title: Gene expression profiles of spleen, liver and head kidney in turbot (Scophthalmus maximus) along the infection process with Philasterides dicentrarchi using an immune-enriched oligo-microarray

status: Public on Jan 24 2012

city: Lugo

first: Adrian

middle: Millan

last: Perez

state: Lugo

address: Facultad Veterinaria, Campus Universitario Pabellon IV 2 superior

department: Acuigen

country: Spain

institute: Universidad Santiago Compostela

summary: We evaluated the expression profiles of turbot in spleen, liver and head kidney across five temporal points of the Philasterides dicentrarchi infection process using an 8x15K Agilent oligo-microarray. The microarray included 2,176 different 5-fold replicated gene probes designed from a turbot 3’ sequenced EST database. We were able to identify 221 differentially expressed (DE) genes (8.1% of the whole microarray), 113 in spleen, 83 in liver and 90 in head kidney, in at least one of the 5 temporal points sampled for each organ. Most of these genes could be annotated (83.0%) and functionally categorized using GO terms (69.1%) after the additional sequencing of DE genes from the 5’ end. Many DE genes were related to innate and acquired immune functions. A high proportion of DE genes were organ-specific (70.6%), although their associated GO functions showed notable similarities in the three organs. The most striking difference in functional distribution was observed between the up- and down-regulated gene groups. Up-regulated genes were mostly associated to immune functions, while down-regulated ones mainly involved metabolism-related genes. Genetic response appeared clustered in a few groups of genes with similar expression profiles along the temporal series. The information obtained will aid to understand the turbot immune response and will specifically be valuable to develop strategies of defense to P. dicentrarchi to achieve more resistant broodstocks for turbot industry.

overall_design: We were interested in analyzing the response of turbot as species to P. dicentrarchi in three of the main immune organs (spleen, liver and head kidney) along a temporal series representing the main episodes of infection (1d, 3d, 7d, 15d, 25d). Accordingly, individual samples were pooled at each sampling point to average interindividual variation. A single control point (time 0; non-injected) was used since a very slight effect of injection on gene expression was previously reported in these three organs in turbot. Five fish were sacrificed on day 0 to be used as the unique control in the experiment and one hundred fifty were challenged with a highly virulent strain of P. dicentrarchi as previously described (Paramá et al., 2003).  Groups of five fish were sacrificed at 1d, 3d, 7d, 15d and 25d post-challenging. Equal amounts of spleen, liver and head kidney were sampled from each fish, pooled per organ at each sampling point and immediately stored in liquid nitrogen.

first: B

middle: G

last: Pardo

first: A

last: Millán

last: Gómez-Tato

first: C

last: Fernández

last: Bouza

first: J

last: Álvarez-Dios

first: S

last: Cabaleiro

last: Lamas

middle: M

last: Leiro

first: P

last: Martínez


title: Recurrent genomic instability of chromosome 1q in neural derivatives of human embryonic stem cells

status: Public on Jan 25 2012

city: Evry

first: nathalie

last: lefort

address: 5 rue Henri Desbruères

country: France

institute: INSERM

type: Genome variation profiling by genome tiling array

summary: array-CGH analysis of human neural stem cells derived from human ES cells during long term in vitro culture

overall_design: array-CGH analysis of human neural stem cells derived from human ES cells comparing control genomic DNA

first: Christine

last: Varela

first: Jérome

middle: A

last: Denis

last: Polentes

first: Maxime

last: Feyeux

first: Sophie

last: Aubert

first: Benoite

last: Champon

first: Geneviève

last: Piétu

first: Marc

last: Peschanski

first: Nathalie

last: Lefort


title: Genome-wide transcriptional profiling of the cell envelope stress response of Listeria monocytogenes

city: Groningen

first: Maarten

last: Mols

address: Nijenborgh 7

country: Netherlands

institute: University of Groningen

summary: The Gram-positive bacterium Listeria monocytogenes is widely distributed in the environment and capable of causing food-borne infections in susceptible individuals. In this study, we investigated the cell envelope stress response in L. monocytogenes. Whole-genome transcriptional profiling was performed to investigate the response upon exposure to the cell wall antibiotic cefuroxime. Differential expression (≥ 2-fold difference) of 558 genes was observed, corresponding to 20% of the L. monocytogenes genome. The majority of genes strongly induced by cefuroxime exposure have cell envelope-related functions, including the dlt-operon, genes encoding penicillin-binding proteins, and members from the LiaRS regulon. The virulence-associated genes dacA and lmo2714 were up-regulated upon cefuroxime exposure, whereas PrfA-regulated virulence genes, required for invasion and intracellular replication, were repressed. A large overlap was observed between the cefuroxime stimulon and genes known to be induced in L. monocytogenes in blood and during intracellular infection, indicating that the cell envelope stress response is active at various stages of the infectious process. Genes involved in stress tolerance (htrA, ctc) and signal transduction (lisRK) were also found among the highly up-regulated genes. We analysed the roles of the two-component systems LisRK and CesRK, showing that activation of the most highly cefuroxime-induced genes was LisR- and CesR-dependent. Using genetic analyses, we showed that several genes of the cefuroxime stimulon contribute to the innate resistance of L. monocytogenes to cefuroxime and tolerance to other cell envelope-perturbing conditions. Collectively, these findings demonstrate central roles for LisRK and CesRK in orchestrating the cell envelope stress response in L. monocytogenes.

overall_design: Cefuroxime induced expression was measured in the wildtype, lisR deletion mutant and, cesR deletion mutant after 60 minutes of exposure and compared to unexposed control samples. Multiple technical and biological replicates where analyzed with or without the dyes-swapped.

first: Pia

middle: K

last: Nielsen


title: The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair

status: Public on Jan 20 2012

city: Würzburg

first: Kai

last: Papenfort

state: Würzburg

address: Josef-Schneider Str.2/BAU D15

department: RNA Biology

country: Germany

institute: IMIB Würzburg

summary: SgrS RNA is a model for the large class of Hfq-associated small RNAs that act to post-transcriptionally regulate bacterial mRNAs. The function of SgrS is well-characterized in non-pathogenic Escherichia coli where it was originally shown to counteract glucose-phosphate stress by acting as a repressor of ptsG mRNA which encodes the major glucose transporter. We have discovered new SgrS targets in Salmonella Typhimurium, a pathogen related to E. coli, which recently acquired a quarter of all genes by horizontal gene transfer. We demonstrate that the conserved short seed region of SgrS that recognizes ptsG was recruited to target the Salmonella-specific sopD mRNA of a secreted virulence protein. The SgrS-sopD interaction is exceptionally selective; we find that sopD2 mRNA whose gene arose from sopD duplication during Salmonella evolution, is deaf to SgrS owing to a non-productive G:U pair in the potential SgrS-sopD2 RNA duplex versus G:C in SgrS-sopD. In other words, SgrS discriminates the two virulence factor mRNAs at the level of a single hydrogen bond. Our study suggests that bacterial pathogens employ their large suites of conserved Hfq-associated regulators to integrate horizontally acquired genes into existing post-transcriptional networks, just as conserved transcription factors are recruited to tame foreign genes at the DNA level. The results graphically illustrate the importance of the seed regions of bacterial small RNAs to select new targets with high fidelity, and argue that target predictions must consider all-or-none decisions by individual seed nucleotides.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: To determine the targets of the small regulatory RNA SgrS in S. Typhimurium, we looked at the effect of a short pulse of SgrS over-expression on the Salmonella transcriptome. To achieve over-expression, the sgrS gene was cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. A strain carrying the pBAD plasmid w/o insert was used as negative control. 3 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674–1688.

first: Dimitri

last: Podkaminski

first: Jay

last: Hinton

first: Jörg

last: Vogel


title: Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (Expression)

city: Lausanne

first: Ruben

middle: C

last: Hartkoorn

state: Vaud

address: SV 3533 (Bâtiment SV) Station 19

department: GHI/SV

country: Switzerland

institute: EPFL

type: Expression profiling by genome tiling array

summary: The genome wide transcriptome analysis to identify the M.tuberculosis sigma factor Rv3286c (SigF) dependent transcripts as well as Pristimaycin induced transcripts

overall_design: Pristinamycin induced transcripts were identified by comparing the cDNA extracted from H37Rv::pMY769 with and without pristinamycin (3 biological replicates). SigF controlled transcripts were identified by comparing the cDNA extracted from H37Rv::pMYsigF with and without pristinamycin (4 biological replicates).

first: Claudia

last: Sala

first: Swapna

last: Uplekar

first: Philippe

last: Busso

first: Jacques

last: Rougemont

first: Stewart

middle: T

last: Cole


title: Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (ChIP-chip)

type: Genome binding/occupancy profiling by genome tiling array

summary: The genome wide ChIP-on-chip analysis to identify the DNA binding sites for the M.tuberculosis sigma factor Rv3286c (SigF)

overall_design: SigF binding sites were determined by microarray analysis of anti-sigF immunoprecipitated DNA from H37Rv(ΔrsbW/sigF)::pmySigF compared to  H37Rv(ΔrsbW/sigF)::pMY769 (both cultured with pristinamycin for 3 days). 4 biological replicates were performed.


title: Gene expression profile of Candida albicans in response to murine IL17A

status: Public on Jan 18 2012

city: PERUGIA

first: LUIGINA

last: ROMANI

address: VIA DEL GIOCHETTO

department: Department of Experimental Medicine and Biochemical Sciences

country: Italy

institute: University of Perugia

summary: Global transcriptional profiling revealed that IL-17A induced artificial nutrient starvation conditions in Candida albicans, resulting in a downregulated target of rapamycin (TOR) signaling pathway and in increased autophagic responses and intracellular cAMP.

overall_design: We used microarray to detail the global programme of gene expression underlying IL17A sensing by Candida albicans at different time points (T0_0h T1_4h, T2_24h) and identified distinct classes of up-regulated and down regulated genes.

first: Luigina

last: Romani


title: Binding pattern and chromatin modifications induced by AML1/ETO in human hematopoietic stem/progenitor cells

city: Madrid

first: Sara

last: Alvarez

address: C/Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

summary: The AML1/ETO fusion protein, which is present in 10% to 15% of cases of acute myeloid leukemia, is known to repress myeloid differentiation genes through DNA binding and recruitment of chromatin-modifying proteins and transcription factors in target genes. ChIP-chip analysis of human hematopoietic stem/progenitor cells transduced with the AML1/ETO fusion gene enabled us to identify 1168 AML1/ETO target genes, 103 of which were co-occupied by HDAC1 and had lost the hyperacetylation at histone H4 marks and 264 of which showed a K9 trimethylation at histone H3. Enrichment of genes involved in hematopoietic differentiation and in specific signaling pathways was observed in the presence of these epigenetic modifications associated with an inactive chromatin status. Furthermore, AML1/ETO target genes had a significant correlation between the chromatin marks studied and transcriptional silencing.

