title: Gene expression profiles in bone marrow of human gastric adenocarcinoma at stage III and stage IV

status: Public on Oct 22 2013

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: A secreted factor in bone marrow associated with metastatic gastric cancer was indentified through expression profiling in bone marrow of stage III and stage IV gastric adenocarcinoma.

overall_design: In the study presented here, bone marrow samples from patients with stage III or stage IV gastric adenocarcinoma were used to acquire expression profiles.

first: Koshi

last: Mimori


title: STOP2 activated transcription in the stop1-mutant: STOP2-complemented lines (stop1-mutant with transformed STOP2) vs. stop1-mutant of Arabidopsis

status: Public on Oct 21 2013

city: Gifu

first: Yuriko

last: Kobayashi

address: 1-1, Yanagido Gifu

department: Faculty of Applied Biological Sciences

institute: Gifu University

summary: Transcriptional profiling of genes recoverd by STOP2-complementation in the stop1-mutant (STOP2 expression is repressed in the stop1-mutant). The roots were exposed to Al and low pH stressed conditions, then genes recovered expression were analyzed. Goal is identifying the genes can be actevated the expression by STOP2.

overall_design: Two-condition experiment, STOP2-complemented lines (stop1-mutant backgoround) v.s. stop1-mutant. Biological replicates: 3 of low pH treatments replicates, 3 Al treatment replicates.

first: Yasufumi

first: Hiroyuki

last: Koyama


title: Gene expression profiling of articular cartilage reveals functional pathways and networks of candidate genes for osteochondrosis in pigs

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary:
Osteochondrosis disorder is characterized by a failure of endochondral ossification of the articular-epiphyseal cartilage and the physeal growth cartilage. The number and identity of relevant genes are unknown.
Simultaneously, 24,123 probe-sets were screened, of which 12,292 had present in at least 50% of the samples of either affected or non-affected and were used for further analysed of differential expression.

overall_design: Total RNAs of articular cartilage tissues from  affected and non-affected sib-pairs animals were hybridized to Affymetrix Porcine Genome Arrays.

first: Siriluck

last: Ponsuksili

first: Eduard

last: Murani

first: Noppawan

last: Rangkasenee


title: Transcription landscape at the HoxD locus in developing caeca

status: Public on Oct 23 2013

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

type: Expression profiling by genome tiling array

summary: Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit.

overall_design: Transcriptional activity at the HoxD locus in developing caeca at E13.5, Array data were quantile normalized within cDNA/genomic DNA replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 80 bp. For each tissue, two independent RNA extractions, cDNA synthesis and array hybridizations were performed, except for del(1-4i) and del(9-11) mutant caeca.

first: S

last: Delpretti

first: D

last: Duboule


title: Expression analysis of fast-fermenting high-gravity maltose Saccharomyces cerevisiae Y55 mutants

status: Public on Oct 25 2013

city: Copenhagen V.

first: Richard

last: Baerends

state: Sealland

address: Gamle Carlsberg Vej 10

department: Yeast Biology

country: Denmark

institute: Carlsberg Laboratory

summary:
Investigation of whole genome gene expression level changes in three S. cerevisiae Y55 mutants, compared to the wild-type strain.  The UV-induced mutations enable the mutant strains to ferment  high-gravity maltose faster than the WT.
The mutants analyzed in this study are further described in Baerends, R.J.S., J.L. Qiu, L. Gautier, and A. Brandt. A high-throughput system for screening of fast-fermenting Saccharomyces cerevisiae strains. Manuscript in preparation.

overall_design: A single-dye 12-plex array chip study using double-stranded DNA prepared from messenger RNA purified from total RNA recovered from three separate Saccharomyces cerevisiae Y55 wild-type cultures and 3x three separate cultures each corresponding to a fast-fermenting UV-induced mutant (mutant 1, 2 and 3), during fermentation of high-gravity maltose at day 2. Each array on the 12-plex chip measures the expression level of 5,777 genes from Saccharomyces cerevisiae S288C with eight 60-mer probes per gene, with three-fold technical redundancy.

middle: J


title: E. coli rnpb mutants: wild type proxy strain DW2/pFLP-Ec vs. DW2/pFLP-Bs strain

city: Stanford

first: Jasmine

middle: L.

last: Loveland

state: California

address: 371 Serra Mall Rm 320

department: Biology

country: USA

institute: Stanford University

summary:
Transcriptional profiling of DW2 E. coli cells in exponential growth phase that have a chromosomal deletion of the rnpb gene (which encodes the catalytic subunit of Ribonuclease P).
We compared the test strain DW2/pFLP-Bs that expresses Bacillus subtilis rnpb from plasmid pFLP-Bs to reference strain DW2/pFLP-Ec, which expresses E. coli rnpb from plasmid pFLP-Ec.

overall_design: Two-strain experiment, wildtype proxy strain DW2/pFLP-Ec (reference) vs DW2/pFLP-Bs RT-10-2 (test) on each array. Biological replicates: 1 reference, 2 test. Four slides plus one dyeflip slide

middle: L

first: Robert

last: Dorit


title: ArcA Chip-chip from Escherichia coli MG1655 K-12, WT and ∆arcA strains

status: Public on Oct 17 2013

city: Madison

first: Dan

last: Park

state: WI

address: 440 Henry Mall

institute: UW Madison

type: Genome binding/occupancy profiling by genome tiling array

summary:
Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12.
Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli

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

overall_design: Mapping of occupancy of ArcA in the genome of Escherchia coli MG1655 K-12 during anaerobic fermentation and aerobic respiration.  Immunoprecipitated DNA compared to INPUT for each sample.

first: Sohail

last: Acktar

first: Aseem

last: Ansari

last: Landick

first: Patricia

last: Kiley


title: Effects of mating on gene expression profiles of mature ant queens

status: Public on Oct 26 2013

first: Yannick

last: Wurm

address: Biophore

department: Ecology and Evolution

institute: University of Lausanne

summary: Will be added/updated once the manuscript is finalized.

overall_design: Cardiocondyla obscurior queens. Three treatments: virgin queens, queens mated by real males, queens sham-mated (by sterile males). Queens collected 1 week and 8 week after mating. seven loops for queens collected 1 week after mating; nine loops for queens collected 8 weeks after mating. Five direct comparisons (with dye-swaps... so 10 arrays) were done of between 1 week and 8 week samples of queens mated by real males. Each sample is RNA from two queens (from different colonies). Samples were hybridized against Solenopsis invicta microarrays (signal was detectable for most clones!)

first: Jan

last: Oettler

first: John

last: Wang

first: Laurent

last: Keller

first: Jürgen

last: Heinze


title: Differential expression of miRNAs in Retinoblastoma cells (Y79) in response to anti-HMGA2 siRNA treatment

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: The main objective of the study is to identify the de-regulated miRNAs in association with HMGA2 (oncogene) in the Retinoblastoma tumorus. The present experiment was carried out using Y79 (Retinoblastoma cell line), as the invitro model of Retinoblastoma tumor. The HMGA2 transcripts were silenced using siRNA and the post-silenced RB cells (at the end of 48 hours) were subjected to miRNA profiling using agilent platform.The key miRNAs de-regulated in this experiment has been validated using qRT-PCR and further their role has been evaluated by addition of specific antagomirs in RB cell lines (Y79 and Weri Rb 1).

overall_design:
Agilent one-color experiment,Organism: Homo sapiens ,Agilent Human miRNA 8x15k Arrays AMADID: 021827 [Agilent miRNA labeling reagent and Hybridization Kit Cat # 5190-0408]
RB cells (Y79) treated with anti-HMGA2 siRNA or with control

first: Nalini

last: Venkatesan

first: Krishnakumar

last: Subramanian

first: Vikas

last: Khetan

first: Ashwin

middle: M

last: Reddy


title: The cold-induced two-component system CBO0366/CBO0365 regulates metabolic pathways with novel roles in cold tolerance of Group I Clostridium botulinum ATCC 3502

status: Public on Oct 29 2013

city: University of Helsinki

first: Elias

last: Dahlsten

address: P.O. Box 66

department: Faculty of Veterinary Medicine

country: Finland

institute: University of Helsinki

summary: The two-component system CBO0366/CBO0365 was recently demonstrated to have a role in cold tolerance of Group I Clostridium botulinum ATCC 3502. The mechanisms under its control, ultimately resulting in increased sensitivity to low temperature, are unknown. A transcriptomic analysis with DNA microarrays was performed to identify the differences in global gene expression patterns of the wild-type ATCC 3502 and a derivative mutant with insertionally inactivated cbo0365 at 37 °C and 15 °C. Altogether 150 or 141 chromosomal CDSs were found to be differently expressed in the cbo0365 mutant at 37 °C or 15 °C, respectively, and thus considered to be under direct or indirect transcriptional control of the response regulator CBO0365. Of the differentially-expressed CDSs, expression of 141 CDSs was similarly affected at both temperatures investigated, suggesting that the putative CBO0365 regulon was practically not affected by temperature. The regulon involved genes related to acetone-butanol-ethanol (ABE) fermentation, motility, to arsenic resistance, and phosphate uptake and transport. Deteriorated growth at 17 °C was observed for mutants with disrupted ABE fermentation pathway components (crt, bdh and ctfA), arsenic detoxifying machinery components (arsC and arsR), or phosphate uptake mechanism components (phoT), suggesting roles for these mechanisms in cold tolerance of Group I C. botulinum. Electrophoretic mobility shift assays showed recombinant CBO0365 to bind to the promoter regions of crt, arsR, and phoT, as well as to the promoter region of its own operon, suggesting direct DNA-binding transcriptional activation or repression as means for CBO0365 in regulating these operons. The results provide insight to the mechanisms Group I C. botulinum utilize in coping with cold.

overall_design: C. botulinum ATCC 3502 cbo0365 mutant vs. wild type; 3 replicates of each strain; growth at 37C in TPGY broth batch culture and subjected to cold shock to 15C; sampling at mid-log growth phase before cold shock, and 1 h after temperature downshift to 15C (= 2 time points). Dye-swapped hybridization.

