title: Altered microRNA expression associated with chromosomal and epigenetic changes contributes to cervical carcinogenesis

status: Public on Jun 28 2012

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary: Little is known about the alterations in microRNA (miRNA) expression patterns during the consecutive stages of cervical cancer development and their association with chromosomal instability and epigenetic changes. We integrated miRNA expression profiles in normal cervical squamous epithelium, high-grade precancerous lesions (CIN2-3), squamous cell carcinomas (SCC) and adenocarcinomas (AdCAs) with previously generated chromosomal profiles of the same samples. In addition, the DNA methylation status of downregulated miRNAs located in a CpG island was determined.  Significantly differential expression during the consecutive stages of cervical SCC development was observed for 106 miRNAs. Altered expression of 5 significantly differentially expressed miRNAs, hsa-miR-9 (1q23.2), hsa-miR-15b (3q25.32), hsa-miR-28-5p (3q27.3), hsa-miR-100 and hsa-miR-125b (both 11q24.1) was directly linked to frequent chromosomal alterations. Another 9 significantly downregulated miRNAs were located within a CpG island. Three of these 9 miRNAs, hsa-miR-203, hsa-miR-572, and hsa-miR-638, showed increased methylation in cervical cancer cell lines and HPV-immortalised cells compared to primary keratinocytes. Functional analyses were performed for hsa-miR-9, representing a potential oncogene with increased expression linked to a chromosomal gain, and hsa-miR-203, representing a potential tumour suppressor gene silenced by DNA methylation. Hsa-miR-9 and hsa-miR-203 were found to alter cell viability and anchorage independent growth in vitro, respectively, supporting their oncogenic and tumour suppressive function in cervical cancer.  In conclusion, differential expression of 106 miRNAs, partly associated with chromosomal alterations and epigenetic changes, was observed during cervical SCC development. Altered expression of hsa-miR-9 and hsa-miR-203 was shown to be functionally relevant, underlining the importance of deregulated miRNA expression in cervical carcinogenesis.

overall_design: 10 squamous cell carcinomas of the cervix, 9 adenocarcinomas of the cervix, 18 high-grade cervical intraepithelial neoplasias (CIN2-3), and 10 cervical squamous epithelial samples with normal histology were analysed using single channel (Cy3) miRNA microarrays from Agilent (G4471A-016436).

first: Saskia

middle: M

last: Wilting

first: Peter

middle: J

last: Snijders

first: Wina

last: Verlaat

first: Annelieke

last: Bosman-Jaspers

first: Mark

middle: A

last: vandeWiel

first: Wessel

middle: N

last: vanWieringen

first: Gerrit

last: Meijer

first: Gemma

middle: G

last: Kenter

first: Yajun

last: Yi

first: Carlos

last: leSage

first: Reuven

last: Agami

first: Chris

first: Renske

middle: D

last: Steenbergen


title: Using the expression profile of peripheral blood to investigate regulatory pathways in schizophrenia

status: Public on Jun 22 2012

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary:
Schizophrenia is best considered a “two-hit” disease, with a neurodevelopment impairment followed by an additional process in early adulthood. Both are regulated by hormonal (like thyroid and retinols) and signal transduction pathways (like WNT), which in turn have been
previously identified in post-mortem brain studies of schizophrenic individuals. While brain studies are fitted for pathology assessment, there are not suitable for searches of a “diagnostic signature” of schizophrenia. In contrast, peripheral blood is easily accessible, and can be used
for the study of disease pathways and potentially diagnosis markers. Blood from twenty eight males with DSM-IV schizophrenia under three drug regimens (clozapine, risperidone or haloperidol), and from 10 healthy controls was studied in a microarray platform with 1364
genes belonging to hormonal and signal transduction pathways. Seven genes were differentially
expressed between controls and patients with different treatments, and 28 between healthy
controls and specific treatments, with four (CTNNA1, GSTM3, HOXA-13 and KRT18) altered in
all analyses. While none of these genes has been previously reported in schizophrenia brain
studies, many belong to pathways altered in schizophrenia, belonging to chromosomal loci
linked to the disease, which warrants additional replication studies to be performed in larger
samples.

overall_design: Glass arrays with 2,352 elements were prepared with the aid of the Flexis Robot (Genomic Solutions, UK). Bacteria were grown in LB medium containing ampicillin (250mg/ml). Inserts were amplified by PCR using M13 reverse and forward primers and products were submitted to 1% agarose gel for quality control. cDNA clones with single amplicons were filtrated in Sephadex G50 (GE Healthcare, UK), printed onto Corning glass slides (Corning, USA) and fixed by UV crosslink (Eisen & Brown, 1999; Brentani et al., 2005). There were 1364 unique genes in the array. Those genes were defined trough literature search for genes related to neurodevelopmental pathways. 76 samples (1/2 dye-swaps).

first: Helena

last: Brentani

first: Dirce

last: Carraro

first: L

last: Mota

first: C

last: Torres

first: Mariana

last: Maschietto

first: Barbara

last: Mello

first: Ann

last: Goodman

first: Clarissa

last: Gama

first: P

last: Belmonte-de-Abreu

first: Joana

last: Palha


title: Liver miRNA profiles of newborn male Erhualian and Large White piglets using LC Sciences Pig miRNA Array

status: Public on Jun 18 2012

city: Nanjing

first: Runsheng

last: Li

state: Jiangsu

department: Nanjing Agricultural University

country: China

institute: Nanjing Agricultural University

summary:
Erhualian (EHL) is one of the seven strains included in a Chinese indigenous pig breed called Taihu. EHL is famous for its early sexual maturity, large litter size, high adiposity, mild temper, good maternity and high tolerance to roughage and stress. To further investigate the role of miRNAs in different breed-specific metabolic characters, a comparison of miRNA expression profiles in liver of newborn Erhualian (EHL) and Large White (LW) piglets was carried out. Six LC sciences microarrays containing 236 miRNA procine probes based on miRBase Release 16.0 and 100 custom miRNA probes based on the solex deep sequencing results (li et al.,2010) were used. When compaired with LW piglets, 5 down-regulated and 8 up-regulated miRNAs were detected (fold change >1.2 and p value < 0.1) in the liver of EHL among the 236 miRbase probes. When considering the 100 custom miRNA probes, 2 down-regulated and 5 up-regulated miRNAs were observed.
These results were further described in the unpublished paper Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and Large White pigs.

overall_design: Six newborn male piglets were sampled from three litters (2 from each litter) of purebred EHL and LW sows and sacrificed. Liver samples were immersed in liquid nitrogen immediately after collection and then stored at -70 °C. Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions. Total RNAs of the two littermate piglets were pooled for the microarray analysis. The pooled samples were named as EHL1-3 and LW1-3, representing 3 mixed liver RNA samples each from EHL and LW piglets, respectively. Microarray experiment was performed by a service provider (LC sciences).

first: Ruqian

last: Zhao


title: Dynamics of intercellular and extracellular miRNAs in HUVECs co-cultured with K562 cells

status: Public on Jun 12 2012

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

summary:
MicroRNAs (miRNAs) are small (18-22 nucleotides), non-coding RNAs that suppress the translation of target mRNAs by binding to their 3` untranslated region, and regulate gene networks, helping to control cell function and phenotype. Recently, the existence of extracellular miRNAs enclosed in exosomes has raised the possibility that they play an important role in cell-cell communication.
The goals of this study were to elucidate whether or not miRNAs secreted from neoplastic cells transfer into endothelial cells and works functionally active in the recipient cells. In the present study, we investigated the interaction of a leukemia cell line (K562) and human umbilical vein endothelial cells (HUVECs) using a non-contact co-culture system, and assess the expression profiles of intercellular and extracellular miRNAs in HUVECs and K562 cells using Taqman MicroRNA Array v2.0 (Applied Biosystems, Bedford, MA). We compared the miRNA expression profiles between 1) K562 cells or HUVECs; 2) intercellular and extracellular; 3) mono-culture medium and co-culture medium.

overall_design: K562 cells and HUVECs were non-contact co-cultures using Transwell (Corning, pore size: 0.45µm) for 24 hr. The culture medium was collected and filtered through a 0.45 µm PVDF filter (Millipore, Billerica, MA). The intercellular and extracellular RNAs were isolated from K562 cells, HUVECs and each culture medium using the mirVana PARIS kit (Ambion, Austin, TX). The expression profile was determined using the Human Taqman MicroRNA Arrays A (Applied Biosystems). QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler. The thermal cycling conditions consisted of 10 min at 95°C, followed by 40 cycles at 92°C for 15 s and 60°C for 1 min.


title: Ethanol alters microNA expression in zebrafish embryos

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

department: Biology

country: Portugal

institute: University of Aveiro

summary: Prenatal exposure to ethanol leads to a myriad of developmental disorders known as fetal alcohol spectrum disorder, often characterized by growth and mental retardation, central nervous system damage and specific craniofacial dysmorphic features. Although the exact mechanisms of ethanol toxicity are not well understood it is known that ethanol exposure during development affects the expression of several genes involved in cell cycle control, apoptosis and transcription. MicroRNAs (miRNAs) are implicated in some of these processes however it is unclear if they are involved in ethanol-induced toxicity. Here we tested whether ethanol deregulates miRNA expression in zebrafish embryos and if a miRNA deregulation signature could be inferred. For this, zebrafish embryos were exposed to two different ethanol concentrations (1% and 1.5%) from 4 hours post-fertilization (hpf) to 24hpf. MicroRNA expression profiles revealed that ethanol exposure induces deregulation of miRNA expression significantly. Seven miRNAs are commonly up-regulated after both ethanol treatments, namely miR-153a, miR-725, miR-30d, let-7k, miR-100, miR-738 and miR-732, whereas downregulation of miR-23a, miR-203, let-7c, miR-128 and miR-193b is detected after 1% ethanol exposure only. Target prediction of deregulated miRNAs shows that putative targets are involved in cell cycle control, apoptosis and transcription, which are the main processes affected by ethanol toxicity. The overall study shows that the effects of ethanol on miRNA deregulation are dose-dependent and that miRNAs are relevant in the context of alcohol toxicity. Moreover, a miRNA toxicity signature for embryonic ethanol exposure was obtained.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus
Takifugu rubripes

overall_design: Zebrafish embryos were obtained from spawning adults in groups of about 10 males and 10 females. Zebrafish embryos were collected and Petri dishes with approximately 250 eggs each were incubated at 28ºC to allow normal zebrafish development until 4hpf, when blastula is reached. At this stage, embryos were examined under a dissecting microscope and those that had developed normally were selected for EtOH exposure (approximately 200 eggs). Briefly, 200 embryos were randomly distributed into plastic Petri dishes containing 20 mL of EtOH test solutions (1% EtOH, 1.5% EtOH). All solutions were made by dilution of absolute EtOH in system water. Exposure was from 4hpf to 24hpf. At this stage, solutions were changed by system water and embryos were allowed to grow until 24hpf. The control group was allowed to grow in plain system water. Zebrafish embryos were collected at 24hpf for microarray analysis. Two biological replicates were performed for each assay.

