title: Expression profiles of evolved clones isolated at various stages during adaptive experimental evolution of E. coli

city: Kawasaki

first: Yoko

last: Asakura

state: Kanagawa

address: 1-1 Suzuki-cho Kawasaki-ku

department: Institule of Life Sciences

country: Japan

institute: Ajinomoto

summary:
An Eschericia coli strain was constructed in which the PaeR7 restriction-modification gene complex was present under an unstable condition on a partially duplicated chromosomal region so that it may continuously attack the host genome to accelerate its evolution. This strain was grown for more than a hundred of generations through repeated cycles of saturation and dilution. The winners of this competition showed faster growth than the ancestor. Analysis of their genome and transcriptome revealed that they have acquired rearrangements in genes affecting their growth. The global expression pattern changes may have realized growth advantage during the adaptation experiment.

Keywords: time course during adaptive evloution

overall_design: We used microarrays to know the genetic mechanism underlying adaptive evolution process, and to know the global expression changes that realize advantage in growth during adaptation. Four populations of the parent strain (YA027) and two populations of isogenic r-m+ strain (YA074), for control, were grown and serially propagated in amino acid rich medium (Davis’s MM supplied with 20 amino acids) with Cm (chloramphenicol) and Km (kanamycin), daily with 100-fold dilution. One passage corresponds to 6 - 7 generations, though it might be changed with evolution. Their growth was monitored daily. The growth curve shifted upwards every day in every population, reflecting improvement both in the initial growth rate and the saturation cell density through the evolution. To follow genome changes and global expression changes during adaptive evolution, we selected clones that might represent several stages of evolution with respect to growth from an r+m+ population (population #3) at the 11th, 84th, and 172th passage (corresponding 70, 500, and 1000 generations, respectively): 3-11-2, 3-11-4, 3-11-9, and 3-11-10 from the 11th passage; 3-84-2, 3-84-4, 3-84-6, and 3-84-10 from the 84th passage, and 3-172-1, 3-172-9, and 3-172-10 from the 172nd passage.  We subjected them to transcriptome analysis. All gene expression measurements were duplicated or triplicated.

first: Ichizo

last: Kobayashi


title: L. lactis NZ9000 (pNZbcaP-H6) Vs. L. lactis NZ9000 (pNZ8048)

status: Public on Jul 20 2011

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Our transcriptome data shows that the two-component system CesSR, which senses cell envelope stresses of different origins, is one of the major players when L. lactis is forced to overproduce the endogenous membrane protein BcaP, a branched-chain amino acid permease.

sample_organism: Lactococcus cremoris subsp. cremoris NZ9000

platform_organism: Lactococcus cremoris subsp. cremoris MG1363

overall_design: Two-condition experiment: nisin induced overproduction of BcaP vs. control. Biological replicates: 2 controls, 2 overproduction cultures; independently grown and harvested; dye swaped on the second array.

first: Joao

middle: P

last: Pinto

first: Oscar

last: Kuipers

first: Ravi

middle: K

last: Marreddy

first: Bert

last: Poolman

first: Jan

last: Kok


title: affy_dormance_mrnaoxidized_sunflower-Molecular mechanisms of seed dormancy release: transcriptome evolution and ROS signalling during sunflower seed after-ripening.

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary: affy_dormance_sunflower - affy_dormance_mrnaoxidized_sunflower - We focus our research on the release of embryonic dormancy in sunflower seeds and more precisely on the molecular mechanisms controlling seed dormancy release during dry after-ripening. Our data show an increase of ROS during dormancy release associated with an increase of stored mRNA oxidation during after-ripening as shown with determination of the RNA oxidation marker : 8-hydroxyguanosine (8OHG) To assess to role of mRNA oxidation in this process, we isolated 8OHG-containing mRNA to identify oxidized transcript using microarray analysis.-The samples compared are the following: 1) 8OHG containing mRNA isolated from total RNA extracted from a population of 100 embryonic axis of dry dormant seed (Dox) ie. Seed which have been frozen at -30°C after harvest to keep dormancy  2) 8OHG containing mRNA isolated from total RNA extracted from a population of 50 embryonic axis from dry non dormant ie. Seeds which have been after-ripened (stored) at 70% RH during 2 month (NDox)   Replicates correspond to different batches of seeds from the same harvest, which have been treated (after ripened) independently and from which the 8OHG containing fraction have been isolated independently.

overall_design: 4 arrays - SUNFLOWER; dormancy

first: Sandrine

last: Arribat

last: Balzergue

first: Hayat

last: Bouteau

first: Jérémie

last: Bazin

first: Marie-Laure

last: Martin-Magniette


title: Genomic Profiling of mouse mammary tumor models identifies miRNA signatures associated with mammary tumor lineage (mammary normal and tumors in different mice strains)

status: Public on Jul 21 2011

city: Bethesda

first: Jeffrey

middle: E

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

country: USA

institute: NCI

summary:
MicroRNAs (miRNAs) are small, non-coding, endogenous RNAs involved in many human diseases including breast cancer. miRNA expression profiling of human breast cancers has identified miRNAs related to the clinical diversity of the disease and potentially provides novel diagnostic and prognostic tools for breast cancer therapy. In order to further understand the roles of miRNAs in association with oncogenic drivers and in specifying sub-types of breast cancer, we performed miRNAexpression profiling on mammary tumors from eight well-characterized genetically -engineered Mouse (GEM) models of human breast cancer including MMTV–H-Ras, -Her2/neu, -c-Myc, -PymT, –Wnt1 and C3(1)/SV40 T/t-antigen transgenic mice, BRCA1fl/fl;p53+/-;MMTV-cre and the p53fl/fl ;MMTV-cre transplant model.
As supplementary data

overall_design: miRNA expression data for 3 mouse primary mammary tumors and 8 mouse normal mammary glands from different mouse strains

first: Min

last: Zhu

first: Ming

last: Yi

first: Chang

middle: H

last: Kim

first: Chuxia

last: Deng

first: Yi

last: Li

first: Daniel

last: Medina

first: Robert

last: Stephen

first: Jeff


title: hcf-1(-) transcriptional profiling

status: Public on Jul 23 2011

city: Ithaca

first: Gizem

last: Rizki

state: NY

address: 526 Campus Road, 341 Biotech

institute: Cornell University

summary: We used microarrays to identify genes regulated by HCF-1 in a daf-16-dependent manner.

overall_design: Samples from young adult worms were hybridized to Agilent microarrays to identify genes differentially expressed in hcf-1(pk924)/daf-16(mgDf47);hcf-1(pk924) and compared to hcf-1(pk924)/N2 arrays.

first: Coleen

middle: T

last: Murphy

first: Colette

middle: L

last: Picard

first: Siu

middle: S

last: Lee


title: The role of the protein kinase-A pathway in the response to alkaline pH stress in yeast

status: Public on Jul 16 2011

city: Cerdanyola

first: Carlos

last: Casado

address: Edifici IBB, Campus Bellaterra

department: Departament Bioquimica i Biologia Molecular

country: Spain

institute: Universitat Autònoma de Barcelona

summary: Exposure of Saccharomyces cerevisiae to alkaline pH represents a stress condition that generates a compensatory reaction. Here we examine a possible role of the protein kinase-A (PKA) pathway in this response. The phenotypic analysis reveals that mutations that activate the PKA pathway (ira1 ira2, bcy1) tend to cause sensitivity to alkaline pH, whereas its deactivation develops tolerance to this stress. We observe that alkalinization causes a transient decrease in cAMP, the main regulator of the pathway. Alkaline pH causes rapid nuclear localization of the PKA-regulated Msn2 transcription factor which, together with Msn4, mediates a general stress response by binding to STRE sequences in many promoters. Consequently, a synthetic STRE-LacZ reporter shows a rapid induction in response to alkaline stress. An msn2 msn4 mutant is sensitive to alkaline pH, and transcriptomic analysis reveals that after 10 minutes of alkaline stress, the expression of many induced genes (47%) depends, at least in part, on the presence of Msn2 and Msn4. Taken together, these results demonstrate that inhibition of the PKA pathway by alkaline pH represents a substantial part of the adaptive response to this kind of stress and that this response involves Msn2/Msn4-mediated gene remodeling. However, the relevance of attenuation of PKA in high pH tolerance is not restricted to regulation of Msn2 function.

overall_design:
Eight samples were analyzed: WT and the MCY5278 mutant strain, lacking both Msn2 and Msn4, in the presence of 20 mM KOH (pH 8) and in the presence of 20 mM KCl (non-induced conditions) for 10 and 30 min of stress. 2 biological replicates were analyzed for each condition, and dye-swapping was carried out for each comparison of samples.

