title: A novel copper-responsive regulon in Mycobacterium tuberculosis.

city: Rockville

first: Chun-Hua

last: Wan

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

summary: In this study, we report the identification of a five-locus copper-inducible regulon in Mycobacterium tuberculosis. The identification of a copper responsive regulon unique to pathogenic Mycobacteria suggests copper homeostasis must be maintained during an infection.

overall_design: WT and mutant Mtb cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5) and treated with 500 mM copper sulfate (CuSO4) for four hours or the absence

first: Richard

last: Festa

first: Marcus

last: Jones

first: Susan

last: Butler-Wu

first: Daniel

last: Sinsimer

first: Russell

last: Gerads

first: William

last: Bishai

first: Scott

last: Peterson

first: K

middle: H

last: Darwin


title: Potential of the hepatic transcriptome expression profile of the striped seabream (Lithognathus mormyrus) as an environmental biomarker

status: Public on Oct 25 2010

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

institute: Israel Oceanographic and Limnological Research

summary: The potential of an hepatic transcriptome expression profile, evaluated in a sentinel feral fish, to serve as an environmental biomarker was examined. Gene expression profiles of individuals of Lithognathus mormyrus were examined using a cDNA microarray and were correlated to the set of environmental exposure conditions at their site and date of collection. The clusters of individual gene expression profiles were reasonably related to the fish samples and several sample-specific clusters of genes, designated gene signatures of the sample, were determined. The relationship between transcriptome expression and the fish samples indicated a potential for their utilization as an environmental biomarker.

overall_design: Ten fish were sampled at each of two sites (Dor, Israel and Haifa, Israel) each of two years (2007 and 2008) for a total of 40 fish. All fish were hybridized to a common reference RNA population using a dye-swap design. Hence, each fish was hybridized twice vs. the reference RNA. The reference RNA was an equalized pool of the RNAs from all 10 fish comprising sample D7.

first: M

first: Y

last: Yudkovski

last: Auslander


title: S. coelicolor WL6268 R5- medium time course study

city: Minneapolis

first: Marlene

last: Castro-Melchor

state: MN

address: 421 Washington Ave SE

department: Department of Chemical Engineering and Materials Science

country: USA

institute: University of Minnesota

summary: Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) deltaSCO6268::kan mutant strain (WL6268) and compare it to the wild-type M145 strain. SCO6268 is a putative histidine kinase.

overall_design: The time-course study involved analysis of 7 samples (12h, 16h, 18h, 19h, 21h, 25h, 33h). Samples (19h, 21h, 25h, 33h) were analyzed on duplicate arrays (2 technical replicates). Sample 16h was analyzed on triplicate arrays (3 technical replicates). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.

first: Wei-Shou

last: Hu


title: S. coelicolor YSK3654 R5- medium time course study

summary: Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) deltaSCO3654::apr mutant strain (YSK3654) and compare it to the wild-type M145 strain. SCO3654 is a putative two-component system sensor kinase.

overall_design: The time-course study involved analysis of 9 samples (10h, 13h, 16h, 19h, 22h, 25h, 31h, 35h, 37h). All samples were analyzed on duplicate arrays (2 technical replicates). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.


title: Clorgyline treatment of VCaP cells

city: Stanford

first: Hongjuan

last: Zhao

state: CA

address: 300 Pasteur Dr

department: Urology

institute: Stanford

summary:
Purpose: Monoamine oxidase A (MAOA) is a mitochondrial enzyme that degrades neurotransmitters including serotonin and norepinephrine.  Its inhibitors are commonly used to treat neurologic conditions including depression.  Recently, we and others identified high expression of MAOA in normal basal prostate epithelium and in high grade primary prostate cancer (PCa).  Inhibition of MAOA with an irreversible inhibitor, clorgyline, induced differentiation in primary cultures of epithelial cells from normal tissues and high grade cancers.  Furthermore, clorgyline treatment inhibited several oncogenic pathways in PCa cells, suggesting a clinical value of MAOA inhibitors as a pro-differentiation and anti-oncogenic therapy for high risk PCa.  Here, we extended our studies to a model of advanced PCa, VCaP cells, which were derived from castration-resistant metastatic PCa and express a high level of MAOA.
Methods: The growth of VCaP cells in the presence or absence of clorgyline was evaluated in vitro and in vivo. Gene expression changes in response to clorgyline were determined by microarray and validated by quantitative real-time PCR.
Results: Treatment with clorgyline in vitro inhibited growth and altered the transcriptional pattern of VCaP cells in a manner consistent with the pro-differentiation and anti-oncogenic effects seen in treated primary PCa cells.  Src, beta-catenin, and MAPK oncogenic pathways, implicated in androgen-independent growth and metastasis, were significantly downregulated.  Clorgyline treatment of mice bearing VCaP xenografts slowed tumor growth and induced transcriptome changes similar to those noted in vitro.
Conclusions: Our results support the possibility that anti-depressant drugs that target MAOA might find a new application in treating PCa.
Compound Based Treatment: Clorgyline treament of VCaP cells


title: Linkage of behavioral and genomic impacts of a wastewater effluent on the fathead minnow

status: Public on Oct 30 2010

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Rivers containing effluents from water treatment plants are complex soups of compounds, ranging from pharmaceuticals to natural hormones.  Male fathead minnows (Pimephales promelas) were exposed for 3 weeks to effluent waters from the Metropolitan Wastewater Treatment Plant in St. Paul, MN. Fish were tested for their competitive nest holding behavior.   Changes in vitellogenin were measured and these were correlated to changes in gene expression using a 22,000 gene microarray developed specifically for fathead minnows.  Significant changes in gene expression were observed in both liver and gonad, which correlate to phenotypic changes of vitellogenin induction and reduced competitive behavior. We also compared by real-time PCR the expression changes in key genes related to steroid biosynthesis and metabolism in fish exposed to the effluent as well as in fish exposed to a model estrogen and a model androgen.  While the gene expression signature from effluent-exposed fish shared some elements with estrogen and androgen signatures, overall it was different, underscoring the complexity of compounds present in sewage and their different modes of action.

overall_design: Fathead minnow 22,000 gene arrays were designed by EcoArray (Alachua, FL) and were purchased from Agilent.  Array hybridizations were performed using a reference design, where each sample was compared to a reference sample.  The reference consisted of equal amounts of RNA from control female and male tissues (liver, brain and gonad) and was prepared as a standard for several experiments.  Four replicates consisting of four different individuals were analyzed for each of the tissues, liver and gonad for both the control and the effluent-exposed fish.  cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer’s kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit and Agilent 60-mer oligo microarray processing protocol; Agilent, Palo Alto, CA).  Ovarian and liver samples from the fish were labeled with Cy5 while the reference sample was labeled with Cy3.

last: Garcia-Reyero

first: Candice

middle: L

last: Lavelle

first: Barbara

last: Escalon

first: Dalma

last: Martinovic

first: Kevin

middle: J

last: Kroll

first: Peter

middle: S

last: Sorensen

first: Nancy

middle: D

last: Denslow


title: Individual Stress Vulnerability Is Predicted by Short-Term Memory and AMPA Receptor Subunit Ratio in the Hippocampus

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute of Developmental Genetics

country: Germany

institute: Helmholtz Zentrum München, German Research Center for Environmental Health

summary:
Chronic stress is a key risk factor for a variety of diseases, but the determinants of individual stress susceptibility are still unclear. Using a recently developed paradigm for chronic social stress in mice we identified animals that were resistant or susceptible to the persistent effects of chronic stress exposure. Gene expression analysis in laser-microdissected hippocampal subfields of both groups revealed differentially regulated AMPA receptor subunits, which might affect the susceptibility of an individual to chronic social stress. To test this hypothesis, animals were treated with the AMPA receptor potentiator LY451646 or vehicle during the last 4 weeks of chronic stress exposure. Enhanced AMPA receptor function in chronically stressed animals ameliorated the lasting effects of the chronic stress exposure on physiological, neuroendocrine and behavioural parameters. Our data suggest that differences in AMPA receptor function may underlie individual stress susceptibility and support AMPA receptor potentiators as potential medication in stress-related diseases.
Keywords: phenotype, chronic stress, AMPA

overall_design: We have subjected 120 individuals to the chronic social stress procedure, which was recently shown to result in robust effects on neuroendocrine and behavioural parameters (Sterlemann V, 2008). Following the stress procedure all animals were single housed for 7 days. Corticosterone secretion was significantly increased in the chronic stress group compared to controls after one week of single housing. Within the chronic stress group we observed a large variation, where some individuals had recovered from the stress procedure, while others still showed a largely increased corticosterone secretion. After 4 more weeks of single housing, the difference in basal corticosterone secretion between the animals susceptible to chronic stress and unsusceptible or control subjects was still evident. From the group extremes in the chronically stressed animals we selected the 6 most-affected and the 6 most resistant individuals. To investigate the mechanisms underlying the observed differences in individual stress susceptibility between these mice we laser dissected the CA1 and the dentate gyrus region of the hippocampus in the selected mice and performed a gene expression profiling analysis. Pooled amplified RNA samples were then hybridised on Illumina mouse BeadChips (N=4 per group) and detected in the Illumina BeadArray Reader (Illumina, Inc., San Diego, CA).

