title: Molecular profiling of breast cancer cell lines defines relevant tumor models (gene expression)

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

summary: Summary: Breast cancer cell lines have been used widely to investigate breast cancer pathobiology and new therapies.  Breast cancer is a molecularly heterogeneous disease, and it is important to understand how well and which cell lines best model that diversity.  In particular, microarray studies have identified molecular subtypes (luminal A, luminal B, ERBB2-associated, basal-like and normal-like) with characteristic gene-expression patterns and underlying DNA copy number alterations (CNAs).  Here, we studied a collection of breast cancer cell lines to catalog molecular profiles and to assess their relation to breast cancer subtypes.  Whole-genome DNA microarrays were used to profile gene expression and CNAs in a collection of 52 widely-used breast cancer cell lines, and comparisons were made to existing profiles of primary breast tumors.  Hierarchical clustering was used to identify gene-expression subtypes, and Gene Set Enrichment Analysis (GSEA) to discover biological features of those subtypes.  Genomic and transcriptional profiles were integrated to discover within high-amplitude CNAs candidate cancer genes with coordinately altered gene copy number and expression.  Transcriptional profiling of breast cancer cell lines identified one luminal and two basal-like (A and B) subtypes.  Luminal lines displayed an estrogen receptor (ER) signature and resembled luminal-A/B tumors, basal-A lines were associated with ETS-pathway and BRCA1 signatures and resembled basal-like tumors, and basal-B lines displayed mesenchymal and stem-cell characteristics.  Compared to tumors, cell lines exhibited similar patterns of CNA, but an overall higher complexity of CNA (genetically simple luminal-A tumors were not represented), and only partial conservation of subtype-specific CNAs.  We identified 80 high-level DNA amplifications and 13 presumptive homozygous deletions, and the resident genes with concomitantly altered gene-expression, highlighting known and novel candidate breast cancer genes.  Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction.  The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes.

overall_design: HEEBO oligonucleotide microarrays from the Stanford Functional Genomics Facility were used to perform gene expression profiling of 50 human breast epithelial cell lines, in comparison to a universal RNA reference.  Expression data were analyzed by hierarchical clustering to identify subgroups, and gene set enrichment analysis to identify subgroup-specific gene pathways.

first: Jessica

last: Kao

first: Yun

last: Choi

first: Melanie

last: Bocanegra


title: Molecular profiling of breast cancer cell lines defines relevant tumor models (aCGH)

status: Public on Jul 10 2009

country: USA

summary: Breast cancer cell lines have been used widely to investigate breast cancer pathobiology and new therapies.  Breast cancer is a molecularly heterogeneous disease, and it is important to understand how well and which cell lines best model that diversity.  In particular, microarray studies have identified molecular subtypes - luminal A, luminal B, ERBB2-associated, basal-like and normal-like - with characteristic gene-expression patterns and underlying DNA copy number alterations (CNAs).  Here, we studied a collection of breast cancer cell lines to catalog molecular profiles and to assess their relation to breast cancer subtypes.  Whole-genome DNA microarrays were used to profile gene expression and CNAs in a collection of 52 widely-used breast cancer cell lines, and comparisons were made to existing profiles of primary breast tumors.  Hierarchical clustering was used to identify gene-expression subtypes, and Gene Set Enrichment Analysis (GSEA) to discover biological features of those subtypes.  Genomic and transcriptional profiles were integrated to discover within high-amplitude CNAs candidate cancer genes with coordinately altered gene copy number and expression.  Transcriptional profiling of breast cancer cell lines identified one luminal and two basal-like (A and B) subtypes.  Luminal lines displayed an estrogen receptor (ER) signature and resembled luminal-A/B tumors, basal-A lines were associated with ETS-pathway and BRCA1 signatures and resembled basal-like tumors, and basal-B lines displayed mesenchymal and stem-cell characteristics.  Compared to tumors, cell lines exhibited similar patterns of CNA, but an overall higher complexity of CNA (genetically simple luminal-A tumors were not represented), and only partial conservation of subtype-specific CNAs.  We identified 80 high-level DNA amplifications and 13 presumptive homozygous deletions, and the resident genes with concomitantly altered gene-expression, highlighting known and novel candidate breast cancer genes.  Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction.  The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes.

overall_design: cDNA microarrays from the Stanford Functional Genomics Facility were used to carry out array-based Comparative Genomic Hybridization (array CGH) analysis of 52 human breast epithelial cell lines, in comparison to normal female DNA.  Three reference arrays of normal male vs. normal female DNA were also done.  Map positions for arrayed cDNA clones were assigned using the NCBI genome assembly, accessed through the UCSC genome browser database (NCBI Build 36).  The cghFLasso method was used to call DNA gains and losses.

first: Young

last: Kim

first: Kevin

last: Kwei


title: Gene expression in S1 panicles of Ubi1:AtJMT transgenic plants and drought-treated nontransgenic rice plants

city: Yong in

first: Nam-gun

address: Myongi Univ.

country: South Korea

institute: GGBIO

type: Expression profiling by genome tiling array

summary: To identify genes that are regulated by MeJA and drought, global expression profilings were performed on panicles from Ubi1:AtJMT, drought-treated NT, and untreated NT plants. The underlying assumption of this approach was that high levels of MeJA produced either by overexpression of AtJMT in the transgenic panicles or by drought treatment in the NT panicles regulates genes that are involved in spikelet and/or panicle development. Profiling was conducted using the Rice 3’-Tiling Microarray (GreenGene Biotech, Yongin, Korea). RNA samples from S1 panicles of Ubi1:AtJMT, drought-treated NT and untreated NT plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from three biological repeats.

overall_design:
Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image.
The microarray was used to profile gene expression in Ubi1:AtJMT, drought-treated NT, and untreated NT plants. Cy3-labeled target cDNA fragments were synthesized from S1 panicles using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.


title: Mycobacterium tuberculosis gene expression in response to thioridazine (THZ)

status: Public on Jul 08 2009

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

summary: The gene expression profiles of Mtb after treatment at the minimal inhibitory concentration (MIC) or 4 X MIC at an early stage (up to 6 hours) was compared to untreated Mtb.

overall_design: Our experiment is designed to in order to ensure that the primary effects (0-6h) of the drugs and any dose (1X MIC and 4X MIC)  responses would be captured.

first: Noton

middle: K

last: Dutta

first: Smriti

last: Mehra


title: The minimum low-salt stimulon in Vibrio parahaemolyticus

status: Public on Jul 07 2009

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

country: China

institute: Institute of Microbiology and Epidemiology

summary: Global gene expression profiles of V. parahaemolyticus grown under 2% and 0.66% NaCl were compared to define the minimum low-salt stimulon. The ectABC-lysC operon for synthesis of the compatible solute ectoine, as well as three compatible-solute transport systems, namely ProU (glycine betaine), OpuD1 (glycine betaine) and Pot2 (spermidine), was up-regulated under 2% NaCl in relative to 0.66% NaCl. The 2% NaCl condition favored the inducible expression of OmpW, OmpN and OmpA2, while repressed the expression of OmpA1, OmpU and VP1008. These results indicated that, to master the hyperosmotic stress of saline environments, V. parahaemolyticus might not only accumulate osmoprotectants through uptake or endogenous synthesis of compatible solutes, but also remodel its profiles of outer membrane protein to restore its cell membrane. The above differentially regulated genes will provide novel candidates for the further investigation of the molecular mechanisms of osmoadaptation in V. parahaemolyticus.

overall_design: A cDNA microarray imprinted with 4669 genes representing about 97% of V. parahaemolyticus genome was used for transcriptome analysis . For two-sample (reference vs. test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation . Accordingly, for each time point, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias. A ratio of mRNA levels (test/reference) was calculated for each gene. Significant changes of gene expression were identified with the SAM software . After the SAM analysis, only genes with at least 2-fold changes in expression were collected for further analysis.


title: Analysis of Gene Expression in Tissues of Two Turmeric Varieties at Different Developmental Stages

status: Public on Jul 09 2009

city: Tucson

first: David

middle: R

last: Gang

state: AZ

address: 1657 E Helen Street

department: Plant Sciences

institute: The University of Arizona

summary: Two varieties of turmeric, FMO (Fat Mild Orange) and TYA (Thin Yellow Aromatic) were compared. Rhizomes were harvested 3, 5, and 7 months after planting, roots were harvested at 7 months, and leaves were harvested at 7 months. Plants were grown under controlled conditions in the greenhouse.

platform_organism:
Zingiber officinale
Curcuma longa

overall_design: We used an interwoven loop design for hybridizations. There are two interwoven loops included in this experiment, one for rhizome samples from the different developmental stages, and a second for leaf and root 7 month old samples compared to 7 month old rhizome samples. The two loops were connected at the 7 month old rhizome samples.

first: HyunJo

last: Koo

first: Xiaoqiang

last: Ma


title: Thioxotriazole copper(II) complex A0 kills cancer cells inducing endoplasmic reticulum stress and paraptotic cell death

status: Public on Jul 06 2009

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

summary:
Time-course experiment for gene expression profiling of HT1080 cells showed that while cisplatin induced p53 targets, A0 regulates genes involved in response to heavy metals or to unfolded protein, supporting the absence of relation between sensitivities to the two drugs

Keywords: Time-course Experiment

overall_design: Expression Profile Comparison of HT1080 in response to A0 and Cisplatin in a Time-course Experiment Design

first: Saverio

last: Tardito

first: Claudio

last: Isella


title: Tumor T12 Sectors

city: Cold Spring Harbor

first: Nicholas

last: Navin

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

type: Genome variation profiling by genome tiling array

summary: The following CGH experiments were conducted on six sectors (S1-S6) from a single primary ductal carcinoma tumor (T12) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.

