Institute

summary:
To address the mechanisms of suppression, we analyzed time course of mRNA expression of four suppressed smc2-8 mutant strains.
We addressed the question of genomic robustness by systematically screening genomic open reading frames, when induced for high-level expression, for their ability to suppress 55 conditional lethal mutations in yeast, and have discovered 636 suppressor genes participating in 822 novel dosage suppressor interactions.  The suppressor genes are functionally broad and are enriched for overlapping open reading frames where mutually overlapping genes tend to be co-suppressors.  Studies on suppressors of defects in chromosome condensation, telomere stability, and RNA polymerase II function suggest that adding interactions, by making significant connections where only weak or undetectable interactions were present (rewiring of gene regulatory pathways, and interaction within and between protein complexes) are frequent mechanisms of dosage suppression.

overall_design: RNA samples isolated from two individual biological replicates, four time points each (0, 45, 90 and 180 min), of smc2-8 mutant strains harboring pGAL:SMC2, pGAL:UME1, pGAL:MEK1, pGAL:HTA2, pGAL:SNU66, and the negative control MORF plasmid (pGAL:negative, BG1766) and hybridized Affymetrix microarrays.

first: Yoshiko

last: Kon

first: Anthony

last: Sevold

first: Jesse

last: Frumkin

first: Ravishankar

middle: R

last: Vallabhajosyula

first: Ashish

last: Bhan

first: Jenna

last: Tamashiro

first: Bruz

last: Marzolf

first: Arend

last: Hintze

first: Bjorn

last: Ostman

first: Amardeep

last: Kaur

first: Nitin

last: Baliga

first: Elizabeth

last: Grayhack

first: David

last: Galas

first: Alpan

last: Raval

first: Christoph

last: Adami

first: Eric

last: Phizicky

first: Animesh

last: Ray


title: PTC1 mutant Yeast Genomic Expression Patterns in Response to deoxynivalenol

status: Public on Jul 22 2011

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

country: Japan

institute: National Food Rsearch Institute

summary:
The evaluation of the toxicity of deoxynivalenol using yeast gene expressions. Yeast PTC1 mutant strain was used for this study. SDS was used to raise the penetration of the yeast cell membrane.

Keywords: stress response

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Two conditions were compared by the gene expression profiles. Both samples were grown in 0.01% SDS contained YPD media, and one of them was also supplied with 50 ppm of deoxynivalenol.

first: Yumiko

last: Iwahashi


title: Effect of loss of function of Gal11/Med15 and Med3 from the Mediator tail module in budding yeast

status: Public on Sep 01 2011

city: Albany

first: Randall

middle: Heywood

last: Morse

state: NY

country: USA

institute: Wadsworth Center

summary:
Gene expression was compared for wild type yeast (BY4741) and yeast lacking Gal11/Med15 and Med3, or from a gal11-myc med3∆ strain.  The gal11-myc allele shows a partial loss of function when combined with med3∆.  Expression was analyzed for yeast grown in YPD as well as in CSM.
We also examined gene expression of the wild type strain BY4742 grown in YPD and include that data here.

overall_design: Gene expression was compared for wild type yeast (BY4741 and BY4742) and yeast lacking Gal11/Med15 and Med3, or from a gal11-myc med3∆ strain.

middle: H

first: Suraiya

middle: A

last: Ansari


title: Transcription data from Saccharomyces cerevisiae yeast (II)

status: Public on Sep 21 2011

city: Stellenbosch

first: Michael

middle: Christiaan

last: Bester

address: Victoria street

country: South Africa

institute: Institute for Wine Biotechnology

summary:
Effect of either FLO8 or MSS11 deletion and -overexpression on yeast transcript profiles compared to wild type in laboratory yeast strains Σ1278b and S288c - also the effect of FLO11 (MUC1) overexpression in the Σ1278b genetic background
The aim of this study was to (1) perform a repeat analysis (to improve statistical analysis of these data sets) similar to data submitted previously (GSE17716) and also (2) study the effect of FLO11 over-expression on the transcriptome.
Background: The outer cell wall of the yeast Saccharomyces cerevisiae serves as the interface with the surrounding environment and defines cell-cell and cell-surface interactions. Many of these interactions are facilitated by specific adhesins that belong to the Flo protein family. This family of mannoproteins has been implicated in phenotypes such as flocculation and substrate adhesion as well as pseudohyphal growth. Genetic data strongly suggest that individual Flo proteins are responsible for many specific cellular adhesion phenotypes. However, it remains unclear whether such phenotypes are determined solely by the nature of the expressed FLO genes or rather the result of a combination of FLO gene expression and other cell wall properties and cell wall proteins. Mss11p has been shown to be a central element of FLO1 and FLO11 gene regulation and acts together with the cAMP-PKA-dependent transcription factor Flo8p. We use genome wide transcript analysis to identify genes that are direct  ly or indirectly regulated by Mss11p in the genetic backgrounds: Sigma1278b and S288c. Sigma 1278b is the strain historically used for the study of pseudohyphae (FLO11 expression) but we also included S288c as this strain is widely used in the research community and was used to determine the first full genome sequence (Thus correspond with SGD information). We also compare this data with transcriptome data from Sigma 1278b yeast over-expressing FLO8 to compare similarities/differences between these two signalling factors. Finally the effect of FLO11 over-expression in Sigma1278b on global transcription is studied so that we can differentiate between "direct" gene targets of Flo8p or Mss11p, and those regulated as a result by the "indirect" effect caused by modified cell wall Flo11p levels.

overall_design: We used two laboratory yeast strains that behave different with regard to adhesion phenotypes. By comparing yeast deleted in either FLO8 or MSS11 to wild type, or yeast overexpressing these genes, in both genetic backgrounds, we investigate the role of Flo8p and Mss11p on yeast transcription. In addition the effect of the over-expression of the adhesin gene FLO11 was studied in Sigma 1278b. By using similar growth conditions to what we use for adhesion phenotype determination we aim to correlate transcription profile changes to yeast behaviour (phenotypes).

middle: C

first: Florian

middle: F

last: Bauer


title: Expression profiling of rpb1-12XWTCTD and rpb1-12XS2ACTD fission yeast strains.

city: London

first: Jim

last: Karagiannis

state: Ontario

address: 1151 Richmond St. N

department: Biology

country: Canada

institute: University of Western Ontario

summary:
In fission yeast, the nuclear-localized Lsk1p-Lsc1p-Lsg1p cyclin dependent kinase complex is required for the reliable execution of cytokinesis and is also required for Ser-2 phosphorylation RNA pol II carboxy terminal domain.
To address whether alterations in CTD phosphorylation might selectively alter expression of cytokinesis genes, expression profiling of site-directed CTD mutants was performed.

overall_design: Strains bearing the rpb1-12XCTD and rpb1-12XS2ACTD mutations were grown to mid-log phase in YES media and treated with 0.5uM LatA (or the solvent control, DMSO) for three hours at 30C.  Three biological replicates were performed.

first: Reza

last: Saberianfar


title: Responses to multi-inhibitors in industrial stain of yeast and the adapted strains

status: Public on Aug 13 2011

city: Tianjin

first: Bing-Zhi

last: Li

address: Weijin Road 92#

country: China

institute: Tianjin University

summary:
Furfural, phenol and acetic acid, generated during the cellulosic material pretreatment, are the representative inhbitors to yeast used for ethanol production. The responses to multi-inhbitors in industrial yeast and the tolerant strain were analyzed.
We analyzed the transcriptome of the parental and tolerant strains in the presence of multi-inhibitors.

overall_design: Parental and tolerant strains were collected at the exponential stage in the presence of multi-inhibitors. The reference samples for industrial yeast and adapted strains were collected at the same growth stage in the absence of inhibitors.

first: Ying-Jin

last: Yuan


title: Yeast Genomic Expression Patterns in Response to Patulin and Ascorbic acid

status: Public on Jul 31 2011

summary:
The assessment of toxicity about patulin using yeast gene expression comparison analysis. Yeast BY4743 derivative SOD1 mutant was used for this study. Ascorbic acid was used to evaluate the anti-toxic effect to patulin.
Keywords: stress response

overall_design: Four series of samples were compared with each by ANOVA analysis. Each strain was grown in YPD medium, and they were also incubated with 25 ppm of patulin and 10 mM ascorbic acid.


title: Detection of S. cerevisiae fragments in the genome of S. bayanus strains with aCGH on Yeast_2 Affymetrix array.

status: Public on Jun 30 2011

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

country: France

institute: INRA

summary:
The aim of this project was to detect S. cerevisiae fragments in the genome of S. bayanus Type strain CBS380 and pure line NBRC1948 (=IFO1948).
The hybridization signal is compared to S. uvarum BBS7001 whose genome has been sequenced and in which no S. cerevisiae sequence has been detected.

sample_organism:
Saccharomyces bayanus
Saccharomyces uvarum

overall_design: Comparison CBS380 (2 arrays) or IFO1948 (one array) to CBS 7001 (2 arrays).

first: Huu-Vang

last: Nguyen

first: J

middle: L

first: Cecile

last: Neuveglise

first: Claude

last: Gaillardin


title: Gene expression data from yeast exposure to alachlor

status: Public on Aug 28 2011

city: Lisboa

first: Cristina

middle: Anjinho

last: Viegas

address: Av Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Técnico

summary:
The world-wide used herbicide alachlor is among the priority substances listed in the European Water Framework Directive. We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes.
We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to alachlor at concentrations exerting slight to moderate levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the lowest observed effect concentration (LOEC; ~8% growth inhibition) and the 20%-inhibitory concentration (IC20), compared to control cells not exposed to the herbicide (CT02).

overall_design: Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of 110 or 200 mg/L of ALA (corresponding to the LOEC and the IC20, respectively, of alachlor) or in medium non-supplemented with the herbicide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix microarrays. Exposure experiments with each concentration of alachlor versus controls were carried out independently. For each exposure condition, independent biological triplicates were processed and analysed.

first: Jörg

middle: D

last: Becker

first: Fátima

middle: N

last: Gil


title: Expression data from Saccharomyces cerevisiae temperature-sensitive strains specific for SCF core components (Skp1, Cullin (Cdc53), E2 enzyme (Cdc34)) and the F-box protein Cdc4.

city: Los Angeles

first: Mariam

last: Aghajan

state: CA

address: 650 Charles E. Young Drive South, CHS 23-231

institute: UCLA

summary:
The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyper-activation of the mTOR pathway in human cancers, novel strategies to enhance TOR pathway inhibition are highly desirable.
We used a yeast-based high-throughput chemical genetic screen to identify small-molecule enhancers of rapamycin (SMERs) and used whole genome expression analysis to identify their mechanisms of action.

overall_design: We incubated various temperature-sensitive yeast strains at either the permissive (room temperature) or non-permissive (35°C) temperature for 1 hour prior to RNA extraction and hybridization on Affymetrix microarrays.  Comparison of expression profiles enabled identification of gene-signatures specific to inhibition of each gene product.