first: Mathias

middle: V

last: Schmidt

last: Weber

first: Klaus

last: Wagner

first: Sebastian

last: Scharf

first: Claudia

last: Liebl

first: Nicole

last: Datson

first: Christian

last: Namendorf

first: Tamara

last: Gerlach

last: Kühne

first: Manfred

last: Uhr

first: Jan

middle: M

last: Deussing

first: Wolfgang

last: Wurst

first: Elisabeth

middle: B

last: Binder

first: Florian

last: Holsboer

first: Marianne

last: Müller


title: Transcriptional signature of Drosophila wing disc regeneration

status: Public on Oct 22 2010

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

country: Spain

institute: Universitat de Barcelona

summary: Research on the ability of certain organisms to reconstruct missing structures of their bodies is still in its infancy, despite numerous efforts performed in multiple species. Using expression profile analyses on different timepoints that cover wound healing and regeneration processes (0, 24 and 72 hours post injury), we studied the regenerative behaviour of fragmented wing imaginal discs of D. melanogaster implanted into adult flies. First, through the comparison between cut and intact discs, we identified the effect of implantation on the regeneration process. Filtering this information, we then constructed the specific early regeneration gene signature of wing discs in which multiple transcription factors, immune response genes and members of the JNK, Notch and WNT signaling pathways seem to play an important role. We next compared the transcriptomes of discs 24 and 72 hours after fragmentation to characterize the regenerative machinery and observed a temporal decrease in the cellular metabolic processes, RNA processing and gene expression machinery, suggesting the discs normal activity was stopped on this first interval of time in response to injury and implantation offences. Based on the expression patterns, we elaborated a catalogue of genes involved in wing disc regeneration divided into four classes (wound healing, regeneration, quick response, constant response).

overall_design: Imaginal discs from third instar larvae were 3/4 fragmented, implanted into the abdomen of adult flies and cultured. In order to subtract the noise due to implantation, we repeated the same protocol using intact discs that were cultivated for 24h. Therefore, a total of 12 microarrays were hybridized: four microarrays (with total RNA from non cut wing discs at 0 and 24 hours) were used to assess the effect of the implantation procedure in intact wing discs and the rest (8) were used to measure changes in gene expression in the first 24 hours after disc dissection and implantation (total RNA from wing discs at 0 and 24 hours was hybridized) and during the period between 24 and 72 hours after the cut (total RNA from wing discs at 24 and 72 hours was hybridized). At least two independent total RNA extractions were carried out (using the RNeasy Protect Mini Kit from Qiagen Inc.) for each condition. The four microarrays hybridized for each pair of conditions were done in biological replicate pairs with dyes swapped to take dye bias into account. The whole set of microarrays was normalized following the same protocol, extracting in each case the list of significant genes (at least 1.5-fold change, FDR adjusted pvalue < 0.05).

first: Enrique

last: Blanco

first: Marina

last: Ruiz-Romero

first: Manel

last: Bosch

first: AdriÃ

last: Punset

first: Florenci

last: Serras

first: Montserrat

last: Corominas


title: Genome-wide Transcript Profiling of Endosperm without Paternal Contribution Identifies Parent-of-origin Dependent Regulation of AGAMOUS-LIKE 36

status: Public on Oct 20 2010

city: OSLO

first: Paul

middle: E.

last: Grini

address: Blindernveien 31

department: Department of Molecular Biosciences

country: Norway

institute: University of Oslo

summary: Seed development is dependent on a well-orchestrated interplay between different transcriptional programs operating in the embryo, the endosperm and the maternally derived seed coat. In angiosperms, the embryo and the endosperm are products of double fertilization during which the two pollen sperm cells fuse with the egg cell and the central cell of the female gametophyte. In Arabidopsis, mutation of the cell cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) results in pollen that only successfully fertilizes the egg cell. Seeds generated from crosses with cdka;1 pollen develop endosperm with solely maternal and no paternal contribution. Here we have exploited cdka;1 fertilization as a novel tool for genomic dissection of parental effects during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds. By this approach, we identified 11 differentially expressed AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors. Here, AGL36 was chosen for an in-depth study. We show that AGL36 is imprinted and only expressed from the maternal genome. In addition, we demonstrate that AGL36 imprinting is controlled by the activity of METHYLTRANSFERASE1 (MET1) maintenance DNA methyltransferase and DEMETER (DME) DNA glycosylase. Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2). These findings shed novel light on the interplay between maternal and paternal genomes in the seed and how imprinting is coordinated by different mechanisms.

overall_design: 3 biological replicates, each consisting of 35 siliques from 10 individual plants, were used. Arabidopsis thaliana wild type (ecotype Colombia-0 and Ler-0) and cdka;1 mutant (At3g48750 /SALK_109806) were sown out on soil and grown under the following conditions: 18oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 μmol/m2/sek in light intensity. For each replica, 10 Ler plants were emasculated and pollinated after 48 hours, either with individual WT Col or with individual cdka;1 mutant pollen. Three days after pollination (3 DAP), the siliques of each biological replicate were dissected with hypodermic needles to remove carpel walls, the pistil with pollen attached to it and the pedicel with abcsission zone. The remaining seeds attached to the middle lamella were harvested in bulk in liquid nitrogen at the same time of the day. Biological replicas are dye-swapped between slides.

first: Reza

last: Shirzadi

first: Per

last: Winge

middle: E


title: MicroRNA profiling analysis of differences between bone marrow mouse stem cells versus leukemic and teratocarcinomic cell lines

status: Public on Oct 27 2010

city: Salamanca

last: Martin

address: Avd/Universidad de Coimbra s/n

department: CSC Biology

institute: OSP

summary:
Our aim is to identify any hallmark differentially expressed miRNAs between mouse bone marrow cells and different cancer cell lines (leukemic with lymphoid and myeloid origin and teratocarcinomic with dedifferentiated characteristics).
MicroRNAs (miRNAs) are an important member of posttrascriptional regulators and its pathological level changes have been implicated in various cancer types. This is the first step of the study focused at cancer stem cell biology of cancer in our in vivo mouse models.
We conclude by high-throughput microRNA profiling analysis,that exists a group of miRNAs candidates to explore their biological function in mice bone marrow stem cells an its role in carcinogenesis.

overall_design:
We isolated the bone marrow cells from mice by femur and tibial flush, then wash and collected. We isolate the same number of cells from fresh cultures of different cell lines types at passage 3, then wash and collected. Total RNA was extracted for the TaqMan Low Density Array v2.0.RNA quality was assessed using Nanodrop for concentration and purity (OD 260/280 and 260/230) and the Agilent Bioanalyzer 2100 for integrity (RNA integrity number (RIN) > 9).
Normalization was performed with common endogenous controls for A card and B card (MummU6, snoRNA135, snoRNA202 reference snRNAs for mouse).Comparative real-time PCR was performed in 3 replicates, including no-template controls.

first: José

last: Martín-Fernández

first: Francisco

last: González


title: Transcriptional Profile Analysis of RPGRORF15 frameshift mutation

city: Philadelphia

first: Sem

last: Genini

state: PA

address: 3900 Delancey Street

department: Clinical Studies

institute: University of Pennsylvania

summary:
Purpose: To identify genes and molecular mechanisms associated with disease progression during (7 weeks of age) and after (16 weeks) the peak of photoreceptor death in dogs affected with XLPRA2, a canine model of early-onset XLRP caused by a microdeletion in RPGR exon ORF15.
Methods: Expression profiles of diseased and normal dog retinas at both ages were compared using a canine retinal custom cDNA microarray. Data normalization and filtering were performed with GeneSpring, statistical analysis with Significance Analysis of Microarrays. Real-time PCR using Taqman probes, western blot and immunohistochemistry (IHC) were applied on selected genes to confirm and expand the microarray results.
Results: At 7 and 16 weeks, respectively, 56 and 18 transcripts were down-regulated in mutant retinas compared to normals. None of the transcripts was differentially expressed (DE) at both ages, suggesting the involvement of temporally distinct molecular pathways. Down-regulated genes included PAX6, CHML, and RDH11 at 7 weeks and CRX and SAG at 16 weeks, which are necessary for visual system development and function. Genes directly or indirectly active in apoptotic processes were altered at 7 weeks (CAMK2G, NTRK2, PRKCB, RALA, RBBP6, RNF41, SEPT5, SMYD3, SPP1, and TUBB2C) and 16 weeks (SLC25A5 and NKAP). Furthermore, DE genes at 7 weeks (ELOVL6, GLOD4, NDUFS4, and REEP1) and 16 weeks (SLC25A5 and TARS2) are related to mitochondrial functions. Real-time PCR of 11 genes confirmed the microarray results and showed differential expression for additional genes not on the array, such as GFAP, RHO, OPN1SW, CNGB3 and the mutated RPGR. Western blotting and IHC analysis also confirmed the high reliability of the presented transcriptomic data.
Conclusions: A list of mutated genes in RPGRORF15 diseased retinas, which are likely candidates to further study their role in age-related photoreceptor degeneration diseases, is reported at different crucial ages. The results indicate that at 7 weeks a combination of non-classical anti- and pro-apoptotic genes appears to be involved in photoreceptor degeneration, whereas at both 7 and 16 weeks expression of mitochondria related genes indicates they may play a relevant role in the disease process.

overall_design: 3 biological replicates each for normal and XLPRA2 affected retinas were analyzed at 7 and 16 weeks of age. Each individual sample was hybridized in a reference design using a custom-made retinal cDNA microarray against brain pool to enable cross comparison between groups. Retina was labeled with Cy5 in all samples but 5615 (GSM474350).