overall_design: The genomic DNA from each tumor subpopulation was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray.  A normal reference male fibroblast was labeled with Cy3 as a control.  Samples were dye-swapped and the experiments were conducted in color-reversal.  The value data repesents a log ratio of the mean of two dye-swapped samples

middle: E


title: Comparative transcript profiling of plant virus synergism

city: Madrid

first: Francisco

last: Tenllado

state: Madrid

address: Ramiro de Maeztu, 9

department: Plant Biology

country: Spain

institute: Centro de Investigaciones Biológicas, CSIC

summary: Many virus diseases of economic importance to agriculture result from mixtures of different pathogens invading the host at a given time. This contrasts with the relatively scarce studies available on the molecular events associated with virus-host interactions in mixed infections. In comparison to single infections, co-infection of Nicotiana benthamiana with Potato virus X (PVX) and Potato virus Y (PVY) resulted in increased systemic symptoms (synergism) that led to necrosis of the newly emerging leaves, and the plant death. A comparative transcriptional analysis was undertaken to identify quantitative and qualitative differences in gene expression during this synergistic infection, and to correlate these changes with the severe symptoms it caused. Global transcription profiles of doubly-infected leaves were compared with those from singly-infected leaves using gene ontology enrichment analysis and metabolic pathway annotator software. Functional gene categories altered by the double infection comprise suites of genes regulated coordinately, which are associated with chloroplast functions (down-regulated), protein synthesis and degradation (up-regulated), carbohydrate metabolism (up-regulated), and response to biotic stimulus and stress (up-regulated). The expression of reactive oxygen species-generating enzymes as well as several mitogen-activated protein kinases, were also significantly induced. Accordingly, synergistic infection induced a severe oxidative stress in N. benthamiana leaves, as judged by increases in lipid peroxidation, and by the generation of superoxide radicals in chloroplasts, which correlated with the misregulation of antioxidative genes in microarray data. Interestingly, expression of genes encoding oxylipin biosynthesis was uniquely up-regulated by the synergistic infection. Virus-induced gene silencing of alfa-dioxygenase1 delayed cell death during PVX-PVY infection.

overall_design: Using mock inoculated leaf tissue as a reference, we compare the gene expression profiles of Nicotiana benthamiana plants infected with one of two viruses, Potato virus X (PVX) or Potato virus Y (PVY), or the combination PVX plus PVY. 3 biological replicates per treatment were independently grown and haversted.

first: Alberto

last: García-Marcos

first: Remedios

last: Pacheco

first: Justo

last: Martiáñez

first: Pablo

last: González-Jara

first: José

last: Díaz-Ruíz


title: Tumor T8 Sectors

summary: The following CGH experiments were conducted on five sectors (S1-S5) from a single primary ductal carcinoma tumor (T8) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Paralog Specificity in cDNA Microarray Experiments

status: Public on Jul 03 2009

city: Austin

first: Lin

last: Huffman

address: 2400 Speedway, PAT 141

department: Institute for Cellular and Molecular Biology

institute: The University of Texas

summary: cDNA microarrays have become the technology of choice for profiling the expression of thousands of genes simultaneously in a single sample. However, cross-hybridization between targets and probes that do not correspond must be considered carefully during the design, analysis, and interpretation of these experiments. Here, we examined this potentially confounding issue by competitively hybridizing fragments with similar sequence obtained from two paralogous genes to a custom cDNA microarray that contains probes for only one of these two genes. We found that although a large contiguous portion of these two fragments was 84% identical and only one target was represented on the array, there was very little cross-hybridization of the non-represented target to either the paralogous probes or other (non-similar) features. We conclude that cDNA microarrays  are indeed very specific and that promiscuous paralog hybridization adds little noise to the data. More generally, the absence of specific probes for any given gene does not increase the chance for cross-hybridization between non-specific probes and targets, even if sequence similarity is relatively high.

overall_design: PCR products from two paralogs (arginine vasotocin/vasopressin and isotocin/mesotocin/oxytocin) were competitively hybridized onto a glass cDNA microarray platform of the same species. The platform contained probes for only one of the two paralogs in an effort to assess cross-hybridization between paralogous targets and probes.

middle: S

first: Hans

middle: A

last: Hofmann


title: The microRNAs hsa-miR-342 and -494 are upregulated in the brain of BSE-infected macaques

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Although transmissible spongiform encephalopathies are thought to be mediated by the pathogenic isoform of the prion protein PrPSc, the molecular mechanism underlying neurodegeneration is poorly understood. MicroRNAs (miRNAs) have been shown to cause or influence the pathogenesis of several diseases, however, they were not linked to prion disorders yet. We have addressed the regulation of miRNAs in BSE-infected macaques as a model for human Creutzfeldt-Jacob disease. Applying miRNA microarrays and quantitative RT-PCR, we found that two miRNAs, hsa-miR-342 and hsa-miR-494, are upregulated in the brain of BSE-infected monkeys. Predictions of potential target genes revealed functional links to other neurodegenerative disorders with protein aggregation, including Alzheimer’s and Huntington’s disease. Differential miRNA analysis may be a powerful tool to identify common pathways in the pathogenesis of neurodegeneration.

overall_design:
2 Experiments:
1. Comparison Brain_BSE vs. Brain_Control: 2-Color Dye Swap Design with 6 technical replicates
2. miRNA Profiling Brain_Control: 3 technical Replicates

first: Judith

last: Montag

first: Reiner

last: Hitt

first: Lennart

last: Opitz

first: Walter

last: Schulz-Schaeffer

first: Gerhard

last: Hunsmann

first: Dirk

last: Motzkus


title: Plasmodium berghei PbeIK2KO sporozoites

status: Public on Jul 01 2009

city: La Jolla

first: Elizabeth

middle: Ann

last: Winzeler

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

summary: Malaria sporozoites, the form transmitted by mosquitoes, are quiescent while in the insect salivary glands. It is only after the sporozoites are deposited in the host’s skin, migrate to the liver and infect hepatocytes that the parasites continue the life cycle. We show that the sporozoite latency is an active process that requires phosphorylation of the eukaryotic initiation factor-2α (eIF2α) by a sporozoite-specific kinase. Inactivation of the kinase gene leads to an overall enhancement of protein synthesis including of silenced liver stage proteins, and inhibits transmission of malaria. Specific inhibition of the eIF2α phosphatase by salubrinal has the opposite effect. Thus, to prevent premature transformation into liver stages, Plasmodium sporozoites exploit the same mechanism that regulates stress responses in mammalian cells.

platform_organism:
Plasmodium berghei
Plasmodium falciparum

overall_design: 4 samples overall, 2 wt and 2 KO (PbeIK2 knockout) samples

first: Stephan

last: Meister


title: miRNA prognostic profiles in lung cancer

city: Radnor

first: Hongtao

last: Fan

state: PA

address: 145 King of Prussia Rd

department: RDI

institute: Centocor

summary:
Non-small-cell lung cancer (NSCLC), which is comprised mainly of adenocarcinoma and squamous cell carcinoma (SCC), is the cause of 80% of all lung cancer deaths in the US. NSCLC is also associated with a high rate of relapse following clinical treatment and therefore requires robust prognostic markers to better manage therapy options.
The aim of this study was to identify miRNA expression profiles in squamous cell carcinoma (SSC) of the lung that would better predict prognosis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Total RNA from 61 SCC samples and 10 matched normal lung samples was processed for small RNA species and profiled on MirVana miRNA Bioarrays (version 2, Ambion).

first: Mitch

last: Raponi

first: Lesley

last: Dossey

first: Tim

last: Jatkoe

first: Xiaoying

last: Wu

first: David

middle: G

last: Beer


title: Chemoprevention of the hepatocarcinogenesis by celecoxib

city: Mexico

first: Adriana

last: Marquez-Quiñones

state: DF

address: AV. Instituto Politecnico Nacional No. 2508

department: Cell Biology

country: Mexico

institute: CINVESTAV

summary: Microarray analysis is a useful methodology to identify target genes modulated by anticancer drugs. Here, celecoxib effect on gene expression profiles was evaluated in the modified resistant hepatocyte model. Animals subjected to carcinogenic treatment were fed with diet containing 1500 ppm of celecoxib. Two schemes of celecoxib administration were designed. In the progression protocol, celecoxib was administrated between days 18 and 25 post-cancer initiation, a total of 8 celecoxib treatment days, when well established preneoplastic lesions starts to appear. In the initiation protocol, celecoxib was administrated from one week before until 25 days after of cancer initiation, a total of 32 celecoxib treatment days. A rat group was subjected only to the carcinogenic treatment as cancer positive control. Gene expression profiles of all groups were compared to a negative untreated control. The evaluation of gene expression profiles permitted us to identify new target genes that are modulated by celecoxib treatment. A possible mechanism of celecoxib chemoprevention of hepatocarcinogenesis is proposed.

overall_design: 9 weeks old Sprague Dawley rats, 4 rats per group, were subjected to Semple-Roberts' modified hepatocarcinogenesis protocol and sacrificed 25 days post-initiation. In celecoxib-treated groups, celecoxib was administrated mixed in diet at 1500 ppm. Negative and positive cancer progression controls were included to compare gene expression profiles. Microarray analysis was performed on liver samples, one replicate per rat, using dye swap.

first: Jaime

last: Arellanes-Robledo

first: Martha

last: Salcido-Neyoy

first: Rebeca

last: Garcia-Roman

first: Olga

last: Beltran-Ramirez

first: Veronique

last: LeBerre

first: Serguei

last: Sokol

first: Jean-Marie

last: François

first: Saul

last: Villa-Treviño


title: Characterization of boundary cap cells using novel markers obtained by RNA profiling

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

summary: Neural crest (NC) cells are a multipotent, highly migratory cell population that generates most of the components of the peripheral nervous system (PNS), including the glial satellite and Schwann cells. In addition, NC cells also gives rise to another type of PNS glial cell, the boundary cap (BC) cells. These latter cells are located at the interface between central nervous system and PNS, at the exit/entry points of ventral motor and dorsal sensory axons. We have shown that in absence of BC cells motor neurons translocate their cell bodies along their axons into the periphery. Moreover, in vivo tracing of BC cells revealed that they give rise to all Schwann cells in the nerve roots and to a subset of nociceptive neurons and satellite cells in the dorsal root ganglia. To identify novel molecular markers for BC cells, we have performed RNA profiling experiments to compare mouse BC cells with two closely related cell types, NC cells and Schwann cells precursors, and tested the most promising candidates by in situ hybridization. This work defined a set of 10 genes that show specific expression in BC cells and/or in their derivatives located along nerve roots.  Using this collection we show that dorsal and ventral BC cells and their derivatives express different genes, suggesting that they have distinct properties. We also establish that BC cells undergo a major modification between embryonic days 14.5 and 17.5. The identification of these novel makers opens the way for further characterization of BC cells in both mouse and man.

