title: Expression data from Saccharomyces cerevisiae Dnup60, Dada2, and Dnup60 Dada2 cells

status: Public on May 13 2013

city: Washington

first: Kristine

last: Willis

state: DC

address: 37 & O Sts. NW

institute: Georgetown University

summary: In Saccharomyces cerevisiae, specific genes physically relocate from the nucleoplasm to the nuclear periphery concomitant with transcriptional activation, where they associate with the nuclear pore complex (NPC).  We took a genomics approach in order to gain insight into the universality and physiological relevance of the interaction between active genes and the NPC.  Using synthetic genetic array (SGA) approach, we identified interactions between components of the SAGA histone acetyltransferase complex and the Mlp and Nup60 subunits of the NPC.  Cells lacking these SAGA and NPC components display growth defects under optimal growth conditions, in which cells are grown on rich medium containing the preferred sugar glucose as a carbon source and incubated at their optimal temperature.  That growth defects were observed under these non-stress conditions suggests that these interactions are indicative of defects in normal cell physiology.  These results are consistent with a model where physical interactions between the NPC and SAGA are important for transcription of constitutively expressed genes.  To test this hypothesis, we used microarray analysis to assess changes global transcript levels in the absence of Nup60, Ada2, or Nup60 and Ada2.  Microarray analysis reveals that the growth defect in these double mutants is correlated with a synthetic reduction in steady-state transcript levels for numerous genes that are strongly expressed in wildtype cells.  These results suggest that SAGA and Nup60 cooperate in transcriptional regulation, and are consistent with a model for global regulation of SAGA-dependent transcription at the NPC.

overall_design: Wildype, single deletion, and double deletion cells were inoculated to equal starting ODs in 50 mL YEPD media and grown at 30C with shaking.  Cells were collected at mid-log phase, washed with chilled water, and stored at -80C for later processing.  RNA was isolated using TRIzol reagent according to the manufacturer's protocol, with modification for yeast cells.

first: Shana

middle: C

last: Kerr

first: Terry

last: Haley

first: Milo

last: Fasken

first: Kellie

middle: E

last: Barbara-Haley

first: George

last: Santangelo

first: Anita

middle: H

last: Corbett


title: Vimentin DNA Methylation Predicts Survival in Breast Cancer

status: Public on Feb 19 2013

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

country: USA

institute: University of North Carolina at Chapel Hill

summary:
Purpose:The Vimentin gene plays a pivotal role in epithelial-to-mesenchymal transition (EMT) and is known to be over-expressed in the prognostically poor basal-like breast cancer subtype. Recent studies have reported Vimentin DNA methylation in association with poor clinical outcomes in other solid tumors, but not in breast cancer. We therefore quantified Vimentin DNA methylation in breast tumors and matched normal pairs in association with gene expression and survival in a cohort of 83 breast cancer patients.

Materials and Methods:Vimentin methylation was quantified in 14 breast cell lines, 83 breast tumors, and 57 matched normal pairs using MALDI-TOF mass spectrometry. Gene expression data via qRT-PCR in cell lines, and oligo microarray data from breast tissues was correlated with percent methylation in the Vimentin promoter. A threshold of 20 percent average methylation was set for bivariate and multivariate tests of association between methylation and tumor subtype, tumor histopathology, and survival.

Results:Vimentin was differentially methylated in luminal breast cancer cell lines, and in luminal A, luminal B and HER2+ breast tumor subtypes, but was rare in basal-like cell lines and tumors. Increased methylation was strongly correlated with decreased mRNA expression in cell lines, and had a moderate inverse correlation in breast tumors. Importantly, Vimentin methylation predicted poor overall survival independent of race, subtype, stage, nodal status or estrogen receptor positivity.

Conclusion:Vimentin methylation predicts overall survival in breast cancer patients and holds promise as a prognostic biomarker for guiding treatment and prophylaxis.

overall_design: reference x sample

first: Jacob

last: Ulirsch

middle: M

first: Theresa

last: Swift-Scanlan


title: Yeast genomic expression patterns in response to zymolyase treatment

status: Public on Mar 21 2013

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 zymolyase treatment using yeast gene expression comparison analysis. The yeast BY4743 strain was used for this study. Yeast cells were treated with Zymolyase (final conc. 300 U/ml), and incubated at 37 degree for ten minutes. Digestion process was not provided for control sample. Total RNA was isolated with commercial kit (FastRNA Pro Red kit, Q-Biogene), and amplified RNA (aRNA) was synthesized with 3'IVT Express kit (Affymetrix). All samples were hybridized with Gene Chip (Yeast Genome 2.0 Array, Affymetrix), then each array chip was scanned by GeneChip Sanner 3000 (Affymetrix).

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Yeast were treated with zymolyase or left untreated. The only difference in conditions between the treated and untreated samples was the enzymatic digestion process. The conditioned samples were normalized with three replicates.

first: Yumiko

last: Iwahashi


title: Micro-scale genomic copy number aberrations as another means of mutagenesis in breast cancer

status: Public on Apr 22 2013

type: Genome variation profiling by genome tiling array

summary: Introduction: In breast cancers, the basal-like subtype has high levels of genomic instability relative to other breast cancer subtypes with many basal-like-specific regions of aberration. There is evidence that this genomic instability extends to smaller scale genomic aberrations as well, as shown by a previously described micro-event in the PTEN gene in the Basal-like SUM149 breast cancer cell line. Methods: We sought to identify if small regions of genomic change exist by using a high density, gene centric Comparative Genomic Hybridizations (CGH) array on both cell lines and primary tumors. A custom Agilent tiling array for CGH (244,000 probes, 200bp tiling resolution) was created to identify small regions of genomic change and was focused on previously identified basal-like-specific, and general cancer genes. Tumor genomic DNA from 94 patients and 2 breast cancer cell lines was labeled and hybridized to these arrays. Aberrations were called using SWITCHdna and the smallest 25% of SWITCHdna-defined genomic segments being called micro-aberrations (<64 contiguous probes, ~ <15kb). Results: Our data showed that primary tumor breast cancer genomes frequently contained areas of small-scale copy number gains and losses, termed micro-aberrations, which are undetectable using lower-density genome-wide platforms. The basal-like subtype exhibited the highest incidence of these events. These micro-aberrations sometimes altered expression of the involved gene as suggested by data from microarray and mRNA-seq studies. We confirmed the presence of the PTEN micro-amplification in SUM149 and by mRNA-seq showed that this resulted in loss of expression of all exons downstream of this event. Micro-aberrations disproportionately affected the 5’ regions of the affected genes, including the promoter region, and a high frequency of micro-aberrations was associated with poor survival outcomes. Conclusion: Using a high probe density, gene-centric aCGH microarray, we present evidence of small-scale genomic aberrations that contribute to gene inactivation, and thus, genomic instability and tumor formation through a mechanism not detected using conventional copy number analyses.

first: Hann-Hsiang

last: Chao

first: Xiaping

last: He

first: Joel

middle: S

last: Parker


title: Expression data from non sexual flocculation cells of S. pombe

status: Public on Jan 04 2013

city: Nanjing

first: Rongpeng

last: Li

address: Wenyuan Rd 1

department: College of life science

country: China

institute: Nanjing normal university

summary:
Deleting ribosomal protein genes caused haploid cells of S. pombe flocculated in full nutrition YEPD medium. We deleted rpl32-1 and rpl32-2 gene respectively and these two mutant cells cultured in YEPD medium flocculated.
We used microarrays to detail the global programme of gene expression between non flocculated rpl32-1 deleted and rpl32-2 deleted, compared with the non flocculated cells SPQ-01, and identified distinct classes of up-regulated genes during this process.

overall_design: Yeast cells cultured in YEPD medium in the log phase were selected for RNA extraction and hybridization on Affymetrix microarrays. The rpl32-1 deleted cells were conformed as SD1 and rpl32-2 deleted cells were conformed as SD2. Control cells SPQ-01 were conformed as WT.

first: Sheng

last: Yuan


title: Expression data from sexual flocculation cells of S. pombe

status: Public on Jan 03 2013

summary:
The h+ and h- haploid cells of S. pombe mixtures flocculated and formed diploid cells when cultured in carbon limited YEPME medium. We first cultured S. pombe h+ YHL6381 and h- SPQ-01 cells respectively in YEPD medium and then mixed them at an 1:1 ratio and further cultured in YEPME medium. Sexual flocculation occured.
We used microarrays to detail the the global programme of gene expression of flocculated YHL6381 and SPQ-01 mixtures cultured in YEPME, compared with the non flocculated cells mixtures cultured in YEPD, and identified distinct classes of up-regulated genes during this process.

overall_design: We first cultured S. pombe h+ YHL6381 and h- SPQ-01 cells respectively in YEPD medium and then mixed them at an 1:1 ratio and further cultured in a new medium for 90min. The flocculated cells mixtures cultured in YEPME named YSD, while the non flocculated cells mixtures cultured in YEPD named YSM.


title: Gene expression profile of mouse ES cells treated with 1mM valproic acid for 8 hours

status: Public on Mar 29 2013

city: Birmingham

first: John

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: Histone deacetylase inhibitors (HDACi) cause hyperacetylation of bulk histones and H3K4 hypermethylation in a variety of cell types. They find clinical application as anti-epileptics and chemotherapeutic agents, but the pathways through which they alter cell physiology remain unclear. Surprisingly, changes in gene expression caused by HDACi are often limited in extent and can be positive or negative. Here we have explored the ability of the clinically important HDACi valproic acid (VPA) to alter gene expression in mouse embryonic stem (ES) cells.

overall_design: CCE/R mouse embryonic stem cells were treated with 1mM valproic acid for 8 hours.  Four biological replicates were carried out. Treated cells were labelled with Cy5 and untreated controls with cy3 except in replicate 4 which was a dye-swap.

first: Elsa

last: Boudadi

middle: A

first: Bryan

last: Turner


title: mRNA profiling of glucose-repressed 14-3-3 and hdac yeast mutants

status: Public on Jan 15 2013

city: Seattle

first: Kenneth

last: Dombek

state: WA

address: 1959 Pacific St. N.E.

department: Biochemistry

institute: University of Washington

summary: Previous results suggest that Bmh might inhibit the activity of the transcription factor Adr1 after binding to Adr1-dependent promoters. In a strain lacking the two major histone deacetylases, Hda1 and Rpd3 (hdac∆), Adr1 is bound to its target promoters recruiting what appears to be an inactive RNA ploymerase II preinitiation complex (PIC). To determine whether Bmh activity inhibits this inactive PIC and the generality of this effect on glucose-repressed gene expression, the mRNA profiles of wild type, bmh mutant, hdac mutant, and bmh hdac mutant cells grown in high glucose medium were compared.