first: Zhen

last: Zhang

first: Panu

last: Somervuo

first: Nigel

middle: P

last: Minton

first: Miia

last: Lindström

first: Hannu

last: Korkeala


title: Chromatin landscape at the HoxD locus in developing caeca (ChIP-chip)

first: Marion

last: LELEU

overall_design: Distribution of histone marks and RNA Pol2 at the HoxD locus in caeca at E13.5, Array data were quantile normalized within ChIP/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp. For each tissue, two independent ChIP-chip experiments were performed with all mentionned antibodies.

first: S

last: Delpretti

first: D

last: Duboule


title: Identification of the molecular targets of miR-185 in DN3 stage thymocytes

status: Public on Oct 28 2013

city: Dallas

first: Nicolai S.C.

last: van Oers

state: Texas

address: 6000 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

summary: T cell-specific overexpression of miR-185 caused a developmental block at DN3 stage of thymopoiesis.

overall_design: DN3 stage thymocytes were sorted from the wild type (C57BL/6) and miR-185 Tg mice, followed by total RNA isolation.

first: Serkan

last: Belkaya

first: Nicolai

middle: S


title: Transcriptional responses of Acinetobacter baumannii ATCC 17978 to limiting iron availability

status: Public on Oct 18 2013

city: Adelaide

first: Bart

last: Eijkelkamp

state: SA

address: North Tce

country: Australia

institute: University of Adelaide

summary: A. baumannii ATCC 17978 cells were incubated under iron replete (mueller-hinton) and iron limiting (MH + 200 µM 2,2'-dipyridyl) conditions, total RNA was extracted when cultures reached OD600=0.7.

overall_design: The probes on the microarray cover all predicted open reading frames (at least 4 per ORF) and additional replicates of housekeeping genes of the A. baumannii ATCC 17978 genome

first: B

middle: A

first: K

last: Hassan

first: I

middle: T

last: Paulsen

first: M

middle: H

last: Brown


title: Gene expression in response to progestin R5020

status: Public on Oct 14 2013

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary: Breast cancer cell lines containing the progesterone receptor respond to progestins, altering expression of a subset of genes. In a previously published experiment of inducible knock-down of histone H1 isoforms with an shRNA-expression lentivector  (GSE12299), we modified the breast cancer cell line T47D with different vectors. Here, we explored response to progestin R5020 of control cells generated with the empty shRNA-expression vector.

overall_design: Stable breast cancer-derived cell lines containing the empty vector for inducible shRNA expression were grown for two days in the absence of serum. Progestin R5020 or vehicle was added for 6 hours, in duplicate, and RNA was extracted for microarray hybridization.

first: Albert

last: Jordan

first: Mónica

last: Sancho


title: Vibrio vulnificus: normal intracellular c-di-GMP level vs. high intracellular c-di-GMP level

city: Seoul

first: Jin Hwan

last: Park

address: Gwanak-ro 599

country: South Korea

institute: Seoul National University

summary: The profiles of transcripts from the V. vulnificus grown under normal and high c-di-GMP conditions were compared by using a V. vulnificus whole-genome microarray

overall_design:
Two-condition experiment,  normal c-di-GMP condition vs. high c-di-GMP condition. Biological replicates: 3 control, 3 experimental, independently grown and harvested. One replicate per array.
For transcriptome analysis, the V. vulnificus whole genome TwinChip, manufactured and kindly provided by the 21C Frontier Microbial Genomics and Applications Center (Daejeon, South Korea), was used.

first: Jin-Hwan

first: Sang-Ho

last: Choi


title: Analysis of prebiotic carbohydrate utilization by Bifidobacterium lactis Bl-04 using differential transcriptomics

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

state: NC

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

summary: The global transcriptome of the Bifidobacterium animalis subsp. lactis Bl-04 was analyzed during exponential growth on 11 prebiotic carbohydrates and glucose to identify the specific gene cluster differentially upregulated in response to each carbohydrate.

overall_design: Affymetrix hybridization experiments were performed to compare the differential transcriptional profiles of the B. lactis Bl-04 at the early-log (OD600nm 0.3-0.5) phase. 12 carbohydrates were tested with two technical replicates to each condition for a total of 24 hybridizations.

first: Joakim

last: Andersen

first: Yong

last: Goh

middle: R


title: Positive and negative CD4+ T-cell immunoselection: effects on miRNA profile

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: Human CD4+ T-cell miRNAs were profiled by OpenArray after either positive or negative cytoselection

overall_design: CD4+ T-cells were obtained from blood of three human donors by positive and negative immunoselection methods. The miRNA complement of positively and negatively selected cells was determined by OpenArray.

last: Yu

first: D

last: Espinoza

last: McAlexander


title: ENF1 (enlarged fil expression domain1) vs wild-type Col.

city: Okazaki

first: Koichi

last: Toyokura

state: Aichi

address: myodaiji-cho

institute: Nationali institute for basic biology

summary: ENF1 gene (AT1G79440) encodes succinic semialdehyde dehydrogenase. Loss-of-function mutant of ENF1 shows pleiotropic phenotypes, including abnormal gene expression along the adaxial-abaxial axis in leaf development. enf1-1 allele has a point mutation in the splicing accepter site of 11th intron of ENF1. enf1-6 allele has T-DNA insertion in 5th exon of ENF1.

overall_design: Differential gene expression between in enf1 and in wild type was measured at shoot apex of six-day-after-sowing seedlings. Independent experiments for wild type, enf1-1, and enf1-6 were performed four, three, and three times, respectively.

first: Kiyotaka

last: Okada


title: Gene expression of metamorphosis in fire ants

status: Public on Oct 20 2013

first: Yannick

last: Wurm

summary: Ants are among the most successful animals on earth, with societies of a complexity that rivals our own. These societies are characterized by reproductive division of labor between female queens that can live several years and lay thousands of eggs per day, workers that live only a few months and are sterile, and males that live only a few weeks and do not participate in colony tasks. These striking differences in lifespan and roles are echoed by extensive morphological and physiological divergence. Using the fire ant, Solenopsis invicta, we conduct the first genome-wide survey of developmental gene expression levels over 20 time-points from larval to adult stages in workers, queens and males

overall_design: Three castes: Worker, queen & male; four colonies used for each caste (12 colonies total). Timepoints: 0h, 3h, 6h, 12h, 18h, 24h, 36h and 48h (hour timepoints) and once every 24hours until eclosion (day timepoints). Eclosion occured after 15 days for male (21 timepoints), 14 days for queen (20 timepoints) and 12 days for worker larvae (19 timepoints). We used a loop design with direct comparisons of consecutive samples within each cast: two loops in one Dye-direction, two loops in the other for balance. Additionally, 3-5 hybridizations against an unrelated Reference RNA were performed within each replicate loop. Microarray batch is indicated in the description column

first: Michael

last: Nicolas

first: John

last: Wang

first: Laurent

last: Keller


title: Transcriptional profiling of the rust fungus Cronartium quercuum f. sp. fusiforme (Cqf) during vegetative growth on 2 different hosts.

city: Gainesville

last: Davis

state: FL

address: 365 Newins-Ziegler Hall

department: School of Forest Resources and Conservation

institute: University of Florida

summary: The purpose of this study was to make a single comparison between Cqf genes expressed during the vegetative stages of infection on the telial host (oak leaf) versus the aecial host (pine stem). A large proportion of genes were expressed in both hosts and significantly differentially expressed genes were enriched for candidate fungal effectors (small secreted proteins). These results suggest that the Cqf rust fungus uses a largely common set of genes to create two very different infection phenotypes.

overall_design: This study was based on hybridizations to custom microarrays containing features representing 8692 gene models from a Cqf genome sequencing project midpoint assembly. Two Agilent 4 X 44K microarray slides were populated with 60-mer probes (1 to 5 per transcript), designed using Agilent’s web-based eArray software. Labeled target cRNA (complementary RNA) was generated using Agilent’s Low Input Quick Amp Labeling Kit, such that oak and pine samples were labeled with either cy3 or cy5 an equal number of times across the experiment. Each microarray was hybridized with labeled cRNA target derived from a single oak sample and labeled cRNA target derived from a single pine sample. There were a total of eight oak sample replications and eight pine sample replications. Target hybridization and scanning were performed by the University of Florida’s Interdisciplinary Center for Biotechnology Research using standard procedures and an Agilent G250B Scanner.

first: Katherine

middle: E

last: Smith


title: microRNA profiles of EZH2 activation

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: Enhancer of Zeste Homolog 2 (EZH2) is a histone methyltransferase that catalyzes the trimethylation of histone H3 lysine 27 (H3K27me3). EZH2 expression is significantly upregulated in MPNST. In our study, we investigated the function of EZH2 and the molecular mechanisms that are regulated by EZH2 in MPNST pathogenesis. Our findings enhance the knowledge of EZH2’s function and biology, and have the potential to provide a novel therapeutic approach for MPNST patients in the clinic.

overall_design:
An EZH2 knockdown experiment was carried out in MPNST cells. There are one control and one siEZH2 samples for three cell lines (724,462,26T) and two repeats for each cell line, so in total there are 8 samples.  Two group comparison
Two group comparison

first: Lev

last: Dina

first: Yiqun

last: Zhang

first: Pingyu


title: Large scale screening for fusion genes in sarcoma patient samples

city: Oslo

first: Gard

middle: Olav

last: Thomassen

address: Radiumhospitalet, Rikshospitalet HF

department: Institute for Cancer Research

country: Norway

institute: Rikshospitalet

summary:
We have utilized our custom array GPL11054 to screen a set of sarcoma patient samples for fusion genes
One negative control was included in the study.

overall_design: We wanted to investigate the power of our fusion-gene array GPL11054 as a means for fusion gene detection in a series of sarcoma patient samples from two diagnostic laboratories with expertise in fusion gene detection.