overall_design: Two biological replicates each in dye swap

first: Piotr

last: Topilko

first: Coulpier

last: Fanny

first: Stephane

last: Le Crom


title: Expression analysis of Streptomyces avermitilis NRRL8165 delta-aveI mutant

status: Public on Jul 02 2009

city: Shanghai

first: Lei

last: Chen

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
Investigation of whole genome gene expression level changes in Streptomyces avermitilis delta-aveI mutant, compared to the wild-type strain.
The mutants analyzed in this study are further described in Chen L, Lu Y., Chen J, Zhang W, Shu D, Qin Z, Yang S, Jiang W. (2008) Characterization of a negative regulator AveI for avermectin biosynthesis in Streptomyces avermitilis NRRL8165. Appl Microbiol Biotechnol 80(2): 277-86.

overall_design: A six chip study using total RNA recovered from three separate Streptomyces avermitilis NRRL8165 and three separate cultures of a Streptomyces avermitilis NRRL8165 delta-aveI (delta-l) mutant. 3 separate RMA normalizations performed, one for each pair of control and mutant samples.

first: Jun

first: Yuqian

last: Jiang

first: Weiwen

last: Zhang

first: Weihong

first: Yinhua

last: Lu


title: Comparison of gene expression in thyrocytes between wildtype and thyroid-specific IFNg transgenic mice

city: Baltimore

first: Patrizio

last: Caturegli

state: MD

address: 720 Rutland Avenue

institute: Johns Hopkins University

summary: Hürthle cells are found in thyroid tumors and autoimmunity, and have a unique appearance characterized by swollen eosinophilic cytoplasm filled with mitochondria and hyperchromatic nucleus. The pathogenesis of Hürthle cells remains unknown. We have generated transgenic mice expressing IFNg specifically in thyroid gland, and shown they develop changes in the thyroid follicular cell that resemble those of the human Hürthle cell.  Transcriptome analysis by serial analysis of gene expression revealed an increased expression of immunoproteasome subunits in transgenic thyrocytes. LMP2, an immunoproteasome subunit also known as PSMB9 or ib1, provided critical for Hürthle cells and hypothyroidism development. Transgenic mice treated with a proteasome inhibitor ameliorated the Hürthle cell phenotype, and failed to develop it when crossed to LMP2 deficient mice. LMP2 was expressed in Hürthle cells from Hashimoto thyroiditis and thyroidal cancer patients. We propose that LMP2 is a nobel therapeuetic target for Hürthle cell lesions.

overall_design:
We used 16 wildtype female mice for "Thyroid_wildtype_CD45depleted" and 3 thyroid specific IFNg transgenic female mice for "Thyroid_IFNg_transgenic_CD45depleted".
Both wildtype and transgenic mouse thyroids have hematopoiteic cells, especially transgenic mouse have numerous mononuclear cell infiltration.  We purely wanted to study gene expression of thyrocytes, because Hürthle cell is a follicular cell and a majority of thyrocytes are follicular cells. A difference of number of mice between two groups are due to a difference of size of thyroid lobes (Kimura et al. Int J Exp Pathol 86, 97-106, 2005).

first: Hiroaki

middle: J

last: Kimura


title: Analysis of milk removal frequency on bovine mammary gene expression

city: Auckland

first: Matt

middle: D

last: Littlejohn

address: PO Box 109-185 Newmarket

country: New Zealand

institute: DairyNZ

summary: Regulation of milk synthesis and secretion is controlled mostly through local (intra-mammary) mechanisms. To gain insight into the molecular pathways comprising this response, an analysis of mammary gene expression was conducted in 12 lactating cows shifted from twice daily to once daily milking. Tissues were sampled by biopsy from adjacent mammary quarters of these animals during the two milking frequencies, allowing changes in gene expression to be assessed within each animal. Using bovine-specific, oligonucleotide arrays representing 21,495 unique transcripts, a range of differentially expressed genes were found as a result of less frequent milk removal.

overall_design: A total of 12 microarrays were used in this study. Each array was hybridized with RNA derived from a mammary sample taken at each biopsy time point, such that the twice-a-day milked sample and once-a-day milked sample were contained on the same slide for each animal (12 animals). Six of the microarrays represented animals previously shown to demonstrate a ‘large’ reduction in milk yield, whereas the other six arrays represented animals that previously displayed a ‘small’ reduction in milk yield when milked once per day. Half of each yield loss group (three animals) was represented by once-a-day milked/twice-daily-milked samples for Cy5/Cy3 labelling, with the other half labelled with the opposite dye configuration. This meant that six of 12 arrays were 'dye swapped', but with biological replicates as opposed to identical replicates.

first: Hamish

last: Ward

first: Klaus

last: Lehnert


title: Mycobacterium smegmatis: CarD depletion (mgm1703) vs Control (mgm1701)

city: New York

first: Christina

middle: Leigh

last: Stallings

department: Immunology

institute: Sloan Kettering Institute

summary: Transcriptional profiling of Mycobacterium smegmatis comparing the effects of wild type levels of CarD expression with CarD depletion. Transcriptional profile of the mgm1701 control strain was compared with that of mgm1703, a strain where CarD transcription is regulated by a Tet-On system. Both strains were grown in the absence of anhydrotetracline for 13 hours in nutrient rich broth to allow for depletion of CarD transcription in mgm1703.

overall_design: Two condition experiment, control (mgm1701) vs CarD depletion (mgm1703). 3 biological replicates of each strain.

middle: L

first: Michael

last: Glickman


title: Temporal pattern of skeletal muscle gene expression following endurance exercise in Alaskan sled dogs

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

summary:
Background: Muscle responses to exercise are complex, and potentially include acute responses to exercise-induced injury as well as longer-term adaptive training responses.  Using Alaskan sled dogs as an experimental model, changes in muscle gene expression were analyzed to better understand the temporal changes that occur after severe exercise.
Methods: Dogs were randomly assigned to undertake in a 160 km run (n=9), or to remain at rest (n=4).  Biceps femoris muscle was obtained by needle biopsy from the unexercised dogs and two dogs at each of 2, 6 and 12 hours after the exercise and from 3 dogs 24 hours after exercise.  RNA was extracted and microarray analysis used to define gene transcriptional changes.
Results: Nine hundred sixty three transcripts exhibited statistically significant change over time after exercise as compared to the unexercised dogs.  The changes in gene expression after exercise occurred in a clear temporal pattern and included transcripts with increased expression 2 hours after exercise with a return towards resting levels by 6 hours after exercise.  Other transcripts demonstrated increased expression which peaked at six hours after exercise, while other transcripts showed sustained induction or repression over the 24 hours after exercise.  Increases in a number of known transcriptional regulators, including PPAR-α, CERM and CEBPD, were observed 2-hours after exercise.  Pathway analysis demonstrated coordinated changes in expression of genes with known functional relationships, including genes involved in muscle remodeling and growth, intermediary metabolism and immune regulation.
Conclusion: Sustained endurance exercise by Alaskan sled dogs induces coordinated changes in gene expression with a clear temporal pattern.  RNA expression profiling has the potential to identify novel regulatory mechanisms and responses to exercise stimuli.

overall_design:
Subjects were 13 Alaskan sled dogs aged 4.5 + 2.5 years (mean + SD) and weighing 23.3 + 2.5 kg. Dogs were randomly assigned to two groups – one group of 9 dogs subsequently ran 160 km in 24 hours as 2 sessions of 80 km, separated by a 6 hour rest period. The second group consisted of four dogs housed in unheated kennels, their usual housing, for the duration of the experiment. All dogs were from the same kennel. Dogs were fed a commercial kibble (Eukanuba, Iams Company, Dayton, OH) supplemented with frozen meat during the 8 weeks preceding the study and throughout the study period.  The dog’s diet was consistent before, during and after the exercise bout.  All dogs had completed 1590 + 100 km of training runs in the 3 months before the study.  The dogs had not exercised for 72 hors before the start of this study.
Dogs in the exercise group ran as a team pulling a lightly laden sled and driver over packed snow. Ambient temperatures were -20o to -10o C with no wind. Dogs completed the two 80 km runs in 23 hours, including the 6 hour rest period.
Blood samples were collected by jugular venepuncture from all dogs the day before exercise, and within a 10 minute window at 2, 6, 12, and 24 hours after completing the second run. Samples were collected into evacuated glass tubes containing a clot enhancer.
Muscle samples were collected from each of two dogs within a 10 minute window at 2, 6 and 12 hours after completing exercise and from three dogs 24 hours after completing exercise. Muscle samples were collected from each of the four unexercised dogs within two hours of the other dogs initiating their exercise bout.  Each dog had only one biopsy procedure performed. Muscle samples were collected from the biceps femoris muscle using a needle biopsy that yielded approximately 40-60 mg of muscle. The biopsy was performed after clipping and aseptic preparation of the skin overlying the biopsy site. The dog was anesthetized with propofol (6 mg/kg, IV, maintained as necessary with 2 mg/kg additional boluses), a cuffed orotracheal tube placed and the dog ventilated with a hand-held ventilation bag. When adequate anesthesia had been obtained a 5 mm incision was made in the skin. A sterile biopsy needle (12 g PGI EZ Core, Products group International, Inc. Lyons, CO) was then inserted through the incision and a sample of muscle collected. If necessary, repeated collections of muscle were made until a minimum of 40 mg of muscle has been collected from an individual dog. The skin incision was closed with tissue glue and an antibiotic ointment applied. The dog was monitored closely until recovery from anesthesia was complete. Carprofen (4.4 mg/kg, orally) was administered when the dog had recovered sufficiently from anesthesia to have a gag reflex.


title: AURATUS goldfish environmental genomics projects: fadrozole in the telencephalon

city: Ottawa

first: Jason

middle: T.

last: Popesku

state: ON

address: 20 Marie Curie

department: Biology

country: Canada

institute: University of Ottawa

summary: Sexually mature female goldfish were exposed (waterborne) to 50 ug/L fadrozole or untreated water (control) to examine the global gene expression of fadrozole on the telencephalon.

platform_organism:
Carassius auratus
Cyprinus carpio

overall_design:
A common reference design was used:
5 independent groups of telencephalonic tissue from sexually mature female goldfish exposed to 50 ug/L of waterborne fadrozole were hybridized against a common pool of unexposed fish.
Slides 4, 14, 22, 33, 44.

first: Dapeng

middle: T

first: Chris

last: Martyniuk

first: Vance

last: Trudeau


title: Impact of sucrose retrieval upon ex vitro acclimatization

city: Québec

first: Jean-François

last: Dubuc

address: 2440 boul. Hochelaga

institute: Université Laval

summary: Hybridization and study was conducted to measure the impact of short-term sugar deprivation, on an acclimatization time-scale, imposed to plantlet transferred from in vitro to ex vitro culture conditions. We thus submitted in vitro tomato plantlets to sugar deprivation for 24-h in order to better understands the impact of sucrose retrieval upon ex vitro acclimatization.