overall_design: Total RNAs were purified from triplicate cultures of W303-1A (wild type), YLL1087 (bmh1-ts bmh2∆), CTY-TY44 (hda1∆ rpd3∆) and KBY3 (bmh1-ts bmh2∆ hda1∆ rpd3∆) cells exponentially growing in YP broth containing 5% glucose and then profiled using Affymetrix Yeast 2.0 arrays.

first: Katherine

last: Braun

first: Elton

middle: T

last: Young


title: MicroRNA-30c inhibits Human Breast Tumor Chemotherapy Resistance by regulating TWF1 and IL-11: Patient DataSet

status: Public on Jan 18 2013

summary: Chemotherapy resistance frequently drives tumor progression. However, the underlying molecular mechanisms are poorly characterized. Epithelial-to-mesenchymal transition (EMT) has been shown to correlate with therapy resistance, but the functional link and signaling pathways remain to be elucidated. We report here that miR-30c, a human breast tumor prognostic marker, plays a pivotal role in chemo-resistance by a direct targeting of the actin-transporter TWF1, which promotes EMT. An IL-6 family member, IL-11 was identified as a secondary target of TWF1 in the miR-30c signaling pathway. Expression of miR-30c inversely correlated with IL-11 expression in clinical tumors and IL-11 correlated with relapse-free survival in breast cancer patients. Identification of a novel miRNA-mediated pathway that regulates chemo-resistance in breast cancer will facilitate the development of new management strategies.

first: Chika

last: Nwachukwu

first: Olufunmilayo

middle: I

last: Olopade


title: Expression data from Saccharomyces cerevisiae

status: Public on Jan 17 2013

city: Göteborg

first: Tobias

last: Österlund

address: Kemivägen 10

department: Dept. of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary:
In this study we focus on two Saccharomyces cerevisiae strains with varying production of heterologous α-amylase and we compare the metabolic fluxes and transcriptional regulation at aerobic and anaerobic conditions, in particular with the objective to identify the final electron acceptor for protein folding.
We found that anaerobic conditions showed high amount of amylase productions when comparing to aerobic conditions and the genome-scale transcriptional analysis suggested that genes related to the endoplasmic reticulum (ER), lipid synthesis and stress responses were generally up-regulated at anaerobic conditions. Moreover, we proposed a model for the electron transfer from ER to the final electron acceptor, fumarate under anaerobic conditions.

overall_design: Three Saccharomyces cerevisiae strains with varied amylase productions were selected at early glucose phase in batch fermentations for RNA extraction and hybridization on Affymetrix microarrays. Biological triplicates were applied, and strains with empty plasmid (no amylase productions) were used as control strain.

first: Zihe

last: Liu


title: Post-transcriptional regulation of cell-cell interaction protein-encoding transcripts by Zfs1p in S. pombe

status: Public on Nov 06 2012

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Members of the tristetraprolin (TTP) family of CCCH tandem zinc finger proteins can bind directly to AU-rich elements in mRNAs and promote transcript deadenylation and decay.  The yeast Schizosaccharomyces pombe expresses a single TTP family member, Zfs1p, that has been linked to the mating response pathway and septum formation.  We showed previously that Zfs1p can bind to and promote the destabilization of AU-rich element-containing transcripts.  In this study, we identified additional target transcripts by comparing transcript levels in wild type and zfs1 mutant yeast, using deep sequencing and microarray approaches.  We also used direct RNA sequencing to determine the locations of the polyA tails in both wild type and mutant strains, and to confirm the presence of potential Zfs1p target sequences within the mRNA.  These studies identified a set of transcripts containing potential Zfs1p binding sites that accumulated significantly in the zfs1 mutants; a subset of these turned over more slowly in the zfs1 mutant strain, and bound directly to Zfs1p in co-immunoprecipitations.  One apparent direct target encodes the transcription factor Cbf12p, which is known to increase cell-cell adhesion and flocculation when over-expressed.  Studies of zfs1 and cbf12 double mutants demonstrated that the increased flocculation seen in zfs1 mutants is due, at least in part, to a direct effect on the turnover of cbf12 mRNA, leading in turn to changes in the levels of its transcriptionally regulated genes.  These data suggest that Zfs1p can both directly and indirectly regulate the levels of transcripts involved in cell-cell adhesion in this species.

overall_design: Indicated strains were grown in YES media to approximately OD600=1.0 and total RNA was harvested, followed by polyA+ purification.  Three independent microarrays were performed: 1) Project 488 included 3 biological replicates each of WT and zfs1∆ and compared PolyA+ RNA, 2) Project 529 included 5 biological replicates each of WT and zfs1∆, and 3) Project 582  included 3 biological replicates each of WT, zfs1∆, cbf12∆, and zfs1∆cbf12∆.

first: Melissa

middle: L

last: Wells

first: Perry

middle: J

last: Blackshear

first: Weichun

last: Huang

first: Leping

first: Kevin

last: Gerrish

first: David

last: Fargo

first: Fatih

last: Ozsolak


title: Budding yeast Wapl controls sister chromatid cohesion maintenance and the chromosome condensation status [expression]

status: Public on Nov 22 2012

city: London

first: Rahul

last: Thadani

address: 44 Lincoln's Inn Fields

institute: Cancer Research UK

summary: Cohesin acetylation by Eco1 during DNA replication establishes sister chromatid cohesion. We show that acetylation makes cohesin resistant to Wapl activity from S-phase until mitosis. Wapl turns out to be a key regulator of cohesin dynamics on chromosomes by controling cohesin maintenance following its establishment in S-phase and its role in chromosome condensation.

overall_design: The Affymetrix Yeast Genome 2.0 Arrays were used to analyze the expression profile of wt and wapl∆ cells.

first: Lidia

last: Lopez-Serra

first: Armelle

last: Lengronne

first: Vanessa

last: Borges

first: Gavin

last: Kelly

first: Frank

last: Uhlmann


title: Expression profile of S. pombe cells with ribosomal protein L32 paralogs

status: Public on Mar 01 2013

first: Lei

last: Sun

address: 1 Wenyuan Rd

institute: Nanjing Normal University

summary:
We cultured the cells of S. pmbe in EMM2, and harvested them in the OD600 of 0.5 and 10 respectively.
We used microarrays to detail the the global program of gene expression of SP-Q01 and SP-Q01 carrying vevtor pESP3X to overexpress either ribosomal protein L32 paralog in the OD600 of 0.5 and 10 respectively.

overall_design: We constructed the ribosomal protein L32 paralog overexpression strains to mimic the expression pattern of RPL32 paralogs in wild-type cells of S.pombe. We cultured the cells to different growth phase, and used microarray to identify the genes were regulated distinctively by RPL32 paralogs.

first: Sheng

last: Yuan


title: Expression data from S. cerevisiae after evolution under diverse conditions

status: Public on Nov 13 2012

city: Rehovot

first: Avihu

last: Yona

address: Hertzel 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institue of Science

summary: We conducted a set of lab-evolution experiments in yeast and followed the long-term dynamics of aneuploidy under diverse conditions including heat shock and high PH.

overall_design: Each evolution experiment starts with an ancestor strain that was subjected (in several independent repetitions) to certain growth conditions such as high temperature 39°C, permissive temperature 30°C, gradually increasing temperature from 30°C to 39°C, high pH=8.6 and normal PH. In all cases the mRNA extraction was performed on a population sample that was grown for 18 generations under stress-less conditions. This is since we aimed to measure the gene expression changes that are due to stress adaptation and not the physiological response.

first: Yair

last: Manor

first: Gal

last: Romano

first: Rebecca

last: Herbst

first: Amir

last: Mitchell

first: Martin

last: Kupiec

first: Yitzhak

last: Pilpel

first: Orna

last: Dahan


title: Saccharomyces cerevisiae stress responses to HMF and furfural

status: Public on Oct 18 2012

first: Magnus

last: Ask

summary: The inhibitors hydroxymethylfurfural (HMF) and furfural were added to the feed-medium of carbon-limited anaerobic chemostat cultures. Samples were taken for transcriptome analysis at steady-state from cultures with inhibitors and without inhibitors.

overall_design: Three biological replicates from each condition (inhibitors, no inhibitors) were analyzed.

first: Maurizio

last: Bettiga

first: Lisbeth

last: Olsson


title: Budding yeast Wapl controls sister chromatid cohesion maintenance and the chromosome condensation status

first: Rahul

last: Thadani

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Lidia

last: Lopez-Serra

first: Armelle

last: Lengronne


title: Global Regulation of Nucleosome Organization And Transcription By The Yeast Ssn6-Tup1 Corepressor (expression)

status: Public on Oct 10 2012

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

summary: The yeast Ssn6-Tup1 complex regulates gene expression through a variety of mechanisms, including positioning of nucleosomes over promoters of some target genes to limit accessibility to the transcription machinery. To further define the functions of Ssn6-Tup1 in gene regulation and chromatin remodeling, we performed genome-wide profiling of changes in nucleosome organization and gene expression that occur upon loss of SSN6 or TUP1, and observed extensive nucleosome alterations in both promoters and gene bodies of derepressed genes. Our improved nucleosome profiling and analysis approaches revealed low-occupancy promoter nucleosomes (P nucleosomes) at locations previously defined as nucleosome-free regions. In the absence of SSN6 or TUP1, this P nucleosome is frequently lost, whereas nucleosomes are gained at -1 and +1 positions, accompanying up-regulation of downstream genes. Our analysis of public ChIP-seq data revealed that Ssn6 and Tup1 preferentially bind TATA-containing promoters, which are also enriched in genes derepressed upon loss of SSN6 or TUP1. These results suggest that stabilization of the P nucleosome on TATA-containing promoters may be a central feature of the repressive chromatin architecture created by the Ssn6-Tup1 corepressor, and that releasing the P nucleosome contributes to gene activation.

overall_design: Genome-wide expression profiling Yeast gene expression in three cell type, Each cell type is tested in duplicate.

first: Kaifu

last: Chen

first: Marenda

last: Wilson

first: Calley

last: Hirsch

first: Anjanette

last: Watson

first: Shoudan

last: Liang

first: Yue

last: Lu

first: Wei

last: Li

first: Sharon

middle: Y

last: Dent


title: Transcriptomic comparison of tumoric tissues induced by different c58 agrobacterium lines; Quorum-sensing in Agrobacterium-induced tumors

status: Public on Sep 01 2013

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary:
rs11-03_agro
transcriptomic comparison of tumoric tissues induced by different c58 agrobacterium lines
What are the functions and the regulatory pathways of the bacterial quorum-sensing system in the context of Agrobacterium/Arabidopsis interactions?