first: Ana

middle: R

last: Soares

first: Violeta

last: Ferreira

first: Marisa

last: Reverendo

first: João

last: Simões

last: Bezerra

first: Gabriela

last: Moura

first: Manuel

last: Santos


title: Comparison of gene expression profiles in cultivated peanut (Arachis hypogaea L.) under strong artificial selection

status: Public on Jun 19 2012

city: Guangzhou

first: Xiaoping

last: Chen

address: 18# Jinying West 2nd Street

institute: Crops Research Institute, Guangdong Academy of Agricultural Sciences

summary: Comparison of gene expression profiles of widespread peanut cultivars  for exploring the expression data in pod and leaf  with regard to signatures of artificial selection

overall_design: We investigated the overall expression by hybridizing the microarray (GPL13178) with RNA samples from pods and leaves of five selected representative peanut varieties (Fuhuasheng, Shitouqi, Yueyou116, Shanyou523, and Yueyou7), which were widely cultivated in different periods of the past fifty years in southern China. We used the RNA sample from Yueyou7 pod as a reference for all the pod hybridizations, and used the Yueyou7 leaf sample as a reference for all the leaf hybridizations. Field grown plants under normal irrigation were used for sample collection. Replicates with dye-swap were performed for each genotype.

first: Yanbin

last: Hong

first: Erhua

last: Zhang

first: Haiyan

last: Liu

first: Guiyuan

last: Zhou

first: Shaoxiong

first: Fanghe

last: Zhu

first: Baozhu

last: Guo

first: Jiujiang

last: Yu

first: Xuanqiang

last: Liang


title: Comparing two transcriptome technologies - sequencing match microarrays [Array]

status: Public on Jun 10 2012

city: Cadorago

first: Martin

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

country: Italy

institute: Sacco Srl

summary: Next-generation sequencing has emerged as a promising platform for whole genome transcriptome profiling. The microarray technology has in contrast a long track record, but may suffer from issues related to background fluorescence and non-specific hybridization. The two technologies have been compared for eukaryotic transcriptomes in various studies. However, for prokaryotes information on comparative performance of the two technologies is sparse. We thus compared the two technologies for Streptococcus thermophilus. With just single experiments there was a strong correlation between the technologies.

overall_design: We compared our in house spotted DNA microarray platform with the same RNA samples sequenced externally. The aim was to, without replicate arrays or sequencing, to determine if the two technologies correlate well.

first: Thomas

middle: B

last: Rasmussen

first: Shruti

middle: H

last: Dantoft


title: Gene expression comparison of L. reuteri ATCC PTA 6475 grown in a glucose-based media and a sucrose-based media

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

country: USA

institute: Baylor College of Medicine

summary: Gene expression comparison of L. reuteri ATCC PTA 6475 grown (stationary phase) in a defined media with either glucose or sucrose as the carbon source, in anaerobic conditions at 37C.

overall_design: Includes 2 biological replicates and dye-swaps for each comparison. Reference time point is is L. reuteri ATCC PTA 6475 grown in a glucose-based media.

first: Carissa

last: Thomas


title: Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (genomic)

city: Lund

first: David

last: Lindgren

address: Building 404 A3, Scheelevägen 2, Medicon Village

department: Dept of Laboratory Medicine

country: Sweden

institute: Lund University

type: Genome variation profiling by genome tiling array

summary: Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

overall_design: 146 primary bladder cancer tumor samples were analyzed on BAC array containing ~32 000 BAC clones. Arrays were produced at the Swegene Centre for Integrative Biology at Lund University (SCIBLU).

first: Gottfrid

last: Sjödahl

first: Mattias

last: Aine

last: Lauss

last: Höglund


title: MicroRNA expression profiling of Ewing sarcoma spheres vs. adherent cells

status: Public on Jun 20 2012

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

institute: University of Turin

summary: We have recently demonstrated that human paediatric mesenchymal stem cells can be reprogrammed toward a Ewing’s sarcoma family tumor (ESFT) cancer stem cell (CSC) phenotype by mechanisms that implicate microRNAs (miRNAs). Here, we show that the miRNA profile of ESFT CSC is shared by embryonic stem cells and CSC from divergent tumor types. We also provide evidence that the miRNA profile of ESFT CSC is the result of reversible disruption of TARBP2-dependent miRNA maturation. Restoration of TARBP2 activity and systemic delivery of synthetic forms of either of two of its targets, miRNA-143 or miRNA-145, inhibited ESFT CSC clonogenicity and tumor growth in vivo. Our observations suggest that CSC self-renewal and tumor initiation may depend on deregulation of TARBP2-dependent miRNA expression.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: 2 Ewing sarcoma primary samples: comparison between spheres and derived adherent cells.

first: Claudio

last: De Vito

first: Nicolo

last: Riggi

first: Mario-Luca

last: Suvà

first: Karine

last: Baumer

first: Ivan

last: Stamenkovic


title: MicroRNA expression profiling of Ewing sarcoma cancer stem cells

overall_design: 2 samples of primary Ewing sarcomas, divided into CD133+ and CD133- fractions. One sample of EWS-FLI1 expressing human pediatric mesenchymal stem cells, divided into CD133+ and CD133- fractions. One sample of STA-ET-8.2 cells, divided into CD133+ and CD133- fractions.


title: affy_zeawall_ril_maize - Expression studies in 5 early maize RIL with contracted allelic patterns at major QTL posititions

status: Public on Jun 17 2012

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary:
affy_zeawall_ril_maize - Four major QTL explaining lignin content and cell wall degradability variation have been identified in the F288 x F271 RIL progeny (Roussel et al., 2002, Maydica 47: 9-20). Gene expression has been considered as a way in identification of candidate gene underlying QTL. Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). Expression study will be investigated in ear internode at two stages emerging tassel and early silking stages with two replicates. Plants were cropped at INRA Lusignan (Vienne, France) in 2009 in a bloc design with two four-row replicates. Below-ear internodes of five representative RIL plants of one row in each replicate were harvested at the two stages and pooled.

Keywords: genotype comparison, time course

overall_design: 20 arrays - maize

first: Sandrine

last: Balzergue

first: Yves

last: Barrière

first: Audrey

last: courtial

last: Arribat


title: Modeling Formamide Denaturation of Probe-Target Hybrids for Improved Microarray Probe Design in Microbial Diagnostics

status: Public on Jun 30 2012

city: Madison

first: Safak

last: Yilmaz

state: Wisconsin

address: 2 University Houses

institute: UW-Madison

summary:
This study aimed to model formamide-based melting for the optimization of the sensitivity and specifcity of oligonucleotide probes in dignostic high-density microarrays.
Formamide melting profiles of DNA oligonucleotides were obtained with a high-density microarray targeting 16S rRNA genes of Escherichia coli and Rhodobacter sphaeroides.  One or two mismatched versions of perfect match probes were included on the array to systematically analyze the effect of formamide on mismatch stability and mismatch discrimination.
A thermodynamics-based mathematical model of formamide denaturation was developed to predict the formamide melting profiles with sufficient accuracy to help with oligonucleotide design in microbial ecology applications.

sample_organism:
Escherichia coli K-12
Cereibacter sphaeroides 2.4.1

overall_design: 16S rRNA sequences with GenBank accession codes U00006 ( E. coli ) and X53853 (R. sphaeroides) were used for probe design.  The following oligonucleotide probe sets were used for the systematic analysis of the effect of formamide on probe-target hybrids (parenthetic information gives set name followed by the number of probes): 22-mer perfect match probes tiling the 16S rRNA gene of E. coli (TileE, n=1521), perfect match E.coli probes of variable length between 18 and 26 mers (Length, n=1045), E. coli probes with central single mismatches (OneM, n=1563), E. coli probes with single positional mismatches (PosM, n=4092), E. coli probes with single deletion mismatches (Gap, n=248), E. coli probes with single insertion mismatches (Insertion, n=248), E. coli probes with two separate mismatches (TwoM, n=1674), E. coli probes with central tandem mismatches (Tandem, n=558), and 22-mer perfect match probes tiling the 16S rRNA gene of R. sphaeroides.  Also, a probe with no match to 16S rRNA genes was used as a background control. On the array, regular probes were replicated three times and the Nonsense probe ten times.  See the manuscript of Yilmaz et al. for details.

first: L

middle: S

first: Alexander

last: Loy

first: Erik

last: Wright

first: Michael

last: Wagner

first: Daniel

last: Noguera


title: Dietary sterols/steroids and the generalist caterpillar Helicoverpa zea: physiology, biochemistry and midgut gene expression

status: Public on Jun 14 2012

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

country: Germany

institute: Max Planck Institute for Chemical Ecology

summary: Sterols are essential nutrients for insects because, in contrast to mammals, no insect (or arthropod for that matter) can synthesize sterols de novo. Cholesterol is the most common sterol in insects, but it is not found in plants in large quantities; plant-feeding insects typically generate their cholesterol by metabolizing phytosterols. However, different plants species can contain different types of phytosterols, and some phytosterols are not readily converted to cholesterol. In this study we examined, using artificial diets containing single sterols, how typical (cholesterol and stigmasterol) and atypical (cholestanol and cholestanone) sterols/steroids affect the performance of a generalist caterpillar (Helicoverpa zea), restricting this analysis to midgut tissue because this is where sterol/steroid absorption occurs, and the midgut is the putative site of dietary sterol/steroid metabolism. In general, H. zea performed best on the cholesterol and stigmasterol treatments; performance was reduced on cholestanol, and was very poor on cholestanone. We compared the transcript profiles of larval guts in response to differentially suitable sterols, using the optimal sterol, cholesterol, as a control, using a two-color reference design microarray experiment. Midgut gene expression patterns differed between the treatments; relative to cholesterol, differences were lowest on the stigmasterol treatment, intermediate on the cholestanol treatment, and greatest on the cholestanone treatment.