overall_design: A total of six microarrays were used for this experiment. More precisely, three biological replicates represented by individually grown in vitro plantlet from both treatments were hybridized. Dye swap was conducted as technical replicate in order to minimize dye bias.


title: Analysis of Gene Expression in Ginger Tissues at Different Developmental Stages

city: Tucson

first: David

last: Gang

institute: The University of Arizona

summary: Rhizome, root and leaf of Yellow ginger were compared in this study. Rhizomes from 2, 3, 4, 6, and 7 month old plants (after planting) were compared to each other and to root from 2 and 7 month plants and leaves from 2 and 7 month old plants.  Plants were grown under controlled conditions in the greenhouse.

overall_design: We used an interwoven loop design for hybridizations. There are two interwoven loops included in this experiment: one for rhizome developmental stages (2, 3, 4, 6, and 7 months old), the other one for all tissues of 2 and 7 month old plants. These interwoven designs are connected at the 2 month old and 7 month old rhizome samples.

first: HyunJo

last: Koo

first: Xiaoqiang

last: Ma


title: Molecular Analyses of 10q hemizygous deletions and parents

first: Jonathan

last: Pevsner

address: 707 N. Broadway

department: Neurology

institute: Kennedy Krieger Institute

summary: We report on the analyses of four unrelated patients with de novo, overlapping, hemizygous deletions of the long arm of chromosome 10. These include two small terminal deletions (10q26.2 to 10qter), a larger terminal deletion (10q26.12 to 10qter), and an interstitial deletion (10q25.3q26.13). Single nucleotide polymorphism (SNP) studies (Illumina 550 K) established that these deletions resulted in the hemizygous loss of approximately 6.1, approximately 6.1, approximately 12.5, and approximately 7.0 Mb respectively. Additionally, these data establish that Patients 1, 2, and 3 share common, distal, hemizygous deleted regions of 6.09 Mb containing 37 RefSeq genes. Patients 3 and 4 share a 2.52 Mb deleted region corresponding to the proximal deleted region of Patient 3 and the distal deleted region of Patient 4. This common, hemizygous region contains 20 RefSeq genes including two H6 family homeobox genes (HMX2 and HMX3). Based on previous reports that Hmx2/Hmx3 knockout mice have vestibular anomalies, we propose that hemizygous deletions of HMX2 and HMX3 are responsible for the inner ear malformations observed from CT images, vestibular dysfunction, and congenital sensorineural hearing loss found in Patients 3 and 4.

overall_design: Four cases were identified as having hemizygous 10q deletions through g-banding. These were analyzed with SNP microarrays as well as parents (controls) for cases 1 and 4.

first: Nathaniel

last: Miller


title: Expression data from ectodermal explants following activation of hormone-inducible zic1

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

summary: The response of ectodermal explants, neuralized by noggin and treated with cycloheximide, following activation of hormone-inducible zic1 injected into the parent embryos compared to those from beta globin injected embryos as controls, is expected to provide information on the direct targets of the Zic1 transcription factor.

overall_design: Activation of zic1 in ectodermal explants following inhibition of new protein synthesis allowed the direct targets of zic1 to be identified by comparison with controls. After RNA extraction, purification and checks with PCR with actin primers for any mesoderm contamination samples were prepared for hybridization to Xenopus laevis Affymetrix GeneChip arrays.

last: Cornish

first: Sabah

last: Hassan

first: Joshua

last: Martin

first: Shuzhao

last: Li

first: Christa

last: Merzdorf


title: Arabidopsis: C24 vs rst1

status: Public on Jun 30 2009

city: West Lafayette

first: Dong-Ha

last: Oh

state: IN

address: 625 Agriculture Mall Dr

department: HLA

institute: Purdue Univ.

summary: Transcriptional profiling of whole plant comparing C24 vs rst1 mutant

overall_design: Three biological repeat, each sample harvested from 10 4-week old plants, utilizing  the Arabidopsis 70-mer oligonucleotide chips (http://ag.arizona.edu/microarray)

first: Metthew

last: Jenks

first: Hans

last: Bohnert


title: Pituitaries of basal and stressed Crhr1 wild type and knockout mice

city: Munich

first: Cornelia

last: Graf

address: Kraepelinstr. 2-10

institute: MPI of Psychiatry

summary:
Pituitaries of basal and stressed Crhr1-wildtype (wt) and -knockout (ko) mice (Timpl et al., 1998)

As the Crh-system and the HPA-axis are known to be crucially invovled in the onset, development and maintainance of psychiatric disorders like anxiety and depression and regulate the behavioural and endocrine stress responses the further analysis of Crhr1-dependent signaling cascades is essential to understand the molecular mechanisms behind these psychiatric diseases. In this project, new candidate genes involved in Crhr1-dependent signaling cascades were dissected using metyrapone treated stressed Crhr1-wt and -ko (Timpl et al., 1998) mice using 30 min restraint stress. Changes in mRNA expression of pituitaries of basal and stressed Crhr1-wt and -ko mice were analysed 1 and 3h, respectively, after stress begin on the Sentrix Mouse-6 Expression BeadChip.

overall_design: To activate the CRHR1-dependent signaling in the pituitary of CRHR1-wt and -ko mice animals were stressed using 30 min restraint stress in 50 ml Falcon tubes. 12 h before stress mice were injected intraperitonally (i.p.) with 150 mg/kg bodyweight (b.w.) metyrapone. Metyrapone is an inhibitor of the steroid beta-hydroxylase, an enzyme catalyzing the biosynthesis of corticosterone. By this way, the negative feedback of corticosterone on the HPA-axis was blocked. A second metyrapone injection (100 mg/kg b.w.) was applied directly before stress. 1 and 3h, respectively, after stress, mice were anesthetized, decapitated and the pituitaries prepared and flash-frozen. mRNA was isolated according to the TRIzol protocol (Invitrogen). Pooled amplified RNA samples were then hybridised on Illumina mouse BeadChips (N=2 per group) and detected in the Illumina BeadArray Reader (Illumina, Inc., San Diego, CA). The experiment was performed in technical duplicates.

first: Peter

last: Weber

first: Claudia

last: Kühne

first: Benno

last: Pütz

first: Florian

last: Holsboer

first: Wolfgang

last: Wurst

first: Jan

middle: M

last: Deussing


title: Gene expression profiling of M tuberculosis BCG strain during extended stationary and resuscitation phase of growth

city: Lucknow

first: Ranjana

last: Srivatsava

address: Chattar Manzil Palace

country: India

institute: Central Drug Research Institute

summary:
Objective of the study is to find out the differentially regulated genes of Mycobacterium BCG strain in extended stationary phase comparison to log phase growth and resuscitation phase.
Mycobacterium BCG culture was grown in Sauton medium at 37o C without shaking. Cells at A600 0.6-0.8   were harvested as log phase culture. The cells harvested after 5 months incubation at 37oC without shaking became non culturable and were harvested as extended stationary phase cells. The extended stationary phase cells were treated with resuscitation promoting factor (Rpf) from Micrococcus luteus and harvested after 8 days. Cells of this stage were treated as resuscitation phase cells.
Gene expression profiling was carried out using Agilent microarray platform.
Keywords: Extended stationary phase, Log phase growth and Resuscitation phase.

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design:
• Organism: Mycobacterium tuberculosis BCG
• Slides: Agilent’s Mycobacterium tuberculosis custom array 4x44k (G2514F) AMADID No: 016013
• Labeling kit: Ambion Message Amp II Bacteria a RNA Amplification Kit Cat# 1790
• Labeling Method: T7 promoter based-linear amplification to generate labeled complementary RNA
• Total RNA and cRNA Purification Kit: Qiagen’s RNeasy minikit Cat#74104
• Hybridization Kit: Agilent’s In situ Hybridzation kit 5184-3568
• RNA quality was checked using Bioanalyzer.

Hybridization protocol 	825ng each of labeled control cRNA was mixed with 825ng of treated labelled cRNA, mixed with appropriate amount of blocking buffer and hybridization buffer (Agilent Technologies). The hybridization mix was applied on to the backings and hybridized to custom designed 60mer Mycobacterium tuberculosis microarray using sure hyb chambers at 65degC for 17 hours. Slides were washed with gene expression wash buffer 1 and 2 (Agilent Technologies) followed by Acetonitrile.
Scan protocol 	Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.
Description 	Slides were scanned at 5 micron resolution using Agilent scanner.Automated feature extraction was done using Agilent’s Feature Extraction Software.
Data processing 	Analysis of feature extracted data was done using Agilent’s GeneSpring GX V 7.3.1 software. Pre-processing of the replicate experiment data was done to flag the outliers. Normalization of the data was done using per spot per chip intensity dependant lowess normalization and dye swap experiment was data transformed.
Genes with log2 ratio of 1.29 and above in replicate experiments were considered as up regulated and 0.81 and below was considered down regulated. p-value was calculated by GeneSpring GX for each gene on the basis of replicate probes to indicate statistical significance. Biological significance of differentials were analyzed using Genotypics Biointerpreter - Web based tool for biological interpretation of given genelist.

first: Brahm

first: Amita

last: Yadav

first: Ravi

last: Gupta


title: BASE-A space experiment with Rhodospirillum rubrum S1H

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

country: Belgium

summary: R. rubrum S1H inoculated on solid minimal media was sent to the ISS in September 2006 (BASE-A experiment). After 10 days flight, R. rubrum cultures returned back to Earth. These cultures were then subjected to both transcriptomic and proteomic analysis and compared with the corresponding ground control. Whole-genome oligonucleotide microarray and high throughput proteomics, which offer the possibility to survey respectively the global transcriptional and translational response of an organism, were used to test the effect of space flight. Moreover, in an effort to identify a specific stress response of R. rubrum to space flight, ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations, which lead to a more solid dissection of the different factors contribution acting in space flight conditions.

overall_design: Total RNA was extracted from R. rubrum S1H grown after 10 days in space flight or after 10 days in simulated ionizing radiation or simulated microgravity. Each microarray slide contained 3 technical repeats.