first: Marthe

last: Løvf

first: Fredrik

last: Mertens

first: Manuel

last: Texeira

first: Ragnhild

last: Lothe

first: Rolf

last: Skotheim


title: Peripheral blood mononuclear cell- and cortical bone-derived transcriptional profiles

city: Cullowhee

first: Heather

middle: B

last: Coan

address: 132 Natural Science Building

department: Biology Department

institute: Western Carolina University

summary: Large-scale transcriptional profiling has enormous potential for discovery of osteoporosis susceptibility genes and for identification of the molecular mechanisms by which these genes and associated pathways regulate bone maintenance and turnover. A potential challenge in the use of this method for the discovery of osteoporosis genes is the difficulty of obtaining bone tissue samples from large numbers of individuals. In this study, we tested the applicability of using peripheral blood mononuclear cell (PBMC)-derived transcriptional profiles as a surrogate to cortical bone transcriptional profiles to address questions of skeletal genetics. We used a well-established and genetically well-characterized nonhuman primate model for human bone maintenance and turnover. We determined that a high degree of overlap exists in gene expression of cortical bone and PBMCs and that genes in both the osteoporosis-associated RANK Osteoclast and Estrogen Receptor Signaling pathways are highly expressed in PBMCs. Genes within the Wnt Signaling pathway, also implicated in osteoporosis pathobiology, are expressed in PBMCs, albeit to a lesser extent. These results are the first in an effort to comprehensively characterize the relationship between the PBMC transcriptome and bone – knowledge that is essential for maximizing the use of PBMCs to identify genes and signaling pathways relevant to osteoporosis pathogenesis. It is also a first step in identifying genes that correlate in a predictable manner between PBMCs and cortical bone from healthy and osteoporotic individuals, potentially allowing us to identify genes that could be used to diagnose osteoporosis prior to detectible bone loss and with easily obtained PBMCs.

overall_design: Total RNA was isolated from peripheral blood mononuclear cells and cortical bone of a nonhuman primate model (Papio hamadryas ssp.) of bone maintenance and turnover. Both samples were taken from the same animal. Tissue from 15 animals was used for the study.

first: Lorena

last: Havill


title: Bisphenol A Exposure and Multiple Sclerosis Risk

first: Anne

middle: Chinenye

last: Katchy

address: 3605 Cullen Blvd, Room 3021

department: CNRCS, Biology and Biochemistry

institute: University of Houston

overall_design: Comparison of vehicle-treated vs. BPA-treated mouse testes tissue. Each comparison in technical and biological duplicate (Done twice: total 4 replicates)

first: Dimitry

middle: N

last: Krementsov

first: Laure

middle: K

last: Case

first: Frances

last: Carr

first: Barbara

first: Cecilia

last: Williams

first: Cory

last: Teuscher


title: Potential link between biotic defense activation and recalcitrance to induction of somatic embryogenesis in shoot primordia from adult trees of white spruce (Picea glauca)

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

country: Canada

institute: Université Laval

summary: The goal is to examine the molecular aspects underpinning somatic embryogenesis (SE) within shoot tissues of adult white spruce trees by conducting transcriptome-wide expression profiling of shoot explants taken from responsive and nonresponsive genotypes.

platform_organism:
Picea glauca
Picea sitchensis

overall_design: One-color analysis of vegetative buds in somatic embryogenesis responsive and nonresponsive genotypes, before and after 7 days of SE induction. There are 5 biological replicates for each of the 4 combinations of genotype/time of induction for a total of 20 slides. Each replicate is comprised of a pool of 6 buds.

first: Sébastien

last: Caron

first: Robert

middle: G

last: Rutledge

first: Don

last: Stewart

first: Cathy

last: Overthon

first: Brian

last: Boyle

middle: J

first: Krystyna

last: Klimaszewska


title: Expression data from wild type and deltaS4473 Shigella flexneri 2457T

first: David

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

summary: Comparison of wild type S. flexneri 2457T gene expression to deletion mutant of S. flexneri 2457T gene S4473 at three growth phases and intracellularly

platform_organism:
Escherichia coli
Shigella

overall_design: Broth culture was grown to mid-log in LB, intracellular growth was 3 hours post invasion of HCT-8 cell (colonic epithelial cell line).

first: Eileen

last: Barry

first: Carolyn

last: Morris


title: MicroRNA expression profiling of HepG2 liver cells after berberine chloride treatment

city: Taipei

first: Ting-fang

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: Berberine, an isoquinoline alkaloid isolated from many medicinal herbs such as Coptis chinensis, has a wide range of pharmacological effects including anti-cancer effects. Since xenobiotic drug-induced micoRNAs have recently emerged as key regulators in guiding their pharmacological effects and toxicity, we were interested in whether or not micoRNA expression was differentially altered by berberine treatment in HCC. Here, we used miRNA microarray to analyze microRNA expression profiles of HepG2 human hepatoma cell line after berberine chloride treatment or 0.08% DMSO as control.

overall_design: Comparing miRNA profiles of 40 µM berberine-treated HepG2 human hepatoma cell line to those of control cells sampled after 2 and 4 hours treatment. A 50 mM stock solution of Berberine chloride was prepared in DMSO. Cells were treated with 40 µM berberine chloride or 0.08% DMSO as control.

first: Ting-Fang

first: Shui-Tein

last: Chen


title: Spatial organization of chromatin at the HoxD locus in developing caeca (4C tiling chip)

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

institute: EPFL

summary: Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit.

overall_design: Chromosome Conformation Capture-on-chip analysis (4C) at the Hoxd locus in developing caeca at E13.5, Array data were quantile normalized within 4C/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp.

first: S

last: Delpretti

first: D

last: Duboule


title: Gene expression profile affected by Bacillus megaterium in Aspergillus flavus NRRL 3357

city: Qingdao

first: Qing

last: Kong

state: Shandong

address: Yushan Road 5

department: Food Science and Engineering

country: China

institute: Ocean University of China

summary: Aspergillus flavus is one of the major fungal molds that colonize peanut in the field and during storage. The impact to human and animal health and to economy in agriculture and commerce are significant since this mold produces the most potent natural toxins, aflatoxins, which are carcinogenic, mutagenic, immunosuppressive, and teratogenic. A strain of marine Bacillus megaterium isolated from the Yellow Sea of East China was evaluated for its effect to inhibit aflatoxin formation through down-regulating aflatoxin pathway gene expression in A. flavus as demonstrated by genechip analysis in liquid medium and peanuts. The results showed that aflatoxin accumulation in potato dextrose broth liquid medium and liquid minimal medium was almost totally (more than 98%) inhibited by B. megaterium. The expression of many of the aflatoxin biosynthetic genes in the fungus was confirmed to be turned down. Some of the target genes down-regulated by B. megaterium within the whole genome and within the aflatoxin pathway gene cluster (aflF, aflT, aflS, aflJ, aflL, aflX) were identified. These target genes could be used for controlling aflatoxin contamination in crops such as corn, cotton, and peanut. Importantly, the expression of the regulatory gene aflS was found to be significantly down-regulated.

overall_design: The effect of B. megaterium on aflatoxin biosynthesis and genes expression of pathogen was firstly tested in potato dextrose broth (PDB) and glucose minimal salts medium (MM). The cell suspension of B. megaterium (concentration in PDB and MM was finally adjusted to 108 CFU/ml) or sterile distilled water as a control was added into the 100 ml beaker flask containing 15 ml PDB or MM, respectively. Then 100 μl of spore suspension (5 × 106 spores/ml) of A. flavus were added into each beaker flask. After 48 h of incubation at 28°C at 200 rpm, mycelia were collected, fresh frozen with liquid nitrogen, ground to a fine powder in liquid nitrogen, and stored at -80°C for further analysis. The effect of B. megaterium on aflatoxin biosynthesis and genes expression in the A. flavus fungal pathogen was also tested in two types of peanut kernels, UF 715133-1 and Jinhua 1012, respectively. Peanut kernels were wounded (6 mm diameter and approximately 3 mm deep) using a sterile borer and then 20 μl of 1 × 108 CFU/ml cell suspension of B. megaterium was inoculated on wounded peanut kernels respectively. Sterile distilled water was also used for inoculation as control. Two hours after bacterial inoculation, 10 μl A. flavus spore suspension was inoculated into each wound at a concentration of 106 spores/ml. The kernels were placed in artificial weather chamber to maintain high humidity (85%) and incubated at 28°C for 7 days. Each treatment was replicated three times with 20 peanut kernels in each test. The mycelia on kernels were harvested at day 7 and fresh frozen immediately in liquid nitrogen, ground into powder, and stored at -80°C for further analysis.


title: Comprehensive analysis of genic male sterility-related genes in Brassica rapa using Brassica rapa 300k microarray v2.0

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

summary: To identify genes associated with genic male sterility (GMS) that could be useful for hybrid breeding in Chinese cabbage (Brassica rapa ssp. pekinensis), floral bud transcriptome analysis was carried out using a B. rapa microarray with 300,000 probes (Br300K). Among 47,548 clones deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region, a total of 10,622 genes were differentially expressed between fertile and sterile floral buds; 4,774 and 5,848 genes were up-regulated over 2-fold in fertile and sterile buds, respectively. However, the expression of 1,413 and 199 genes showed fertile and sterile bud-specific features, respectively. Genes expressed specifically in fertile buds, possibly GMS-related genes, included homologs of several Arabidopsis male sterility-related genes, genes associated with the cell wall and synthesis of its surface proteins, pollen wall and coat components, signaling components, and nutrient supplies. However, most early genes for pollen development, genes for primexine and callose formation, and genes for pollen maturation and anther dehiscence showed no difference in expression between fertile and sterile buds. Some of the known genes associated with Arabidopsis pollen development showed similar expression patterns to those seen in this study, while others did not. BrbHLH89 and BrMYP99 are putative GMS genes. Additionally, 17 novel genes identified only in B. rapa were specifically and highly expressed only in fertile buds, implying the possible involvement in male fertility. All data suggest that Chinese cabbage GMS might be controlled by genes acting in post-meiotic tapetal development that are different from those known to be associated with Arabidopsis male sterility.

overall_design: A total of 14 chips were used for the microarray experiment. Experiments were performed with two biological replicates.

first: Yoon

last: Hur

first: Dong

last: Xiangshu


title: To examine the influence of the early stress of maternal separation on the hippocampal transcriptome in middle-aged life

status: Public on Oct 11 2013

city: Mumbai

first: Deepika

last: Suri

address: Homi Bhabha Road

department: DBS

institute: TIFR

summary: In this study, we examined the consequences of the early stress (ES) of maternal separation on hippocampal gene expression in middle-aged animals. Middle-aged (15 months old) ES animals exhibit hippocampal transcriptome changes with a significant regulation of genes associated with ion binding, transcriptional regulation, cellular projection, cellular stress responsive pathways, neuronal development and chromatin remodeling.