overall_design: ChIP-chip comparison of human hematopoietic stem/progenitor cells (HSPCs) retrovirally transduced with the AML1/ETO fusion protein with HSPCs transduced with an empty vector (Mulloy et al., Blood, 2002) using antibodies tagging the AML1/ETO fusion protein, the HDAC1 protein, as well as H4Ac and H3K9m3 chromatin modifications.

first: Alba

last: Maiques-Díaz

first: Fu-Sheng

last: Chou

first: Mark

last: Wunderlich

first: Gonzalo

last: Gómez-López

first: Filipe

middle: V

last: Jacinto

first: Sandra

last: Rodrguez-Perales

first: MariaJose

last: Larrayoz

last: Calasanz

first: James

last: Mulloy

first: Juan

last: Cigudosa


title: aCGH study of iPS cells from two normal subjects and two Parkinson's disease patients with parkin mutations

status: Public on Jan 21 2012

city: Buffalo

first: Jian

last: Feng

state: NY

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

country: USA

institute: State University of New York at Buffalo

summary: Parkinson's disease (PD) is defined by the degeneration of nigral dopaminergic (DA) neurons and can be caused by monogenic mutations of genes such as parkin. The lack of phenotype in parkin knockout mice suggests that human nigral DA neurons have unique vulnerabilities. Here we generate induced pluripotent stem cells from normal subjects and PD patients with parkin mutations. We demonstrate that loss of parkin in human midbrain DA neurons greatly increases the transcription of monoamine oxidases and oxidative stress, significantly reduces DA uptake and increases spontaneous DA release. Lentiviral expression of parkin, but not its PD-linked mutant, rescues these phenotypes. The results suggest that parkin controls dopamine utilization in human midbrain DA neurons by enhancing the precision of DA neurotransmission and suppressing dopamine oxidation. Thus, the study provides novel targets and a physiologically relevant screening platform for disease-modifying therapies of PD.

overall_design: Genomic DNA was isolated from each of the four lines of iPSCs and labeled with Cy5. Pooled sex mismatched normal human genomic DNA was labeled with Cy3. Both samples are hybridized together on RPCI 21K BAC aCGH array.

first: Houbo

last: Jiang

first: Yong

last: Ren

first: Eunice

middle: Y

last: Yuen

first: Ping

last: Zhong

first: Mahboobe

last: Ghaedi

first: Zhixing

last: Hu

first: Gissou

last: Azabdaftari

first: Kazuhiro

last: Nakaso

first: Zhen

last: Yan


title: Expression analysis of laser cut germaria vs laser cut apex of testes

city: Urbana

first: Amy

last: Cash

state: IL

address: 1206 W. Gregory Dr

department: Biology

institute: University of Illinois

summary: Here we used laser cutting microdissection and RNA amplification to profile the gene expression in wildtype female germaria and male apex of the testes.  These tissue contain germline stem cells and early dividing germ cells.  Our goal was to identify genes expressed in these cell types.

overall_design: A direct microarray design of laser cut germaria vs laser cut apex of testes.  Four biological replicates are included with two dye-swaps.

first: Justen

last: Andrews


title: Trypanosoma cruzi gene expression study in response to gamma-radiation

city: Belo Horizonte

first: Priscila

last: Grynberg

state: Minas Gerais

address: Avenida Antonio Carlos, 6627

department: Departamento de Bioquímica e Imunologia

country: Brazil

institute: Universidade Federal de Minas Gerais

summary: Trypanosoma cruzi is an organism highly resistant to ionizing radiation. Following a dose of 500 Gy of gamma radiation, the fragmented genomic DNA is gradually reconstructed and the pattern of chromosomal bands is restored in less than 48 hours. Cell growth arrests after irradiation but, while DNA is completely fragmented, RNA maintains its integrity. In this work we compared the transcriptional profiles of irradiated and non-irradiated epimastigotes at different time points after irradiation using microarray. In total, 273 genes were differentially expressed; from these, 160 were up-regulated and 113 down-regulated. We found that genes with predicted functions are the most prevalent in the down-regulated gene category. Translation and protein metabolic processes, as well as generation of precursor of metabolites and energy pathways were affected. In contrast, the up-regulated category was mainly composed of obsolete sequences (which included some genes of the kinetoplast DNA), genes coding for hypothetical proteins, and Retrotransposon Hot Spot genes. Finally, the tyrosyl-DNA phosphodiesterase 1, a gene involved in double-strand DNA break repair process, was up-regulated. Our study demonstrated the peculiar response to ionizing radiation, raising questions about how this organism changes its gene expression to manage such a harmful stress.

overall_design: To evaluate the gamma radiation effect on T. cruzi epimastigote cells, two identical and independent experiments (biological replicates) were performed in triplicate. Each triplicate was composed of seven samples: cell culture growth control (not used in the microarray experiments), non-irradiated cells (used as reference sample in the microarray analysis), and five irradiated samples that had their RNA extracted immediately after irradiation (or i.a.i.), at 4, 24, 48, and 96 hours post-irradiation. Triplicates were pooled after the RNA extraction and before the purification/amplification steps. Each pool corresponding to one of the five time points was hybridized twice against the reference pool from each experiment, applying a reference time-course dye-swap design. Thus, four microarray slides for each time point were produced, two for each biological replicate, totaling 20 slides.

first: Danielle

last: Passos-Silva

first: Marina

last: Mourão

first: Roberto

last: Hirata-Jr

first: Andrea

last: Macedo

first: Carlos

middle: R

last: Machado

first: Daniella

last: Basrtholomeu

first: Gloria

last: Franco


title: Expression analysis of Aspergillus nidulans OE::rsmA

status: Public on Jan 17 2012

city: Carlisle

first: Dana

middle: Jasmine

last: Wohlbach

state: PA

institute: Dickinson College

summary: Investigation of whole genome gene expression level changes in Aspergillus nidulans OE::rsmA compared to wild-type RDIT9.32 (veA).

overall_design: A twelve array study using total RNA recovered from six separate cultures of Aspergillus nidulans wild-type RDIT9.32 (veA) and six separate cultures of Aspergillus nidulans overexpressing rsmA (restorer of secondary metabolism A), using custom-designed, four-plex arrays.  The experiment was divided into two runs.  In the first run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans carrying a plasmid overexpressing rsmA under the control of the gpdA promoter were assayed.  In the second run, three biological replicates each of Aspergillus nidulans wild-type RDIT9.32 (veA) and Aspergillus nidulans overexpressing rsmA at the native locus under the control of the gpdA promoter were assayed.

middle: J

first: Audrey

middle: P

last: Gasch

first: Wenbing

last: Yin

first: Nancy

last: Keller


title: Three commercial array platforms compared for DNA copy number detection with DNA isolated from FFPE tissue [NimbleGen]

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

institute: Vrije Universiteit Medical Center

summary: Formalin-fixed, paraffin-embedded (FFPE) archival tissue is an important source of DNA material. The most commonly used technique to identify copy number aberrations from chromosomal DNA in tumorigenesis is array comparative genomic hybridization (aCGH). Although copy number analysis using DNA from FFPE archival tissue is challenging, several research groups have reported high quality and reproducible DNA copy number results using aCGH.   Aim of the present study is to compare aCGH platforms suitable for copy number analysis using FFPE derived DNA. Two dual channel aCGH platforms (Agilent and NimbleGen) and a single channel SNP based platform (Affymetrix), were evaluated using seven FFPE colon cancer samples, median absolute deviation (MAD), deflection, signal-to-noise ratio (SNR) and DNA input requirements were used as quality criteria.  Large differences were observed in MAD values and deflection between platforms; Agilent and NimbleGen showed better MAD values (0.13 for both) compared to Affymetrix (0.22). Contrary, Affymetrix showed a better deflection of 0.94, followed by 0.71 for Agilent and 0.51 for NimbleGen. Since the deflection compensates for the MAD the Signal to Noise Ratios (SNR) were comparable; Agilent ranks first, Affymetrix second and NimbleGen third with SNRs of 3.9, 3.6 and 3.3 respectively.  DNA input amounts of 40ng are sufficient for high quality profiles with Affymetrix. For Agilent DNA input amounts of 50ng are sufficient for high quality profiles. For results of similar quality NimbleGen requires at least 100ng.  Copy number analysis using DNA derived from FFPE archival material is feasible and shows reproducible results on high-resolution copy number platforms. Input amounts of DNA from FFPE material lower than recommended still yield high quality profiles without additional amplification steps.

overall_design:
Overall study comprises 6 samples analyzed across three platforms with an additional dilution range (5 concentrations) of a seventh sample on two platforms.
This Series represents NimbleGen platform-derived data.

first: Oscar

last: Krijgsman

last: Israeli

first: Josien

last: Haan

first: Hendrik

middle: F

last: van Essen

first: Serge

last: Smeets

first: Paul

last: Eijk

first: Renske

middle: D

last: Steenbergen

first: Klaas

last: Kok

first: Sabine

last: Tejpar

first: Gerrit

last: Meijer

first: Bauke

last: Ylstra


title: Role of the SaeRS two-component regulatory system in Staphylococcus epidermidis autolysis and biofilm formation

status: Public on Jan 12 2012

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:
Background: Staphylococcus epidermidis (SE) has emerged as one of the most important causes of nosocomial infections. The SaeRS two-component signal transduction system (TCS) influences virulence and biofilm formation in Staphylococcus aureus. The deletion of saeR in S. epidermidis results in impaired anaerobic growth and decreased nitrate utilization. However, the regulatory function of SaeRS on biofilm formation and autolysis in S. epidermidis remains unclear.
Results: The saeRS genes of SE1457 were deleted by homologous recombination. The saeRS deletion mutant, SE1457DsaeRS, exhibited increased biofilm formation that was disturbed more severely (a 4-fold reduction) by DNase I treatment compared to SE1457 and the complementation strain SE1457saec. Compared to SE1457 and SE1457saec, SE1457DsaeRS showed increased Triton X-100-induced autolysis (approximately 3-fold) and decreased cell viability in planktonic/biofilm states; further, SE1457DsaeRS also released more extracellular DNA (eDNA) in the biofilms. Correlated with the increased autolysis phenotype, the transcription of autolysis-related genes, such as atlE and aae, was increased in SE1457DsaeRS. Whereas the expression of accumulation-associated protein was up-regulated by 1.8-fold in 1457DsaeRS, the expression of an N-acetylglucosaminyl transferase enzyme (encoded by icaA) critical for polysaccharide intercellular adhesion (PIA) synthesis was not affected by the deletion of saeRS.
Conclusions: Deletion of saeRS in S. epidermidis resulted in an increase in biofilm-forming ability, which was associated with increased eDNA release and up-regulated Aap expression. The increased eDNA release from SE1457DsaeRS was associated with increased bacterial autolysis and decreased bacterial cell viability in the planktonic/biofilm states.