title: MESSAGE 2 space experiment with Rhodospirillum rubrum S1H

summary: R. rubrum S1H inoculated on solid agar rich media was sent to the ISS  in October 2003 (MESSAGE-part 2 experiment). After 10 days flight, R. rubrum cultures returned back to Earth. These cultures were then subjected to both transcriptomic and proteomic analysis and compared with the corresponding ground control. Whole-genome oligonucleotide microarray and high throughput proteomics, which offer the possibility to survey respectively the global transcriptional and translational response of an organism, were used to test the effect of space flight. Moreover, in an effort to identify a specific stress response of R. rubrum to space flight, ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations, which lead to a more solid dissection of the different factors contribution acting in space flight conditions.


title: Gene expression profiling of hepatocarcinogenesis initiation in Fischer-344 rats.

first: Adriana

last: Marquez-Quiñones

summary: Diethylnitrosamine is used as initiator carcinogen in the modiffied resistan model but is not known its effect on gene expression profile on this stage. In other way, CAPE is compound with anticarcinogenic propertie when is administered 12 h before DEN and with the aim to characterize its effect on gene expression profile when is administered alone and in combination with diethylnitrosamine, these analysis were made. Male Fischer-344 rats were we used 4 animal per each treatment and all treatments are compared with not treated rats. Were identified groups of genes related with Carcinogens metabolism, oxidative stress and cell regulation with important differences between treatments.

overall_design: RT-PCR, enzyme activities, wester blots, metabolism assays were performed to validate these results.

first: Olga

last: Beltrán-Ramírez

first: Veronique

last: Le Berre

first: Serguei

last: Sokol

first: Jean-Marie

last: François

first: Saul

last: Villa-Treviño


title: Tiling-set aCGH data for oral dysplasias and oral squamous cell carcinomas

city: Vancouver

first: T

last: Buys

state: BC

address: 675 W.10th Avenue

department: Cancer Genetics and Developmental Biology

institute: British Columbia Cancer Research Centre

summary:
Analysis of DNA from 89 oral lesions by whole genome tiling-path array comparative genomic hybridization.
Keywords: array comparative genomic hybridization

overall_design: Genomic DNA isolated from 89 formalin-fixed paraffin-embedded oral dysplasias and tumors, then profiled by whole genome tiling-path array CGH to identify DNA copy alterations for each case.

first: Cathie

last: Garnis

first: Raj

last: Chari

first: Timon

middle: P

first: Lewei

last: Zhang

first: Raymond

last: Ng

first: Miriam

last: Rosin

first: Wan

last: Lam


title: p53 and p73 ChIP-chip experiments in HCT116-3(6) cells

city: La Jolla

first: Vera

last: Huang

address: 3855 Health Science Drive, Room 4317

department: Medicine

institute: UCSD-Moores Cancer Center

type: Genome binding/occupancy profiling by genome tiling array

summary: The p53-family of transcription factors share a highly homologous DNA binding domain and have overlapping and distinct biological functions. Using chromatin immunoprecipitation in combination with NimbleGen promoter arrays and a Model-based Algorithm for Promoter arrays (MAP), we performed a direct comparison of the promoter occupancy profiles of p53 and p73 before and after treatment with hydroxyurea (HU).  We have found that p53 and p73 bind to common promoters before HU treatment. After HU treatment, we found that p53-bound promoters are likely to also bind p73, but p73 binds to additional promoters that that do not bind p53. Among them, we showed that p73 but not p53 is recruited to the promoter of MLH3, which encodes a mismatch repair protein. The differential effects of HU on the promoter occupancy profiles of p53 and p73 suggest that these related transcription factors have divergent functions in DNA damage response.

overall_design: The main goal of this study is to examine the effect of HU on the promoter occupancy profiles of p53 and p73. One biological sample from HCT116-(6) cells treated with or without Hydroxyurea was subjected to ChIP-chip analysis using a model based algorithm for promoter arrays (MAP).

first: Xin

last: Lu

first: Yong

last: Jiang

first: Jean

middle: Y

last: Wang


title: The alternative complement pathway appears to be a UVA sensor that leads to systemic immunosuppression

status: Public on Jun 29 2009

city: Sydney

first: Michael

middle: Peter

last: Stapelberg

state: NSW

address: The University of Sydney

country: Australia

institute: The University of Sydney

summary: Ultraviolet (UV) wavebands in sunlight are immunomodulatory. About half the amount of UVA within a minimum erythemal dose of sunlight is systemically immunosuppressive, while higher doses protect from UVB immunosuppression in mice. We have previously shown that these responses to UVA are genetically restricted as they occur in C57BL/6 but not Balb/c mice. We used gene set enrichment analysis of microarray data and real-time RT-PCR confirmation to determine the molecular mechanisms associated with UVA immunomodulation. We found up-regulation of mRNA for the alternative complement pathway. The core-enriched genes complement component 3, properdin and complement factor B were all activated by the immunosuppressive dose of UVA only in UVA-responsive C57BL/6 but not unresponsive BALB/c mice. This therefore matched the genetic restriction and dose responsiveness of UVA immunosuppression. The immune-protective higher UVA dose prevented UVB from down regulating chemokine receptor 7 and IL-12B, and decreased IL-10, supporting previous identification of IL-12 and IL-10 in high dose UVA protection from UVB immunosuppression. Our study has identified activation of the alternative complement pathway as a trigger of UVA-induced systemic immunosuppression and suggests that this pathway is likely to be an important sensor of UVA-induced damage to the skin.

overall_design:
24 hours after UVA, UVB and ssUV irradiation, a 1 cm2 uniform section of skin was excised from the dorsal surface of irradiated and control mice. Total RNA was then extracted from the whole skin using TRIzol reagent (Gibco Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions, purified, DNase treated and reverse transcribed into cDNA. For the microarray study a direct incorporation of Cyanine 3-dCTP and Cyanine 5-dCTP fluorescent dyes (Perkin Elmer Life Sciences, Inc. Boston, MA, USA) was used for cDNA synthesis. For each UV dose, a reference design was used to compare an unirradiated control against an irradiated sample. Microarray experiments used compugen 22k mouse oligonucleotide microarray slides (The Clive and Vera Ramaciotti Centre for Gene Function Analysis, Sydney Australia (http://www.ramaciotti.unsw.edu.au).
Lower and higher UVA doses were used. C57BL/6 mice were irradiated with lower UVA, higher UVA, UVB, or ssUV; Balb/C mice were irradiated with lower or higher UVA.  Experiments were replicated 6 times for each UV dose. A fluorescent dye swap was done for each alternate hybridisation to reduce systematic dye bias of incorporated fluorescent dyes.

first: Rohan

middle: B

last: Williams

first: Scott

middle: N

last: Byrne

first: Gary

last: Halliday


title: Effect of Xpcl1 integration and p27Kip1 deletion on gene expression in MuMLV lymphomas

city: Albuquerque

first: Matthew

middle: Luke

last: Fero

state: NM

address: 1201 Camino de Salud

department: Internal Medicine

institute: University of New Mexico

summary: Mice lacking the p27Kip1 Cdk inhibitor (Cdkn1b) exhibit increased susceptibility to lymphomas from the Maloney murine leukemia virus (M-MuLV), and exhibit a high frequency of viral integrations at Xpcl1 (Kis2), a locus on the X-chromosome. Xpcl1 encodes miR-106a~363, a cluster of microRNAs that are expressed in response to adjacent retroviral integrations. We report the first large-scale profile of microRNA expression in MuLV-induced lymphomas, in combination with microarray gene expression analysis. The source material was T-cell lymphomas induced by M-MuLV in p27Kip1 knockout mice and normal thymus. Surprisingly, the overall levels of miRNA expression were equivalent in lymphomas and normal thymus. Nonetheless, the expression of specific microRNAs was altered in tumors. The miR-106a~363 miRNA were over-expressed in lymphomas, particularly those with viral integrations at the Xpcl1 locus. In contrast, p27Kip1 deletion itself was associated with a different pattern of microRNA expression. Gene expression was dramatically altered in lymphomas, yet paralleled data from T-cell lymphomas induced by other mechanisms. Genes with altered expression in association with the p27Kip1 null genotype were of similar functional classes to those associated with Xpcl1 integration, but with the opposite pattern of expression. Thus, the effect of p27Kip1 deletion may be to oppose an anti-oncogenic effect of Xpcl1 rather than enhancing its oncogenic functions. A subset of miR-106a~363 target genes was consistently reduced in lymphomas with Xpcl1 integrations, particularly genes with cell cycle and immune functions. We identify four predicted target genes of miR-106a~363 miRNA, including N-Myc (Mycn), and the TGF-beta receptor (Tgfbr2) using 3'UTR reporter assays. Still, bioinformatic miRNA target predictions were poor predictors of altered gene expression in lymphomas with Xpcl1 integration. Confirmation of miR- 106a~363 gene targeting relevant to the tumor phenotype requires in vivo validation, because only a subset of predicted targets are consistently reduced in tumors that overexpress miR- 106a~363.

overall_design: Total RNA was prepared from 17 lymphoma samples arising in MuMLV infected mice.  A subset of the animals had homozygous p27 deletions.  In addition 3 samples of normal thymic RNA were collected as a comparison group.  Equal amounts of RNA from of all samples were pooled as a common reference for co-hybridization on 2-color expression arrays.  Each sample was run in duplicate with a dye (Cy5 vs Cy3) swap.

first: Peter

last: Linsley

first: Bruce

middle: E

last: Clurman

first: Daniel

last: Kuppers

first: Aimee

last: Jackson

first: Harry

middle: C

last: Hwang


title: NT roots and NTwithNaB roots and OsHDAC1 roots

city: Pyeongchang

first: Pil Joong

last: Chung

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

institute: Seoul National University

summary:
In conjuction, microarray experiments by using RNA sources from 14-d-old NT and NT with NaB roots and OsHDAC1 overexpressor roots were performed and compared to the microarrays of NT with NaB roots and OsHDAC1 overexpressor roots.

Keywords: Epigegetic regulation

overall_design: Two-conditional experiments, NT vs. NTwithNaB and NT vs. OsHDAC1. Biological replications : 3

first: PJ

first: YS

last: Kim

first: JS

last: Jeong

first: S-H

last: Park

first: BH

last: Nahm

first: J-K


title: A Transcriptomic Analysis of Land Use Impacts on the Oyster, Crassostrea virginica, in the South Atlantic Bight.