overall_design: Transcriptional profiling comparing Helicoverpa zea gut tissue from third instar larvae exposed to four different dietary sterols, namely Cholesterol (CON), Cholestanol (ChStanol), Cholestan-3-one (Ch3one) and Stigmasterol (Stigma). Two-color reference design. Biological replicates: 4 (5 individuals per replicate). 12 samples total.

first: Spencer

last: Behmer


title: Development of a high-density oligo microarray of cassava, an important tropical crop

status: Public on Jun 15 2012

city: Yokohama

first: Tetsuya

last: Sakurai

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

institute: RIKEN

summary: We developed a 60-mer oligonucleotide Agilent microarray representing about 20,000 cassava genes and applied it to expression profiling under drought stress. We demonstrated that our microarray is an useful tool for analyzing the cassava transcriptome and that it can be applied to various cassava species.

sample_organism:
Manihot esculenta
Manihot esculenta subsp. peruviana

overall_design: After cutting of shoots from the cassava plants, the shoots were grown in  a glass bottle containing MS medium supplemented with 2% sucrose and 0.3% gelrite for 4 weeks (16 hours light / 8 hours dark). The plantlets were subjected to drought treatment by removing the plantlets from the gelrite plate, placing on a plastic plate and keeping them for  1 hour under 40-80 μmol photons m-2 sec-1 at 30ºC in 50% of relative humidity. Then total RNA was prepared from the shoots and used for the microarray hybridization. Three replicative hybridization experiments were carried out using the independent biological samples.

first: Yoshinori

last: Utsumi

first: Maho

last: Tanaka

first: Morosawa

last: Taeko

first: Akihiro

last: Matsui

first: Atsushi

last: Kurotani

first: Takuhiro

last: Yoshida

first: Yoshimi

last: Umemura

first: Manabu

last: Ishitani

first: Kazuo

last: Shinozaki

first: Motoaki

last: Seki


title: Micro-Array Profiling Exhibits Remarkable Intra-Individual Stability of Human Platelet micro-RNA

city: Bad Krozingen

first: Thomas

last: Nuehrenberg

state: Baden-Württemberg

address: Südring 15

department: Klinik für Kardiologie II

institute: Universitäts-Herzzentrum Freiburg • Bad Krozingen

summary:
Results: MiRNA expression profiling of 1281 human miRNAs revealed relevant expression of 221 miRNAs consistently expressed in all samples at all time points. Correlation of platelet miRNA ranks was highly significant with data from other studies. Global distribution of miRNA expression was relatively similar in all subjects. No miRNA exhibited a significant effect of time at level 0.05. This finding was supported by exploratory analysis of predicted time effects from the mixed effects models. Furthermore, no significant effect of ASA could be found. Concerning the functional implication of the 20 most abundantly expressed miRNAs, we found 6 functional themes: nuclear import, cell cycle, transmembrane receptor protein serine/threonine kinase signaling pathway, regulation of kinase activity, pathways in cancer, and leukocyte differentiation.
Conclusion: Our study shows that the platelet miRNA profile is remarkably stable in healthy subjects and is not affected by single-dose ASA treatment. For this reason, single-point analysis of platelet miRNA profile is reasonable when inter-individual differences are studied. The functional annotation network points toward additional extra-platelet effects of platelet miRNAs.

overall_design: We assessed the platelet miRNA profile blood in 5 volunteers at five time points over a time course of 10 days; 24 h prior to the last blood sampling, all subjects took 500 mg acetylsalicylic acid (ASA) once. Platelet miRNA was isolated from platelet-rich plasma which was leucocyte-depleted by negative bead separation. Then miRNA array analysis was performed on the isolated platelet miRNA. Temporal patterns and the effect of ASA were explored by a linear mixed effects model for each miRNA. For the 20 most abundantly expressed platelet miRNAs, a target gene search was performed by using miRWalk for validated and predicted targets. To visualize which molecular functions arerelated to those miRNAs, an annotation network was created by ClueGO, a Cytoscape plug-in.

first: Christian

last: Stratz


title: Expression analysis of Desulfovibrio africanus strain Walvis Bay

status: Public on Jun 07 2012

city: Oak Ridge

first: James

last: Moberly

state: TN

address: 1 Bethel Valley Rd

department: Biosciences Division

institute: Oak Ridge National Laboratory

summary: Investigation of partial genome gene expression level changes in a Desulfovibrio africanus during exponential and stationary phase growth in the presence and absence of 5 ug/L Hg2+ (as HgNO3). Desulfovibrio africanus is a known mercury methylating bacteria

sample_organism: Desulfocurvibacter africanus subsp. africanus str. Walvis Bay

overall_design: A 3 chip study using total RNA recovered from three separate cultures of Desulfovibrio africanus with 5 ug/L Hg during exponential phase growth, three seperate cultures of Desulfovibrio africanus with 5 ug/L Hg during stationary phase growth, three cultures of Desulfovibrio africanus without Hg during exponential phase growth, and Desulfovibrio africanus without Hg during stationary phase growth.  Each chip measures the expression level of 4,585 genes and intergenic regions from Desulfovibrio africanus strain Walvis Bay on a custom Nimblegen format with 75-mer probes with tiled in 4-plex format.

first: Moberly

last: James

first: Dwayne

last: Elias

first: Steven

last: Brown


title: The retinoblastoma gene is targeted for rearrangements in BRCA1-deficient basal-like breast cancer.

status: Public on Jun 27 2012

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

summary: Breast tumors from BRCA1 germ line mutation carriers typically exhibit features of the basal-like molecular subtype. However, the specific genes recurrently mutated as a consequence of BRCA1 dysfunction have not been fully elucidated. In this study, we utilized gene expression profiling to molecularly subtype 577 breast tumors, including 73 breast tumors from BRCA1/2 mutation carriers. Focusing on the RB1 locus, we analyzed 33 BRCA1-mutated, 36 BRCA2-mutated and 48 non-BRCA1/2-mutated breast tumors using a custom-designed high-density oligomicroarray covering the RB1 gene. We found a strong association between the basal-like subtype and BRCA1-mutated breast tumors and the luminal B subtype and BRCA2-mutated breast tumors. RB1 was identified as a major target for genomic disruption in tumors arising in BRCA1 mutation carriers and in sporadic tumors with BRCA1 promoter-methylation, but rarely in other breast cancers. Homozygous deletions, intragenic breaks, or microdeletions were found in 33% of BRCA1-mutant tumors, 36% of BRCA1 promoter-methylated basal-like tumors, 13% of non-BRCA1 deficient basal-like tumors, and 3% of BRCA2-mutated tumors. In addition, RB1 was frequently inactivated by gross gene disruption in BRCA1-related hereditary breast cancer and BRCA1-methylated sporadic basal-like breast cancer, but rarely in BRCA2-hereditary breast cancer and non-BRCA1-deficient sporadic breast cancers. Together, our findings demonstrate the existence of genetic heterogeneity within the basal-like breast cancer subtype that is based upon BRCA1-status.

overall_design: Gene expression profiling of breast tumors. Dual color common reference gene expression study using 55K oligonucleotide microarrays.

first: Göran

last: Jönsson

last: Vallon-Christersson

first: Markus

last: Ringner

first: Sofia

last: Gruvberger-Saal

first: Lao

last: Saal

first: Karolina

last: Holm

first: Cecilia

last: Hegardt

first: Adalgeir

last: Arason

first: Rainer

last: Fagerholm

first: Camilla

last: Persson

first: Dorthe

last: Grabau

first: Ellinor

last: Johnsson

first: Kristina

last: Lövgren

first: Linda

last: Magnusson

first: Paivi

last: Heikkilä

first: Bjarni

last: Agnarsson

first: Oskar

middle: T

last: Johannsson

first: Per

last: Malmström

first: Mårten

last: Fernö

first: Håkan

last: Olsson

first: Niklas

last: Loman

first: Heli

last: Nevanlinna

first: Rosa

last: Barkardottir

first: Ake

last: Borg


title: Identification Atg5-related microRNAs involved in the regulation of tumor formation

status: Public on Jun 26 2012

city: Hsinchu

first: Yen-Ju

last: Lin

address: 195, Sec. 4, Chung Hsing Rd., Chutung

country: Taiwan

institute: Industrial Technology Research Institute

summary: Autophagy plays an important role in physiology and tumorigenesis. We and others have demonstrated that Ha-ras overexpression induces autophagy in NIH3T3 cells. Autophagic machinery is regulated by a family of autophagy associated genes (Atg). The inducible Ha-ras oncogene was introduced into mouse embryo fibroblast Atg5 wild type [MEF-Atg5(+/+)] and Atg5 knock-out [MEF-Atg5(-/-)] cells and the stable cell lines MR and M5R were established, respectively. Our results showed that M5R cell induced larger tumor formation compared with MR cells while these two cell lines were subcutaneously injected into SCID mice under Ha-ras overexpression conditions. It indicates that Atg5 is involved in the suppression of Ras-related tumor formation. MicroRNA (miRNA), approximately 22 nucleotide of non-coding RNA, regulates transcription and translation of the target genes and is involved in cell differentiation and tumorigenesis. A miRNA microarray (932 probes) screening was conducted to identify the autophagy-tumorigenesis-related miRNAs.  Among the significant genes, miR-224 was highly expressed in autophagy deficient cell and it induced tumors. Overexpression miR-224 enhanced the activity of migration and invasion in vitro and tumor formation in vivo. In conclusion, this is the first report to demonstrate that autophagy suppresses tumor formation through down-regulation of microRNA in this case miR-224.

overall_design: MR and M5R cell lines were treated with IPTG for 48 hr. In addition, these cell lines were subcutaneously injected into mice to induce tumor formation. The RNA samples were extracted from above cell lines and tumors. In this research, BEL/ITRI 15K V1.0 miRNA microarray chips were used to evaluate the miRNA expression profile.