first: Nao

last: Jonai

first: Karin

last: Flick

first: Fei

last: Fu

first: Manlin

last: Luo

first: Xiaolu

last: Cai

first: Ikram

last: Ouni

first: Nathan

last: Pierce

first: Xiaobo

last: Tang

first: Brett

last: Lomenick

first: Robert

last: Damoiseaux

first: Rui

last: Hao

first: Pierre

middle: M

last: del Moral

first: Rati

last: Verma

first: Ying

first: Cheng

first: Kendall

last: Houk

middle: E

last: Jung

first: Ning

last: Zheng

first: Lan

last: Huang

first: Raymond

middle: J

last: Deshaies

first: Peter

last: Kaiser

first: Jing


title: Transcriptional responses of sympathetic neurons during BMP-induced primary dendritogenesis

city: Davis

first: Pamela

last: Lein

address: 2161 Haring Hall

institute: UC Davis

summary: The objective of this study was to identify genes that are differentially regulated in cultured sympathetic neurons during BMP-induced dendritic growth and to determine the temporal expression patterns of these genes.

overall_design: We determined that inhibiting transcription within the first 24 hours after adding exogenous BMP-7 blocks BMP-induced dendritic growth in cultured sympathetic neurons dissociated from the superior cervical ganglia of embryonic rat pups.  Thus, we determined the transcriptional profiles of cultured sympathetic neurons at 6 and 24 hours after addition of BMP-7 to identify early and later transcriptional responses that may drive dendrite formation.  We isolated total RNA from sympathetic neurons exposed to three different experimental conditions:  (1) no BMP-7 treatment; (2) treatment with BMP-7 for 6 hours; and (3) treatment with BMP-7 for 24 hours.  Total RNA was labeled and hybridized to Affymetrix Rat Genome U34A oligonucleotide microarrays.  This experiment was independently repeated three times using cultures derived from three independent dissections, such that a total of nine arrays were used.  The nine samples were processed over two batches and the batching was balanced across the treatment conditions.  Image data was processed using Affymetrix GCOS software to generate numeric, probe level data (CEL) and CEL data was then pre-processed using the RMA algorithm implemented by Partek Genomics Suite (St. Louis, MO).  Following batch correction of the probe set level, normalized data using Partek, differential gene expression was determined by two-way ANOVA and linear contrasts between all treatment conditions were applied to generate fold-change values along with the statistical p-value.  Lists of significantly changed transcripts were uploaded to MetaCore (GeneGo, ) for mining biological annotation and network analysis.

first: Michelle

last: Garred

first: Michael

last: Wang

first: Christina

last: Harrington

first: Xin

last: Guo


title: Expression data from Saccharomyces cerevisiae Met30 temperature-sensitive strain

first: Mariam

last: Aghajan

overall_design: We incubated Met30 temperature-sensitive yeast strain at either the permissive (room temperature) or non-permissive (35°C) temperature for 1 hour prior to RNA extraction and hybridization on Affymetrix microarrays.  Comparison of expression profiles enabled identification of gene-signature characteristic of Met30 inhibition.

first: Nao

last: Jonai

first: Karin

last: Flick

first: Fei

last: Fu

first: Manlin

last: Luo

first: Xiaolu

last: Cai

first: Ikram

last: Ouni

first: Nathan

last: Pierce

first: Xiaobo

last: Tang

first: Brett

first: Robert

last: Li


title: Measurements of mRNA abundance and decay for two strains 211 (wt) and 212 (mutant)

status: Public on Jul 30 2011

city: Rehovot

first: Ophir

last: Shalem

address: Hertzel

country: Israel

institute: Weizmann Inst.

summary: For each strain two time courses for mRNA abundance: Oxidative and MMS and two time courses for decay: reference decay and following oxidative stress

overall_design: We used Affymetrix microarrays to quantify changes in mRNA abundance following oxidative stress and DNA damage stress and also decay following transcription inhibition with and without oxidative stress. Each of the experiments were done for both strains 211 (wt) and 212 (mutant)

first: Bella

last: Groisman

first: Mordechai

last: Choder

first: Orna

last: Dahan

first: Yitzhak

last: Pilpel


title: Expression profiling of nhp6 mutants and wildtype yeast cells (Saccharomyces cerevisiae)

status: Public on May 19 2011

city: Oxford

first: Jiannis

last: Ragoussis

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre For Human Genetics, University of Oxford

summary: The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. However, nucleosome number in cells was considered fixed, and no condition was described where nucleosome number was reduced. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker and variant histones, and a correspondingly reduced number of nucleosomes. Yeast nhp6 mutants lacking NHP6A and –B proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform, and our results can be modelled assuming that different nucleosomal sites compete for the available histones: sites with high affinity are almost always packaged into nucleosomes both in wt and nucleosome-depleted cells, whereas sites with low affinity are less frequently packaged in nucleosome-depleted cells. We suggest that by modulating the occupancy of nucleosomes histone availability may constitute a novel layer of epigenetic regulation.

overall_design:
This microarray experiment forms part of a larger study of the effects of nucleosome depletion on transcription
Using the Affymetrix Yeast Genome 2.0 Array, yeast nhp6 mutants (lacking NHP6A and NHP6B proteins) were compared to wildtype yeast cells  (3 biological replicates per condition)

first: Barbara

last: Celona

first: Assaf

last: Weiner

first: Francesca

last: Di Felice

first: Francesco

last: Mancuso

first: Elisa

last: Cesarini

first: Riccardo

last: Rossi

first: Lorna

last: Gregory

first: Dilair

last: Baban

first: Helen

last: Lockstone

first: Grazisa

last: Rossetti

first: Massimiliano

last: Pagani

first: Tiziana

last: Bonaldi

first: Nir

last: Friedman

first: Giorgio

last: Camilloni

first: Marco

last: Bianchi

first: Alessandra

last: Agresti


title: Expression data from yeast strain VIN13 in pure-culture fermentations and in mixed fermentations with co-inoculated Oenococcus oeni strain S6

status: Public on Jun 02 2011

first: Debra

last: Rossouw

state: Western Cape

address: Cnr Neethling and Victoria rd

department: Institute for Wine Biotechnology

institute: University of Stellenbosch

summary:
The yeast Saccharomyces cerevisiae is an important component of the wine fermentation process and determines various attributes of the final product. However, lactic  acid  bacteria  (LAB)  are  also an  integral  part  of  the microflora of  any  fermenting must. Various wine microorganism engineering projects have been endeavoured in the past in order to change certain wine characteristics, namely aroma compound composition, ethanol concentration, levels of toxic/ allergenic compounds etc. Most of these projects focus on a specific gene or pathway, whereas our approach aims to understand the genetically complex traits responsible for these phenotypes in a systematic manner by implementing a transcriptomic analysis of yeast in mixed fermentations with the LAB O. oeni.  Our aim is to investigate interactions between yeast and LAB on a gene expression level to identify targets for modification of yeast and O. oeni in a directed manner.
Our goal was to identify the impact that the common wine microorganism O. oeni (malolactic bacteria) has on fermenting yeast cells on a gene expression level. To this end we co-inoculated the yeast and bacteria at the start of fermentation in a synthetic wine must, using yeast-only fermentations witout O. oeni as a control.

sample_organism:
Oenococcus oeni
Saccharomyces cerevisiae Vin13

overall_design: Fermentations were carried out in synthetic wine must in triplicate for both the control S. cerevisiae VIN13 strain and the mixed fermentation of VIN13 and O. oeni (strain S5). Sampling of yeast for RNA extractions were performed at day 3 of fermentation, during the exponential growth phase of the yeast cells, and again at day 7 of fermentation, during the early stationary growth phase.

first: Florian

last: Bauer


title: Expression data for haploid Saccharomyces cerevisiae strains growing in a defined low glucose medium.

status: Public on May 20 2011

city: Mississauga

first: Lucas

last: Parreiras

address: 3359 Mississauga Road N.

department: Cell and Systems Biology

institute: University of Toronto

summary: We used microarrays to assess differences in gene expression associated with single nucleotide polymorphisms occurred in three genes, PMA1, MDS3 and MKT1, as compared to a reference strain devoid of any mutations (Progenitor strain).

overall_design: Haploid yeast strains carrying no evolved alleles (progenitor - reference strain) or different combinations of the studied evolved alleles (PMA1e, MDS3e and MKT1e) and devoid of all other evolved alleles were used. The following genotypes were studied: ancestral, MDS3e, MKT1e, MDS3e_MKT1e and PMA1e_MKT1e (2 replicates each). Cells of the studied strains were grown overnight on liquid yeast peptone dextrose (YPD) medium and used to inoculate defined low glucose medium.

middle: S

first: Linda

last: Kohn

first: James

middle: B

last: Anderson


title: Expression data from Saccharomyces cerevisiae strains deleted for different subunits of the THO/TREX complex

status: Public on Jun 29 2011

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

summary:
THO/TREX is a conserved nuclear complex that functions in mRNP biogenesis at the interface of transcription-RNA export with a key role in preventing transcription-associated genome instability.
We used microarrays to analyze the impact of different THO/TREX mutations on gene expression and found that THO-Sub2 deletions have a high functional impact on highly expressed, long and G+C-rich genes regardless of gene function.

overall_design: S. cerevisiae strains were grown in YPAD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays.

first: Belén

last: Gómez-González

first: Cristina

last: Tous

first: Hélène

last: Gaillard

first: Antonio

last: Marín


title: Expression data from diclofenac-treated yeast cells

status: Public on May 17 2011

city: Amsterdam

last: Vos

address: de Boelelaan 1083

department: Chemistry and Pharmaceutical Sciences

country: Netherlands

institute: Vrije Universiteit

summary: Diclofenac is a widely used analgesic drug that can cause serious adverse drug reactions. We used Saccharomyces cerevisiae as model eukaryote to elucidate the molecular mechanisms of diclofenac toxicity and resistance. Although most yeast cells died during initial diclofenac treatment, some survived and started growing again. Microarray analysis of the adapted cells identified three major processes involved in diclofenac detoxification and tolerance. Especially pleiotropic drug resistance genes and genes under control of Rlm1p, a transcription factor in the protein kinase C (PKC) pathway, were upregulated in diclofenac-adapted cells. Genes involved in ribosome biogenesis and rRNA processing were downregulated, as well as zinc-responsive genes.

overall_design: Five independent yeast cultures were incubated with 100 µM diclofenac for 75 hours. Every 24h, cultures were diluted to OD600 ~0.1 in YNB containing 100 µM diclofenac. Five independent control cultures were grown in the absence of diclofenac.