first: Barbara

last: Zangerl

first: J

last: Slavik

first: Gregory

last: Acland

first: William

middle: A

first: Gustavo

last: Aguirre


title: Somatic CNV profile of congenital ectopic thyroids

city: Montreal

first: Johnny

middle: Yvan

last: Deladoëy

state: QC

address: 3175 Côte Sainte-Catherine

department: Pediatrics; U of Montreal

country: Canada

institute: Research Center CHU Sainte-Justine

type: Genome variation profiling by genome tiling array

summary: To assess whether specific genes have relevant somatic genetic or epigenetic alterations in ectopic tissue, we used a combined analysis of transcriptome (confirmed by qRT-PCR on 68 genes), methylome, structural genome variations (copy number variants, CNVs) and miRNA profile of ectopic compared with orthotopic thyroids.

overall_design: DNA form three ectopic thyroid compared with matched leucocytes.

first: Rasha

last: Abu-Kuhdir

first: Jean

last: Paquette

first: Anne

last: Lefort

first: Frederick

last: Libert

first: Jean-Pierre

last: Chanoine

first: Gilbert

last: Vassart

first: Guy

last: Van Vliet


title: CGH profiles of sporadic basal-like breast tumors

status: Public on Oct 26 2010

city: Hamburg

first: Simon

last: Joosse

address: Martinistrasse 52

department: Institute of Tumor Biology

institute: University Medical Center Hamburg-Eppendorf

summary:
Genomic DNA from sporadic breast tumours was isolated and analysed using array CGH. The NKI 1MB BAC/PAC micro array was used to identify chromosomal aberrations of all tumours. Other profiles are located at: GSE9114
Keywords: sporadic breast tumour, CGH.

overall_design: Locate chromosomal aberrations in sporadic breast tumors.


title: Methylome analysis of congenital ectopic thyroids

type: Methylation profiling by genome tiling array

overall_design: The MeDIP-chip was performed using pair of enriched methylated fraction (IP) and nomal fraction (IN) of genomic DNA from the three available cases and the three controls. The methylated fraction of genomic DNA was enriched using the methylated DNA immunoprecipitation (MeDIP) assay (Weber et al. Nat Genetics, 2005) and interrogated on human Promoter plus CpG Island Tiling Arrays with a ChIP design for CpG islands and promoter regions (n=28,226)  from HG18 using 385,020 Probes selected from CGH probe bank with a median spacing of  101bp (Roche NimbleGen, Madison, WI).


title: S. coelicolor M752 SMM medium time course study

first: Marlene

last: Castro-Melchor

summary: Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M752 mutant strain, which has an in frame deletion of scbR (SCO6265) and compare it to the wild-type M145 strain. scbR encondes a gamma-butyrolactone binding protein (Takano, E., Chakraburtty, R., Nihira, T., Yamada, Y., and Bibb, M. A complex role for the gamma-butyrolactone SCB1 in regulating antibiotic production in Streptomyces coelicolor A3(2). Mol. Microbiol. 2001 41(5), 1015-1028).

overall_design: The time-course study involved analysis of 8 samples (14hr, 15hr, 16hr, 17hr, 19hr, 20hr, 22hr, 39hr). Sample 22hr was analyzed on duplicate arrays (2 technical replicates). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.

first: Eriko

last: Takano

first: Wei-Shou

last: Hu


title: Inhibitors that block initiation of wall teichoic acid biosynthesis sensitize methicillin-resistant Staphylococcus aureus to beta-lactams

city: Normal

first: Arunachalam Muthaiyan

email: amuthai@gmail.com, bjwilkin@ilstu.edu

state: IL

address: Julian Hall

department: Biological Sciences

institute: Illinois State University

summary: Methicillin resistance in Staphylococcus aureus depends on the production of mecA, which encodes penicillin-binding protein 2A (PBP2A), an acquired peptidoglycan transpeptidase with reduced susceptibility to beta-lactam antibiotics. Here, we show that preventing the expression of wall teichoic acids (WTAs) genetically or with a TarO inhibitor sensitizes MRSA strains to beta-lactams although PBP2A is still expressed. Using S. aureus microarrays and array data analysis protocols (NIAID's Pathogen Functional Genomics Resource Center) we have characterized the transcriptomes of S. aureus COL. in order to further understand the sensitization of strain COL to methicillin by tunicamycin we determined the tunicamycin and methicillin transcriptomes alone and in combination. Methicillin treatment of COL at 500 µg/mL had almost no effect on cell growth rate and, remarkably, the only gene in the transcriptome that showed a more than two-fold change in expression was lytM, which was downregulated. The tunicamycin transcriptome of COL, acquired at 0.4 µg/mL, shows modest changes compared to the untreated control both in terms of the total numbers of affected genes and in the degree of up- or downregulation. Several of the genes upregulated upon tunicamycin treatment are part of the cell wall stress stimulon.COL was grown with methicillin to an OD600 ~0.4, and challenged with tunicamycin for 2 hrs whereas the control culture contained methicillin alone. transcriptome for COL growing in the presence of both agents showed extensive changes in gene expression. , the cell wall stress stimulon, which was not induced by methicillin when tunicamycin was absent, was clearly induced in its presence and the changes were far more dramatic than observed with tunicamycin alone. ). vraS and vraR, which encode a two component signaling system dedicated to the cell wall regulon, were upregulated 3.8 and 3.7 fold, respectively. Other upregulated cell wall stress stimulon genes include pbp2, fmtA, mvaD (mevalonate diphosphate decarboxylase), crtN (dehydrosqualene desaturase) mvak1 (mevalonate kinase), recU, SAV1424 (methionine sulfoxide reductase A), prsA (peptidyl-prolyl cis/trans isomerase), tcaA (Tca protein) and cwrA. A considerable number of genes were also downregulated upon challenge of COL with the combination of tunicamycin and methicillin. These included sspB, lrgA, dltA, capL, SAS0988, sspA, pflB, and spa. Several of these genes have been found to be downregulated in previous studies of cell wall-active antibiotic challenge of S. aureus.

overall_design:
Growth conditions for microarray analysis- For transcriptional profiling, an overnight-grown COL culture was diluted (2% vol/vol) to 20 ml TSB medium in a 50-ml Erlenmeyer flask and grown at 30°C with shaking at 200 rpm. For the sensitization experiment, COL was grown with methicillin to an OD600 ~0.4, and challenged with tunicamycin for 2 hrs whereas the control culture contained methicillin alone. Total bacterial RNA was isolated as previously described from S. aureus COL (30°C, 200 rpm). The RNA samples were then converted to fluorescently-labeled cDNA and hybridized to S. aureus microarrays version 7 (NIAID's Pathogen Functional Genomics Resource Center). Hybridization signals were scanned using an Axon4000B scanner (Molecular Devices, Sunnyvale, CA ) with Acuity 4.0 software and scans were saved as TIFF image. Scans were analyzed using TIGR-Spotfinder (www.tigr.org/software/) software and the local background was subsequently subtracted. The data set was normalized by applying the LOWESS algorithm using TIGR-MIDAS (www.tigr.org/software/) software. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded. The averaged log2 ratio for each remaining gene on the four replicate slides was ultimately calculated. Significant changes of gene expression were identified with SAM (significance analysis of microarrays; www.tat.stanford.edu/~tibs/SAM/index.html. Genes analyzed using these programs were further sorted and grouped based on their function using our in-house software Staphylococcus aureus Gene Sorter (SAGS). Several controls were employed to minimize the technical and biological variations and to ensure that the data obtained were of good quality. First, each ORF was present in triplicate on the array. Second, each RNA preparation was used to make probes for at least two separate arrays for which the incorporated dye was reversed.

Contents of raw data files:

Channel A = Cy3 dye
Channel B = Cy5 dye

File names ending with S1,S3 = Cy3 untreated, Cy5 treated
File names ending with S2,S4 = Cy5 untreated, Cy3 treated

first: Jennifer

last: Campbell

first: Atul

middle: K

last: Singh

first: John

middle: P

last: Santa Maria

first: Younghoon

last: Kim

first: Stephanie

last: Brown

first: Jonathan

middle: G

last: Swoboda

first: Eleftherios

last: Mylonakisc

first: Brian

last: Wilkinson

first: Suzanne

last: Walker


title: Aspergillus niger WT: Control vs. xylan induction

status: Public on Oct 21 2010

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

summary: Transcriptional profiling of the A. niger WT (N402) strain treated with xylan (1%, w/v) for 6, 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases after treatment with the polysaccharide xylan. The experiment was further validated by enzymatic assays.

overall_design: Three-condition experiment: WT-Xylan for 6, 12 and 24 h at 30oC in batch culture. Firstly, the WT (N402) strain was grown in minimal medium with fructose as carbon source (control), and then transferred to 1% (w/v) xylan as carbon source. 2 biological replicates per time point.