first: Sheng-Hui

last: Lan

first: Shan-Ying

last: Wu

first: Roberto

last: Zuchin

first: Xi-Zhang

first: Ih-Jen

last: Su

first: Ting-Fen

last: Tsa

first: Cheng-Tao

first: Hsiao-Sheng

last: Liu


title: Molecular mechanisms underpinning physiological tolerances to salinity and alkaline salinity in Brassica juncea

city: Melbourne

first: Muhammad

last: Javid

state: Victoria

address: Building 142, cnr Tin Alley, Parkville

department: Agriculture and Food Systems

country: Australia

institute: The University of Melbourne

summary: In low rainfall regions soils are naturally conditioned with frequent co-occurrence of salinity and alkalinity. Plant salinity responses both at physiological and molecular level have been extensively researched. However, effects of the combined treatment of alkaline salinity that could greatly reduce plant growth and the mechanisms responsible for tolerance remain indeterminate. In Brassica juncea, large reductions in biomass and increased leaf Na+ concentration under alkaline salinity indicates that the combined treatment had greater negative effect than salinity on both growth and the physiological responses of the plant. To determine molecular mechanisms potentially controlling adaptive tolerance responses to salinity and alkaline salinity, the moderately tolerant genotype NDR 8501 was further investigated using microarray analysis. The transcripts of treated leaf tissues verses those of the untreated control sample were analysed after prolonged stress of four weeks. In total, 528 salinity responsive and 1245 alkaline salinity responsive genes were indentified and only 101 genes were expressed jointly in either of the two treatments. Transcription of 37% more genes involved in response to alkaline salinity than salinity alone, which suggests the increased impact and severity of the combined stress on the plant, indicating the transcription of a far greater number of genes likely involved in mitigation and damage control. Transcription of KUP2 and KUP7 genes involved in potassium homeostasis under salinity alone and NHX1 and ENH1 genes for ion (K+ and Na+) homeostasis under alkaline salinity, clearly demonstrated that different genes and genetic pathways are involved in response to each stress. They further provide supporting evidence for the physiological responses that occur in the plant, with massive reprogramming of the transcriptome leading to partial ion exclusion, shuttling and compartmentation.

overall_design: Salinity and alkaline salinity induced gene expression in Brassica juncea leaf was measured at 4 weeks of prolonged treatment of 50 mM NaCl alone and combined with 2.5 mM HCO3- versus non-stressed control. A single experiment was conducted using Brassica juncea genotype NDR 8501 at a single time point (fours weeks after treatment) with three replications per treatment.

first: Marc

middle: E

last: Nicolas

first: Rebecca

last: Ford


title: Analysis of ethanologenic E.coli strain GLBRCE1 during fermentation of alkaline-pretreated corn stover hydrolysate

first: Michael

last: Schwalbach

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin-Madison

summary: The physiology of ethanologenic Escherichia coli grown anaerobically in alkaline-pretreated plant hydrolysates is not well studied. To gain insight into how E. coli responds to such hydrolysates, we studied an E. coli K-12 ethanologen fermenting a hydrolysate prepared from corn stover pre-treated by ammonia fiber expansion. Despite the high sugar content (~6% glucose, 3% xylose) and relatively low toxicity of this hydrolysate, E. coli ceased growth long before glucose was depleted. Nevertheless, the cells remained metabolically active and continued conversion of glucose to ethanol until all glucose was consumed. Gene expression profiling revealed complex and changing patterns of metabolic physiology and cellular stress responses throughout the different stages of growth. During the exponential and transition phases of growth, high cell maintenance and stress response costs were mitigated, in part, by free amino acids available in the hydrolysate media. However, after the majority of amino acids were depleted from the media cells entered stationary phase and ATP derived from glucose fermentation was consumed entirely by the demands of cell maintenance in the hydrolysate. Comparative gene expression profiling and metabolic modeling of the ethanologen suggested that the high energetic cost of mitigating osmotic, lignotoxin and ethanol stress collectively limits growth, sugar utilization rates and ethanol yields in alkaline-pretreated lignocellulosic hydrolysates.

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

overall_design: 38 samples in total.  24 samples were derived from biological replicate fermentations of alkaline-pretreated cornstover hydrolysate (12 datapoint time-series per fermentation).  The remaining samples were obtained from fermentations conducted in defined media (Glucose Minimal Media (GMM, n=7), Synthetic Hydrolysate media (SynH, n=7)).


title: Gene expression profiles of M. tuberculosis constitutively expressing the transcriptional regulator DosR (Rv3133c).

status: Public on Jun 13 2012

city: Guadalajara

first: Mario

last: Flores Valdez

state: Jalisco

address: Av. Normalistas No. 800

department: Col. Colinas de la Normal

country: Mexico

institute: Centro de Investigación y Asistencia en Tecnología y diseño del Estado de Jalisco, A.C.

summary:
Background: Conflicting results have been reported about the role of the two-component sensor and transcriptional regulator DosS/DosR, controlling the expression of the dormancy DosR regulon, for in vivo virulence of M. tuberculosis. Here, we have used a new approach to further analyze the relevance of the dosRS system, by driving DosR (Rv3133c) expression under the control of a constitutive promoter (phsp60).
Methodology/Principal Findings: M. tuberculosis H37Rv constitutively expressing the transcriptional regulator DosR (Mtb::DosR) was compared to wild type M. tuberculosis (Mtb+/+) for in vitro growth kinetics and expression of the target genes of the DosR dormancy regulon, for in vivo virulence and for immunogenicity in mice. Under aerobic conditions, hsp60-driven DosR induced the expression of 28 out of 39 tested DosR regulon genes. In vitro growth characteristics were comparable for both strains, but Mtb::DosR showed an attenuated in vivo phenotype in immunocompetent mice, as indicated by reduced bacterial replication, reduced pulmonary immunopathology, reduced cachexia and significantly prolonged survival time as compared Mtb+/+. In immunodeficient SCID mice, Mtb::DosR was fully virulent. RT-qPCR analysis revealed a strong and comparable pulmonary TNF-?? and IL-23 expression following intratracheal infection, whereas IL-12 and IL-17 expression was slightly higher with wild type Mtb+/+. Finally, mice persistently infected with Mtb::DosR for 8 months showed five to tenfold higher lung IFN-?? responses against ten of the 48 DosR regulon encoded antigens (Rv1733c, Rv1734, Rv1738, Rv1996, Rv1997, Rv2029c, Rv2623, Rv2627c, Rv2628 and Rv3127) than mice actively infected with Mtb+/+. In spleen however, DosR regulon encoded antigen specific IFN-?? responses were similar in both groups.
Conclusions/Significance. Collectively, these results suggest that increased DosR regulon encoded antigen specific pulmonary T cell responses are responsible for the attenuated phenotype of Mtb::DosR and that infection with Mtb::DosR could be used as a new animal model for studying key aspects of latent tuberculosis.

overall_design: Set of arrays that are part of repeated experiments

first: M

last: Flores-Valdez


title: Exercise training effects on disease resistance are dependent on training regimes and inherent swimming performance in Atlantic salmon

status: Public on Jun 09 2012

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Atlantic salmon juveniles were screened for swimming performance and separated into either poor or good swimmers. After ten weeks of rearing in fresh water, during which both swimming performance groups were part of an exercise training experiment, fish were transferred to seawater and challenged with infectious pancreatic necrosis virus (IPNV) in a co-habitation test. When mortality curve levelled out (45 days post commencement of challenge test), fish that had previously been categorized as good swimmers displayed a significantly higher survival (86.1%) compared to poor swimmers (77.6%). Global gene expression analyses were performed to search for disease resistance correlates. Cardiac ventricle expression of 21 genes was greater in poor swimmers than in good swimmers. These genes were previously classified as virus-responsive genes (VRGs), being reliable markers of viral load. This suggested that inherent swimming performance is associated with higher disease resistance.

overall_design: Atlantic salmon post-smolts belonging to groups previously classified as either poor or good swimmers were challenged with infectious pancreatic necrosis virus (IPNV). Heart ventricle was sampled from challenged and unchallenged fish on day 45 post-commencement of the challenge (when no more mortalities were registered). Nine poor swimmers and nine good swimmers were hybridized against a common reference sample composed of nine unchallenged fish.

first: Vicente

last: Castro

first: Sven

last: Jørgensen

first: Harald

last: Takle


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 the presence of environmental change, natural selection can shape the transcriptome. Under a scenario of environmental change, genotypes that are better able to modulate gene expression to maximize fitness will tend to be favored. Therefore, it is important to examine gene expression at the population level in order to distinguish random or neutral gene expression variation from the pattern produced by natural selection. This study investigates the natural variation in transcriptional response to a cactus host shift utilizing the mainland Sonora population of Drosophila mojavensis.  Drosophila mojavensis is a cactophilic species composed of four cactus host populations endemic to the deserts of North America. Overall, the change in cactus host was associated with a significant reduction in larval viability, as well as the differential expression of 21% of the genome (3,109 genes). Among the genes identified were a set of genes previously known to be involved in xenobiotic metabolism, as well as genes involved in cellular energy production, oxidoreductase/carbohydrate metabolism, structural components and mRNA binding. Interestingly, of the 3,109 genes whose expression was affected by host use, there was a significant overrepresentation of genes that lacked an orthologous call to the D. melanogaster genome, suggesting the possibility of an accelerated rate of evolution in these genes.  Of the genes with a significant cactus effect, the majority, 2,264 genes, did not exhibit a significant cactus-by-line interaction. This population level approach facilitated the identification of genes involved in past cactus host shifts.
Dataset from Population transcriptomics of cactus host shifts in Drosophila mojavensis, Matzkin, LM. Molecular Ecology.

overall_design: Nine isofemale lines of Drosophila mojavensis from the Sonoran cactus host race were utilized.  Each line was reared in either their native host (necrotic organpipe cactus) or an alternative host (necrotic agria cactus).  For each line, two replicates were done for a grand total of 36 hybridizations.


