title: Human Rheumatoid Arthritis Synovial Fibroblasts: Control vs. Tenascin-C Stimulated

status: Public on Mar 27 2012

city: Sapporo

first: Asano

last: Tsuyoshi

address: Kita-15, Nishi-7, Kita-ku

department: Graduate School of Medicine

country: Japan

institute: Hokkaido University

summary: Transcriptional profiling of human rheumatoid arthritis synovial fibroblasts comparing control cells treated with BSA with cells treated with Tenascin-C.

overall_design: Two-condition experiment, BSA vs. Tenascin-C stimulated cells. One replicate per array.

first: Tsuyoshi

last: Asano

first: Masashi

last: Kanayama


title: apc transcriptome-Transcriptome on Arabidopsis APC hypomorphic lines

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: rs07-03_apc - apc transcriptome - Which genes are misregulated when the APC complex activity is reduced? - Wild Type Col0, APC10S and CDC16S lines (down regulation of APC10 and CDC16 endogenous genes due to overexpression of a sequence corresponding to a part of APC10 or CDC16 gene, respectively) are grown in growth chamber (16h photoperiod 22°C) for 15 days. Whole seedlings are then frozen in liquid nitrogen and total RNA are extracted.

overall_design: 4 dye-swap - normal vs rnai mutant comparison

first: Pascal

last: Genschik

first: Samira

last: Elftieh

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Developmental shifts in gene expression in the auditory forebrain during the sensitive period for song learning

status: Public on Mar 24 2012

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

country: USA

institute: University of Illinois

summary: A male zebra finch begins to learn to sing by memorizing a tutor’s song during a sensitive period in juvenile development. Tutor song memorization requires molecular signaling within the auditory forebrain. Using microarray and in situ hybridizations, we tested whether the auditory forebrain at an age just before tutoring expresses a different set of genes compared with later life after song learning has ceased. Microarray analysis revealed differences in expression of thousands of genes in the male auditory forebrain at posthatch day 20 (P20) compared with adulthood. Furthermore, song playbacks had essentially no impact on gene expression in P20 auditory forebrain, but altered expression of hundreds of genes in adults. Most genes that were song-responsive in adults were expressed at constitutively high levels at P20. Using in situ hybridization with a representative sample of 44 probes, we confirmed these effects and found that birds at P20 and P45 were similar in their gene expression patterns. Additionally, eight of the probes showed male–female differences in expression. We conclude that the developing auditory forebrain is in a very different molecular state from the adult, despite its relatively mature gross morphology and electrophysiological responsiveness to song stimuli. Developmental gene expression changes may contribute to fine-tuning of cellular and molecular properties necessary for song learning.

overall_design: Post-hatch day 20 male zebra finches that had been raised in acoustic isolation with a foster female or adult male zebra finches were placed in a song playback chamber. The next day, birds heard either silence (control) or 30 minutes of novel song. All samples were hybridized against the universal SoNG RNA reference pool, 6 biological replicates per group in each of 4 groups.

first: Sarah

middle: E

last: London

first: Shu

last: Dong

first: David

middle: F

last: Clayton


title: nitrogen starvation-miRNA and Nitrogen starvation and resupply

status: Public on Mar 22 2012

summary: adt07-01_mirna-n - nitrogen starvation - Do nitrogen starvation and resupply change miRNAs ? - young plantlets were grown on N-sufficient medium and transfered on N-starvation medium for time course transcription analyses (T0, 24h, 4 days, 10 days.

overall_design: 12 dye-swap - time course

first: Richard

last: Berthome

first: Frederique

last: Bitton


title: comparison_cul4_as_light-Functional analysis of the SKP2 and CUL4 proteins

summary: rs04-04_skp2_cul4 - comparison_cul4_as_light - Antisense and mutants of the SKP2 and CUL4 genes are compared to the Wt in order to identify the genes controlled by those SCF proteins. - The seeds have been sown every two days on MS 255 (Duschefa) without 1% sugar. These plates stayed 6 days in the dark at 4 °C. Then they were transfered to the light for 6 more days.