first: Jolanda

last: van Leeuwen

first: Nico

middle: P

last: Vermeulen

first: J


title: In the absence of H2A.Z, the SWR1 histone replacement complex causes genetic instability, stress and genome transcription misregulation

status: Public on May 18 2011

city: SEVILLE

first: ELOISA

last: ANDUJAR

state: SEVILLE

address: AVDA. AMERICO VESPUCIO S/N

department: GENOMICS

institute: CABIMER-CSIC

summary: The SWR1 complex replaces the canonical histone H2A with the variant H2A.Z (Htz1 in yeast) at specific chromatin regions. This dynamic alteration in nucleosome structure provides a molecular mechanism to regulate transcription. Here we analysed the transcription profiles of single and double mutants and wild-type cells by whole-genome microarray analysis. Our results indicate that genome-wide transcriptional misregulation in htz1∆ can be partially or totally suppressed if SWR1 is not formed (swr1∆), if it forms but cannot bind to chromatin (swc2∆), or if it binds to chromatin but has no histone replacement activity (swc5∆). These results suggest that in htz1∆ the nucleosome remodelling activity of SWR1 affects chromatin integrity because of an attempt to replace H2A with Htz1 in the absence of the latter.

overall_design: Three biological independent replicates were use for each strain

first: Macarena

last: Morillo-Huesca

first: Marta

last: Clemente-Ruiz

first: Eloisa

last: Andujar

first: Felix

last: Prado


title: Expression data from yeast cells with pop2 deletion and overexpressing STM1 or STM1 R237K mutant

status: Public on Apr 22 2011

city: Taipei

first: yu-chen

last: Huang

address: Academia Sinica. 128 Sec. 2

country: Taiwan

institute: Institute of Molecular Biology

summary:
A880 has pop2 deletion and a very slow-growth phenotype with glycerol as carbon source. A880 transformed with 2-micron plasmids encoding STM1 can grow robustly on glycerol plates. The Arg237 on Stm1p can be methylated by Hmt1p. A880 transformed with 2-micron plasmids encoding the Stm1p R237K mutant retain the slow-growth phenotype on glycerol plates.
We used microarrays to assess the transcription profiles of A880, and A880 transformed with STM1 or STM1 R237K mutant. The goal is to identify genes that are up- or down-regulated in the presence of STM1 R237K mutant but not in the presence of the wild type STM1.

overall_design: BY4741 (wild type control), A880 (BY4741 with pop2 deletion), A880STM1 (A880 transformed with STM1) and A880STM1K (A880 transformed with STM1 carrying an Arg237 to lysine substitution) cells were grown in SC medium with glucose as carbon source to early log phase. The cells were shifted to SC medium containing 2% glycerol and incubated for 12 hours before harvesting.  Total RNAs were extracted for microarray analysis. Two data sets were generated from separate experiments and cell cultures.

first: Yu-Chen

first: Ming

last: Tam


title: Mutations in cohesin-associated genes impair protein translation

status: Public on Apr 01 2011

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: The cohesin protein complex is well known for playing a role in chromosome segregation. However, it has additional less understood roles in transcription, DNA repair, and chromosome condensation. Mutants in two yeast orthologues (Eco1 and Scc2) of human cohesinopathy disease alleles were examined by transcriptional profiling in response to perturbation of the transcriptional program by amino acid starvation.

overall_design: Two cohesin mutants were compared to wt in a time course of amino acid starvation consisting of 4 time points, 3 replicates of each, for a total of 36 samples.

first: Tania

last: Bose

first: Kenny

last: Lee

first: Shuai

last: Lu

first: Bethany

last: Harris

first: Alexander

last: Garrett

first: William

last: McDowell

first: Karin

last: Zueckert

first: Scarlett

last: Gard

first: Jennifer

last: Gerton


title: Dot1 and Histone H3K79 Methylation in Natural Heterochromatic and HML/HMR Silencing

status: Public on Feb 12 2011

summary: Dot1 is a methyl transferase that has been shown through a reporter gene to be involved in position effect variegation of gene expression in heterochrmatic regions such as telomeres and the mating type loci in yeast. This study examines the effect of mutation of DOT1 and two other proteins involved in H3K79 methylation, SWI4 and ARD1, on gene expression relative to wt cells.

overall_design: Wt, and mutants of Dot1, Swi4, or Ard1 were grown, in duplicate, in liquid media to midlog phase for extraction of RNA and comparison of gene expression on Affymetrix arrays.

first: Yoh-Hei

last: Takahashi

first: Julia

last: Schulze

first: Jessica

last: Jackson

first: Thomas

last: Hentrich

first: Sue

last: Jaspersen

first: Michael

last: Kobor

first: Ali

last: Shilatifard


title: System level characterization of galactose mutants of yeast

status: Public on Mar 31 2011

city: Gothenburg

first: Kuk-Ki

last: Hong

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: Adaptively evolved mutants of yeast on galactose were characterized by feremtation physiology and tools from systems biology.

overall_design: Three evolved mutants of yeast grown on aerobic batch with galactose as carbon source

first: K

first: W

last: Vongsangnak

first: G

last: Vemuri

first: J

last: Nielsen


title: Expression data from yeast strain VIN13 in small and large scale alcoholic fermentations.

status: Public on Mar 02 2011

first: Debra

last: Rossouw

summary: Transcriptomic analyses of fermenting yeast are increasingly being carried out under small scale simulated winemaking conditions. It is not known to what degree data generated from such experiments are a reflection of transcriptional processes in large-scale commercial fermentation tanks. In this experiment we set out to determine the effect of scale, or fermentation volume, on the transcriptional respone of wine yeast strains. Parallel fermentations were carried out in laboratory fermentation vials and commercial fermentation tanks using the same wine media and inoculated yeast strain. Comparative transcriptomic analyses were carried out at three time points during alcoholic fermentation.

overall_design: Fermentations were carried out in Chardonnay wine must in triplicate for both the lab-scale (80ml) and commercial scale (300L) fermentations. Sampling of yeast for RNA extractions were performed at day 2 of fermentation (during the exponential growth phase of the yeast cells), and again at day 5 (early stationary growth phase) and day 10 (late stationary growth phase) of fermentation.

first: Florian

last: Bauer


title: Neonatal beta cells lack the specialized metabolic phenotype of mature beta cells

status: Public on Feb 22 2011

city: Boston

first: Susan

last: Bonner-Weir PhD

state: MA

address: One Joslin Place

department: Section on Islet Cell and Regenerative Biology

institute: Joslin Diabetes Center

summary:
Fetal and neonatal beta cells have poor glucose-induced insulin secretion and only gain robust glucose responsiveness several weeks after birth. This unresponsiveness may be due to a generalized immaturity of the metabolic pathways normally found in beta cells.
Gene expression profile of neonatal (1 day old) and young adult (6 weeks old) Sprague-Dawley rat islets were evaluated and compared.

overall_design: Frozen sections were obtained from pancreases of neonatal (1 day old) and young adult (6 weeks old) Sprague-Dawley rats. The beta cell enriched cores of the islets were excised using laser capture microdissection. RNA was extracted, amplified and subjected to microarray analysis.

first: Agnes

last: Jermendy

first: Elena

last: Toschi

first: Tandy

last: Aye

first: Angela

last: Koh

first: Cristina

last: Aguayo-Mazzucato

first: Arun

last: Sharma

first: Gordon

last: Weir

first: Dennis

last: Sgroi

last: Bonner-Weir


title: Chronological Aging of Yeast in the Absence of Caloric Restriction: Cell Immobilization Uncouples Reproduction from Metabolism

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary:
Studies using yeast have advanced our understanding of both replicative and chronological aging, leading to the discovery of longevity genes that have homologues in higher eukaryotes. Chronological lifespan in yeast is conventionally defined as the lifespan of a non-dividing cell. To date, this parameter has only been estimated under calorically restricted (CR) conditions, mimicked by starvation. Since post-mitotic cells in higher eukaryotes are rarely calorically-restricted, we sought to develop an alternative experimental system where non-dividing yeast would age chronologically, in the presence of excess nutrients. We report here on a system wherein alginate-encapsulated yeast are packed in a pH- and temperature-controlled bioreactor, then continuously fed non-limiting substrate for extended periods of time. We present demographic, physiological and genomic evidence indicating that after ~120 hrs, immobilized cells cease dividing, remain metabolically very active and retain >95% viability for periods of 17 days. Over the same time interval, starved planktonic cells, cultured using the same media, and also controlled for temperature and pH, retained < 1 % viability in both aerobic and anaerobic cultures,. Unlike planktonic yeast, continuously-fed immobilized cells hyper-accumulate glycogen. FACS analysis of SYTOX green-stained yeast confirms that immobilized cells completely arrest within 5 days of culture, and unlike starving planktonic cells, remain free thereafter of replicative stress and are non-apoptotic. This unusual state is supported by a global gene expression profile that is stable over time, repeatable across replicate experiments, and altogether distinct from planktonic cells cultured in the presence and absence of limiting nutrients. DNA expression profiling, performed here for the very first time on immobilized cells, reveals that glycolytic genes and their trans-acting regulatory elements are upregulated, as are genes involved in remodeling the cell wall and resisting stress; by contrast, many genes that promote cell cycle progression and carry out oxidative metabolism are repressed. Stress resistance transcription factor MSN4 and its upstream effector RIM15 are conspicuously upregulated in the immobilized state, suggesting that nutrient-sensing pathways may play a role in cell viability and longevity when yeast are immobilized and placed in prolonged culture under calorically-unrestricted conditions. The cell cycle arrest in the immobilized state is mediated by RIM 15. Over the time-course of our experiments, well-fed, non-diving immobilized cells do not appear to age.