title: Silver nano-colloids disrupt medaka embryogenesis through vital gene expressions

city: Itakura-machi

first: Shosaku

last: Kashiwada

state: Ora-gun, Gunma

address: 1-1-1 Izumino

department: Department of Life Sciences

institute: Toyo University

summary: Using medaka fish embryo model, toxic effects of silver nanocolloids (SNC, 3.8±1.0nm diameter) on developmental morphology and gene expression profile were investigated. SNC caused morphological changes in embryos including cardiovascular malformations, ischemia, underdeveloped central nervous system and eyes, and kyphosis at exposures of 0.5mg/L and 1.0mg/L.. To determine in vivo distribution of SNC, medaka embryos were exposed to 0.5mg/L for 6 days and subjected to ICP-OES analyses. Silver was detected in medaka embryos and chorion at levels of 16.6±9.3pg and 720±29pg, respectively. TEM analyses showed SNC adhered to the chorion surface and inside the chorion. On investigation of oxidative mechanism, NAC (0.05mM) rescued all embryos by 96-hr post treatment, while 0.5mM GSH did not. NAC blocked lipid peroxidation. Furthermore, medaka oligo DNA microarray and qRT-PCR were used for gene expression profiling in embryos exposed for 48-hr to 0.05mg/L SNC. Six genes relative to embryogenesis and morphogenesis such as ctsL, Tpm1, RBP, mt, atp2a1 and hox6b6 turned out to be affected and their involvement to the above malformations was implied.  In conclusion, SNC causes gross malformations in the cardiovascular and central nervous systems in developing medaka embryos through potentially SNC-affected differential expression of a series of genes related to oxidative stress, embryonic cellular proliferation, and morphological development.

overall_design: Three of the stage-21 medaka embryos per sample were exposed in triplicate to 0mg/L (control) and 0.05mg/L SNC for 48 hours.  Therefore, for each exposure condition nine of the stage-21 embryos were prepared and used in the SNC exposure test.

first: G

last: Chandler

first: Yoshihiro

last: Kagami


title: Dissecting modes of action of non-genotoxic carcinogens in primary mouse hepatocytes.

city: Bilthoven

first: Mirjam

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

institute: RIVM

summary:
Under REACH, the European Community Regulation on chemicals, the testing strategy for carcinogenicity is generally based on in vitro and in vivo genotoxicity assays. Given that non-genotoxic carcinogens are negative for genotoxicity, this class of carcinogens will not be detected. Therefore, alternative test are urgently needed. Non-genotoxic carcinogens, however, act through different modes of action, which complicates the development of such an assay.
The aim of this study was to investigate whether gene expression profiling in primary mouse hepatocytes can be used to distinguish different modes of action of non-genotoxic carcinogens.

overall_design: Primary mouse hepatocytes were exposed to 16 non-genotoxic carcinogens with diverse modes of action. Upon profiling, pathway analysis was performed to obtain insight into the biological relevance of the observed changes in gene expression. To recognize similarities in mode of action at the transcriptomic level, both a supervised and an unsupervised comparison approach was applied.

first: Edwin

middle: P

last: Zwart

first: Paul

middle: F

last: Wackers

first: Ilse

last: Huijskens

first: Bob

last: van de Water

first: Timo

last: Breit

first: Harry

last: van Steeg

first: Martijs

last: Jonker

last: Luijten


title: MicroRNA expression profiling of Ewing sarcoma cell lines upon TARBP2 depletion

first: Paolo

last: Provero

overall_design: 3 Ewing sarcoma cell lines: comparison between TARBP2 silencing by shRNA and control.

first: Claudio

last: De Vito

first: Nicolo

last: Riggi

first: Mario-Luca

last: Suvà

first: Karine

last: Baumer

first: Ivan

last: Stamenkovic


title: miRNA expression in the spleen of C57BL mice, p53-knockout C57BL mice, and NO2-knockout C57BL mice.

city: Bethesda

first: Ewy

last: Mathe

state: MD

address: 37 Convent Dr.

institute: National Cancer Institute/National Institutes of Health

summary: The goal of the study is to assess whether inflammation-induced oxidative and nitrosative stress modulates miRNA expression in mouse model deficient in either p53 or NOS2

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA was extracted from the spleen of C57BL mice (WT, NOS2 knockout, and p53 knockout) that were C. Parvum treated or saline control treated. 4 or 5 mice were utilized for each grouping.

first: Mathe

last: Ewy

first: Hussain

last: Perwez


title: Cellular Response of the bacterium Cupriavidus metallidurans CH34 to Strontium: bio-precipitation as strontium carbonate.

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary: The physiological and transcriptomic response of the metal resistant bacterium Cupriavidus metallidurans strain CH34 in response to stable (non-radioactive) strontium ions (Sr) was investigated. C. metallidurans CH34 could survive and proliferate in the presence of relatively high concentrations of SrCl2 (D10 is 70mM, MIC is 120 mM). Precipitation of Sr as strontium carbonate was observed in the culture during aerobic growth of CH34 in the presence of 60 mM SrCl2. To identify the cellular mechanisms involved in the bioprecipitation process, gene expression in the cells was analyzed after short-time (30 min) exposure to low (5 mM) and high (60 mM) concentrations of SrCl2. The transcription of the gene clusters annotated as hmyFCBA and czcCBADRS, coding for ion efflux pumps, was significantly induced following exposure to Sr, and not with Ca.  There were also significant changes is the transcription of the genes encoding TctCBA proteins involved in citrate uptake  and two hypothetical porin coding genes  following exposure Sr and Ca. These results highlight a specific molecular response of bacterium Cupriavidus metallidurans CH34 to Sr, including the identification of putative Sr specific efflux pumps, and thus the potential of this bacterium to distinguish Sr from Ca. These findings will help to better understand natural Sr (and Ca) microbial weathering or mineralization processes in the environment, and could be of interest for bioremediation or bioprocessing of (radioactive) Sr-containing water, soil or waste.

overall_design: Two-condition experiments. Comparing samples after induction with metals (Sr, Ca) versus non-induced samples. Biological triplicate. Each array contains 3 technical replicates.

first: Issam

last: Ben Salem

first: Haïtham

last: Sghaier

first: Karim

last: Mezhoud

first: Pieter

last: Monsieurs

first: Hugo

last: Moors

first: Sami

last: Fattouch

first: Mouldi

last: Saidi

first: Ahmed

last: Landolsi

first: Natalie

last: Leys


title: microRNA expression data from Ewing's sarcoma tumor samples

city: Paris

first: Loredana

last: Martignetti

address: 26, rue d'Ulm

institute: Insitut Curie/ INSERM U900 / Mines Paris Tech

summary: Ewing sarcoma a rare pediatric tumor characterized by EWSR1-ETS fusions. We performed expression profiling of both miRNA and mRNA from the same Ewing's sarcoma tumors.  We propose a novel statistical measure of non-linear dependence between miRNA and mRNA expression, In order to infer miRNA-target interactions. This approach, That we name antagonism pattern detection, Is based on the statistical recognition of a triangular-shaped pattern in miRNA-target expression profiles. This pattern is observed in miRNA-target expression measurements since their simultaneously elevated expression is statistically under-represented in the case of miRNA silencing effect. The proposed method enables miRNA target prediction to strongly rely on cellular context and physiological conditions reflected by expression data.

overall_design: Total RNAs issued of 39 Ewing tumors were used for mRNA and miRNA microarray analyses. The microRNA data were collected using the Illumina human-6 V1 BeadChip.

first: Olivier

last: Delattre

last: Laud-Duval

first: Franck

last: Tirode

first: Gaelle

last: Pierron

first: Stephanie

last: Reynaud


title: Expression and differential expression analysis of HFF cells in G0 phase compared to cells in G1

status: Public on Jun 06 2012

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: Expression and differential expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway.  In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850.  HFF cells were synchronised by serum starvation and reside in G0 phase or G1 phase of mitotic cell cycle.

overall_design: We analyzed three arrays each for HFF cells in G0 phase and cells in G1 phase

first: Jörg

last: Hackermüller

first: Levin

last: Böhlig

first: Kurt

last: Engeland

first: Friedemann

last: Horn


title: miRNA signatures of antigen specific CD8+ T cells at different stages of immune response to LCMV infection

status: Public on Jun 05 2012

city: ATLANTA

first: Tuoqi

last: Wu

state: GA

address: 1510 Clifton Rd, Room G211

institute: Emory University

summary: miRNAs play an important role in regulating CD8+ T cell response. We used the microarray approach to profile the miRNA signatures of naïve, day 5 effector, day 8 effector, and memory CD8+ T cells. We identified a miRNA signature associated with rapidly proliferating effector CD8+ T cells.

overall_design: CD8+ T cells from P14 TCR transgenic mice were transferred to C57BL6 recipients which were subsequently infected with LCMV Armstrong. Donor P14 CD8+ T cells were sorted on day 5, day 8, or >day 60 post-infection. Naïve P14 CD8+ T cells were sorted directly from naive P14 splenocytes. The total RNA including miRNAs was extracted from sorted samples, labeled, and hybridized to Agilent Mouse miRNA microarray.

first: Rafi

last: Ahmed


title: AURATUS goldfish environmental genomics projects: lumiestrone in the liver

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

country: Canada

institute: University of Ottawa

summary: Sexually inactive male goldfish were injected i.p. with lumiestrone (0.5 µg/g) or control vehicle (in charcoal-stripped peanut oil; 5 µL/g) to investigate the biological activity of lumiestrone.

platform_organism:
Carassius auratus
Cyprinus carpio

overall_design:
A common reference design was used:
4 independent groups of sexually inactive male goldfish treated with 0.5 ug/g lumiestrone hybridized against a common vehicle control.
Slides 2, 15, 20, 43.

first: Kate

middle: L

last: Crump

first: Emily

last: Gerrie

first: Vance

last: Trudeau


title: Gene expression profile of chicken lung in response to Avian influenza virus challenge in broiler chickens

city: Davis

first: Huaijun

last: Zhou

state: CA

address: RM 3307 Meyer Hall

institute: UC Davis

summary:
To determine the host response to AIV in chicken lungs, a whole chicken genome array was used to analyze RNA isolated from chicken lungs infected with AIV (4dpi) or medium control (NS). Dual-color, direct comparisons were carried between AIV infected and non-infected controls. Each comparison includes four biological replicates. There were
508 mRNAs (347 down-regulated) were differentially expressed following AIV infection. From the results, MX1, IL-8, IRF-7, TNFRS19 are identified as strong candidate genes involved in regulating the host response to AIV infection in the lungs of broiler chickens. Further gene specific knock-down assay is warranted to elucidate underlying mechanism of AIV infection regulation in the chicken.

overall_design: Dual-color, common reference comparisons were carried between AIV infected and non-infected controls. Four biological replicates, with dye swap labeling, were included in the comparisons. Background subtracted signal intensity were collected from 4 arrays and normalized before data analysis.