We compared the expression profiles of:

1) WT +KOH vs. WT +KCl after 10 min
2) msn2 msn4 mutant +KOH vs. msn2 msn4 +KCl after 10 min
3)WT +KOH vs. WT +KCl after 30 min
4) msn2 msn4 mutant +KOH vs. msn2 msn4 +KCl after 30 min

Total number of chips analyzed: 16.

first: Asier

last: González

first: Maria

last: Platara

first: Amparo

last: Ruiz

first: Joaquín

last: Ariño


title: Mouse expression analysis

status: Public on Jul 19 2011

city: Rostock

first: Markus

last: Krohn

address: Gehlsheimer Str. 20

country: Germany

institute: University of Rostock

summary: Comparison between APPPS1-FVB and APPPS1-FVBxABCC1ko mice

overall_design: Mouse brain expression analysis

first: Cathleen

last: Lange

first: Jacqueline

last: Hofrichter

first: Katja

last: Scheffler

first: Jan

last: Stenzel

first: Johannes

last: Steffen

first: Toni

last: Schumacher

first: Thomas

last: Brüning

first: Anne-Sophie

last: Plath

first: Franziska

last: Alfen

first: Anke

last: Schmidt

first: Felix

last: Winter

last: Rateitschak

first: Andreas

last: Wree

first: Jörg

last: Gsponer

first: Lary

middle: C

last: Walker

first: Jens

last: Pahnke


title: Alterations in the transcriptome and antibiotic susceptibility of Staphylococcus aureus grown in the presence of diclofenac

city: Tampa

first: James

last: Riordan

state: FL

address: 4202 E Fowler Ave

department: CMMB

institute: University of South Florida

summary: Diclofenac is a non-steroidal anti-inflammatory drug (NSAID) which has been shown to increase the susceptibility of various bacteria to antimicrobials and demonstrated to have broad antimicrobial activity.  This study describes transcriptome alterations in S. aureus strain COL grown with diclofenac and characterizes the effects of this NSAID on antibiotic susceptibility in laboratory, clinical and diclofenac reduced-susceptibility (DcRS) mutant S. aureus strains.

overall_design: Four hybridizations, including a biological replicate and a dye-swap experiment for each replicate was carried out. LOWESS normalization was performed on the raw data to correct for dye-bias. Statistical analysis was performed using a significance analysis of microarrays (SAM, MultiExperiment Viewer, ver. 4.0) unpaired contrast.  A d-statistic was calculated for each gene based on repeated permutations, and a false discovery rate FDR of 0.01 was used to assign a critical cutoff for significance.

first: JoAnne

middle: M

last: Dupre

first: Stephanie

middle: A

last: Cantore-Matyi

first: Atul

last: Kumar-Singh

first: Yang

last: Song

first: Shahrear

last: Zaman

first: Sonia

last: Horan

first: Nada

last: Helal

first: Vijayaraj

last: Nagarajan

first: Mohamed

middle: O

last: Elasri

first: Brian

middle: J

last: Wilkinson

first: John

last: Gustafson


title: Copy number profiling of 13 IDH1 WT and 8 IDHI mutants newly diagnosed, previously untreated Glioblastoma specimens

city: South San Francisco

first: Zhaoshi

last: Jiang

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc

summary: Genomic DNA extracted from tumor samples were profiled on Agilent Human 1X1M aCGH Array

overall_design: Profiling copy number changes of GBM samples

first: Samir

last: Kharbanda

first: Heidi

last: Phillips

first: Robert

last: Soriano

first: Zora

last: Modrusan


title: Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Benzene vs. Phenol)

city: Amherst

first: Dawn

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

summary: Anaerobic benzene oxidation coupled to the reduction of Fe(III) was studied in Ferroglobus placidus in order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions.  F. placidus conserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor.  The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [14C]-benzene to [14C]-carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III).  Benzoate, but not phenol or toluene, accumulated at low levels during benzene metabolism and [14C]-benzoate was produced from [14C]-benzene.  Analysis of gene transcript levels revealed increased expression of genes encoding enzymes for anaerobic benzoate degradation during growth on benzene versus growth on acetate, but genes involved in phenol degradation were not up-regulated during growth on benzene.  A gene for a putative carboxylase that was more highly expressed in benzene- versus benzoate-grown cells was identified.  These results suggest that benzene is carboxylated to benzoate and that phenol is not an important intermediate in the benzene metabolism of F. placidus.  This is the first demonstration of a microorganism in pure culture that can grow on benzene under strict anaerobic conditions and for which there is strong evidence for degradation of benzene via clearly defined anaerobic metabolic pathways.  Thus, F. placidus provides a much needed pure culture model for further studies on the anaerobic activation of benzene in microorganisms.

overall_design: A six-chip study using total RNA recovered from three separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM  benzene (experimental condition) and three separate cultures of Ferroglobus placidus DSM 10642 grown on 0.5 mM phenol (control condition).  Each chip measures the expression level of 2,613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Carla

last: Risso

first: Jessica

last: Smith

first: Derek

last: Lovley


title: Mycobacterium smegmatis: I-SceI homing endonuclease generated genomic DNA damage in Darr strains expressing ArrWT, ArrH18A, ArrD83A, or an empty vector vs WT M. smegmatis Mc2155 (mgm182, site(+))

status: Public on Jul 15 2011

city: St Louis

first: Christina

middle: Leigh

last: Stallings

state: Mo

address: 660 South Euclid Avenue, Box 8230

department: Molecular Microbiology

institute: Washington University School of Medicine

summary:
Transcriptional profiling of Mycobacterium smegmatis comparing strains undergoing I-SceI generated DNA damage at a single genomic locus
Gene designations are the updated annotation

overall_design: Four comparisons were made, all with log phase cultures and no ATc added. Darr Site(+) with an empty vector compared to wild-type M. smegmatis Site(+), Darr Site(+) with a vector expressing WT Arr compared to wild-type M. smegmatis Site(+), Darr Site(+) with a vector expressing ArrH18A compared to wild-type M. smegmatis Site(+), Darr Site(+) with a vector expressing Arr D83A compared to wild-type M. smegmatis Site(+). 3 biological replicates of each strain for each experiment.

first: Michael

last: Glickman


title: Wnt signaling involved in mouse myoblast differentiation

city: Kurashiki

first: Tsutomu

last: Nohno

address: 577 Matsushima

department: Molecular and Developmental Biology

institute: Kawasaki Medical School

summary: Wnt/β-catenin signaling is involved in various aspects of skeletal muscle development and regeneration. In addition, Wnt3a and β-catenin are required for muscle-specific gene transcription in embryonic carcinoma cells and satellite-cell proliferation during adult skeletal muscle regeneration. Downstream targets of canonical Wnt signaling are cyclin D1 and c-myc. However, both target genes are suppressed during differentiation of mouse myoblast cells, C2C12. Underlying molecular mechanisms of β-catenin signaling during myogenic differentiation remain unknown. Using C2C12 cells, we examined intracellular signaling and gene transcription during myoblast proliferation and differentiation. We confirmed that several Wnt signaling components, including Wnt9a, Sfrp2 and porcupine, were consistently upregulated in differentiating C2C12 cells. Troponin T-positive myotubes were decreased by Wnt3a overexpression, but not Wnt4. TOP/FOP reporter assays revealed that co-expression with Wnt4 reduced Wnt3a-induced luciferase activity, suggesting that Wnt4 signaling counteracted Wnt3a signaling in myoblasts. FH535, a small-molecule inhibitor of β-catenin/Tcf complex formation, reduced basal β-catenin in cytoplasm and decreased myoblast proliferation. K252a, a protein kinase inhibitor, increased membrane-bound β-catenin and enhanced myoblast fusion. Treatments with K252a or Wnt4 resulted in increased cytoplasmic vesicles containing phosphorylated β-catenin (Tyr654) during myogenic differentiation. These results suggest that various Wnt ligands control subcellular β-catenin localization, which regulate myoblast proliferation and myotube formation. Wnt signaling via β-catenin likely acts as a molecular switch that regulates the transition from cell proliferation to myogenic differentiation.

overall_design: Control cells (day 0) prior to differentiation induction with n=4; differentiated for two days with n=3; differentiated for four days with n=3.

first: Shingo

last: Tanaka


title: Identification of Hoxb1b regulated genes in zebrafish embryos

city: Aurora

first: Charles

last: Sagerstrom

state: CO

address: 12801 East 17th Avenue

department: Pediatrics

institute: University of Colorado Medical School

summary: Microarrays containing the Compgen/Sigma-Genosys XEBLIB96 oligo set (which represents about 12,500 unique genes) was used to identify 100 genes up-regulated more than 2-fold by hoxb1b in zebrafish embryos

overall_design: Fertilized zebrafish embryos were injected with hoxb1+meis3 mRNA or meis3 mRNA alone and raised to 14 hpf followed by dissection of the anterior 1/3 of the embryo to identify genes ectopically induced by Hoxb1b.

first: Seong-Kyu

last: Choe

first: Xiaolan

last: Zhang

first: Nicolas

last: Hirsch


title: ChIP-chip of the Cryptococcus neoformans transcription factor GAT201 and expression profiling of gat201KO

city: San Francisco

first: Cheryl

last: Chun

institute: UC San Francisco

type: Genome binding/occupancy profiling by genome tiling array

summary:
identify binding sites of Gat201 in C. neoformans cells grown in DMEM at 37C in 5% CO2
The anti-phagocytic polysaccharide capsule of the yeast C. neoformans is a major virulence attribute. However, previous studies of the pleiotropic virulence determinant Gat201, a GATA-family transcription factor, suggested that capsule-independent antiphagocytic mechanisms exist. We have determined that Gat201 controls the mRNA levels of ~1100 genes (16% of the genome) and binds the upstream regions of ~130 genes. Seven Gat201-bound genes encode for putative and known transcription factors⎯including two previously implicated in virulence⎯suggesting an extensive regulatory network. Systematic analysis pinpointed two critical Gat201-bound genes, GAT204 (a transcription factor) and BLP1, which account for much of the capsule-independent antiphagocytic function of Gat201. A strong correlation was observed between the quantitative effects of single and double mutants on phagocytosis in vitro and on host colonization in vivo. This genetic dissection provides the first clear evidence that capsule-independent anti-phagocytic mechanisms are pivotal for successful mammalian infection by C. neoformans.

overall_design:
two biological replicates were performed of wild type strains without any tagged ORF and strains carrying a CBP-FLAG tag at the Gat201 ORF.  Whole cell extract (WCE) is in the Cy3 channel, the IP material is in the Cy5 channel.

expression profiling of wild-type and gat201KO cells grown in YPAD or DMEM/5% CO2
two separate experiments: comparison of YPAD-grown samples and comparison of DMEM/5% CO2-grown samples
samples on arrays CHM7-251, CHM7-253, CHM7-254, and CHM7-260 were grown in DMEM; samples on arrays CHM7-256, CHM7-257, CHM7-258, and CHM7-259 were grown in YPAD

middle: D

last: Brown

first: Hiten

last: Madhani


title: Design of a Diagnostic Pan-Pathogen Oligonucleotide Microarray including a sub-Array for Detection of Meningitis-Causing Bacterial Pathogens

city: Salisbury

first: Karen

middle: Elizabeth

last: Kempsell

state: Wiltshire

address: Porton Down

department: Science Group

country: United Kingdom

institute: UK Health Security Agency

summary: Meningitis is a complex disease which can be caused by infection with either viral or bacterial pathogens. Viral meningitis is usually a sterile self-limiting disease with a good clinical prognosis, while bacterial meningitis is a potentially more serious disease with a higher mortality rate. Early diagnosis of bacterial meningitis is of paramount importance, as intervention with antimicrobial therapy increases the likelihood of a favourable clinical outcome.  Routine diagnosis in many laboratories is still dependent to some degree on traditional methods e.g. culture, though molecular methods have been developed which can give a shorter time to diagnosis.  However, there is not as yet a single test format that can detect all bacterial pathogens capable of causing meningitis.  In addition, many tests e.g. real-time PCR have a finite limit for multiplexing and do not provide additional information such as strain or serogroup which is useful during outbreaks and for retrospective epidemiological surveillance. To this end we have developed a microarray probe set for detection of meningitis-associated bacterial pathogens including those in the N. meningitidis serogroups. Here we demonstrate utility of this array in specific detection of represented bacterial species and strains and in detection of pathogen signals in cerebrospinal fluid samples from patients with suspected bacterial meningitis. This method shows promise for development as a diagnostic tool; however, we discuss the technical issues encountered and suggest mechanisms to improve resolution of pathogen-specific signals in complex clinical samples.