overall_design:
Arabidopsis WT Col0 plants were grown in greenhouse till stage 1.03-1.04 (growth conditions 1). They were then confined in short day conditions and at 22°C (growth conditions 2). At stage 5.10 plants were wounded at the base of the stem and part of them were inoculated with 3 different C58 Agrobacterium strains (WT, accR or traI). Eighteen days post inoculation, wounded but non-infected tissues (control) as well as tumoric tissues were collected and processed for RNA extraction.
21 dye-swap

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Julien-

last: Lang

first: Marie-Laure

last: Martin-Magniette


title: Expression analysis of Dickeya dadantii 3937 infecting an aphid (Acyrthosiphon pisum clone LL01) host

status: Public on Dec 01 2012

city: Villeurbanne

first: Yvan

last: Rahbé

address: INSA-Lyon, 20 ave. A.-Einstein

department: SPE

summary:
Investigation of whole genome gene expression level changes in the phytopathogenic Dickeya dadantii wild-type strain 3937 during an acute per os  infection of an aphid body, in comparison with a colony grown in standard LB medium.
The pathosystem described in this study has been analysed and first published in Grenier et al.  2006, and further detailed in Costechareyre et al. 2011

overall_design: A two chip study using total RNA recovered from three separate (aphid-, or in vitro-grown) samples

first: Denis

last: Costechareyre

first: Guy

last: Condemine


title: The Fun30 ATP-dependent nucleosome remodeler promotes resection  of DNA double-strand break ends

status: Public on Oct 04 2012

first: kaifu

last: chen

type:
Expression profiling by array
Genome variation profiling by array

summary: Chromosomal double-strand breaks (DSBs) are resected by 5’-nucleases to form 3’ single-strand DNA (ssDNA) substrates for binding by homologous recombination and DNA damage checkpoint proteins. Two redundant pathways of extensive resection were described both in cells and in vitro, one relying on Exo1 exonuclease and the other on Sgs1 helicase and Dna2 nuclease. However, it remains unknown how resection proceeds within the context of chromatin where histones and histone-bound proteins represent barriers for resection enzymes. Here, we have identified the yeast nucleosome remodeling enzyme Fun30 as novel factor promoting DSB end resection. Fun30 is the major nucleosome remodeler promoting extensive Exo1- and Sgs1-dependent resection of DSBs while the RSC and INO80 chromatin remodeling complexes play redundant roles with Fun30 in resection adjacent to DSB ends. ATPase and helicase domains of Fun30, which are needed for nucleosome remodeling, are also required for resection. Fun30 is robustly recruited to DNA breaks and spreads around the DSB coincident with resection. Fun30 becomes less important for resection in the absence of the histone-bound Rad9 checkpoint adaptor protein known to block 5’ strand processing and in the absence of either histone H3 K79 methylation or γ-H2A, which mediate recruitment of the Rad9 . Together these data suggest that Fun30 helps to overcome the inhibitory effect of Rad9 on DNA resection.

overall_design:
Genome-wide expression profiling of Yeast gene expression in two cell type including the wild type and a FUN30 knockout cell, each cell type is tested in two duplicates.
Test relative gene integration efficiency in yeast genome-wide homozygous diploid deletion mutants.

first: Xuefeng

first: Dandan

last: Cui

first: Alma

last: Papusha

first: Xiaotian

last: Zhang

first: Chia-Dwo

last: Chu

first: Jiangwu

last: Tang

first: Xuewen

last: Pan

first: Grzegorz

last: Ira


title: Autotoxicity mechanism of Oryza Sativa: Microarray analysis of rice plants in response to allelochemical ferulic acid

status: Public on Jul 22 2013

city: Tainan

first: Wen-Chang

last: Chi

state: Taiwan

address: No.1, University Road, Tainan City

department: Life Science

country: Taiwan

institute: National Cheng Kung University

summary: Autotoxicity plays an important mechanism in regulating plant productivity. Ferulic acid (FA) is phytotoxic and was identified in extracts and residues of rice plants as a candidate for rice allelochemicals. To help characterize the autotoxicity mechanism of rice, we present the first large-scale, transcriptomic analysis of rice root responses to ferulic acid.

overall_design: Two-condition experiment, short exposures and long exposures. Comparison of mock control and rice seedlings treated with 50 ppm ferulic acid (FA) during short (pooled from 1- and 3-h treatments), as compared to long (24 h) exposures.; Biological replicates: 3 control replicates (short and long exposures), 3 FA-treated replicates (short and long exposures).

first: Yun-An

last: Chen

first: Yu-Chywan

last: Hsiung

first: Chang-Hung

last: Chou

first: Hao-Jen

last: Huang


title: Yeast genomic expression patterns in response to type B trichothecenes

status: Public on Sep 12 2012

first: Tadahiro

last: Suzuki

summary: The evaluation of mycotoxicity of type B trichothecenes using a yeast gene expression comparison analysis. The yeast BY4743 derivative PDR5 mutant was used for this study. The yeast cells were treated with trichothecene mycotoxins, and incubated at 25 degree for two hours, respectively. Total RNA was isolated with commercial kit (FastRNA Pro Red kit, Q-Biogene), and amplified RNA (aRNA) was synthesized with 3'IVT Express kit (Affymetrix). All samples were hybridized with Gene Chip (Yeast Genome 2.0 Array, Affymetrix), then each array chip was scanned by GeneChip Sanner 3000 (Affymetrix).

overall_design: The yeast strain was grown in YPD medium with 25 ppm of trichothecene mycotoxin (deoxynivalenol (DON), 3-acetyldeoxynivalenol (3ADON), 15-acetyldeoxynivalenol (15ADON), nivalenol (NIV), or fusarenone-X (FusX)). The same volume of DMSO was added to the control samples. The conditioned samples were normalized with three replicates.

first: Yumiko

last: Iwahashi


title: Transcriptional profile of an eca39∆ mutant fission yeast

status: Public on Sep 21 2012

city: Okayama

first: Hidekazu

last: Takahashi

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

summary:
An branched-chain amino acids auxotroph eca39∆ mutant fission yeast exhibits an unusual adaptive growth phenotype on solid minimal media containing Ile, Leu and Val when other strains are growing nearby.
The transcriptional profiles of an eca39∆ mutant before and after the adaptation were determined using Affymetrix DNA microarrays.

overall_design: Wild-type, the eca39∆ mutant, and the adapted eca39∆ mutant fission yeasts were inoculated in YE+2mM Ile, Leu and Val, and harvested at OD ~ 1. Total RNAs were purified from the 3 samples.

first: Xiaoying

last: Sun

first: Makiko

last: Hamamoto

first: Yoko

last: Yashiroda

first: Minoru

last: Yoshida


title: Expression data of Saccharomyces cerevisiae CEN.PK.113-7D grew in Batch and Chemostat condition using for comparison of RNA-seq and Microarray data

status: Public on Sep 14 2012

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: High throughput sequencing is a powerful tool to investigate complex cellular phenotypes in functional genomics studies. Sequencing of transcriptional molecules, RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared to traditional expression analysis based on microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in analysis of RNA-seq data and to cross-compare the results with those obtained through a microarray platform. We used the well-characterized Saccharomyces cervevisiae strain CEN.PK 113-7D grown under two different physiological conditions (batch and chemostat) as a case study. In our work, we addressed the influence of genetic variability on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and Tophat), the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and noiSeq) and we explored the consistency between the two main approaches for RNA-seq: reference mapping and de novo assembly. High reproducibility in data generated through RNA-seq among different biological replicates (correlation ≥ 0.99) and high consistency with the results identified with RNA-seq and microarray data analysis (correlation ≥ 0.91) were observed. The results from differential gene expression identification as well as the results of integrated analysis based on the different methods are in good agreement. Overall, our study provides a useful and comprehensive comparison of the workflow for transcriptome analysis using RNA-seq technique.

overall_design: Microarray ananlysis were perfomed from the same RNA extraction then compare the result with RNA-seq analysis

first: Marta

last: Papini

first: Gionata

last: Scalcinati

first: Jens

last: Nielsen


title: Adaptively evolved yeast mutants on galactose shows trade-offs in carbon utilization on glucose.

status: Public on Aug 01 2012

city: Gothenburg

first: Kuk-Ki

last: Hong

department: Department of Chemical and Biological Engineering

summary:
Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast

Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in    the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level.

overall_design: Yeast galactose evolved mutants having improved galactose availability were grown on aerobic batch with glucose as carbon source

first: K

middle: K

first: J


title: Expression data of Schizosaccharomyces pombe deletions involved in DNA damage response

status: Public on Sep 11 2012

city: Shanghai

first: Wenjuan

last: Mo

address: No. 220 Handan Road

department: Life School

institute: Fudan University

summary:
DNA damage response (DDR) plays pivotal roles in maintaining genome integrity and stability. An effective DDR requires the involvement of hundreds of genes that compose a complicated network. To identify novel genes involved in DDR, we screened a genome-wide Schizosaccharomyces pombe (S. pombe) haploid deletion library against six different DNA damage reagents. We identified 52 genes that were actively involved in DDR. Among the 52 genes, 20 genes were linked to DDR for the first time.
For a better understanding of DDR genes function, we performed a DNA microarray assay to analyze the gene expression profiles of eight deletions.

overall_design: Cells of wild type and eight deletions involved in DDR were collected during the expontentially growing stage, and were subjected to RNA extraction and hybridization on Affymetrix microarrays. We tried to understand the role of genes in DDR by comparing the expression profiles of deletions with that of wild type.

first: Xian

last: Pan

first: Hong

last: Lu


title: Analysis of postnatal gene expression in a transgenic rat kidney

status: Public on Oct 02 2012

city: Cardiff

first: David

middle: Allan

last: Carter

state: Cardiff

address: Museum Avenue

department: School of Biosciences

institute: Cardiff University

summary: We have generated a transgenic rat model with postnatal pathology. In order to investigate the potential contribution of changes in kidney gene expression to the pathology, we have conducted microarray-based gene expression profiling of postnatal kidney.

overall_design: Rat kidneys were sampled at mid-day of postnatal day 6 for RNA extraction and hybridization to Affymetrix Genechip arrays. Two biological replicates of both wild-type and transgenic kidneys were included in the study.

