title: Imatinib treatment causes substantial transcriptional changes in adult Schistosoma mansoni in vitro exhibiting pleiotropic effects

status: Public on Jun 20 2014

city: São Paulo

first: Katia

middle: Cristina Pereira

last: Oliveira

state: O

address: Av Prof lineu prestes 748

department: Centro de Parasitologia e Micologia

country: Brazil

institute: Instituto Adolfo Lutz

summary: Transcriptional profiling of  Imatinib-treated paired adult S. mansoni vs. Non-treated (control) paired adult S. mansoni during 24 and 48 hours

overall_design: Two conditions (Imatinib-treated vs. Non-treated ) for each time of treatment (24 hours and 48 hours) with three biological samples of each conditions. For each biological sample (three Imatinib-treated and three Non-treated for each time of treatment) were performed two technical replicas.

first: Christin

last: Buro

first: Svenja

last: Beckmann

middle: C

first: Colette

last: Dissou

last: Cailliau

first: Sergio

last: Verjovski-Almeida

first: Christoph

middle: G

last: Grevelding


title: Juvenile hormone (JH) response in integuments of silkworm larvae

status: Public on Jun 29 2014

city: Chongqing

first: Daojun

last: Cheng

address: No 2, Tiansheng, Beibei

country: China

institute: Southwest University

summary: Expression changes in silkworm integuments after JH analogue (JHA) methoprene treatment.

overall_design: Two-condition experiments, namely JH analogue (JHA) methoprene treatment (Test) and acetone treatment (Control). Time course: 12 hours after treatment (Hat), 24 Hat, 36 Hat, and 48 Hat.

first: Jian

last: Peng

first: Qingyou

last: Xia


title: Identification of direct target genes of the tomato FRUITFULL homologs during ripening by promoter ChIP-chip

status: Public on Jun 23 2014

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

country: Japan

institute: National Food Research Institute

type: Genome binding/occupancy profiling by genome tiling array

summary: Tomato (Solanum lycopersicum) has two MADS-box FRUITFULL homologs, FUL1 and FUL2, both of which are able to interact with the master ripening regulator RIN.  Here, we performed chromatin immunoprecipitation coupled with a DNA microarray (ChIP-chip) for the 2-kb upstream putative promoters of whole tomato predicted genes (ITAG2) for a large-scale identification of the direct target genes of FUL1 and FUL2 during ripening. The ChIP-chip with antibodies of FUL1 and FUL2 identified 1,877 and 1,919 of FUL1- and FUL2-binding sites, respectively, each of which was assigned a significantly high peak score (FDR<0.05) in at least two of the three biologically independent analyses. Using the information about genomic position of the FUL1- and FUL2-binding sites, we found 1,943 and 2,051 potential direct targets of FUL1 and FUL2, respectively, that carried one or more binding sites in the putative promoter or in other gene regions, such as exons, introns or a downstream region from the translation termination site (1-kb), where the promoter region of a neighbor gene are overlapped.  The majority of the direct target genes are common between FUL1, FUL2 and RIN, suggesting that FUL1 and FUL2 act redundantly in the regulation of fruit ripening, and that these factors regulate the expression of their targets in a form of heteromer complex.  Interestingly, the analysis also found direct targets unique to each of FUL1, FUL2 and RIN, implying their exclusive roles during ripening.

overall_design: Three biologically independent samples (chromatin-immunoprecipitated DNA and input DNA) recovered from the ripening tomato fruits.

first: M

last: Fujisawa

first: Y

last: Shima

first: T

last: Nakano


title: Human cells infected with Mucormycosis-causing strains from clinical settings

status: Public on Jun 19 2014

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

country: USA

institute: University of Maryland School of Medicine

type: Expression profiling by high throughput sequencing

summary:
Mucormycosis is an increasingly common, life-threatening fungal infection caused by fungi belonging to the subphylum Mucormycotina, order Mucorales. The major risk factors for mucormycosis include uncontrolled diabetes mellitus, treatment with corticosteroids, organ or bone marrow transplantation, neutropenia, trauma and burns, malignant hematological disorders, and deferoxamine-therapy in patients receiving hemodialysis. Amphotericin B (AmB) remains the only antifungal agent approved for the treatment of invasive mucormycosis. Because fungi belonging to the mucorales order are relatively resistant to AmB, high doses are required, which frequently causes nephrotoxicity and other adverse effects. In the absence of surgical removal of the infected focus (such as excision of the eye in patients with rhinocerebral mucormycosis), antifungal therapy alone is rarely curative. Even when surgical debridement is combined with high-dose AmB, the mortality associated with mucor¬mycosis is >50%. In patients with prolonged neutropenia or disseminated disease, mortality is 90-100%. Rhizopus oryzae is by far the most common organism isolated from patients with mucormycosis, and is responsible for approximately 70% of all cases of mucormycosis.

Recent epidemiological data collected from transplant centers have demonstrated a striking increase in the number of reported cases of mucormycosis. Furthermore, mucormycosis outbreaks are also known to follow natural disasters as was the case following the tsunami that devastated Indonesia in 2004 and the tornadoes that destroyed Joplin, Missouri in June 2011.  Hence, there exists a large impetus to identify particular virulence factors and biomarkers associated with mucormycosis, which would lead to a rational approach to develop new antifungals and vaccines to prevent deaths specifically due to mucormycosis. In order to better understand the complex nature of the host pathogen interaction during mucormycosis, we performed dual species RNA-seq on 5 different Mucorales strains during in vitro infection of endothelial or epithelial cells.

overall_design:
5 different strains of Mucorales (see below) were used to infect two different types of human tissue culture monolayers of either epithelial cells or endothelial cells. RNA from the infection mixtures were harvested at 90 minutes post infection.

Sample name|title|source name|infection|organism|cell type|molecule|description|processed data file |SRA accession
Absidia corymbifera 008-049 + endothelial cells|A1|Absidia corymbifera in Endothelial cells|Absidia corymbifera 008-049|human|Endothelial cells|total RNA|Absidia corymbifera in Endothelial cells|A1.genic.coverage.stats.rpkm.txt|SRX365460
Absidia corymbifera 008-049 + HUVEC media alone|A2|Absidia corymbifera in HUVEC media|Absidia corymbifera 008-049|human|HUVEC media|total RNA|Absidia corymbifera in HUVEC media||SRX365522
Absidia corymbifera 008-049 + epithelial cells|A3|Absidia corymbifera in epithelial cells|Absidia corymbifera 008-049|human|epithelial cells|total RNA|Absidia corymbifera in epithelial cells|A3.genic.coverage.stats.rpkm.txt|SRX365523
Absidia  corymbifera008-049 + epithelial media alone|A4|Absidia corymbifera in epithelial cell media|Absidia corymbifera 008-049|human|epithelial cell media|total RNA|Absidia corymbifera in epithelial cell media||SRX365541
Cunninghamella bertholttiae 175 + endothelial cells|C1|Cunninghamella bertholttiae in Endothelial cells|Cunninghamella bertholttiae 175|human|Endothelial cells|total RNA|Cunninghamella bertholttiae in Endothelial cells|C1.genic.coverage.stats.rpkm.txt|SRX365542
Cunninghamella bertholttiae 175 + HUVEC media alone|C2|Cunninghamella bertholttiae in HUVEC media|Cunninghamella bertholttiae 175|human|HUVEC media|total RNA|Cunninghamella bertholttiae in HUVEC media||SRX365619
Cunninghamella bertholttiae 175 + epithelial cells|C3|Cunninghamella bertholttiae in epithelial cells|Cunninghamella bertholttiae 175|human|epithelial cells|total RNA|Cunninghamella bertholttiae in epithelial cells|C3.genic.coverage.stats.rpkm.txt|SRX365620
Cunninghamella bertholttiae 175 + epithelial media alone|C4|Cunninghamella bertholttiae in epithelial cell media|Cunninghamella bertholttiae 175|human|epithelial cell media|total RNA|Cunninghamella bertholttiae in epithelial cell media||SRX365623
Mucor ramosissumus 97-1192 + endothelial cells|M1|Mucor ramosissumus in Endothelial cells|Mucor ramosissumus 97-1192|human|Endothelial cells|total RNA|Mucor ramosissumus in Endothelial cells| M1.genic.coverage.stats.rpkm.txt|SRX365603
Mucor ramosissumus 97-1192 + HUVEC media alone|M2|Mucor ramosissumus in HUVEC media|Mucor ramosissumus 97-1192|human|HUVEC media|total RNA|Mucor ramosissumus in HUVEC media||SRX365655
Mucor ramosissumus 97-1192 + epithelial cells|M3|Mucor ramosissumus in epithelial cells|Mucor ramosissumus 97-1192|human|epithelial cells|total RNA|Mucor ramosissumus in epithelial cells| M3.genic.coverage.stats.rpkm.txt|SRX365662
Mucor ramosissumus 97-1192 + epithelial media alone|M4|Mucor ramosissumus in epithelial cell media|Mucor ramosissumus 97-1192|human|epithelial cell media|total RNA|Mucor ramosissumus in epithelial cell media||SRX365664
Rhizopus oryzea 99-880 + endothelial cells|880_1|Rhizopus oryzea in Endothelial cells|Rhizopus oryzea 99-880|human|Endothelial cells|total RNA|Rhizopus oryzea in Endothelial cells|880_1.genic.coverage.stats.rpkm.txt|SRX365613
Rhizopus oryzea 99-880 + HUVEC media alone|880_2|Rhizopus oryzea in HUVEC media|Rhizopus oryzea 99-880|human|HUVEC media|total RNA|Rhizopus oryzea in HUVEC media||SRX365624
Rhizopus oryzea 99-880 + epithelial cells|880_3|Rhizopus oryzea in epithelial cells|Rhizopus oryzea 99-880|human|epithelial cells|total RNA|Rhizopus oryzea in epithelial cells|880_3.genic.coverage.stats.rpkm.txt|SRX365628
Rhizopus oryzea 99-880 + epithelial media alone|880_4|Rhizopus oryzea in epithelial cell media|Rhizopus oryzea 99-880|human|epithelial cell media|total RNA|Rhizopus oryzea in epithelial cell media||SRX365629
Rhizopus oryzea 99-892 + endothelial cells|892_1|Rhizopus oryzea in Endothelial cells|Rhizopus oryzea 99-892|human|Endothelial cells|total RNA|Rhizopus oryzea in Endothelial cells|892_1.genic.coverage.stats.rpkm.txt|SRX365618
Rhizopus oryzea 99-892 + HUVEC media alone|892_2|Rhizopus oryzea in HUVEC media|Rhizopus oryzea 99-892|human|HUVEC media|total RNA|Rhizopus oryzea in HUVEC media||SRX365656
Rhizopus oryzea 99-892 + epithelial cells|892_3|Rhizopus oryzea in epithelial cells|Rhizopus oryzea 99-892|human|epithelial cells|total RNA|Rhizopus oryzea in epithelial cells|892_3.genic.coverage.stats.rpkm.txt|SRX365657
Rhizopus oryzea 99-892 + epithelial media alone|892_4|Rhizopus oryzea in epithelial cell media|Rhizopus oryzea 99-892|human|epithelial cell media|total RNA|Rhizopus oryzea in epithelial cell media||SRX365658

Cells from each of the Mucorales strains were used to infect endothelial cells or epithelial cells in tissue culture media for 90 minutes at 37 degrees celcius. The negative control samples were the host or C. albicans cells alone in tissue culture media for the same amount of time.
RNA extractions were performed using RiboPure RNA Purification Kit, yeast (Life Technologies, AM1926) following manufacturer's protocols
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq

Base calls were performed using the bulit in Illumina basecaller.
Sequenced reads were mapped to each fungal genome and the human genome using TopHat v. 1.4.
RPKM values were calculated for the genes in the human genome.