sample_organism:
Neisseria flavescens
Neisseria lactamica
Neisseria meningitidis
Haemophilus influenzae
Staphylococcus aureus
Streptococcus agalactiae
Streptococcus pneumoniae
Listeria monocytogenes
Homo sapiens

overall_design: We designed as part of a larger pan-pathogen microarray a sub-set of probes to meningitis-associated bacterial pathogens. We present here data confirming the pathogen-specificity of many of these probes and their potential use in clinical diagnosis through testing on a  small number of patient clinical samples using human DNA and no added nucleic acid controls. These data are from single channel Cy3-labelled nucleic acids. Four technical replicates for each feature are included on the array.

first: Stephanie

last: Vollmer

first: Sonal

last: Shah

last: Watson

last: Elmore

first: W

last: Telfer Brunton

first: Pete

last: Marsh

first: Steve

last: Green

first: Richard

last: Vipond

first: Nigel

last: Silman


title: Mycobacterium smegmatis: I-SceI homing endonuclease generated genomic DNA damage (site(+), mgm182) vs control (site(-), mgm181)

first: Christina

last: Stallings

summary:
Transcriptional profiling of Mycobacterium smegmatis comparing a strain undergoing I-SceI generated DNA damage at a single genomic locus versus a control strain with no I-SceI recognition sequence in its genome (and thus not undergoing double strand DNA breaks
Gene designations are from the original annotation, not the updated

overall_design: Five conditions investigated: Log phase cultures without induction of I-SceI expression (T=0, -Atc), Log phase cultures induced to express I-SceI by the addition of ATc for 45 minutes (T=45, +ATc), Stationary cultures control without induction of I-SceI expression (T=0, -Atc), Stationary phase cultures induced to express I-SceI by the addition of ATc for 15 minutes (T=15, +ATc), and Stationary cultures induced to express I-SceI for 45 minutes by the addition of ATc (T=45, +ATc). 3 biological replicates of each strain for each experiment.

first: Michael

last: Glickman


title: Expression analysis of Pseudomonas fluorescens Pf0-1 (Wt) and delta-pst mutant grown in K10T-1 medium

status: Public on Jul 14 2011

city: Hanover

first: Peter

last: Newell

state: NH

address: 1 North College Street

department: Microbiology and Immunology

institute: Dartmouth Medical School

summary:
Whole genome gene expression study comparing Pseudomonas fluorescens Pf0-1 (Wt) relative to a delta-pst mutant (deletion of the pstSCAB operon) that consitutively expresses the Pho regulon
Mutants used in this study are further described  in Monds, R.D. Newell, P.D., Gross, R.H., O'Toole, G.A. (2007) Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA. Mol. Microbiol. 63(3): 656-679

overall_design: A four chip study using total RNA recovered from two independent wild-type cultures of wild type strain Pseudomonas fluorescens Pf0-1 and two independent cultures of  Pseudomonas fluorescens Pf0-1 delta pst mutant (deletion of the pstSCAB operon). Each chip measures the expression level of 5733 open reading frames (ORFs) genes from Pseudomonas fluorescens Pf0-1 (Refseq: NC_007492) with twenty 60-mer postive match (PM) probes per gene, with three-fold technical redundancy.

first: Russell

last: Monds

first: George

last: O'Toole


title: Anaerobic Oxidation of Benzene by the Hyperthermophilic Archaeon Ferroglobus placidus (Phenol vs. Benzoate)

first: Dawn

last: Holmes

overall_design: A five-chip study using total RNA recovered from three separate cultures of Ferroglobus placidus DSM 10642 grown with 0.5 mM phenol (experimental condition) and two separate cultures of Ferroglobus placidus DSM 10642 grown on 1 mM benzoate (control condition). Each chip measures the expression level of 2,613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Carla

last: Risso

first: Jessica

last: Smith

first: Derek

middle: R

last: Lovley


title: In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh

status: Public on Jul 12 2011

city: Boston

first: Richelle

middle: C.

last: Charles

state: MA

address: 55 Fruit Street, Gray 504

department: Infectious Diseases

institute: Massachussetts General Hospital

summary: We applied an RNA capture and amplification technique, Selective Capture of Transcribed Sequences (SCOTS), and microarray hybridization to identify S. Typhi transcripts expressed in the blood of five humans infected with S. Typhi in Bangladesh.  In total, we detected the expression of mRNAs for 2046 S. Typhi genes (44% of the S. Typhi genome) in human blood; expression of 912 genes was detected in all 5 patients, and expression of 1100 genes was detected in 4 or more patients.  Identified transcripts were associated with the virulence-associated PhoP regulon, Salmonella pathogenicity islands, the use of alternative carbon and energy sources, synthesis and transport of iron, thiamine, and biotin, and resistance to antimicrobial peptides and oxidative stress.  The most highly represented group were genes currently annotated as encoding proteins designated as hypothetical, unknown, or unclassified.  Of the 2046 detected transcripts, 1320 (29% of the S. Typhi genome) had significantly different levels of detection in human blood compared to in vitro cultures; detection of 141 transcripts was significantly different in all 5 patients, and detection of 331 transcripts varied in at least 4 patients.  These mRNAs encode proteins of unknown function, those involved in energy metabolism, transport and binding, cell envelope, cellular processes, and pathogenesis.  We confirmed increased expression of a subset of identified mRNAs by quantitative-PCR.

sample_organism: Salmonella enterica subsp. enterica serovar Typhi

overall_design: We compared transcriptional profiles of S. Typhi from the blood of infected humans to S. Typhi grown in vitro

first: Alaullah

last: Sheikh

first: Nusrat

last: Sharmeen

first: Sean

last: Rollins

first: Jason

middle: B

last: Harris

first: Md

last: Bhuiyan

first: Mohammad

last: Arifuzzaman

first: Farhana

last: Khanam

first: Archana

last: Bukka

first: Anuj

last: Kalsy

first: Steffen

last: Porwollik

first: Daniel

last: Leung

last: Brooks

first: Regina

last: LaRocque

last: McClelland

first: Elizabeth

last: Hohmann

first: Tanya

last: Logvinenko

first: Alejandro

last: Cravioto

first: Stephen

last: Calderwood

first: James

last: Graham

first: Firdausi

last: Qadri

first: Edward

last: Ryan


title: A unique iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis [Expression Array]

status: Public on Jul 13 2011

first: Changbin

last: Chen

state: California

address: HSE450, 513 Parnassus Avenue

department: Department of Microbiology & Immunology

institute: University of California, San Francisco

summary: The mammalian gastrointestinal tract and the bloodstream are highly disparate biological niches, and yet certain commensal-pathogenic microorganisms are able to thrive in both environments.  Here, we report the evolution of a unique transcription circuit in the yeast, Candida albicans, which determines its fitness in both host niches.  Our comprehensive analysis of the DNA-binding proteins that regulate iron uptake by this organism suggests the evolutionary intercalation of a transcriptional activator called Sef1 between two broadly conserved transcriptional repressors, Sfu1 and Hap43.  The Sef1 activator of iron uptake genes promotes virulence in a mouse model of bloodstream infection, whereas the Sfu1 repressor is dispensable for virulence but promotes gastrointestinal commensalism.  We propose that the ability to alternate between genetic programs conferring resistance to iron depletion in the bloodstream versus iron toxicity in the gut may be a fundamental attribute of gastrointestinal commensal-pathogens.

overall_design: The Wild type strain (SN250) was grown in either YEPD or YEPD supplemented with iron chelator bathophenanthroline disulfonate (BPS); The sfu1Δ (SN515) mutant was grown in YEPD medium; The sef1Δ(SN330) or hap43Δ (SN694) mutant was grown YEPD supplemented with iron chelator bathophenanthroline disulfonate (BPS). 5-6 biological replicates were performed per strain per condition. RNA was prepared from these strains and samples were hybridized on custom Agilent C. albicans ORF arrays (15,000 spots/array, 70-mer probes).

first: Kalyan

last: Pande

first: Sarah

last: French

first: Brian

last: Tuch

first: Suzanne

last: Noble


title: Identification of Plasmodium vivax genes whose expression is spleen-dependent

status: Public on Jul 10 2011

city: Barcelona

first: Hernando

last: del Portillo

state: Barcelona

address: rosello, 132 (4a)

institute: Barcelona Centre for International Health Research

summary: The goal of this study is to identify P. vivax genes whose expression is dependent on the intact spleen in experimental infections in Aotus monkeys.