Keywords: comparison of growth states and a time course of immobilized cells

overall_design: Nine growth conditions or time points with two to four replicates each

first: Saisubramanian

last: Nagarajan

first: Arle

last: Kruckeberg

first: Morgan

last: Hamilton

first: Ryan

last: Summers

first: Timothy

last: Taylor

first: Frank

last: Rosenzweig


title: Expression profile of ypr045c∆ mutant

status: Public on Feb 23 2011

first: Sonia

last: Jimeno

state: Seville

address: Americo Vespucio s/n

department: Molecular biology

summary: We report a new protein complex with a role in transcription elongation that is formed by Ypr045c (Thp3) and the Csn12 component of the COP9-signalosome. Thp3-Csn12 is recruited to transcribed genes. Their mutations suppress the gene expression defects of mutants of the THO complex involved in mRNP biogenesis and export and show defects in mRNA accumulation. In vivo transcription elongation impairment of thp3∆ mutants is shown by reduction of RNAPII recruitment throughout an active gene and in transcript run on analysis performed in G-less systems. This new complex establishes a novel link between transcription and mRNA processing.

overall_design: Tthree repeats of the wild type control and three of the ypr045c∆ mutant (BY4741 background).

first: Andrés

last: Aguilera


title: Expression data from yeast strain VIN13 overexpressing the transcription factor SOK2

status: Public on Feb 11 2011

city: Stellenbosch

first: Debra

last: Rossouw

summary:
Industrial wine yeast strains are geno- and phenotypically highly diversified, and have adapted to the ecological niches provided by industrial wine making environments. These strains have been selected for very specific and diverse purposes, and the adaptation of these strains to the oenological environment is a function of the specific expression profiles of their genomes. It has been proposed that some of the primary targets of yeast adaptation are functional binding sites of transcription factors (TF) and the transcription factors themselves. Sequence divergence or regulatory changes related to specific transcription factors would lead to far-reaching changes in overall gene expression patterns, which will in turn impact on specific phenotypic characteristics of different yeast species/ strains. Variations in transcriptional regulation between different wine yeast strains could thus be responsible for rapid adaptation to different fermentative requirements in the context of commercial wine-making. In this study, we compare the transcriptional profiles of five different wine yeast strains in simulated wine-making conditions: Comparative analyses of gene expression profiles in the context of TF regulatory networks provided new insights into the molecular basis for variations in gene expression in these industrial strains. We also show that the metabolic phenotype of one strain can indeed be shifted in the direction of another by modifying the expression of key transcription factors.
SOK2 was one target transcription factor identified in this study. This expression factor was overexpressed in order to validate our hypotheses that altered expression levels of key transcription factors could shift metabolism in a directed, predicted manner.

overall_design: Fermentations were carried out in synthetic wine must in triplicate for both the control VIN13 strain and the SOK2 overexpressing strain. Sampling for RNA extractions were performed at day 2 of fermentation, during the exponential growth phase of the yeast cells.

first: Florian

last: Bauer


title: Phosphoglycerate mutase knock-out mutant Saccharomyces cerevisiae: physiological investigation and transcriptome analysis

status: Public on Jan 24 2011

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: Characterize the gpm1 mutant growth on dual substrate of ethanol and glycerol

overall_design: We used microarrays to detail the responses of the gpm1 mutant compare with reference

first: Marta

last: Papini

first: Gionata

last: Scalcinati

first: Verena

last: Siewers

first: Jens

last: Nielsen


title: Profiling oxidative stress in Saccharomyces cerevisiae by oxidation of transcription factor Swi6p

status: Public on Jan 31 2011

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

summary:
Cell cycle sensing of oxidative stress in Saccharomyces cerevisiae by oxidation of a specific cysteine residue in the transcription factor Swi6p.
Yeast cells begin to bud and enter S phase when growth conditions are favourable during G1 phase. When subjected to oxidative stress, cells arrest at G1 delaying entry into the cell cycle allowing repair of cellular damage. Hence, oxidative stress sensing is coordinated with the regulation of cell cycle. We identified a redox sensing cysteine residue in the cell-cycle regulator of Saccharomyces cerevisiae, Swi6p, at position 404. Mutation of Cys404 to alanine abolished the ability of the cells to arrest at G1 upon treatment by lipid hydroperoxide. By constructing a truncated form of Swi6p, the Cys404 residue was found to be oxidised when cells were subjected to the oxidant. Furthermore, microarray analysis revealed that mutation of Cys404 to alanine led to loss of suppression of G1-cyclins CLN1 and PCL1 when the cells were exposed to lipid hydroperoxide. In conclusion, oxidation of Cys404 serves as a molecular sensor of oxidative stress and inhibits entry into the cell cycle by suppression of G1-cyclin expression.

overall_design: We used a gene expression approach to assess the involvement of Cys404 in oxidative stress by mutating this residue to alanine in order to study whether it contributes to Swi6p, a transcriptional factor, function for redox regulation of the cell cycle. Wild type, swi6-deletant, and swi6 C404A-mutated yeast cells were treated with either linoleic acid hydroperoxide (LoaOOH) or control. Three replicates per group/treatment.

first: Joyce

last: Chiu

first: Carole

last: Tactacan

first: Ian

last: Dawes


title: Transcriptional profile analysis of Saccharomyces cerevisiae in second fermentation

status: Public on May 31 2011

city: LOGROÑO

first: Vanessa

last: Penacho

state: LA RIOJA

address: c/ Madre de Dios, 51

department: Oenology & Viticulture

institute: ICVV/CSIC

summary:
Second fermentation in a bottle supposes such specific conditions that undergo yeasts to a set of stress situations like high ethanol, low nitrogen, low pH or sub-optimal temperature. Also, yeast have to grow until 1 or 2 generations and ferment all sugar available while they resist increasing CO2 pressure produced along with fermentation. Because of this, yeast for second fermentation must be selected depending on different technological criteria such as resistance to ethanol, pressure, high flocculation capacity, and good autolytic and foaming properties.

All of these stress factors appear sequentially or simultaneously, and their superposition could amplify their inhibitory effects over yeast growth. Considering all of the above, it has supposed interesting to characterize the adaptive response of commercial yeast strain EC1118 during second-fermentation experiments under oenological/industrial conditions by transcriptomic profiling. We have pointed ethanol as the most relevant environmental condition in the induction of genes involved in respiratory metabolism, oxidative stress, autophagy, vacuolar and peroxisomal function, after comparison between time-course transcriptomic analysis in alcoholic fermentation and transcriptomic profiling in second fermentation. Other examples of parallelism include overexpression of cellular homeostasis and sugar metabolism genes. Finally, this study brings out the role of low-temperature on yeast physiology during second-fermentation.

overall_design: S. cerevisiae EC1118 pre-adapted to ethanol cells and sucrose (20 g/L) were added to 20 L of base wine (Cavas Freixenet, Sant Sadurní D’Anoia, Spain). Complete volume was bottled with 350 mL each one. All were sealed and incubated in static conditions at 16ºC for approximately 40 days after tirage. Three samples were taken during the process for transcriptional study of the physiological adaptation of yeast cells to industrial second fermentation conditions. A sample corresponding to exponential-growth phase under unstressed conditions (in YPD at 28ºC) was used as an external reference. Three timepoints from second-fermentation were monitored and three biological replicates from each timepoint were analyzed.

first: Eva

last: Valero

first: Ramon

last: Gonzalez


title: Identification of histone codes and crosstalk in fission yeast

status: Public on Jan 05 2011

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

institute: Karolinska Inst

type: Genome binding/occupancy profiling by array

summary: Aims: To map histone modifications with unprecedented resolution both globally and locus-specifically, and to link modification patterns to gene expression. Materials & methods: Using correlations between quantitative mass spectrometry and chromatin immunoprecipitation/microarray analyses, we have mapped histone post-translational modifications in fission yeast (Schizosaccharomyces pombe). Results: Acetylations at lysine 9, 18 and 27 of histone H3 give the best positive correlations with gene expression in this organism. Using clustering analysis and gene ontology search tools, we identified promoter histone modification patterns that characterize several classes of gene function. For example, gene promoters of genes involved in cytokinesis have high H3K36me2 and low H3K4me2, whereas the converse pattern is found ar promoters of gene involved in positive regulation of the cell cycle. We detected acetylation of H4 preferentially at lysine 16 followed by lysine 12, 8 and 5. Our analysis shows that this H4 acetylation bias in the coding regions is dependent upon gene length and linked to gene expression. Our analysis also reveals a role for H3K36 methylation at gene promoters where it functions in a crosstalk between the histone methyltransferase Set2KMT3 and the histone deacetylase Clr6, which removes H3K27ac leading to repression of transcription. Conclusion: Histone modification patterns could be linked to gene expression in fission yeast.

overall_design:
The combined microarray strategy in this study was performed essentially as outlined in Wiren et al, 2005.
We used the S. pombe spotted microarrays (Eurogentec, Belgium). For histone modification maps, ChIP-CHIP method was essentially used according to Robyr and Grunstein (2003). Antibodies against H3K9Ac, H3K14Ac, H3K18Ac, H3K23Ac, H3K27Ac, H3K56Ac , H4K5Ac, H4K8Ac, H4K12Ac, H4K16Ac (Suka, Suka et al. 2001; Xu, Zhang et al. 2007) and H3K36Me2 (Millipore) were used. The histone ?H3cter? antibody (Upstate) was used for ChIP according to Wiren et al, 2005. Spotted microarrays were hybridized using Cy3 and Cy5. For normalization of the data (in Series supplementary file) all the different modification channels were divided by average input value and then divided by ?H3cter? value to correct the histone loss calculations followed by 50th percentile normalization. For our cluster analysis we have used variance normalization method. To reduce the variations between different sample preparations we used same extracts for all IPs. The standard S.pombe laboratory strain Hu303(972h-) was used for this study. For Wt, set1D and set2D expression studies we have used Affymetrix genechip yeast Genome 2.0 microarray. Wt, set1D and set2D cells were grown to mid logarithmic phase (5*10 power 6 cells/ml) in rich medium. RNA was extracted and hybridized according to Affymetrix protocol. For each expression profile at least two independent cultures were analyzed with microarray experiments.

first: Indranil

last: Sinha

first: Luke

last: Buchanan

first: Michelle

last: Rönnerblad

first: Carolina

last: Bonilla

first: M

last: Durand-Dubief

first: Andrej

last: Shevchenko

first: Michael

last: Grunstein

first: Francis

last: Stewart


title: Expression data from oxidant treated yeast

status: Public on Dec 30 2010

city: Memphis

first: Thomas

middle: R

last: Sutter

state: TN

address: 3774 Walker Ave.

institute: University of Memphis

summary:
Yeast transcription factor Yap1 mediates adaptive response against H2O2 and the cystein thiol reactive Michael acceptor, N-ethylmaleimid (NEM) and acrolein.  The response against H2O2 was found to be distinct from that against NEM and acrolein.
We used microarray experiment to identify two subsets of Yap1-dependent genes that correspond to these two adaptive responses.

overall_design: Wild-type yeast BY4741 cells were grown in early exponential phase and treated with H2O2, NEM, or acrolein.  RNAs were then extracted and hybridized on Affymetrix microarrays.

first: Xiaoguang

last: Ouyang

first: Quynh

middle: T

last: Tran


title: Gene expression response to the antifungal compound plakortide F acid in S. cerevisiae

status: Public on Jan 28 2011

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

summary:
Plakortide F acid (PFA), a marine-derived polyketide endoperoxide, exhibits strong inhibitory activity against the opportunistic fungal pathogens Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus.  In the present study, transcriptional profiling coupled with mutant and biochemical analyses were conducted using the model organism Saccharomyces cerevisiae, to investigate the mechanism of action of this compound.  PFA elicited a transcriptome response indicative of a Ca2+ imbalance, affecting the expression of genes known to be responsive to altered cellular calcium levels.  Several additional lines of evidence obtained supported a role for Ca2+ in PFA's activity.  First, mutants lacking calcineurin and various Ca2+ transporters including pumps (Pmr1 and Pmc1) and channels (Cch1 and Mid1) showed increased sensitivity to PFA.  In addition, the calcineurin inhibitors FK506 and cyclosporine A strongly enhanced PFA activity in wild-type cells.  Furthermore, PFA activated the transcription of a lacZ reporter driven by the calcineurin-dependent response element.  Finally, elemental analysis indicated a significant increase in intracellular calcium levels in PFA-treated cells.  Collectively, our results demonstrate that PFA mediates its antifungal activity by perturbing Ca2+ homeostasis, thus representing a potentially novel mechanism distinct from that of currently used antifungal agents.
DNA microarray analysis of gene expression response to the antifungal compound plakortide F acid in yeast

overall_design: S. cerevisiae S288C cells at OD 0.2 were treated with either plakortide F acid (PFA) at IC50 concentration (0.62 ug/ml), or solvent (0.25% DMSO), allowed to grow to OD 0.5, then harvested and frozen.  Three biological replicate samples were analyzed for each treatment.