first: Ying

last: Wang

first: Vinayak

last: Brahmakshatriya

first: Blanca

last: Lupiani

first: Sanjay

last: Reddy

first: Ron

last: Okimoto


title: Transcriptional analysis of fluorescence-activated sorted Mesp-GFP-labeled B7.5 founder trunk ventral cell lineage cells from Ciona intestinalis

city: Tucson

first: Bradley

middle: J

last: Davidson

state: AZ

department: Molecular Cardiovascular Research Program

institute: University of Arizona

summary: The Ciona heart progenitor lineage (TVC, trunk ventral cells) is first specified by Fibroblast Growth Factor/Map Kinase (FGF/MapK) activation of the transcription factor Ets1/2 (Ets). For this analysis, B7.5 lineage cells were labeled with the Mesp-GFP reporter. In the first experiment, we targeted a dominant-negative form of the sole Ciona FGF receptor (FGFRdn) to the B7.5 lineage using the Mesp enhancer (Mesp-FGFRdn). In the second experiment, we targeted a dominant repressor form of Ets1/2 to the B7.5 lineage using the Mesp enhancer (Mesp-EtsWRPW). This construct is designed to repress Ets1/2 target gene transcription and has previously been shown to abolish TVC induction.

overall_design: We employed whole-genome microarray analysis of sorted B7.5 lineage cells to identify primary FGF:MapK:Ets1/2 target genes.

first: Maximilian

last: Haeussler


title: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue.

status: Public on Jun 04 2012

city: New delhi

first: Padmalatha

state: Delhi

address: Pusa campus

department: Plant Biotechnology

country: India

institute: NRCPB

summary:
Transcriptome analysis in cotton under drought stress.
To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out in leaf tissue. Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Leaf samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. Gene expression profiles in drought induced and their respective control samples were analyzed using Affymertix cotton Genechip Genome arrays to study the global changes in the expression of genome.

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Total RNA was isolated from leaf tissue. Samples were collected from both drought induced and control plants. Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following the Affymetrix protocols. Three biological replicates were maintained.

first: K

middle: V

last: Padmalatha

first: G

last: Dhandapani

first: M

last: Kanakachari

first: Saravanan

last: Kumar

first: Palakolanu

first: Neha

last: Jain

first: Amolkumar

middle: U

last: Solanke

first: H

middle: M

last: Vamadevaiah

first: I

last: Katageri

middle: K

first: S

last: Leelavathi

first: V

first: P

middle: A


title: Streptomyces coelicolor A3(2) SigR regulon

status: Public on Jun 03 2012

city: Madison

first: Yann

last: Dufour

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

type: Genome binding/occupancy profiling by genome tiling array

summary: We determined the genomic locations of the SigR binding sites by chromatin immuno-precipitation of cross-linked DNA and hybridization on a tilling oligonucleotide array after 20 minutes of diamide treatment on cell cultures.

overall_design: Three independent biological samples were prepared separately from the wild-type cells and pooled before hybridization on a single array. Three more independent biological samples were prepared from sigR deletion mutant cells, pooled, and hybridized on another single array. After normalization, the signal from the mutant cells was subtracted from the signal from the wild-type cells to recover SigR specific signal.

first: Min-Sik

last: Kim

first: Ji-Sun

last: Yoo

first: Yoobok

last: Cho

first: Joo-Hong

last: Park

first: Gi-Baeg

last: Nam

first: HaeMin

first: Timothy

last: Donohue

first: Jung-Hye

last: Roe


title: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress during fibre development stages.

first: Padmalatha

summary:
Transcriptome analysis in cotton during fibre development stages.
To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out at fibre development stages (0, 5, 10 and 20 dpa/Days post anthesis). Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. Gene expression profiles in drought induced and their respective control samples were analyzed using Affymertix cotton Genechip Genome arrays to study the global changes in the expression of genome.

overall_design: Total RNA was isolated from 0 dpa, 5 dpa, fibre bearing ovules of 10 dpa, and fibre bearing ovules of 20 dpa. Samples were collected from both drought induced and control plants. Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following the Affymetrix protocols. Three biological replicates were maintained.

first: K

last: Padmalatha

first: G

first: M

first: Saravanan

first: Palakolanu

last: Reddy


title: miRNA Expression Profiling Using Human TaqMan Low Density Array Cards

status: Public on Jun 01 2012

city: Boston

first: Diana

last: Cirstea

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

summary:
miRNA expression profiling was performed on MM.1S MM cells cultured 8 hours in control media or 50nM RGB-286638, with or without BMSCs.
The emerging role of miRNAs in the pathogenesis of multiple myeloma (MM) led us to hypothesize that the miRNA network might be among the inducible transcriptional alterations consequent to MM-bone marrow stromal cell (BMSC) interactions. Our data suggests that BMSC induced MM transcription led to aberrant miRNA expression. We therefore hypothesized that agents interfering with RNAPII transcription might inhibit aberrant miRNA expression in MM. To test this hypothesis we used RGB-286638, a novel protein kinase inhibitor, which works primarily via RNAPII inhibition followed by transcriptional arrest in MM cells. miRNA profiling of RGB-286638-exposed MM cells resulted in RNAPII arrest associated with reduced miRNA levels. RGB-286638 abrogated BMSCs-induced miRNAs, which correlated with growth arrest in MM cells. Analysis of RGB-286638-induced differentially-expressed miRNAs in MM cells, in the presence or absence of BMSCs, revealed RNAPII regulation of expression of BMSC-inducible miRNAs with established oncogenic functions in MM Our findings demonstrate the role of RNAPII in regulating miRNA network, suggesting a new rationale for using agents interfering with RNAPII transcription in the treatment of MM.

overall_design: TaqMan Low-Density Array (TLDA) using human miRNA version 2.0A and version 3.0B cards (Applied Biosystems) were applied to examine the global change of miRNA expression levels in MM.1S cells when co-cultured with BMSCs, with or without RGB-286638 treatment. A total of 756 mature miRNA updated in the Sanger miRBase v.15.0 were quantified according to the manufacturer's instructions as previously described. miRNAs with Ct values higher than 37 were excluded from the analysis. Normalization was carried out with the mean of RNU44 and RNU48. Relative quantification of miRNA expression was calculated with the 2−ΔΔCt Ct method using the ddCt program (Shannon McCormack Advanced Molecular Diagnostics Laboratory Research Services). The data was presented as log10 of the relative quantity of each miRNA.

first: Sigitas

last: Verselis

first: Noopur

last: Raje


title: Does ketoprofen or diclofenac pose the lowest risk to fish?

city: Gothenburg

first: Marija

last: Cvijovic

address: Chalmers Tvärgata 3

institute: Chalmers Univeristy of Technology

summary: Ketoprofen and diclofenac are non-steroidal anti-inflammatory drugs (NSAIDs) often used for similar indications, and both are frequently found in surface waters. Diclofenac affects organ histology and gene expression in fish at around 1 µg/L. Here, we exposed rainbow trout to ketoprofen (1, 10 and 100 µg/L) to investigate if this alternative causes less risk for pharmacological responses in fish. The bioconcentration factor from water to fish blood plasma was <0.05 (4 for diclofenac based on previous studies). Ketoprofen only reached up to 0.6‰ of the human therapeutic plasma concentration, thus the probability of target-related effects was estimated to be fairly low. Accordingly, a comprehensive analysis of hepatic gene expression revealed no consistent responses. In some contrast, trout exposed to undiluted, treated sewage effluents bioconcentrated ketoprofen and other NSAIDs much more efficiently, according to a meta-analysis of recent studies. Neither of the setups is however an ideal representation of the field situation. If a controlled exposure system with a single chemical in pure water is a reasonable representation of the environment, then the use of ketoprofen is likely to pose a lower risk for wild fish than diclofenac, but if bioconcentration factors from effluent-exposed fish are applied, the risks may be more similar.

overall_design:
Ketoprofen (purity ≥98%) (Sigma-Aldrich, Steinheim, Germany) was dissolved in water (500 mg/L concentrated solution), stirred vigorously and diluted stepwise to obtain stock concentrations (0.5 mg/L, 5 mg/L and 50 mg/L). Juvenile rainbow trout (Oncorhynchus mykiss) of both sexes (age: approximately six months, weight: 39.4±6.6g) were obtained from Vänneåns fiskodling AB, Sweden, and kept in 500 L holding tanks with sand-filtered, aerated fresh water in a flow-through system for one week prior to the experiment. Eight experimental 48 L glass aquaria, semi-covered in black plastic bags to reduce visual stress from the outside (12:12 h light:dark photocycle), were supplied with filtered, aerated freshwater at a flow rate of 0.25 L/min. At the onset of the experiment 80 trout were randomly divided among the aquaria (ten fish in each). Peristaltic pumps (500 µl/min) from each stock solution were used to reach target ketoprofen concentrations of 0 (control), 1 (low), 10 (intermediate) and 100 (high) µg/L with two aquaria for each concentration. Water samples were taken from each aquarium at day 1, 7 and 14 and stored at -20°C until analysis. To minimize biological variation due to variable food intake, the fish were not fed during the exposure period. It should be stressed that trout readily cope with food deprivation for much longer periods at these temperatures [Kullgren et al., 2010]. To ensure a stable water quality, temperature (12.9±0.1°C), pH (7.4±0.2) and oxygen saturation (88.3%±1.3) were monitored every third day. The total organic carbon content of the supply water was 2.5 mg/L.
At the experiment termination on day 14, the fish were killed by a rapid blow to the head and blood was collected from the caudal vessels by the use of heparinized syringes. The plasma was instantly separated by centrifugation at 10,000 rpm for 2 min and snap frozen in liquid nitrogen. The length and weight of the fish were measured and their sex determined by macroscopical observation of their gonads. Liver samples for gene expression analyses were collected and snap frozen in liquid nitrogen. Both liver and plasma samples were stored at −70°C until analysis. All animal experiments were approved by the local animal committee in Gothenburg (permission number 216-2010).
A 15k rainbow trout gene expression microarray was designed for the RT analyzer platform (febit, Heidelberg, Germany) using The Institute for Genomic Research (TIGR) Rainbow Trout Gene Index (RTGI) database version 7.0 (http://compbio.dfci.harvard.edu/tgi/). Details on the probe design strategy, but for eelpout (Zoarces viviparus), and transcript selection strategy are described elsewhere [Cuklev et al., 2011, Kristiansson et al., 2009, Cuklev et al., 2012]. When available, transcripts at GenBank (http://www.ncbi.nlm.nih.gov/nucleotide) were used. Results from similar microarrays, performed by our research group using the same platform, have shown good correlation with qPCR data [Cuklev et al., Kristiansson et al., 2009, Cuklev et al., 2012, Gunnarsson et al., 2009, Lennquist et al., 2011].