overall_design: These studies were carried-out at the facilities of the “Fundación Centro de Primates de la Universidad del Valle”, Cali, Colombia and in the “Barcelona Centre for International Health Resarch” - CRESIB, Barcelona, Spain.  This protocol was approved from the Ethical Committees of both Centres. A total of 4 Aotus lemurinus griseimembra naive animals were used in these experiments.  Three animals were splenectomized whereas another had an intact spleen. A donor monkey was infected with P. vivax Sal-I strain and after peak parasitemias appeared a time-series infections into Sp-1, Sp-2, Sp-3, and Sp+2 animals were performed. Parasites from each infection were obtained from peripheral blood, monkey leukocytes were removed by MidMacs and only purified schizont stages were used for RNA extractions. Dual-hybridizations Cy3/Cy5 comparing the global expression of parasites obtained from different infections (Cy5) with a reference pool PvSp-1 obtained from splenectomized monkeys from CDC (PvSp-1) were perfomed using an Agilent's 60-mer platform representing the complete coding genome of P. vivax (1 oligonucleotide/2 kb coding sequences) GPL6667

first: Carmen

last: Fernandez-Becerra

first: Ricardo

middle: N

last: Vencio

first: Socrates

last: Herrera

first: Myriam

last: Arevalo-Herrera

first: John

last: Barnwell


title: Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeceae)

city: Gainesville

first: Andre

last: Chanderbali

address: Museum Road

institute: Univrsity of Florida

summary: Current understanding of floral developmental genetics comes primarily from the core-eudicot model Arabidopsis thaliana. Here we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. Several thousand Nuphar genes with significantly up-regulated floral expression are identified, including homologs of the well-known ABCE floral regulators. However, strong similarities in the expression profiles of different organ categories contradict the organ-specific spatial expression domains predicted by the ABCE model. The broadly overlapping transcriptional programs observed among floral organs in Nuphar are shared with the magnoliid Persea americana (avocado), supporting the inference that this is the ancestral condition in angiosperms. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived. The transcriptional landscapes in Arabidopsis correlate with a shift toward morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. In contrast to most eudicots, perianth organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Our findings suggest that genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.

overall_design: Custom microarrays targeting 6,220 unique Nuphar floral transcripts were used to measure expression levels in eight tissues using an interwoven double-loop design for 16 arrays.

first: Mi-Jeong

last: Yoo

first: Naomi

last: Altman

first: Pamela

last: Soltis

first: Douglas

middle: E


title: Effect of Advanced Paternal Age on Copy Number Variation in Offspring (custom array)

city: Brisbane

first: Traute

last: Flatscher-Bader

state: Queensland

address: The University of Queensland, Upland Road, QBI Building (79)

department: The Queensland Brain Institute

country: Australia

institute: The University of Queensland

type: Genome variation profiling by genome tiling array

summary:
The offspring of older fathers have an increased risk of neurodevelopmental disorders such as schizophrenia and autism. It has been proposed that de novo point mutations and copy number variants (CNVs) in the continually dividing spermatogonia underlie this association. In light of the evidence implicating CNVs with schizophrenia and autism, here we use a mouse model to test the hypothesis that the offspring of older males have an increased risk of de novo CNVs.

Three-month-old and fourteen- to sixteen-month-old C57BL/6J sires were mated with three-month-old dams to create control offspring and offspring of old sires, respectively. Applying genome-wide microarray screening technology, seven distinct CNVs were identified in a discovery set of twelve offspring and their parents. Competitive quantitative PCR was employed to confirm the variants and establish their frequency in a replication set of 77 offspring and their parents. Six de novo CNVs were detected in the offspring of older sires, while none were detected in the control group. One of the de novo CNVs involved Auts2 (autism susceptibility candidate 2), and other CNVs included genes linked to schizophrenia, autism and brain development. Two of the CNVs were associated with behavioural and/or neuroanatomical phenotypic features. This is the first experimental demonstration that the offspring of older males have more de novo CNVs. The results suggest that offspring of older fathers may be at increased risk of neurodevelopmental disorders such as schizophrenia and autism via the generation of de novo CNV in the male germline. In light of the trends for delayed parenthood in many societies, and in light of the potential for these CNVs to accumulate over subsequent generations, the impact of these mechanisms on the health of future generations warrants closer scrutiny.

overall_design: 2 sires of advanced paternal age (12-16 months of age) and 2 control (3 months of age) sires were mated to dams (3 months of age) to create 6 offspring of advanced paternal age (APA) and 6 control offspring (C), respectively, with an even number of sexes within each group of offspring. A commerical aCGH and a custom CNV array (both supplied by Agilent) were used in combination to detect copy number variations in the genomes of the offspring and their parents. DNA from all male animals was hybridized against a male reference animal and that from all female animals against a female reference animal.

first: Claire

last: Foldi

first: Saying

last: Chong

first: Emma

last: Whitelaw

first: Ralf

last: Moser

first: Thomas

middle: H

last: Burne

first: Darryl

middle: W

last: Eyles

last: McGrath


title: Effect of Advanced Paternal Age on Copy Number Variation in Offspring (commercial array)


title: The different epidemiologic subtypes of Burkitt Lymphoma share a largely homogenous micro RNA profile distinct from diffuse large B-cell lymphoma.

status: Public on Jul 18 2011

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

institute: Charité-Universitätsmedizin Berlin

summary: Sporadic Burkitt lymphoma (sBL) can be delineated from diffuse large B-cell lymphoma (DLBCL) by a very homogeneous mRNA expression signature. However, it remained unclear whether all three BL variants – sBL, endemic BL (eBL) and immunodeficiency-associated BL (HIV-BL) – represent a uniform biological entity despite their differences in geographical occurrence, association with immunodeficiency and/or incidence of EBV infection. To address this issue, we generated micro RNA (miRNA) profiles from 18 eBL, 31 sBL and 15 HIV-BL cases. In addition, we analyzed the miRNA expression of 86 DLBCL to determine whether miRNA profiles recapitulate the molecular differences between BL and DLBCL evidenced by mRNA profiling. A signature of 38 miRNAs enriched in MYC regulated and NF-kB pathway associated miRNAs was obtained that differentiated BL from DLBCL. The miRNA profiles of sBL and eBL displayed only 6 differentially expressed miRNAs, whereas HIV and EBV infection had no impact on the miRNA profile of BL. In conclusion, miRNA profiling confirms that BL and DLBCL represent distinct lymphoma categories and demonstrates that the three BL variants are representatives of the same biological entity with only marginal miRNA expression differences between eBL and sBL.

overall_design: Archival tumor specimens of 86 diffuse large B-cell lymphoma (DLBCL) and 64 Burkitt lymphoma (BL) patients were obtained. The DLBCL samples have previously been reviewed by a panel of expert hematopathologists and their clinical data were published as part of the RiCOVER-60 trial. The diagnosis of all BL cases was confirmed by histopathology review according to the criteria of the WHO classification. Based on their geographical origin, 31 BL samples were designated as sporadic BL (sBL) and 18 samples as endemic BL (eBL). Fifteen BL cases were diagnosed as immunodeficiency-associated BL (HIV-BL). Of the 18 eBL 14 cases were EBV+ (87.5%), 2 samples were EBV- (12.5%) and for 2 eBL cases the EBV status was unknown. Of the sBL samples 26 were EBV- (86.7%), 4 cases were EBV+ (13.3%) and for 1 case the EBV status was not evaluable. Among the HIV-BL 5 (33.3%) were EBV+, whereas 10 (66.7%) were EBV-.


title: miRNA expression of human samples of hepatoblastoma (HB) and normal and fetal liver

status: Public on Jul 08 2011

city: Evry

first: stefano

last: cairo

address: 4 rue Pierre Fontaine

institute: Xentech

summary: Forty-nine hepatoblastoma (HB) tumor specimens were profiled on a microarray containing 250human miRNA, in order to identify miR classifiers that could discriminate HBs with diverse prognosis, and to get insight on the functional mechanisms in which miRNAs are involved.

overall_design: Hierarchical unsupervised clustering of HB samples according to their miRNA expression profile identifies 2 tumor subgroups associated with different degree of differentiation, proliferation rate and invasive phenotype. As subset of these tumors is used as training set to build a mir classifier. When the signature is applied to an independent test set, an independent series of HB is classified patients into two groups associated with the clinical features identified in the first set of patients.

first: Stefano

last: Cairo

first: Marie-Annick

last: Buendia


title: affy_diversity_maize-Understanding the Diversity of Maize Cell Wall

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary:
affy_diversity_maize - affy_diversity_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of two maize lines Cm484 (line of good digestibility) and F98902 (line of bad digestibility) at the same developmental stage (male flowering).

Keywords: organ comparison

overall_design: 4 arrays - maize

first: Magalie

last: Pichon

first: Stephanie

last: Huguet

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: The use of the glycoarray chip to investigate VHL-dependent protein glycosylation changes in renal cancer Renal cell carcinoma (RCC)

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: Renal cell carcinoma (RCC) accounts for around 2-3% of all adult neoplasms and its incidence is increasing. RCC is largely resistant to standard cancer treatment regimens including chemotherapy and radiation therapy, whilst immunotherapy modestly provides benefit to only a small subset of patients. As a result, prognosis for RCC patients with advanced disease is very poor, with a 5-year survival rate of less than 10%. An early event in the development of familial and up to 90% of sporadic RCC is the loss and/or mutation/methylation of the von Hippel-Lindau (VHL) tumour suppressor gene. The tumor suppressor role of VHL relies primarily on its ability to target members of the hypoxia-inducible factors (HIF) for proteosomal degradation, however it has also been implicated in other biological processes linked to oncogenesis, such as the extracellular matrix assembly and the regulation of  actin cytoskeleton, that are less clearly defined. Targeting the VHL/HIF pathway may dramatically improve RCC treatment, as demonstrated by an increasing number of novel agents that have shown promising activity in recent clinical trials6. Identification of other possible proteins regulated by VHL that may be involved in tumour suppression will improve our understanding of RCC pathobiology and also provide novel disease biomarkers or potential targets.

overall_design:
A number of our studies have identified changes in glycosylation in RCC, at least some of which appear to alter as a result of changes in the VHL gene.  Lectin binding immunohistochemistry shows altered reactivity with a number of lectins in the malignant tissue compared with the normal tissue.  Comparison of plasma membrane protein enriched fractions from human RCC cells stably transfected with control vector or with wild type VHL led to the identification of VHL-associated changes in the forms of several plasma membrane proteins which we beelive to be due to differential glycosylation. For one of these we have now shown that it is differentially O-glycosylated and this has been confimed in cell lysates and patient tissue by Western blotting. A parallel approach using 2D-PAGE analysis of RCC cell line conditioned medium (CM) has also identified a tumour-specific glycoform of a secretory protein that appears to undergo differential N-glycosylation in RCC and this has been confirmed in analysis of some matched primary tumour/normal pairs. These findings are potentially very interesting, as these proteins could serve as prognostic or diagnostic markers, or even as targets for improving RCC therapy. We are therefore keen to explore the underlying mechanism of differential glycosylation that may be associated to VHL dependent gene expression. As there are an immense number of enzymes involved in the conjugation of N- and particularly O-glycans to proteins, the glyco-microarray is an ideal tool to elucidate this further.
For chip analyses we have three cell lines generated from human RCC cells (RCC4, 786-0 and UMRC2) that have been stably transfected with control vector or with wild type VHL i.e. 6 cell lines in total.  Whole RNA was extracted from each cell line in 3 replicates per line.