middle: K


title: Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

status: Public on Dec 22 2010

first: wanwipa

last: vongsangnak

summary:
The needs for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where selective pressure is applied to a partially genetically engineered strain to confer a desirable phenotype. The exact genetic modification or resulting genotype that leads to the improved phenotype is often not identified or understood to enable further metabolic engineering. In this work we establish proof-of-concept that whole genome high-throughput sequencing and annotation can be used to identify single nucleotide polymorphisms (SNPs) between Saccharomyces cerevisiae strains S288c and CEN.PK113-7D. The yeast strain S288c was the first eukaryote sequenced, serving as the reference genome for the Saccharomyces Genome Database, while CEN.PK113-7D is a preferred laboratory strain for industrial biotechnology research. A total of 13,787 high-quality SNPs were detected between both strains (reference strain: S288c). Considering only metabolic genes (782 of 5,873 annotated genes),  a total of 219 metabolism specific SNPs are distributed across 158 metabolic genes, with 85 of the SNPs being non-silent (e.g., encoding amino acid modifications). Amongst metabolic SNPs detected, there was pathway enrichment in the galactose uptake pathway (GAL1, GAL10) and ergosterol biosynthetic pathway (ERG8, ERG9). Physiological characterization confirmed a strong deficiency in galactose uptake and metabolism in S288c compared to CEN.PK113-7D, and similarly, ergosterol content in CEN.PK113-7D was significantly higher in both glucose and galactose supplemented cultivations compared to S288c. Furthermore, DNA microarray profiling of S288c and CEN.PK113-7D in both glucose and galactose batch cultures did not provide a clear hypothesis for major phenotypes observed, suggesting that genotype to phenotype correlations are manifested post-transcriptionally or post-translationally either through protein concentration and/or function. With an intensifying need for microbial cell factories that produce a wide array of target compounds, whole genome high-throughput sequencing and annotation for SNP detection can aid in better reducing and defining the metabolic landscape. This work demonstrates direct correlations between genotype and phenotype that provides clear and high-probability of success metabolic engineering targets. The genome sequence, annotation, and a SNP viewer of CEN.PK113-7D are deposited at www.sysbio.se/cenpk.

Keywords: Two strains and two different carbon sources

overall_design: Two conditions (glucose and galactose) with two biological replicates for S. cerevisiae strains S288c and CEN.PK113-7D

first: J

last: Otero*

first: W

last: Vongsangnak*

last: Asadollah

first: R

last: Olivares-Hernandes

last: Maury

first: L

last: Farinelli

last: Barlocher

last: Schalk

first: A

last: Clark

last: Nielsen


title: Transcriptional response of Sacchromyces cerevisiae to change in oxygen provision

city: VTT

first: Eija

last: Rintala

country: Finland

institute: VTT Technical Research Centre of Finland

summary: In industrial fermentations of Saccharomyces cerevisiae, transient changes in oxygen concentration commonly occur and it is important to understand the behaviour of cells during these changes. Saccharomyces cerevisiae CEN.PK113-1A was grown in glucose-limited chemostat culture with 1.0% and 20.9% O2 in the inlet gas (D= 0.10 /h, pH5, 30C). After steady state was achieved, oxygen was replaced with nitrogen and cultures were followed until new steady state was achieved. The overall responses to anaerobic conditions of cells initially in different conditions were very similar. Independent of initial culture conditions, transient downregulation of genes related to growth and cell proliferation, mitochondrial translation and protein import, and sulphate assimilation was seen. In addition, transient or permanent upregulation of genes related to protein degradation, and phosphate and amino acid uptake was observed in all cultures. However, only in the initially oxygen-limited cultures was a transient upregulation of genes related to fatty acid oxidation, peroxisomal biogenesis, oxidative phosphorylation, TCA cycle, response to oxidative stress, and pentose phosphate pathway observed. Furthermore, from the initially oxygen-limited conditions, a rapid response around the metabolites of upper glycolysis and the pentose phosphate pathway was seen, while from the initially fully aerobic conditions, a slower response around the pathways for utilisation of respiratory carbon sources was observed.

overall_design: Time series analysis starting from two (1% and 20.9%) levels of oxygen provision. Seven timepoints from both time series and two biological replicates from each timepoint were analysed.


title: Comparative transcriptome analysis of yeast expressing the fungal desaturases

status: Public on Dec 27 2010

summary:
To study how the presence of PUFAs influences central cellular processes, and in order to perform lipidome, transcriptome and molecular studies we decided to use yeast as a model organism. We therefore co-expressed Δ12-desaturase and Δ6- desaturase genes from Mucor rouxii in S. cerevisiae with the objective to obtain a yeast strain that contains PUFAs, especially linoleic acid (LA, C18:2Δ9,12) and γ-linolenic acid (GLA, C18:3Δ6,9,12), in its membranes.
The resulting yeast strain was analyzed in details in order to quantify the fluxes through the fatty acid biosynthetic pathways and the genome-wide transcriptional response to production of LA and GLA.

overall_design: Three recombinant yeasts were constructed and grown in glucose-limited condition. Steady-state cultures were harvested for RNA extraction and hybridization on Affymetrix microarrays. Comparative transcriptome analysis between S. cerevisiae recombinants expressing M. rouxii D12-desaturase (D12) and co-expressing D12-desaturase and D6-desaturase genes (D126) and the reference strain (REF) was implemented.

first: Rawisara

last: Ruenwai

first: Andrea

last: Neiss

first: Kobkul

last: Laoteng

first: Wanwipa

last: Vongsangnak

first: Arastoo

last: Dalfard

first: Supapon

last: Cheevadhanarak

first: Dina

last: Petranovic

first: Jens


title: Expression data from wild-type FY4 and the BAS1-deletion strain

status: Public on Dec 01 2010

city: Zurich

first: Uwe

last: Sauer

address: Auguste-Piccard-Hof 1

department: Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

summary: The impact on mRNA expression of the transcription factors Bas1, Pho2, Gcn4 and Gcr2p  was investigated in the corresponding deletion strains during exponential growth in glucose minimal media batch cultures.

overall_design: All strains were grown in the same media and harvested during exponential growth, at the same cell density, for gene expression analysis. Gene expression analysis of each deletion mutant can be compared relative to the reference strain FY4. Three replicates each strain.

first: Sarah-Maria

last: Fendt

first: Ana

last: Oliveira


title: Expression data from wild-type FY4 and the PHO2-deletion strain

overall_design: All strains were grown in the same media and harvested during exponential growth, at the same cell density, for gene expression analysis. Gene expression analysis of each deletion mutant can be compared relative to the reference strain FY4. Three replicates for wild-type and two replicates for the Pho2 deletion mutant.


title: Expression data from wild-type FY4 and the GCN4-deletion strain


title: Transcriptional profiling of fetal hypothalamic TRH neurons

status: Public on May 27 2011

city: Cuernavaca

first: Leonor

last: Perez-Martinez

state: Morelos

address: Avenida Universidad 2001

department: Medicina Molecular y Bioprocesos

country: Mexico

institute: University of Mexico

summary:
During murine hypothalamic development, different neuroendocrine cell phenotypes are generated in overlapping periods; this suggests that cell-type specific developmental programs operate to achieve complete maturation. A balance between programs that include cell proliferation, cell cycle withdrawal as well as epigenetic regulation of gene expression characterizes neurogenesis. Thyrotropin releasing hormone (TRH) is a peptide that regulates energy homeostasis and autonomic responses. To better understand the molecular mechanisms underlying TRH neuron development, we performed a genome wide study of its transcriptome during fetal hypothalamic development.
In primary cultures, TRH cells constitute 2% of the total fetal hypothalamic cell population. To purify these cells, we took advantage of the fact that the segment spanning –774 to +84 bp of the Trh gene regulatory region confers specific expression of the green fluorescent protein (GFP) in the TRH cells. Transfected TRH cells were purified by fluorescence activated cell sorting, various cell preparations pooled, and their transcriptome compared to that of GFP- hypothalamic cells. TRH cells undergoing the terminal phase of differentiation, expressed genes implicated in protein biosynthesis, intracellular signaling and transcriptional control. Among the transcription-associated transcripts, we identified the transcription factors Klf4, Klf10 and Atf3, which were previously uncharacterized within the hypothalamus.
To our knowledge, this is the first report identifying transcripts with a potentially important role during the development of a specific hypothalamic neuronal phenotype. This genome-scale study forms a rational foundation for identifying genes that might participate in the development and function of hypothalamic TRH neurons.

overall_design: Hypothalamic primary cultures were prepared from E17 rat embryos. Twenty-four hours after seeding, cells were transfected using the minimal Trh promoter (-776/+84 bp) upstream of the GFP. Forty-eight hours after transfection, cells were trypsinized and subjected to FACS. TRH+ cells were purified from a pool of five 60-mm dishes using the FACS Vantage (Becton Dickinson, San Jose, CA) and the exclusion method at high speed (60 µl/min). In general, 20,000 GFP+ cells were purified from 5 X 106 cells. The microarray analysis was performed as described in the Affymetrix expression analysis technical manual (http://www.affymetrix.com). Total RNA (10 µg) was extracted from three different cell populations: i) sorted TRH-GFP+ cells (GFP+); ii) TRH-GFP+ and GFP- mixed cells (GFP+/-) passed through the FACS but not sorted, and iii) non transfected cells (NT). To obtain a sufficient amount of RNA for each cell population, the number of independent experiments pooled for the GFP+ sample was higher than for the other samples. Therefore, a pool of six independent experiments was used to prepare total RNA from the GFP+ and three independent experiments for GFP+/- or NT cells.

first: Magdalena

last: Guerra-Crespo

first: Carlos

last: Pérez-Monter

first: Sarath

last: Chandra Janga

first: Santiago

last: Castillo-Ramírez

first: Rosa

last: Gutierrez-Rios

first: Patricia

last: Joseph-Bravo

last: Pérez-Martínez

first: Jean-Louis

last: Charli


title: Building Prognostic Models for Breast Cancer Patients Using Clinical Variables and Gene Expression Signatures

status: Public on Oct 25 2010

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Our findings indicate that the integration of expression signatures and clinicopathological factors can better determine the individual risk of recurrence for newly diagnosed patients with lymph-node negative ER-positive breast cancer. Models incorporating other variables yet to be discovered will be needed to obtain robust prognostic models for ER-negative and HER2-positive breast cancer patients.