first: Timothy

last: Wells


title: Expression data from lack of DNA topoisomerase I, DNA topoisomerase II and complete lack of both topoisomerases

city: Aarhus

first: Jakob

middle: Madsen

last: Pedersen

state: Aarhus

address: CF Mollers Alle 3

department: Molecular Biology

country: Denmark

institute: Aarhus University

summary: To investigate the role of DNA topoisomerases in transcription, we have studied global gene expression in Saccharomyces cerevisiae cells deficient for topoisomerases I and II and performed single-gene analyses to support our findings. The genome-wide studies show a general transcriptional down-regulation upon lack of the enzymes, which correlates with gene activity but not gene length. Furthermore, our data reveal a distinct subclass of genes with a strong requirement for topoisomerases. These genes are characterized by high transcriptional plasticity, chromatin regulation, TATA box presence, and enrichment of a nucleosome at a critical position in the promoter region, in line with a repressible/inducible mode of regulation. Single-gene studies with a range of genes belonging to this group demonstrate that topoisomerases play an important role during activation of these genes. Subsequent in-depth analysis of the inducible PHO5 gene reveals that topoisomerases are essential for binding of the Pho4p transcription factor to the PHO5 promoter, which is required for promoter nucleosome removal during activation. In contrast, topoisomerases are dispensable for constitutive transcription initiation and elongation of PHO5, as well as the nuclear entrance of Pho4p. Finally, we provide evidence that topoisomerases are required to maintain the PHO5 promoter in a superhelical state, which is competent for proper activation. In conclusion, our results reveal a hitherto unknown function of topoisomerases during transcriptional activation of genes with a repressible/inducible mode of regulation

overall_design: wild type versus top1Δ, top2ts and top1Δtop2ts. 3 biological replicates for each mutant versus wild type counterpart amounting to 12 microarrays.

first: L

last: Andreasen

last: Fredsoe

last: Mundbjerg

first: M

last: Kruhoeffer

first: B

middle: R

last: Knudsen

first: A

last: Andersen


title: Integrated analysis of the transcriptome-lipidome reveals the interactions of inositol-choline and SNF1 in controlling lipid biosynthesis

status: Public on Aug 29 2012

first: Intawat

last: Nookaew

summary: Characterize the transcriptional response to inositol-choline and snf1

overall_design: We used microarrays to capture the global responses of inositol-choline concentration and snf deletion in Carbon and Nitrogen limited growth

first: Pramote

last: Chumnanpuen

first: Jie

last: Zhang


title: Distinct Signaling Roles of Ceramide Species in Yeast Revealed Through Integromics Analyses

status: Public on Aug 28 2012

city: Pittsburgh

first: Xinghua

state: PA

address: 5607 Baum Blvd

department: Dept Biomedical Informatics

institute: University of Pittsburgh

summary: Yeast cells were subjected to different combination of the following perturbations: heat stress, myriocin (ISP1) treatment and lipid (myristate) supplement.  Then gene expression and lipidomic data were collected under each experimental condition with triplicates.

overall_design: heat stress, myriocin (ISP1) treatment and lipid (myristate) supplement in triplicates

last: Montefusco


title: Gene expression profiles of S. cerevisiae under heat stress

status: Public on Aug 30 2012

city: Tsukuba

first: Toshihide

last: Nakamura

address: 2-1-12 Kannondai

institute: National Food Research Institute

summary: Genes whose expression correlated to the degree of thermotolerance in S. cerevisiae were identified by DNA microarray analysis.

overall_design: Gene expression profiles of three S. cerevisiae strains showing different levels of thermotolerance were compared and a thermotolerance-related gene chosen.

first: Mami

last: Yamamoto


title: Expression profile in wild type, fkh2delta and fkh2-S2A mutants

status: Public on Jul 13 2012

first: Claes

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

institute: Gothenburg University

summary:
Mitotic entry is accompanyed by the expression of a cluster of so called mitotic genes, whose activation is critical for mitosis in human and yeast cells. We found a link between the transcription machinery and cell cycle control network at mitosis in fission yeast, involving the Cdk8 kinase dependent phosphorylation of the fork head transcription factor Fkh2. We have generated a non-phosphorylatable fkh2 mutant (fkh2-S2A) also.
We have used microarrays to study the gene expression changes in fkh2 deletion and phosphomutants vs Wt in exponentially growing fission yeast cells to detect how the phosphorylation may affect global and mitotic gene expression.

overall_design: RNA samples were taken from exponentially growing fission yeast cells and hybridized to affymetrix microarrays: wild type, fkh2delta and fkh2-S2A mutants

first: Zsolt

last: Szilagyi


title: The Influence of Sleep Deprivation on Hippocampal CA1 Gene Expression: Relation to Stress and Aging

status: Public on Jul 17 2012

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary: Sleep deprivation (SD) in young adults is associated with metabolic, stress and cognitive responses that are also characteristic of brain aging. Given that sleep architecture changes with age, including increased fragmentation and decreased slow wave activity, it seems reasonable to investigate potential molecular relationships between SD and aging in brain tissue. Here, we tested the hypothesis that young rats exposed to 24 or 72 hour SD would respond with stress and aging-like shifts in brain hippocampal CA1 gene expression. SD animals showed blood corticosterone and weight changes consistent with a stress response. Microarray results, validated by Western blot and comparison to prior SD studies, pointed to disruptions in neurotransmission, sleep pressure signaling, and macromolecular synthesis. In a separate experiment, animals exposed to 24 or 72 hour novel environment stress recapitulated nearly one third of the SD transcriptional profile, particularly upregulated apoptotic and immune signaling pathways. Compared to aging (based on three previously published independent hippocampal aging studies), SD transcriptional profiles agreed for neurogenesis and energy pathways. However, immune signaling, glial activity, macromolecular synthesis and neuronal function all showed an SD profile that was, at least in part, opposed by aging. We conclude that while stress and SD have discrete molecular signatures, they do show a subset of highly similar changes. However, the same could not be said of aging and SD, where a similar subset of genes is changed, but in partially divergent directions. Finally, this work identifies presynaptic vesicular release and intercellular adhesion molecular signatures as novel targets for future SD-countering therapeutics.

overall_design: Subjects: Male Fischer 344 rats (3-5 months old, Harlan, Indianapolis): 37 in cohort 1 and 32 in cohort 2. Subjects were assigned to one of 5 treatment groups: Home Cage-HC n =17; 24 hour sleep deprivation- 24SD n = 16; 72 hour sleep deprivation- 72SD n = 20; 24 hour novel environment stress- 24NES n = 10; 72 hour novel environment stress- 72NES n = 6. Cohorts 1 and 2 were combined for microarray analyses. Sleep Deprivation: The multiple platform modification (Coenen and van Luijtelaar, 1985) of the classic ‘flower pot’ (Mendelson et al., 1974) technique in which animals are placed on an elevated platform over water was used. Pairs of SD animals (cage mates) were sleep deprived for 24 or 72 hours. Novel Environment Stress (NES): NES animals were exposed to a novel environment, but were not constrained from sleeping. These NES animals paralleled the sleep deprivation exposure duration (24 hour- n = 10, and 72 hour- n = 6). Tissue Isolation: On the day that animals were removed from the SD chambers, they were anesthetized with CO2 gas and decapitated. Brains were removed and immediately placed in oxygenated artificial cerebrospinal fluid (aCSF) containing (in mM) 114NaCl, 2.5 KCl, 2MgCl2, 30 NaHCO3, 10 Glucose and 2.2CaCl2.  Hippocampi were dissected as described previously (Blalock et al., 2003; Kadish et al., 2009). Briefly, dissected hippocampi were immersed in 0 °C oxygenated aCSF and placed on a chilled glass petri dish. The CA1 region was dissected along the long axis of the hippocampus. CA1 tissue was flash frozen and stored at -80° C until further use. Microarray Protocol: GCOS quality control measures of background signal (74.9 ± 2.1 cohort 1; 59.8 ± 2.3 cohort 2) and RawQ (2.3 ± 0.1 cohort 1; 1.9 ± 0.1 cohort 2), as well as a chip x chip correlation matrix of signal intensity data pointed to a global decrease in background signal intensity in Cohort 2. To control for this, each gene’s expression values for HC, 24SD and 72SD was standardized separately within cohort 1 and cohort 2, and then the two cohorts were combined. This retained the variability of each cohort, but removed the ‘cohort effect’ from the data. Pre-statistical filtering retained ‘A’ grade probe sets that were uniquely annotated (Affymetrix, June 2011) with gene symbols and had at least 6 presence calls across all 71 chips. This criterion was selected based on factorial analysis demonstrating < 5% probability of 6 or more chips being rated present for a given probe set by chance (Blalock, unpublished observations).

first: Nada

last: Porter

first: Julia

last: Bohannon

first: Meredith

last: Rauhut

first: Michael

last: Bridges

first: Heather

last: Buechel

first: Amy

last: Dowling

first: Jelena

last: Popovic

first: Veronique

last: Thibault

first: Donald

last: Cohen

first: Susan

middle: D

last: Kraner

first: Kuey-Chu

last: Chen


title: Expression data from dietary restricted budding yeast

status: Public on Jun 21 2012

city: Liverpool

first: Daniel

last: Wuttke

state: Meyerside

address: Crownstreet

department: Department of Functional and Comparative Genomics

institute: University of Liverpool

summary:
Dietary restriction (also known as caloric/calorie restriction; CR) extends the lifespan of species from all three eukaryotic kingdoms. The restriction of the diet interferes directly with the aging process by triggering a tightly controlled genetic program where specific sets of genes are either upregulated downreguled.
We used microarray-technology to detail the global program of gene expression underlying the anti-aging effect of dietary restriction and identified distinct classes of up- and down-regulated genes.

overall_design: In order to apply dietary restriction in budding yeast we cultured cells on a reduced glucose medium (0.5% vs. 2.0%), which is known as moderate DR regimen. We then compared mRNA expression of yeast cells cultured under dietary restricted (0.5% glucose) and ad libitum (2.0% glucose) conditions.

first: Fusheng

last: Tang


title: Effect of brain death on gene expression in liver from rhesus macaque

status: Public on Jun 28 2012

city: Madison

first: Jamie

last: Sperger

state: WI

address: 1111 Highland Ave.