first: Roz

last: Banks


title: Comparison between GT and SigE overexpressed strains of cyanobacteria

status: Public on Jul 09 2011

city: Kawasaki

first: Takashi

last: Osanai

address: 1-1-1, Higashimita, Tamaku

department: School of Agriculture

institute: Meiji University

summary: SigE is a global regulator for sugar catabolism in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed SigE-overexpressing strain, named GOX50, by introducing the sigE genes fusing psbAII promoter by homologous recombination. The transcript profiles of parental wild-type strain GT and GOX50 were compared by microarray CyanoChip (Takrara bio.). Experiments were performed by three times with biologically independent RNA. The results showed that genes for the oxidaditive pentose phosphate pathway and glycogen catabolism were induced by SigE overexpression.

overall_design: Total RNAs from three independent wild-type (GT) and three independent SigE-overexpression strains were differently labeled by Cy3 or Cy5, followed by hybridyzation on CyanoChip.


title: Screening  of influenza A virus infection related microRNA

status: Public on Jul 07 2011

city: Beijing

first: zhenpeng

last: li

address: Taiping Road, Haidian District

country: China

institute: Beijing Institute of Radiation Medicine

summary: In the study presented here,  A549 cells infected with influenza virus A /JingFang/86-1(H1N1) for 4 and 24 hours and intervention by Flutide,  was used to acquire expression profiles of a total of 471 standard mature miRNAs based on Sanger miRBase Release 9.2.

overall_design: 4 samples: uninfected, 4 h and 24 h after infection, and 24 h infection then treated with Flutide

first: Xiao-ran

last: Ding


title: Transcriptional profiling of M. tuberculosis CDC1551 wild type vs aprABC null, aprBC null, aprC null and phoP transposon mutants.

city: Ithaca

first: David

last: Russell

address: C5 171 Veterinary Medical Center

department: College of Veterinary Medicine

institute: Cornell University

summary: Following phagocytosis by macrophages, Mycobacterium tuberculosis (Mtb) senses the intracellular environment and remodels its gene expression for growth in the phagosome. Abramovitch et.al. in this current study identified an Acid and Phagosome Regulated (aprABC) locus that is unique to the Mtb complex and whose gene expression is induced during growth in acidic environments in vitro and in macrophages. The authors propose a model where phoP senses the acidic pH of the phagosome and induces aprABC expression to fine-tune processes unique for intracellular adaptation of Mtb complex bacteria.

overall_design: This study uses microarray analyses to compare transcriptional responses of wild type Mycobacterium tuberculosis (CDC1551) to  aprABC locus deletion mutants and the phoP transposon mutant. The bacteria were grown to early log phase in vented T-75 standing flasks containing 12 mL of pH 7.0 7H9 OADC medium. Transcript levels of the wild type bacteria were compared to the following mutants: aprABC null, aprBC null, aprC null, phoP::Tn mutant.


title: Metabolomics reveals phospholipids as important nutrient sources during Salmonella growth in bile in vitro and in vivo

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

state: BC

department: Michael Smith Laboratories

country: Canada

institute: The University of British Columbia

summary: During the colonization of hosts, bacterial pathogens are presented with many challenges that must be overcome for colonization to successfully occur. This requires bacterial sensing of the surroundings and adaptation to the conditions encountered. One of the major impediments to pathogen colonization of the mammalian gastrointestinal tract is the antibacterial action of bile. Salmonella enterica serovar Typhimurium has specific mechanisms involved in resistance to bile. Besides being resistant to it, Salmonella can also successfully multiply in bile, using it as a source of nutrients. This accomplishment is highly relevant to pathogenesis, as Salmonella colonizes the gallbladder of hosts, where it can be carried asymptomatically and promote further host spread and transmission. In order to gain insights into the mechanisms used by Salmonella to grow in bile, we studied the changes elicited by Salmonella in the chemical composition of bile during growth in vitro and in vivo through a metabolomics approach. Our data suggest that phospholipids are an important source of carbon and energy for Salmonella during growth in the laboratory as well as during gallbladder infections of mice. Further studies in this area will generate a better understanding of how Salmonella exploits this generally hostile environment for its own benefit.

overall_design: For in vitro studies, bile was extracted from C57BL/6 mice and used immediately. An overnight culture of Salmonella enterica serovar Typhimurium SL1344 was used to inoculate 10 μL of bile at an approximate density of 5x10^6 cells/mL. The experiment was performed in duplicate, and a total of 2 uninfected and 2 infected bile samples were studied. Samples were incubated for 24 hours at 37 oC with shaking. After incubation, samples were centrifuged to remove bacteria and the supernatant was saved for metabolomic analyses. For in vivo studies, C57BL/6 mice were infected with approximately 10^8 bacterial cells by oral gavage. Four groups of three to four mice each were either infected with Salmonella or kept uninfected (total of 11 mice per treatment group). Five days after infection, all mice were sacrificed and bile was collected. Samples were centrifuged and supernatants saved for metabolomic analyses. Samples were prepared by mixing equal volumes of bile from three to four mice, generating three samples per treatment (uninfected and infected), which were used in the subsequent steps. Seven microliters of each sample was evaporated and the residue resuspended in 50% acetonitrine. Extracts were infused into a 12-T Apex-Qe hybrid quadrupole-FT-ICR mass spectrometer equipped with an Apollo II electrospray ionization source, a quadrupole mass filter and a hexapole collision cell. Raw mass spectrometry data were processed as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140). To identify differences in metabolite composition between different groups of samples, we filtered the list of masses for metabolites which were present on one set of samples but not the other. Additionally, we calculated the ratios between averaged intensities of metabolites from each group of mice. To assign possible metabolite identities to the masses selected as described above, the monoisotopic neutral masses of interest were queried against the Human Metabolome Database (HMDB, http://www.hmdb.ca), with a tolerance of 0.001 Da.

first: L

first: Sarah

middle: K

last: Andersen

first: Alfredo

last: Menendez

first: Ellen

middle: T

last: Arena

first: Jun

last: Han

first: Rosana

last: Ferreira

first: Christoph

last: Borchers

first: B

last: Finlay


title: Farnesyl Diphosphate (FPP) Toxicity in E. coli, M9 medium

city: Emeryville

first: Robert

last: Dahl

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

summary: This experiment studied the effect of FPP accumulation on E. coli.  E. coli cells transformed with pMBIS (the S. cerevisiae mevalonate pathway enzymes converting mevalonate to FPP) and fed mevalonate produce large amounts of FPP, which causes toxicity when it accumulates.  When coupled with an active amorphadiene synthase (pADS) the cells produce amorphadiene, a non-toxic isoprenoid.  To accumulate FPP, but maintain similar protein burden, an amorphadiene synthase with 3 mutations to render it inactive was used (pADSmut) to accumulate FPP.  E. coli was transformed with pMBIS and pADS or pMBIS and pADSMut and grown in M9+glucose with varying magnesium concentrations and fed 20 mM mevalonate and induced with 0.5 mM IPTG, then sampled at subsequent time points.

overall_design:
This comparison is between E. coli DH1 cells accumulating FPP via the heterologous mevalonate pathway (pMBIS/pADSmut) to cells producing amorphadiene via the same pathway (pMBIS/pADS).  Samples were collected 6, 10, 14, and 26.5 hr after addition of IPTG and mevalonate.
One biological replicate was used.  Total RNA was extracted, reverse transcribed, labeled, and hybridized to multiple slides for technical replicates.

first: Jay

last: Keasling


title: Expression profiling of 4q-linked and phenotypic FSHD in different steps of myogenic differentiation

city: monza

first: raffaella

last: meneveri

state: italia

address: via cadore 48

department: Dept of Experimental Medicine

country: Italy

institute: Univ. Milano Bicocca

summary:
The specific gene(s) responsible for FSHD phenotype have not yet been identified. We used the Human GeneChip Exon 1.0 ST platform to analyze the global gene expression profiles of FSHD-1, FSHD-2 and controls during myogenic differentiation.
In this dataset, we include the expression data of human primary myoblasts obtained from three FSHD-1 and two FSHD-2 patients, and three healthy controls (CN). This data are used to evaluate the molecular perturbation of FSHD upon muscle differentiation; we compared patients and CN proliferating myoblasts as well as the corresponding myotubes obtained after 8 days of cell differentiation.

overall_design: 16 expression profiles were generated from 6 different cell types: including myoblasts and myotubes from healthy donors and FSHD-1 and FSHD-2 patients. Gene probesets with P < 0.01 and FC > 2 were selected in FSHD-1 assay, whereas P < 0.001 and FC > 2 were used in FSHD-2, in the attempt to overcame problems due to the small sample size analyzed.

first: Stefania

last: Cheli

first: Raffaella

last: Meneveri


title: Diagnosis of Alzheimer's Disease Based on Disease-Specific Autoantibody Profiles

city: Stratford

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

summary: Alzheimer's Disease (AD) and Non-Demented Control (NDC) human sera were probed onto human protein microarrays in order to identify differentially expressed autoantibody biomarkers that could be used as diagnostic indicators.

overall_design: In the study presented here, 50 AD and 40 NDC human serum samples were probed onto human protein microarrays in order to identify differentially expressed autoantibodies.  Microarray data was analyzed using several statistical significance algorithms, and autoantibodies that demonstrated significant group prevelance were selected as biomarkers of disease.  Prediction classification analysis tested the diagnostic efficacy of the identified biomarkers; and differentiation of AD samples from other neurodegeneratively-diseased and non-neurodegeneratively-diseased controls (Parkinson's disease and breast cancer, respectively) confirmed their specificity.