Genome Build: Homo sapiens.GRCh37.71

first: Ashraf

last: Ibrahim


title: Genome-wide transcriptional changes of Sphingomonas wittichii RW1 during inoculation and growth in contaminated sand [experiment 1]

city: Lausanne

first: Silvia

middle: K.

last: Moreno-Forero

state: Vaud

address: Batiment Biophore, Unil Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

summary: The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions.

overall_design: We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. We compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during exponential growth and at stationary phase, all in carefully controlled and replicated experimental conditions.

middle: K

first: Jan

middle: R

last: van der Meer


title: Effect of antimicrobial peptide PR-39 on the gene expression of porcine intestinal epithelial cell line (IPEC-J2)

status: Public on Jun 28 2014

city: Hangzhou

first: Xi

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Feed Science

institute: Zhejiang University

summary:
To gain a more complete understanding of how porcine cathelicidin PR-39 influence the  porcine intestinal epithelial cells,
we profiled gene expression patterns in IPEC-J2 cell line in the presence or the absence of PR-39.

overall_design: two groups(control and PR-39),each group has three replicates

first: Yizhen

last: Wang


title: Global Analysis of Carbohydrates Utilization of the Alkaline Hemicellulytic Bacteria Bacillus sp. N16-5

status: Public on Jun 17 2014

city: Beijing

first: song

last: yajian

address: N0.1 Beichen Road

institute: institute of microbiology, chinese acadmy of science

summary: Alkaline hemicellulytic bacteria Bacillus sp. N16-5 has abroad substrate spectrum and exhibits great growth ability on complex carbohydrates. In order to get insight into its carbohydrate utilization mechanism, global transcriptional profiles were separately determined for growth on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan, pectin and carboxymethyl cellulose by using one-color microarrays.

overall_design: Substrate induced gene expression was measured when culture was grown on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan and CMC to mid-logarithmic phase.

first: Yajian

last: Song

first: Yanfen

last: Xue

first: Yanhe

last: Ma


title: GdpS contributes to Staphylococcus aureus biofilm formation by regulation of eDNA release

status: Public on Jun 30 2014

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary: In Staphylococcus aureus, the role of the GGDEF domain containing protein GdpS remains poorly understood. Previous studies reported that gdpS mutant strains had decreased biofilm formation due to changes in icaADBC expression that were independent of cyclic-di-GMP levels. We deleted gdpS in three unrelated S. aureus isolates, and analyzed the resultant mutants for alterations in biofilm formation, metabolism and transcription. Dynamic imaging during biofilm development showed that GdpS inhibited early biofilm formation in only two out of the three strains examined, without affecting bacterial survival. However, quantification of biofilm formation using crystal violet staining revealed that inactivation of gdpS affected biofilm formation in all three studied strains. Extraction of metabolites from S. aureus cells confirmed the absence of cyclic-di-GMP, suggesting that biofilm formation in this species differs from that in other Gram-positive organisms. In addition, targeted mutagenesis demonstrated that the GGDEF domain was not required for GdpS activity. Transcriptomic analysis revealed that the vast majority of GGDEF-regulated genes were involved in virulence, metabolism, cell wall biogenesis and eDNA release. Finally, expression of lrgAB or deletion of cidABC in a strain lacking gdpS confirmed the role of GdpS on regulation of eDNA production that occurred without an increase in cell autolysis. In summary, S. aureus GdpS contributes to cell-to-cell interactions during early biofilm formation by influencing expression of lrgAB and cidABC mediated eDNA release. We conclude that GdpS acts as a negative regulator of eDNA release.

overall_design: Three strains UAMS-1, SA113 and SA564 were used in this study to compare wt with gdpS mutant after 5 hours of growth in static conditions (biofilm formation).

first: Adrien

last: Fischer

first: Kumiko

last: Kambara

first: Hanna

last: Meyer

first: Ludwig

last: Stenz

first: Eve-Julie

last: Bonetti

first: Myriam

last: Girard

first: Michael

last: Lalk

first: Patrice

last: François

first: Jacques

last: Schrenzel


title: Effect of lymphotoxin beta receptor blockade on microRNA expression in the spleen [ExiqonMicroRNA]

city: Midlothian

first: Neil

middle: A.

last: Mabbott

address: Easter Bush

department: The Roslin Institute & Royal (Dick) School of Veterinary Sciences

country: United Kingdom

institute: University of Edinburgh

summary: Follicular dendritic cells (FDC) are important stromal cells within the B cell follicles and germinal centres (GC) of secondary lymphoid tissues.  FDC trap and retain native antigens on their surfaces in the form of immune complexes which they display to B cells, in order to select those cells with the highest antigen affinity.  MicroRNAs are short, non-coding RNAs of approximately 18-25 nucleotides in length that regulate gene expression at the post-transcriptional level by repressing the translation of target genes.  In the current study in vivo and in vitro systems were used to identify microRNAs that are differentially expressed as a result of FDC depletion.   Constitutive lymphotoxin-β receptor (LTβR) stimulation is required to maintain FDC in their differentiated state.  We show that the rapid de-differentiation of spleen FDC that followed LTβR-blockade, coincided with a significant decrease in the expression of mmu-miR-100-5p, mmu-miR-138-5p and mmu-miR-2137.  These microRNAs were shown to be expressed in the FDC-like cell line, FL-YB, and specific inhibition of mmu-miR-100-5p significantly enhanced expression of Il6, Ptgs1/2 and Tlr4 in this cell line.  The expression of each of these genes by FDC plays an important role in regulating GC size and promoting high-affinity antibody responses, suggesting that mmu-miR-100-5p may help regulate their expression during GC reactions.

overall_design: C57BL/6 mice were given a single intravenous injection of 100 µg of LTβR to temporarily deplete their FDC.  At intervals after treatment 4 spleens from each group were harvested and RNA prepared.   For each group samples were pooled into 2 groups of 2 and microRNA expression levels compared.  Spleens from LTb-/- mice were also analysed.  One channel was used for the actual sample, the second channel was used for internal QC reference.

first: Susan

last: Aungier

first: Hotshi

last: Ohmori

last: Clinton

middle: A


title: Expression data from liver of WNIN/Ob lean and obese rats

status: Public on Jun 18 2014

city: Hyderabad

first: Vajreswari

last: Ayyalasomayajula

state: Telangana

address: Tarnaka

department: Lipid Chemistry Division

country: India

institute: National Institute of Nutrition

summary:
Obesity is risk factor for development of fatty liver. Analysis of altered gene expression gives better understading about the mechanisms involved/alterted in the development of obesity-induced fattyliver  in this new obese rat model.
We used Microarrays to delinate the alted gene expression in liver of WNIN/Ob obese rats

overall_design: Liver was collected from 4 month old WNIN/Ob lean and obese rats for RNA extraction and hybridization on Affymatrix Rat gene 1ST arrays. Four RNA samples from each phenotype were pooled and used for the study.

first: Siva

middle: S

last: Sakamuri


title: Deciphering the genetic basis of Moraxella catarrhalis complement resistance: Gene expression analysis of Moraxella catarrhalis BBH18 upon exposure to normal human serum.

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

summary: The complement system is an important part of the innate defense against invading pathogens. The ability to resist complement-mediated killing is considered to be an important virulence trait for the human-restricted respiratory tract pathogen M. catarrhalis, as most disease-associated M. catarrhalis isolates are complement-resistant. Here we studied the molecular basis of M. catarrhalis complement-resistance by transcriptome profiling upon exposure to 10% normal human serum (NHS).

overall_design: After 1h exposure of M. catarrhalis BBH18 to 10% NHS (n = 5) or the NHS dilution buffer alone (control, n = 5), total RNA was isolated and labeled cDNA was generated according to standard Nimblegen gene expression array protocols and hybridized to 4x72K Nimblegen M. catarrhalis expression arrays for read-out.

first: Stefan

middle: P

last: de Vries

first: Rob

middle: J

last: Rademakers

first: Christa

middle: E

last: van der Gaast - de Jongh

first: Marc

last: Eleveld

first: Peter

middle: W

last: Hermans


title: Microarray analysis of laser-microdissected tissues indicates the biosynthesis of suberin in the outer part of roots during formation of a barrier to radial oxygen loss in rice (Oryza sativa).