overall_design: Agilent one-color experiment, Agilent-024724 Genotypic-designed Custom Rattus Norvegicus 8x15k; Organism: Rattus norvegicus; Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442); Biological replicates: 5 per early stress group, 3 per control group

first: Vidita

last: Vaidya


title: To examine the influence of the early stress of maternal separation on the hippocampal transcriptome in young adulthood

summary: In this study, we examined the consequences of the early stress (ES) of maternal separation on hippocampal gene expression in young adulthood. Young adult (2 months old) ES animals exhibit hippocampal transcriptome changes with a significant regulation of genes associated with intracellular signaling, MAP kinase signaling, plasma membrane function, neurotransmitter and neuropeptide receptors and cytoskeletal components.

overall_design: Agilent one-color experiment, Agilent-024724 Genotypic-designed Custom Rattus Norvegicus  8x15k; Organism: Rattus norvegicus; Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442); Biological replicates: 4 per treatment group.


title: Hippocampal transcriptome of young adult and middle-aged ES animals

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

overall_design: Refer to individual Series


title: Transcriptional profiles of Campylobacter jejuni NCTC 11168 to 0.125mg/L erythromycin treatment

status: Public on Oct 10 2013

city: Ames

first: Qingqing

last: Xia

state: IA

address: 1116 VMPM Iowa State University

institute: Iowa State University

summary: Erythromycin is the drug of choice to treat campylobacteriosis, but resistance to this antibiotic is rising. The adaptive mechanisms employed by Campylobacter jejuni to erythromycin treatment remain unknown. The aim of this study is to determine the molecular basis underlying Campylobacter’s immediate response to Ery treatment.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni wild type strain NCTC 11168. One hybridizations were performed: sham-treated NCTC 11168 v.s. sub-lethal dose erythromycin treated NCTC 11168. Samples were  independently grown and harvested.  There were three biological replicates of each sample.

first: Zuowei

last: Wu

first: Qijing

last: Zhang


title: Discovery of the genes controlled by the second messenger cyclic di-GMP in Mycobacterium tuberculosis

status: Public on Oct 09 2013

city: Hefei

first: Yuzhi

last: Hong

state: Anhui Province

address: 3 Feixi Road

department: Modern Experiment Technology Center

institute: Anhui University

summary: Cyclic di-GMP (c-di-GMP) is a ubiquitous second messenger that regulates many biological processes in bacteria. The genome in Mycobacterium tuberculosis encodes a single copy of the diguanylate cyclase gene (dgc) responsible for c-di-GMP synthesis. To determine the role of c-di-GMP signaling in M. tuberculosis, the mutant strain of Δdgc was generated in the virulent H37Rv strain. We used whole genome microarray expression profiling as a discovery platform to identify the genes controlled by c-di-GMP in M. tuberculosis, providing molecular proof for the phenotypes modulated by the signaling.

overall_design: Wild-type H37Rv and Δdgc cultures were analyzed under aerobic conditions or in an in vitro dormancy model. Bacteria were collected at OD600 =1.3 for the aerobic cultures and upon the beginning of anaerobiosis for the cultures in the dormancy model. One culture for each experiment was assayed except for Δdgc under anaerobiosis (2 independent cultures).

first: Haihong

last: Fang


title: Transcriptional profiles of Campylobacter jejuni macrolide resistant strain JL272 to 4mg/L erythromycin treatment

overall_design: The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni macrolide resistant strain JL272. One hybridizations were performed: sham-treated JL272 v.s. lethal dose erythromycin treated JL272. Samples were  independently grown and harvested.  There were three biological replicates of each sample.


title: Effect of FGF8 on bovine granulosa cells

city: St-Hyacinthe

first: Christopher

last: Price

state: QC

address: 3200 rue Sicotte

institute: University of Montreal

summary: FGF8 induction of immediate-early response genes

overall_design: Cells treated for 2 h vs untreated controls. Three biological replicates


title: Bovine granulosa cell response to FGF18

summary: Determining immediate-early response genes to FGF18 treatment.

overall_design: Cells treated for 2 h vs non-treated cells. Three biological replicates.


title: Transcriptional profiles of Campylobacter jejuni NCTC 11168 to 4mg/L erythromycin treatment

overall_design: The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni wild type strain NCTC 11168. One hybridizations were performed: sham-treated NCTC 11168 v.s. lethal dose erythromycin treated NCTC 11168. Samples were  independently grown and harvested.  There were three biological replicates of each sample.


title: Comparison between a first and a last run of industrial serial repitching

status: Public on Oct 02 2013

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

summary: The aim of this study was to identify differently expressed genes between first and last runs of serial repitchings from four different German breweries. In the breweries the number of successive runs varied from 4 to 22. A run describes the industrial fermentation of brewery wort. By the end of fermentation the yeast slurry is cropped. These cells are reused for inoculation of another cylindro-conical vessel (CCVs).

overall_design: Results from eight microarrays are summarized in this study. The samples were taken from four German breweries. Microarrays were hybridized in a dye swap approach: Dye-swap 1: brewery A runs 1 vs. 22; Dye-swap 2: brewery B runs 1 vs. 5; Dye-swap 3: brewery C runs 1 vs. 4; Dye-swap 4: brewery D runs 1 vs. 8

first: Franziska

last: Bühligen

first: Philipp

last: Rüdinger

first: Ingo

last: Fetzer

first: Thomas

last: Scheper

first: Hauke

last: Harms

first: Susann

last: Müller


title: Comparison between all runs of industrial serial repitching 4

summary: The aim of this study was to identify differently expressed genes between all runs of four serial repitchings from a German brewery. In the brewery the number of successive runs varied from 17 to 20. A run describes the industrial fermentation of brewery wort. By the end of fermentation the yeast slurry is cropped. These cells are reused for inoculation of another cylindro-conical vessel (CCVs).

overall_design: Results from four loops are summarized in this study. The samples were taken from four serial repitchings of a German brewery (brewery A). Microarrays were hybridized in a loop approach.


title: Comparison between stationary phase S. cerevisiae H155 cells, exponential phase cells and stressed cells

summary: The sensibility of the used low-density arrays was tested by applying the lab strain S. cerevisiae H155. Important abiotic parameters were tested as they were introduced as elevated osmotic, pH or ethanol stress to the cells.

overall_design: Results from one loop including samples from cells in five different conditions are summarized in this study. Microarrays were hybridized in a loop approach.


title: Comparison between all runs of industrial serial repitching 3


title: Comparison between all runs of industrial serial repitching 2


title: Transcriptional profiles of Campylobacter jejuni NCTC 11168 and JL272 to erythromycin treatment


title: Serial industrial repitching and stress


title: Comparison between all runs of industrial serial repitching 1


title: Two histone deacetylases, FfHda1 and FfHda2, are important for secondary metabolism and virulence in Fusarium fujikuroi

status: Public on Oct 05 2013

city: Neuherberg, Germany

first: Christian

last: Sieber

address: Ingolstädter Landstraße 1

department: Institute of Bioinformatics and Systems Biology

institute: Helmholtz Zentrum München

summary:
Histone modifications have been shown to be crucial for secondary metabolism in various filamentous fungi. Here we studied the influence of histone acetylation on secondary metabolite production in the phytopathogenic fungus Fusarium fujikuroi, a known producer of several secondary metabolites including pigments and mycotoxins. Deletion of the classical HDACs FfHdF1, FfHdF2 and FfHdF3 indicated that FfHdF1 and FfHdF2 are major regulators of secondary metabolism, whereas FfHdF3 is involved in developmental processes but dispensable for secondary metabolite production in F. fujikuroi. Microarray analysis with the major HDAC FfHdF2 revealed differential regulation of several secondary metabolite gene clusters, subsequently verified by a combination of chemical and biological approaches. These results indicate that HDACs are responsible for gene silencing but also gene activation. Chromatin immunoprecipitation assays with ΔffhdF2 revealed significant alterations regarding the acetylation state in the landscape of secondary metabolite gene clusters thereby providing insights into the regulatory mechanism. In addition, the class I HDAC FfHdF1 also has major impact on secondary metabolism in F. fujikuroi. Furthermore, deletion of both ffhdF1 and ffhdF2 resulted in de-repression of secondary metabolites under normally repressing conditions. Thus, manipulation of HDAC encoding genes might provide a powerful tool for the activation of cryptic secondary metabolites.
Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289, ΔffhdF2 mutant under nitrogen starvation and nitrogen sufficient conditions.

overall_design: In this study we hybridized in total 12 microarrays using total RNA recovered from a wild-type culture of F. fujikuroi IMI58289 and ΔffhdF2 mutant culture. All cultures were grown on a 6 mM Gln (10%) and a 60 mM Gln medium (100%). For each combination of culture and medium a biological replicate was created. Each chip measures the expression level of 14,397 genes from F. fujikuroi IMI58289 with eight 60-mer probes.

first: Lena

last: Studt

first: Florentin

last: Schmidt

first: Leonie

last: Jahn

first: Kristina

last: Smith

middle: M

first: Eva

last: Niehaus

first: Michael

last: Freitag

first: Hans

middle: U

last: Humpf

first: Bettina

last: Tudzynski


title: Which role for genomics in environmental risk assessment? A case study in Venice Lagoon.

status: Public on Oct 01 2013

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: DNA microarray analyses of Ruditapes philippinarum sampled in Venice lagoon areas subjected to different anthropogenic impact.

overall_design: A comparative analysis of gene expression was conducted between Manila clam from lowly-polluted Chioggia and Colmata area and polluted Marghera site.

first: Milan

last: Massimo

first: Bargello

last: Luca


title: The cell death negative regulator, CaRLK1 gene, causes metabolic alterations of pyruvate and alanine via the glyoxylate cycle under hypoxia

first: Yeon-Ki

last: Kim

summary: A custom-made microarray was used for comparative transcriptome analysis of transgenic suspension cell line of Nicotiana tabacum that overexpresses the CaRLK1 gene. Ectopic expression of the CaRLK1 preferentially upregulated many amino acid biosynthetic genes under hypoxia: a 1.7-fold higher steady-state concentration of total free amino acids. Free Ala level was predominantly increased by 3-4 times and reached more than half of total free amino acid content. A significantly and markedly increased pyruvate content was also observed. These accumulations are associated with the glyoxylate cycle positively regulated by the CaRLK1.