middle: R


title: Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Mutation Accumulation Lines)

status: Public on Oct 19 2010

first: Daniel

middle: Francis

last: Simola

address: 1041 BRB II/III

department: Cell and Developmental Biology

summary:
45 genome-wide microarray measurements for 23 mutation accumulation lines grown in YPD liquid culture
MA lines obtained by single-colony transfer on YPD plates for 600 generations, starting from a BY4741 derived strain (see Zeyl C, DeVisser JA: Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae. Genetics 2001, 157:53–61)

overall_design: Two biological replicates for each strain in a common reference design (no dye-swap)

middle: F

first: Helen

last: Murphy


title: Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes (Natural Strain Timecourse)

summary:
Multi-genome, time series transcriptome measurements across the budding yeast cell cycle
378 genome-wide microarray measurements, 18 timepoints, nine strains of S. cerevisiae and one strain of S. paradoxus

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

overall_design: Dye-swap technical replication at each strain,timepoint pair in a common reference design


title: Gene expression from beagle dog mandible

city: Matsdo

first: Jian

last: Zhao

address: 2-870-1 Sakaecho-nishi

country: Japan

institute: Nihon University School of Dentistry at Matsudo

summary:
In this study, beta-TCP was implanted in dog mandibles, after which the gene expression profiles and signaling pathways were monitored using microarray and Ingenuity Pathways Analysis (IPA). Following the extraction of premolars and subsequent bone healing, beta‑TCP was implanted into the artificial osseous defect. Total RNA was isolated from bone tissues and gene expression profiles were examined using microarray analysis.
We used microarrays to detail the global programme of gene expression and identified distinct classes of up- and down- regulated genes during this process.

overall_design: Waiting 3 months healing after tooth extraction from beagle dog mandibles, we drilled the holes in the dog mandibles, and implanted without and with beta-TCP. And these dog mandibles were selected for RNA extraction and hybridization on Affymetrix microarrays. After implanting beta-TCP in the dog mandibles 4, 7, 14 days, we selected sample at 3 time points: Control_4d, beta-TCP_4d, Control_7d, beta-TCP_7d, Control_14d, beta-TCP_14d.

first: Takao

last: Watanabe

first: Ujjal

last: Bhawal

first: Eiro

last: Kubota

first: Yoshimitsu

last: Abiko


title: The effect of tert-butyl hydroperoxide on hepatic multi-transcript patterns of the sentinel fish Lithognathus mormyrus

first: Moshe

last: Tom

summary: The study was aimed at examining the effect of the model organic oxygen reactive species (ROS) tert-Butyl Hydroperoxide (tBHP) on hepatic multi-gene expression patterns of the fish Lithognathus mormyrus. Fish were exposed to injected tBHP followed by extraction of RNA from their livers. The corresponding labeled cDNAs of treated versus control fish were applied onto a cDNA microarray of ~1500 unique sequences and differentially expressed genes were identified. The hepatic profile of the in individual fish versus a reference RNA was the basic biomarker parameter. M, the log2 ratio of gene expression (M) was calculated from the imaged hybridization results by the LIMMA software (R environment) used also to statistically determine the differentially expressed genes in the various treatments. EXPANDER4.1 software was used to hierarchically cluster M profiles of individual fish across genes. This clustering was used as a preliminary step aimed at distinguishing groups of similarly expressed genes across the treatments. Gene annotation was aimed at more educated interpretation of the results.

overall_design:
The study is composed of two experiments, Experiments 1 and 2.
Experiment 1 – (samples GSM476020, GSM476029, GSM476030). Three groups with five fish in each of them were injected by three tBHP doses, 0.5, 5, 50 mg/kg body weight/injection. Three injections were applied to each fish in three days intervals between consecutive injections. A control group of five fish was sham-injected with saline, the tBHP carrier. Both the control and the treated fish were sacrificed three days after the last injection.
Experiment 2 - (samples GSM476074, GSM476112) Two groups with 18 fish in each of them were injected by two tBHP doses, 5, and 30-50 mg/kg body weight/injection. Five injections were applied daily to each fish. The first injection of the high dose contained 50 mg/kg body weight, but was reduced to 30 mg/kg body weight due to mortality of two fish several hours after the first injection. A control group of 18 fish was sham-injected by saline, the tBHP carrier. Six fish of each of the treatment and control groups were sacrificed at three time intervals: 2, 20 and 68 hours after the last injection.
RNA preparations resulted from the two exposure experiments were labeled and hybridized on the cDNA microarray. The hybridization design of Experiment 1 is composed of dual hybridizations of randomly selected treated fish with randomly selected control fish. Four replicate slides were used for each fish pair, applying dye swap design. Experiment 2 is similarly designed, with only one replicate slide per fish pair. Alternate labeling in the each half of the biological replicates is aimed at partial compensation of dye effect. Please see 'hybridization_design.txt' file for sample label details.

first: Meirav

last: Auslander

first: Peter

last: Neumann


title: Identification of Altered MicroRNA Expression Patterns in Synovial Sarcoma

city: Kamakura

first: Toshihiko

last: Kuroda

institute: Toray industries inc.

summary: MicroRNAs (miRNAs) are non-coding small RNAs that function as an endogenous regulator of gene expression. Their dysregulation has been implicated in the development of several cancers. However, the status of miRNA in soft tissue sarcomas has not yet been thoroughly investigated. This study examined the global miRNA expression in synovial sarcoma and compared the results to those in another translocation-associated sarcoma, the Ewing family of tumors, and in normal skeletal muscle. The 3D-Gene miRNA microarray platform (Toray, Kamakura, Japan) and unsupervised hierarchical clustering revealed a distinct expression pattern of miRNAs in synovial sarcoma from Ewing tumors and skeletal muscle. Thirty-five of the more than 700 miRNAs analyzed were differentially expressed in synovial sarcomas in comparison to other tissue types. There were 21 significantly up-regulated miRNAs, including some miRNAs, such as let-7e, miR-99b and miR-125a-3p, clustered within the same chromosomal loci. Quantitative reverse transcription-polymerase chain reaction also demonstrated that these miRNAs were over-expressed in synovial sarcomas. The down-regulation of let-7e and miR-99b by anti-miR miRNA inhibitors resulted in the suppression of the proliferation of synovial sarcoma cells, and modulated the expression of their putative targets, HMGA2 and SMARCA5, suggesting that these molecules have a potential oncogenic role. The unique miRNA expression pattern including the over-expressed miRNA clusters in synovial sarcoma warrants further investigation in order to develop a better understanding of the oncogenic mechanisms and future therapeutic strategies for synovial sarcoma.

overall_design: Ten synovial sarcomas, five Ewing tumors and five normal skeletal muscle specimens are analyzed.

first: Masanori

last: Hisaoka

first: Atsuji

last: Matsuyama

first: Yuichi

last: Nagao

first: Lan

last: Luan

first: Hideo

last: Akiyama

first: Satoshi

last: Kondo

first: Hiroshi

last: Hashimoto


title: DNA methylation data from a separate set of human iPS cells and fibroblasts, and ES cells

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

summary: We used custom Nimblegen microarrays to determine the DNA methylation profiles of iPS cells, ES cells, and fibroblasts.

overall_design: We isolated genomic DNA from iPS cells, ES cells, and fibroblasts and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).

first: In-Hyun

last: Park

first: Bo

last: Wen

last: Murakami

first: George

middle: Q

last: Daley

first: Andrew

last: Feinberg


title: Part 7/7: Fibroblasts_6hpi_activevirus_dendrimer

status: Public on Oct 16 2010

city: Bethesda

first: Falko

last: Schmeisser

address: 8800 Rockville Pike, building 29A, room 3C-05

department: DVP

institute: FDA/CBER

summary: Differentiated NT2 cells are a potentially useful model system to study herpes simples virus (HSV) replication in human neurons.  These cells can be irreversibly differentiated into NT-neurons in the presence of retinoic acid and non-dividing cultures NT-neurons can be maintained for up to several months without retinoic acid.  HSV is capable of infecting and replicating in differentiated NT-neurons and thus differentiated NT-neurons provide a ready source of human post-mitotic cells which can be useful to study certain aspects of the interaction of HSV and the neuron.  Microarray analysis was used to examine how HSV-1 infection modulates cellular transcription in human NT-neurons, focusing on changes that take place during the first 24 hours following infection and compared to changes resulting from infection with inactivated virus.  In addition, the transcriptional changes resulting from virus infection of neurons were compared to those observed in primary human fibroblasts.  At early times after HSV infection a small number of cellular transcripts in NT-Neurons appear to be increased in abundance.  Most of these transcripts that are up-regulated after infection are not unique to neuronal cells, and possibly represent a common cellular response to HSV infection.  A few transcripts were not detected in infected human fibroblasts and may represent part of a transcriptional profile specific to this type of human neuronal cell.  In contrast to the situation at early times after infection, analysis of cellular transcripts in NT-neurons at late times after infection is complicated by the overall profound decrease in cellular transcription.  Thus, microarray analysis appeared to be most useful as a screening method for transcription changes following infection at early times after virus infection of NT-neurons.

overall_design: Two-condition experiment, HSV-1 infected versus uninfected fibroblasts, 3 independent biological replicate sets (uninfected/infected) in dual channel array setup (Cy3/Cy5).

first: Jerry

last: Weir


title: Part 4/7: NTNeurons_24hpi_inactivatedvirus_dendrimer

overall_design: Two-condition experiment, NTNeurons infected with inactivated HSV-1 versus uninfected NTNeurons, 4 independent biological replicate sets (uninfected/infected) in dual channel array setup (Cy3/Cy5).