status: Public on Jun 26 2014

city: Eiheiji

first: Katsuhiro

last: Shiono

state: Fukui

address: 4-1-1 Matsuoka-Kenjyojima

department: Department of Bioscience

institute: Fukui Prefectural University

summary: Internal aeration is crucial for root growth in waterlogged soil. A barrier to radial oxygen loss (ROL) can enhance long- distance oxygen transport via the aerenchyma to the root tip; a higher oxygen concentration at the apex enables root growth into anoxic soil. The ROL barrier is formed within the outer part of roots (OPR). Suberin and/or lignin depos- ited in cell walls are thought to contribute to the barrier, but it is unclear which compound is the main constituent. This study describes gene expression profiles during ROL barrier formation in rice roots to determine the relative responses of suberin and/or lignin biosyntheses for the barrier. OPR tissues were isolated by laser microdissection and their transcripts were analysed by microarray. A total of 128 genes were significantly up- or downregulated in the OPR during the barrier formation. Genes associated with suberin biosynthesis were strongly upregulated, whereas genes associated with lignin biosynthesis were not. By an ab initio analysis of the promoters of the upregulated genes, the putative cis-elements that could be associated with transcription factors, WRKY, AP2/ERF, NAC, bZIP, MYB, CBT/DREB, and MADS, were elucidated. They were particularly associated with the expression of transcrip- tion factor genes containing WRKY, AP2, and MYB domains. A semiquantitative reverse-transcription PCR analysis of genes associated with suberin biosynthesis (WRKY, CYP, and GPAT) confirmed that they were highly expressed during ROL barrier formation. Overall, these results suggest that suberin is a major constituent of the ROL barrier in roots of rice.

overall_design: 23-d-old plants were either continued in aerated solution or transplanted into N2-flushed or stagnant deoxygenated solution for 9 h. After treating the roots of plants in aerated, stagnant, or N2-flushed conditions for 9h, the basal parts (12.5 -22.5mm below the root - shoot junction) of the adventitious roots were collected. Cells in OPR (including exodermis and sclerenchyma) were isolated using laser microdissection. RNA extracted from the isolated OPR was analysed with a 44k rice oligo-DNA microarray. Total RNAs were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (10 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.

first: Takaki

last: Yamauchi

first: So

last: Yamazaki

first: Yoshiaki

last: Nagamura

first: Naoko

last: Nishizawa

first: Mikio

last: Nakazono


title: PRPF6 regulated alternative splicing in colon cancer cell lines

city: South San Francisco

first: Jinfeng

last: Liu

state: CA

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

summary: PRPF6, an RNA binding component of the pre-mRNA spliceosome, is an essential driver of oncogenesis in colon cancer. PRPF6 is both amplified and overexpressed in colon cancer and cells with high PRPF6 levels are sensitive to its loss.  Here we investigate alternative splicing changes in colon cancer cell lines following PRPF6 silencing by three different siRNA sequences.

overall_design: Two colon cancer cell lines (SW620 and KM-12), silencing of PRPF6 and control, 3 biological replicate samples for each group.

first: Ron

last: Firestein

first: Zora

last: Modrusan


title: Correlation of transcriptomic responses and metal bioaccumulation in Mytilus edulis L. reveals early indicators of stress

city: Boston

first: Helen

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

summary: Marine biomonitoring programs in the U.S. and Europe have historically relied on monitoring tissue concentrations of bivalves to monitor contaminant levels and ecosystem health.  By integrating ‘omic methods with these tissue residue approaches we can uncover mechanistic insight to help link tissue concentrations to toxic effects.  In an effort to identify novel biomarkers and better understand the molecular toxicology of metal bioaccumulation in bivalves, we exposed the blue mussel, Mytilus edulis L., to sub-lethal concentrations (0.54 M) of cadmium, lead, and a Cd+Pb mixture. Metal concentrations were measured in gill tissues at 1, 2, and 4 weeks, and increased linearly over the 4 week  duration.  In addition, there was evidence that Pb interfered with Cd uptake in the mixture treatment.  Using a 3025 sequence microarray for M. edulis, we performed transcriptomic analysis, identifying 57 differentially expressed sequences. Hierarchical clustering of these sequences successfully distinguished the different treatment groups demonstrating that the expression profiles were reproducible among the treatments. Enrichment analysis of gene ontology terms identified several biological processes that were perturbed by the treatments, including nucleoside phosphate biosynthetic processes, mRNA metabolic processes, and response to stress.  To identify transcripts whose expression level correlated with metal bioaccumulation, we performed Pearson correlation analysis.   Several transcripts correlated with gill metal concentrations including mt10, mt20, and contig 48, an unknown transcript containing a wsc domain.  In addition, three transcripts directly involved in the Unfolded protein response (UPR) were induced in the metal treatments at 2 weeks and were further up-regulated at 4 weeks.  Overall, correlation of tissue concentrations and gene expression responses indicates that as mussels accumulate higher concentrations of metals, initial stress responses are mobilized to protect tissues.  However, given the role of UPR in apoptosis, it serves as an early indicator of stress, which once overwhelmed will result in adverse physiological effects.

overall_design: A total of 52 samples including initial samples and 3 time-points following exposure to cadmium, lead, or a mixture.  There were four replicate samples for each treatment and time-point.  An additional three replicate samples were used for RT-qPCR.

first: William

last: Robinson

first: Bonnie

last: Blalock


title: The gene expression changes in darkcd4 apoptosis-deficient mutant flies

city: Bunkyo-ku

first: Masayuki

last: Miura

state: Tokyo

department: Genetics

institute: the University of Tokyo, Grad. Sch. Pharm. Sci

summary: Apoptosis is required not only for proper morphogenesis and tissue size regulation during development, but also for removing damaged or unwanted cells to maintain homeostasis. Apoptosis is mainly executed by evolutionally-conserved signaling process including caspases and its activator, dark. We performed microarray analysis of darkcd4 mutant flies to reveal the changes in gene expression. We found the elevated immune reaction, suggesting that inflammatory response was triggered by necrosis in darkcd4 .

overall_design: We collected total RNA from day 5 adult of darkcd4 mutant flies backcrossed six generations to w1118. w1118 was used as control. N=4 for each sample.

first: Fumiaki

last: Obata

first: Katsura

last: Tomioka


title: Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program [microarray: PGC1a_vs_GFP]

status: Public on Jun 16 2014

city: Basel

first: Christoph

last: Handschin

address: Spitalstrasse 41

institute: Biozentrum, University of Basel

summary: Skeletal muscle tissue shows an extraordinary cellular plasticity, but the underlying molecular mechanisms are still poorly understood. Here we use a combination of experimental and computational approaches to unravel the complex transcriptional network of muscle cell plasticity centered on the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α), a regulatory nexus in endurance training adaptation. By integrating data on genome-wide binding of PGC-1α and gene expression upon PGC-1α over-expression with comprehensive computational prediction of transcription factor binding sites (TFBSs), we uncover a hitherto underestimated number of transcription factor partners involved in mediating PGC-1α action. In particular, principal component analysis of TFBSs at PGC-1α binding regions predicts that, besides the well-known role of the estrogen-related receptor α (ERRα), the activator protein-1 complex (AP-1) plays a major role in regulating the PGC-1α-controlled gene program of hypoxia response. Our findings thus reveal the complex transcriptional network of muscle cell plasticity controlled by PGC-1α.

overall_design: We used microarrays to detect changes in gene expression in C2C12 cells following PGC-1alpha over-expression or GFP (control) over-expression. We used 3 biological replicates for each condition.

first: Mario

last: Baresic

first: Silvia

last: Salatino

first: Erik

last: van Nimwegen

first: Barbara

last: Kupr


title: Genome-wide transcriptional changes of Sphingomonas wittichii RW1 during inoculation and growth in contaminated sand [experment 2]

last: Moreno-Forero

summary: The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions

overall_design: We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. we compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during lag phase, all in carefully controlled and replicated experimental conditions.

first: Jan

last: van der Meer


title: Expression data from adipose tissue of WNIN/Ob lean and obese rats

first: Vajreswari

last: Ayyalasomayajula

summary:
Obesity is characterised by increased adipocyte size and number. Analysis of altered gene expression gives better understading about the mechanisms involved/alterted in the development of obesity in this new obese rat model.
We used Microarrays to delinate the alted gene expression in adipose tissue of WNIN/Ob obese rats

overall_design: Retroperitioneal adipose tissue was collected from 4 month old WNIN/Ob lean and obese rats (n=2 per phenotype) for RNA extraction and hybridization on Affymatrix Rat gene 1ST arrays.

first: Siva

last: Sakamuri


title: HIV-specific B cells are enriched within abnormal memory subsets in infected individuals

status: Public on Jun 24 2014

city: Bethesda

first: Susan

last: Moir

address: 9000 Rockville Pike

department: NIAID

institute: NIH

summary: Recently, several neutralizing anti-HIV antibodies have been isolated from memory B cells of HIV-infected individuals. However, despite extensive evidence of B-cell dysfunction in HIV disease, little is known about the cells from which these rare HIV-specific antibodies originate. Accordingly, HIV envelope gp140 and CD4 or co-receptor (CoR) binding site (bs) mutant probes were used to evaluate HIV-specific responses in the peripheral blood B cells of individuals at various stages of infection. In contrast to non-HIV responses, HIV-specific responses against gp140 were enriched within abnormal B cells, namely activated and exhausted memory subsets, which are largely absent in the blood of uninfected individuals. Responses against the CoRbs (a poorly-neutralizing epitope) arose early whereas those against the CD4bs (a well-characterized neutralizing epitope) were delayed and infrequent.  Enrichment of the HIV-specific response within resting memory B cells, the predominant subset in uninfected individuals, did occur in certain infected individuals who maintained low levels of plasma viremia and immune activation with or without antiretroviral therapy. These findings were corroborated by transcriptional profiles. Taken together, our findings provide valuable insight into virus-specific B-cell responses in HIV infection and demonstrate that memory B-cell abnormalities may contribute to the ineffectiveness of the antibody response in infected individuals.

overall_design: HIV-specific responses against gp140 were enriched within abnormal B cells, namely activated (AM) and exhausted (tissue-like; TLM) memory subsets, which are largely absent in the blood of uninfected individuals. These responses are highest during the early stage of HIV infection, significantly decreased following the initiation of antiretroviral therapy (ART), and most importantly, enriched in normal resting memory B cells (RM) when HIV viremia and immune activation are controlled either naturally or as a result of ART. These HIV-specific B cells (AM and TLM) and resting memory B cells (RM) were sorted from peripheral blood mononuclear cells (PBMCs) of 6 HIV infected individuals. In addition, gp140-specific IgG+ B cells were sorted from individuals with either a strong (n= 6) or weak (n= 6) pro-resting memory profile. TaqMan gene expression assay was performed on these HIV-specific B cells and B cell subset. The array consisted of 29 genes.