department: Dept. of Surgery

institute: University of Wisconsin - Madison

summary: The majority of transplanted organs are recovered from deceased donors after brain death (BD).   BD has been hypothesized to compromise organ quality in part from the activation of systemic inflammation.  The objective of this study was to characterize the immune response induced by BD in a well controlled non-human primate (NHP) model.  Assessment of physiologic parameters (blood pressure, heart rate, urinary output, catecholamines, and cerebral angiograms) was used to confirm BD.  After 6h of BD, we monitored changes in the peripheral blood by flow cytometry, liver gene expression by microarray and liver protein expression by Western blotting and immunohistochemistry (IHC).  BD was indicated by a rapid increase in blood pressure followed by hemodynamic instability, hypotension, diabetes insipidus and the absence of cerebral blood flow and brain stem reflexes.  Within the peripheral blood IL-6 levels and neutrophils increased and myeloid dendritic cells decreased in BD NHP when compared to living donor controls.  Genes related to innate inflammatory response and apoptosis were significantly upregulated in BD NHP.  BD livers showed increased expression of suppressor of cytokine signaling 3 (SOCS3) protein and the danger associated molecular pattern protein S100A9.  Increased expression of intracellular cellular adhesion molecule 1 (ICAM-1) and major histocompatibility complex (MHC) II, neutrophil accumulation, and products of oxidative stress (carboxy methyl lysine (CML) and hydroxynonenal (HNE)) were detected by IHC in livers.  Conclusion:  These data indicate that BD leads to the rapid activation of an inflammatory response within the liver involving components of the innate immune response at the gene and protein levels.  The activation of these inflammatory pathways may provide one explanation for the reduced post-transplant function of organs from brain dead donors.

overall_design: Microarray analysis was performed to compare gene expression patterns from livers recovered after 5 hours of brain death (n=5) and from "living donor" non-brain dead controls (n=5).

first: Luis

last: Fernandez


title: HIRA, a Conserved Histone Chaperone, Plays an Essential Role in Low-dose Stress Response via Transcriptional Stimulation in Fission Yeast

status: Public on Jul 22 2012

city: Kyoto

first: Fuyuki

last: Ishikawa

address: Yoshida-Konoe-cho, Sakyo-ku

institute: Kyoto University

summary:
Cells that have been pre-exposed to mild stress (priming stress) acquire transient resistance to subsequent severe stress even under different combinations of stresses. This phenomenon is called cross-tolerance. Although it has been reported that cross-tolerance occurs in many organisms, the molecular basis is not clear yet. Here, we identified slm9+ as a responsible gene for the cross-tolerance in the fission yeast Schizosaccharomyces pombe. Slm9 is a homolog of mammalian HIRA histone chaperone. HIRA forms a conserved complex and gene disruption of other HIRA complex components, Hip1, Hip3, and Hip4, also yielded a cross-tolerance-defective phenotype, indicating that the fission yeast HIRA is involved in the cross-tolerance as a complex. We also revealed that Slm9 was recruited to the stress-responsive gene loci upon stress treatment in an Atf1-dependent manner. The expression of stress-responsive genes under stress conditions was compromised in HIRA disruptants. Consistent with this, Pol II recruitment and nucleosome eviction at these gene loci were impaired in slm9D cells. Furthermore, we found that the priming stress enhanced the expression of stress-responsive genes in wild-type cells that were exposed to the severe stress. These observations suggest that HIRA functions in stress response through transcriptional regulation.
To determine whether fission yeast HIRA specifically regulates stress-responsive genes under stress condition, we performed genome-wide analysis by using Affymetrix GeneChip oligonucleotide microarrays.

overall_design: Fission yeast cells (WT, slm9D, hip1D) were grown in quadruplicate at 32°C to the logarithmic phase and an aliquot was collected as the unstressed control. The other three aliquots were exposed to 40°C for 1 h, 25 mM H2O2 for 1 h, or 40°C for 1 h followed by 25 mM H2O2 for 1 h, respectively. Total RNA was purified and all the 12 RNA samples were analyzed with GeneChip Yeast Genome 2.0 Array (Affymetrix).

first: Moeko

last: Chujo

first: Yusuke

last: Tarumoto

first: Koichi

last: Miyatake

first: Eisuke

last: Nishida


title: Gene expression profiles of S. cerevisiae under acetic acid stress

first: Toshihide

last: Nakamura

department: Applied Microbiology Division

summary: Genes whose expression correlated to the acetic acid tolerance in S. cerevisiae were identified by DNA microarray analysis.

overall_design: Gene expression profiles of two S. cerevisiae strains showing different levels of acetic acid tolerance were compared and an acetic acid tolerance-related gene chosen.

first: Yutaka

last: Haitani

first: Mami

last: Yamamoto

first: Jun

last: Shima


title: Genome sequecing of yeast strain evolved under high glucose

status: Public on Jul 11 2012

city: Albuquerque

first: Anthony

last: Aragon

state: NM

address: Castetter Hall Room 214

institute: University of New Mexico

summary: A population of Saccharomyces cerevisiae was cultured for approximately 450 generations in the presence of high glucose to select for genetic variants. This experiment allows for a controlled model of adaptive evolution under natural selection. Using the parental strain BY4741 as the starting population, an evolved culture was obtained after continuous aerobic growth in a glucose-high medium for approximately 450 generations. After the evolution period three single colony isolates were selected for analysis.  Next-generation Ion Torrent sequencing was used to evaluate genetic changes.  Greater than 100 deletion/insertion changes were found with approximately half of these effecting genes.  Additionally, over 180 single-nucleotide polymorphisms (SNPs) were identified with more than one quarter of these resulting in a non-synonymous mutation. Affymetrix DNA microarrays and RNseq analysis were used to determine differences in gene expression in the evolved strains compared to the parental strain. It was established that approximately 900 genes demonstrated significantly altered expression in the evolved strains relative to the parental strain. Many of these genes showed similar alterations in their expression in all three evolved strains. Interestingly, genes with altered expression in the three evolved strains included genes with a role in the TCA cycle. Overall these results are consistent with the physiological observations of decreased ethanol production and suggest that the underlying metabolism switched from fermentation to respiration during aerobic growth.

overall_design: Yeast strains were grown in the presence of high glucose for approximately 450 generations.  Individual isolates were then grown and total RNA was collected to compare difference between the evolved strains and the parental strain.


title: Gene expression profiles of WT and ime4-/- mutant yeast cells, under vegetative and meiosis-inducing conditions

status: Public on Apr 25 2012

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

department: Cancer Research Center

institute: Sheba Medical Center

summary: Inactivation of the yeast IME4 gene, the yeast homologue of METTL3, was shown to result in the loss of m6A in mRNA of mutant cells grown in sporulation medium. We attempted to  characterize the effects of ime4 deletion on gene expression under vegetative and meiosis-inducing conditions. The results show that in vegetatively-growing ime4-/- cells there is an increased expression of the RME1 gene (repressor of meiosis) which prevents precocious entry into the meiotic program. Mutant yeast cells showed reduced expression levels of genes involved in ribosome biogenesis and gene expression processes. Surprisingly, despite the fact that a diploid strain was analyzed, there was also a striking change in the expression level of haploid-specific genes, suggesting that RNA methylation may be used to enforce the sexual identity of diploid cells, required for the implementation of the gametogenesis program. Consistently, when cells were induced to undergo meiosis, ime4-/- diploids failed to undergo the meiotic divisions. Among the genes showing reduced expression in the mutant were IME1 and IME2, the two known inducers of meiosis. Thus, the yeast IME4 gene plays an important role in the regulation of the developmental switch from vegetative cells into gametogenesis.

overall_design: WT and ime4 -/- yeast cells were grown vegetatively in YPD (Yeast extract, Peptone, Dextrose) medium, and transferred to sporulation medium(1% Kacetate) for induction of sporulation for 4 hrs. RNA was purified from the cells and hybridized to Affymetrix microarrays. Experiments were conducted in biological replicates.

first: Dan

last: Dominissini

first: Lior

last: Ungar

first: Martin

last: Kupiec

first: Jasmine

last: Jacob-Hirsch

first: Mali

last: Salmon-Divon

first: Gideon

last: Rechavi


title: Identification of a complex genetic network involved in Saccharomyces cerevisiae colony morphology

status: Public on Apr 28 2012

city: Leuven

first: Dries

last: De Maeyer

address: Gaston Geenslaan 1

country: Belgium

institute: CMPG/Bioincubator

summary: When grown on solid substrates, different microorganisms often form colonies with very specific morphologies.  Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much recent attention.  In this study, we use a genome-wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. We show that several major signaling cascades, including the MAPK, TORC, SNF1 and RIM101 pathways play a role, indicating that morphological changes are a reaction to changing environments. Other genes that affect colony morphology are involved in protein sorting and epigenetic regulation. Interestingly, the screen reveals only few genes that are likely to play a direct role in establishing colony morphology, one notable exception being FLO11, a gene encoding a cell-surface adhesin that has already been implicated in colony morphology, biofilm formation, and invasive and pseudohyphal growth. Using a series of modified promoters to tune FLO11 expression, we confirm the central role of Flo11 and show that differences in FLO11 expression result in distinct colony morphologies.  Together, our results provide a first comprehensive looks at the complex genetic network that underlies the diversity in the morphologies of yeast colonies.

overall_design: Microarrays were used to measure gene expression between WT and FLO11 mutants in both liquid and solid medium to assess which genes induce altered colony morphology through FLO11.

first: Elisa

last: van der Zande

first: Kevin

last: Verstrepen


title: Genome wide transcriptional oscillation for Saccharomyces cerevisiae CEN.PK122

status: Public on Apr 17 2012

city: Duarte

first: shwe

middle: lynn

last: chin

address: 1500 E Duarte Rd.

department: Biology

institute: Beckman Research Institute

summary: Genetic and environmental stresses are known factors that influence an organisms phenotype. Time is rarely taken into consideration when studying phenotypic changes in cells. Time-resolved microarray data revealed genome-wide transcriptional changes in yeast strain CEN.PK122 oscillating with~2 periods. We mapped the global patterns of transcriptional oscillationsinto a 3-dimensional map to represent different cellular phenotypes ofoscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other.

overall_design: High-resolution samples over time were collected for CEN.PK122 oscillating with 2 h period.

first: Shwe

last: Chin

first: Ian

last: Marcus

first: Robert

last: Klevecz

first: Caroline

last: Li


title: Dynamics of two oscillation phenotypes in S. cerevisiae [4hr]

summary: Genetic and environmental factors influence the phenotype of an organism. Time is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional changes in cells oscillating with ~2 and ~4 h periods. We mapped the global patterns of transcriptional oscillations into a 3-dimensional map to represent different cellular phenotypes of oscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. This ordered timing of biological process may allow cells to grow energetically efficient.  Decreased glucose levels in the media were found to increase the redox cycles of yeast strain CEN.PK113-7D. Glucose may have acted as signaling molecules for timing longer catabolic processes in the cell population. As oscillation period lengthened, the peak to trough ratio of transcripts increased and the percent of cells in the unbudded (G0/G1) phase of the cell cycle increased. Gene transcripts appear to be coordinated with metabolic functions and the cell cycle.

overall_design: High-resolution samples over time were collected for CEN.PK113-7D oscillating with 4 hour period.


title: Dynamics of two oscillation phenotypes in S. cerevisiae reveal a network of genome-wide transcriptional and cell cycle oscillators.