The frozen liver tissue was homogenized using Tissuelyser (Qiagen) and total hepatic RNA was isolated using QIAcube and RNeasy® Plus Mini Kit (Qiagen). The RNA quantity was determined with spectophotometric measurements (Nanodrop 1000, NanoDrop Technologies) and the quality was assessed by Experion automated electrophoresis using RNA StdSense chip (Bio-Rad, Sundbyberg, Sweden). Biotinylated aRNA was synthesized using MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion®). The aRNA samples (20 µg) were vacuum dried in a vacuum centrifuge, dissolved in 10 µl water and fragmented according to the manufacturer’s protocol.
The following steps described in this subchapter were all performed by febit. Oligonucleotide arrays were synthesized by photo-controlled in situ synthesis using the Geniom One system (febit). Each biochip consists of eight individually accessible micro-channels, each of which is referred to as a microarray in this manuscript. Four individuals (of both sexes) from each control aquarium and each high exposure concentration aquarium were included in the analysis, i.e. eight fish per exposure concentration. In total, two biochips were analyzed corresponding to 16 microarrays.
Pre-hybridization and hybridization were performed based on a customized protocol, described in detail by Cuklev et al. [2011]. The samples were randomly allocated on the biochips. Signals were detected using the internal CCD-camera system of the RT analyzer instrument (febit) and quantified using the Geniom Wizard software. Integration times were 266 and 273 ms, determined automatically by the instrument software.
All statistical calculations were done in R-2.12.2 (www.r-project.org) [ R Development Core Team, 2010]. The quality of pre- and post-normalized arrays was verified with Box and MA plots. The data analysis was performed in the R-package LIMMA [Smyth, 2004]. Data were normalized using the ‘quantile’ method. Moderated t-statistics and adjusted p-values of differential expression were calculated using the empirical Bayes model. As we found no clear differences between the two control aquaria or between the two aquaria with the highest concentration of ketoprofen (100 µg/L), all fish from the same treatment were treated as a single group, i.e. we compared one control group to one group of fish exposed to 100 µg/L of ketoprofen.

first: Filip

last: Cuklev

first: Jerker

last: Fick

first: Erik

last: Kristiansson

first: Lars

last: Förlin

first: DGJoakim

last: Larsson


title: Bacillus subtilis spores, PROTECT experiment, Space-exposed and Mars-exposed vs. Earth-control

city: Merritt Island

first: Wayne

last: Nicholson

state: FL

address: 505 Odyssey Way, Rm. 201-B

department: Microbiology and Cell Science

institute: University of Florida

summary: Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted and fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.


title: Primitive erythropoiesis is regulated by miR-126 via non-hematopoietic Vcam-1+ cells

city: Chapel Hill

first: Scott

last: Hammond

state: NC

department: Dept Cell and Developmental Biology

institute: University of North Carolina

summary: Using classical overexpression/knockout studies, we find that miR-126 regulates the duration of the primitive erythroid program, and confirm this in embryonic miR-126-/- yolk sacs.

platform_organism:
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: MicroRNA microarray analysis was performed on samples from ES cell differentiation

first: S

first: C

last: Sturgeon


title: LmnaN195K Mouse Model

first: Ravi

middle: C

last: Balijepalli

address: 1300 University Ave, B370 SMI

department: Medicine

institute: University of Wisconsin School of medicine and Public Health

type: Expression profiling by genome tiling array

summary: Lamin A/C proteins, encoded by the LMNA gene, are intermediate filament proteins of the nuclear lamina, and predominantly expressed in differentiated cells including cardiomyocytes. Mutations in LMNA are associated with laminopathies, congenital diseases affecting muscle and homeostasis. One of the laminopathies associated with a missense mutation (N195K) in the A-type lamins results in dilated cardiomyopathy (DCM) with arrhythmias and sudden death. However it is unknown how the mutation in this LMNA gene contributes to the mechanism of arrhythmia and sudden death.  To investigate this a mouse line expressing the Lmna-N195K (LmnaN195K/N195K) was used. Mutant mice demonstrated reduced fractional shortening, LV mass, wall thickness and dilated cardiomyopathy by echocardiography at 6 weeks consistent with human DCM, and died at an early age (6-7 weeks). Comparative cDNA microarray analysis from LmnaN195K/N195K and the wild type (WT) control ventricles at 6 weeks age revealed significant alterations in the expression of ion channels, transporter proteins, caveolins and associated proteins such as MAP kinases. Transmission electron microscopy analysis showed structural alterations of the ventricular myocytes with increase in number of caveolae. Quantitative Western blot analysis confirmed reduced expression for Cavβ (2 fold) subunits of the L-type Ca2+ channel. In contrast the expression levels of Cav3 (2.5 fold) was significantly increased. To investigate the functional impact of Lmna N195K on the ICa,L, we transiently expressed either the WT LMNA+GFP, Lmna N195K+GFP or GFP (control) in isolated neonatal mouse ventricular myocytes and performed whole cell patch clamp analysis. Transient expression of Lmna N195K significantly reduced (58 %) peak ICa,L (-6.0 ± 2 pA/pF, n=9) compared to GFP control (-14 ± 2 pA/pF, n=8). Expression of WT LMNA did not affect the ICa,L (-14.2 ± 2.5 pA/pF, n=8) compared to control. Conclusion: We conclude that Lmna N195K mutation results in reduced expression of ion channels and scaffolding proteins in the left ventricle with a significant reduction in peak ICa,L in ventricular myocytes and these may contribute to the mechanism of arrhythmia and dilated cardiomyopathy.

overall_design: 6 samples

first: Amina

last: Saqib


title: Role of intracellular calcium in Drosophila larval growth and viability

status: Public on Jun 02 2012

city: Bangalore

first: Gaiti

last: Hasan

address: GKVK Campus,

institute: NCBS, TIFR

summary: Intracellular Ca2+ release through the Inositol 1,4,5-Triphosphate Receptor (InsP3R) is a feature of all multicellular organisms in which it shapes the temporal and spatial aspects of calcium signaling in cells, affecting several developmental and physiological processes. Mutants in the InsP3R gene of Drosophila (itpr) exhibit a range of defects which include growth defects and larval lethality.The Drosophila Insulin-like peptides (ILPs) are encoded by multigene families that are expressed in the brain and other tissues. Upon secretion, these peptides likely serve as hormones, neurotransmitters, and growth factors. In Drosophila melanogaster, molecular genetic studies have revealed Drosophila ILPs as elements of a conserved insulin signaling pathway, and as in other animal models, it appears to play a key role in metabolism, growth, reproduction, and aging. Previous work from our group has shown that InsP3R function can be rescued by ectopically expressing InsP3R in dilp cells  or can be compensated by altering the activity of Sarco-Endoplasmic Reticulum Calcium-ATPase (SERCA). To understand the molecular basis of larval lethality and growth defect in Drosophila InsP3R mutants and to decipher possible cross talk of itpr gene with other signaling pathways we have carried out genome wide microarray experiments. We have compared the transcript profiles of i) itpr mutant larvae and wild type larvae, ii) dilp rescue larvae with itpr mutant larvae iii) itpr and SERCA double mutant larvae with itpr mutant larvae. By this we have identified genes whose levels are altered in itpr mutants and are restored towards wild type in dilp rescue larvae with itpr mutant larvae and itpr and SERCA double mutants. Our experiments help in identify genes that are regulated by changes in intracellular Ca2+ in the context of larval viability may contribute to the better understanding of the major human pathologies caused by calcium misbalance or by dysregulation of the insulin/IGF pathway.

overall_design: The 8x60k array AMADID: 27326 slide was scanned immediately by PerkinElmer Scan array Gx Microarray scanner. The Scan array software (PerkinElmer) was used for grid wise normalization of array images. Three were used with Mutant, three for Dilp Rescue and two for Kum Rescue experiments . The data was analysed by GeneSpring GX Agilent . The differential expression was considered if the Log 2 mean of at least -1 for the down regulated genes and +1 for the upregulated genes. We considered only the genes that were reproducible from biological triplicates for Mutant, biological treplicates for Dilp Rescue and biological duplicates for Kum Rescue.

first: Satish

last: Kumar

first: Debleena

last: Dey


title: arcole / pgpr-Nitrogenous nutrition efficiency of canola in spring : identification of targets for plant breeding

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: pc_arcole - arcole / pgpr - What are the genes implicated in the efficiency of nitrogenous nutrition when A.thaliana is inoculated with a PGPR (Plant Growth Promoting Rhizobacteria)? - A.thaliana seeds germinated and grew during ten days until they were transfered in 6 different media: 0,5 mM nitrate with PGPR (Plant Growth Promoting Rhizobacteria), 0,5mM nitrate without PGPR, 2mM nitrate with PGPR, 2mM nitrate without PGPR, 20 mM nitrate with PGPR, 20 mM nitrate without PGPR. Young plantlets grew 7 days in these new mediums. Shoots are collected in eppendorf.

overall_design: 6 dye-swap - dose response,organ comparison,treated vs untreated comparison

first: Bruno

last: Touraine

first: Linhda

last: Couvelard

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: ChIP-chip of lymphocytes using H3K9Ac, H3K4me3, H3K9me3, H3K27me3 and H4K16Ac antibodies

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: Both genetic and environmental factors are implicated in Type 1 Diabetes (T1D). Since environmental factors can trigger epigenetic changes, we hypothesized that variations in  histone posttranslational modifications (PTMs) at the promoter/enhancer regions of T1D susceptible genes may be associated with T1D. We therefore evaluated histone PTM variations at known T1D susceptible genes in blood cells from T1D patients versus healthy non-diabetic controls, and explored their connections to T1D. We used the chromatin-immunoprecipitation-linked-to-microarray approach to profile key histone PTMs, including H3-lysine-4 trimethylation (H3K4me3), H3K27me3, H3K9me3, H3K9 acetylation (H3K9Ac) and H4K16Ac at genes within the T1D susceptible loci in lymphocytes, and H3K4me3, H3K9me2, H3K9Ac and H4K16Ac at the IDDM1 region in monocytes of T1D patients and healthy controls separately. We screened for potential variations in histone PTMs using computational methods to compare datasets from T1D and controls. Interestingly, we observed marked variations in H3K9Ac levels at the upstream regions of HLA-DRB1 and HLA-DQB1 within the IDDM1 locus in T1D monocytes relative to controls. Additional experiments with THP-1 monocytes demonstrated increased expression of HLA-DRB1 and HLA-DQB1 in response to interferon- and TNF-treatment that were accompanied by changes in H3K9Ac at the same promoter regions as that seen in the patient monocytes. These results suggest that the H3K9Ac status of HLA-DRB1 and HLA-DQB1, two genes highly associated with T1D, may be relevant to their regulation and transcriptional response towards external stimuli. Thus, the promoter/enhancer architecture and chromatin status of key susceptible loci could be important determinants in their functional association to T1D susceptibility.