first: Lela

last: Kardava

first: Naisha

last: Shah

first: Wei

last: Wang

first: Richard

last: Wilson

first: Clarisa

middle: M

last: Buckner

first: Brian

last: Santich

first: Leo

last: Kim

first: Emily

last: Spurlin

first: Amy

last: Nelson

first: Adam

last: Wheatley

first: Christopher

last: Harvey

first: Adrian

middle: B

last: McDermott

first: Kai

last: Wucherpfennig

first: Tae-Wook

last: Chun

first: John

last: Tsang

first: Yuxing

last: Li

first: Anthony

last: Fauci


title: Skin Deep: Early Mucosal Responses in Blue Catfish (Ictalurus furcatus) Skin to Aeromonas hydrophila Infection

city: AUBURN

first: chao

last: li

address: 203 swingle hall

institute: auburn university

summary: Fish skin is a critical regulatory organ, serving not only as a physical barrier to pathogen entry, but also as a sophisticated integrator of aquatic environmental, social and nutritional cues through roles in immunity, osmoregulation, and endocrine signaling. Integral to the complexity of teleost skin is the mucus layer secreted by epidermal goblet cells.  Pathogen invasion can disrupt this delicate homeostasis with profound impacts on signaling throughout the organism. Here, we investigated the transcriptional effects of virulent A. hydrophila infection in blue catfish skin, Ictalurus furcatus. We utilized an 8X60K Agilent microarray to examine gene expression profiles at critical early timepoints following challenge—2 h, 12 h, and 24 h. Expression of a total of 1,155 unique genes was significantly perturbed during at least one timepoint. We observed dysregulation of a number of genes involved in including antioxidant/apoptosis, cytoskeletal rearrangement, immune response, junctional/adhesion, and proteases.  In particular, A. hydrophila infection rapidly altered a number potentially critical lectins, chemokines, interleukins, and other mucosal factors in a manner predicted to enhance its ability to adhere and invade the catfish host.

overall_design: Two-condition experiment, control vs. infected skin. Biological replicates: 3 control replicates, 3 infected replicates.3 timepoints

first: Chao

first: Benjamin

last: Beck

first: Baofeng

last: Su

first: Jeffery

last: Terhune

first: Eric

last: Peatman


title: Expression data from sympathetic nervous system of KI Alk F1178L mice

city: paris

first: Alex

last: Cazes

state: Please select...

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary:
Neuroblastoma is an embryonal neoplasm that remains of dramatic prognosis in its aggressive forms. Activating mutations of the ALK tyrosine kinase receptor have been identified in sporadic and familial cases of this cancer. We generated knock-in mice carrying an F1178L Alk mutation corresponding to the ALK F1174L mutation observed in neuroblastoma patients
We used microarrays to detail the global programme of gene expression underlying the impact of ALK F1178L mutation on sympathetic nervous system ganglia

overall_design: We selected sympathetic nervous system ganglia (superior cervical and stellate ganglia) for RNA extraction and hybridization on Affymetrix microarrays. We profiled a total number of 12 Po (4 Wt; 4 Hz; 4 Ho) and 5 P18 (3 Wt; 2 Hz)

first: Isabelle

last: Janoueix-Lerosey


title: Expression profiling in N2 (wild-type) early embryo

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St.

department: Molecular, Cell, and Developmental Biology

institute: UC Santa Cruz

summary: Determination of gene expression levels in wild-type early embryo. First published in Rechtsteiner et al. 2010 PLoS Genetics.

overall_design: 4 replicates of total RNA from wild-type early embryo

first: Thea

last: Egelhofer

first: Andreas

last: Rechtsteiner

first: Teruaki

last: Takasaki

last: Stromen


title: Influence of intrauterine low protein diet on ductal morphogenesis of the rat mammary gland.

city: Erlangen

first: Fabian

last: Fahlbusch

address: Loschgestr. 15

department: Kinder- und Jugendklinik

country: Germany

institute: Universität Erlangen

summary: Following intrauterine low protein diet, the lumbar mammary gland of control and low protein rats were removed for further analysis via genarray on day 21 and day 28 postpartum.

overall_design: Virgin female Wistar rats came from Charles River. Throughout pregnancy the NP rats received 25g/d of Altromin C1000 containing 17.0% protein, while LP animals were fed 25g/d of Altromin C1003 containing 8.8% protein. At birth, litter size was reduced to 6 females in both groups, which were left to suckle for 21 days. During lactation (d1-d21) and after weaning (d21-d28) NP and LP animals were fed a standard chow and tap water ad libitum. At d21 and d28 3 dams were sacrificed under isofluran narcosis. The lumbar mammary gland (4th and 5th pair) were removed and cleared of visible lymph nodes before snap-freezing in liquid nitrogen.

first: Lea

last: Beinder

first: Nina

last: Faehrmann

first: Rainer

last: Wachtveitl

first: Ilona

last: Winterfeld

first: Andrea

last: Hartner

first: Carlos

last: Menendez-Castro

first: Manfred

last: Rauh

first: Matthias

last: Ruebner

first: Hanna

last: Huebner

first: Stephanie

last: Noegel

first: Helmuth-Guenther

last: Doerr

first: Wolfgang

last: Rascher


title: Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program [microarray: kD_AP1]

first: Christoph

last: Handschin

overall_design: We used microarrays to detect changes in gene expression in C2C12 cells following PGC-1alpha over-expression and either Atf3, Fos, Jun or control knockdown. We used 2 biological replicates for each condition.

first: Mario

last: Baresic

first: Silvia

last: Salatino

first: Erik

last: van Nimwegen

first: Barbara

last: Kupr


title: Populus 717 wildtype versus 35S::EVE1

city: Gainesville

first: Cintia

middle: Leite

last: Ribeiro

state: FL

address: 2033 Mowry Road room 320F

institute: University of Florida

summary: RNA was extracted from xylem tissue of the first 5cm of the lower stem of four replicates of three overexpression lines and wild-type. Samples were collected from 3-month-old Populus from growth-chamber experiments at 25oC and 35oC.

overall_design: 2 treatments (growth at 25C and 35C temperature), 4 genotypes (wildtype and 3 35S::EVE1 independent lines) and 4 biological reps per genotype

first: Matias

last: Kirst

middle: L


title: Genome-wide transcriptional changes of Sphingomonas wittichii RW1 during inoculation and growth in contaminated sand

city: Lausanne

last: Moreno-Forero

address: Batiment Biophore, Unil Sorge

institute: University of Lausanne

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

overall_design: Refer to individual Series


title: RSV vs BSA

status: Public on Jun 21 2014

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary:
Rationale: Respiratory syncytial virus (RSV) and Streptococcus pneumoniae are major respiratory pathogens. Co-infection with RSV and S. pneumoniae is associated with severe and often fatal pneumonia but the molecular basis for this remains unclear.

Objectives: To determine if interaction between RSV and pneumococci enhances pneumococcal virulence.

Methods: We used confocal microscopy and western blot to identify the receptors involved in direct binding of RSV and pneumococci, the effects of which were studied in both in vivo and in vitro models of infection. Human ciliated respiratory epithelial cell cultures were infected with RSV for 72h and then challenged with pneumococci. Pneumococci were collected after 2h exposure and changes in gene expression determined using qRT-PCR.

Results: Following incubation with RSV or purified G protein, pneumococci demonstrated a significant increase in the inflammatory response and bacterial adherence to human ciliated epithelial cultures and markedly increased virulence in a pneumonia model in mice. This was associated with extensive changes in the pneumococcal transcriptome and significant upregulation in the expression of key pneumococcal virulence genes, including the gene for the pneumococcal toxin, pneumolysin. We show that mechanistically this is due to RSV G glycoprotein binding penicillin binding protein 1a.

Conclusion: The direct interaction between a respiratory virus protein and the pneumococcus resulting in increased bacterial virulence and worsening disease outcome is a new paradigm in respiratory infection.

overall_design:
Comparison of the Streptococcus pneumoniae D39 RSV treated compared to BSA Treated in BEBM medium
One condition design comparision of two strains including a dye swap

first: Oscar

last: Kuipers

first: Claire

last: Smith

first: Christopher

last: O’Callaghan


title: RSV increases the virulence of Streptococcus pneumoniae by binding to PBP1a: a new paradigm respiratory infection


title: Expression of Nodule Cysteine-Rich (NCR) Defensin-Like (DEFL) genes among four different accessions of Medicago truncatula inoculated with two different rhizobial strains.

city: Minneapolis

first: Kevin

last: Silverstein

state: MN

address: 599 Walter Library, 117 Pleasant St SE

department: Minnesota Supercomuting Institute

institute: Universtiy of Minnesota

summary: We have undertaken a detailed study to identify expression polymorphism of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in four different accessions of Medicago truncatula. Each accession was inoculated with two different rhizobial strains to assess the NCR expression differences caused by host-symbiont specificity. The NCRs displayed significant expression differences among the ecotypes but had subtle differences in gene expression because of strain difference.

overall_design: We used a custom Affymetrix chip containing 684 probe sequences of Medicago DEFLs to explore the expression polymorphism of NCRs in nodules inoculated with Sinorhizobium meliloti 1021(Sm1021) and Sinorhizobium medicae (SmA321) totalling 8 different treatments. Each treatment was supported by three biological replicates giving a grand total of 24 samples.

first: Sumitha

last: Nallu

first: Kathryn

last: VandenBosch

first: Peter

last: Tiffin

first: Nevin

middle: D

last: Young

first: Peng

last: Zhou


title: Next Generation Sequencing of  non-heading Chinese cabbage (Brassica rapa ssp. chinensis)

status: Public on Jun 14 2014

city: Shanghai

first: Liu

last: Xuxin

address: 300 Fengling Road

institute: Institute of Plant and Physiology & Ecology

type: Non-coding RNA profiling by high throughput sequencing

summary: Next-generation sequencing has been applied on seedling of two genotypes of noheading Chinese cabbage, Huaq and Wut. The goals of this study are to compare the different expression of small RNAs which is possible effect the phynotype of close genetic relation cultivars.

overall_design: Two genotypes small mRNA profiles of 21-day old Huaq and Wut seedling were generated by deep sequencing, using Illumina GAIIx.