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

overall_design: Refer to individual Series


title: Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering

status: Public on Feb 29 2012

first: Kuk-Ki

last: Hong

address: Kemivägen 10

institute: Chalmers University of Technology

summary: Reconstructed mutants of yeast by inverse metabolic engineering were characterized by fermentation physiology and tools from systems biology.

overall_design: Six reconstructed mutants of yeast were grown on aerobic batch with galactose as carbon source

first: K

first: J

last: Nielsen


title: Expression data from S. cerevisiae, S288C with graded GCN5 F221A

status: Public on May 03 2012

city: AUSTIN

first: Amanda

middle: Morgan

last: Lanza

state: TX

address: 1 University Station C0400

department: Chemical Engineering

institute: University of Texas at Austin

summary:
S288C was transformed with plasmids expressing the GCN5 F221A mutant at varying levels.  We sought to examine the global impact on gene expression
using the Affymetrix yeast 2.0 arrays.

overall_design: TEF promoter strength varied from 32, 68 and 95% of the wild-type expression.  Controls included wild-type with empty & GCN5 null strain with empty plasmid.  Strains were grown for approximately 7 dblings in triplicate, followed by a mid-log phase RNA extraction.  Whole cell RNA was processed for Affymetrix yeast 2.0 arrays.

first: John

last: Blazeck

first: Nathan

middle: C

last: Crook

first: Hal

last: Alper


title: Microarray analysis of Saccharomyces cerevisiae expressing the Hsp90 mutant hsc82-W296A

status: Public on Apr 16 2012

city: Moscow

first: Jill

last: Johnson

state: ID

department: Biological Sciences

institute: University of Idaho

summary: Altered mRNA levels of HBT1 were observed in S. cerevisiae cells expressing hsc82-W296A compared to WT HSC82. We conducted microarray analysis to determine the extent of other changes in that strain.

overall_design: The yeast strain used contained chromosomal deletions of HSC82 and HSP82. WT HSC82 or hsc82-W296A was supplied on a plasmid so that it was the only Hsp90 present in the cell. Yeast were grown overnight in rich media at 30° and harvested during exponential growth phase. RNA was harvested from three cultures expressing WT Hsc82 and 3 cultures expressing the Hsp90 mutant..

first: Gary

last: Flom


title: Revealing the beneficial effect of protease supplementation to high gravity beer fermentations  using “–omics” techniques

status: Public on Feb 12 2012

first: wanwipa

last: vongsangnak

summary:
Addition of sugar syrups to the basic wort is a popular technique to achieve higher gravity in beer fermentations, but it results in dilution of the free amino nitrogen (FAN) content in the medium. The multicomponent protease enzyme Flavourzyme has beneficial effect on the brewer´s yeast fermentation performance during high gravity fermentations as it increases the initial FAN value and results in higher FAN uptake, higher specific growth rate, higher ethanol yield and improved flavour profile. In the present study, transcriptome and metabolome analysis were used to elucidate the effect on the addition of the multicomponent protease enzyme Flavourzyme and its influence on the metabolism of the brewer´s yeast strain Weihenstephan 34/70. The study underlines the importance of sufficient nitrogen availability during the course of beer fermentation. The applied metabolome and transcriptome analysis allowed mapping the effect of the wort sugar composition on the nitrogen uptake. Both the transcriptome and the metabolome analysis revealed that there is a significantly higher  impact of protease addition for maltose syrup supplemented fermentations, while addition of glucose syrup to increase the gravity in the wort resulted in increased glucose repression that lead to inhibition of amino acid uptake and hereby inhibited the effect of the protease addition.

Keywords: 21 Plato with two carbon  sources (glucose and maltose) and with/without enzyme supplementation

sample_organism: Saccharomyces pastorianus Weihenstephan 34/70

overall_design: Fermentation, transcriptome and metabolome analysis of industrial lager beer yeast strain Weihenstephan 34/70

first: M

last: Piddocke

first: A

last: Fazio

first: W

last: Vongsangnak

last: Wong

first: H

last: Heldt-Hansen

first: C

last: Workman

first: L

last: Olsson


title: Effect of dDAVP on outer medullary gene expression in Brattleboro rats

status: Public on Mar 01 2012

city: Berlin

first: Alexander

last: Paliege

address: Philippstr. 12

department: Anatomy

country: Germany

institute: Charité

summary:
Activation of the renal urine concentrating mechanism by vasopressin requires the coordinated regulation of multiple gene products including ion transporters, and water channels as well as regulatory proteins like protein kinases and phosphatases or enzymes involved in the energy-metabolism of the cells.
We used microarray analysis of AVP-regulated gene products in a rat model of central diabetes insipidus (DI) to generate a comprehensive database documenting these changes.

overall_design: For microarray studies young (8 weeks) adult male Brattleboro rats were randomly divided into 2 groups (n = 3 per group) and treated for 3 days with either 1-desamino-8-D-Arg vasopressin (dDAVP; 5ng/h; Sigma Aldrich, Germany) or vehicle via osmotic minipump (ALZET minipump model 2001, Charles River, Sulzfeld, Germany). At the end of the treatment period animals were sacrificed and the kidneys removed. The outer medulla was isolated and used for cDNA generation and subsequent microarray analysis using [Rat230_2] Affymetrix Rat Genome 230 2.0 Array.

first: Sebastian

last: Bachmann


title: Ecological success of a group of Saccharomyces cerevisiae / Saccharomyces kudriavzevii hybrids in the Northern European wine making environment.

status: Public on Feb 09 2012

city: Montpellier cedex1

first: Jean-Luc

last: Legras

address: 2, place Viala

department: UMR1083, Science pour l'Oenologie

institute: INRA

summary: The aim of this project was to evaluate the ploidy of a S. cerevisiae *S. kudriavzevii hybrid  in comparison to the lab strain S288C. Other wine yeast have been icluded in the project for the global analysis.

sample_organism: Saccharomyces cerevisiae x Saccharomyces kudriavzevii

overall_design: Comparison of Eg8 (2 arays) ,  to S288C (3 arrays), other strains V5, U13, Eg25 (2 arrays) are used to enable signal normalization acccross arrays with RMA package.

last: Erny

first: P

last: Raoult

last: Alais

first: G

last: Butterlin

first: F

last: Matei-Radoi

first: S

last: Casaregola

first: JL


title: Dynamics of two oscillation phenotypes in S. cerevisiae [2hr]

first: shwe

last: chin

overall_design: High-resolution samples over time were collected for CEN.PK113-7D oscillating with 2 hour period.

first: Shwe

last: Chin

first: Ian

last: Marcus

first: Robert

last: Klevecz

first: Caroline

last: Li


title: Gene expression response to the antifungal compound 6-Nonadecynoic acid (6-NDA) in Saccharomyces cerevisiae and Candida albicans

status: Public on Feb 08 2012

city: University

first: Ameeta

last: Agarwal

state: MS

address: NCNPR, Room 2049

department: National Center for Natural Products Research

institute: University of Mississippi

summary: 6-Nonadecynoic acid (6-NDA), a plant-derived acetylenic acid, exhibits strong inhibitory activity against the human fungal pathogens Candida albicans, Aspergillus fumigatus, and Trichophyton mentagrophytes.  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.  6-NDA elicited a transcriptome response indicative of fatty acid stress, altering the expression of genes known to be affected when yeast cells are grown in the presence of oleate.  Mutants of S. cerevisiae lacking transcription factors that regulate fatty acid beta-oxidation showed increased sensitivity to 6-NDA.  Fatty acid profile analysis indicated that 6-NDA inhibited the formation of fatty acids longer than 14 carbons in length.  In addition, the growth inhibitory effect of 6-NDA was rescued in the presence of exogenously supplied oleate.  To investigate the response of a pathogenic fungal species to 6-NDA, transcriptional profiling and biochemical analyses were also conducted in C. albicans.  The transcriptional response and fatty acid profile of C. albicans were comparable to those obtained in S. cerevisiae, and the rescue of growth inhibition with exogenous oleate was also observed in C. albicans.  In addition, 6-NDA enhanced the potency of the antifungal drug fluconazole  in a fluconazole-resistant clinical isolate of C. albicans.  Collectively, our results indicate that the antifungal activity of 6-NDA is mediated by a disruption in fatty acid homeostasis, and that this compound has potential utility in combination therapy in the treatment of drug-resistant fungal infections.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Candida albicans

overall_design:
Cultures of S. cerevisiae strain S288C were started at OD600 of 0.1, allowed to grow to OD600 of 0.2, then treated with either DMSO (0.25%) or 6-NDA at the IC50 concentration (2.2 ug/ml).  When OD600 of 0.5 was reached, cells were harvested and frozen.  Two biological replicate cultures were grown for each treatment, and RNA from each replicate was hybridized to 2 independent arrays, resulting in 4 hybridizations for each treatment.
Cultures of C. albicans strain SC5314 were started at OD600 of 0.1, allowed to grow to OD600 of 0.2, then treated with either DMSO (0.25%) or 6-NDA at the IC50 concentration (4 ug/ml).  When OD600 of 0.5 was reached, cells were harvested and frozen.  Three biological replicate cultures were grown for each treatment, and RNA from each replicate was hybridized as dye-swap pairs, resulting in 6 hybridizations for each treatment.


title: Expression data from yeast (wild type, rlm1 and swi3 mutants) exposed to Congo Red

status: Public on May 25 2012

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

summary: We did transcription profiling on the effect of rlm1 (MAPK Slt2 transcription factor) deletion and swi3 (component of SWI/SNF complex involved in chromatin remodeling) deletion in genes involved in cell wall stress (Congo Red) response.