title: Part 5/7: NTNeurons_6hpi_activevirus_aminoallyl

overall_design: Two-condition experiment, HSV-1 infected versus uninfected NTNeurons, 3 independent biological replicate sets (uninfected/infected) in dual channel array setup (Cy3/Cy5).


title: Part 6/7: NTNeurons_24hpi_activevirus_aminoallyl

overall_design: Two-condition experiment, HSV-1 infected versus uninfected NTNeurons, 4 independent biological replicate sets (uninfected/infected) in dual channel array setup (Cy3/Cy5).


title: Validation data for Lawrence Livermore Microbial Detection Array version 1

status: Public on Oct 15 2010

city: Livermore

first: Kevin

last: McLoughlin

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

summary: We designed a pan-Microbial Detection Array (MDA) to detect all known viruses (including phage), bacteria, and plasmids. Family-specific probes were selected for all sequenced viral and bacterial complete genomes, segments, and plasmids. Probes were designed to tolerate some sequence variation to enable detection of divergent species with homology to sequenced organisms. The array has wider coverage of bacterial and viral targets based on more recent sequence data and more probes per target than other microbial detection/discovery arrays in the literature. In blinded lab testing on spiked samples with single or multiple viruses, the MDA was able to correctly identify species or strains. In clinical fecal, serum, and respiratory samples, the MDA was able to detect and characterize multiple viruses, phage, and bacteria in a sample to the family and species level, as confirmed by PCR.

sample_organism: Human respiratory syncytial virus A strain Long

overall_design: Testing of microbial detection array with mixtures of known viruses, blinded clinical samples and viral cell culture samples.

first: Shea

middle: N

last: Gardner

first: Crystal

middle: J

last: Jaing

middle: S

first: Tom

last: Slezak


title: Evaluation of the effect of antimiR-122 administration on the liver, spleen and heart miRNome

city: Heidelberg

first: Mirco

last: Castoldi

address: Im Neuenheimer Feld 156

department: Department of Pediatric Oncology, Hematology and Immunology

institute: University of Heidelberg

summary: To determine the effect of antimiR-122 administration on the mouse miRNome.

overall_design: To functionally investigate a possible link between miR-122 and iron metabolism we inhibited miR-122 by a single, intraperitoneal injection of Locked Nucleic Acid (LNA)-modified antimiR oligonucleotides into age- and sex-matched C57Bl/6 WT mice. To inhibit miR-122 specifically, we injected an antimiR compound with perfect complementarity to miR-122 [perfect match (PM); PM_antimiR-122]. As negative controls, mice were either injected with an LNA control compound with two mismatches (2MM, 2MM_antimiR-122) or the vehicle control (SAL; 0.9% NaCl). Mice were sacrificed three and six weeks after injection. Independent of treatment, mice were viable and exhibited no overt physical or behavioral abnormalities. To exclude that PM_antimiR-122 administration disturbs the expression of other miRNAs we analyzed miRNA expression profiles in the livers, hearts and spleens of the same mice.


title: Part 1/7: NTNeurons_6hpi_activevirus_dendrimer


title: Bypass mechanisms of the AR pathway in castration-resistant PC346 prostate cancer cells

city: Rotterdam

first: Rute

last: Marques

address: Dr Molewaterplein 50

country: Netherlands

institute: Erasmus MC

summary:
Prostate cancer is initially dependent on androgens for survival and growth, making hormonal therapy the cornerstone treatment for invasive tumors. However, despite initial remission, the cancer will inevitably recur. The present study was set to investigate how androgen-dependent prostate cancer cells eventually survive and resume growth under androgen-deprived and antiandrogen supplemented conditions
Microarray technology was used to analyze differences in gene expression between androgen-responsive and hormone-refractory prostate cancer cell lines. As model system, we used the androgen-responsive PC346C cells and its castration-resistant sublines: PC346DCC, PC346Flu1 and PC346Flu2. These sublines were derived from the parental PC346C by long-term androgen ablation (PC346DCC), supplemented with the antiandrogen hydroxyflutamide (PC346Flu1 and PC346Flu2). Previous studies revealed distinct AR modifications in all three castration-resistant sublines: AR overexpression (PC346Flu1), AR down-regulation (PC346DCC) and  T877A AR mutation (PC346Flu2).

overall_design: Each of the hormone-refractory sublines were cultured in their respective selection medium (steroid-stripped medium for PC346DCC, supplemented with 1 mM OH-Flutamide for PC346Flu1 and Flu2) and hybridized on the microarrays, together with the parental androgen-responsive PC346C (cultured in complete medium supplemented with 0.1 nM R1881). To account for the biological variability and dye-preferential binding to oligonucleotides on the microarray, four replicate arrays were performed per cell line, using two independent cell passages in dye-swap.

first: Guido

last: Jenster


title: Validation data for Lawrence Livermore Microbial Detection Array version 2

sample_organism:
Chlorocebus aethiops
Homo sapiens
Vaccinia virus Lister
Bovine viral diarrhea virus 1
Human betaherpesvirus 6B


title: Gene array analysis of human CD34+ hematopoietic cells exposed during 24h to HOXB4 or HOXC4 homeoproteins

city: paris

first: isabelle

middle: catherine

last: vigon

address: 22 rue Méchain

country: France

institute: Institut Cochin, inserm u1016, cnrs umr8104, Université Paris-Descarte

summary: At the molecular level, the mechanisms of action of Hox genes during hematopoiesis remain elusive. Although reports have described the implication of Hox genes in some molecular pathways in mice, the targets of HOX proteins in human hematopoietic cells are mostly unidentified. Since HOXB4 and HOXC4 are transcription factors encoded by paralogous genes that display similar effects on HSCs and progenitors, we presumed that HOXB4 and HOXC4 regulate the same target genes during human HSC expansion. This hypothesis was supported by the fact that HOXB4 and HOXC4 have similar molecular structure and similar roles and expression patterns during development.  To identify early factors and signaling pathways involved in hematopoietic cell expansion consecutive to the action of HOXB4 or HOXC4, we performed a differential transcriptome analysis of RNAs from cord blood-derived CD34+ cells cultured for 24 hours in the presence of MS-5 cells engineered to secrete HOXB4 or HOXC4 proteins. MS-5/GFP cells were used as control in separate co-cultures to exclude nonspecific changes in gene expression that may be associated with the presence of lentivirus-transduced MS-5 cells.

overall_design:
Human CD34+ cord blood (4.106) cells were co-cultured for 24 hours with irradiated EGFP-, HOXB4-, or HOXC4-transduced MS-5 cells.   12 arrays were analysed. Three competitive hybridizations to the arrays were performed in duplicate using each time two dye-swap following this experimental design:
AVZ056 : CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+GFP)
AVZ059 : CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXB4)
AVZ064 : CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXB4)
AVZ067 : CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+GFP)
AVZ057 : CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXC4)
AVZ058 : CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+GFP)
AVZ060 : CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+GFP)
AVZ068 : CY5 (CD34+/MS5+GFP) / CY3 (CD34+/MS5+HOXC4)
AVZ061 : CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+HOXC4)
AVZ062 : CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+HOXB4)
AVZ065 : CY5 (CD34+/MS5+HOXC4) / CY3 (CD34+/MS5+HOXB4)
AVZ066 : CY5 (CD34+/MS5+HOXB4) / CY3 (CD34+/MS5+HOXC4)

first: Cathy

last: Philippe

first: Simon

last: Tendil

first: Vincent

last: Frouin

first: Xavier

last: Gidrol


title: Kinetic gene expression profiles of chicken macrophage HD11 cells in response to endotoxin from Salmonella typhimurium-798

city: Ames

first: Susan

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

summary:
HD11 cells were stimulated with 1 ug/ml endotoxin from ST-798 for 1, 2, 4 and 8 hours
Cells were harvested at 1, 2, 4 and 8 hrs post stimulation and RNA was isolated from these cells and microarray was conducted for these RNA samples using affymetrix genechips

overall_design: The microarray experiment was conducted using three replications.  The first two replications each used one experimental unit and one Affymetrix GeneChip for each of the eight combinations of endotoxin dose (treated vs. control) and time (1, 2, 4, or 8 hours after treatment).  The third replication was analyzed with four GeneChips for four endotoxin-treated experimental units measured at 1, 2, 4, and 8 hours after treatment, respectively.

first: Ceren

last: Ciraci

first: Christopher

last: Tuggle

first: Dan

last: Nettleton

first: Michael

last: Wannemuehler


title: A domino effect in drug action: From metabolic assault towards parasite differentiation

status: Public on Oct 18 2010

first: Martin

last: Wurst

address: INF 282

institute: Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)

summary: Glycolysis is the sole free-energy source for the deadly parasite Trypanosoma brucei and is therefore a possible target pathway for anti-trypanosomal drugs. Plasma-membrane glucose transport exerts high control over trypanosome glycolysis and hence the transporter is a promising drug target. Here we show that at high inhibitor concentrations, inhibition of trypanosome glucose transport causes cell death. Most interestingly, sublethal concentrations initiate a domino effect in which network adaptations enhance inhibition.