first: Eric

middle: P

first: Min

first: Cassandra

last: DeMarshall

first: Benjamin

last: Belinka


title: Expression data of sweet orange in response to Candidatus Liberibacter asiaticus infection at advanced stage

city: Lake Alfred

first: Fred

middle: G.

last: Gmitter

email: fgmitter@ufl.edu, fanjing7758@126.com

address: 700 Experiment Station Rd

institute: University of Florida

summary:
Citrus Huanglongbing (HLB, or greening) is one of the most severe diseases of citrus. Plant disease symptom development is considered to be the consequence of a number of molecular, cellular and physiological changes, and may also be associated with host defense responses. Understanding citrus host response to HLB may contribute to the development of new strategies to control this destructive disease.
We performed microarray analysis to identify the differentially expressed genes in sweet orange in response to HLB infection using the Affymetrix GeneChip® citrus genome array.

overall_design: Two-year-old seedlings of ‘Madam Vinous’ sweet orange (Citrus sinensis L. Osbeck) were inoculated by grafting with bud sticks from HLB-diseased, PCR positive sweet orange plants. For mock-inoculated controls, the same types of plants were grafted with bud sticks from HLB-free, PCR negative sweet orange. At 7 months after inoculation, mature leaves were sampled from 3 individual HLB-diseased plants, and healthy leaves from 3 mock-inoculated plants as control. Total RNA was extracted from leaf samples and hybridized on Affymetrix microarrays.

first: Jing

last: Fan

first: Abeer

last: Khalaf

first: Chunxian

last: Chen

first: Qibin

last: Yu

first: Ron

last: Brlansky

first: Gloria

middle: A

last: Moore

first: Zhengguo

last: Li


title: Transciptional profile of Escherichia coli O157:H7 TUV93-0 inhibitor mutants in MEM-HEPES

status: Public on Jul 05 2011

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

summary: Tpx, FolX and WrbA were identified as a targets for type 3 secretion inhibititors in pull-down assays.The transcriptional profile of Escherichia coli O157:H7 and isogenic mutants grown in MEM-HEPES were determined.

overall_design: Total RNA from triplicate cultures growing exponentially in MEM-HEPES media were labelled with Cy5 (wild type) and Cy3 (tpxC61S). Labelled cDNAs were hybridised to UBEC3 arrays.

first: Dai

last: Wang


title: Mouse hypothalamus and whole brain: control vs. sodium craving

status: Public on Jul 04 2011

city: Durham

first: Andreas

middle: Robert

last: Pfenning

state: NC

address: Duke University Medical Center, Box 3209, Department of Neurobiology

department: Neurobiology

institute: Duke University

summary:
Sodium appetite is an instinct that involves avid specific intention. It is elicited by sodium deficiency, stress-evoked ACTH and by reproduction. Genome-wide microarrays in sodium deficient mice, or following ACTH infusion, showed upregulation of hypothalamic genes, including DARPP-32, dopamine receptors-1 and  -2, alpha-2C-adrenoceptor, and STEP. Both DARPP-32 and neural plasticity regulator, ARC were upregulated in lateral hypothalamic orexinergic neurons by sodium deficiency. Administration of dopamine D1- (SCH23390) and D2-receptor (raclopride) antagonists  reduced gratification of sodium appetite triggered by sodium  deficiency. SCH23390 was specific, having no effect on  osmotic-induced water drinking, whereas raclopride also reduced  water intake. D1-receptor knockout mice had normal sodium appetite, indicating compensatory regulation. It was  insensitive to SCH23390, confirming the absence of off-target effects. Bilateral microinjection of SCH23390 (100nM in 200nL) into rats? lateral hypothalamus greatly reduced sodium appetite.
Gene Set Enrichment Analysis  in  hypothalami of mice with sodium appetite showed significant enrichment of gene sets previously linked to addiction (opiates, cocaine). This finding of concerted gene regulation was attenuated upon gratification with perplexingly rapid kinetics of only 10 minutes, anteceding significant absorption of salt from the gut.  Salt appetite and hedonic liking of salt taste have evolved over more than  a  hundred million years e.g. being present in Metatheria. Drugs causing pleasure and addiction are comparatively recent and likely reflect usurping of evolutionary ancient systems with high survival value by the gratification of contemporary hedonic indulgences.  Our findings outline a novel molecular logic for instinctive behavior encoded by the brain with  possible  important translational-medical implications.

overall_design:
Transcripts were profiled in the hypothalamus and whole brain of control and salt craving animals to determine the gene expression profile corresponding to that behavioral state.  We show an over-representation of addiction-related genes in the set that is common to different methods of salt craving.
Mouse hypothalamus and whole brain under three conditions:  control, furosemide treated, and ACTH treated.  4 or 5 biological replicated per group.  Two channels - experimental and reference are used.

first: Wolfgang

last: Liedtke

first: Michael

last: McKinley

first: Lesley

last: Walker

first: John

last: Drago

first: Andrew

last: Lawrence

first: Derek

last: Denton


title: Ustilago maydis rak1 mediated gene expression during exponential growth

status: Public on Jul 06 2011

city: Marburg

first: Regine

last: Kahmann

state: Hesse

address: Karl-von-Frisch Str. 10

department: Organismic Interactions

institute: MPI für terrestrische Mikrobiologie

summary: In mammalian cells RACK1 serves as a scaffold protein that has a role in integrating inputs from different signaling pathways and affects translation through association with ribosomes. U. maydis contains a seven-WD40 repeat motif protein designated Rak1, which shows 68% identity to RACK1 and is homologous to Asc1p of Saccharomyces cerevisiae. The asc1 mutant could be complemented by introduction of U. maydis rak1. The deletion of rak1 affected cell growth, cell wall integrity and specifically attenuated cell fusion. This latter defect was caused by reduced expression of prf1 encoding the regulator for pheromone and pheromone-receptor genes. Rak1 interacts with a variety of ribosomal proteins and microarray analysis revealed that the deletion of rak1 led to severely reduced expression of rop1, an activator prf1. The constitutive expression of rop1 could rescue the defect of mfa1 expression as well as conjugation tube formation in response to pheromone induction in the rak1 mutant. Moreover, a solopathogenic rak1 mutant failed to respond to plant derived stimuli, resulting in attenuated filamentation and pathogenicity. This could be partially rescued by constitutive expression of the b heterodimer. These data suggest that rak1 is a regulator of rop1 expression with additional roles after cell fusion.

overall_design: Ustilago maydis strains FB1 and FB1∆rak1 were grown on a rotary shaker (200 rpm) in liquid Ustilago complete medium with 1% glucose at 28°C to an OD600 of 0.5. The experiment was performed using three independent biological replicates per strain.

first: Lei

first: Patrick

last: Berndt

first: Xiaojuan

last: Xia

first: Jörg

last: Kahnt


title: Peroxide stress in Desulfovibrio vulgaris Hildenborough

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

summary:
Using data from microarray experiments, we investigated the effects of excess hydrogen peroxide on D. vulgaris.

Keywords: stress response, time course

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of cells treated with 1 mM H2O2,sterile water Peroxide to untreated cells at times of 0,120,240,30,480,60 min.


title: Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state

city: Raleigh

first: Pete

last: Pascuzzi

address: 851 Main Campus Drive

institute: North Carolina State University

summary: DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4) during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac) was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated with initiation zones and replication origins.

overall_design: Replicating DNA in cultured Arabidopsis cells was labeled with BrdU for 1 hour. Cells were harvested, nuclei extracted, and the nuclei were sorted by FACS as Early, Mid or Late S phase based on DNA content (DAPI signal).  Newly replicated DNA was isolated by immunoprecipitation to BrdU, amplified, and labeled with Cy5/Cy3. Input DNA served as a reference and was labeled with Cy3/Cy5.  Equal amounts of DNA was hybridized to a spotted cDNA that covers Arabidopsis chr4.  Each S phase sample has 3 biological replicates with a dye swap serving as a technical replicate for a total of 18 arrays.

first: Tae-Jin

last: Lee

first: Sharon

last: Settlage

first: Randall

last: Shultz

first: Milos

last: Tanurdzic

first: Pablo

middle: D

last: Rabinowicz

first: Margit

last: Menges

first: James

last: Murray

first: Bryon

last: Sosinski

first: George

middle: C

last: Allen

first: Robert

last: Martienssen

first: Linda

last: Hanley-Bowdoin

first: Matthew

last: Vaughn

first: William

middle: F

last: Thompson


title: Hydrogen peroxide Stress in Desulfovibrio vulgaris Hildenborough

platform_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of wild type and deletion mutant cells treated with 1 mM H2O2 to untreated cells at times of 0 and 120 min. See also Series GSE4447 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE4447)


title: Organ-specific light-responsive gene expression profiling assay using 18kA and 18kB soybean cDNA microarrays

city: New York

first: Ying

last: Li

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

summary: An expression profiling assay comparing dark-grown soybean seedlings with seedlings treated with 1 h far-red light using different organs including cotyledons, hook, and hypocotyl with the soybean cDNA 18kA and 18kB microarrays.

overall_design: Pairwise comparisons of far-red-light-treated samples and dark-grown samples in three organs: cotyledons, hook, and hypocotyl. Each comparison was done with 4 biological replicates with a dye swap.

last: Hudson


title: DNA methylation data from AML12 cells during EMT

status: Public on Jul 03 2011

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

type: Methylation profiling by genome tiling array

summary: We investigated genome-wide DNA methylation during EMT in AML12 cells using comprehensive high throughput arrays for relative methylation (CHARM). We used custom Nimblegen microarrays.

overall_design: We isolated genomic DNA from cells at different timepoints post-TGF-β stimulation and hybridized to custom-designed Nimblegen microarrays (CHARM arrays). AML12 cells from 4 representative experiments were collected and used for the genome-wide DNA methylation analysis.