overall_design: A large data set was created by combining five different publicly available microarray datasets of node-negative breast cancer patients treated with local therapy only. The microarray gene expression data was combined using the batch effect adjustment by the Distance Weighted Discrimination method.

first: Cheng

last: FAN

first: Aleix

last: Prat Aparicio

first: Joel

last: Parker

first: Yufeng

last: Liu


title: Experimental systems biology: Lessons from an integrated, multi-laboratory study in yeast

city: Kgs. Lyngby

first: Jie

last: Zhang

address: Kemitorvet 220

department: CFB

country: Denmark

institute: Technical University of Denmark

summary: We undertook an inter-laboratory effort to generate high-quality quantitative data for a very large number of cellular components in yeast using transcriptome and metabolome analysis. We ensured the high-quality of the experimental data by evaluating a wide range of sampling and measurement techniques. The data were generated for two different yeast strains, each growing under two different growth conditions and based on integrated analysis of the high-throughput data we hypothesize that differences in growth rates and yields on glucose between the two strains are due to differences in protein metabolism.

overall_design: Two yeast strains, YSBN2 and CEN.PK 113-7D, were grown in aerobical batch as well as glucose-limited chemostat (dilution rate 0.1h-1) in biological triplicates

first: André

last: Canelas

first: Nicola

last: Harrison

first: Alessandro

last: Fazio

first: Juha-Pekka

last: Pitkänen

first: Joost

last: van den Brink

first: Barbara

last: Bakker

first: Lara

last: Bogner

first: Jildau

last: Bouwman

first: Juan

middle: I

last: Castrillo

first: Ayca

last: Cankorur

first: Pramote

last: Chumnanpuen

first: Pascale

last: Daran-Lapujade

first: Duygu

last: Dikicioglu

first: Karen

last: van Eunen

first: Jennifer

middle: C

last: Ewald

first: Joseph

last: Heijnen

first: Betul

last: Kirdar

first: Ismo

last: Mattila

first: Femke

last: Mensonides

first: Anja

last: Niebel

first: Merja

last: Penttilä

first: Jack

last: Pronk

first: Matthias

last: Reuss

first: Laura

last: Salusjärvi

last: Sauer

first: David

last: Sherman

first: Martin

last: Siemann-Herzberg

first: Hans

last: Westerhoff

first: Johannes

last: de Winde

first: Dina

last: Petranovic

first: Stephen

middle: G

last: Oliver

first: Christopher

last: Workman

last: Zamboni

first: Jens

last: Nielsen


title: Potential Molecular Basis for Impaired Collateral Artery Growth in the Spontaneously Hypertensive Rat

status: Public on Dec 15 2010

city: Indianapolis

first: Joseph

last: Unthank

state: IN

address: 1001 West Tenth St

country: USA

institute: Indiana University

summary:
Analysis of global gene expression in mesenteric control and collateral arteries was used to investigate potential molecules, pathways  and mechanisms responsible for impaired collateral growth in the Spontaneously Hypertensive rat (SHR).  A fundamental difference was observed in the overall gene expression pattern in SHR vs. Wistar Kyoto (WKY) collaterals (only 6% of the genes altered in collaterals were similar).  IPA analysis identified major differences between WKY and SHR in networks and biological functions related to cell growth and proliferation and gene expression.  Canonical pathways identified by IPA in WKY but not SHR included nitric oxide and renin angiotensin system signaling.  The angiotensin type 1 receptor (AT1R) exhibited up-regulation in WKY collaterals, but down-regulation in SHR; pharmacological blockade of the AT1R with losartan prevented collateral luminal expansion in WKY.
In SHR control arteries, several mechano-sensitive and redox-dependent transcription regulators were down-regulated including Jun (-5.2X, P=0.02), Egr-1 (-4.1X, P=0.01), and NFkB1 (-1.95X, P=0.04).   Predicted binding sites for NFkB and AP-1 were present in the genes altered in WKY but not SHR collaterals.    Immunostaining demonstrated increased NFkB nuclear translocation in WKY but not SHR collaterals, and in collaterals of SHR treated with apocynin to restore a normal redox status.  Based upon these results, we propose redox-dependent modulation of mechano-sensitive transcription factors as a mechanism to explain, at least in part, the fundamental differences in collateral gene expression between WKY and SHR and the impairment of collateral growth during chronic oxidative stress.

Key words: arteriogenesis, microarray analysis, peripheral vascular disease, gene expression

overall_design: two strains: two vessel types

middle: L

first: Jeanette

last: McClintick

first: Carlos

middle: A

last: Labarrer

first: Lang

last: Li

first: Matthew

last: DiStasi

first: Steven

last: Miller


title: cAMP/PKA signaling balances respiratory activity with mitochondria dependent apoptosis via transcriptional regulation

status: Public on Nov 24 2010

city: Canterbury

first: Campbell

middle: William

last: Gourlay

state: Kent

address: Giles Lane

department: Biosciences

institute: University of Kent

summary: This data provides evidence that elevation of cAMP levels has a dramatic effect on the transcriptome of yeast cells, with particular emphasis on mitochondrial function and the promotion of ROS production

overall_design: S. cerevisiae cells lacking the high affinity phosphodiesterase PDE2or both PDE2 and the PKA subunit TPK3 were grown for 24h in rich media in the presence of 4mM exogensously added cAMP. 8 samples.

first: Jane

last: Leadsham


title: Expression data from wild-type and H2B K37A mutant yeast histones

status: Public on Sep 27 2010

first: Brian

last: Strahl

address: 120 Mason Farm Rd.   3060 Genetic Medicine, CB# 7260

department: Biochemistry and Biophysics

institute: University of North Carolina School of Medicine

summary: We identified lysine 37 of histone H2B as a novel site of histone lysine methylation in budding yeast.  Microarray analysis was performed to determine global changes in gene expression upon mutation of this lysine residue to a unmodifiable form.

overall_design: Histones were acid-extracted from asynchronously grown yeast expressing wild-type H2B or H2B harboring a K37A mutation.


title: O-glycosylation inhibition and O-glycosylation mutants

status: Public on Sep 30 2010

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

institute: Facultad de Farmacia (UCM)

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

overall_design: Refer to individual Series


title: Transcription profile of fission yeast

status: Public on Nov 04 2010

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

summary: Wild-type cells were cultured at 30 deg and cells were harvested. Total RNAs were purified from 3 populations.

overall_design: Microarray data of 3 samples were background-corrected with Mas5.0.

first: Hideki

last: Tanizawa

first: Osamu

last: Iwasaki

first: Atsunari

last: Tanaka

first: Joe

last: Capizzi

first: Ken-ichi

last: Noma


title: Equivalent mutations in the eight subunits of the chaperonin CCT produce dramatically different cell phenotypes.

status: Public on Jul 01 2010

city: Rehovot

first: Amnon

last: Horovitz

address: P.O.Box 26

department: Structural Biology

institute: Weizmann Institue of Science

summary:
The eukaryotic cytoplasmic chaperonin-containing TCP-1 (CCT) is a complex formed by two back-to-back stacked hetero-octameric rings that assists the folding of actins, tubulins and other proteins in an ATP-dependent manner.  Here, we decided to test the significance of the hetero-oligomeric nature of CCT for its function by introducing, in each of the eight subunits in turn, an identical mutation at a position involved in ATP binding and conserved in all the subunits, in order to establish the extent of ‘individuality’ of the various subunits.  Our results show that these identical mutations lead to dramatically different phenotypes.  For example, cells with the mutation in CCT2 have an excess of actin patches and are the only pseudo-diploid strain.  By contrast, cells with the mutation in CCT7 are the only ones to accumulate juxta-nuclear protein aggregates that may reflect the absence of stress response in this strain.  System-level analysis of the strains using RNA microarrays reveals connections between CCT and several cellular networks including ribosome biogenesis and TOR2 that help to explain the phenotypic variability observed
We used microarrays to reveal the differences in mRNA expression caused by the different mutations.

overall_design: All yeast strains were grown at 30 °C to OD(600)=0.5. Their total RNA was extracted and reverse transcribed to cDNA and transcribed back to RNA in the presence of biotinylated nucleotide analog. The biotinylated RNA was fragmented and hybridized to GenCHip Yeast Genome 2.0 array.

first: Maya

last: Amit

first: Sarah

last: Weisberg

first: Michal

last: Nadler-Holly

first: Ester

last: Feldmesser

first: Daniel

last: Kaganovich

first: Keith

last: Willison


title: Analysis of cohesin-dependent gene regulation in fission yeast

status: Public on Aug 13 2010

city: Bordeaux

first: Sonia

last: Dheur

address: 1, Rue Camille Saint-Saëns

department: Université Bordeaux 2

institute: IBGC CNRS UMR5095

summary: In addition to its well-know function in chromosome segregation, increasing evidence implicates cohesin in the control of gene expression. It has been previously reported that inactivation of the cohesin loader Mis4 in G1-arrested cells leads to the dissociation of cohesin from chromatin. We exploited this experimental situation to ask whether this loss of cohesin would affect gene expression on a genome-wide scale.

overall_design: Three independent inoculates (biological replicates) of cells carring either the thermosensitive mis4-367 or the wild-type mis4+ allele were grown at permissive temperature of 25°C. Cells were G1-arreted by titrating out the Cdc10 transcription factor by overexpression of the C-terminal fragment of its binding partner Res1, and then shifted for 2 hours at 37°C. Cells were harvested before and after the temperature shift to proceed to total RNA extraction.

first: Jean-Paul

last: Javerzat


title: Metabolic and transcriptional dynamics during the transition from carbon limitation to nitrogen limitation in Saccharomyces cerevisiae

status: Public on Jul 23 2010

city: Göteborg

first: Goutham

middle: N

last: Vemuri

address: Kemivagen 10

department: Chemical and Biological Engineering

institute: Chalmers University of Technology

summary:
Microorganisms are exposed to large variations in nutrient availability in nature. To cope with these variations and sustain growth, they maximize the utility of the available nutrients and adapt to nutritional deficiencies. We studied the transcriptional and metabolic dynamics in Saccharomyces cerevisiae in response to a gradual transition from glucose-limited growth to ammonia-limited growth under aerobic or anaerobic conditions.
Through exposing yeast to a gradual increase in glucose availability, we discovered new aspects of regulation that ensured a balanced metabolism of glucose and ammonia to sustain growth. This required tight coordination of metabolism with different cellular processes. The coordinated expression of the genes involved in key cellular processes implicated the role of signaling pathways mediated by Tor1, Pka1 and Hog1. This is in contrast to the rapid increase in glucose availability, when Snf1 appeared to be the key regulator. The results presented here provide clear insight into key cellular processes that are affected by nutrient limitation and have direct implications in further studies on genome-scale regulation of metabolism.