overall_design: total of 5 slides, including 3 biological replicates and dyeswap

first: Jurgen

last: Haanstra

first: Eduard

last: Kerkhoven

first: Arjen

last: van Tuijl

first: Marjolein

last: Blits

first: Rick

last: van Nuland

first: Marie-Astrid

last: Albert

first: Paul

last: Michels

first: Jildau

last: Bouwman

first: Christine

last: Clayton

first: Hans

middle: V

last: Westerhoff

first: Barbara

middle: M

last: Bakker


title: Transcriptional profiling of the luteinizing hormone surge in bovine granulosa cells (GC) during the pre-ovulation period comparing 2 h pre-LH GC, 6 h post-LH GC and 22 h post-LH GC

city: Quebec

first: Isabelle

last: Gilbert

state: Quebec

address: Pavillon INAF

department: Sciences Animales

institute: Universite Laval

summary: The LH surge induces panoply of events that are essential for ovulation and corpus luteum formation. The transcriptional responses to the LH surge of pre-ovulatory granulosa cells are complex and still poorly understood. In the present study, a genome wide bovine oligo array was used to determine how the gene expression profiles of granulosa cells are modulated by the LH surge. Granulosa cells from three different statuses were used (1) 2 h before the induction of the LH surge, (2) 6 h and (3) 22 h after the LH surge to assess the short and long term effects of this hormone on follicle differentiation. The results obtained were a list of differentially expressed transcripts for each granulosa cell group. To provide a comprehensive understanding of the processes at play, biological annotations were used to reveal the different functions of transcripts, confirming that the LH surge acts in a temporal manner. The pre-LH group is involved in typical tasks such as cell division, development and proliferation, while the short response of the LH surge included features such as response to stimulus, vascularisation and lipid synthesis, which are indicative of cells preparing for ovulation. The late response of granulosa cells revealed terms associated with protein localization and intra-cellular transport corresponding to the future secretion task that will be required for the transformation of granulosa cells into corpus luteum. Overall, results described in this study provide new insights into the different transcriptional steps that granulosa cells go through during ovulation and before luteinization.

overall_design: Three biological granulosa cells samples: 2 h pre-LH vs. 6 h post-LH vs. 22 h post-LH. Biological replicates: 3 with a technical dye-swap replicates (Dy 547 and Dy 647) for each biological replicate. Hybridizations were performed in a loop design for a total a 9 hybridizations.

first: Marc-Andre

last: Sirard

first: Claude

last: Robert

first: Patrick

last: Blondin


title: Sciatic nerve FAIRE-chip and ChIP-Chip with Egr2/Krox20 and Sox10

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

type: Genome binding/occupancy profiling by genome tiling array

summary:
Egr2/Krox20 and Sox10 regulate genes involved in formation of myelination in the peripheral nervous system. ChIP-chip assays were performed on rat sciatic nerve at P15, a peak timepoint of myelination. In addition, Faire was used to identify areas of open chromatin.
This experiment includes a custom ChIP-chip design incorporating many genes that are dynamically regulated during peripheral nerve myelination. Two antibodies were used for Egr2, Abcam and Covance PRB-236P.

overall_design: Egr2 and Sox10 ChIP samples were hybridized along with total input. In addition, FAIRE samples were hybridized relative to input DNA

first: Rajini

last: Srinivasan

first: Erin

last: Jones


title: Comparative expression analysis between TTHA0101-deficient mutant and wild-type of Thermus thermophilus HB8

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

summary: We observed the expression profile of the total mRNA of TTHA0101 deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70°C compared with that of wild type.

overall_design: Four wild-type and three mutant T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 680 min, and then crude RNA was extracted. In order to compare mRNA expression in the TTHA0101 deletion mutant with that of wild type, the expression of each mRNA was analyzed on a GeneChip.

first: Yoshihiro

last: Agari

first: Miwa

last: Ohmori

first: Seiki

last: Kuramitsu


title: Part 3/7: NTNeurons_6hpi_inactivatedvirus_dendrimer

first: Falko

last: Schmeisser

first: Jerry

last: Weir


title: Part 2/7: NTNeurons_24hpi_activevirus_dendrimer


title: Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor

city: St. Paul

first: Steve

last: Eichten

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

summary: Different individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. In order to investigate the potential contribution of CNV and PAV to genomic diversity in maize we used array comparative genomic hybridization (CGH) to compare gene content and copy number variation among 25 diverse maize inbreds 14 genotypes of the wild ancestor of maize, teosinte. The microarray included multiple probes for each of the ~32,500 stringently filtered genes identified in the B73 reference genome. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3,410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes that are present in B73 but missing from the genome of several other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes and the majority of events are observed in both maize and teosinte suggesting that these reflect relatively old variants that are not associated with domestication or maize improvement. Many of the genes affected by CNV/PAV are either maize-specific or members of genes families suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. Many plant genomes are relatively large and contain the remnant of whole genome duplications which may provide the ability to tolerate high levels of structural variation. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation.

sample_organism:
Zea mays
Zea mays subsp. parviglumis

overall_design: 1-2 replications of 25 maize inbred and 14 teosinte genotypes were hybridized to an array designed from the ~32,400 genes in the maize B73 reference genome.

first: Ruth

last: Swanson-Wagner

first: Sunita

last: Kumari

first: Peter

last: Tiffin

first: Joshua

middle: C

last: Stein

first: Doreen

last: Ware

first: Nathan

last: Springer


title: MicroRNA expression profiling in adult mouse liver following benzo(a)pyrene (BaP) treatment [Agilent miRNA array]

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

summary:
Lack of change in microRNA expression in adult mouse liver following treatment with benzo(a)pyrene (BaP), as detected using Agilent miRNA arrays.
We have investigated the effect of exposure to 150 mg/kg benzo(a)pyrene (BaP) for 3 days on mRNA and miRNA expression levels in adult mouse liver. We used Agilent miRNA array platforms to assess effects of BaP exposure on miRNA expression levels. Our results indicate a distinct lack of effect of BaP of miRNA expression, despite widespread changes in mRNA levels.

Keywords: Toxicology, miRNA

overall_design: Adult male B6C3F1 mice were exposed to a daily dose of corn oil (vehicle control group) or 150 mg/kg BaP (treatment group) for 3 d (n=6 per group). Mice were sacrificed at 4 h or 24 h following the last dose and liver lobes were extracted and flash frozen. Agilent miRNA arrays were used to examine changes in miRNA transcript levels in random liver lobe sections.

first: Carole

middle: L

last: Yauk

first: Kelly

middle: A

last: Jackson

first: Lynn

last: Berndt-Weis

first: Morie

last: Malowany


title: Overexpression of PtaHB1, Homeodomaine-leucine-Zipper class III, in hybrid poplar

city: Québec

first: John

last: MacKay

state: Québec

address: 1030 avenue de la medecine

department: Wood and forestery Departement

institute: Laval University - ARBOREA

summary:
Transcriptional profiling of primary xylem tranformed cells comparing control empty vector to PtaHB-1 overexpressed
Over-expression constructs were obtained by inserting the complete coding sequences of PtaHB1 and PtaHB7 from P. tremula x P. alba between the maize ubiquitin promoter (Christensen et al., 1992) and a 35S terminator into the pCambia1305.2 vector (www.cambia.org). The resulting plasmids were then transferred into A. tumefaciens strain C58 pGV2260 (Hellens et al., 2000).

overall_design: 4 control trees vs 4 PtaHB-1 trees, and dye-swap

last: Mackay

first: Caroline

last: Côté

first: Vicky

last: Roy

first: Janice

last: Cooke


title: Time course of the mRNA expression after phage ϕYS40 infection in crp deletion mutant of Thermus thermophilus HB8

first: Akeo

last: Shinkai

summary: We observed the expression profile of the total mRNA in crp (TTHA1437) deletion mutant strain of Thermus thermophilus HB8 during infection of bacteriophage ϕYS40.

overall_design: Three crp (TTHA1437) delection mutant strain of T. thermophilus HB8 were pre-cultured at 70 C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C until A600 value being ~0.8 (1.7 108 cells/ml) that corresponds to logarithmic growth phase. Then the FYS40 phage was infected to the medium at multiplicity of infection (m.o.i.) being ~1, and continued cultivation. Cells were collected after 0, 75 and 100 min infection, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip..

first: Yoshihiro

last: Agari

first: Keiko

last: Sakamoto

first: Aimi

last: Osaki

first: Miwa

last: Ohmori

first: Seiki

last: Kuramitsu


title: Expression profile of TTHA0167-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA0167 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0167-deficient strain grown in a rich medium at 70°C for 480 min.

overall_design: Three TTHA0167-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 480 min, and then, the expression of each mRNA was analyzed.


title: T. thermophilus HB8 wild-type strain in response to iron (2008)

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 30 min after the addition of FeSO4.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 4 hours in 5 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells diluted 100 fold by the synthetic medium and then cultivated at 70°C until A600 value being 1.0 . Then the 1.0 mM of FeSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of iron ion, and then crude RNA was extracted. The expression of each mRNA was analyzed on a GeneChip as described under Sample Description Sheet of each sample.

first: Takushi

last: Ooga


title: Abf1 and Rap1 effect on nucleosome occupancy in yeast

city: Albany

first: Randall

middle: Heywood

last: Morse

state: NY

institute: Wadsworth Center

summary: We grew wild type and corresponding mutant abf1 and rap1 temperature sensitive yeast at 25 C, then for one hour after shifting to 37 C.  We then prepared nucleosomal (mostly mononucleosomal) DNA and hybridized to tiling arrays.