overall_design: Comparision between SE1457 wild type strain and SA1457 SaeRS mutant strain after 4 hours and 12 hours of growth

first: Qiang

last: Lou

first: Tao

last: Zhu

first: Jian

last: Hu

first: Haijing

last: Ben

first: Jinsong

last: Yang

first: Fangyou

last: Yu

first: Jingran

last: Liu

first: Yang

last: Wu

first: Adrien

last: Fischer

first: Patrice

last: Francois

first: Jacques

last: Schrenzel

first: Di

last: Qu


title: Effect of Doxycycline on Wolbachia and Brugia malayi adult female worms in vivo

status: Public on Jan 16 2012

city: St. Louis

first: Michael

last: Heinz

state: MO

address: 4320 Forest Park Blvd.

department: Genetics

institute: Washington University School of Medicine

summary: Doxycycline treatment affects gene expression in Wolbachia and Brugia malayi adult female worms in vivo

platform_organism: Wolbachia endosymbiont strain TRS of Brugia malayi

overall_design: Two biological replicates of female RNA used for hybridization, in duplicate, to examine the gene expression changes in Wolbachia and Brugia

first: Ramakrishna

last: Rao

first: Seth

last: Crosby

first: Gary

last: Weil


status: Public on Jan 15 2012

city: Albuquerque

first: Anne

last: Ruffing

state: NM

department: Bioenergy and Defense Technologies

institute: Sandia National Laboratories

summary: Gene Expression Analysis of Curdlan Production in Agrobacterium sp. ATCC 31749

overall_design: Two conditions are compared with four biological replicates of each condition, corresponding to eight total samples. The control condition was sampled at 22 hours during the exponential growth phase when no curdlan is produced. The second condition was sampled at 70 hours after the initiation of curdlan production, corresponding to approximately 100 hours.

first: Marlene

last: Castro-Melchor

first: Wei-Shou

first: Rachel

last: Chen


title: SNAI1 induced epithelial to mesenchymal transition miRNA study in time course

status: Public on Jan 13 2012

city: Luxembourg

first: Antony

last: Le Bechec

address: 162a avenue de la faïencerie

department: Life sciences research unit

country: Luxembourg

institute: University of Luxembourg

summary: To identify miRNAs participating in SNAI1-orchestrated regulatory pathways, we analysed time-resolved microarray data of SNAI1-induced EMT, obtained during conditional expression of SNAI1 in a “Tet-Off” MCF7-SNAI1 breast carcinoma cell model (Vetter et al, 2009).

overall_design: miRNA time series study for 7 times points (4h, 8h, 12h, 24h, 48h, 72h, 96h) in 3 replicates. For each time point, we compared induced and non-induced samples. Overall, we have 42 samples (21 hybridizations).

first: Michèle

last: Moes

last: Le Béchec

first: Christina

last: Laurini

first: Aliaksandr

last: halavatyi

first: Guillaume

last: Vetter

first: Evelyne

last: Friederich


title: The expression profiles of extracellular matrix-related genes in the presence or absence of IL-17A or -17F as measured with the PCR array in systemic sclerosis (SSc) dermal fibroblasts

status: Public on Jan 01 2012

city: Kumamoto

first: Taiji

last: Naashima

address: 1-1-1 Honjo

department: Department of Dermatology and Plastic Surgery

country: Japan

institute: Faculty of Life Sciences, Kumamoto University

summary: We examined the effect of IL-17 signaling pathway on extracellular matrix (ECM) expression and the involvement of IL-17 signaling pathway in pathogenesis of SSc. To identify differences in the expression pattern of ECM genes in IL-17A- or IL-17F-treated cells, we performed PCR array analysis, consisting of 84 ECM-related genes. Normal human dermal fibroblasts were cultured until they were confluent, and then stimulated with IL-17A or IL-17F for 12 hours, and total RNA was extracted. A mixture of equal amounts of mRNAs from three normal fibroblasts was prepared in the presence or absence of IL-17A or -17F, and mRNA expression profile was evaluated using PCR Array.

overall_design: Normal fibroblasts were obtained by skin biopsies from 3 healthy donors.  Fibroblasts from donors were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was pooled prior to gene expression analysis.

last: Nakashima


title: Real-time quantitative PCR analysis of 88 microRNAs involved in human cell differentiation and development  in systemic sclerosis (SSc) dermal fibroblasts

summary: Normal fibroblasts and SSc fibroblasts between the third and six subpassages were used for experiments. Total RNA was extracted from culture cells with ISOGEN (Nippon Gene, Tokyo, Japan). MicroRNA isolation from total RNA was performed using RT2 qPCR-Grade miRNA Isolation Kit (SA Bioscience). For RT2 Profiler PCR Array (SABioscience), microRNAs were reverse-transcribed into first strand cDNA using RT2 miRNA First Strand Kit (SABiosciences). A mixture of equal amounts of cDNAs from 5 normal fibroblasts or 5 SSc fibroblasts was prepared. The cDNA was mixed with RT2 SYBR Green/ROX qPCR Master Mix and the mixture was added into a 96-well RT2 miRNA PCR Array (SABiosciences) that included primer pairs for 88 human microRNAs.

overall_design: Human dermal fibroblasts were obtained by skin biopsy from the affected areas (dorsal forearm) of 5 patients with diffuse cutaneous SSc and <2 years of skin thickening. Control fibroblasts were obtained by skin biopsies from 5 healthy donors. Control donors were each matched with a SSc patient for age, sex, and biopsy site.

first: Noritoshi

last: Honda


title: Thermotoga species transcription on glucose and a mix of polysaccharides

status: Public on Jan 05 2012

city: Raleigh

first: Andrew

last: Frock

state: NC

address: 840 Main Campus Drive, Partners II, Room 3304

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

summary: Hyperthermophilic bacteria of the genus Thermotoga are known to utilize a wide range of simple and complex polysaccharides. T. maritima's transcriptional response to a variety of mono- and poly-saccharides was previously studied to assign functions to genes involved in carbohydrate uptake and utilization. To compare and contrast closely-related members of the Thermotoga genus, a four-species microarray was developed by expanding a whole genome T. maritima array to include unique genes from three other species (T. neapolitana, T. petrophila, and T. sp. RQ2). This multi-species array was used to investigate the diversity of the genus, specifically the response of each of the four species to a mixture of polysaccharides (galactomannan, glucomannan, xylan, pectin, lichenan, and carboxymethyl cellulose).

sample_organism:
Thermotoga maritima
Thermotoga neapolitana
Thermotoga petrophila
Thermotoga sp. RQ2

overall_design: RNA derived from glucose-grown cultures (glu) was compared to RNA derived from polysaccharide-grown cultures (poly) using a dye swap setup.

first: A

first: S

last: Gray

first: R

last: Kelly


title: Expression data from chick cochlea and utricle

city: Portland

first: Peter

last: Gillespie

state: OR

address: L335A / 3181 SW Sam Jackson Pk Rd

department: Oregon Hearing Research Center

institute: Oregon Health & Science University

summary: Inner ear auditory and vestibular tissues differ in their responses to mechanical stimuli.

overall_design: Chick cochlea and utricle sensory epithelia were microdissected at E20-E21.  RNA was extracted and cRNA hybridized to Affymetrix microarrays.

first: Kateri

last: Spinelli


title: Candidate SNPs association with APOC3

status: Public on Jan 11 2012

city: houston

first: Ariel

last: Brautbar

address: 1 baylor plaza

institute: Baylor College of Medicine

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: ApoC-III is a proatherogenic protein associated with elevated triglycerides; its deficiency is associated with reduced atherosclerosis. Mixed dyslipidemia, characterized by elevated triglyceride and apoC-III levels and low HDL cholesterol level, with or without elevated LDL cholesterol, increases cardiovascular disease risk and is commonly treated with combined statin and fibrate therapy. We sought to identify single nucleotide polymorphisms (SNPs) associated with apoC-III level response to combination therapy with statins and fenofibric acid (FA) in individuals with mixed dyslipidemia. Participants in a multicenter, randomized, double-blind, active-controlled study examining response to FA alone and in combination with statin were genotyped for candidate SNPs. Association between genotyed SNPs and APOC3 response to therapy was conducted

overall_design: We sought to identify single nucleotide polymorphisms (SNPs) associated with apoC-III level response to combination therapy with statins and fenofibric acid (FA) in individuals with mixed dyslipidemia. Participants in a multicenter, randomized, double-blind, active-controlled study examining response to FA alone and in combination with statin were genotyped for candidate SNPs. Genomic DNA extracted from peripheral blood was genotyped using a custom GoldenGate bead array encompassing 384 SNPs (Illumina). Multivariate linear regression and 2-way ANOVA for percent change in apoC-III level were performed between the groups receiving FA alone compared with FA+statin compared with statin alone.


city: Huntsville

first: Luciano

middle: Matias

last: Matzkin

state: Alabama

address: 301 Sparkman Drive

department: Biological Sciences

institute: University of Alabama in Huntsville

summary:
In internally fertilizing organisms, mating involves a series of highly coordinated molecular interactions between the sexes that occur within the female reproductive tract.  In species with promiscuous mating systems, traits involved in postcopulatory interactions are expected to evolve rapidly, potentially leading to postmating-prezygotic (PMPZ) reproductive isolation between diverging populations.  Here, we use a novel study design to investigate the postmating transcriptional response of Drosophila mojavensis female reproductive tracts following copulation with either conspecific or heterospecific (D. arizonae) males at three time points postmating.  Relatively few genes (15 total) were transcriptionally regulated in the female lower reproductive tract in response to conspecific mating.  Heterospecifically-mated females exhibited significant perturbations in the expression of the majority of these genes, and also downregulated transcription of a number of others, including several involved in mitochondrial function.  These striking regulatory differences indicate failed postcopulatory molecular interactions between the sexes consistent with the strong PMPZ isolation observed for this cross.  We also report, for the first time, the transfer of male mRNA transcripts to females during copulation.  These included transcripts from male accessory-gland proteins (ACPs), a finding with potentially broad implications for understanding postcopulatory molecular interactions between the sexes.
Dataset from Postmating transcriptional changes in reproductive tracts of con- and heterospecifically-mated Drosophila mojavensis females Bono, JM, Matzkin,LM, Kelleher, ES, and Markow, MA, Proceedings of the National Academy of Sciences, USA.