first: Yuke

last: He

first: Xuxin

last: Liu


title: Target repression induced by endogenous microRNAs: large differences, small effects

status: Public on Jun 12 2014

city: Manchester

first: Suzanne

last: Hunt

address: Dover Street

department: Life Sciences

institute: University of Manchester

summary: MicroRNAs are small RNAs that regulate protein levels.  It is commonly assumed that the expression level of a microRNA is directly correlated with its repressive activity – that is, highly expressed microRNAs will repress their target mRNAs more. Here we investigate the quantitative relationship between endogenous microRNA expression and repression for 32 mature microRNAs in Drosophila melanogaster S2 cells.  In general, we find that more abundant microRNAs repress their targets to a greater degree. However, the relationship between expression and repression is nonlinear, such that a 10-fold greater microRNA concentration produces only a 10% increase in target repression. The expression/repression relationship is the same for both dominant guide microRNAs and minor mature products (so-called passenger strands/microRNA* sequences). However, we find examples of microRNAs whose cellular concentrations differ by several orders of magnitude, yet induce similar repression of target mRNAs.  Likewise, microRNAs with similar expression can have very different repressive abilities. We show that the association of microRNAs with Argonaute proteins does not explain this variation in repression.  The observed relationship is consistent with the limiting step in target repression being the association of the microRNA/RISC complex with the target site. These findings argue that modest changes in cellular microRNA concentration will have minor effects on repression of targets.

overall_design: Two replicates of S2-DRSC cells under normal conditions


title: Probing the RyhB-2 regulon in Salmonella Typhimurium

status: Public on Jun 10 2014

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: Typically, the expression of sRNAs is activated in response to environmental stimuli in order to regulate gene expression through post-transcriptional mechanisms. In the present work we show that the Salmonella Typhimurium paralog sRNAs RyhB-1 and RyhB-2 are induced in response to the nitrosating agent S-nitrosoglutathione (GSNO). Inactivation of these sRNAs decreased S. Typhimurium resistance to GSNO and increased the levels of nitrosylated proteins. These results prompted us to evaluate a possible role of these sRNAs in nitrosative stress resistance. RNA profiling was used as a screening to identify novel RyhB-1 and RyhB-2 regulated targets, and a subset of genes was filtered based on their potential role in the response to nitrosative stress. To confirm our observation, expression of the candidate targets was analyzed by quantitative RT-PCR in a wild type, single and double mutant strains (ΔryhB1, ΔryhB2 and ΔryhB1 ΔryhB2) treated with GSNO. In response to GSNO RyhB-1 and RyhB-2 negatively regulate the expression of the genes cyoABC (cytochrome o oxidase complex), cydB (cytochrome d oxidase complex), cybC (cytochrome b-562), and positively regulate the nirBCD operon (nitrite reductase system). Together, these results suggest that RyhB-1 and RyhB-2 finely tune the expression of genes coding for cytochrome and the nitrate reductase system, allowing the cell to cope with GSNO-induced stress.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Total RNA was harvested from two biological replicates of wt S. Typhimurium overexpressing the sRNA RyhB-2 grown in LB medium, in order to identify RhyB-2 targets that might be implicated in reactive nitrogen stress resistance.

first: Eduardo

middle: H

last: Morales

first: Ivan

last: Calderon

first: Steffen

last: Porwollik


title: Role of mRNA stability during bacterial adaptation

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

summary: Bacterial adaptation involves extensive cellular reorganization. In particular, growth rate adjustments are associated with substantial modifications of gene expression and mRNA abundance. In this work we aimed to assess the role of mRNA degradation during such variations.   A genome-wide transcriptomic-based method was used to determine mRNA half-lives. The model bacterium Lactococcus lactis was used and five growth rates were studied in continuous cultures under isoleucine-limitation and in batch cultures during the adaptation to the isoleucine starvation.   During continuous isoleucine-limited growth, the mRNAs of different genes had different half-lives. The stability of most of the transcripts was not constant, and increased as the growth rate decreased. This half-life diversity was analyzed to investigate determinants of mRNA stability. The concentration, length, codon adaptation index and secondary structures of mRNAs were found to contribute to the regulation of mRNA stability in these conditions. However, the growth rate was, by far, the most influential determinant.   The respective influences of mRNA degradation and transcription on the regulation of intra-cellular transcript concentration were estimated. The role of degradation on mRNA homeostasis was clearly evidenced: for more than 90 % of the mRNAs studied during continuous isoleucine-limited growth of L. lactis, degradation was antagonistic to transcription. Although both transcription and degradation had, opposite effects,, the mRNA changes in response to growth rate were driven by transcription. Interestingly, degradation control increased during the dynamic adaptation of bacteria as the growth rate reduced due to progressive isoleucine starvation in batch cultures.  This work shows that mRNA decay differs between gene transcripts and according to the growth rate. It demonstrates that mRNA degradation is an important regulatory process involved in bacterial adaptation. However, its impact on the regulation of mRNA levels is smaller than that of transcription in the conditions studied.

overall_design: In the study presented here mRNA stabilities were analyzed at 5 growth rates. For each growth rate mRNA levels were measured in a time course experiment following rifampicin addition. At least 12 time points per growth rate are available, including 3 replicates of the zero.

first: Clémentine

last: Dressaire

first: Flora

last: Picard

first: Emma

last: Redon

first: Pascal

last: Loubière

first: Isabelle

last: Queinnec

first: Laurence

last: Girbal


city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary:
inra12-05_mut_flg_ii-FLG-MPKs
ra12-05_mut_flg_ii - inra12-05_mut_flg_ii - Analysis of flg22-induced transcriptional changes in mpk3, mpk4 and mpk6 mutants. - 2 weeks old seedlings compared for transcriptome after a 30min mock or 1µM flg22 treatment.

overall_design: 21 dye-swap - gene knock out,normal vs mutant comparison,treated vs untreated comparison

first: Heribert

last: Hirt

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: MicroRNA-223 and miR-143 are important systemic biomarkers for disease activity in psoriasis

city: Hellerup

first: Marianne

middle: Bengtson

last: Løvendorf

address: Niels Andersens Vej 65

department: Dermato-Allergology

country: Denmark

institute: Gentofte Hospital

summary: Background: Psoriasis is a systemic inflammatory skin disease. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that recently have been found in the blood to be relevant as disease biomarkers. Objective: We aimed to explore miRNAs potential as blood biomarkers for psoriasis. Methods: Using microarray and quantitative real-time PCR we measured the global miRNA expression in whole blood, plasma and peripheral blood mononuclear cells (PBMCs) from patients with psoriasis and healthy controls. Results: We identified several deregulated miRNAs in the blood from patients with psoriasis including miR-223 and miR-143 which were found to be significantly upregulated in the PBMCs from patients with psoriasis compared with healthy controls (FCH=1.63, P<0.01; FCH=2.18, P<0.01, respectively). In addition, miR-223 and miR-143 significantly correlated with the PASI score (r = 0.46, P<0.05; r=0.55, P<0.02, respectively). Receiver-operating characteristic analysis (ROC) showed that miR-223 and -143 have the potential to distinguish between psoriasis and healthy controls (miR-223: Area under the curve (AUC) = 0.80, miR-143: AUC = 0.75). Interestingly, after 3-5 weeks of treatment with methotrexate following a significant decrease in psoriasis severity, miR-223 and miR-143 were significantly downregulated in the PBMCs from patients with psoriasis. Conclusion: We suggest that changes in the miR-223 and miR-143 expressions in PBMCs from patients with psoriasis may serve as novel biomarkers for disease activity in psoriasis; however, further investigations are warranted to clarify their specific roles.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the present study, we compared the global miRNA expression profile between whole blood samples obtained from 24 patients with psoriasis (5 samples were excluded due to poor quality control) compared with 15 healthy controls.

first: John

last: Zibert

first: Mette

last: Gyldenløve

first: Mads

last: Røpke

first: Lone

last: Skov


title: The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner [ChIP-chip]

status: Public on Jun 06 2014

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such as histone H3 lysine 9 (H3K9) methylation. In Arabidopsis thaliana DNA methylation and H3K9 methylation are usually colocated and set up a mutually self reinforcing and stable state. Here, in contrast, we found that SUVR5, a plant Su(var)3-9 homolog with a SET histone methyltransferase domain, mediates H3K9me2 deposition and regulates gene expression in a DNA-methylation-independent manner. SUVR5 binds DNA through its zinc fingers and represses  the expression of a subset of stimulus response genes. This represents a novel mechanism for plants to regulate their chromatin and transcriptional state, which may allow for the adaptability and modulation necessary to rapidly respond to extracellular cues.

overall_design:
Investigation of H3K9me2 levels in WT Col0 and suvr5-1 mature leaves
4 ChIP-chip experiments.

first: Elena

last: Caro

first: Steve

last: Jacobsen


title: Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis

status: Public on Jun 03 2014

city: Cambridge

first: Fatima

last: Al-Shahrour

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard


title: Identification of long non-coding RNAs as prognostic indicators of astrocytoma

status: Public on Jun 07 2014

city: Changzhou

first: Yilin

last: Yang

state: Jiangsu

address: 185#, Juqian Road

department: Modern Medical Research Center

institute: Third Affiliated Hospital of Soochow University

summary: Background: Long noncoding RNAs (lncRNAs) are pervasively transcribed and play a key role in tumorigenesis. The aim of the present study was to determine the lncRNA expression profile in astrocytoma patients and to assess the potential clinical value of the findings.  Methods: The global lncRNA expression profile in astrocytoma was measured by lncRNA microarray. Next, the differentially expressed lncRNAs were validated using a Taqman probe-based quantitative real time-PCR (qRT-PCR) assay in 130 astrocytoma and 60 normal adjacent tissue (NAT) samples, which were randomly divided into a training set and a validation set. Finally, the correlation of the lncRNA levels with survival of the astrocytoma patients was estimated by performing a Kaplan-Meier survival analysis and a univariate/multivariate Cox proportional hazard regression analysis.  Results: After a two-phase selection and validation process, 7 lncRNAs were found to have a significantly different expression profile in astrocytoma samples compared to the NAT samples. Unsupervised clustering analysis further revealed the potential of the 7-lncRNA profile to differentiate between tumors and NAT samples. Using Kaplan-Meier survival analysis, we found that the low expression of XLOC_005285 and XLOC_010967 and the high expression of HIT000260843.11 were significantly associated with poor patient survival. Moreover, Cox proportional hazard regression analysis revealed that this prognostic impact was independent of other clinicopathological factors.

overall_design: The lncRNA expression profiles of 3 astrocytoma tissues and 3 normal adjacent tissues  were studied by microarray.