overall_design: A total of 12 chips were used for microarray. Total RNAs were extracted from BY-2 suspension cells (control), RLK1ox suspension cells (RLK), auxin-free RLK1ox suspension cells (RA), and 10 uM DPI-treated RLK1ox suspension cells (RD) with triple biological replicates.

first: Dong

last: Lee

first: Ji

middle: Y

first: Go-woo

last: Choi

first: Youn

last: Chi


title: Expression data from porcine cells infected with TGEV wild-type (rTGEV-wt) or mutant (rTGEV-delta7) coronaviruses

status: Public on Sep 30 2013

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: Innate immune response is the first line of antiviral defense resulting, in most cases, in pathogen clearance with minimal clinical consequences. Viruses have developed diverse strategies to evade innate immune response and to ensure their survival. Using transmissible gastroenteritis virus (TGEV) as a model, we previously reported that accessory gene 7 counteracts host antiviral response by its association with the catalytic subunit of protein phosphatase 1 (PP1c). A transcriptomic analysis was performed to further investigate the effect of gene 7 absence on the host cell.

overall_design: A recombinant TGEV virus lacking gene 7 expression (rTGEV-delta7) was previously generated in our laboratory. Porcine ST cells were mock infected or infected with wild type (rTGEV-wt) or mutant (rTGEV-delta7) virus. Gene expression was analyzed at 6 and 12 hours post infection (hpi) by using porcine Affymetrix microarray. Three biological replicates were made for each sample type.

first: Jazmina

last: Cruz

first: Martina

last: Bécares

first: Isabel

last: Sola

middle: C

first: Luis

last: Enjuanes

first: Sonia

last: Zúñiga


title: Genomic and physiological responses to strong selective pressure during late organogenesis: how natural Fundulus heteroclitus populations cope with persistent environmental pollution Superfund Site

city: Miami

first: Marjorie

middle: F.

last: Oleksiak

address: 4600 Rickenbacker Causeway

department: Marine Biology and Fisheries

institute: University of Miami

summary: This study explores the synergistic effects of two model PAHs, an aryl hydrocarbon receptor (AHR) agonist (β-naphthoflavone) and a cytochrome P4501A (CYP1A) inhibitor (α-naphthoflavone), on gene expression in stage 31 embryos from two different population.  One population (Elizabeth River population) is relatively resistant to the pollutants in its environment.

overall_design: A loop design (Figure 5) was used for the microarray hybridizations where each sample is hybridized to 2 arrays using both Cy3 and Cy5 labeled fluorophores (Kerr and Churchill, 2001).  The loop consisted of Cy3 and Cy5 labeled embryo aRNAs from 4 biological samples and six different treatments (T1-T6: control, 1 μg/L BNF, 50 μg/L ANF, 100 μg/L ANF, 1 μg/L BNF + 50 μg/L ANF, 1 μg/L BNF + 100 μg/L ANF).  In total, 48 biological samples were hybridized to 24 microarrays.  Each array had different combinations of biological samples, so that the most direct comparisons (i.e., 50 µg/L ANF resistant embryo and 50 µg/L sensitive embryo) are hybridized to the same array.  The loop formed was T1S→ T1R → T2S→ T2R →T3S→ T3R→ T4S→ T4R→ T5S→ T5R → T6S→T6R→ T1S→ T2S → T3S → T4S → T5S → T6S → T1S → T1R → T2R → T3R → T4R → T5R → T6R, where each arrow represents a separate hybridization (array) with the biological sample at the base of the arrow labeled with Cy3 and the biological pool at the head of the arrow labeled with Cy5.  T1-6 is treatment, and S and R represent sensitive and resistant embryos.

middle: F


title: Rat intervertebral disc cell was stimulated by NGF

city: TAIPEI

first: chien yu

last: wang

institute: ndmc

summary: The rat-tail intervertbral disc cells was incubated with NGF at a concentration of 100 ng/ml/day for a total of five days.

overall_design: Primary culture of 8 weeks rat-tail interverbral disc cells. The control group was incubated with PBS and the experimental group was incubated with NGF at a concentration of 100 ng/ml/day for a total of five days.

first: Herng-Sheng

first: Ting-Hsien

last: Kao


title: Mice Exposed in situ to Urban Air Pollution Exhibit Pulmonary Alterations in Lipid Droplet Synthesis Pathways

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

summary: In the present study, we investigate pulmonary transcriptional responses in mice following exposure in situ to ambient air in a heavily polluted urban environment. Mature C57BL/CBA male mice were caged in sheds located in an urban area near two working steel mills and a major highway in Hamilton, Ontario, Canada. Control mice were housed in the same environment but received only high-efficiency particle-filtered air. Whole lung tissues were collected from mice exposed for 3 weeks, 10 weeks or for 10 weeks followed by 6 weeks in the laboratory (16 weeks total). DNA microarrays were used to explore changes in pulmonary gene expression in mice breathing ambient air versus HEPA-filtered air. Transcriptional profiling revealed changes in the expression of genes implicated in the lipid droplet synthesis pathway (plin, dgat2, lpl, s3-12, agpat2), antioxidants (ucp1). We postulate that exposure to particulate matter adsorbed with polycyclic aromatic hydrocarbons triggers lipid droplet synthesis (holding depots for lipids and malformed/excess proteins tagged for degradation) in the lungs, which act to sequester particulates adsorbed with toxic chemicals. Increased lipid droplet synthesis could potentially lead to endogenous/stressor-induced synthesis of reactive oxygen species and activation of antioxidant mechanisms. Further investigation into the stimulation of lipid droplet synthesis in the lung in response to air pollution is warranted in order to better understand these mechanistic changes and the resulting health implications.

overall_design: Mature male C57BL/6 x CBA F1 hybrid mice were exposed to either HEPA-filtered or ambient air in Hamilton, ON, Canada. Animals were exposed starting May 14, 2004 for 3 weeks (3wk), 10 weeks (10wk), or for 10 weeks followed by 6 weeks of recovery (16wk). Each treatment group consisted of five mice, for a total of 30 mice. Total RNA was isolated from a random section of the whole lung using TRIzol reagent (Invitrogen) and purified using the RNeasy Mini Kit (Qiagen). RNA quality was confirmed by UV spectrophotometry and using an Agilent Bioanalyzer. Total RNA (200 ng) from HEPA-filtered air or whole air-exposed mice and Universal Mouse Reference RNA (Stratagene) were used to synthesize double-stranded cDNA and cyanine-labelled cRNA according to the manufacturer's instructions (Agilent Linear Amplification Kits, Agilent Technologies). Biological samples were labelled with Cy5 dye while the commercially available Stratagene mouse reference RNA was labelled with Cy3 dye. At each of the three time points, ambient air-exposed samples and HEPA-filtered samples were hybridized to Agilent microarrays. Arrays were washed, and scanned on an Agilent G2505B scanner. Data were acquired using the Agilent Feature Extraction software version 9.5.3.1.

first: Andrea

last: Rowan-Carroll

first: Sabina

last: Halappanavar

first: Chris

last: Somers

first: Carole

last: Yauk


title: Host plant genotypes affect miRNA gene expression in Hessian fly larvae

city: Lincoln

first: Chitvan

last: Khajuria

state: NE

address: 103 Entomology Hall

institute: University of Nebraska-Lincoln

summary: MicroRNAs (miRNAs) are small noncoding RNAs that play critical roles in regulating post transcriptional gene expression.  Gall midges encompass a large group of insects that are of economic importance and also possess fascinating biological traits.  The gall midge Mayetiola destructor, commonly known as the Hessian fly, is a model organism for studying gall midge biology and insect – host plant interactions. In this study, we systematically analyzed miRNAs from the Hessian fly.  Deep-sequencing a Hessian fly larval transcriptome led to the identification of 89 miRNA species that are either identical or very similar to known miRNAs from other insects, and 184 novel miRNAs that have not been reported from other species.  Microarray analyses revealed the expression of miRNA genes was strictly regulated during Hessian fly larval development and abundance of many miRNA genes were affected by host genotypes.  The identification of a large number of miRNAs for the first time from a gall midge provides a foundation for further studies of miRNA functions in gall midge biology and behavior.

overall_design: Two wheat lines “Molly” and “Newton” were used in the experiment. Newton is a susceptible winter wheat that contains no Hessian fly R gene, and Molly is a nearly isogenic line of Newton, but contains the R gene H13. Larvae were collected one and three days after egg hatch from susceptible Newton and resistant Molly plants. Total RNA extracted from the collected larvae was used for microarray analysis. Three biological replications were used for each treatment and at each time point.

first: Ming-Shun

last: Chen


title: Screening for novel immungenic proteins of Salmonella Enteritidis 125109

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: The screening of a cDNA derived expression library of Salmonella Enteritidis 125109 expressed in E. coli using a fusion construct and specific HaloTag interaction to a modified surface is shown. Thus, 1536 different clones were screened including positive (fimA) and negative (argC, gapA) reference proteins. The goal of the screening was to identify potential novel immunogenic proteins from S. Enteritidis by selecting clones showing a high signal intensity in comparison to the known antigens used as positve markers. Afterwards, the most promising clones were sequenced to identify the gene and corresponding protein and these proteins were then investigated further. Consequently, 9 novel immunogenic proteins could be identified.