first: Oliver

last: McDonald

first: Andrew

last: Feinberg


title: microRNA expression signatures in colorectal cancer cell lines with demethylating treatment

status: Public on Jul 01 2011

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: To screen for epigenetically silenced miRNAs, wecarried out miRNA microarray analysis in three colorectal cancer (CRC) cell lines (HCT116, DLD-1 and RKO) treated with or without 5-aza-2'-deoxycytidine (aza).  HCT116 and RKO cells were also treated with aza plus 4-phenylbutyric acid (PBA).  In addition, we analyzed HCT116 cells in which the DNA methyltransferase genes DNMT1 and DNMT3B were genetically disrupted (double knockout; DKO cells), thereby abrogating DNA methylation.  Expression of a majority of miRNAs was downregulated in all three CRC cell lines tested, as compared to normal colonic mucosa. DAC treatment upregulated expression of a large number of miRNAs in all three CRC cell lines, and combination treatment with DAC plus PBA induced even greater numbers of miRNAs in CRC cells.  The most profound effect on the miRNA expression profile was induced by genetic disruption of DNMT1 and DNMT3B in HCT116 cells.

overall_design: CRC cells were treated with 5-aza-2’-deoxycytidine (aza) or aza plus 4-phenylbutyrate (PBA). Nomal colon RNA was purchased from BioChain. Expression of 470 miRNAs was analyzed using Human miRNA Microarray V1 (G4470A; Agilent technologies, Santa Clara, CA, USA).

first: Minoru

last: Toyota


title: Maize gene expression during infection with Ustilago maydis strains SG200Dpit1 and SG200Dpit2

first: Gunther

last: Doehlemann

state: Hessen

address: Karl von Frisch Str.

institute: Max Planck Institue for Terrestiral Microbiology

summary:
Ustilago maydis is a basidiomycete fungus that causes smut disease in maize. Most prominent symptoms of the disease are plant tumors, which can be induced by U. maydis on all aerial parts of the plant. We identified two linked genes, pit1 and pit2, which are specifically expressed during plant colonization. Deletion mutants for either pit1 or pit2 are unable to induce tumor development and elicit plant defense responses.
We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to deletion pit1 and pit2 mutants and found plant responses to both mutants being not significantly distinguishable.

overall_design: U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200Dpit1 and SG200Dpit2, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023, 4d mock and 4d SG200 Samples). These data served as controls for this experiment.

first: Stefanie

last: Reissmann

first: Regine

last: Kahmann


title: Genome-wide transcriptomic profiling of oxaliplatin response

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

institute: University of Navarra/ Clínica Universidad de Navarra

summary: Oxaliplatin (OXA) is a member of the family of Pt-containing chemotherapeutic agents that also include cisplatin (CDDP) and carboplatin. OXA is distinguished from these two older drugs by its different spectrum of activity both in preclinical models and in clinical trials. It is the only platinum analogue to have activity in colon cancer, a disease for which this drug has now become a mainstay of therapy. It mainly forms intrastrand adducts between two adjacent guanine residues or guanine and adenine, disrupting DNA replication and transcription. OXA has been reported to be involved in the Nucleotide Excision Repair Pathway (NER), p38 kinase activation, PI3K/AKT pathway and caspase cascade activation through the apoptotic intrinsic pathway. However, not all colon cancer cells show the same sensitivity to OXA. In this study we have compared the changes in RNA expression profiles of colon cancer cell lines with different sensitivity to OXA, determined by IC50.

overall_design: The goal of our experiment was to identify genes that are differentially activated or inhibited commparing OXA sensitive and OXA resistent colon cancer cell lines upon OXA treatment. We treated 6 OXA-sensitive colorectal cancer cell lines: LoVo, LS513, SW1116, SW1417, SW48 and LS174TT and 8 resistant cell lines: LS411NN, HCT116, HCT15, SW480, SW948, CACO2, DLD1 and HT29, to identify genes and pathways that could play a role in OXA sensitivity. The experimental design used was “RNA-Reference” and “Dye-Swap”. Each cell line was analyzed in duplicate with RNA reference (Stratagene) as reference sample and labeled each biological condition once by Cy3 and once by Cy5. We took the average of the dye-swapped arrays to cancel the dye effect on any particular gene. In total we used 56 slides.

first: Anna

last: Martinez-Cardús

first: Eva

last: Martinez-Balibrea

last: Bandres

first: Alba

last: Ginés

first: José

middle: L

last: Manzano

first: Jesús

last: García-Foncillas

first: Albert

last: Abad


title: CpG methylation patterns and decitabine treatment response in acute myeloid leukemia cells and normal hematopoietic precursors

city: Cleveland

first: Kwok Peng

last: Ng

state: OH

address: 9500 Euclid Avenue

department: Ophthalmic Research

institute: Cleveland Clinic

summary: The DNA hypomethylating drug decitabine maintains normal hematopoietic stem and progenitor cell (HSPC) self-renewal but induces terminal differentiation in acute myeloid leukemia (AML) cells. To better understand the basis for this contrasting treatment effect, the baseline expression of key lineage-specifying transcription factor (TF) (eg., CEBPa) and key late differentiation TF (CEBPe), was examined in normal, myelodysplastic (MDS) and AML primary cells and cell lines. To appreciate the role of differentiation in hypomethylation of some CpG by decitabine treatment but not others, promoter CpGs, analyzed by microarray and mass spectrometry, were categorized by the direction of methylation change during normal myeloid differentiation. In MDS/AML cells, high expression of CEBPa, relatively low expression of CEBPe (a gene target of CEBPa), hypermethylation of CEBPe promoter CpG, and the methylation pattern at differentiation sensitive promoter CpGs analyzed by microarray, suggested lineage-commitment and aberrant epigenetic repression of late differentiation genes. DNA hypomethylation in response to decitabine was greatest at CpGs that are hypomethylated during normal myeloid differentiation. In contrast, normal HSPC treated with decitabine retained immature morphology, and methylation significantly decreased at CpG that are hypermethylated during myeloid differentiation. Partial differentiation at baseline, and repression of key late differentiation genes by epigenetic means, likely plays a role in methylation and phenotype responses of AML cells treated with decitabine.

overall_design: Bisulphite converted DNA from the 208 samples were hybridised to the Illumina Cancel Panel 1 GPL9183 methylation assay

first: Kwok

first: Yogen

last: Saunthararajah


title: Microgenomic Analysis in Skeletal Muscle: Expression Signatures of Individual Fast and Slow Myofibers

status: Public on Jul 21 2011

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

summary:
Background: skeletal muscle is a complex, versatile tissue composed of a variety of functionally diverse fiber types. Although the biochemical, structural and functional properties of myofibers have been the subject of intense investigation for the last decades, understanding molecular processes regulating fiber type diversity is still complicated by the heterogeneity of cell types present in the whole muscle organ.
Methodology/Principal Findings: we have produced a first catalogue of genes expressed in mouse slow-oxidative (type 1) and fast-glycolytic (type 2B) fibers through transcriptome analysis at the single fiber level (microgenomics). Individual fibers were obtained from murine soleus and EDL muscles and initially classified by myosin heavy chain isoform content. Gene expression profiling on high density DNA oligonucleotide microarrays showed that both qualitative and quantitative improvements were achieved, compared to results with standard muscle homogenate. First, myofiber profiles were virtually free from non-muscle transcriptional activity. Second, thousands of muscle-specific genes were identified, leading to a better definition of gene signatures in the two fiber types as well as the detection of metabolic and signaling pathways that are differentially activated in specific fiber types. Several regulatory proteins showed preferential expression in slow myofibers. Discriminant analysis revealed novel genes that could be useful for fiber type functional classification.
Conclusions/Significance: as gene expression analyses at the single fiber level significantly increased the resolution power, this innovative approach would allow a better understanding of the adaptive transcriptomic transitions occurring in myofibers under physiological and pathological conditions.

overall_design: EDL and soleus muscles were incubated with type I collagenase to dissociate intact myofibres that were separated under stereo microscope from the bulk of hyper contracted fibres. Isolated myofibres were divided in two parts: one was immersed in Laemmli buffer for fibre typing; the other was placed in RNA extraction buffer for RNA amplification. We analyzed the transcription profiles of 10 biological replicas of type 2B single muscle fibres from EDL and 10 biological replicas of type 1 single muscle fibres from soleus. Microarray competitive hybridizations were carried out against an artificial control with a balanced composition of type 1 and type 2B fibres (20 hybridizations). Each oligonucleotide is spotted in two replicates on the glass slide, so for every data two intra-slide replicas are present. The control was created as follows: three couples of soleus and EDL muscles were removed from 3 different mice and treated with collagenase. Total RNA was extracted separately from EDL and soleus muscles. By mixing about 1/3 RNA from EDL and 2/3 RNA from soleus muscles the control had approximately the same contributions of type 1 and type 2B fibres. Purified RNA samples from single fibres and from control were amplified twice using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion).

first: Francesco

last: Chemello

first: Camilla

last: Bean

first: Paolo

last: Laveder

first: Giorgia

last: Busolin

first: Stefano

last: Cagnin

first: Pasqua

last: Cancellara

first: Carlo

last: Reggiani


title: Expression profiling of a spf deletion mutant suggests biological roles and mRNA targets for Spot 42 in the fish pathogen Aliivibrio salmonicida

city: Tromsø

first: Erik

last: Hjerde

address: Breivika

department: Department of chemistry

country: Norway

institute: University of Tromsø

summary: Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role remained obscure until it was shown to cause discoordinate expression of the galactose operon (gal operon). Recently Spot 42 has also been implicated in having broader roles in the central and secondary metabolism. Spot 42 is encoded by the spf gene. The gene is ubiquitous in the Vibrionaceae family of gamma-proteobacteria, which includes a number of serious pathogens of humans and animals, including the infamous Vibrio cholerae. One member of this family, Aliivibrio salmonicida, causes cold-water vibriosis in farmed Atlantic salmon. Its genome encodes Spot 42 with 84 % identity to E. coli Spot 42 (spf). We generated a A. salmonicida spf deletion mutant. We then and used microarray and Northern blot analyses to monitor global effects on the transcriptome in order to provide insights into the biological roles of Spot 42 in this bacterium. In the presence of glucose we found a surprisingly large number of ≥2× differentially expressed genes, and several major cellular processes were affected, such as carbohydrate metabolism and transport, motility and chemotaxis, iron homeostasis and quorum sensing. A gene encoding a pirin-like protein (VSAL_I1200) showed an on/off expression pattern in the presence/absence of Spot 42, which suggests that Spot 42 plays a key regulatory role in the central metabolism by regulating the switch between fermentation and respiration. Interestingly, in a global search we discovered a sRNA, named VSsrna24, which is encoded immediately downstream of spf. This new sRNA has an expression pattern opposite to that of Spot 42, and its expression is highly dependent on glucose. Our hypothesis is that this novel sRNA works in concert with Spot 42 to regulate carbohydrate metabolism and uptake.