overall_design: We evaluated histone PTM variations at known T1D susceptible genes in blood cells from T1D patients versus healthy non-diabetic controls, and explored their connections to T1D. We used the ChIP-chip approach to profile key histone PTMs, including histone H3K4me3, H3K27me3, H3K9me3, H3K9 acetylation (H3K9Ac) and H4K16Ac, at genes within the T1D susceptible loci in lymphocytes.

first: Rama

last: Natarajan

first: Feng

last: Miao

first: Zhuo


title: Mammary stem cells: molecular profiling to identify novel biomarkers and the stem cell niche

city: Beltsville

first: Anthony

middle: V.

last: Capuco

address: 10300 Baltimore Ave., Bldg 200, Rm 14

department: Beltsville Agricultural Research Center

institute: USDA-ARS

summary: Identification and transcriptome analysis of mammary stem cells (MaSC) are important steps toward understanding the molecular and cellular bases of mammary epithelial growth, homeostasis and tissue repair. We identified MaSC based upon their ability to retain bromodeoxyuridine (BrdU) for an extended period. Using laser microdissection, we isolated four categories of cells from the mammary epithelium of female bovine calves. These categories included label retaining epithelial cells (LREC) from the basal layer (LRECb), basal control cells (ECb), LREC from embedded layers (LRECe) and embedded control cells (ECe). Microarray analysis revealed 592 genes that were differentially expressed between LRECb and ECb, and 110 genes between LRECe and ECe. Our analysis supported classification of LRECb as MaSC and LRECe as progenitor cells. Enriched expression of genes in LRECb were associated with stem cell attributes and identified enrichment of Wnt, Notch and MAPK pathways of self renewal and proliferation. Genes expressed in LRECe revealed retention of some stem-like properties along with up-regulation of differentiation factors and the Notch pathway involved in lineage commitment. The basal epithelium provided for the stem cell niche, characterized as a microenvironment containing numerous survival and proliferation factors, growth suppressors and chromatin modifiers in balance state. We conclude that BrdU label retention identifies stem and progenitor cells, wherein MaSC are located in the basal epithelial layer and committed progenitor cells are localized in more apical layers. Results provide novel candidate markers for bovine MaSC with potential applicability to the study of MaSC in other species.

overall_design: Five Holstein heifers were injected with bromodeoxyuridine (BrdU) for five consecutive days and sacrificed 45 days later, at which time mammary samples were obtained and processed. Cryosections were prepared and immunostained to detect epithelial cells that retained BrdU label (LREC). Four classes of cells were excised by laser microdissection, which included LREC and control cells in the basal and in the suprabasal layers of the mammary epithelium. For each cell type, cells were lysed, RNA was reverse transcribed and cDNA amplified for microarray analysis. Twenty microarrays were utilized for sample hybridization and another array for hybridization of amplified cDNA from a water blank.

first: Ratan

last: Choudhary

first: Robert

middle: W

last: Li

first: Christina

last: Evock-Clover


title: ChIP-chip of monocytes using H3K9Ac, H3K4me3, H3K9me2 and H4K16Ac antibodies

overall_design: We used ChIP-chip to profile key histone PTMs, including H3K4me3, H3K9me2, H3K9Ac and H4K16Ac, at the IDDM1 region in monocytes of T1D patients and healthy controls.


title: Trastuzumab produces therapeutic actions by upregulating miR-26a and miR-30b in breast cancer cells

city: Kyoto

first: Akira

last: Myomoto

address: Yoshida-Shimoadachi

institute: Kyoto Univ.

summary: Objective: Trastuzumab has been used for the treatment of HER2-positive breast cancer (BC). However, a subset of BC patients exhibited resistance to trastuzumab therapy. Thus, clarifying the molecular mechanism of trastuzumab treatment will be beneficial to improve the treatment of HER2-positive BC patients. In this study, we identified trastuzumab-responsive microRNAs that are involved in the therapeutic effects of trastuzumab.  Methods and results: RNA samples were obtained from HER2-positive (SKBR3 and BT474) and HER2-negetive (MCF7 and MDA-MB-231) cells with and without trastuzumab treatment for 6 days. Next, we conducted a microRNA profiling analysis using these samples to screen those microRNAs that were up- or downregulated only in HER2-positive cells. This analysis identified miR-26a and miR-30b as trastuzumab-inducible microRNAs. Transfecting miR-26a and miR-30b induced cell growth suppression in the BC cells by 40% and 32%, respectively. A cell cycle analysis showed that these microRNAs induced G1 arrest in HER2-positive BC cells as trastuzumab did. An Annexin-V assay revealed that miR-26a but not miR-30b induced apoptosis in HER2-positive BC cells. Using the prediction algorithms for microRNA targets, we identified cyclin E2 (CCNE2) as a target gene of miR-30b. A luciferase-based reporter assay demonstrated that miR-30b post-transcriptionally reduced 27% (p=0.005) of the gene expression by interacting with two binding sites in the 3’-UTR of CCNE2.  Conclusion: In BC cells, trastuzumab modulated the expression of a subset of microRNAs, including miR-26a and miR-30b. The upregulation of miR-30b by trastuzumab may play a biological role in trastuzumab-induced cell growth inhibition by targeting CCNE2.

overall_design: We obtained microRNA expression profiles of breast cancer cell lines, MCF7, MDA-MB-231, SKBR3, and BT474, with or without trastuzumab (4microgram/mL) treatment.

first: Takehiro

last: Ichikawa

first: Fumiaki

last: Sato

first: Kazuya

last: Terasawa

first: Soken

last: Tsuchiya

first: Tasakazu

last: Toi

first: Gozoh

last: Tsujimoto

first: Kazuharu

last: Shimizu


title: Transcriptional profiling of turkey muscle satellite cells transfected with versican-siRNA during proliferation and differentiation

city: East Lansing

first: Kelly

middle: R

last: Sporer

state: MI

address: 3365 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

summary: In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene versican (VCAN) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788).  The VCAN gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the VCAN-mediated effects on the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted).

overall_design: This experiment was designed to investigate the role of VCAN expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation.  Satellite cells were isolated from 7-week-old turkeys from the RBC2 line.  Cells were transfected with either VCAN siRNA or a lipofectamine control; VCAN expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted).  Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction.   Microarrays directly compared the VCAN-knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of VCAN expression in satellite cell development and function.  Hybridizations were performed in random order.

first: Sandra

middle: G

last: Velleman

last: Tempelman

first: Gale

last: Strasburg


title: Expression data from 0dpa ovules of GhHD-1 silenced and over-expression transgenic cotton lines

city: Canberra

first: Sally

middle: Ann

last: Walford

state: ACT

address: Clunies Ross street

department: Plant Industry

institute: CSIRO

summary:
Cotton (Gossypium hirsutum L.) fibres are specialised trichomes that extend from the seedcoat. To date only a few genes directly involved in the differentiation of these epidermal cells have been identified. We have identified a HD-ZIP transcription factor, GhHD-1, expressed in trichomes and early fibres that might play a role in cotton fibre initiation. Here we characterise GhHD-1 from G. hirsutum and show, using reporter constructs and qRT-PCR, that they are expressed predominantly in epidermal tissues during early fibre development and in other tissues bearing epidermal trichomes. GhHD-1 silencing caused reduced trichome formation and delayed the timing of fibre initiation whereas constitutive over-expression of GhHD-1 increased the number of fibres initiating on the seed, but did not affect leaf trichomes. Expression of GhHD-1 in transgenic cotton silenced for different fibre MYBs suggest that in ovules it acts downstream of GhMYB25-like. Microarray analysis of silencing and over-expression lines of GhHD-1 indicated that it potentially functions through a WRKY transcription factor and calcium-signalling pathway genes that are shared with some biotic stress reactions.
Microarray analysis of 2 biological replicates each of GhHD-1 silenced and over-expression transgenic lines relative to wild-type were used to identify downstream targets of this transcription factor during early fibre development.

overall_design: 0 dpa (Days post anthesis) ovules from GhHD-1 silenced and over-expression lines and wild-type cotton plants were selected for RNA extraction and hybridisation on Affymetrix cotton arrays. Cotton fibre development initiates on the epidermal surface of each ovule within a cotton boll on the day of flowering and GhHD-1 has been shown to be most highly expressed at this stage (0 dpa). Ovules were obtained from 0dpa flowers for hybridisation to cotton arrays to identify genes that may be regulated by GhHD-1 during this early fibre development stage (initiation).

first: Sally-Ann

first: Yingru

last: Wu

first: Danny

last: Llewellyn

first: Elizabeth

last: Dennis


title: Differentially regulated genes induced in Mycobacterium avium subspecies paratuberculosis by in vitro infection of THP-1 human macrophage cell line

city: Amherst

first: Andrea

last: Cossu

state: MA

address: 102 Holdsworth way

department: Department of Food Science

institute: University of Massachusetts, Amherst

summary: Transcriptional profile of Mycobacterium avium subspecies paratuberculosis in in vitro THP-1 (ATCC TIB-202) cell line infection, comparing bacteria grown in host medium and intracellular bacteria recovered from infected THP-1 cells.

platform_organism: Mycobacterium avium subsp. paratuberculosis K-10

overall_design: Two-condition experiment, MAP-K vs. intracellular MAP-THP-1. Biological replicates: 10 controls, 10 intracellular MAP-THP-1, independently grown and harvested. In controls and  intracellular MAP-THP-1 cells, good quality RNA samples obtained from each pellet were pooled together and used for microarray experiments to get an average of 10 separate experiments, four replicates per array.

first: Valentina

last: Rosu