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: In total 1536 different lysates were spotted on different microarray slides. Each slides contained 3600 distinct spots, seperated into two compartments of 1800 spots each. Each compartment comprised quadruplicate replicates of each sample lysate with controls being analysed with more replicates. As controls we used: fimA from 3 different samples (40 replicates) as positive reference proteins, as it has been described as immunogenic before. GapA from Klebsiella pneumoniae and Campylobacter jejuni (40 replicates) as negative reference proteins, additionally two sets of E.coli cell lysates without fusionprotein expressed, namely Acella electrocompetent cells (40 replicates) and KRX (32 replicates). Last but not least a buffer control (24 replicates) was included. Therefore, each set of replicate slides contained 384 different samples. Each screening was performed with three replicate slides. Consequently, a total number of 12 slides were screened (4 sets of samples x 3 replicates each). For identification rabbit polyclonal antibody to S. enterica (Abcam ab35156) as primary and Goat polyclonal to Rabbit IgG conjugated with ChromeoTM-546 (Abcam ab60317) as secondary antibody were used. The top compartment was incubated first with primary antibody, while the bottom compartment was incubated with PBS at the same time. Afterwards both compartments were incubated with secondary antibody.


title: Transcriptome characterization of venous endothelium during the formation of neointimal hyperplasia and stenosis in a rat arteriovenous fistula model for kidney dialysis

city: Amsterdam

first: Oscar

middle: L

last: Volger

state: Noord Holland

address: De Boelelaan 1117

department: Molecular Cell Biology and Immunology

country: Netherlands

institute: VU University Medical Center

summary: In patients with severe kidney disease AVF are surgically placed in order to create good access for hemodialysis. In these dialysis patients the failure rates of AVF can be as high as 24% within 6 months after surgery, causing ineffective dialysis and necessitating additional clinical interventions. The pathological processes known to lead to AVF failure are beginning to be unravelled include the formation of venous neointimal hyperplasia (VNIH), thrombosis (Chang et al. PMID 16105066), and venous stenosis (Kanterman et al. PMID7892454, Tang et al. 1998), resulting in a reduced blood flow through the fistula. We established a rat model for AVF failure in human kidney dialysis patients. The characterization of this model has been previously described (Globerman et al. 2011, PubmedID:22002501). In this model the AVFs are surgically constructed in the right leg by connecting the superficial epigastric vein SEV to the common femoral artery (CFA), resulting in exposure of the SEV to arterial pressure with pulsatile and low resistant flow patterns (Globerman et al. 2011, PMID22002501). In the present study we utilized this AVF model in order to assess the effects of arterialized flow, with consequent pathological changes of the vessel wall due to surgical AVF instalment, on the transcriptome of endothelium from the SEV. Within the SEV these pathologies of the vessel wall include the formation of NIH in the main branch, and stenosis in the side branches. By employing this rat model we assessed the changes of the endothelial transcriptome in relation to these pathologies in order to gain mechanistic understanding of the potential roles of venous endothelium in AVF failure, as well as to identify potential biomarkers preceding AVF failure.

overall_design: AVF surgery was performed on N=6 rats, and 13-14 days after surgery the rats were sacrificed. AVFs were extracted from the rats, and microarray transcriptome analyses were performed on luminal endothelial cells that isolated from four different sites of the AVF by employing Laser Capture Microdissection (LCM). These sites included (i) N=5 AVF sections of the superficial epigastric vein (SEV) with neointimal hyperplasia (NIH), (ii) N=3 AVF sections of SEV side branches with luminal stenosis, (iii), N=6 sections of the SEV located distally from a ligation thereby omitting exposure to arterialized flow and consequently preventing the development of NIH or stenosis, and (iv) N=3 sections of the AVF common femoral artery without signs of NIH or stenosis.

first: Anat

middle: S

last: Globerman

first: Anton

last: Horrevoets

first: Eli

last: Keshet


title: The formation of the intestine at the juvenile stage is raised by the Hox10 gene through the migration of endodermal strand cells in ascidian

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

institute: Okayama University

summary: Hox cluster genes play crucial roles in the establishment of the body plan along the antero-posterior axis during animal development. Hox genes are expressed in the chordate endodermal tissues, and unraveling functions there is necessary for elucidating the mechanisms of endoderm specification. In the invertebrate chordate Ciona intestinalis, the endodermal tissues are in the premature state at the larval stage, and they form the differentiated digestive tract during metamorphosis. In this study, we showed that a Hox gene Ci-Hox10 is required for the formation of the intestine during metamorphosis. To know the downstream genes that are controlled by Hox10, microarray analysis of Hox10 knock-down embryos was performed.

overall_design: Gene expressions in the tail region of Hox10 knockdown embryos that were injected with Hox10 morpholino (MO) and control embryos of Ciona intestinalis were examined by comparative analysis with two color detection. Dye-swap analysis was carried out.

first: Narudo

last: Kawai

first: Yosuke

last: Ogura

first: Tetsuro

last: Ikuta

first: Hidetoshi

last: Saiga

first: Nori

last: Satoh

first: Yasunori

last: Sasakura


title: NanoString miRNA profiling of THP1-differentiated macrophages treated with LPS derived from A. aggregatibacter, P. gingivalis and Pg LPS treated with cigrate smoke extract (Pg CSE)

status: Public on Sep 19 2013

city: Chapel Hill

first: Afsar

middle: Raza

last: Naqvi

state: North Carolina

address: Brauer Hall 111

department: Periodontics

institute: University of North Carolina chapel Hill

summary: To examine the early (4h) miRNAs responses of differentiated macrophages to LPS challenge, we performed global miRNA profiling using the Nanostring nCounter technology, a multiplexed, color-coded probe assay. Of the 653 probes present on the assay, we detected expression of ~200 (30%) miRNAs across all samples.

overall_design: THP-1 differentiated cells were treated in duplicates with Aa, Pg and Pg (CSE) LPS for 4h and the cells were harvested after washing twice with PBS. Total RNA was isolated using miRNeasy kit (Qiagen). Samples were then processed for Nanostring profiling.

middle: R

first: Jezrom

last: Self-Fordham

first: Salvador

last: Nares


title: Maize coleoptilar node development: WT vs. rtcs

status: Public on Sep 01 2013

city: Bonn

first: Frank

last: Hochholdinger

state: BW

address: Katzenburgweg 1a

department: INRES - Crop Functional Genomics

institute: University of Bonn

summary: Maize (Zea mays L.) and other monocot cereals develop extensive shoot-borne root systems from nodal structures of the shoot to secure water and nutrient uptake and provide anchorage in the soil. In the present study, the early stages of coleoptilar node (first shoot-node) development of maize were subjected to a detailed morphological and histological analysis followed by a comprehensive microarray profiling via 105 k oligonucleotide microarrays. Expression profiling identified 1,179 microarray features corresponding to 974 unique transcripts which were differentially expressed between three stages of wild-type B73 coleoptilar node development within the first four days after the initiation of this structure. Significantly, all but one of these microarray features were preferentially expressed at day four compared to day zero of coleoptilar node formation. Moreover, comparative microarray profiling of wild-type versus mutant rtcs coleoptilar nodes which do not initiate shoot-borne roots revealed 958 microarray features corresponding to 828 unique transcripts that were expressed in a RTCS dependent fashion. Differential gene expression during wild-type coleoptilar node development and between wild-type and rtcs coleoptilar nodes was confirmed for a subset of 24 genes by qRT-PCR. In order to identify direct downstream targets of RTCS in silico promoter analyses revealed 191 differentially expressed genes that contained at least one LBD motif in a 1 kb promoter region upstream of the ATG start codon. For six promoter sequences containing LBD motives EMSA experiments demonstrated RTCS binding, hence supporting the notion that differentially accumulated genes containing LBD motifs are direct downstream targets of RTCS. The complex RTCS dependent regulation of coleoptilar node development and crown root formation was illustrated by a wide variety of cellular functions represented by the differentially accumulated genes and in particular by the differentially accumulated genes containing LBD promoter motifs.

overall_design: 24 samples in total: 3 developmental stages (0, 2, 4) * 2 genotypes (WT, rtcs) * 4 biological replicates

first: Nils

last: Muthreich

first: Christine

last: Majer

first: Mary

last: Beatty

first: André

last: Schützenmeister

first: Yan

last: Fu

first: Patrick

last: Schnable

first: Hans-Peter

last: Piepho

first: Hajime

last: Sakai


title: YG001: A Usp7-Tip60 pathway regulates early adipogenesis

status: Public on Aug 28 2013

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: USP7, a dominant DUB activity in 3T3-L1 adipocytes and in mouse adipose tissue, increases Tip60 protein levels, and deubiquitinates Tip60 both in intact cells and in vitro. Treatment with a pan deubiquitinase (DUB) inhibitor, or knockdown of USP7, decreases adipogenesis. Transcriptome analysis reveals a common set of cell cycle genes to be co-regulated by both Tip60 and USP7. Knock down of either factor results in impaired mitotic clonal expansion, an early step in adipogenesis. These results therefore reveal deubiquitination of a transcriptional coregulator to be a key mechanism in the regulation of early adipogenesis

overall_design: Mature 3T3-L1 adipocytes were subjected to RNAi-mediated knock down with control(C), USP7(U)- or Tip60(T)-specific oligonucleotides. For this, 4 replicates of differentiated 3T3-L1 cells were transfected with Amaxa technology. Two days after transfection cells were washed twice with PBS twice and lysed in 0.5ml Trizol (Invitrogen). mRNA expression of Tip60 and USP7 was assessed by qRT-PCR. Amplified cRNA samples were labeled with either cy3 or cy5 and put on microarray together with and oppositely labeled common reference sample consisting of cRNA derived from undifferentiated 3T3-L1 cells.

first: Yuan

last: Gao

first: Olivier

last: van Beekum

first: Arjen

last: Koppen

first: Nicole

last: Hamers

first: Dik

last: van Leenen

last: Koerkamp

first: Ruud

last: Berger

last: Holstege

first: Arjan

middle: B

last: Brenkman

first: Huib

last: Ovaa

first: Eric

last: Kalkhoven


title: Effect of waterborne exposure to carcinogenic PAHs on adult zebrafish hepatic transcriptome

city: Leioa

first: Unai

last: Vicario

state: Bizkaia

address: Barrio Sarriena SN

department: Zoology and Animal Cell Biology

institute: University of the Basque Country (UPV/EHU)

summary: Several environmental pollutants, especially organic compounds such as polycyclic aromatic hydrocarbons (PAHs) are potent carcinogenic chemicals. Exposure of different fish species to PAHs causes a high prevalence and variety of tumor lesions. To identify and compare the mode of action (MOA) of different model carcinogenic PAHs, a transcriptomic study was carried out in adult zebrafish (Danio rerio) after exposure to 0.3 mg/l of benzo(a)pyrene (B(a)P) or to 7,12-dimethylbenz(a)anthracene (DMBA), both of them dissolved in dimethyl sulfoxide (DMSO; final concentration of 0.01%). Samples for microarray analysis were taken after 1 and 2 weeks of exposure. The changes in the mRNA transcription levels over the corresponding controls were compared among treatments. Correspondence analysis was able to discriminate among treatments; factor 1 separated both sampling times while factor 2 separated the compounds. A total number of 3043 transcripts was shown to be differentially regulated in at least one of the treatments. B(a)P treatment produced regulation of sequences related to GO categories associated to cell cycle and cell division whereas DMBA regulated GO terms related to oxidation/reduction responses, responses to chemicals and response to bacterium. Both compounds were able to alter many xenobiotic metabolism related genes, especially upregulating the transcription of phase I metabolism-related genes such as cytochrome P450 members (cyp1a or cyp1b), and many cancer-related genes such as the Jun B proto-oncogene (junb). Overall, these results indicated that the exposure to both PAHs was able to differentially alter the transcription levels of genes involved in both the detoxification metabolism and the cell-cycle control, including different tumor-supressor genes and oncogens. These alterations have been often related to the appearance of tumor lesions.