overall_design: Gene expression was measured in Saccharomyces cerevisiae as it was exposed to gradualy increasing amounts of glucose under aerobic or anaerobic conditions. Eight samples were collected in each case and gene expression measured.


title: Expression data of yeast with and without ribosomal protein Rpl12ap or Rpl12bp

city: Taipei

first: yu-chen

last: Huang

address: Academia Sinica. 128 Sec. 2

institute: Institute of Molecular Biology

summary: Ribosomal protein Rpl12p is encoded by duplicated genes RPL12A and RPL12B.  The gene products have identical primary protein sequence but reportedly cells harboring either Rpl12ap or Rpl12bp exhibit subtle functional differences. We use microarrays to screen for genes which might express differently in the presence of Rpl12ap or Rpl12bp.

overall_design: Total RNAs were extracted from W303 (wild type control), 6EA1 (cells with both RPL12A and RPL12B deletion), and 6EA1 transformed with high copy number plasmids carrying either RPL12A or RPL12B. These samples were hybridized to Affymetric microarrays, and up- or down-regulated genes were identified.

first: Huang

last: Yu-Chen

first: Tam

last: Ming F.


title: Wild type 3 hours exposure to 1 microM OGT2468

first: Javier

last: Arroyo

summary: We did transcription profiling on the effect of O-glycosylation inhibitor OGT2468 in Saccharomyces cerevisiae using strains SEY6210 (wild type). Yeast cells exposed to OGT2468 in YPD growth medium show a significant inhibition of mating, filamentation and induction of cell wall compensatory mechanism.

overall_design:
Three biological samples were analyzed for each condition, and a microarray experiment were carried out for each sample
1. absence of the drug (but the corresponding amount of DMSO 1%)
2. presence of 1 microMolar of OGT2468


title: Sodium arsenate response of wild type and slt2 deficient cells

status: Public on Jul 25 2010

first: Miguel

middle: Angel

last: Rodriguez-Gabriel

address: Campus Cantoblanco

department: Molecular Biology

institute: Universidad Autonoma de Madrid

summary:
Wild type (BY4741) Saccharomyces cerevisiae strains and their isogenic slt2 deficient counterparts, were treated for 2 hours with sodium arsenate 100 micromolar. Control (untreated) cells were also collected. Total RNA was extracted and analyzed by microarray hybridization.
The data obtained from these experiments allows to determine those genes that are regulated by Slt2 activity after arsenate treatment.

overall_design:
The experiments was designed as follows:
Four types of samples were used: untreated wild type cells, treated wild type cells, untreated slt2- cells and treated slt2- cells. 3 independent replicates were performed for each experiment.

first: Ana

middle: M

last: Matia


title: Expression data from Saccharomyces cerevisiae treated with Small Molecule Enhancers of Rapamycin (SMERs)

status: Public on Jun 28 2010

city: Los Angeles

first: Mariam

last: Aghajan

state: CA

address: 650 Charles E. Young Drive South, CHS 23-231

institute: UCLA

summary:
The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyper-activation of the mTOR pathway in human cancers, novel strategies to enhance TOR pathway inhibition are highly desirable.
We used a yeast-based high-throughput chemical genetic screen to identify small-molecule enhancers of rapamycin (SMERs) and used whole genome expression analysis to identify their mechanisms of action.

overall_design: We treated yeast individually with SMERs 1-5, rapamycin, or DMSO (solvent control) for 30 minutes prior to RNA extraction and hybridization on Affymetrix microarrays.  Expression profiles of SMER-treated samples were compared to that of DMSO (solvent control) and rapamycin-treated samples to identify gene expression signatures unique to SMER-treated samples.

first: Nao

last: Jonai

first: Karin

last: Flick

first: Fei

last: Fu

first: Manlin

last: Luo

first: Xiaolu

last: Cai

first: Ikram

last: Ouni

first: Nathan

last: Pierce

first: Xiaobo

last: Tang

first: Brett

last: Lomenick

first: Robert

last: Damoiseaux

first: Rui

last: Hao

first: Pierre

last: del Moral

first: Rati

last: Verma

first: Ying

last: Li

first: Cheng

first: Kendall

last: Houk

first: Michael

middle: E

last: Jung

first: Ning

last: Zheng

first: Lan

first: Raymond

middle: J

last: Deshaies

first: Peter

last: Kaiser

first: Jing


title: Microarray analysis of rat pulmonary artery smooth muscle cells before or after exposure to S-nitrosoglutathione (GSNO)

status: Public on Jun 01 2010

city: Boston

first: Andrea

middle: U

last: Steinbicker

address: 55 Fruit Street

institute: Massachusetts General Hospital

summary: Nitric oxide (NO) regulated pulmonary vascular function and structure, in part, via its effect on gene expression. We used microarrays to determine the up- and downregulated genes in rat pulmonary artery smooth muscle cells exposed to the NO donor S-nitrosoglutathione (GSNO) for 1, 2, and 4 hours.

overall_design: Two independent preparations of RPaSMCs were untreated or exposed to GSNO (100 μmol/L) for 1, 2, and 4 hours (h). RNA, cDNA, and labeled cRNA were generated. Fragmented cRNA was hybridized to Affymetrix rat U-34A GeneChips containing 8798 gene entries with the GeneChip Fluidics Station 450 and scanned with the GeneChip® Scanner 3000. Affymetrix GeneChip 5.0 software was used for data analysis according to Affymetrix protocols.

first: Heling

last: Liu

first: Kenneth

middle: D

last: Bloch


title: Yeast genomic expression patterns in response to deoxynivalenol

status: Public on May 31 2010

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

country: Japan

institute: National Food Rsearch Institute

summary:
The assessment of toxicity about deoxynivalenol (DON) using yeast gene expression comparison analysis. Two yeast strains, parental BY4743 and PTC1 mutant, were used for this study. SDS was used to raise the penetration of the yeast cell membrane.

Keywords: stress response

overall_design: Four conditions are compared with three replicates each. Each of the two strains was grown in either 0.01% SDS-containing YPD media or  0.01% SDS-containing YPD media with 25 ppm of deoxynivalenol.

first: Yumiko

last: Iwahashi


title: Expression data from wild-type FY4 and the TF-KOs BAS1-, PHO2-, GCN4- and GCR2-deletion strains

first: Uwe

last: Sauer

address: Auguste-Piccard-Hof 1

institute: ETH Zurich


title: Wild type 3 hours exposure to 0.1 microM OGT2468

first: Javier

last: Arroyo

overall_design:
Three biological samples were analyzed for each condition, and a microarray experiment were carried out for each sample
1. absence of the drug (but the corresponding amount of DMSO 0.1%)
2. presence of 0.1 microMolar of OGT2468


title: Expression data of β-subunit of Snf1 kinase in yeast Saccharomyces cerevisiae

status: Public on May 10 2010

first: Jie

last: Zhang

summary: The conserved Snf1/AMPK (AMP-activated protein Kinase) family is one of the central components in nutrient sensing and regulation of carbon metabolism in eukaryotes. It is also involved in several other processes such as stress resistance, invasive growth and ageing. Snf1 kinase is composed of a catalytic α-subunit Snf1, a regulatory γ-subunit Snf4 and one of three possible β-subunits, Sip1, Sip2 or Gal83. We used a systematic approach to study the role of the three β-subunits by analyzing all 7 possible combinations of β-subunit deletions together with the reference strain.

overall_design: 7 mutant strains together with 1 reference strain grown under glucose-limited condition with three biological replicates for each strain

first: J

first: L

last: Olsson

last: Nielsen


title: Effect of 52 weeks of chronic exposure to TCDD AND PCB126 on hepatic gene expression

status: Public on Jun 10 2010

city: Buffalo

first: Corie

last: Ellison

state: NY

address: 102 Farber hall

department: Pharmacology and Toxicology

institute: University at Buffalo

summary: This study investigates the effects of the aryl hydrocarbon receptor (AhR) ligands TCDD and PCB126  on hepatic gene expression in female sprague dawley rats. Rats were treated with toxicological equivalent doses of TCDD (100ng/kg/day) (Toxic equivalence factor (TEF) = 1.0), PCB126 (30ng, 300ng or 1000ng/kg/day) (TEF = 0.1) or a vehicle control of corn oil:acetone (99:1) 5 days a week for 52 weeks.

overall_design: There are 3 control chips and representing animals treated with vehicle control. There are 3 biological replicates (3 chips) for each treatment group (eg. TCDD, PCB126), each biological replicate is derived from 2 individual animals. A total of 15 chips were analyzed.

first: Bladimir

last: Ovando

first: Chad

last: Vezina

first: James

middle: R

last: Olson


title: Expression data of Saccharomyces cerevisiae treated with clioquinol

status: Public on May 21 2010

city: Beijing

first: Chenghua

last: Li

address: Qinghuayuan

department: Biological Sciences and Technology

institute: Tsinghua University

summary:
Clioquinol (CQ or iodochlorhydroxyquin, 5-chloro-7-iodo-8-hydroxyquinoline) is a hydrophobic chelator of copper, zinc, and iron. It was extensively used as an antibiotic for the treatment of diarrhea and skin infection in the mid-1900s, but then withdrawn because it was reported to be associated with subacute myelo-optic neuropathy (SMON) in Japan. Interest in this drug was recently revived as it was shown that CQ specifically kills cancer cells and significantly decreases Aβ level. Nevertheless, the underlying mechanisms of CQ’s drug effects and side effects are still unclear.