first: Feng

last: Zhi

first: Qiang

last: Wang

first: Lian

last: Xue

first: Naiyuan

last: Shao

first: Rong

first: Danni

last: Deng

first: Suinuan

first: Xiwei

last: Xia


title: Microarray analysis of genes regulated by SpxA1 and SpxA2 in Streptococcus suis serotype 2

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

institute: Yangzhou University

summary: To reveal the scope of the Spx regulation and explore the differences in the regulatory roles of SpxA1 and SpxA2, the global gene transcription profiles of the WT, ∆spxA1 and ∆spxA2 strains were determined by DNA microarray analysis performed using an Agilent custom-designed oligonucleotide microarray.

overall_design: S. suis strains were grown in TSB with 10% (vol/vol) newborn bovine serum to mid-exponential phase. Total RNA was isolated using an SV total RNA isolation system (Promega), according to the manufacturer’s recommended protocol. RNA concentrations and integrity were determined using an Agilent 2100 Bioanalyzer.Two biological replicates of total RNA from WT strain and three from each mutant strain were used for array.

first: Weicheng

last: Bei


title: The functional  study of zebrafish Bad gene

status: Public on Jun 01 2014

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary: Transcriptional profiling of zebrafish embryo comparing wild type untreated embryos with embryos injected with morpholino of zf-bad. This assay is used for determination of expression profiling at 24 hpf and 48 hpf under Bad deficiency.

overall_design: Two-condition experiment, wild type vs. MO-Bad treated cells. Biological replicates: each group contains 200 embryos.

first: Gen-Hwa

last: Lin

first: Jiann-Ruey

last: Hong

first: Jen-Leih

last: Wu


title: Acrolein-mediated changes in HUVEC miRNA

city: Louisville

first: Timothy

last: O'Toole

state: KY

address: 302E. Muhammad Ali Blvd

institute: University of Louisville

summary: Acrolein is a major reactive component of vehicle exhaust, cigarette and wood smoke. It is also present in several food substances and is generated endogenously during inflammation and lipid peroxidation. Although previous studies have shown that dietary or inhalation exposure to acrolein results in endothelial activation, platelet activation and accelerated atherogenesis, the basis for these effects is unknown. Moreover, the effects of acrolein on microRNA (miRNA) have not been studied. Using AGILENT miRNA microarray high throughput technology, we have thus characterized the effects of acrolein exposure on miRNA expression in human umbilical vein endothelial cells (HUVEC).

overall_design: 2 condition, acrolein-exposed and vehicle exposed; 4 replicates of each

first: Wesley

last: Abplanalp

first: Xiaohong

last: LI

first: Nigel

last: Cooper

first: Daniel

first: Petra

last: Haberzettl

first: Aruni

last: Bhatnagar


title: Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis [MPN patients]

first: Fatima

last: Al-Shahrour

summary: We used expression profiling, SNP arrays, and mutational profiling to investigate a well-characterized cohort of MPN patients. MPN patients with homozygous JAK2V617F mutations were characterized by a distinctive transcriptional profile. Notably, a transcriptional signature consistent with activated JAK2 signaling is seen in all MPN patients regardless of clinical phenotype or mutational status.  In addition, the activated JAK2 signature was present in patients with somatic CALR mutations.  Conversely, we identified a gene expression signature of CALR mutations; this signature was significantly enriched in JAK2-mutant MPN patients consistent with a shared mechanism of transformation by JAK2 and CALR mutations. We also identified a transcriptional signature of TET2 mutations in MPN patent samples. Our data indicate that MPN patients, regardless of diagnosis or JAK mutational status are characterized by a distinct gene expression signature with upregulation of JAK-STAT target genes, demonstrating the central importance of the JAK-STAT pathway in MPN pathogenesis.

overall_design: [MPN patients]  We have performed microarray gene expression analysis in 93 patients with MPNs (28 PV, 47 ET, 18 MF) and 11 age-matched normal donors.

first: Raajit

last: Rampal

first: Omar

last: Abdel-Wahab

first: Jay

last: Patel

first: Jean-Philippe

last: Brunel

first: Craig

last: Mermel

first: Adam

last: Bass

first: Jennifer

last: Pretz

first: Jihae

last: Ahn

first: Todd

last: Hricik

first: Outi

last: Kilpivaara

first: Martha

last: Wadleigh

first: Lambert

last: Busque

first: D

middle: G

last: Gilliland

last: Golub

first: Benjamin

last: Ebert

first: Ross

last: Levine


title: Effect of human TGF-β on the gene expression profile of Echinococcus granulosus protoscoleces

city: Urumqi

first: Guodong

last: Lü

state: Xinjiang

address: Liyushan north road

department: State Key Lab Cultivation Base for Xinjiang Major Diseases Research and Xinjiang Key Laboratory of Echinococcosis

institute: First Affiliated Hospital of Xinjiang Medical University

summary: TGF-β is a crucial cytokine participate in the interplay between the intermediate host and helminthes. TGF-β receptors were discovered in many cestode, and could bind the human TGF-β. However, the function of host TGF-β on the Echinococcus is still not elucidated, and this paper aim to explore the question at transcription level. Microarray analysis was used to investigate differential expression genes in protoscolices of Echinococcus granulosus cultured in the presence or absence of human TGF-β at different time points (4h, 8h and 24h) in vitro. A total of 523 genes were up- or down-regulated in response to TGF-β, compared with control group, 390 genes were up-regulated and 47 genes were down-regulated at 8h, and 376 genes were up-regulated and 19 genes were down-regulated at 12h, including 310 differential genes were regulated at both time point. Only 1 gene down-regulated at 4 h. Gene ontology (GO) analysis showed that the biological process of the up-regulated genes in protoscolex were predominantly involved in DNA packaging, nucleosome assembly, chromatin assembly, etc. And the cellular component gene were located in cell nucleus. TGF-β appeared to promote growth or development of the protoscolex by up-regulated the gene related with mitosis. In addition, the study also indicated that TGF-β has a multiple influence on the protoscolex, as reflected in the increased stimulation of gene expression of the ErbB signaling pathway, MAPK signaling pathway, Notch signaling pathway and VEGF signaling pathway.

overall_design: Isolated E. granulosus protoscoleces were treated with human TGF-β at different time points (4h, 8h and 24h) in vitro, and replicated 3 times. Each samples independently grown and harvested. And was extracted of total RNA using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each RNA sample separately on the GeneChip of Echinococcus granulosus Genome Array (Capitalbio) at CapitalBio Corporation (Beijing, China). The reference samples are protoscoleces treated by human TGF-β(0 h)

first: Jianqin

last: Zhao


title: Application of a 9k-cDNA microarray for identification of albendazole and artemisinin targeting genes in Echinococcus granulosus larval protoscoleces

summary: A cDNA microarray composed of 9065 uniEST probes was constructed and applied to detect the gene expression profile of protoscoleces of E. granulosus treated with albendazole and artemisinin in vitro, respectively. Compared with the untreated parasite, 7 genes were up-regulated and 38 genes were down-regulated in protoscoleces treated with albendazole and 100 genes were up-regulated and 6 genes were down-regulated in protoscoleces treated with artemisinin. The differential expression genes in protoscoleces induced by albendazole were clustered into energy metabolism, cell cycle and assembly of cell structure. And the differential expression genes affected by artemisinin were clustered into genetic information, the transduction of environmental signals, metabolism. Under transmission electron microscope observation, albendazole intervention damaged the cell structure, and form the heterochromatin in protoscoleces cells was mainly increased in the artemisinin group.

overall_design: Isolated E. granulosus protoscoleces were treated with albendazole and artemisinin respectively and was extracted of total RNA using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each RNA sample separately on the GeneChip of Echinococcus granulosus Genome Array (Capitalbio) at CapitalBio Corporation (Beijing, China).


title: Streptococcus mutans UA159 grown in the presence of glucose or maltose pH7 and pH5

city: Rochester

first: Roberta

middle: C

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

summary: Transcriptional analysis of the effects of sugar source in S. mutans

overall_design: RNA was extracted from 4 replicate samples of S. mutans UA159, UA159 grown in glucose or maltose in continuous culture to steady-state pH values of 7 or 5.  RNA was labeled with Cy3.  For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cultures grown to mid-log.

first: Andrew

last: Buckley

first: Robert

last: Quivey Jr


title: Gene expression profiling of liver cancers

city: Bethesda

first: Henry

last: Zhang

state: MD

address: 49 Convent Drive

department: NICHD Bioinformatics and Scientific Programming Core

institute: NICHD

summary: Analysis of the gene expression in  primary heptocarcinoma tissue.

overall_design:
Total 24 pairs of primary heptocarcinoma sample and its adjacent tissue were anayzed with Affymetrix HG-U133A chips.

Deposited by the Laboratory of Population Genetics, National Cancer Institute, NIH


title: REG3γ-deficient mice have altered mucus distribution and increased mucosal inflammatory responses to the microbiota and enteric pathogens in the ileum

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

institute: Wageningen University

summary: Objective: Reg3g has been proposed to have a protective role against infection due to its bactericidal effect on Gram-positive bacteria, but evidence from in vivo studies is lacking. Therefore we generated a Reg3g-/- mouse, to determine its role in intestinal homeostasis and protection against experimental infection. Methods: Reg3g-/- mice were phenotyped using histological methods and a range of innate and immune markers. To investigate the antimicrobial role of Reg3g we experimentally infected mice with Gram-positive Listeria monocytogenes and Gram-negative Salmonella entertitidis and measured translocated bacteria, mucosal and systemic markers of infection. Results: Reg3g-/- mice display altered ileal mucus distribution and increased bacterial contact with the epithelium. , concomitant with This increased the inflammatory status in of the ileal mucosa and increased expression of Il-22, myeloperoxidase (MPO) and serum chemokines in serum. In response to infection, Reg3g-/- mice showed transcriptome changes and elevated levels of mucosal MPO in the ileum, but no increased bacterial translocation to the organs. Conclusions: Reg3g is equally distributed throughout the mucus of wild type (wt) mice and its absence results in an altered distribution of the ileal mucus. Reg3g deficiency also results resulted in increased bacterial contact with the epithelium and heightened  inflammatory responses in the ileal mucosa. We propose that Reg3g binds pathogens suggesting it and contributes to mucus barrier function by ensnaring bacteria. Compared to wt mice, Reg3g-/- mice infected with S. enteritidis and L. monocytogenes show an increase of mucosal inflammatory markers indicating the protective, anti-microbial roles of Reg3g in defence against both Gram-positive and -negative bacteria.