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
2. presence of 30 µg/ml of Congo Red


title: LPS-induced expression in rat lung epithelial cells

first: Hitendra

last: Chand

address: 2425 Ridgecrest Dr SE

institute: Lovelace Respiraotry Research Institute

summary:
Acute lung inflammation can alter the pulmonary function of susceptible individuals and exacerbate the pathogenesis of chronic inflammatory lung diseases including chronic obstructive pulmonary disease (COPD), cystic fibrosis and asthma.  Exposure to lipopolysaccharide (LPS) or endotoxin, a constituent of outer cell membrane of gram negative bacteria, induces airway inflammation that is primarily characterized by increased polymorphonuclear neutrophils (PMNs) at early time points.  Because LPS is present in variety of occupational and home environments and is an active constituent of cigarette smoke it is a risk factor for increasing prevalence and severity of non-occupational COPD, for adult onset of asthma and for wheezing in children. In airway epithelial cells, LPS stimulation increases mucin gene expression and mucous production.  Hypersecretion of mucus overwhelms the ciliary clearance and obstructs airways, causing morbidity and mortality in chronic inflammatory respiratory lung diseases. In addition, acute bacterial infection contributes to the exacerbation of chronic airway diseases, specifically in advanced COPD and CF subjects, leading to increased healthcare burden and higher mortality. Bcl-2, a prosurvival protein that inhibits cell death plays a key role in normal cellular homeostasis and regulates the integrity of the mitochondrial and endoplasmic reticulum membranes.  Gain- and loss-of-function studies showed that Bcl-2 expression sustains hyperplastic epithelial cells, and Bcl-2 expression is elevated in airway epithelial cells of subjects with cystic fibrosis and asthma.  The present study investigated which inflammatory mediators induce mucous cell metaplasia and Bcl-2 expression following LPS exposure.  Microarray analyses of mRNA from airway epithelial cells captured by laser microdissection from rat lungs snap-frozen at day 0 and 2 post LPS exposure were analyzed.
Microarray analysis of mRNA from airway epithelial cells captured by laser microdissection from rat lungs snap-frozen at day 0 and day 2 post LPS exposure was performed to identify inflammatory mediators modulated by LPS exposure.

overall_design: Specific pathogen-free F344/NCrR male rats of 8–10 wk of age (from NCI, Frederick, MD) were exposed to LPS (1000 ug in 0.5 ML Saline) and rats were sacrificed on day 0 and day 2 of LPS exposure. Right lungs were snap-frozen in OCT and airway epithelial cells were captured by laser-dissection microsopy to extract RNA.  Gene expression data from nonexposed rats (0d) was used a  control.

first: Yangde

last: Chen

first: Paul

last: Wright


title: Transcriptomic analysis of the oxygen response in Saccharomyces cerevisiae EC1118 under wine fermentation conditions

status: Public on Jan 11 2012

city: Santiago

first: Felipe

middle: F

last: Aceituno

address: Vicuña Mackena 4860

department: Chemical Engineering and Bioprocesses

country: Chile

institute: PUC

summary: Oxygen additions play a critical role in winemaking. However, few studies have focused on how this oxygen affects yeast metabolism and physiology in wine making conditions. We performed microarrays to unveil the oxygen response in wine making conditions.

overall_design: We extracted RNA from  nitrogen-limited chemostats, simulating wine making conditions, sparged with nitrogen and 1%, 5% and 20% oxygen-nitrogen mixtures, at different flux regimes, to achieve different dissolved oxygen levels representative of those found during wine making. These correspond to 0, 1.2, 2.7, 5 and 21 micromolar dissolved oxygen

first: Marcelo

last: Orellana

first: Jorge

last: Torres

first: Sebastian

last: Mendoza

first: Alex

middle: W

last: Slater

first: Francisco

last: Melo

first: Eduardo

last: Agosin


title: Expression data from kidney transplantations in a Fisher-Lewis rat model: placebo and 13cisRA treatment

status: Public on Jan 07 2012

city: Neuherberg

first: Christine

last: von Toerne

address: Ingoldstädter Landstraße 1

department: Proteinanalytik

institute: HelmholtzZentrum

summary:
Most kidney allograft losses are caused by chronic allograft dysfunction (CAD). The aim of the study was to correlate changes in gene expression over time during the development of chronic damage in contrast to13cisRA Treated animal that demonstrated morphologically healthy kidneys by the end of teh study. Renal allografts were harvested from placebo and13cisRA Treatment groups for time points 0d, 7d, 14d and 56d (n=3-5) and examined for steady state mRNA expression using Affymetrix microarray RG-U34A. The effect of the13cisRA Treatment on dysregulated pathways was examined. In order to verify the microarray analysis, qPCR has been performed.
Microarray data was used to obtain transcriptomic changes reflecting signaltransduction pathway dysregulation

overall_design: Progression of rejection was observed in untreated animals at timepoints 7d, 14d and 56d after transplantation that could be prevented by 13cisRA treatment

first: Herrmann-Josef

last: Gröne

first: Peter

last: Nelson


title: Multiple chronic pain states are associated with a common amino acid-changing allele in KCNS1

status: Public on Jul 15 2011

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Not all patients with nerve injury develop neuropathic pain. The extent of nerve damage and age at the time of injury are two of the few risk factors identified to date. In addition, preclinical studies show that neuropathic pain variance is heritable. To define such factors further, we performed a large-scale gene profiling experiment which plotted global expression changes in the rat dorsal root ganglion in three peripheral neuropathic pain models. This resulted in the discovery that the potassium channel alpha subunit KCNS1, involved in neuronal excitability, is constitutively expressed in sensory neurons and markedly downregulated following nerve injury. KCNS1 was then characterized by an unbiased network analysis as a putative pain gene, a result confirmed by single nucleotide polymorphism association studies in humans. A common amino acid changing allele, the 'valine risk allele', was significantly associated with higher pain scores in five of six independent patient cohorts assayed (total of 1359 subjects). Risk allele prevalence is high, with 18-22% of the population homozygous, and an additional 50% heterozygous. At lower levels of nerve damage (lumbar back pain with disc herniation) association with greater pain outcome in homozygote patients is P = 0.003, increasing to P = 0.0001 for higher levels of nerve injury (limb amputation). The combined P-value for pain association in all six cohorts tested is 1.14 E-08. The risk profile of this marker is additive: two copies confer the most, one intermediate and none the least risk. Relative degrees of enhanced risk vary between cohorts, but for patients with lumbar back pain, they range between 2- and 3-fold. Although work still remains to define the potential role of this protein in the pathogenic process, here we present the KCNS1 allele rs734784 as one of the first prognostic indicators of chronic pain risk. Screening for this allele could help define those individuals prone to a transition to persistent pain, and thus requiring therapeutic strategies or lifestyle changes that minimize nerve injury.

overall_design: Microarrays were run on mRNA extracted from adult rat L4 and L5 DRGs cells after 3,7,21,40 hours after three different sciatic nerve lesions [Spared Nerve Injury (SNI); Chronic Constriction Injury (CCI); Spinal Nerve Ligation (Ch) with Sham controls (SH)].

first: M

last: Costigan

first: I

last: Belfer

first: R

middle: S

last: Griffin

first: F

last: Dai

first: L

middle: B

last: Barrett

first: G

first: T

last: Wu

first: C

last: Kiselycznyk

last: Poddar

first: Y

last: Lu

last: Diatchenko

first: S

last: Smith

first: E

last: Cobos

first: D

last: Zaykin

first: A

last: Allchorne

last: Gershon

first: J

last: Livneh

first: P

middle: H

last: Shen

last: Nikolajsen

last: Karppinen

last: Männikkö

last: Kelempisioti

last: Goldman

first: W

last: Maixner

last: Geschwind

last: Max

first: Z

last: Seltzer

last: Woolf


title: Pseudomonas putida KT2440 : Control vs. recG gene mutant with untreated or paraquat (PQ) treated

status: Public on Dec 15 2011

city: Seoul

first: Jinki

last: Yeom

address: Anam-Dong, Sungbuk-Gu

department: Life Science

country: South Korea

institute: Korea University

summary: Transcriptional profiling of P. putida KT2440 cells comparing control untreated wild type cells with untreated recG gene mutant cells or PQ  treated recG gene mutant cells

overall_design: Three-condition experiment, Control vs. untreated recG gene mutant and PQ treated recG gene mutant. Biological replicates: 4 samples independently grown and harvested


title: Pseudomonas putida KT2440 : Control vs. paraquat (PQ) or cumen hydroperoxide (CHP) treated

summary: Transcriptional profiling of P. putida KT2440 cells comparing control untreated cells with PQ or CHP treated cells

overall_design: Three-condition experiment, Control vs. treatment. Biological replicates: 1 control, 3 treated, independently grown and harvested


title: Phytochemical variations in medicinal herbs affecting bioefficacy: Equisetum arvense extracts in the global market place as a case study

status: Public on Dec 31 2011

city: Campbelltown

first: Rebekah

last: Cook

state: NSW

address: Narellan Road

department: CompleMED

country: Australia

institute: University of Western Sydney

summary: We used phytochemical profiling techniques to generate a list of compounds present in each of 13 Equisetum arvense samples sourced globally. We used microarrays to detail the global programme of gene expression underlying the treatment of the model system Saccharomyces cerevisiae to a chosen number of these extracts. A thorough bioinformatic analysis was performed to identify the relationship between phytochemical and gene expression response profiles.

overall_design: We analysed 18 Equisetum arvense microarrays. Six samples were chosen from the original 13 for microarray analysis, 5 of which were performed in duplicate and the sixth in quadruplicate. Control arrays were also performed in quadruplicate.

first: James

last: Hennell

first: Maria

last: Carles

first: Vincent

last: Higgins

first: Nikolaus

last: Sucher


title: Expression profile of nab2-1 mutant

status: Public on Dec 01 2011

city: Sevilla

first: Cristina

last: González-Aguilera

email: cgonagu@upo.es, aguilo@us.es

address: Avda Américo Vespucio s/n

department: Molecular Biology

institute: Universidad de Sevilla-CSIC/CABIMER

summary:
Gene expression in eukaryotes is an essential process that includes transcription, pre-RNA processing and RNA export. All these steps are coupled and normally, any failure in one step affects the other steps and could cause nuclear mRNA retention. One important player in this interface is the poly(A)-RNA binding protein Nab2, which regulates the poly(A)-tail length of mRNAs protecting their 3’-ends from a second round of polyadenylation and facilitating their nucleo-cytoplasmic export. Interestingly, here we show that Nab2 has additional roles in mRNA transcription elongation, tRNA metabolism and rRNA export.
We use Genome-wide analysis of expression of nab2-1 mutant to demosntrate that the role of Nab2 in RNAPII transcription and RNAPIII metabolism is not the result of a secondary effect. Our results identify primary targets of nab2 revealing novel functions for Nab2 in transcription and metabolism of most types of RNAs, not only poly(A) mRNAs, indicating that Nab2 function is more ubiquitous than previously anticipated, being a central player in the general and coordinated control of gene expression from transcription elongation to translation initiation.