overall_design: The treatments were con- and heterospecific mated D. mojavensis females.  Three different post-copulation times points were assayed, 15 minutes, 2 hours and 6 hours.  For each time point there were two independent replicates.  Additionally, two replicates of a virgin D. mojavensis female control were assayed.  A total of 14 arrays.  All RNA extractions were from the lower reproductive tract of females.

first: Jeremy

last: Bono

first: Erin

middle: S

last: Kelleher

first: Therese

last: Markow


title: Health Status, Infection and Disease in California Sea Lions (Zalophus californianus) studied using a canine microarray platform and machine-learning approaches

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

institute: University of Ferrara

summary: In this study we assessed the utility of a microarray to identify changes in gene expression predictive of health status by interrogating blood samples from California sea lions in rehabilitation.

overall_design: 73 California sea lion blood samples. 28 Females and 45 males. Animals were divided into 4 groups based on preliminary diagnosis at the rehabilitation center: domoic acid toxicosis (n=33, DAT), Leptospirosis infection (n=24, Lepto), control (n=4, Healthy) and other diseases (n=12, Outgroup).

first: James

last: Ryan


title: Transcriptional analysis of common carp (Cyprinus carpio L.) immune response against Cyprinid herpesvirus 3 (CyHV-3).

city: Liege

first: Leonor

last: Palmeira

address: Bd Colonster 20

department: Faculty of Veterinary Medicine

country: Belgium

institute: University of Liege

summary: Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV), is the aetiological agent of an emerging and lethal disease in common and koi carp. In this work we studied the immune response of two genetically different lines of common carp (Polish K and Polish R3) infected with CyHV-3 by immersion. The two carp lines presented a 20% difference in survival rate and, furthermore, significant difference in virus loads measured at day 3 post infection (p.i.). Microarray analysis revealed that 581 genes in line K (330 up-regulated, 251 down-regulated) and 107 genes in line R3 (77 up-regulated, 30 down-regulated), were at least 2-fold differentially expressed at day 3 p.i. compared to day 0. Genes which were at least 4-fold differentially expressed in both lines were selected as potential markers of an infection of common carp by CyHV-3. This group includes 17 up-regulated and only 1 down-regulated genes. In addition, microarray analysis revealed no significant differences in gene expression between line K and R3 at day 0. At day 3 p.i. there were, however, 76 genes that were at least 2-fold differentially expressed between the two lines. The kinetics of expression of T cell markers and selected cytokines indicate for higher activation of immune response in more resistant R3 line. Thus, our study revealed that differences in resistance to CyHV-3 between two carp lines can be correlated with differentially expressed immune-related genes.

platform_organism:
Cyprinus carpio
Cyprinid herpesvirus 3

overall_design: The experiment included four biological replicates with no dye swaps for (i) each strain (K and R3) and (ii) each condition (day 0 and day 3).


title: IgE reactivity profiling in an asthma affected cohort

status: Public on Jan 03 2012

city: Perugia

first: tania

last: dottorini

address: via del Giochetto

department: Dept. Exp.Medicine and Bichem. Sci.

institute: University of Perugia

summary: Background: Most asthmatic patients have high serum levels of IgE directed against common environmental allergens such as house dust mite, animal danders and moulds. However the presence of specific IgE against individual allergens alone does not account for asthma. Many individuals are atopic but not asthmatic. Precise knowledge of the serum IgE specificity repertoire in asthmatic and non-asthmatic patients would substantially help in understanding the pathogenesis of the disease and at the same time facilitate the treatment and the implementation of preventive measures.  Methods: We developed a microarray immunoassay containing 103 common allergens to study the IgE reactivity profiles of 485 asthmatic and 342 non-asthmatic individuals from families whose members had a documented history of asthma and atopy. The results were analyzed using k-means clustering to investigate whether IgE reactivity profiles correlated with asthma, disease severity and age of onset as well as with other atopic conditions such as rhinitis, conjunctivitis and eczema. We trained an artificial neural network (ANN) using the serum reactivity data to identify individuals as asthmatic and non-asthmatic.   Results: Individual sera showed clear differences in the number and the combinations of allergens recognized as well as in the level of specific IgE. While the presence of specific IgE against single allergens correlated poorly with the pathological conditions examined k-means clustering analysis unraveled that a particular profile was significantly associated with asthma (p <1E-8). An ANN-based algorithm, calibrated with the profile reactivity data correctly classified as asthmatic or non-asthmatic 78% of the individual examined.  Conclusions: Our analysis demonstrates that asthma may be a higher-order phenomenon related to patterns of response and not attributable to single antibody reactions. This information sheds new light on the risk of developing the disease and can be readily utilized in combination with an ANN-based tool to distinguish asthmatic and non-asthmatic individuals on the basis of their serum reactivity profile.

overall_design:
The study consisted of a total of 872 sera samples: 485 individuals were diagnosed with asthma, 342 were classified as non asthmatic, a remaining 45 were classified as unconfirmed asthma diagnosis. The serum IgE reactivity profiles were analyzed against 103 allergens representative of 11 distinct allergen classes.
Quantification of bound IgE: The fluorescence signal was acquired using ProScanArray Express™ version 3.0 software. PMC reading values of individual spots were corrected against the internal negative control to identify signals above background. Duplicate measurements of individual allergens were utilized. The signal collected from the allergens was interpolated with an external calibration curve to obtain the IU/ml value (see supplementary file GSE20020_IU_ml values.txt), and translated into a Class Score by plotting the data in a standard reactivity scale (see Sample data tables). Class Score values: (CLASS 0 (less than 0.35 IU/ml); CLASS 1 (0.35-0.7 IU/ml); CLASS 2 (0.71-3.5 IU/ml); CLASS 3 (3.51-17.5 IU/ml); CLASS 4 (17.51-50 IU/ml); CLASS 5 (50.01-100 IU/ml).

first: Tania

last: Dottorini

first: Gabriella

last: Sole

first: Luisa

last: Nunziangeli

first: Francesca

last: Baldracchini

first: Lenuta

last: Balaci

first: Nazario

last: Olla

first: Nicola

last: Senin

first: Silvia

last: Naitza

first: Andrea

last: Crisanti


title: Role of a Candida albicans Whi5/Nrm1 homolog in cell cycle and hyphal-specific gene expression

city: Memphis

first: Katherine

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

summary: Candida albicans is an opportunistic pathogenic fungus that is able to assume several morphologies, including yeast and hyphal growth forms. The hyphal morphology can be induced by various environmental stimuli and is accompanied by expression of a large set of hyphal-specific genes (HSGs). Cell cycle and morphogenetic programs are interconnected: notably, inhibition of cell cycle progression often causes a switch to filamentous growth. Here we identify and characterize CaNrm1, a C. albicans homolog of the S. cerevisiae Whi5 and Nrm1 transcription inhibitors that, analogous to mammalian Rb, regulate the cell cycle transcription program in the G1 phase and at the G1/S transition. CaNRM1 is able to complement the phenotypes of both whi5 and nrm1 mutants in S. cerevisiae. Deletion of CaNRM1 causes a reduction in cell size and results in increased resistance to hydroxyurea (HU), an inhibitor of DNA replication; analysis of the expression of ribonucleotide reductase, the target of HU, suggests that its transcriptional induction in response to HU is mainly dependent upon CaNrm1. Genetic epistasis analysis suggests that CaNrm1 interacts with the SBF and MBF transcription factors in S. cerevisiae and with the MBF functional homolog in C. albicans. At the transcription level, deletion of CaNRM1 causes an induction of many G1 and G1/S-specific genes. Induction of the HSGs is dampened under certain conditions in the Canrm1-/- mutant, suggesting that the cell cycle transcription program influences the morphogenetic transcription program of C. albicans.

overall_design: One aspect of the characterization of the C. albicans Whi5/Nrm1 gene was to examine how this molecule influences global gene expression.  To that end, we isolated total RNA from log-phase nrm1-/nrm1- (as well as parent/background strain) cells in two independent replicate experiments.  These samples were processed, labeled, and subsequently used for hybridization of custom C. albicans Affymetrix arrays.

first: Ayala

last: Ofir

first: Kay

last: Hofmann

first: Julia

last: Gutman

first: P

last: Rogers

first: Daniel

last: Kornitzer


title: MicroRNA expression in HMVECs: control vs. VEGF-treated vs. PEDF/VEGF-treated

status: Public on Dec 31 2011

city: Chicago

first: Dauren

last: Biyashev

address: 300 E.Superior St.

institute: Northwestern University

summary:
MicroRNA expression profiling of human microvascular endothelial cells (HMVECs) treated with either vascular endothelial growth factor (VEGF) only or in combination with the natural angiogenesis inhibitor pigment epithelial-derived factor (PEDF).

Originally we were interested in the microRNA-mediated regulation of angiogenesis by the endogenous anti-angiogenic PEDF. To identify the microRNAs involved in PEDF signaling in activated endothelial cells,  we compared the levels of microRNAs in non-treated microvascular endothelial cells, cells treated with VEGF, and cells treated with a combination of VEGF and PEDF. After treatment, total RNA content was isolated and sent for analysis to LC Sciences, LLC. They performed expression profiling and completed statistical analysis, based on which we confirmed the regulation of one of the microRNAs, mir-27b. In the following experiments, we identified the targets of mir-27b relevant for angiogenesis and confirmed our findings in zebrafish and mouse models. The manuscript describes the key role of mir-27b in determination of the endothelial tip cell fate and venous differentiation by regulating Notch ligand Delta-like ligand 4 (Dll4) and Sprouty homologue 2 (Spry2).