overall_design: Zebrafish were waterborne exposed to 0.3ppm BaP or DMBA for 1 and 2 weeks. After 1 and 2 weeks hepatic samples were collected from each treatment group as well as from the control group. 3 biological replicates have been collected per exposure group and time point. Each biological replicate is a pool of  5 livers. Samples from the different treatments were hybridized in an n+2 (n = 9) A-optimal loop design. Additionally, these two designs were linked by two extra hybridizations to enable comparison between time points

last: Vicario-Parés

first: Lucia

last: Vergauwen

first: Dries

last: Knapen

first: Ronny

last: Blust

first: Miren

middle: P

last: Cajaraville

first: Amaia

last: Orbea


title: Analysis of miRNA expression in lung (CC10) VEGF transgenic mice and their wild type litters

status: Public on Sep 06 2013

city: New haven

first: seyedtaghi

last: takyar

state: CT

address: 300 Cedar street

department: Medicine

institute: Yale School of Medicine

summary: Vascular Endothelial Growth Factor (VEGF) is a critical regulator of pulmonary Th2 inflammation but the underlying mechanism and the roles of miRNAs in this process have not been defined. We analyzed the effect of VEGF on lung microRNAs by microarray analysis and validated the findings by Taqman qRT-PCR. We compared the levels of microRNAs in the lungs of transgenic mice with their wild type litters after overexpression of VEGF from a lung epithelium-restricted transgene.  VEGF was overexpressed in the lung epithelium of CC10-rtTA-VEGF transgenic mice by adding Doxycycline to their drinking water for 7-10 days. RNA from the lungs of VEGF transgenic mice and their wild type litters were extracted and analyzed by microarray. The expression levels of microRNAs that were significanly altered were validated in another group of mice.

overall_design: Lung RNA from each transgenic mouse was labeled with Cy5 and lung RNA from wild type mice were labeled with Cy3. The two labeled RNAs were hybridized to the miRNA array. This array (chip ID 01_M9.1_070362) detects miRNA transcripts listed in Sanger miRBase Release 9.1 (http://www.sanger.ac.uk/Software/Rfam/mirna/).      Multiple control probes are included in each chip.  The control probes are used for quality controls of chip production, sample labeling and assay conditions.  Among the control probes, PUC2PM-20B and PUC2MM-20B are the perfect match and single-based match detection probes, respectively, of a 20-mer RNA positive control sequence that is spiked into the RNA samples before labeling.  One may assess assay stringency from the intensity ratio of PUC2PM-20B and PUC2MM-20B, which is normally larger than 30.  When the option for custom probes is selected, custom probes are also included.  After hybridization three imaged were obtained. From Cy3 and Cy5 images one may directly read miRNA profiles and from Ratio images one may get a quick sense of differential expressions between the corresponding samples.  The images are displayed in pseudo colors so as to expand visual dynamic range.  In the Cy3 and Cy5 intensity images, as signal intensity increases from 1 to 65,535 the corresponding color changes from blue to green, to yellow, and to red.  In the Cy3/Cy5 ratio image, when Cy3 level is higher than Cy5 level the color is green; when Cy3 level is equal to Cy5 level the color is yellow; and when Cy5 level is higher than Cy3 level the color is red.

first: Seyedtaghi

last: Takyar


title: Methylation profiles of Human kidney tubules

status: Public on Aug 09 2013

city: Philadelphia

first: Yi-An

last: Ko

state: Pennsylvania

address: 415 curie blvd

department: Genetics & Gene Regulation

institute: UPeenn

type: Methylation profiling by genome tiling array

summary: Epigenetic information in the human kidneys is yet to be studied. In this work, we collected 26 human kidney samples and profiled the genome-wide cytosine methylation patterns using HELP assay.

overall_design: We sought to decrease the cell type heterogeneity of kidney tissues to increase the resolution of methylation profiles. To that end, microdissected human kidney tissue are used for the HELP-assay (HpaII tiny fragment Enrichment by Ligation-mediated PCR) and hybridization on Roche NimbleGen microarrays.

first: Davoud

last: Mohtat

first: Masako

last: Suzuki

first: Ae

last: Park

first: Maria

last: Izquierdo

first: Sang

last: Han

first: Hyun

last: Kang

first: Han

last: Si

first: Thomas

last: Hostetter

first: James

last: Pullman

first: Melissa

last: Fazzari

first: Amit

last: Verma

first: Deyou

last: Zheng

first: John

last: Greally

first: Katalin

last: Susztak


title: Primate genome architecture linked with formation mechanisms and functional consequences of structural variation

status: Public on Aug 10 2013

city: Boston

first: Charles

last: Lee

state: MA

address: 221 Longwood Ave., EBRC-422

department: Pathology

institute: Brigham and Women's Hospital/Harvard Medical School

type: Genome variation profiling by genome tiling array

summary: While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, comprising thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques. Non-allelic homologous recombination, linked with genomic architecture, primarily shaped the genomes of great apes resulting in different SV formation mechanism landscapes across species, with distinct functional consequences. Transcriptome analyses across nonhuman primates and humans revealed significant effects of species-specific gene duplications on gene expression, with these effects displaying remarkable diversity in direction and magnitude. Thirteen inter-species gene duplications coincided with the species-specific gain of expression in a new tissue, implicating these duplications in function acquisition.

sample_organism:
Macaca mulatta
Pan troglodytes
Pongo abelii

platform_organism:
Macaca mulatta
Pan troglodytes
Pongo pygmaeus

overall_design: Agilent arrays were custom designed for probes to be relatively evenly spaced across the reference genomes of chimpanzee, orang-utan, and rhesus macaque. For each species 9 one million probe arrays were used to cover the autosomes and a single 400k probe array was used for the sex chromosomes.

first: Omer

last: Gokcumen

first: Verena

last: Tischler

first: Jelena

last: Tica

first: Qihui

last: Zhu

first: Rebecca

last: Iskow

first: Eunjung

first: Markus

middle: H

last: Fritz

first: Amy

last: Langdon

first: Adrian

last: Stütz

first: Pavlos

last: Pavlidis

first: Vladimir

last: Benes

first: Ryan

last: Mills

first: Peter

first: Jan

middle: O

last: Korbel


title: Changes of miRNAs during osteogenic differentiation of PDGFRa+ mesenchymal progenitors derived from human skeletal muscle

status: Public on Aug 01 2013

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Comprehensive analyses of miRNAs expression were performed using miRNA microarrays during osteogenic differentiation of PDGFRa+ mesenchymal progenitors isolated from human skeletal muscle to identify miRNAs that are involved in osteogenesis of PDGFRa+ mesenchymal progenitors.

overall_design: PDGFRa+ mesenchymal progenitors were isolated from the gluteus medius muscles of two different patients, and then subjected to osteogenic induction. Expression of miRNAs was examined using miRNA microarrays at the time points of one week and two weeks after osteogenic induction and were compared with that of uninduced cells.

first: Teruyo

last: Oishi

first: Asami

last: Yamaguchi


title: Genome-wide expression profiling of PpABI1 disruptants

status: Public on Jul 31 2013

city: Setagaya-ku

first: Kenji

last: KOMATSU

state: Tokyo

address: 1-1-1 Sakuragaoka

department: Department of Bioproduction Technology

institute: Tokyo University of Agriculture

summary: To investigate the disruption effect of Group A PP2C on global gene expression in Physcomitrella patens, we performed microarray analysis of wildtype plant and PpABI1 disruptants using a custom Physcomitrella oligonucleotide microarray, which carries probes for 33,942 gene models of Physcomitrella genome version 1.1. on a 4 x 44 K Agilent platform.

overall_design: Gene expression in wildtype plant and ppabi1 disruptants were measured at 0, 1, 3, 6 and 12 hours after exposure to 10 μM ABA.  Three biologically independent experiments were performed at 0 hour. Also to discover the early ABA-responsive genes, gene expression in wildtype was measured at 0 and 3 hours after exposure to 1 μM ABA.

last: Komatsu

first: Norihiro

last: Suzuki

first: Mayuri

last: Kuwamura

first: Yuri

last: Nishikawa

first: Mao

last: Nakatani

first: Hitomi

last: Ohtawa

first: Daisuke

last: Takezawa

first: Motoaki

last: Seki

first: Maho

last: Tanaka

first: Teruaki

last: Taji

first: Takahisa

last: Hayashi

first: Yoichi

last: Sakata


title: The global gene expression pattern by RCK1 over-expression

city: Seoul

first: miwha

last: Chang

address: anam dong 5ga

department: School of Life Sciences and Biotechnology

institute: Korea university

summary: We did transcription profiling on the effect of RCK1 over-expression. rck1 mutant strain was transformed with empty high copy vector pRS425 empty vector), or  with RCK1 cloned into pRS425 (the RCK1-overexpressing strain: RCK1 cloned into pRS425).

overall_design: Analysis was performed with rck1 (Empty vector, pRS425) mutant and RCK1 over-expressed cells (pRS425-RCK1). Yeast cells were grown on SD-leu medium. Yeast cells were grown overnight at 30°C . The culture was refreshed to 0.2 O.D and grown at 30°C  for 2h 30min. Cell wall stress was applied by addition of zymolyase to a final concentration of 5 unit/ml .  Cells were collected at 2 hours of growth and processed for RNA extraction.