overall_design: Three repeats of the wild type and nab2-1 mutant

last: González-Aguiera

first: Andrés

last: Aguilera


title: Expression profile of the “heat-inducible N-degron” of Nab2 (nab2-td)

summary:
Gene expression in eukaryotes is an essential process that includes transcription, pre-RNA processing and RNA export. All these steps are coupled and normally, any failure in one step affects the other steps and could cause nuclear mRNA retention. One important player in this interface is the poly(A)-RNA binding protein Nab2, which regulates the poly(A)-tail length of mRNAs protecting their 3’-ends from a second round of polyadenylation and facilitating their nucleo-cytoplasmic export. Interestingly, here we show that Nab2 has additional roles in mRNA transcription elongation, tRNA metabolism and rRNA export.
We use Genome-wide analysis of expression of a conditional degron nab2 mutant that allows the depletion of the protein in 15 minutes, to demosntrate that the role of Nab2 in RNAPII transcription and RNAPIII metabolism is not the result of a secondary effect. Our results identify primary targets of nab2 revealing novel functions for Nab2 in transcription and metabolism of most types of RNAs, not only poly(A) mRNAs, indicating that Nab2 function is more ubiquitous than previously anticipated, being a central player in the general and coordinated control of gene expression from transcription elongation to translation initiation.

overall_design: Two and three repeats of the wild type control and the nab2-td mutant respectively at time 0, 30 and 75 minutes after the degron induction.


title: Balancing Protein Folding and Disulfide Bond Formation Rates is Key to Mitigating Secretory Stress

city: Göteborg

first: Keith

middle: EJ

last: Tyo

department: Chemical and Biological Engineering

summary:
The protein secretory pathway must maintain homoeostasis while producing a wide assortment of proteins in different conditions.  It is also used extensively to produce many useful proteins in biotechnology.   As such, secretory pathway dysfunction can be highly detrimental to the cell, resulting in the molecular basis for many human diseases, and can drastically inhibit product titers in biochemical production.  Because the secretory pathway is a highly-integrated, multi-organelle system, dysfunction can happen at many levels and dissecting the root cause can be challenging.

To better understand some of these dysfunctions, we measured multiple systems-level states of the cell (physiology, transcriptome, metabolism) while secreting a small protein (insulin precursor) or a large protein (α-amylase).  This was carried out in the presence and absence of HAC1, a key transcription factor in maintaining secretory homeostasis.  Clear trends in cellular stress were apparent across multiple data resulting from our perturbations.  In particular, processes involving (1) degradation of protein / recycling amino acids, (2) overall transcription/translation repression, and (3) oxidative stress.

Apparent runaway oxidative radical production was explained by a thermodynamic model that we put forward for disulfide formation in the endoplasmic reticulum.  This model predicts that balancing the relative rates of protein folding and disulfide bond formation are key to easing oxidative stress.  These predictions have direct implications in how to engineer a broad range of recombinant proteins for secretion and provide potential hypotheses for the root causes of several secretory-associated diseases.

overall_design:
Yeast strains were constructed that produce and secrete (a) IP or (b) α-amylase and were compared to yeast strains containing (c) an empty vector in both wild-type and HAC1 deletion backgrounds.

These strains are named WN (WT with empty vector), WI (WT secreting IP), WA (WT secreting α-amylase), dN (Δhac1 with empty vector), dI (Δhac1 secreting IP), and dA (Δhac1 secreting α-amylase).  Strains were characterized in batch fermentation and samples were taken in mid-exponential phase.  Triplicate fermentations were carried out for each strain.

middle: E

first: Zihe

last: Liu

first: Dina

last: Petranovic

first: Jens

last: Nielsen


title: Effect of Concentration and type of Dietary Fatty Acid on Development of Nonalcoholic Fatty Liver Disease

status: Public on Oct 24 2011

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: The current study was designed to determine if dietary fatty acid concentration and composition affects the development and progression of nonalcoholic fatty liver disease. Male SD rats were overfed diets low (5%) or high (70%) fat diets via total enteral nutrition where the fat source was olive oil (monounsaturated), or corn oil (polyunsaturated). Overfeeding 5% corn oil produced little steatosis relative to feeding 5% olive oil. This was associated with lower fatty acid synthesis and reduced SREBP-c signaling in the 5% corn oil group. Overfeeding 70% fat diets increased steatosis and lead to increased liver necrosis in the 70% corn oil but not olive oil group. Increased injury after feeding polyunsaturated fat diets was linked to peroxidizability of hepatic free fatty acids and triglycerides and appearance of peroxidaized lipid products HETES and HODES previously linked to clinical nonalcoholic steatohepatitis.

overall_design: Male SD rats were overfed diets low (5%) or high (70%) fat diets via total enteral nutrition where the fat source was olive oil (monounsaturated) or corn oil (polyunsaturated).

first: M

middle: J

last: Ronis

middle: N

last: Baumgardner

last: Marecki

last: Badeaux

last: Sharma

middle: L

last: Blackburn

first: R

last: Till

first: X

last: Wu

first: K

last: Shankar

middle: A

last: Cleves

first: H

first: T

middle: M

last: Badger


title: Chemical Genetics of TOR Identifies an SCF Family E3 Ubiquitin Ligase Inhibitor

status: Public on Jun 30 2011

first: Mariam

last: Aghajan

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

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.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression profiling of wild-type and set3D fission yeast strains

status: Public on Jan 01 2012

city: London

first: Jim

last: Karagiannis

state: Ontario

address: 1151 Richmond St. N

country: Canada

institute: University of Western Ontario

summary:
In fission yeast the SET domain protein, Set3p  is required for the reliable execution of cytokinesis.
To address whether the deletion of the set3 gene might selectively alter expression of cytokinesis genes, expression profiling of wildtype and set3D strains was performed.

overall_design: Wild-type or set3D strains were grown to mid-log phase in YES media and treated with 0.5 mM LatA (or the solvent control, DMSO) for three hours at 30 degrees C.  Three biological replicates were performed.

first: Reza

last: Saberianfar

first: Stefan

last: Rentas


title: Transcription data from Saccharomyces cerevisiae yeast

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 FLO8 or MSS11 deletion and -overexpression on yeast transcript profiles compared to wild type in laboratory yeast strains Σ1278b and S288c.

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. By using similar growth conditions to what we use for adhesion phenotype determination we aim to correlate transcription profile changes to yeast behaviour (phenotypes).

first: Florian

last: Bauer


title: Expression data from the partially synthetic yeasts SynIXR-1D, -6B,  -22D, and controls.

status: Public on Sep 14 2011

city: Baltimore

first: Jessica

last: Dymond

state: MD

address: 733 N. Broadway BRB 320

department: High Throughput Biology Center

country: USA

institute: Johns Hopkins University School of Medicine

summary:
We have replaced the right arm of chromosome IX in Saccharomyces cerevisiae with a synthetic version to generate synIXR haploids.  The synthetic chromosome features multiple sequeunce modifications.
We analyzed gene expression by microarray analysis in three synIXR haploids (1D, 6B, and 22D) to detect any changes in synIXR transcripts or global compensatory changes.

overall_design: Biological triplicates of three synIXR haploids (1D, 6B, and 22D) and corresponding controls (either BY4741 or BY4742) were grown to mid-log phase and collected for mRNA isolation.

first: Jef

middle: D

last: Boeke


title: Interaction of Snf1 with TORC1 in yeast Saccharomyces cerevisiae

status: Public on Oct 20 2011

city: Kgs. Lyngby

first: Jie

last: Zhang

address: Kemitorvet 220

department: CFB

institute: Technical University of Denmark

summary: Snf1 and TORC1 are two global regulators that sense the nutrient availability and regulate the cell growth in yeast Saccharomyces cerevisiae. Here we undertook a systems biology approach to study the effect of deletion of these genes and investigate the interaction between Snf1 and TORC1 in regulation of gene expression and cell metabolism.

overall_design: 3 mutant strains (snf1Δ, tor1Δ, snf1Δtor1Δ) together with 1 reference strain grown under both glucose-limited or amonia-limited defined media with three biological replicates for each strain

first: J

first: S

last: Vaga

first: P

last: Chumnanpuen

last: Kumar

first: G

last: Vemuri

last: Aebersold

last: Nielsen


title: Genome-wide Response of Saccharomyces cerevisiae upon Arsenate Exposure

status: Public on Nov 04 2011

city: Oeiras

first: Liliana

middle: Batista

last: Nascimento

address: Avenida da Republica

department: Biological Chemistry

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica

summary: Arsenic metalloid is a double-edge sword. On the one hand it is a very toxic and powerful carcinogen, and on the other it has been successfully used in the treatment of acute promyelocytic leukemia. In order to prevent the deleterious effects caused by arsenic compounds, almost all living organisms have developed mechanisms to eliminate it.  In this study genome-wide response of S. cerevisiae to arsenic shows that this metal interferes with genes involved in the iron homeostasis including those encoding proteins that function in iron uptake, incorporation into Fe–S clusters, and more. In addition our data indicate that Yap1 transcriptionally controls the iron homeostasis regulator AFT2 as well as its direct target, MRS4. Most importantly in response to arsenate exposure Yap1 strongly regulates the expression of several genes involved in the Fe-S proteins biosynthesis, namely NBP35 and YFH1.    Interestingly mRNA levels encoding Fet3, Ferro-O2-oxidoreductase required for high-affinity iron uptake, are drastically destabilized upon arsenic exposure. Such destabilization is due to the 5’ to 3’ exonuclease Xrn1 localized in the P Bodies. Moreover FET3 mRNA decay is not mediated by Cth2 and is independent on the formation of ROS responsible for the toxic effects of arsenic compounds. Strikingly, in presence of arsenate fet3 mutant shows resistance over the wild-type which leads us to suggest that Fet3 has a role in arsenic toxicity. Unexpectedly arsenic treatment seems to activate the non-reductive iron uptake in order to maintain the cellular iron homeostasis. Furthermore our genetic, biochemical, and physiological analysis demonstrate that aft1 mutant is sensitive to arsenic compounds and such phenotype is reversible upon addition of iron. We also show that arsenic exposure induces iron deficiency in aft1 mutant.   In conclusion this work shows for the first time that arsenic, a chemotherapy drug used to treat a specific type of acute promyelocytic leukemia (APL), disrupts iron homeostasis and our results suggest that this disruption is independent on ROS generation. Finally we provide preliminary data confirming that such disruption also takes place in mammalian cells, an observation that can be very relevant in term of clinical applications.

overall_design: yap1yap8 mutant cells independently transformed with pRS416 and YcpLac111, YcpLac111-YAP1, or pRS416-YAP8 were grown in triplicates in SC-URA-LEU containing 2mM of AsV until exponential growth phase, and RNA was extracted, labeled, and hybridized to Affymetrix Yeast Genome S98 arrays.