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

summary:
Increasing utilization and human population density in the coastal zone is widely believed to place increasing stresses on the resident biota, but confirmation of this belief is somewhat lacking. While we have solid evidence that highly disturbed estuarine systems have dramatic changes in the resident biota (black and white if you will), we lack tools that distinguish the shades of grey. In part this lack of ability to distinguish shades of grey stems from the analytical tools that have been applied to studies of estuarine systems and perhaps more important is the insensitivity of the biological end points that we have used to assess these impacts. In this paper we will present data on the phenotypic adjustments as measured by transcriptomic signatures of a resilient organism (oysters) to land use practices in the surrounding watershed using advanced machine learning algorithms. We will demonstrate that such an approach can reveal subtle and meaningful shifts in oyster gene expression in response to land use.  Further, the data shows that gill tissues are far more responsive and provide superior discrimination of land use classes than hepatopancreas and that transcript encoding proteins involved in energy productions, protein synthesis and basic metabolism are more robust indicators of land use than classic biomarkers such as metallothioneins, GST and cytochrome P450.

Keywords: Comparative genomics, ecogenomics. Tissue differences, impacts of land use and contaminants on gene expression.

platform_organism:
Crassostrea virginica
Magallana gigas

overall_design: Oysters were collected from 11 tidal creeks in Georgia, South Carolina and North Carolina at sites variously impacted by human development. A total of 267 individuals were examined for gene expression profiles in gill and hepatopancreas tissues for a total of 534 arrays. The data were filtered though standard tools and ultimately analyzed using advance machine learning techniques.

first: Robert

middle: W

last: Chapman

first: Annalaura

last: Mancia

first: Marion

last: Beal

first: Artur

last: Veloso

first: Charles

last: Rathburn

first: Anne

last: Blair

first: Denise

last: Sanger

first: A

middle: F

last: Holland

first: G

last: Warr

first: Guy

last: DiDonato


title: Comparative analysis of the human and mouse placental transcriptome and proteome

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

institute: University of Toronto

summary:
An important question for the use of the mouse as a model for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human and mouse placenta show structural similarities but there have been no systematic attempt to assess their molecular similarities or differences. We built a comprehensive database of protein and microarray data for the highly vascular exchange region micro-dissected from the human and mouse placenta near-term. Abnormalities in this region are associated with two of the most common and serious complications of human pregnancy, maternal preeclampsia (PE) and fetal intrauterine growth restriction (IUGR), each disorder affecting ~5% of all pregnancies. Over 7,000 orthologs were detected with 70% co-expressed and over 80% of genes known to cause placental phenotypes in mouse were co-expressed. These genes form a tight protein-protein interaction network with novel candidate genes likely to be important in placental structure and/or function. The entire data is available as a web-accessible database to guide the informed development of mouse models to study human disease.

This experiment is now fully represented in the NCBI Peptidome database with accession PSE115.

sample_organism:
Homo sapiens
Mus musculus

overall_design: Microdissection of human villous trees and mouse placental labyrinth. Tissues were split for microarray and protein analysis. For protein analysis samples were first fractionated by differential sucrose gradients into mitochrondria, cytosol, microsomes and nuclei. Mitochrondira and neuclei were each extracted by two different methods for soluble and insoluble material. Each subcellular fraction for each tissue was analysed in quintuplet by 9 step 2 dimensional LC/MSMS. This generated a total of 270 mzXML files for each tissue.

first: Thomas

last: Kislinger

first: Andreas

middle: I

last: Evangelou

first: S

last: Adamson

first: Janet

last: Rossant

first: Vladimir

last: Ignatchenko

first: Alex


title: Expression profiling of Ruminococcus flavefaciens FD-1 with growth on cellulose or cellobiose

city: Urbana

first: Bryan

middle: A

last: White

state: IL

address: 1207 W. Gregory Drive

department: Animal Sciences

institute: University of Illinois

summary:
This study compares growth of Ruminococcus flavefaciens FD-1 with cellulose or cellobiose as the carbohydrate substrate.
Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides.  Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application to improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels.  These results show that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components.

overall_design: 1 species (Ruminococcus flavefaciens FD_1), 2 conditions (cellulose, cellobiose), 4 biological replicates.  Direct design with biological dye swap.

first: Margret

last: Berg Miller

first: Dionysios

last: Antonopoulos

first: Marco

last: Rincon

first: Mark

last: Band

first: Albert

last: Bari

first: Tatsiana

last: Akraiko

first: Alvaro

last: Hernandez

first: Jyothi

last: Thimmapuram

first: Bernard

last: Henrissat

first: Pedro

last: Coutinho

first: Ilya

last: Borovok

first: Sadanari

last: Jindou

first: Raphael

last: Lamed

first: Harry

middle: J

last: Flint

first: Edward

last: Bayer


title: Microarray Analysis of Acid-Stress Induced Changes in EHEC O157:H7

status: Public on Jun 26 2009

first: Debora

last: Foster

address: 350 Victoria Street

department: Chemistry and Biology

institute: Ryerson University

summary:
While significant advances have been made in EHEC pathogenesis, we still do not fully understand the impact of environmental stress on EHEC virulence. During the course of infection, EHEC must evade or overcome several biological barriers, the first of which is the gastric acidity encountered during passage through the stomach.  EHEC is remarkable in its ability to tolerate this acidity.  There are four different acid resistance systems that provide E. coli O157:H7 protection against exposure to low pH (2-2.5). Interestingly, EHEC uses these acid resistance systems differentially for survival in foods versus the bovine intestinal tract. The glutamate-dependent acid-resistance system is thought to offer the best protection below pH 3.  Since the infectious dose of EHEC is so low (50-100 organisms), acid resistance becomes an important virulence trait.

Studies of EHEC response to acid stress have focused primarily on levels of acid tolerance and the molecular basis of tolerance. However, the impact of acid stress on EHEC virulence is less well understood. In the related pathogen, EPEC, the plasmid-encoded regulator, Per, that regulates expression of many EPEC virulence factors, is regulated negatively at pH 5.5 and positively at pH 8.0, suggesting that virulence gene expression is repressed during mild acid stress and enhanced in alkaline pH typical of the small intestine. Expression of EPEC type III secreted factors involved in A/E lesion formation has been shown to be influenced by factors including culture media, iron and calcium levels. Protein secretion was inhibited at pH 6 and 8.  In a third study, a gadE (encoding acid resistance regulator) mutation resulted in increased adhesion of E.coli O157:H7 to colonic epithelial cells, suggesting negative regulation of one or more adhesins.  Other studies have reported that shiga toxin production is sensitive to culture conditions including pH. However, there are no studies of EHEC virulence changes after more severe acid stress nor studies linking stressed EHEC virulence phenotype with transcriptional changes.

The goal of this study was to determine how acid stress affects EHEC virulence properties and through microarray analysis, define the genetic basis for these changes.  Understanding how acid stress modulates the virulence potential of this pathogen is essential for delineating the pathogenesis of disease caused by EHEC infection and may offer novel approaches to prevent and treat EHEC infections.

overall_design:
Bacteria were grown in LB broth overnight, then subcultured into DMEM and grown at 37C, 5%Co2. Bacteria were then subjected to one of three acid stress protocols: 1) UA30: growth in DMEM pH 7.4 followed by growth in DMEM pH 3.0 for 30 minutes; 2) AA30: growth in DMEM pH 5.0 (adaptation) followed by growth in DMEM pH 3.0; 3) UA15: growth in DMEM pH 7.4 followed by growth in DMEM pH 3.0 for 15 minutes.
DMEM was supplemented with 25 mM MES (pH 5.0) and in the case of the control (unadapted, unshocked) 25 mM MOPS (pH 7.4) and the adaptation step was again carried out at 37C and 5% CO2.  Acid shocking was done at pH 3.0 (unbuffered) at room temperature for all treatments

first: Belinda

last: House

first: Julianne

middle: V

last: Kus

first: Nita

last: Prayitano

first: Richard

last: Mair

first: Lynne

last: Que

first: Victor

last: Gannon

first: Dennis

middle: G

last: Cvitkovitch

last: Barnett Foster


title: Remodeling of global transcription patterns of C. neoformans genes mediated by stress-activated HOG signaling pathways

status: Public on Jun 27 2009

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

institute: Yonsei University

summary: The ability to sense and adapt to a hostile host environment is a crucial element for virulence of pathogenic fungi, including Cryptococcus neoformans.  These cellular responses are evoked by diverse signaling cascades, including the stress-activated HOG pathway.  Despite previous analysis of central components of the HOG pathway, its downstream signaling network is poorly characterized in C. neoformans.  Here we performed comparative transcriptome analysis with HOG signaling mutants to explore stress-regulated genes and their correlation with the HOG pathway in C. neoformans.  In this study we not only provide important insights into remodeling patterns of global gene expression for counteracting external stresses, but also elucidated novel characteristics of the HOG pathway in C. neoformans.  First, inhibition of the HOG pathway increases expression of ergosterol biosynthesis genes and cellular ergosterol content, conferring a striking synergistic antifungal activity with amphotericin B and providing an excellent opportunity to develop a novel therapeutic method for treatment of cryptococcosis.  Second, a number of cadmium-sensitive genes are differentially regulated by the HOG pathway, and their mutation causes resistance to cadmium.  Finally, we have discovered novel stress-defense and HOG-dependent genes, which encodes a sodium/potassium efflux pump, protein kinase, multidrug transporter system, and elements of the ubiquitin-dependent system.

overall_design: There is more than 95% genome homology between JEC21 (Cryptococcus neoformans var. neoformans serotype D) and H99 (Cryptococcus neoformans var. grubii serotype A). Therefore, 100 slides of JEC21 70-mer oligo arrays are used in this analysis. 3 biological replicate experiments are performed. Total RNAs are extracted under 3 conditions (1M NaCl, 20ug/ul Fludioxonil, 2.5mM Hydrogen peroxide) at 3 time points (0time, 30min, 60min) with 4 strains from H99 (wild type, hog1Δ , ssk1Δ , skn7Δ). We use a mix of all the total RNAs from this experiment as the control RNA. We use Cy5 as the sample dye and Cy3 as the control dye. Several samples are dye swapped.