first: Miwha

first: Cheol-won

last: Yun


title: Effect of clpX overexpression in Synechococcus

city: Hirakata, Osaka

first: Keiko

last: Imai

address: 2-5-1 shinmachi

institute: Kansai medical university

summary: In the unicellular cyanobacteriuIn the cyanobacterium, Synechococcus elongatus PCC 7942, most genes show rhythmic expression controlled by the Kai-based clock under continuous light conditions (LL). Overexpression of clpX led to a decrease in kaiBC promoter activity, disruption of circadian rhythm, and eventually cell death. We found that overexpression of clpX upregulated mRNA levels of ribosomal protein subunits, after which expression of other genes containing the clock genes was decreased.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Wild type (WT) and inducible clpX-overexpressor (ox-clpX) S. elongatus PCC 7942 strains were analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: WT at hours 16 in LL (IPTG-free): WT under LL 20 in LL (addition of 100 µM IPTG for 4 hours): ox-clpX cells at hours 16 in LL (IPTG-free): ox-clpX cells at hours 20 in LL (addition of 100 µM IPTG for 4 hours)

first: Yhoko

last: Kitayama


title: Identification of transcription factors potentially involved in the juvenile to adult phase transition in rough lemon (C. jambirhi Lush.)

status: Public on Jul 27 2013

city: Moncada

first: Gema

last: Ancillo

state: Valencia

address: Ctr. Moncada-Naquera Km 4.5

department: Protección Vegetal y Biotecnología

institute: Instituto Valenciano de Investigaciones Agrarias (IVIA)

summary: The main objective of the present study was to identify citrus transcrition factors putatively involved in the juvenile to adult transition in citrus. A  oligonucleotide microarray containing 1152 putative unigenes of citrus transcription factors was used.

overall_design:
Rough lemon (C. jambirhi Lush.), were analyzed in two diferent developmental stages, junenile and adult. Four replicates for each sample category  were generated and for each genotipe juvenile versus adult samples were compared .
Comparative transcriptomic hybridization

first: M

last: Castillo

first: Javier

last: Forment

first: José

last: Gadea

last: Juarez

first: Luis

last: Navarro


title: Identification of transcription factors potentially involved in the juvenile to adult phase transition in Pineapple sweet orange (C. sinensis (L.)

overall_design:
Pineapple sweet orange (C. sinensis (L.) was analyzed in two diferent developmental stages, junenile and adult. Four replicates for each sample category  were generated and for each genotipe juvenile versus adult samples were compared .
Comparative transcriptomic hybridization


title: Gene expression of abnormal uric acid synthesis animal model of silk worm Bombyx mori.

status: Public on Jul 24 2013

city: Mishima

first: Hiromasa

last: Ono

state: Shizuoka

address: National Institute of Genetics, Yata 1111

department: Database Center for Life Science (DBCLS)

institute: Research Organization of Information and Systems

summary: Uric acid (UA) is the final product of purine metabolism and plays an important role as a physiological antioxidant. In recent years, several different groups have reported a correlation between decreased UA in Parkinson’s disease (PD) and clinical progression and stage of PD. However, little is known about the molecular mechanisms of decreased UA under oxidative stress. We used our systematic functional annotation pipeline for silkworm genes to identify a novel UA metabolic pathway regulator under oxidative stress in a UA metabolism mutant silkworm Bombyx mori model.

overall_design: Gene expression was measured in 3day of fifth instar larvae of abnormal uric acid synthesis Bombyx mori mutant of op.

first: Hiroko

last: Tabunoki

first: Yuki

last: Nakamura

first: Kazuhiro

last: Ishikawa

first: Hidemasa

last: Bono


title: Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.):  custom genetic tools for exploring herbivore ecology

status: Public on Jul 30 2013

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

summary: We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds.  We generated a liver transcriptome of the desert woodrat (Neotoma lepida) with the Roche 454 platform.  The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only:  one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness).  The resulting one-color arrays had high technical and biological quality.  Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus).  Biotransformation processes and functions were highly represented in the results.  Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species.  The conspecific comparison had overall fewest differences.

sample_organism:
Neotoma lepida
Neotoma bryanti

overall_design: Gene expression was compared across 3 groups of woodrats:  Neotoma lepida (n=4), N. bryanti Palm Springs (n=4), and N. bryanti Caspers Wilderness (n=4).  Animals were fed a rabbit chow diet, called control; intake was monitored over 10 days, after which RNA was extracted from hepatic tissue.  One-color arrays were performed.

first: Jael

last: Malenke

first: Aaron

last: Miller

middle: D

last: Dearing


title: Quantitative real-time RT-PCR analysis of HEK293 cells stably transfected with PRL-1 (PTP4A1) or empty pcDNA4 vector control.

city: Indianapolis

first: Carmen

middle: M.

last: Dumaual

state: IN

address: 723 West Michigan St., Room SL306

department: Biology

institute: Indiana University-Purdue University Indianapolis

summary: The protein tyrosine phosphatase PRL-1 (Gene Symbol:  PTP4A1) has been identified as an important oncogene with roles in promoting cell proliferation, survival, migration, invasion, and metastasis.  However, little is currently known about the signaling pathways through which it mediates its effects.  Studies have shown a relationship between PRL-1 and the expression or activity levels of various molecules involved in integrin-mediated cell signaling.  These integrin-responsive players can promote re-arrangements in the actin cytoskeleton that are central to cell motility, invasion, and metastasis.  Therefore, to investigate the effects of PRL-1 overexpression in human embryonic kidney 293 (HEK293) cells, we used qRT-PCR to examine the expression levels of 184 genes which either were identified by microarray and proteomic analysis to be differentially expressed in response to PRL-1 or have known associations to integrin-mediated signaling, cytoskeletal remodeling, and/or cell motility.

overall_design: Total RNA was extracted from duplicate cultures of HEK293 cells stably overexpressing PRL-1 (HEK293-PRL-1) and HEK293 cells stably transfected with empty pcDNA4 vector (HEK293-Vector).   Samples were analyzed using custom TaqMan Array 96-well Plates to examine the expression of 184 genes with known involvement in or association with signaling pathways related to integrin-mediated cell adhesion, cytoskeletal remodeling, and/or cell motility.

first: Boyd

middle: A

last: Steere


title: Transcriptional profiling of Salmonella typhimurium in the ceca of gnotobiotic mice

status: Public on Jul 23 2013

city: Stanford

first: Justin

last: Sonnenburg

state: CA

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University

summary: Transcriptional profiling of Salmonella typhimurium in the ceca of germ-free and Bacteroides thetaiotaomicron-monoassociated gnotobiotic mice. Comparison with response in MM-Glucose.

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

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: In vivo transcriptional profiles of Salmonella typhimurium obtained from biological triplicate samples taken from cecal contents of germ-free and Bacteroides thetaiotaomicron-monoassociated mice 5 days post-infection with S. typhimurium. Biological duplicate samples from in vitro culture of S. typhimurium in MM-Glucose used for comparision.

first: K

middle: M

last: Ng

first: J


title: Wild-type yeast vs delta esl1/ delta esl2 mutant strain

status: Public on Jul 18 2013

city: Clayton

first: traude

middle: Helene

last: Beilharz

state: Victoria

address: Monash University

department: Biochemistry & Molecular Biology

institute: Monash University

summary:
Transcript profiling of the double  delta esl1/ delta esl2 mutant versus wild-type growning at log phase in rich meda.
During its natural life cycle, budding yeast (Saccharomyces cerevisiae) has to adapt to drastically changing environments, but how environmental sensing pathways are linked to adaptive gene expression changes remains incompletely understood. Here, we describe two closely related yeast hEST1A-B (SMG5-6)-like proteins termed Esl1 and Esl2 that contain a 14-3-3-like domain and a putative PIN ribonuclease domain.  We found that, unlike their metazoan orthologues, Esl1/2 were not involved in nonsense-mediated mRNA decay or telomere maintenance pathways. However, in genome-wide expression array analyses, absence of Esl1 and Esl2 led to >2-fold deregulation of ~50 transcripts, most of which were expressed inversely to the appropriate metabolic response to environmental nutrient supply; for instance, normally glucose-repressed genes were de-repressed in esl1Δ esl2Δ double mutants during growth in a high-glucose environment. Likewise, in a genome-wide synthetic gene array screen, esl1Δ esl2Δ double mutants were synthetic sick with null mutations for Rim8 and Dfg16, which form the environmental sensing complex of the Rim101 pH response gene expression pathway. Overall, these results suggest that Esl1 and Esl2 contribute to the regulation of adaptive gene expression responses of environmental sensing pathways.

overall_design: 3 biological replicates of each strain (wt & mutant) were analysed by competitive hybridisation.  One dye-swap exeperiment was additionally performed.

first: Traude

first: Jörg

last: Heierhorst


title: Gene expression profiles of Hyalella azteca populations with different pyrethroid sensitivities

status: Public on Jul 17 2013

first: Helen

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

summary: The goal of the study was to investigate gene expression differences in Hyalella azteca exposed to pyrethroid insecticides and compare a laboratory strain to a wild population believed to be resistant to the pesticides.  H. azteca reared in the laboratory at the University of CA, Berkeley (UCB) were exposed to cyfluthrin, a commerical pyrethroid insecticide for 96-h.  A wild population collected from Grayson Creek (GC), CA was reared in the laboratory for several days and also exposed to cyfluthrin.  Toxicity testing revealed that GC animals were two orders of magnitude less sensitive to cyfluthrin compared to the laboratory animals with the no observed effect concentration (NOEC) for UCB = 0.4 ng/L and GC= 170 ng/L.  Unexposed, control animals and animals exposed to 0.4 ng/L (GC and UCB) or 170 ng/L cyfluthrin were collected following 96-h treatments.  Differences in gene expression were measured using a custom Hyalella azteca microarray.  Gene expression profiles revealed that laboratory H. azteca responded to cyfluthrin through differential expression of genes involved in neurological system processes.   In contract, H. azteca from Grayson Creek showed a pattern of oxidative stress through the differential expression of glutathione-S-transferases, heat shock proteins, and other genes involved in oxidation-reduction processes.

overall_design: Four replicate exposures consisting of  ten animals were collected for each treatment or control.  A one-color hybridization protocol was used so that each sample was labeled with cy3 and only one sample was hybridized to each array.

first: Don

last: Weston

first: Bonnie

middle: J

last: Blalock

first: Maria

last: Sepulveda

first: John

last: Colbourne