overall_design: Two-condition experiment, wild type cells (control samples) vs. spf mutants grown in A. salmonicida-specific minimal media (ASMM) (stimulated samples). Samples were prepared by culturing the A. salmonicida wild type and a spf deletion mutant strains at 12 °C in ASMM without any added carbon source to OD 600nm 0.4. At this density glucose to 44.4 mM was added. Samples were collected 15 min after stimulation. Biological replicates for each sample: 3 wild type, 3 spf mutant, independently grown and harvested. One replicate per array.

first: Geir

last: Hansen

first: Rafi

last: Ahmad

first: Christopher

last: Fenton

first: Nils-Peder

last: Willassen

first: Peik

last: Haugen


title: Comparative genomics and transcriptomics of Propionibacterium acnes

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary:
The anaerobic Gram-positive bacterium Propionibacterium acnes is a human skin commensal, but is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with health. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a sequence type (ST) 18 strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits, differ between phylotypes. Comparative transcriptome analysis revealed that 225 genes of strain KPA171202 (type I-2, ST34) were differentially transcribed in strain 266 during exponential growth. 47% of these genes belong to the strain-specific gene content of strain KPA171202, indicating that strain-specific functions are utilized.
Next, we studied differential expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by up-regulation of genes involved in the stress response and amino acid metabolism. Taken together, our data highlight the genomic basis for strain diversity and identify, for the first time, the transcribed part of the genome, underling the important role active growth plays in the inflammatory activity of P. acnes. We argue that the disease-causing potential of different P. acnes strains is not only determined by variable genome content but also, and to a greater degree, by variable transcriptomes.

overall_design: Microarray experiments were performed as dual-color hybridizations. In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed. Two different labeling methods were applied. RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies) using FullSpectrum MultiStart Primer for T7 IVT RNA Amplification (BioCat GmbH, Heidelberg, Germany) as random T7 labeling. Alternatively, the total RNA samples were amplified with the TransPlex Whole Transcriptome Amplification Kit (Sigma-Aldrich, Munich, Germany) and labeled with BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Karlsruhe, Germany) as WTA BioPrime indirect. Both methods were compared and combined for final data analysis.

first: Elzbieta

last: Brzuszkiewicz

first: Thomas

last: Meyer

first: Holger

last: Brueggemann


title: FAIRE-chip in CHRF-288-11 and K562 cells

city: Hinxton

first: Dirk

middle: Stefan

last: Paul

address: Wellcome Trust Genome Campus

department: Human Genetics

institute: Wellcome Trust Sanger Institute

summary:
Maps of open chromatin in a megakaryocytic (CHRF-288-11) and an erythroblastoid (K562) cell line using the formaldehyde-assisted isolation of regulatory elements (FAIRE) method.
We profiled chromatin structure at 62 non-redundant genetic loci representing all known associations (as of November 2009, CEU population) with 11 cardiovascular traits: coronary artery disease (CAD), (early-onset) myocardial infarction (MI), mean platelet volume (MPV), platelet counts (PLT), platelet signaling (PLS), white blood cell counts (WBC), red blood cell counts (RBC), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), systolic blood pressure (SBP), diastolic blood pressure (DBP), hypertension (HYP).

overall_design: A total of 4 experiments: FAIRE using two different cross-linking times (8 and 12 min) in two cell types (CHRF-288-11 and K562 cells).

middle: S

first: Panos

last: Deloukas


title: High-frequency stimulation of the ventrolateral thalamus regulates gene expression in hippocampus, motor cortex and caudate-putamen

city: Girona

first: Gemma

last: Huguet

address: Campus de Montilivi

institute: Universitat de Girona

summary: Transcriptional profiling of rat hippocampus comparing  rats subjected to chronic (1 hour daily during 14 days) vetrolateral thalamus stimulation  (DBS group) with sham operated rats (with electrode placement but without stimulation) and with naive rats.

overall_design:
Three-condition experiment, DBS, sham and naive. Every sample consisted of pooled hippocampi from three rats. Slices between Bregma levels -2 and -4 were used for dissections of the hippocampi.  Common reference design, comparing every condition versus a brain pooled tissue consisting of pooled hippocampal, thalamic and cortical brain tissue of the naive (n=4), sham-operated (n=5) and stimulated (n=4) rats. Biological replicates: 4 DBS, 4 sham and 3 naive.  One replicate per array.
Deep brain stimulation

first: Elisabet

last: Kádár


title: Liver-expressed antimicrobial peptide-2 is downregulated in Eimeria maxima-infected chickens

city: Blacksburg

first: Huifeng

last: Li

state: VA

address: 3570 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Tech

summary: Avian coccidiosis is a major disease of poultry caused by the intestinal protozoa Eimeria.  Aviagen line A and line B birds show differential susceptibility to Eimeria infection, with line B birds exhibiting higher lesion scores and mortality.  The objective of this study was to examine differential intestinal gene expression between line A and B chicks in response to a challenge with Eimeria maxima.  Following challenge with 1 x 10^4 oocysts/chick, greater than 40% of line A chicks had lesion scores of 0 to 1 (on 0 to 4 scale), similar to controls.  In contrast, all line B challenged chicks at this same dose had lesion scores of 2 to 4.

overall_design:
Total RNA was extracted from the jejunum of control and challenged chicks from both lines A and B.  Microarrays were used for detecting the expression-changed genes which responded to the Eimeria challenge.

Samples included: four control A chicks, two challenged A chicks with a lesion score of 1 (A/LS1), two challenged A chicks with lesion scores of 3 to 4 (A/LS3-4), four control B chicks, two challenged B chicks with lesion scores of 2 to 3 (B/LS2-3) and two challenged B chicks with lesion scores of  4 (B/LS4). The DNA microarrays were processed at the Virginia Bioinformatics Institute (Virginia Tech) core facility.  The raw array data were normalized using GC-robust multiple array (GC-RMA) normalization.  Analysis of variance was used for differentially expressed genes based on Welch ANOVA (P < 0.05) and probe set lists were ordered using the fold change analysis provided by GeneSpring software.

first: Samantha

last: Casterlow

first: Elizabeth

middle: R

last: Gilbert

first: Rami

last: Dalloul

first: Audrey

last: McElroy

first: Derek

last: Emmerson

first: Eric

last: Wong


title: Pyrus communis: 'Ercolini' cultivar vs. 'Rocha' cultivar

status: Public on Jul 02 2011

city: Lisbon

first: Vanessa

middle: Tolentino

last: Pereira

address: Ed. ICAT, Campus da FCUL, Campo Grande

department: Unit of Molecular Biology and Plant Biotechnology

country: Portugal

institute: FCUL/ICAT/BioFIG

summary:
Transcriptional profiling of pear tree comparing a resistant/tolerant cultivar with a susceptible cultivar to the Stemphylium vesicarium fungus
Rocha' pear is an economically important portuguese Pyrus communis L. cultivar very susceptible to the Stemphylium vesicarium pathogenic fungus, the brown spot agent, causing huge decrease on fruit quality and yield production. Field control of brown spot disease is based in systemic application of antifungal chemicals with high economic costs and dramatic consequences to public health and environmental pollution. Plant-pathogen interactions involve a series of events encompassing constitutive and induced plant defence responses whose dissection has been a research target for control many crop diseases. The biosynthesis of cell wall polymers and antifungal compounds appear to be an efficient physical and chemical barrier to infection.To understand the molecular responses behind defence mechanisms of resistant/tolerant and susceptible cultivars of Pyrus communis L. to the S. vesicarium fungus, cDNA microarray technology was used to identify the genes differentially expressed along a time course leaf inoculation between 'Rocha' pear cultivar (a high susceptible cultivar) and 'Ercolini' pear cultivar (a resistant/tolerant pear cultivar). This study aims to contribute with information on the molecular mechanisms involved in host-pathogen interactions responsible for pear tree brown spot disease and resistance to Stemphylium vesicarium.

overall_design: Experimental condition: 'Ercolini' vs 'Rocha' (each experiment including 5 plants from each cultivar). 3 time-points: water-inoculation (T0h), 6 hours after inoculation with S. vesicarium (T6h) and 24 hours after inoculation with S. vesicarium. Biological replicates: 3 in each time-point. One replicate per array.

first: Lisete

last: Sousa

first: Antonio

first: Sandra

last: Fonseca

first: Maria

last: Pais


title: miR expression after treatment with anti-miR-191 or control

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

country: Israel

institute: Rosetta Genomics

summary:
The goal of this experiment was to study the effectivity of miR down regulation by using an anti-miR molecule.
Hepatocellular carcinoma (HCC) is a fatal disease with currently very limited beneficial therapies. MicroRNAs (miRs), which are considered to be master regulators of gene expression, have significant influence on cellular pathways and phenotype, and are de-regulated in HCC, and hence are thought to be of great therapeutic potential as novel targets. We identified hsa-miR-191 as a potential target for HCC therapy. Inhibition of this miR causes decreased cell proliferation and induction of apoptosis in vitro as well as a significant reduction of tumor mass in vivo in an orthotopic liver xenograft model. This miR was also found to be up-regulated by a dioxin, a known liver carcinogen, and was found to be a key regulator of cancer related pathways.

overall_design: HCC cell line treated with anti-miR-191, and treated with negative control anti-miR. Although this experiment was done with dual channel, chanels are not compared, irrelevant samples were on the reciprocal channel.  Sample data tables represent relevant, single channel data.

first: Noga

last: Yerushalmi

first: Eran

last: Elyakim

first: Avital

last: Dov