We used yeast, Saccharomyces cerevisiae, as a model to study how CQ affects molecular and cellular functions. Genechip analysis was utilized to examine the effect of CQ on gene expression at the genomic level.

overall_design: To study gene expression profiles of yeast treated with CQ, yeast cells were treated with CQ or DMSO for 5 hours and RNAs were extracted for microarray analysis.

first: Bing

last: Zhou


title: Gate-Keeping transcription through histone H3 K42, a novel site of methylation in the yeast nucleosome core

city: Baltimore

first: Edel

middle: Maria

last: Hyland

state: MD

address: 733 North broadway, Rm 320

department: Molecular Biology and Genetics

institute: Johns Hopkins School of MEdicine

summary: A new site of methylation was identified on histone H3 K42 in Saccharomyces cerevisiae. Mutations were engineered at this site to mimic either a constitutively modified state, K42L, or a constitutively unmodified state, K42Q in addition to an alanine substitution. K42A. The effects of these mutations on global transcription was monitored in yeast cells whose sole source of histone H3 was from a plasmid expressing these mutant proteins, and compared to that of an isogenic strain expressing the wild-type histone H3 protein from the same plasmid.

overall_design: Two biological replicates are included for each yeast strains expressing a specific histone H3 mutant. Three reference strains were also analyzed in the same way which expressed the wild-type histone protein. All strains were handled in the same way. A fresh culture of each strain was inoculated from a saturated overnight culture and grown to an OD A600 of approximately 0.7. Cells were harvested and total RNA extracted.

first: Henrik

last: Molina

first: Akhilesh

last: Pandey

first: Jef

last: Boeke


title: A Med15 - Hrp1 complex associates with fission yeast Mediator

status: Public on Sep 21 2010

city: Gothenburg

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

institute: Gothenburg University

summary:
The multiprotein Mediator complex is an important regulator of RNA polymerase II-dependent genes in eukaryotic cell. In contrast to the situation in many other eukaryotes, the conserved Med15 protein is not a stable component of Mediator isolated from fission yeast. We now demonstrate that Med15 exists in a protein complex together with Hrp1, an ATP-dependent chromatin remodeling protein. The Med15/Hrp1 subcomplex is not a component of the core Mediator complex, but can interact with the repressive L-Mediator conformation. Deletion of MED15 and HRP1 cause similar effects on global steady-state levels of mRNA, but only MED15 is required for galactose-dependent activation of the inv1 gene. Hrp1 has been found in complex with other proteins and genome-wide analysis demonstrates that Med15 only associates with a distinct subset of Hrp1-bound gene promoters. Global analysis reveals that Hrp1-binding normally is associated with increased histone H3 density, but at promoters also bound by Med15, histone H3 density is instead increased. Our findings reveal that Med15 functions as a separate entity in fission yeast and indicate that the function and organization of the Mediator complex may differ significantly between eukaryotes.
Keywords: ChIP-chip

overall_design:
Genome-wide binding of the Mediator subunit Med15 was analysed using a ChIP-on-chip approach. a-myc ChIP DNA purified from a Med15-myc strain was amplified, labeled and hybridised onto Eurogentec IGR+ORF arrays together with input DNA from the same sample.
Similarly, global H3 density was analysed using an anti-H3 antibody for ChIP-on-chip. The analysis of histone density was carried out in three strains: wildtype (711) and knockout strains lacking either Med15 or Hrp1.
Furthermore, expression analysis of wildtype, delta-Med15 and delta-Hrp1 strains was carried out using Affymetrix arrays.

In each case, 2-3 biological replicates were analysed, and for the Eurogentec experiments dye-swap was always performed.

first: Olga

last: Khorosjutina

first: Paulina

last: Wanrooij

first: Julian

last: Walfridsson

first: Karl

last: Ekwall


title: Transcriptional response to serum stimulation of Rat1 fibroblasts in the presence or absence of the Myc interfering molecule termed Omomyc.

status: Public on Dec 21 2010

city: Roma

first: Sergio

last: Nasi

state: Italia

address: P.le A. Moro 5

department: IBPM - Sapienza Università di Roma

country: Italy

institute: CNR - Consiglio Nazionale delle Ricerche

summary:
Myc is a multifaceted bHLHZip transcription factor deregulated in the majority of human cancers. How to target Myc for cancer therapy is unclear, given its involvement in a variety of key functions in healthy cells. We used microarrays to capture the cellular transcriptional response to Omomyc – a Myc interfering molecule acting at the level of protein protein interactions that demonstrated a remarkable therapeutic efficacy in transgenic mouse cancer models.
We found that Omomyc differently affects Myc induced gene repression and activation, channelling the Myc interactome activity to repression.

overall_design: To determine whether Omomyc causes widespread changes of the cell transcriptome, we analysed the transcriptional response to serum stimulation of Rat1 fibroblasts stably infected with an Omomer – Omomyc fused to the tamoxifen inducible oestrogen receptor ERTM – producing retrovirus (Rat1_Omomer) as compared to Rat1 cells infected with a control virus (Rat1_Control). Endogenous c-Myc is known to be sharply induced by serum and is critical for cell cycle re-entry. Cells were grown, serum-starved for 48 h in presence of tamoxifen (4-OHT) and stimulated by addition of fresh serum. Total RNA was collected from Rat1_Control and Rat1-Omomer cells at the time of serum re-addition (T0) and 90' thereafter (T90'), in the presence of tamoxifen.

first: Mauro

last: Savino

first: Laura

last: Soucek


title: Microarray studies on effect of Pneumocystis carinii infection on global gene expression in alveolar macrophages

status: Public on Apr 12 2010

first: Chao-Hung

last: Lee

address: 1120 South Dr., FH 419

department: Pathology & Lab Medicine

institute: Indiana University

summary: With a filter of false-discovery rate less than 0.1 and fold change greater than 1.5, 115 genes were found to be up- and 137 were down-regulated in alveolar macrophages during Pneumocystis carinii infection.

overall_design: Total RNA samples from 4 each of normal, dexamethasone-treated, and Pneumocystis carinii-infected Sprague-Dawley rats were analyzed by the Affymetrix GeneChip RG-U34A

first: Bi-Hua

last: Cheng


title: SWISS MADE: Standardized WithIn class Sum of Squares to evaluate Methodologies And Dataset Elements

status: Public on Mar 26 2010

city: Chapel Hill

first: Charles

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

institute: University of North Carolina at Chapel Hill

summary:
Contemporary high dimensional biological assays, such as mRNA expression microarrays, regularly involve multiple data processing steps, such as experimental processing, computational processing, sample selection, or feature selection (i.e. gene selection), prior to deriving any biological conclusions.  These steps can dramatically change the interpretation of an experiment.  Evaluation of processing steps has received limited attention in the literature.  It is not straightforward to evaluate different processing methods and investigators are often unsure of the best method.
We present a simple statistical tool, Standardized WithIn class Sum of Squares (SWISS), that allows investigators to compare alternate data processing methods, such as different experimental methods, normalizations, or technologies, on a dataset in terms of how well they cluster a priori biological classes.  SWISS uses Euclidean distance to determine which method does a better job of clustering the data elements based on a priori classifications.
We apply SWISS to three different gene expression applications.  The first application uses four different datasets to compare different experimental methods, normalizations, and gene sets.  The second application, using data from the MicroArray Quality Control (MAQC) project, compares different microarray platforms.  The third application compares different technologies: a single Agilent two-color microarray versus one lane of RNA-Seq.  These applications give an indication of the variety of problems that SWISS can be helpful in solving.
The SWISS analysis of one-color versus two-color microarrays provides investigators who use two-color arrays the opportunity to review their results in light of a single-channel analysis, with all of the associated benefits offered by this design.  Analysis of the MACQ data shows differential intersite reproducibility by array platform.  SWISS also shows that one lane of RNA-Seq clusters data by biological phenotypes as well as a single Agilent two-color microarray.

overall_design: Total RNA from eight tumors were hybridized with Stratagene universal human reference on Agilent 22K Custom arrays.

first: Cabanski

last: Christopher

first: Yuan

last: Qi

first: Xiaoying

last: Yin

first: Eric

last: Bair

first: Michele

last: Hayward

first: Cheng

last: Fan

first: Jianying

first: Matthew

last: Wilkerson

first: J

middle: S

last: Marron

first: D

last: Hayes


title: Yeast Genomic Expression Patterns of  PTC1 null mutant in Response to  Aflatoxin B1 (AFB1)

status: Public on Apr 01 2010

first: Tadahiro

last: Suzuki

summary: The evaluation of the toxicity of Aflatoxin B1 using yeast gene expressions. Yeast strain; BY4743 PTC1 mutant, was used for this study. SDS was used to raise the penetration of the yeast cell membrane.

overall_design: Two conditions are compared with three replicates each. Mutant strain was grown in 0.01% SDS containing YPD media or 0.01% SDS, 25 ppm ABF1 containing YPD media.

first: Yumiko

last: Iwahashi


title: Yeast expression data from conditions that inhibit sirtuins

status: Public on May 11 2010

city: Charlottesville

first: Jeffrey

last: Smith

email: jss5y@virginia.edu, sb3de@virginia.edu

state: VA

address: 1340 Jefferson Park Avenue

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary:
Sir2 is an NAD+-dependent histone deacetylase, and is the founding member of a large, phylogentically conserved, family of such deacetylases called the Sirtuins. The budding yeast, Saccharomyces cerevisiae, harbors 4 paralogs of Sir2, known as Hst1, Hst2, Hst3, and Hst4. Reducing the intracellular NAD+ concentration is inhibitory for the Sirtuins, and raising the intracellular nicotinamide (NAM) concentration is inhibitory. Microarray gene expression analysis was used to identify novel classes of yeast genes whose expression is altered when either NAD+ concentration is reduced or NAM is elevated. A subset of genes involved in thiamine biosynthesis was identified as being upregulated when Sir2 or Hst1 was inactivated.
Several mutants in the NAD+ biosynthesis and salvage pathways were tested, along with WT and WT grown in the presence of 5 mM nicotinamide, which inhibits the Sirtuins.

overall_design: Duplicate cultures in rich YPD media were grown into log phase and then harvested. The deletion mutants npt1∆, bna1∆, tna1∆, and pnc1∆ were compared to a wild-type (WT) strain. Additionally, a WT strain grown in the presence of 5 mM NAM was compared to WT without NAM. Total RNA was isolated and used for microarray hybridizations onto Affymetrix Yeast 2.0 Gene arrrays.

first: Mingguang

last: Li

first: Brian

last: Petteys

first: Julie

last: McClure

first: Veena

last: Valsakumar

first: Stefan

last: Bekiranov

first: Elizabeth

last: Frank


title: Yeast Genomic Expression Patterns in Response to Zymolyase Treatment

status: Public on Mar 31 2010

summary:
We used microarray to investigate the influence of zymolyase treatment which is used for degradation of yeast cell wall. Two types of RNA extraction methods were used, and zymolyase preprocessing was applied to one among them. The qualities of total RNA extracted by two extraction methods were checked, and then RNAs were used for generating cloned DNA and RNA. Finally, two types of cRNA were hybridized to Affymetrix yeast genome 2.0_array.

Keywords: comparison of RNA extraction process

overall_design: Yeast BY4743 was grown in YPD media containing 0.01% SDS, and was applied for two types of RNA extraction method.


title: Yeast background with high-concentration spikes

status: Public on Mar 21 2010

city: Lyngby

first: Aron

last: Eklund

address: Kemitorvet, Building 208

department: Center for Biological Sequence Analysis

institute: Technical University of Denmark

summary:
Microarray measurements are susceptible to error caused by cross-hybridization and bulk hybridization. To characterize the effect of these off-target interactions, we analyzed samples made from baseline (S. cerevisiae) alone or mixed with a high-concentration 1kb spike.
The spike is a 1 kb sequence amplified from the Schizosaccharomyces pombe gene SPAC27D7.10c, with an added oligo(dT)-T7 promoter. The baseline and spike samples were mixed at the double-stranded cDNA stage.

overall_design: Three arrays: 100% baseline, 99% baseline + 1% spike, 90% baseline + 10% spike. There are no replicates.

first: Pia

last: Friis

first: Rasmus

last: Wernersson

first: Zoltan

last: Szallasi