overall_design: 4 dye-swap - gene knock out, normal vs antisense mutant comparison

first: Hajer

last: Hadji


title: cadmium-mirna-cadmium stress on suspension cells.

status: Public on Mar 25 2012

summary: rs06-03_cd-mirna - cadmium-mirna - trancriptional and post-transcriptional response to cadmium. - After 5 days of grown in a fresh medium (5% PCV at day0), CdCl2 was added to tested cells (Cad) to a final concentration of 200uM. Nothing was added to control cells (Tem). After 12 and 24 hours of growth +/- cadmium, cells were harvested and frozen in liquid nitrogen.

overall_design: 4 dye-swap - treated vs untreated comparison

first: Tomas

last: Morosinotto

first: Ludivine

last: Taconnat


title: The transcriptome response of leaves of the resurrection plant Xerophyta humilis to desiccation

status: Public on Mar 30 2012

city: Rondebosch

first: Nicola

last: Illing

state: Western Cape

address: Chemistry Rd

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

summary: Measurement of changes in the mRNA transcript abundance of 1709 cDNAs in Xerophyta humilis leaves at 6 relative water contents (RWC) (100%, 80%, 60%, 40%, 20% and 5%RWC respectively).

overall_design: 3105 cDNA clones (corresponding to 1709 unique cDNAs) were randomly selected from X. humilis cDNA libraries (Leaf Dehydration (LD), Leaf Rehydration (LR), Root Dehydration (RD) and Root Rehydration (RR)), amplified by PCR, and printed on each glass slide multiple times (ranging from 4 to 12X), such that each printed block contained a random unbiased mixture of cDNAs from the 4 different cDNA libraries. Total RNA extracted from each X. humilis leaf sample was linearly amplified, labelled with Cy3, and simultaneously hybridized with Cy5 labelled common reference RNA, to the printed cDNA arrays. The reference RNA comprised equal amounts of total RNA pooled from 6 different RWC experimental samples. Data was recorded for five biological replicates for each of the 6 RWC stages being investigated.

first: Arthur

last: Shen

first: Sally-Ann

last: Walford


title: The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

type: Genome binding/occupancy profiling by genome tiling array

summary: Pax5 is a critical regulator of B cell commitment. Here we identified direct Pax5 target genes by streptavidin-mediated ChIP-chip analysis of pro-B cells expressing in vivo biotinylated Pax5. By binding to promoters and enhancers, Pax5 directly regulates the expression of multiple transcription factor, cell surface receptor and signal transducer genes. One of the newly identified enhancers was shown by transgenic analysis to confer Pax5-dependent B-cell-specific activity to the Nedd9 gene controlling B cell trafficking. Profiling of histone modifications in Pax5-deficient and committed wild-type pro-B cells demonstrated that Pax5 induces active chromatin at activated target genes, while eliminating active chromatin at repressed genes in committed pro-B cells. Pax5 rapidly induces these chromatin and transcription changes by recruiting chromatin-remodeling, histone-modifying and basal transcription factor complexes to its target genes. These data provide novel insight into the regulatory network and epigenetic regulation, by which Pax5 controls B cell commitment.

overall_design: Analysis of chromatin and TF binding in rag2-/- and pax5-/- rag2-/- pro-B cells. Chip-Chip with 1-3 experiments for each antibody and celltype combination.

first: Shane

last: McManus

first: Anja

last: Ebert


title: Activation of seed-specific genes in leaves and roots of the desiccation-tolerant plant, Xerophyta humilis

summary: Measurement of changes in the mRNA transcript abundance of 1709 cDNAs in desiccated (5% RWC) and hydrated (100% RWC) Xerophyta humilis leaves and roots, and in mature seeds.