first: Young-Joon

last: Ko

first: Yeong-Man

last: Yu

first: Gyu-Bum

last: Kim

first: Gir-Won

last: Lee

first: Pil-Jae

last: Maeng

first: Sang-Soo

first: Anna

last: Floyd

first: Jeseph

last: Heitman


title: The unique roles of DosT and DosS in DosR regulon induction and Mycobacterium tuberculosis dormancy

city: Aurora

first: Ryan

middle: William

last: Honaker

state: CO

institute: University of Colorado Denver

summary: In Mycobacterium tuberculosis, the sensor kinases DosT and DosS activate the transcriptional regulator DosR, resulting in the induction of the DosR regulon, important for anaerobic survival and perhaps latent infection. The individual and collective roles of these sensors has been postulated biochemically, but their roles have remained unclear in vivo. This work demonstrates distinct and additive roles for each sensor during anaerobic dormancy. Both sensors are necessary for wild type levels of DosR regulon induction, and concomitantly, full induction of the regulon is required for wild type anaerobic survival. In the anaerobic model, DosT plays an early role, responding to hypoxia. DosT then induces the regulon and with it DosS, which sustains and further induces the regulon. DosT then loses its functionality as oxygen becomes limited, and DosS alone maintains induction of the genes from that point forward. Thus, M. tuberculosis has evolved a system whereby it responds to hypoxic conditions in a stepwise fashion as it enters an anaerobic state.

platform_organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

overall_design: Various DosS and DosT mutant strains were analyzed against wild type (reference strain H37Rv, identical conditions as mutant) under various conditions: day 6 in an anaerobic dormancy model, 4 or 24 hours in a GasPak model, or log phase with the addition of a nitric oxide donor. Experiments were repeated in triplicate or quadruplicate.

first: Rachel

middle: L

last: Leistikow

first: Iona

last: Bartek

first: Martin

last: Voskuil


title: Halobacterium sp. NRC-1 ChIP-chip for TFBa, TFBd and TFBf, high resolution array

status: Public on Jun 25 2009

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

summary: A detailed map of genomic locations where TFs bind DNA and modulate transcription is essential to model mechanisms of gene regulation on a systems-scale. Chromatin immunoprecipitation of transcription complexes coupled to microarray (ChIP-chip (Ren et al, 2000)) or sequencing (ChIP-seq (Robertson et al, 2007)) is a commonly used approach to construct such maps. In ChIP-chip, the resolution to which the protein-DNA binding sites (TFBSs) can be identified is often limited by the genomic spacing of the probes in the array. We utilized the MeDiChI algorithm (Reiss et al, 2008) to estimate precise TFBS locations and their corresponding local false discovery rates (LFDRs) from high-resolution arrays for TFBa, TFBd and TFBf. This regression-based method deconvolves the ChIP-chip enrichment ratios along the genome by fitting them with a 'peak profile' model of binding events, assuming a distribution in enriched DNA fragment lengths. A comparison of the peak intensities derived from MeDiChI for all three TFs (TFBd, TFBf and TFBa) for which there were biological replicate measurements using 2 different microarray platforms (500 nt resolution spotted arrays, see series GSE7045 vs. 13 nt resolution Nimblegen arrays) provided strong validation (with R2 of 0.66, 0.52, and 0.81, respectively) of most TFBSs. Visualizations comparing the two microarray platforms are available at: http://baliga.systemsbiology.net/regulatory_logic/

overall_design: IP sample of Cmyc tagged TFBs expressed in Halobacterium NRC-1 cells transformed with pMTFcmyc gene expressing TFBf in standard growth media with 20microgram/ml mevinolin versus a whole cell extract from the same sample. Three biological replicates for TFBd are available.

first: Marc

last: Facciotti

first: Min

last: Pan

first: David

last: Reiss

first: Nitin

middle: S

last: Baliga


title: Comparison of gene expression in Staphylococcus aureus strain SH1000 wildtype vs mepR

city: Pearl River

first: Ellen

last: Murphy

state: NY

address: 401 N. Middletown Road

department: Vaccines

institute: Wyeth Research

summary:
MepR is a substrate-responsive repressor of mepR and mepA, which encode itself and a MATE family multidrug efflux pump.  Microarray analyses of Staphylococcus aureus SH1000 and its mepR-disrupted derivative revealed changes in expression of many genes in addition to mepR and mepA, notably several involved in virulence
Keywords: Staphylococcus aureus, MATE efflux pump, MepR

overall_design: Staphylococcus aureus strains SH1000 wildtype and mepR were grown in duplicate to exponential and post-exponential phase (corresponding to an A550 nm of 0/4 and 2.0 respectively).  RNA was harvested, converted to cDNA, labelled with Biotin and used to probe custom-designed Affymetrix antisense S.aureus GeneChips.  Eight samples in total were prepared and analyzed.

first: Carmen

last: DeMarco

first: Fionnuala

middle: M

last: McAleese

first: Susan

last: Seo

first: Steven

last: Projan

first: Glenn

last: Kaatz


title: Comparative genomics using microarrays studied in Metarhizium anisopliae 2575 and 324

city: College Park

first: Sibao

last: Wang

address: Baltimore Avenue

department: Entomology

institute: University of Maryland

summary: The entomopathogen Metarhizium anisopliae contains strains with wide host ranges and specialist strains adapted to particular hosts. Patterns of gene duplication, divergence and deletion in three generalist and three specialist strains were investigated by heterologous hybridization of genomic DNA to genes from the generalist strain ARSEF 2575. Many sequences from 2575 that are highly conserved in fungi showed rapid evolution and loss in specialist Metarhizium genomes. Some poorly hybridizing genes in specialists were functionally coordinated, including several involved in toxin biosyntheses and sugar metabolism in root exudates, indicative of reductive evolution. This suggests that specialists are loosing genes required to live in alternative hosts or as saprophytes. Several components of mobile genetic elements were also highly divergent or lost in specialists. Exceptionally, the genome of the specialist strain ARSEF 443 contained extra insertion elements that might play a role in generating evolutionary novelty.

overall_design: Three microarray slides were used  in comparison (cDNAs are replicated in triplicate on each slide). 324 strain’s DNA was co-hybridized with strain ARSEF 2575 DNA in dye swapping replicate experiments and the relative hybridization efficiency (fluorescence ratio) of their DNA for strain ARSEF 2575 genes was compared. This array harbors PCR amplified fragments from the unique cDNA clones from M. anisopliae var. anisopliae ARSEF 2575 and a few genes from M. anisopliae var. acridum ARSEF 324 absent from the libraries of ARSEF 2575. In total, 1730 amplified clones were printed in triplicates on the slides. Additional background control was provided by 30 randomly distributed spots of 3×SSC buffer. Printing, hybridization, and scanning of slides was as described before (Freimoser et al., 2005).

first: Stleger

last: Raymond


title: Male Fundulus exposed to 1,720ppb arsenic, and their parentally exposed offspring

status: Public on Jun 24 2009

city: Pendleton

first: Lisa

last: Bain

address: P. O. Box 709

department: Biological Sciences

institute: Clemson University

summary: The present study investigated arsenic’s effects on mummichogs (Fundulus heteroclitus), while also examining what role that gender or age of exposure might play.  Adult male and female mummichogs were exposed to 172ppb, 575ppb, or 1,720ppb arsenic as sodium arsenite for 10 days immediately prior to spawning.  No differences were noted in the number or viability of eggs between the groups, but there was a significant increase in deformities in the 1,720ppb arsenic exposure group.  Total RNA from adult livers or 6-week-old juveniles was used to probe custom macroarrays for changes in gene expression.  In females, 3% of the genes were commonly differentially expressed in the 172 and 575ppb exposure groups.  In the males, between 1.1-3% of the differentially expressed genes were in common between the exposure groups.  Several genes, including apolipoprotein, serum amyloid precursor, lysozyme, and tributyltin-binding protein, were commonly expressed in either a dose-responsive or dose-specific, but across genders, manner.  These patterns of regulation were confirmed by QPCR.   These findings will provide us with a better understanding of the effects of dose, gender, and exposure age on the response to arsenic.

platform_organism:
Fundulus heteroclitus
Pseudopleuronectes americanus

overall_design:
Adult mummichogs (Fundulus heteroclitus) were exposed to either 0 or 1,720ppb sodium arsenite for 10 days before the full moon. Each treatment group had 5 20-gallon plastic tanks with 2 male and 5 female fish per tank.  The fish were exposed via a static renewal, with renewals every 48 hours. Mummichogs were housed at 25C in a 14/10 light/dark cycle at 18% salinity.  On the 3 days surrounding the full moon, spawning substrates were provided and eggs collected.

Adult males: After the last day of egg collection, the adults were euthanized.  The livers were removed from the males, placed in TRI-Reagent® for RNA isolation (Sigma Chemical Co, St. Louis, MO), and then stored at -80C.

Juveniles: Eggs were transferred to clean water and allowed to hatch.  The juveniles were grown out in clean water for 6 weeks and then were euthanized.  Whole juveniles (7-10 per exposure per tank) were placed in TRI-Reagent® for RNA isolation (Sigma Chemical Co, St. Louis, MO), and then stored at -80C.

first: Horacio

middle: O

last: Gonzalez


title: Halobacterium salinarum NRC-1 conditional ChIP-chip for transcription initiation factor IIB 4 (TFBd)

type: Genome binding/occupancy profiling by array

summary: Conditional ChIP-chip for TFBd at different growth stages.

overall_design: cmyc-tagged TFBd was immunoprecipitated at different growth stages (early log, stationary and late stationary phases) and hybridized to microarrays.

middle: T


title: Rat liver: Control vs. Chemical treated, 14 days

status: Public on Jun 23 2009

city: Ibaragi

first: kohei

last: inoue

address: Sunayama

country: Japan

institute: Mitsubishi Chemical Medience Corporation

summary:
The final goal of this study is to develop a short term and highly accurate prediction method of carcinogenicity based on gene expression profiles of rats subjected to carcinogen exposure.
We conducted 3 day-, 14 day- and 28 day-repeated dose experiments in male F344 rats with 47 carcinogens and 26 non-carcinogens, and the gene expression profiles in liver were investigated by custom glass microarrays.