overall_design: Three abf1 ts mutant and corresponding wild type, and three rap1 ts mutant and corresponding wild type (note not the same wild type; BY4741 for Rap1, but TMY86 for Abf1)

middle: H

first: Kyle

last: Tsui

first: Corey

last: Nislow


title: Time course of the mRNA expression in wild-type Thermus thermophilus HB8 strain grown in a rich medium (labeling:ENZO)

summary: In order to observe altered expression profile of wild-type T. thermophilus HB8 strain grown in a rich (TT) medium at 70°C. we analyzed time-dependent mRNA expression profile of the total mRNA from the strain, which corresponds the logarithmic phase to the early stationary phase.

overall_design: Three wild-type T. thermophilus HB8 strains were pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 180, 240, 300, 360, 420, 480, 540, 600, 680, and 760 min, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.

first: Aiko

last: Kashihara

first: Emi

last: Ishido-Nakai


title: Expression profile of TTHA0175-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA0175 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0175-deficient strain grown in a rich medium at 70°C for 300, 480, and 600 min.

overall_design: Two TTHA0175-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 300, 480, and 600 min, respectively, and then, the expression of each mRNA was analyzed.


title: Differential expression analysis of T. thermophilus HB8 TTHA0995-deficient strain in response to iron

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 TTHA0995 deficient strain at 0 and 30 min after the addition of FeSO4.

overall_design: Three TTHA0995 deficient strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5.5 hours (A600 value being ~1.53). Then the 1.0 mM of FeSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of iron ion, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.


title: Expression profile of TTHA0845-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA0845 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0845-deficient strain grown in a rich medium at 70°C for 420 min.

overall_design: Three TTHA0845-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 1 L of the same medium and then cultivated at 70°C. Cells were collected after 420 min, and then, the expression of each mRNA was analyzed.

first: Satoshi

last: Kira


title: T. thermophilus HB8 alternative sigma factor sigE (TTHB211) deletion mutant strain, TT medium, 8 h

summary: We observed the expression profile of the total mRNA of sigE (TTHB211) deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70 degC.

overall_design: Three TTHB211 deletion mutant T. thermophilus HB8 strains were each pre-cultured at 70 degC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70 degC. Cells were collected after 8 h, and then crude RNA was extracted. The expression of each mRNA were analyzed on a GeneChip.


title: Expression profile of crp-deficient Thermus thermophilus HB8 strain

summary: We observed the expression profile of the total mRNA of crp (TTHA1437) deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70 degC

overall_design: Three crp-deletion mutant T. thermophilus HB8 strains were each pre-cultured at 70 degC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70 degC. Cells were collected after 6 h and 8 h, and then crude RNA was extracted. The expression of mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.


title: Transcriptional profiling of the T. thermophilus HB8 response to ethanol

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 30 min after the addition of 5% ethanol.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (0.5 mL) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 6 hours (A600 value being ~0.95). Then the 5% (v/v) of ethanol was added into the medium, and continued cultivation. Cells were collected at 30 min time point after the addition of ethanol, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.


title: Transcriptional profiling of the T. thermophilus HB8 response to tetracycline (low concentration)

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 5 min after the addition of 10 mM tetracycline.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 1 L of the same medium and then cultivated at 70°C for 5 hours (A600 value being ~0.47). Then the 10 mM of tetracycline was added into the medium, and continued cultivation. Cells were collected at 5 min time point after the addition of tetracycline, and then crude RNA was extracted. The expression of each mRNA was analyzed on a GeneChip.


title: Expression profile of TTHA1939-deficient Thermus thermophilus HB8 strain

summary: We observed the expression profile of the total mRNA of the TTHA1939-deficient strain grown in a rich medium at 70°C for 800 min.

overall_design: Wild-type and the mutant strains were precultured in rich medium (TR medium) for two times at 70 oC and then subcultured to minimum essential medium (CS medium). These cells were harvested during the logarithmic growth phase (800 minutes from the start of culture). Total RNA were extracted from each strain and used for the cDNA synthesis. For the biological replication, above experiments were performed four times independently.


title: Expression profile of TTHA1431-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA1431 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA1431-deficient strain grown in a rich medium at 70°C for 360 min.

overall_design: Three TTHA1431-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 1 L of the same medium and then cultivated at 70°C. Cells were collected after 360 min, and then, the expression of each mRNA was analyzed.


title: Expression profile of TTHA0101-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA0101 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0101-deficient strain grown in a rich medium at 70°C for 680 min.

overall_design: Three TTHA0101-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 680 min, and then, the expression of each mRNA was analyzed.


title: Expression profile of TTHB186-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHB186 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHB186-deficient strain grown in a rich medium at 70°C for 360, and 480 min.

overall_design: Three TTHB186-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 500 mL of the same medium and then cultivated at 70°C. Cells were collected after 360, and 480 min, respectively, and then, the expression of each mRNA was analyzed.


title: Transcriptional profiling of the T. thermophilus HB8 response to tetracycline

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 10 min after the addition of 50 mM tetracycline.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 4 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 1 L of the same medium and then cultivated at 70°C for 6 hours (A600 value being ~0.62). Then the 50 mM of tetracycline was added into the medium, and continued cultivation. Cells were collected at 0 and 10 min time point after the addition of tetracycline, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.


title: Transcriptional profiling of the T. thermophilus HB8 response to hydrogen peroxide

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 0, 5, 15 and 30 min after the addition of 10 mM H2O2.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 2 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (1 mL) were inoculated into 1000 mL of the same medium and then cultivated at 70°C for 6.5 hours (A600 value being ~0.55). Then the 10 mM of H2O2 was added into the medium, and continued cultivation. Cells were collected at 0, 5, 15 and 30 min time point after the addition of H2O2, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.

first: Kenji

last: Fukui


title: Expression profile of TTHA0252-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA0252 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0252-deficient strain grown in a rich medium at 70°C for 360,540, and 680 min.

overall_design: Two TTHA0252-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 500 mL of the same medium and then cultivated at 70°C. Cells were collected after 360, 540, and 680 min, respectively, and then, the expression of each mRNA was analyzed.

last: Ishido


title: Expression profile of TTHA1634-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA1634 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA1634-deficient strain grown in a rich medium at 70°C for 420, and 600 min.

overall_design: Two TTHA1634-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 1 L of the same medium and then cultivated at 70°C. Cells were collected after 420, and 600 min, respectively, and then, the expression of each mRNA was analyzed.


title: Expression profile of TTHA1359-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA1359 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the sdrP-deficient strain grown in a rich medium at 70°C for 300, 480, and 600 min.

overall_design: TTHA1359-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 680, 1120, and 1240 min, respectively, and then, the expression of each mRNA was analyzed.


title: Differential expression analysis of Thermus thermophilus HB8 wild-type strain in response to NaCl

summary: In order to investigate response of T. thermophilus HB8 wild-type strain for high salt stress, we observed the expression profile of the total mRNA in the strain at 30 min after the addition of NaCl to a final concentration of 0.5% and/or 1.5%, and compared them with that of non-treated cells.

overall_design: Three T. thermophilus HB8 wild-type strains were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH.  The cells were inoculated into 1 L or 250 ml of TT medium to a 1/500 dilution, and then cultivated at 70°C for 6 hours.  Then NaCl was added into the medium to a final concentration of 0.5 or 1.5%, and the cultivation was continued. Cells were collected at 0 and 30 min time point after the addition of excess NaCl, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.


title: Expression analysis of Thermus thermophilus HB8 wild-type strain in response to high growth temperature

summary: In order to observe the heat-shock response of extremely thermohilic bacterium T. thermophilus HB8 strain, we analyzed the altered expression profile of the total mRNA in T. thermophilus HB8 wild-type strain after the growth temperature was shifted from 70°C to 80°C for 30 min.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70°C for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (0.5 mL) were inoculated into 250 mL of TT medium and then cultivated at 70°C for 6 hours. After the cells were collected from 50 ml culture medium, the remaining medium was cultured at 80°C for 30 min.  The cells were collected, and then crude RNA was extracted from each lot of cells. The expression of each mRNA at each time point was analyzed on a GeneChip.


title: Expression profile of TTHA0655-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA0655 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0655-deficient strain grown in a rich medium at 70°C for 360 and 680 min.

overall_design: Three TTHA0655-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 360 or 680 min, respectively, and then, the expression of each mRNA was analyzed.


title: mRNA expression analysis of T. thermophilus HB8 wild-type strain cultivated in a synthetic medium for 10 and 20 h

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 10 and 20 h.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 500 mL of the synthetic medium and then cultivated at 70°C.  Then, cells were collected at 10 and 20 h time point, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.


title: Expression profile of TTHA0973-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA0973 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0973-deficient strain grown in a rich medium at 70°C for 680 min.

overall_design: Three TTHA0973-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 680 min, respectively, and then, the expression of each mRNA was analyzed.


title: Expression profile of TTHA0344-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA0344 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA0344-deficient strain grown in a rich medium at 70°C for 680 min.

overall_design: Three TTHA0344-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 680 min, and then, the expression of each mRNA was analyzed.


title: Transcriptional profiling of the T. thermophilus HB8 response to diamide

summary: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 10 min after the addition of 10 mM diamide.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 4 mL of systhetic medium. The cells (2 mL) were inoculated into 250 mL of the same medium and then cultivated at 70°C for 8 hours (A600 value being ~0.34). Then the 10 mM of diamide was added into the medium, and continued cultivation. Cells were collected at 0 and 10 min time point after the addition of diamide, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.