overall_design: This study was set up according to a one-treatment, one-control design; treatments were inoculation with either Listeria monocytogenes or Salmonella enteritidis bacterial pathogens. The study results contain transcriptional profiles from infected and sham-infected control C57Bl/6 mice. In total, this study includes data from 2 treatments and 1 control of (pooled) wild-type C57Bl/6 mice and Reg3g-/- KO mutant C57Bl/6 mice = 6 arrays.

first: Linda

last: Loonen

first: Jerry

last: Wells


title: transcriptome analysis of differentially expressed genes in the harlequin (hlq) mutant

city: Lubbock

first: Christopher

middle: Dale

last: Rock

address: Flint and Main Sts.

department: Biological Sciences

institute: Texas Tech University

summary: Plant growth and development is continuous and modular, a combination that allows morphogenesis by controlled cell division and elongation and serves to facilitate plants’ adaptations to changing environments.  Plasticity is achieved through integration of external and internal signals to regulate meristem activities.  We previously characterized the pleiotropic phenotypes of the harlequin (hlq) mutant, isolated on the basis of ectopic expression of ABA- and auxin-inducible proDc3:GUS in roots and hypocotyls.  Mutants are skotomorphogenic (dark development of true leaves and chlorophyll accumulation), have deformed and collapsed epidermal cells that accumulate callose and starch and stain strongly with the vital dye fluorescein diacetate, brittle stems and leaves, cell walls with a relative abundance of pectins and cell wall proteins, and abnormal and reduced root hairs and leaf trichomes.  We cloned hlq and show it is an allele of brassinosteroid-insensitive3/hypocotyl6/root hairless3/Topoisomerase6B.  Mutants affecting the cell wall and inhibitors of cellulose synthesis and N-glycosylation phenocopy several of the traits of hlq such as ectopic proDc3:GUS expression, lignin accumulation, and bulging root tips and epidermal cells.  We performed a microarray analysis of genes differentially expressed in hlq mutants and observed coordinated expression of adjacent pairs/sets of genes suggesting a direct effect on chromatin remodeling, and significantly mis-regulated genes for histones, WRKY and IAA/AUX transcription factors, aquaporins, ubiquin E3-ligase mediated proteolysis and autophagy, biotic stress response markers, as well as numerous other cellular and metabolic processes affecting carbon partitioning into secondary metabolites lignin and anthocyanin.  Our results shed light on the molecular mechanisms underlying the det/cop/fus-like pleiotropic phenotypes of hlq and support a broader role for TopoVI regulation of chromatin remodeling that mediates cell wall metabolism, growth, and development in response to environmental and hormonal signals.

overall_design: Seven samples; four mutant, three wild type in a dual color competitive hybridization to four microarray slides.  One 'quasi-technical' replicate slide made up of pools of the three biological replicates plus a fourth mutant replicate.


title: Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis [HEL cell lines]

first: Fatima

last: Al-Shahrour

overall_design: [HEL cell lines]  We have performed gene expression profiling in the JAK2V617F homozygous mutant HEL cell line following treatment with 2 independent shRNAs targeting JAK2 or 2 different control shRNAs

first: Raajit

last: Rampal

first: Omar

last: Abdel-Wahab

first: Jay

last: Patel

first: Jean-Philippe

last: Brunel

first: Craig

last: Mermel

first: Adam

last: Bass

first: Jennifer

last: Pretz

first: Jihae

last: Ahn

first: Todd

last: Hricik

last: Kilpivaara

middle: R


title: FOXO3 in control of circadian rhythms via direct regulation of Clock

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

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

overall_design: Refer to individual Series


title: MH003B:FOXO3 in control of circadian rhythms via direct regulation of Clock. Part 2: knockdown of FoxO3.

summary: Circadian rhythms are responsive to a variety of external cues, light and metabolism being the most important. In mammals, the light signal is sensed by the retina and transmitted to the SCN master clock, where it is translated into the molecular oscillator via regulation of clock gene transcription. The signalling pathways governing the molecular translation from metabolic signals to circadian output in peripheral oscillators, in contrast, are less understood. FOXO transcription factors are known to translate external metabolic cues to internal transcriptional programs. In the past couple of years it has become evident that both FOXO transcription factors and the circadian clock are of key importance in the underlying mechanisms of ageing and the regulation of metabolism. We now show FOXO3 to be a crucial modulator of circadian rhythmicity via direct transcriptional regulation of Clock, a core component of the molecular oscillator, and identify FOXO3 as a novel link in the circadian feedback loop, which is required for circadian rhythms in liver. We propose that FOXO3 directly feeds back into the circadian oscillator in response to metabolic cues.

overall_design: We performed a microarray study on synchronized NIH 3T3 cells upon transient knock-down of FoxO3 (siO3). Cells were harvested for RNA isolation 24h (time1), 30h(time2), 36h(time3) and 42h(time4) after synchronization. Experimental samples were hybridized against a reference pool of cRNA, which was derived from unsynchronized NIH 3T3 cells. AS controlgroup a scrambled siRNA was transfected. Experiments were performed 4 times, of each sample group two samples were labeled with cy5 and co-hybridized with reference RNA labeled with cy3, and two samples were labeled and hybridized in the opposite way. Microarrays used were Mouse Whole Genome Gene Expression Microarrays V1 (Agilent Technologies, Belgium)

first: Inês

last: Chaves

first: Gijsbertus

middle: T

last: van der Horst

first: Raymond

last: Schellevis

first: Romana

last: Nijman

last: Koerkamp

first: Frank

last: Holstege

first: Marten

last: Smidt

first: Marco

middle: F

last: Hoekman


title: Genomic Determinants of Gene Regulation by 1,25-Dihydroxyvitamin D3 During Osteoblast-Lineage Cell Differentiation [gene expression]

status: Public on Jun 02 2014

city: Madison

first: Mark

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

summary: The biological effects of 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) on osteoblast differentiation and function differ significantly depending upon the cellular state of maturation.  To explore this phenomenon mechanistically, we examined the impact of 1,25(OH)2D3 on the transcriptomes of both pre-osteoblastic (POBs) and differentiated osteoblastic (OBs) MC3T3-E1 cells, and assessed localization of the vitamin D receptor (VDR) at sites of action on a genome-scale using ChIP-seq analysis. We observed that the 1,25(OH)2D3-induced transcriptomes of POBs and OBs were quantitatively and qualitatively different, supporting not only the altered biology observed but the potential for a change in VDR interaction at the genome as well.  This idea was confirmed through discovery that VDR cistromes in POBs and OBs were also strikingly different.  Depletion of VDR binding sites in OBs, due in part to reduced VDR expression, was the likely cause of the loss of VDR-target gene interaction. Continued novel regulation by 1,25(OH)2D3, however, suggested that factors in addition to the VDR might also be involved.  Accordingly, we show that transcriptomic modifications are also accompanied by changes in genome binding of the master osteoblast regulator RUNX2 and the chromatin remodeler C/EBPβ.  Importantly, genome occupancy was also highlighted by the presence of epigenetic enhancer signatures which were selectively changed in response to both differentiation and 1,25(OH)2D3. The impact of VDR, RUNX2, and C/EBPβ on osteoblast differentiation is exemplified by their actions at the Runx2 and Sp7 gene loci.  We conclude that each of these mechanisms may contribute to the diverse actions of 1,25(OH)2D3 on differentiating osteoblasts.

overall_design: RNA was isolated and applied to gene expression microarrays in undifferentiated MC3T3-E1 cells as well as post 15 day osteogenic differentiation MC3T3-E1 cells, which were treated for 24 hours with 10-7M 1,25(OH)2D3.  For the vehicle matched samples, please refer to study GSE41955.  The samples were completed in biological triplicate.

first: Nancy

middle: A

last: Benkusky

first: J

last: Pike


title: Rice cultivar Lijiangxintuanheigu under cold stress: control vs. 8℃ treated

city: Guangzhou

first: Junliang

last: Zhao

address: 29 Jinying Road, Tianhe District

institute: Guangdong Academy of Agricultural Science

summary: Transcriptional profiling of a Oryza sativa L. land race Lijiangxintuanheigu (LTH) under cold stress (8℃) comparing to control (26℃)

overall_design: 4 time points experiment, 3 biological replicates for stressed and control samples of all time points

first: Bin

last: Liu


title: Diethyl maleate inhibits MCA+TPA transformed cell growth via modulation of GSH, MAPK, and cancer pathways

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

institute: Indian Institute of Toxicology Research

summary: Murine or human cancer cells have high glutathione levels. Depletion of the elevated GSH inhibits proliferation of cancer cells. Molecular basis for this observation is little understood. In an attempt to find out the underlying mechanism, we reproduced these effects in transformed C3H10T1/2 and BALB/c 3T3 cells using diethyl maleate and studied cytogenomic changes in the whole mouse genome using spotted 8 × 60K arrays. Transformed cells revealed an increase in GSH levels. GSH depletion by DEM inhibited the growth of transformed cells. The non-cytotoxic dose of DEM (0.25 mM) resulted in GSH depletion, ROS generation, cell cycle arrest, apoptosis, decrease in anchorage independent growth, gene expression changes and activation of all three members of the MAPK family. Increase in intracellular GSH levels by GSHe countered the effect of DEM. These results support the physiological importance of GSH in regulation of gene expression for transformed cell growth restraint. This study is of interest in not only understanding the molecular biology of the transformed cells, but also in identifying new targets for development of gene therapy together with the chemotherapy.

overall_design: Agilent one-color experiment; Organism: Mus musculus; Agilent Custom Mouse Whole Genome Mouse 8x60k gene expression designed by Genotypic Technology Private Limited; Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442).

first: Shivam

last: Priya

first: Sushil


title: Differential transcription of fathead minnow immune-related genes following infection with an emerging pathogen of ectothermic vertebrates, Frog virus 3