Supplementary file "73 Compounds for training" indicates 47 carcinogens and 26 non-carcinogens.
Supplementary file "15 Compounds for test" lists the other compounds which are for test.

overall_design: Two-condition experiment, control vs. chemical treated rat liver. Biological replicates: 4 control, 4 treated, control samples were pooled. One replicate per array.

first: Koji

last: Nakayama

first: Hideki

last: Miyaura

first: Kayo

last: Sumida

first: Hiroshi

last: Matsumoto

first: Fumiyo

last: Saito

first: Koichi

first: Masaru

last: Sekijima

first: Masanori

last: Otsuka

first: Yoshikuni

last: Yakabe

first: Tomoyuki

last: Shirai


title: Male and female Fundulus exposed to 575ppb arsenic, and their parentally exposed offspring

overall_design:
Adult mummichogs (Fundulus heteroclitus) were exposed to either 0 or 172ppb sodium arsenite for 10 days before the full moon. Each treatment group had 5 20-gallon plastic tanks with 2 male and 5 female fish per tank.  The fish were exposed via a static renewal, with renewals every 48 hours. Mummichogs were housed at 25C in a 14/10 light/dark cycle at 18% salinity.  On the 3 days surrounding the full moon, spawning substrates were provided and eggs collected.

Adult males and females: After the last day of egg collection, the adults were euthanized.  The livers were removed from the males and females, placed in TRI-Reagent® for RNA isolation (Sigma Chemical Co, St. Louis, MO), and then stored at -80C.

Juveniles: Eggs were transferred to clean water and allowed to hatch.  The juveniles were grown out in clean water for 6 weeks and then were euthanized.  Whole juveniles (7-10 per exposure per tank) were placed in TRI-Reagent® for RNA isolation (Sigma Chemical Co, St. Louis, MO), and then stored at -80C.


title: Male and female Fundulus exposed to 172ppb arsenic, and their parentally exposed offspring


title: Sigma factor B (sigB) response to stress conditions (0.05% SDS and 5mM Diamide)

first: Martin

last: Voskuil

summary: The numerous sigma factors present in Mycobacterium tuberculosis (MTB) are indicative of adaptability to different environmental conditions. In this report we describe the sigma factor B (sigB) regulon and the phenotypes of a MTB sigB mutant strain exposed to different stresses like SDS and Diamide. This experiment set compares expression profiles between H37Rv wild type and H37Rv sigB null mutant as well as under different stress conditions. Both H37Rv wild type and H37Rv sigB null mutants were treated with either 0.05% SDS or 5mM Diamide for 60 min and their expression profiles were compared with untreated wild type or mutant controls.

overall_design: Biological Replicate


title: Expression profiles during cell death programmed by a restriction-modification system in E. coli

city: Kawasaki

first: Yoko

last: Asakura

state: Kanagawa

address: 1-1 Suzuki-cho Kawasaki-ku

department: Institule of Life Sciences

institute: Ajinomoto

summary:
Genetically programmed deaths play important roles in the biology of unicellular prokaryotic cells. Some gene complexes force their maintenance on the host bacterial cells by killing cells that have lost them. This form of programmed death called post-segregational killing or genetic addiction is brought about by several Type II restriction-modification gene complexes, through restriction attack on the undermethylated chromosome, and underlie their behavior as selfish mobile elements. To learn the genetic steps to death, we examined how carriage and loss of PaeR7I restriction-modification gene complex affect host Escherichia coli cells through transcriptome and experimental analyses. The PaeR7I complex was on a temperature-sensitive plasmid so that the killing was induced by a temperature shift.
We used microarrays to detail the global program of gene expression underlying cell death process mediated by PaeR7I restriction-modification system in E. coli.
Keywords: time course

overall_design: Post-segregational cell killing was induced by blocking replication of a temperature sensitive plasmid carrying PaeR7I RM gene complex by shifting up the cultivation temperature. At 30℃, the permissive temperature for the plasmid replication, growth as monitored by OD660, of MG1655/pTN9 (r+m+) was indistinguishable from those of MG1655/pTN11 (r-m+) and MG1655/pHSG415 (vector). Cell death was observed at least 4 h after the temperature shift only in MG1655/pTN9 (r+m+) as in the previous works; the increase in viable cell counts stopped and resulted in decrease of cell viability. To analyze global gene expression when cells went to death, we performed transcriptome analysis 0 h, 1h, 1 h 50 min, and 3h after the temperature shift.  We used Affimetrix E. coli antisense genome array. Experiments were performed independently twice.

first: Ichizo

last: Kobayashi


title: Transcriptome analyses of 2.5% and 5% NaCl-stressed B. cereus ATCC 14579

status: Public on Jun 22 2009

city: Wageningen

first: Heidy

last: den Besten

address: Bomenweg 2

country: Netherlands

institute: Wageningen University

summary: Bacteria are able to cope with the challenges of sudden increase of salinity by activating adaptation mechanisms. In this study, exponentially growing cells of the food-borne pathogen Bacillus cereus ATCC 14579 were exposed to both mild (2.5% NaCl w/v) and severe (5% NaCl w/v) salt stress conditions. B. cereus continued growth at a reduced rate when shifted to mild salt stress. Exposure to severe salt stress resulted in a lag period, and after 60 min cellular growth was resumed filamentously. Whole-genome expression analyses of cells exposed to 2.5% salt stress revealed an overlap with that of cells exposed to 5% salt stress, suggesting that the corresponding genes (n = 147) were involved in a general salt stress response. Up-regulation of osmolyte, Na+/H+ and di-/tripeptide transporters and activation of an oxidative stress response were important aspects of this general salt stress response. Activation of this response may confer cross-protection towards other stresses, and increased resistance to heat and H2O2 was indeed observed. Notably, a temporal shift was observed between the observed transcriptome and phenotype responses of severely salt-stressed cells including cellular filamentation, reduced chemotaxis performance, catalase activity and optimal oxidative stress resistance. The linkage of transcriptomes and phenotypic characteristics can contribute to a better understanding of cellular stress adaptation strategies and possible cross protection mechanisms.

overall_design: ATCC 14579 was grown to an OD600 of ~0.5, after that 2.5% or 5% NaCl (w/v) was added. Before addition of NaCl and after 10, 30 and 60 minutes of NaCl-exposure a sample was taken for RNA isolation. Comparisons (untreated versus salt-treated) performed were in duplicate with dye swap.

first: HMW

first: M

last: Mols

first: R

last: Moezelaar

first: MH

last: Zwietering

first: T

last: Abee


title: Site-specific impacts on gene expression and behavior in fathead minnows exposed to streams adjacent to STPs

status: Public on Jun 19 2009

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

summary: Environmental monitoring for pharmaceuticals and endocrine disruptors in the aquatic environment traditionally employs a variety of methods including analytical chemistry, as well as a variety of histological and biochemical endpoints that correlate with the fish fitness.  It is now clear that analytical chemistry alone is insufficient to identify aquatic environments that are compromised because these measurements do not identify the biologically available dose.   The biological endpoints that are measured are important because they relate to known impairments, however, they are not specific to the contaminants and often focus on only a few known endpoints. These studies can be enhanced by looking more broadly at changes in gene expression, especially if the analysis focuses on biochemical pathways. The present study was designed to obtain additional information on well-characterized sites adjacent to sewage treatment plants in MN that are thought to be impacted by endocrine disruptors. Here we examine five sites that have been previously characterized and examine changes in gene expression in fathead minnows (Pimephales promelas) that have been caged for 48 h in each of the aquatic environments.   We find that the gene expression changes are characteristic and unique at each of the five sites.  Also, fish exposed to two of the sites, 7 and 12, display a more aggressive behavior compared to control fish. Our results show that short-term exposure to sewage treatment plant effluents was able to induce a site-specific gene expression pattern in the fathead minnow gonad and liver. The short-term exposure was also sufficient to affect fish sexual behavior. Our results also show that microarray analysis can be very useful for determining potential exposure to chemicals, and could be used routinely as a tool for environmental monitoring.

overall_design:
To conduct the field exposures at each field site, FHM were transported from the laboratory to the field site in aerated, insulated tanks.  At each site, 25 males and 25 females were placed in separate wire mesh minnow traps with the entrance funnel plugged.  The traps were anchored to the bottom in the stream current with the top of the traps submerged. Fish were removed from the traps 48 h later and transported back to the laboratory in aerated, insulated tanks containing the stream water.  Immediately upon arrival at the laboratory, four males and four females were sacrificed as described for the laboratory exposures. Liver and gonads were removed and stored in liquid nitrogen until processed for arrays. All procedures involving live fish were reviewed and approved by the University of Minnesota Institutional Animal Care and Use Committee (IACUC).

Fathead minnow 22,000 gene arrays were designed by EcoArray (Alachua, FL) and purchased from Agilent.  Array hybridizations were performed using a reference design, where each sample was compared to a reference sample.  The reference sample consisted of equal amounts of RNA from control female and male tissues (liver, brain and gonad).  Four replicates, each consisting of a different individual, were analyzed for each of the treatment sites (sites 7, 11, 12, 13 and 21).  cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer’s kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit and Agilent 60-mer oligo microarray processing protocol; Agilent, Palo Alto, CA).

last: Reyero

first: Ira

last: Adelman

first: Dalma

last: Martinovic

first: Li

last: Liu

first: Nancy

last: Denslow


title: Differential microRNA expressions during development of mouse cornea

status: Public on Jun 28 2009

city: Bethesda

first: Yan

last: Li

state: MD

address: 5625 Fishers Lane, Room 1S-02

institute: NIH\NEI

summary: Expression of microRNAs (miRNA) was examined in the wild type mouse cornea at postnatal day 9 (PN9) before stratification of the corneal epithelium and at 6 weeks of age when the epithelium is fully stratified.

overall_design: Using Sanger miRBase Version 10.0, we analysed 568 miRNAs across 4 biological replicates of the developing (PN9) and mature (6-week-old) mouse cornea.

last: Yan

first: Piatigorsky

last: Joram


title: Tumor T1 Sectors

status: Public on Jul 10 2009

city: Cold Spring Harbor

first: Nicholas

last: Navin

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T1).

overall_design: The genomic DNA from each tumor sector was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray.  A normal reference male fibroblast was labeled with Cy3 as a control.  Samples were dye-swapped and the experiments were conducted in color-reversal.  The value data repesents a log ratio of the mean of two dye-swapped samples


title: Epigenetic profiling at mouse imprinted gene clusters

status: Public on Jun 16 2009

city: College Station

first: Scott

last: Dindot

state: TX

address: Texas Veterinary Medical Center, 4467 TAMU

department: Veterinary Pathobiology

institute: Texas A&M University

type: Methylation profiling by genome tiling array

summary: Epigenetic profiling of DNA methylation, histone H3 lysine 4 trimethylation and histone H3 lysine 9 trimethylation at imprinted gene clusters in the mouse.

overall_design: Imprinted control regions were identified by comparing DNA and histone methylation patterns between sperm, heart and cerebellum.

first: Arthur

last: Beaudet