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Three-condition experiment: untreated (control) HMVECs vs. VEGF-treated HMVECs vs. PEDF/VEGF-treated HMVECs.

first: Olga

last: Volpert


title: miRNA expression profile in leprosy skin biopsy specimens

city: Los Angeles

first: Philip

middle: T.

last: Liu

state: CA

address: 615 Charles E Young Drive South, 410 OHRC

department: Department of Orthopaedic Surgery

institute: University of California at Los Angeles

summary:
Skin biopsy specimens of skin lesions were profiled for miRNA expression.
In this study, we indentified miRNA species that were differentially expressed in the skin lesions of either the lepromatous or tuberculoid forms of leprosy.  One miRNA species, hsa-mir-21, found in the lepromatous lesions was capable of downregulating the vitamin D-dependent antimicrobial pathway.

overall_design: Scalpel or punch skin biopsy specimens were obtained after informed consent from patients with tuberculoid leprosy and patients with lepromatous leprosy at the time of diagnosis.  Specimens were embedded in OCT medium, snap-frozen in liquid nitrogen and stored at  80°C until sectioning.

first: Robert

middle: L

last: Modlin


title: The scr circuit in Vibrio parahaemolyticus: output targets and transcriptional regulation by a c-di-GMP responsive protein

city: Iowa City

first: Linda

last: McCarter

state: Iowa

address: 3-401 BSB  51 Newton Rd

department: Microbiology

institute: University of Iowa

summary: Vibrio parahaemolyticus scr genes modulate expression of gene sets pertinent to swarming and biofilm formation. They do so by affecting the level of the second messenger c-di-GMP. Here we explore the extent of this regulation by comparing the transcriptomes of a scrABC mutant and its wild-type parental strain.  The scope of transcriptional effects modulated by c-di-GMP includes ~100 genes that are positively and negatively regulated. An elevated cellular level of c-di-GMP represses the surface sensing regulon including the genes encoding the lateral flagellar and type three secretion systems while inducing expression of genes encoding cell surface molecules and capsular polysaccharide. Expression of a few transcriptional regulators was also affected, and here we describe the role of one, CpsQ. CpsQ is one of four V. parahaemolyticus homologs in the CsgD/VpsT family of regulators, members of which have been implicated in c-di-GMP signaling. Mutations in cpsQ, like defects in another previously identified capsule regulator, cpsR, suppress the sticky phenotype of scr mutants. By using a combination of mutant and reporter analyses in Vibrio and E. coli, CpsQ is shown to be the direct positive regulator of cpsA transcription and its cpsA-activating ability is found to be responsive to the cellular level of c-di-GMP. Unexpectedly, we find that a low level of this nucleotide diminishes the stability of CpsQ. The molecular interplay in this signaling circuit is further defined by demonstrating that CpsQ is epistatic to CpsS, a negative regulator of capsule. CpsR activates cpsQ, and CpsQ can also regulate its own transcription.

overall_design: Wildtype Vibrio parahaemolyticus (LM5674) and scrABC mutant (LM6567) were grown on rich mediim agar plates and gene expression profiles were compared.

first: Rosana

middle: B

last: Ferreira

middle: M

last: Chodur

first: Luis

last: Antunes

first: E

last: Greenberg


title: Microarray analysis reveals novel regulatory genes associated with the non-aflatoxigenic Aspergillus parasiticus mutants obtained by 5-azacytosine treatment or serial mycelial transfer

city: Beaumont

first: Jeff

last: Wilkinson

state: tx

address: 635 Parson

summary: Aflatoxins are carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and Aspergillus parasiticus. Repeated serial mycelial transfer or treatment of A. parasiticus with 5-azacytidine produced mutants with a fluffy phenotype and loss of aflatoxin production. To understand how these treatments affect aflatoxin production and development, we carried out expressed sequence tag (EST)-based microarray assays to identify differentially expressed genes in clones obtained from these treatments.  Expression of 183 genes was significantly dysregulated. Of these, 38 had at least two-fold or lower expression compared to the untreated control and only two had two-fold or higher expression. The most frequent change was downregulation of genes predicted to be membrane-bound. Dysregulation of some of these may be responsible for the fluffy phenotype. Of the aflatoxin biosynthesis pathway genes only aflJ (aflS) was significantly affected by either treatment. A gene for a protein homologous to a key regulator of secondary metabolite biosynthesis (LaeA) was one of the upregulated genes and possibly could affect the activity of LaeA. Other genes known to be required for fungal developmental or aflatoxin production were not affected by the treatments. Consistent with the fluffy phenotype and the non-aflatoxigenicity of the clones obtained by either treatment, we hypothesize that the mutations cause improper development of conidiophores and specialized biosynthesis vacuoles (aflatoxisomes) needed for AF production.

overall_design: A. parasiticus wild-type (WT) and clones from serial mycelial transfer (SerTrans), and 5-azacytidine-treated (5-AC)  fungi were grown for 16 and 24 h on PDA medium. RNA was isolated from the mycelia at each time point and cDNAs were labeled with Cy3 or Cy5 dyes prior to microarray assay.


title: A novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network

city: Hong Kong

first: Hao

last: Sun

address: 306G LiHS biomedical Sciences Building

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: microRNAs (miRNAs) are non-coding RNAs that regulate gene expression post-transcriptionally, and mounting evidences support the prevalence and functional significance of their interplay with transcription factors (TFs). Here we describe the identification of a regulatory circuit between muscle miRNAs (miR-1, miR-133 and miR-206) and Yin Yang 1 (YY1), an epigenetic repressor of skeletal myogenesis.  Genome-wide identification of potential YY1 down-stream targets by combining computational prediction with expression profiling data reveals a large number of putative miRNA targets of YY1 during skeletal myoblasts differentiation into myotubes with muscle miRs rank on top of the list.

platform_organism:
Homo sapiens
Mus musculus

overall_design: Murine skeletal muscle cells (C2C12 cells) were differentiated for 0, 1 or 3 days. Total RNAs were isolated from the cells and used for array profiling of miRNA expression.

first: Huating

last: Wang


title: [URE3] Prion formation by the Candida albicans Ure2p (but not by C. glabrata Ure2p)-CgUre2

city: Bethesda

first: Huei-Fung

last: Tsai

state: MD

address: 10 Center Dr. Bldg. 10 Rm. 11N228

department: LCID

institute: NIH/NIAID

summary: [URE3] is a prion (infectious protein) of the Saccharomyces cerevisiae Ure2p, a regulator of nitrogen catabolism. We find that the Ure2p of Candida albicans and C. glabrata also regulate nitrogen catabolism. Conservation of amino acid sequence within the prion domain of Ure2p has been proposed as evidence that the [URE3] prion helps its host. We show that the C. albicans Ure2p, which does not conserve this sequence, can nonetheless form a [URE3] prion, but the C. glabrata Ure2p, which does have the conserved sequence, cannot form [URE3]. These results suggest that the sequence is not conserved to preserve prion forming ability.

overall_design: Two groups (Wild type and ure2 mutants) consisted of 4 biological replicates in which a Ure2 mutant sample was paired with the wild type strain BG14 sample. Each group included 1 reciprocally labeled sample.


title: Genome-wide gene expression analysis of human whole-blood samples in  in response to dengue disease

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

summary:
We looked at the whole-blood transcriptional profiling on dengue patients sampled within 72h of fever presentation and compared the signatures with autologous samples drawn at defervescence and convalescence and to control patients with fever of other etiology.
Our data show that the early response in patients mimics those previously only described in vitro and suggests that this innate immune responses may initiate the later adaptive immune responses.

overall_design: Total RNA obtained from whole-blood of dengue patients with fever presentation, defervescence and convalescence are compared. Also, dengue patients with fever presentation are compared with control patients which are with fever of other etiology. 119 samples are analysed, which include 31 dengue patients and 26 control patients.

first: Ling

last: Ling

first: Thomas

last: Tolfvenstam

first: Anna

last: Lindblom

first: Martin

last: Hibberd


title: MicroRNA expression profiling of quiescent and activated muscle stem cells

city: Palo Alto

middle: A

last: Rando

address: 3801 miranda ave.

department: Department of Neurology and Neurological Sciences

institute: Stanford University School of Medicine

summary: MicroRNA expression profiling during muscle stem cell activation. Quiescent muscle stem cells from uninjured muscles and activated muscle stem cells from injured muscles at indicated time points were isolated by FACS.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
MicroRNA expression profiling during muscle stem cell activation using real-time PCR based miRNA arrays. Muscle stem cells were harvested at indicated time points (0hr, 36hr, 60hr and 72hr) after injury. 3 technical replicates were performed.

Supplementary files: Raw data (Ct) and complete processed data (dCt, ddCt, fold-change) by platform.

first: Tom

middle: H

last: Cheung


title: Viral Detection Microarray Analysis of Unknown Tropical Febrile Illness Cases

city: San Francisco

first: Joseph

last: DeRisi

address: Byers Hall, Rm s403c, 1700 4th St.

department: Department of Biochemistry and Biophysics

institute: University of California San Francisco

summary:
This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua.  This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection.  We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses.  The Virochip microarray is capable of detecting known viruses and discovering novel viruses.  This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls.

Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip

overall_design: From each serum sample, total nucleic acid was extracted and used to prepare a randomly-primed dsDNA library.  These libraries were fluorescently labeled and hybrized to Virochip arrays.

first: Nathan

last: Yozwiak

first: Peter

last: Skewes-Cox

first: Mark

last: Stenglein

first: Don

last: Ganem

first: Eva

last: Harris


title: Role of the srrb in the Staphylococcus aureus gene expression

city: Rockville

first: Fatma

last: Onmus-Leone

address: 9704 Medical Center Dr.

institute: JCVI

summary: Staphylococcus aureus is a Gram-positive human pathogen causing a variety of human diseases in both hospital and community settings. This bacterium is so closely associated with prophages that it is rare to find S. aureus isolates without prophages. Two phages are known to be important for staphylococcal virulence: the beta-hemolysin (hlb) converting phage and the Panton-Valentine Leukocidin (PVL) converting phage. The hlb-converting phage is found in more than 90% of clinical isolates of S. aureus. This phage produces exotoxins and immune modulatory molecules, which inhibit human innate immune responses. The PVL-converting phage produces the two-component exotoxin PVL, which can kill human leucocytes. This phage is wide-spread among community-associated methicillin resistant S. aureus (CA-MRSA).  It also shows strong association with soft tissue infections and necrotizing pneumonia. Several lines of evidence suggest that staphylococcal prophages increase bacterial virulence not only by providing virulence factors but also by altering bacterial gene expression: 1) Transposon insertion into prophage regulatory genes, but not into the genes of virulence factors, reduced S. aureus killing of Caenorhabditis elegans.; 2) Although the toxins and immune modulatory molecules encoded by the hlb- converting phages do not function in the murine system, deletion of phiNM3, the hlb-converting phage in S. aureus Newman,  reduced staphylococcal virulence in the murine abscess formation model. 3) In a preliminary microarray experiment, prophages in S. aureus Newman altered the expression of more than 300 genes.  In this research proposal, using microarray and high-throughput quantitative RT-PCR (qRT-PCR) technologies, we will identify the effects of the two important staphylococcal phages on the gene expression of S. aureus in both in vitro and in vivo conditions. This project is intended to be completed within one year. All the data – microarray, qRT-PCR and all the primer sequences- will be made available to public 6 month after completion. Data from this project will help us to understand the role of prophages in the S. aureus pathogenesis and can lead to development of a strategy to interfere with the pathogenesis process.

overall_design: Staphylococcus aureus subsp.aureus strain Newman (reference) and Staphylococcus aureus subsp.aureus strain Newman srrb knockout(query) were grown in TSA broth.RNA samples were harvested at early log (30 min), mid log (60 min), late log(90 min), early stationary(120 min) and late stationary phase (240 min).Samples were hybridized on aminosilane coated slides with 70-mer oligos.

first: Marcus

last: Jones

first: Rosslyn

last: Maybank

first: Kenneth

last: Shatzkes

first: Fei

first: Taeok

last: Bae

first: Scott

middle: N

last: Peterson


title: Mussel (Mytilus galloprovincialis) digestive gland tissue: effects of 17β-estradiol injection in reference and Chlorpyrifos pre-exposed animals

city: Alessandria

first: Francesco

last: Dondero

address: Via Michel 11

department: Department of Environmental and Life Sciences

institute: University of Piemonte Orientale "Amedeo Avogadro"

summary:
Transcriptional profiling of mussel (Mytilus galloprovincialis) digestive gland tissue comparing control tissue with tissue obtained from animals exposed to sublethal amounts of Chlorpyrifos, animals injected into the posterior adductor muscle with 25 pico-moles 17β-estradiol (E2) and animals pre-exposed for three days to the pesticide and further injected with E2.