title: Time course of the mRNA expression after bacteriophage ϕYS40 infection in wild-type T. thermophilus HB8 strain

summary: We observed the expression profile of the total mRNA of wild-type Thermus thermophilus HB8 strain during infection of bacteriophage ϕYS40.

overall_design: Wild-type T. thermophilus HB8 cells were pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C until A600 value being ~0.8 (1.7   108 cells/ml) that corresponds to logarithmic growth phase. Then the FYS40 phage was infected to the medium at multiplicity of infection (m.o.i.) being ~1, and continued cultivation. Cells were collected after 0, 25, 50, 75 and 100 min infection, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.


title: Expression profile of TTHA1438-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHA1438 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHA1438-deficient strain grown in a rich medium at 70°C for 240, 360, 480, 600 and 760 min.

overall_design: Two TTHA1438-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 240, 360, 480, 600, 680 and 760 min, respectively, and then, the expression of each mRNA was analyzed.


title: Expression profile of TTHB099-deficient Thermus thermophilus HB8 strain

summary: In order to find function of TTHB099 protein from T. thermophilus HB8, we observed the expression profile of the total mRNA of the TTHB099-deficient strain grown in a rich medium at 70°C for 360 and 420 min.

overall_design: Four TTHB099-deficient T. thermophilus HB8 strains were each pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 360 or 420 min, respectively, and then, the expression of each mRNA was analyzed.


title: Transcriptional profiling of the acuM null mutant

status: Public on Oct 12 2010

city: Rockville

first: Natalie

last: Fedorova

address: 9704 Medical Center Dr

department: Infectious Disease

institute: JCVI

summary: Deletion of AcuM caused attenuated virulence in mouse models of Aspergillosis, we carried out the microarry to figure out pathways have been changed to affect the virulence.

overall_design: Transcriptional profiling of Aspergillus fumigatus  mycelium comparing mutant ΔacuM with wild type Af293, and complemented strain ΔacuM ::acuM  with mutant  ΔacuM .  Three time points comparison under RPMI: 8 hour, 18 hour, 24 hour. Biological replicates: 2, independently grown and harvest. One replicate per array.

first: Scott

middle: G

last: Filler

first: Hong

last: Liu

first: Dan

last: Chen

first: William

last: Nierman


title: silkworm temporal expression profiles

city: Shanghai

first: Shuai

last: Zhan

address: 300 Fenglin Road

country: China

institute: Shanghai Institutes for Biological Sciences

summary: comparison among egg, larva, pupa, and adult stages

overall_design: Egg vs larva, larva vs pupa, and pupa vs adult

first: Yongping

last: Huang


title: Influence of cold shock on total mRNA expression profile during harvesting Thermus thermophilus HB8 cells.

first: Akeo

last: Shinkai

summary: In order to investigate the influence of the cold shock during harvesting the cells, we compare the expression profile of mRNA between in T. thermophilus HB8 cells harvested after arrested the growth on ice and in those harvested after addition of cold ethanol.

overall_design: Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70°C for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 mL) were inoculated into 1000 mL of same medium and then cultivated at 70°C for 8 hours (A600 value being ~2.57). For normal cells (harvested after arrested the growth on ice), 15 mL of culture medium was centrifuged 4270G for 5 min at 4°C. For cold-shock avoided cells (harvested after addition of cold ethanol), 15 mL of culture medium was cooled down immediately by addition of the same volume of ethanol which pre-cooled to -80°C, and then centrifuged in same way as normal cells.  Then crude RNA was extracted from each sample.

first: Yoshihiro

last: Agari

first: Miwa

last: Ohmori

last: Kuramitsu


title: Oligoarray analysis of semi-global gene expression in ripening Japanese pear fruit

city: Tsukuba

first: Chikako

last: Nishitani

state: Ibaraki

institute: National Institutes of Fruit Tree Science

summary: A custom oligoarray of Japanese pear (Pyrus pyrifolia) based on 9,812 independent ESTs from different tissues (fruits at various growth stages, vegetative and flower tissues) was designed and used for comprehensive investigation of gene expression before and during ripening (105 to 147 days after full bloom).

overall_design: Gene expression in fruit development of Japanese pear was measured from 105 to 147 days after full bloom (DAFB). 147 DAFB is the optimum maturity for eating. Two to three independent experiments were performed at each time (105 to 147 DAFB) using different trees for each experiment.

first: Tokurou

last: Shimizu

first: Hiroshi

last: Fujii

first: Fumiko

last: Hosaka

first: Shingo

last: Terakami

first: Yuri

last: Nakamura

first: Akihiro

last: Itai

first: Toshiya

last: Yamamoto


title: Time-course of mRNA expression in wild-type Thermus thermophilus HB8 grown on rich medium_long (labeling:Affymetrix)

summary: In order to observe the growth phase-dependent expression profile of each mRNA of wild-type Thermus thermophilus HB8 strain grown in a rich medium at 70°C, we cultured the strain in a medium, and then the expression of total mRNA at the time points corresponding to logarithmic growth phase and early to late stationary growth phases was analyzed by using DNA microarray (GeneChip).

overall_design: Wild-type T. thermophilus HB8 strains were pre-cultured at 70°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 180, 360, 540, 680, 880, 1000, 1120, and 1240 min, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.

first: Aiko

last: Kashihara

first: Emi

last: Nakai

first: Noriko

last: Nakagawa

first: Seiki


title: Time course of the mRNA expression in wild-type Thermus thermophilus HB8 strain grown on a synthetic medium

summary: We observed the expression profile of the total mRNA of wild-type Thermus thermophilus HB8 strain grown in a synthetic medium at 70°C.  Keywords: time course

overall_design: Wild-type T. thermophilus HB8 strains were pre-cultured at 70°C for 16 h in 3 ml of synthetic medium. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C. Cells were collected after 360, 480, 600, 720, 840, 960, 1080, 1200, 1320 and 1440 min, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under 'Description' field of each Sample.


title: Vibrio parahaemolyticus gene expression affected by 0.04% bile

status: Public on Oct 10 2010

city: Suita

first: Toshio

last: Kodama

state: Osaka

address: 3-1 Yamadaoka

institute: OSAKA university

summary: Vibrio parahaemolyticus is a Gram-negative marine bacterium. Strain RIMD 2210633, the wild type strain of the organism, causes acute gastroenteritis in humans. Human intestinal factor bile often affects the global gene regulation in some species of enteropathogenic bacteria. To determine the genes in V. parahaemolyticus that respond to bile, we investigated the differences in the transcriptomes of the wild type strain and the vtrA-null strain grown in Luria-Bertani medium cultivated with or without 0.04% crude bile. The vtrA gene encodes the previously identified T3SS2 regulator. Our goal is to demonstrate bile regulon controlled by VtrA in V. parahaemolyticus.

overall_design: Total RNA from WT and vtrA-null strains in response to 0.04% crude bile or no bile were analyzed. Samples grown with or without bile were labeled with Cy3 and Cy5, respectively, and cohybridized on a single array. Labeling and hybridization were performed three times independently in wild type and vtrA-null samples.

first: Kazuyoshi

last: Gotoh

first: Tetsuya

last: Iida


title: Silicon effect on suberization and lignification in roots of rice (Oryza sativa)

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

summary:
This study was performed to study the effect of silicon (Si) nutrition on suberization and lignification in roots of rice. Besides physiological and histochemical examinations of the roots, transcription of candidate genes related to synthesis of suberin and lignin was investigated using microarray analysis.
14 days old rice seedlings (Oryza sativa, cv. Selenio) were cultivated for 28 days in non-aerated nutrient solution (mM: 1.43 NH4NO3, 0.32 NaH2PO4 x H2O, 0.51 K2SO4, 1 CaCl2 x 2 H2O, 1.6 MgSO4 x 7 H2O; µM: 1.82 MnSO4, 0.03 (NH4)6Mo7O24, 9 H3BO3, 0.3 ZnSO4 x 7 H2O and 0.15 CuSO4). The pH-value was adjusted to 6.0 by addition of 10 % (v/v) H2SO4 and 0.75 M KOH.Plants were supplied with Si in form of K2SiO3 at concentrations 0 ppm Si (control) and 50 ppm Si (1.78 mM) and potassium in the control treatment was balanced with K2SO4 supply. The plants were grown in a growth chamber (photoperiod: 14 h light, 10 h dark; temperature 25°C day / 20°C night; relative humidity 75 %; light intensity 220 µmol m2 s-1). Adventitious roots were harvested at 0-2 cm and 4-6 cm distance from the root tip and frozen immediately in liquid nitrogen. For RNA isolation, roots were ground under liquid nitrogen and total RNA was isolated using TRIsure® Reagent (Bioline, Luckenwalde, Germany) following the instructions of the manufacturer.
To examine transcription of genes related to suberin and lignin synthesis, a self developed microarray containing amongst others ABC transporter, aclytransferases, ß-ketoacyl-CoA synthases and peroxidases was used .

overall_design:
Results from four microarrays are summarized in this study. The samples originate from two root zones (0-2 and 4-6 cm) with each two Si treatments (0 ppm and 50 ppm Si) as mentioned above. Microarrays were hybridized in a  dye swap approach:
Dye-swap1: 0-2 cm with and without Silicon.
Dye-swap2: 4-6 cm with and without silicon

first: Alexander

last: Fleck

first: Philipp

last: Rüdinger