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Frog virus 3 (FV3) and other ranaviruses are responsible for an increasing number of die-offs involving wild, farmed, and captive amphibians, fish, and reptiles.  Studies in Lithobates pipiens (Leopard frogs) and Xenopus laevis (African clawed frog) indicate that embryos and tadpoles are more likely to succumb to FV3 infection than adult animals.  The heightened susceptibility of embryos and tadpoles to ranaviral disease likely reflects the immaturity of their immune system.   To ascertain which elements of the immune system respond to ranavirus infection, we explored cellular transcriptional responses following infection of fathead minnow (Pimephales promelas) cells with either wild type (wt) FV3 or a knock out (KO) mutant targeting the 18kDa immediate early gene (18K).   At 8 hr post infection (p.i.), a time when late viral gene expression has begun and host protein synthesis has been inhibited, we observed marked up-regulation of multiple cellular transcripts encoding proteins affecting innate and acquired immune responses.  We found 2367 target sequences expressed 4-fold or higher in wt-infected cells versus 530 target sequences that were 4-fold or more downregulated.  For example, in cells infected with wt virus, interferon (IFN) transcripts were elevated compared to mock-infected cells, along with those encoding IFN regulatory factors (IRFs), IFN stimulated genes (ISGs) such as Mx and MHC class I, and other immune related gene products such as the interleukins IL-1β, IL-8, IL-17C and IL-12.  Cells infected with the 18K KO mutant (∆18K) showed generally similar levels of induction although quantitative and qualitative differences were noted.  Collectively, these results indicate that ranavirus infection induced expression of multiple cellular genes affecting both innate and acquired immunity.   It is likely that induction of various immune-related genes may slow or limit viral infection through the activation of multiple components of the innate immune system and, in a whole animal, enhance the development of acquired immunity and protect from disease.

overall_design: To ascertain which elements of the immune system respond to ranavirus infection, we explored cellular transcriptional responses following infection of fathead minnow (Pimephales promelas) cells with either wild type (wt) FV3 or a knock out (KO) mutant targeting the 18kDa immediate early gene (18K). Replicate confluent monolayers of FHM cells grown on 35 mm dishes were mock-infected or infected with wt- or ∆18K-FV3 at a MOI of 10 PFU/cell.   At 8 hr p.i., total RNA was isolated from samples RNeasy (Qiagen, Valencia, CA, USA) for microarray analysis. Five or six replicates were used per treatment.

first: Kwang

last: Chen

first: Lynn

last: Escalon

first: Gregory

last: Chinchar


title: Expression profiles of human oral cancer cell lines under hypoxic conditions

city: Hiroshima

first: Keiji

last: Tanimoto

address: Kasumi 1-2-3, Minami-ku

institute: Research Institute for Radiation Biology and Medicine, Hiroshima University

summary: A gene expression profiles of human oral squamous cell carcinoma lines, HSC-2 and Ca9-22, cultured under hypoxic conditions (1% pO2 for 24 or 48 hours) were compaired with those under normoxic conditions (21% pO2).

overall_design: Six arrays for 2 cell lines in 3 conditions were analyzed.

first: Hideaki

last: Nakamura


title: Effect of NaCl concentration on the transcriptional network of E. coli in glucose minimal medium with glycine betaine

status: Public on May 26 2014

city: Norwich

first: Aline

last: Metris

state: Norfolk

address: Norwich research Park

department: GHFS

institute: Institute of Food Research

summary: The growth rate of E. coli decrease continuously with NaCl concentration, however the pattern for metabolic efficiency as measured by optical density is corralated to a  change in pattern in transcription data and proteomics.The analysis of the data suggest that between 4.5 and 5% NaCl, the metabolism switched from aerobic to fermentative pathways. The response to osmotic stress is similar to a response to oxidative stress. An example how  a stagewise metabolic answer may be the result of continuously increasing stress.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Study of the pattern of gene expression as a function of NaCl concentrations (2%, 3.5% -2 replicates-, 4.5%, 5%, 5.5%). To compare the different conditions, cDNA was normalised to genomic DNA, gDNA.

first: Susan

last: George

first: Andrew

last: Carter


title: Global gene expression of Ruegeria pomeroyi DSS-3 during ammonium-limited, ribose phosphate-, methylphosphonate-, or potassium phosphate-excess growth regimes or during potassium phosphate-limited, ammonium-excess regime

city: Athens

first: Leong-Keat

last: Chan

state: GA

address: 325 Sanford Drive

department: Marine Sciences

institute: University of Georgia

summary: We used the previously designed oligonucleotide microarrays (Bürgmann et al., 2007, Environmental Microbiology, 9: 2742-2755) to detect the mRNA transcripts of R. pomeroyi DSS-3 when the cells were cultured under steady-state conditions limited with ammonium (NH4Cl, 0.26 mM) but with an excess of D-ribose-5-phosphate (C5H9Na2O8P*2H2O, 0.5 mM), methylphosphonic acid (CH5PO3, 0.5 mM), or potassium phosphate (KH2PO4, 0.5 mM), or during ammonium excess (NH4Cl, 2.8 mM) but were limited with potassium phosphate (KH2PO4, 9.2 μM).

overall_design: A total of 13 microarray hybridizations were performed: three biological replicates each from ribose phosphate, methylphosphonate, or potassium phosphate excess growth regimes, three biological replicates from potassium phosphate limited growth regime, and one technical replicate for the potassium phosphate excess growth regime. Data for the technical replicates were averaged and combined, resulted in a total of 12 samples.

first: Mary-Ann

last: Moran

first: Ryan

middle: J

last: Newton

first: Shalabh

last: Sharma


title: Cardiac left ventricular physiological hypertrophy in swine

city: Rotterdam

first: Diederik

last: Kuster

address: Dr Molewaterplein 50

department: Experimental Cardiology

institute: Erasmus University Medical Center

summary: The molecular mechanism underlying cardiac remodeling following exercise have been incompletely understood. Until now, most studies have been performed in rodents. We studied cardiac remodeling in the physiologically more relevant animal model, the swine.  Microarray analysis was performed on animals that underwent either and exercise protocol or remained sedentary. RNA was isolated from tissue samples from the endocardial layer of the free wall of the left ventricle.

overall_design: RNA was isolated from 8 exercise-trained and 8 sedentary animals 4-5 weeks after start of the protocol. Each group contained 4 males and 4 females. Animals used for the study were 2-3 months old Yorkshire x Landrace swine. Only neutered males entered the study.

middle: W

first: Dirk

last: Duncker


title: DNA methylation profiles across different brain regions in healthy mice (control samples)

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

summary: Genome wide DNA methylation profiling of normal and disease samples from different mice models. A custom Illumina Golden Gate DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 800 CpGs.

overall_design: Bisulphite converted DNA from the 7 control samples were hybridised to the Illumina custom golden gate DNA methylation array.

first: Jose

middle: V

last: Sanchez-Mut


title: Contrasted transcriptomic responses to a rhabdovirus and a togavirus in zebrafish embryo

status: Public on May 17 2014

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary: Characterization of the zebrafish embryonic host response to viral infection (CHIKV, IHNV) by means of global expression analysis

overall_design: Three  sets of larvae infected by CHIKV or IHNV were analyzed (2 color hybridizations against control sets of larvae)

first: Valérie

last: Briolat

first: Luc

last: Jouneau

first: Ralph

last: Carvalho

first: Nuno

last: Palha

first: Christelle

last: Langevin

first: Philippe

last: Herbomel

first: Olivier

last: Schwartz

first: Herman

middle: P

last: Spaink

first: Pierre

last: Boudinot

first: Jean-Pierre

last: Levraud


title: Existence of conventional dendritic cells in Gallus gallus revealed by comparative gene expression profiling

status: Public on May 01 2014

city: Jouy en Josas

first: pierre

last: Sibille

address: domaine de Vilvert, bât 440

department: Virologie et Immunologie Moléculaires

summary: The existence of conventional dendritic cells (cDCs) has not yet been demonstrated outside mammals. In this paper, we identified bona fide cDCs in chicken spleen. Comparative profiling of global and of immune response gene expression, morphology, and T cell activation properties show that cDCs and macrophages (MPs) exist as distinct mononuclear phagocytes in chicken, resembling their human and mouse cell counterparts. Using computational analysis, core gene expression signatures for cDCs, MPs, T and B cells across chicken, human and mouse were established, which will facilitate the identification of these subsets in other vertebrates. Overall this study, by extending the newly uncovered cDC and MP paradigm to chicken, suggests that the generation of these two phagocyte lineages occurred before the reptile to mammal and bird transition in evolution. It opens avenues for the design of new vaccines and neutraceuticals that are mandatory for the sustained supply of poultry products in the expanding human population.

overall_design: Four independent replicates of RNA from 4 cellular populations have been purified  from histocompatible chicken spleens, based on surface markers and fluorecence cell sorting: putative conventional Dendritic cells  (F2+, MHC-II+ cells) ;  control B cells (BU-1+ cells; only 3 replicates  could be included in the study);  T cells  (CD3+ cells) and macrophage spleen population (MHC-II+, KUL-01+ cells).

first: Thien-Phong

last: Vu Manh

first: Hélène

last: Marty

first: Yves

last: Le Vern

first: Bernd

last: Kaspers

first: Marc

last: Dalod

first: Isabelle

last: Schwartz-Cornil

first: Pascale

last: Quéré


title: siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-1_0 ENST)

status: Public on May 15 2014

city: Regensburg

first: Julia

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

institute: University of Regensburg

summary:
Short interfering RNAs (siRNA) are widely used as tool for gene inactivation in basic research and therapeutic applications. One of the major shortcomings of siRNA experiments are sequence-specific Off-target effects. Such effects are largely unpredictable because siRNAs can affect partially complementary sequences and function like microRNAs (miRNAs), which inhibit gene expression on mRNA stability or translational levels.
Here we demonstrate that novel, enzymatically generated siRNA pools - referred to as siPools - containing up to 60 accurately defined siRNAs eliminate Off-target effects. This is achieved by the low concentration of each individual siRNA diluting sequence-specific Off-target effects below detection limits. In fact, whole transcriptome analyses reveal that single siRNA transfections can severely affect global gene expression. However, when complex siRNA pools are transfected, almost no transcriptome alterations are observed. Taken together, we present enzymatically-produced complex but accurately defined siRNA pools with potent On-target silencing but without detectable Off-target effects.

overall_design: To demonstrate the reduction of Off-target gene deregulation by use of complex siRNA pools (siPools), a single siRNA targeting human SCYL1 was transfected alone or in combination with 14 or 59 other siRNAs at a total siRNA concentration of 3 nM in human Hela cells. Mock transfected cells served as negative control. Every sample was tested in biological triplicates. Total RNA was extract 48h after transfection for affimetrix expression analysis.

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