Background: Many pesticides have been shown to act as endocrine disrupters. Although the potencies of currently used pesticides as hormone agonists/antagonists in vitro are low compared with those of natural ligands, their ability to act via multiple mechanisms might enhance the biological effect. The organophosphate Chlorpyrifos (CHP) has been shown to be weakly estrogenic and cause adverse neurodevelopmental effects in mammals. However, no information is available on the possible endocrine effects of CHP in aquatic organisms. In the digestive gland of the bivalve Mytilus galloprovincialis, a target tissue for the action of both estrogens and pesticides, the possible effects of CHP on the responses to the natural estrogen 17β-estradiol (E2) were investigated.

Methodology/Principal findings: Mussels were exposed to CHP (4.5 mg/l, 72 hrs) and subsequently injected with E2 (6.75 ng/g dw). Responses were evaluated in CHP, E2 and CHP/E2 treatment groups at 24 h p.i. by a biomarker/transcriptomic approach. CHP and E2 induced additive, synergistic, and antagonistic effects on lysosomal biomarkers (lysosomal membrane stability, lysosome/cytoplasm volume ratio, lipofuscin and neutral lipid accumulation). Additive and synergistic effects were also observed on the expression of estrogen-responsive genes (GSTπ, catalase and 5-HTR) evaluated by RT-Q-PCR. The use of a 1.7K cDNA Mytilus microarray showed that CHP, E2 and CHP/E2, induced 81, 44, and 65 Differentially Expressed Genes (DEGs), respectively. 24 genes were exclusively shared between CHP and CHP/E2, only 2 genes between E2 and CHP/E2. Moreover, 36 genes were uniquely modulated by CHP/E2. Gene ontology annotation was used to elucidate the putative mechanisms involved in the responses elicited by different treatments.

Conclusions: The results show complex interactions between CHP and E2 in mussel digestive gland, indicating that the combination of certain pesticides and hormones may give rise to unexpected effects at the molecular/cellular level. Overall, these data demonstrate that CHP can interfere with the mussel responses to natural estrogens.

overall_design: Four-condition experiment.  Dual color competitive hybridizations. Common reference (vehicle treated animals, 0.02% Dimethyl sulfoxide, injected with 50 μl of a solution of Artificial Sea Water containing 0.05 % ethanol); Pools of six animals. Biological replicates: 4 controls, 4 Chlorpyrifos, 4 17β-estradiol, 4 Chlorpyrifos-17β-stradiol. One replicate per array.

first: Aldo

last: Viarengo

first: Laura

last: Canesi


title: Expression data from murine cardiac tissue

city: Riyadh

first: Kate

last: Collison

address: Department Biological & Medical Research

country: Saudi Arabia

institute: King Faisal Specialist Hospital & Research Centre

summary:
Gender dimorphism exists in the physiological response to diet and other environmental factors. Trans-hydrogenated fatty acid (TFA)  intake is associated with an increase in coronary heart disease (CHD), and gender differences in the incidence of CHD are well documented. Neonatal administration of Monosodium Glutamate (MSG) causes stunted heart growth and hypoplasticity; and gender dimorphism at the growth hormone axis has been demonstrated in MSG-treated rodents. The identification of gender dimorphism in cardiac nutrigenomics may provide the basis for gender-specific medicine in the future.
We used microarray analysis to examine changes in cardiac gene transcription in response to TFA and/or MSG feeding in male and female C57Bl/6J mice.

overall_design: Our study animals were bred from female C57Bl/6J mice fed a standard chow diet until 6 weeks of age whereupon they were placed on one of 4 different dietary regimens for a period of 3 weeks prior to mating. The four dietary regimens used in this study were: [1] Standard Chow (Control diet) with ad lib drinking water. [2] Standard Chow, with ad lib drinking water containing 0.64 g/L Monosodium Glutamate (MSG diet). [3] Trans fat diet of 20% (w/w) Partially Hydrogenated Vegetable Shortening containing 8.68% w/w Trans fatty acids(TFA diet).  [4] Trans fat Diet #5C4M together with ad lib drinking water containing 0.64 g/L Monosodium Glutamate (TFA+MSG diet). Following mating, the 4 groups of dams were maintained on their respective diets throughout the gestation and nursing period. Male and female offspring used in the following experiments were weighed, weaned onto the same diets and maintained on their respective dietary regimens until they reached 32 weeks of age.Cardiac tissues (8 per diet group) were used at 32 weeks for RNA extraction and hybridization on Affymetrix microarrays.

first: Marya

middle: Z

last: Zaidi


title: A specific miRNA signature correlates with complete pathological response to neoadjuvant chemo-radiotherapy in locally advanced rectal cancer

status: Public on Apr 25 2012

city: Milano

first: Francesca

last: Falcetta

address: Via La Masa, 19

department: Oncology

institute: Istituto di ricerche farmacologiche Mario Negri

summary: Background:  MicroRNAs (miRNAs) are small, non-coding, RNA molecules which regulate numerous cellular processes. Specific miRNA may be abnormally down-regulated or up-regulated in colorectal cancer and have been found associated with prognosis or response to treatments. However, no study has ever addressed their predictive role in rectal cancer. Therefore, we used microarray technology and RT-PCR to profile miRNA expression patterns in patients (pts) with rectal cancer, with the aim to identify a specific “signature” associated with pathological complete response after neoadjuvant chemo-radiotherapy.  Methods: 38 pts with locally advanced rectal cancer (cT3-4/N+) were treated with capecitabine-oxaliplatin and pelvic conformal radiotherapy (45 cGy) followed by surgery (after 6-8 weeks). Pathologic response was scored according to the tumor regression grade (TRG) scale. MiRNA expression profile was analysed by microarray on fresh frozen biopsies obtained before treatment start and confirmed by RT-PCR. The correlation between miRNA expression profile and the TRG coded as TRG1 (pathologic Complete Response-pCR) versus TRG >1 (no pCR) was assessed by statistical analysis methods specifically designed for this study.  Findings: 14 miRNAs were selected by arrays analysis as differentially expressed in TRG1 pts and 13 were confirmed by RT-PCR. In particular, 11 miRNAs (miR-1183, miR-483-5p, miR-622, miR-125a-3p, miR-1224-5p, miR-188-5p, miR-1471, miR-671-5p, miR-1909*, miR-630 and miR-765) were significantly up-regulated in TRG1 pts, while 2 miRNAs were under -expressed (miR-1274b and miR-720). miR-622 and miR-630 showed 100% sensitivity and specificity in selecting TRG1 cases and were significantly correlated with EGFR (χ2=11•793; p= 0•001) and TS expression (χ2=10•589; p= 0•001).  Interpretation: A set of 13 miRNAs is strongly associated with pathologic complete response and may represent a specific marker of response to chemo-radiotherapy in locally advanced rectal cancer.

overall_design: Experiments were performed on purified RNA from preoperatory biopsies of 38 patients with histological diagnosis of rectal adenocarcinoma invading through the intestinal wall and/or with pelvic lymph node involvement as evaluated by endorectal ultrasonography (uT3-T4 and/or uN+). Patients were treated with neoadjuvant chemo-radiotherapy (capecitabine + oxaliplatin in combination with  45 Gy of pelvic conformal radiotherapy). Patients have been divided in the following two groups:  group A those who had obtained a pathologic complete response – TRG 1, including the patient without detectable disease who  refused surgery,   group B any pathologic response other than complete.

first: Giuseppina

last: Della Vittoria

first: Sergio

last: Marchini

first: Singh

middle: V

last: Kumar

first: Paolo

last: Ubezio


title: Marine and freshwater three-spined stickleback (Gasterosteus aculeatus) gene expression differences

status: Public on Dec 30 2011

first: Haili

last: Zhang

address: 279 Campus Dr. Beckman Center

department: Developmental Biology

institute: Stanford University

summary: In order to identify gene expression difference between marine and freshwater stickleback populations, we compared the transcriptomes of seven adult tissues (eye, gill, heart, hypothalumus, liver, pectoral muscle, telencephalon) between a marine population sampled from the mouth of the Little Campbell river in British Columbia (LITC) and a freshwater population (Fishtrap Creek, FTC) from northern Washington.   For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents.

overall_design: Four to five fish from each population were used as biological replicates for each of the seven tissues. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents. All fish were of similar age and were raised in the same aquarium (salinity: 3.5 ppt), with a plastic divider separating the marine and freshwater groups. One male and four females were sampled from each population. Microarray experiments were performed in a 2-color format on custom Agilent arrays: experimental RNA samples were labeled with Cy5, and the common reference RNA sample was labeled with Cy3. The reference RNA was total RNA isolated from a large number of 7-day-post-hatch embryos from the freshwater population of Bear Paw Lake, Alaska (BEPA). One technical replicate was used for each array, and one of the hypothalamus samples (Hyp_FTC#3) was excluded from further analysis due to poor quality indicators. FTC#1 liver and LITC#2 pectoral muscle samples did not yield RNA of sufficient quality for the microarray experiment, and were also excluded from hybridization.

first: Tim

last: Howes

first: Alex

last: Pollen

first: David

last: Kingsley


title: Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer

city: Sao Paulo

first: Vinicius

last: Maracaja-Coutinho

state: Sao Paulo

address: Av. Prof. Lineu Prestes 748, sala 1200

department: Departamento de Bioquimica, Instituto de Quimica

institute: Universidade de Sao Paulo

summary:
Pancreatic ductal adenocarcinoma (PDAC) is known by its aggressiveness and lack of effective therapeutic options. Thus, improvement in current knowledge of molecular changes associated with pancreatic cancer is urgently needed to explore novel venues of diagnostics and treatment of this dismal disease. While there is mounting evidence that long noncoding RNAs (ncRNAs) transcribed from intronic and intergenic regions of the human genome may play different roles in the regulation of gene expression in normal and cancer cells, their expression pattern and biological relevance in pancreatic cancer is currently unknown. In the present work we investigated the relative abundance of a collection of ncRNAs in patients’ pancreatic tissue samples aiming at identifying gene expression profiles correlated to pancreatic cancer and metastasis. To investigate the relative abundance, we used a custom 3,355-element spotted cDNA microarray interrogating protein-coding genes and putative ncRNA were used to obtain expression profiles from 38 clinical samples of tumor and non-tumor pancreatic tissues. Bioinformatics analyses were performed to characterize structure and conservation of ncRNAs expressed in pancreatic tissues, as well as to identify expression signatures correlated to tissue histology. Strand-specific reverse transcription followed by PCR and qRT-PCR were employed to determine strandedness of ncRNAs and to validate microarray results, respectively. We found that long intronic/intergenic ncRNAs are ubiquitously expressed across tumor and non-tumor pancreatic tissue samples. Enrichment of promoter-H3K4me3 associated chromatin marks and over-representation of conserved DNA elements and stable secondary structure predictions suggest that these transcripts are generated from  independent transcriptional units and that at least a fraction is under evolutionary
selection, and thus potentially functional.  Statistically significant expression signatures comprising protein-coding mRNAs and long ncRNAs that correlate to PDAC or to pancreatic cancer metastasis were identified. Interestingly, loci harboring intronic ncRNAs differentially expressed in PDAC metastases were enriched in genes associated to the MAPK pathway. Orientation-specific RT-PCR documented that intronic transcripts are expressed in sense, antisense or both orientations relative to protein-coding mRNAs. Differential expression of a subset of intronic ncRNAs (PPP3CB, MAP3K14 and DAPK1 loci) in metastatic samples was confirmed by Real-Time PCR.  All this results reveal sets of long intronic ncRNAs expressed in pancreatic tissues whose abundance is correlated to PDAC or metastasis, thus pointing to the potential
relevance of this class of transcripts in biological processes related to malignant transformation and metastasis in pancreatic cancer.

overall_design: Fluorescent labeled cDNA targets derived from pancreatic tumor and non-tumor tissue from each patient were combined and hybridized to spotted cDNA microarrays. For each patient, a replicate hybridization was performed. For each sample, there are 4 replicate measurements for each probe.

first: Ana

middle: C

last: Tahira

first: Márcia

last: Kubrusly

first: Michele

last: Faria

first: Bianca

last: Dazzani

first: Rogério

last: Fonseca

last: Verjovski-Almeida

first: Marcel

last: Machado

first: Eduardo

last: Reis


title: Clinical Impact of Circulating miR-92a Levels in Non-Hodgkin’s Lymphoma

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

institute: Tokyo Medical University

summary: To identify the differentially expressed miRs in the plasmas of non-Hodgkin's lymphoma (NHL) patients, we screened NHL samples using microarrays.

overall_design: Experiments were performed with three pooled total RNA isolated from the plasmas of four patients with diffuse large B-cell lymphoma (DLBCL), four patients with follicular lymphoma (FL), and eight control samples.

first: Kazuma

last: Ohyashiki

first: Tomohiro

last: Umezu

first: Sei-ichiro

last: Yoshizawa

first: Yoshikazu

last: Ito

first: Hisashi

last: Kawashima

first: Masahiko

last: Kuroda

first: Junko


title: Genome wide analysis of mouse gastrointestinal stromal tumors (GIST) in a mouse model of spontaneous GIST.

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Analysis of mouse GIST tumors at the gene expression level. The purpose of the study was to identify immunomodulatory genes in mouse GIST tumors after in vivo treatment with the specific tyrosine kinase inhibitor imatinib mesylate.

overall_design: Total RNA obtained from mouse GIST tumors after in vivo treatment with imatinib or vehicle control injected intraperitoneally.

first: Vinod

last: Balachandran

first: R

last: DeMatteo


title: Transcriptome analysis of the Tap efflux pump mutant in Mycobacterium bovis BCG.

city: Vancouver

first: Santiago

last: Ramon-Garcia

state: BC

address: 2350 Health Sciences Mall

department: Microbiology & Immunology

country: Canada

institute: University of British Columbia

summary: We used DNA microarrays to define the physiological roles of the Tap efflux pump in M. bovis BCG during the exponential and the stationary phase of in vitro growth. For this purpose we constructed a M. bovis BCG strain in which the tap gene was inactivated by the insertion of a hygromycin resistance cassette (Ω-hyg). When the gene expression patterns of the tap mutant were compared to the wild-type strain, almost no differences were observed during exponential growth; only seven genes slightly increased their expression. In contrast, more that 100 genes showed a variation in their level of expression during stationary growth. More than ten representative genes were chosen from the microarray experiments and their expression was measured by quantitative RT-PCR using sigA as invariant internal control. In support to the gene expression profiling data, the mRNA levels of all selected genes was significantly different in the tap mutant strain relative to control. A functional category analysis (http://tuberculist.epfl.ch/index.html) of the genes differentially expressed revealed a high proportion belonging to the Virulence, Detoxification, Adaptation (VDA), Intermediary Metabolism and Respiration (IMR), Conserved Hypotheticals (CH), and Cell Wall and Cell Processing (CWCP) categories suggesting a major adaptation to a stress generated by inactivation of the tap efflux pump gene.

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design: We compared the global gene expression of the tap mutant versus the wild-type strain of M. bovis BCG during the exponential (one week; OD540= 0.2-0.3) and stationary (six weeks; OD540= 0.8-1.0) growth. Hybridizations were performed using RNA extracted from two different biological samples. Each sample was hybridized twice through swap labeling of the respective cDNAs.

first: Riccardo

last: Manganelli

first: Elisa

last: Dainese


title: Neurological defects in CAIX knockout mice

city: Tampere

first: Pei-wen

last: Pan

address: Biokatu 6

country: Finland

institute: Institute of Medical Technology, University of Tampere

summary: To further identify transcriptomic responses to CAIX deficiency in the brain, genome-wide cDNA microarray analyses were performed. Thirty-one and 37 genes were up- and down-regulated in the brain of Car9-/- mice as compared to wild-type mice. Functional annotation revealed that genes with increased expression are mainly involved in alternative splicing, nucleotide binding, RNA binding, and regulation of cellular protein metabolic process; whereas genes with reduced expression are chiefly implicated in cellular cation homeostasis, positive regulation of ion transport, Ubl conjugation, phosphorus metabolic process, and regulation of cell proliferation. Notably, the biological processes behaviour and locomotory behaviour are two prominent over-representation terms among the down-regulated genes, which is consistent with the results obtained from behavioural tests.

overall_design: Brain tissue samples were collected from five wild-type and four CAIX KO mice, respectively, at the age of eight months. Total RNAs were purified and used for cDNA microarray.

first: Peiwen

first: Anna-Kaisa

last: Parkkila

first: Salla

last: Järventausta

first: Mika

last: Hilvo

first: Silvia

last: Pastorekova

first: Jaromir

last: Pastorek

first: Seppo


title: Gene expression profiles in Arabidopsis plants during the treatment of AgNO3.

status: Public on Dec 22 2011

city: Sakai

first: Hirohisa

last: Saga

state: Osaka

address: Gakuen-cho 1-1

institute: Osaka Prefecture University

summary: Camalexin, an indolic secondary metabolite, is the magor phytoalexin produced by Arabidopsis thaliana. Camalexin biosynthesis is induced by abiotic stresses such as heavy metal treatment (e.g AgNO3). With the aim of identifying positive regulators of camalexin biosynthesis in Arabidopsis, we listed putative transcription factor genes strongly induced during the time course of AgNO3 treatment from a transcriptome analysis.

overall_design:
AgNO3 induced gene expression in Arabidopsis was measured at 48 and 72 hours after the 0.1 mM AgNO3 treatment.
Arabidopsis seedlings were germinated under sterile conditions on GM-agar plates. Seedlings (one-week after germination) were then transferred to GM liquid culture and shaken for two weeks. Plants were then treated with 0.1 mM AgNO3 and sampled at 0 h, 48 h and 72 h after the treatment. Three independent experiments were performed at each time (0, 48, or 72 h) using different plants for each experiment.


title: Expression analysis of Nanog-like-MO1 injected zebrafish embryos at the sphere stage

status: Public on Dec 28 2011

city: Boston

first: Cong

last: Xu

state: MA

address: 1 Blackfan Circle

institute: Harvard Medical School

summary:
Investigation of whole genome gene expression level changes in nanog-like knockdown embryos , compared to the control-MO injected embryos. Knockdown of nanog-like impaired early gastrulation.
To globally analyze which target genes Nanog-like regulates during early embryogenesis, we performed a genome-wide transcription analysis using sphere stage (4 hpf) nanog-like morphants.

overall_design: A six chip study using total RNA recovered from three separate control-MO injected embryos and three separate nanog-like-MO1 injected embryos at the sphere stage

first: Leonard

middle: I

last: Zon


title: TGFb receptor 1 (TGFBR1) inhibitor treatment of zebrafish embryos vs. controls

status: Public on Dec 17 2011

city: St. Louis

first: Seth

middle: Daniel

last: Crosby

address: 660 S. Euclid

department: Genetics

institute: Washington Univeristy School of Medicine

summary:
The effect of transforming growth factor beta receptor 1 (TGFBR1) inhibitor (LY-364947) treatment was compared to untreated embryos.
Experimental details and analyzed data are available in Willaert et al. Human Molecular Genetics 2011; doi: 10.1093/hmg/ddr555

overall_design: Two-condition experiment, LY-364947 (40microM) treatment vs untreated controls. Biological replicates: 3 LY-364947 treatment replicates compared to a pooled sample of 3 untreated control replicates with dye swap.

first: Zsolt

last: Urban


title: Mussel (Mytilus galloprovincialis) digestive gland tissue: Control vs. Nickel, Chlorpyrifos and their mixture.

first: Francesco

last: Dondero

summary:
Transcriptional profiling of mussel (Mytilus galloprovincialis) digestive gland tissue comparing control tissue with tissue obtained from animals exposed for four days to sublethal amounts of Nickel, Chlorpyrifos, or their mixture.
Background: Mixtures of chemicals present in aquatic environments may elicit toxicity due to additive or synergistic effects among the constituents or ‘vice versa’ the adverse outcome may be reduced by antagonistic interactions. Deviations from additivity should be explained either by the perturbations of toxicokinetic parameters and/or chemical toxicodynamics. We addressed this important question in marine mussels exposed subchronically to a binary mixture made of two wide-spread pollutants: the heavy metal Nickel and the organic phosphorus pesticide Chlorpyrifos. To this aim, we proposed the use of a systems approach based on the evaluation and integration of different disciplines, i.e. high throughput gene expression profiling, functional genomics, stress biomakers and toxicokinetics.
Results: Stress biomarkers showed statistically significant antagonistic deviations from the reference model systems to predict mixture toxicity which are based either on simple additivity or non-interaction. While toxicokinetic modeling did not explain mixture interactions, gene expression profiling and further functional genomics analysis provided clues that the decrement of toxicity may arise from the development of specific toxicodynamics. Multivariate statistics of microarray and quantitative PCR data showed two separate patterns for the single chemicals and a composite complex profile for the mixture suggesting the occurrence of interactive molecular responses. The latter signature accounted for differentially expressed genes whose relative expression values were either in trend or in contrast with those found due to single substance treatments and a relevant set of sequences which were exclusive of the mixture gene list.
Conclusion: The functional genomics assessment fits with biological data to indicate the occurrence of different toxicodynamic events and ‘in general’ a decrease of toxicity, driven by the mitigation or even abolishment of lysosomal responses such as the lipid metabolic disorder observed exclusively in single chemical-exposed samples. Furthermore, our results emphasized the importance of the application of mechanistic approaches and the power of systems assessment to study toxicological responses in ecological relevant organisms.

overall_design:
Mussel MytArray 1.0 (Platform GPL1799)-based arrays: Three-condition experiment.  Dual color competitive hybridizations. Common reference (vehicle treated animals, 0.02% Dimethyl sulfoxide); Pools of six animals. Biological replicates: 4 controls, 4 Nickel, 4 Chlorpyrifos. One replicate per array.
Mussel MytArray 1.1 (Platform GPL10269)-based arrays: Four-condition experiment.  Dual color competitive hybridizations. Common reference (vehicle treated animals, 0.02% Dimethyl sulfoxide); Pools of six animals. Biological replicates: 5 controls, 1 Nickel, 3 Chlorpyrifos, 5 mixture. One replicate per array.

first: Aldo

last: Viarengo


title: Novel anti-inflammatory activity of chlorojanerin isolated from Sausurrea heteromalla (D. Don) Hand.-Mazz.

status: Public on Dec 14 2011

city: Mumbai

first: Muralidhara

last: Padigaru

state: Maharashtra

address: 1, Nirlon Compex, Off Western Express Highway

department: Translational Research

country: India

institute: Piramal Lifesciences India Limited

summary: Medicinal plants have shown great promise as a source of novel drug compounds for the treatment of inflammatory disorders.  In our search for new entities with anti-inflammatory potential, the extracts of the whole plant of Saussurea heteromalla (family-Asteraceae), collected from Himalayas, were evaluated in the high throughput screen for TNF-α and IL-6 inhibitors. The plant has been found as a new source of chlorojanerin, a guaianolide type of sesquiterpene lactone. This is the first report on the potent anti-inflammatory activity of the compound. Chlorojanerin was shown to be significantly effective in inhibiting TNF-α and IL-6 production in LPS induced THP-1 cells (TNF-α, IC50 = 3µM and IL-6, IC50 = 0.8µM).  The compound also blocked TNF-α and IL-6 production from LPS induced human monocytes and synovial cells from RA patients. Chlorojanerin also inhibited the binding of NF-κB in a GFP reporter assay system.  Transcriptional profiling of the LPS stimulated THP-1 cells revealed that chlorojanerin exerted its anti-inflammatory effect by inhibiting the expression of genes involved in activating the transcription factor – NF-κB.  Real time analysis of these genes validated the effect of chlorojanerin on the classical downstream targets of NF-κB.  Thus, this study clearly delineated 8 targets specific for the effect of chlorojanerin on NF-κB induced signaling at the mRNA level.  This work is a step towards the isolation and characterization of lead anti-inflammatory agents from the extract of Saussurea heteromalla, which can be developed into better therapeutic molecules targeted towards some specific inflammatory diseases.

overall_design: Single dye labelling with Cy3 for all treatment RNA samples. Treatments included unstimulated, LPS stimulated, Chlorjanerin treatment and dexamethasone treatment.

first: Debarshi

last: Chakrabarti

first: Asha

last: Kulkarni-Almeida


title: MicroRNA-22 upregulation by vitamin D mediates its protective action against colon cancer.

status: Public on Dec 20 2011

city: MADRID

first: Luis

last: LOMBARDIA

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Molecualr Pathology Programme

country: Spain

institute: CNIO (Spanish National Cancer Center)

summary: Vitamin D deficiency is associated with high risk of colon cancer and a variety of other diseases. The active vitamin D metabolite 1alpha,25-dihydroxyvitamin D3 (1,25(OH)2D3) regulates gene transcription via its nuclear receptor (VDR), and posttranscriptional regulatory mechanisms of gene expression have also been proposed. We have identified microRNA-22 (miR-22) and several other miRNA species as 1,25(OH)2D3 targets in human colon cancer cells. Remarkably, miR-22 is induced by 1,25(OH)2D3 in a time-, dose-, and VDR-dependent manner. In SW480-ADH and HCT116 cells, miR-22 loss-of-function by transfection of a miR-22 inhibitor (anti-miR-22) suppresses the effect of 1,25(OH)2D3. Additionally, miR-22 inhibition increases cell migration per se and decreases the antimigratory effect of 1,25(OH)2D3 in both cell types. In silico analysis shows a significant overlap between genes suppressed by 1,25(OH)2D3 and miR-22 putative target genes. Consistently, miR-22 inhibition abrogates the reduction by 1,25(OH)2D3–mediated suppression of NELL2, OGN, HNRPH1, and NFAT5 genes. In 39 out of 50 (78%) human colon cancer patients, miR-22 expression was found lower in the tumor than in the matched normal tissue and correlated directly with that of VDR. Our results indicate that miR-22 is induced by 1,25(OH)2D3 in human colon cancer cells and it may contribute to its antitumor action against this neoplasia.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We have analysed a human colon cancer cell line, SW480-ADH, treated with  1,25(OH)2D3 or isopropanol (vehicle) at three different time points (24, 48 and 96 hours). Each experiment was replicated 2 times by dye swap.

last: Álvarez-Díaz

first: Noelia

last: Valle

first: Gemma

last: Ferrer-Mayorga

last: Lombardía

first: Mercedes

last: Herrera

first: Orlando

last: Domíguez

first: Miguel

last: Segura

first: Félix

last: Bonilla

first: Eva

last: Hernando

first: Alberto

last: Muñoz


title: A five-species transcriptome array for oral mixed-biofilm studies

status: Public on Dec 09 2011

city: Rostock

first: Sylvio

last: Redanz

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Institute of microbiology, virology and hygiene

institute: hospital university rostock

summary:
Investigation of whole genome gene expression levels of P. gingivalis W83, F. nucleatum DSMZ 25586, S. sanguinis SK36, A. actinomycetemcomitans HK1651, S. mutans UA159 in an 24 h old culture. Additionally, whole genome gene expression level changes of S. mutans UA159  biofilm cells after co-cultivation with S. mitis ATCC 11843 were compared to its single species biofilm growth after 24 h.
Aim: Demonstration of the usefulness of a five-species gene expression array. Multiple probes per gene enabled identification of single inter-species cross-hybridizing probes. The deletion of such probes lead almost not to the deletion of the whole gene. This was investigated and confirmed by a two-species biofilm expression analysis: The here described array was used for the identification of genes of S. mutans influenced by the presence of S. mitis. Materials and Methods: P. gingivalis W83, F. nucleatum DSMZ 25586, S. sanguinis SK36, A. actinomycetemcomitans HK1651,and S. mutans UA159 were grown in CDM/succrose or artificial saliva/galactose in a single-species culture for 24 h anaerobically resulting in biofilm structures or monolayers. Total RNA was isolated and used for microarray analysis. Probes were analysed for the presence of biological false positive signals caused by cross-hybridizing probes of one of the other species presented on the chip. Further, a simple procedure was developed for automatical identification and deletion of false positive signals caused by washing artefacts, resulting in a more reliable outcome. In the case of the S. mutans/S. mitis mixed-species biofilm, both species were cultured together for 24 h like previously described. The found gene regulations were verified by RT-PCR.  Results: Experiments with cDNA from 24 h old single-species cultures allowed the identification of cross-species hybridizing probes on the array, which can be eliminated in mixed-species experimental settings without the need to exclude the whole genes from the analysis. Between 69 % and almost 100 % represented genomes on this array were found actively transcribed under the mono-species monolayer and biofilm conditions used here. S. mutans / S. mitis co-culture: Physiological investigations revealed an increase in S. mutans biofilm mass with a decrease in pH-value under the influence of S. mitis, thereby confirming previously published data. A stringent fold change cut-off of 2 (p<0.05) identified 19 S. mutans transcripts with increased abundance, and 11 with decreased abundance compared to a S. mutans mono-species biofilm. Many of the genes have previously been found differentially regulated under general and acid stress, thereby confirming the value of this array.  Conclusions: Taken together, this new array allows transcriptome studies on multi-species oral biofilm interactions and could become an important asset in future oral biofilm and inhibitor/therapy studies.

overall_design: The chip study used pooled total RNA recovered from three biologically independent mono-species biofilms or adherent cells/monolayers of P. gingivalis W83, F. nucleatum DSMZ 25586, S. sanguinis SK36, A. actinomycetemcomitans HK1651, and S. mutans UA159. In the case of  gene expression analysis of S. mutans/S.mitis biofilm structures compared to the single species biofilm of S. mutans three separate single and three separate two-species biofilm cultures were analysed. Each chip measured the expression level of all together 10186 genes (1883 genes of P. gingivalis W83, 1964 genes of F. nucleatum DSMZ 25586, 2244 genes of S. sanguinis SK36, 2168 genes of A. actinomycetemcomitans HK1651, 1927 genes of S. mutans UA159) with up to thirteen 60-mer probes per gene and with a three-fold technical redundancy.

first: Kerstin

last: Standar

first: Andreas

last: Podbielski

first: Bernd

last: Kreikemeyer


title: Knockdown of slc2a10/glut10 in zebrafish embryos vs. controls

first: Seth

last: Crosby

state: MO

summary:
A zebrafish model of arterial tortuosity syndrome (ATS) was generated by knocking down the slc2a10/glut10 gene using antisense morpholino oligonucleotides (MO). Control morpholino treated embryos were used as controls. The samples were collected for gene expression profiling at 48 hours post fertilization.
Experimental details and analyzed data are available in Willaert et al. Human Molecular Genetics 2011; doi: 10.1093/hmg/ddr555

overall_design: Two-condition experiment, slc2a10 MO (7.5ng) treatment vs control MO (5ng) treatment. Biological replicates: 3 slc2a10 MO replicates, compared to a pooled sample of 3 control MO replicates with dye swap.

first: Zsolt

last: Urban