overall_design: 3105 cDNA clones (corresponding to 1709 unique cDNAs) were randomly selected from X. humilis cDNA libraries (Leaf Dehydration (LD), Leaf Rehydration (LR), Root Dehydration (RD) and Root Rehydration (RR)), amplified by PCR, and printed on each glass slide multiple times (ranging from 4 to 12X), such that each printed block contained a random unbiased mixture of cDNAs from the 4 different cDNA libraries. Total RNA extracted from each X. humilis leaf, root and seed sample was labelled with Cy3 and hybridized to the printed cDNA arrays. Data was recorded for three biological replicates for each of the samples being investigated.


title: comparison_col0vsskp2-Functional analysis of the SKP2 and CUL4 proteins

first: Soubigou-Taconnat

last: Ludivine

summary: rs04-04_skp2_cul4 - comparison_col0vsskp2 - Antisense and mutants of the SKP2 and CUL4 genes are compared to the Wt in order to identify the genes controlled by those SCF proteins. - Comparison Col0 versus skp2

overall_design: 2 dye-swap - wt vs mutant comparison

first: Pascal

last: Genschik

first: Gaetan

last: Lemonnier

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue


title: Deinococcus radiodurans R1: wildtype strains vs. DR0199-deletion strains

status: Public on Mar 29 2012

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

department: Institute of Nuclear-Agricultural Sciences

country: China

institute: Zhejiang University

summary: Transcriptional profiling of  comparing wildtype strains with DR0199-deletion strains under normal growth conditions.

overall_design: One-condition experiment, wild type strains vs. DR0199-deletion strains. Three biological replicates were carried out.

first: Hu

last: Wang


title: cells-C/N balance in cells

status: Public on Mar 23 2012

summary: adt07-02_c-n_cells - cells - How does the C/N balance act in cells ?  - 3 doses of sugar (Carbon) and 3 doses of nitrogen were applied to cells : C : 7,5g, 15g, 30g; and N : 25mM, 2.5mM and 0.25mM

overall_design: 16 dye-swap - dose response

first: Richard

last: Berthome

first: Frederique

last: Bitton

first: Marie-Laure

last: Martin-Magniette


title: carbonic anhydrase (1 or 2) simple or double mutants-Comparative transcriptome analysis between carbonic anhydrase mutants and wild type Arabidopsis

summary: cea05-01_carbonic-anhydrase - carbonic anhydrase (1 or 2) simple or double mutants - Identification of genes differentially expressed in leaves of single CA1 and CA2 T-DNA insertional mutants and in the corresponding double mutant vs wild type - CA1 (At3g01500) and CA2 (At5g14740) T-DNA insertional mutant lines, the double (CA1+CA2) mutant and wild type Arabidopsis seeds were sown in soil in a phytotron. Leaves were harvested 40 days later for RNA extraction

overall_design: 6 dye-swap - gene knock out

first: Ludivine

last: Taconnat

first: Dominique

last: Rumeau


title: Pho85, Pcl1, and Hms1 Signaling Governs Candida albicans Morphogenesis Induced by Elevated Temperature or Hsp90 Compromise [ChIP-chip]

status: Public on Mar 20 2012

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

summary: The capacity to sense and transduce temperature signals pervades all aspects of biology, and temperature exerts powerful control over the development and virulence of diverse pathogens. In the leading fungal pathogen of humans, Candida albicans, temperature has a profound impact on morphogenesis, a key virulence trait.  Many cues that induce the transition from yeast to filamentous growth are contingent on a minimum temperature of 37ºC, while further elevatation to 39ºC serves as an independent inducing cue.  The molecular chaperone Hsp90 is a key regulator of C. albicans temperature-dependent morphogenesis, as induction of filamentous growth requires relief from Hsp90-mediated repression of the morphogenetic program. Compromise of Hsp90 function genetically, pharmacologically, or by elevated temperature induces filamentation in a manner that depends on protein kinase A (PKA) signaling, but is independent of the terminal transcription factor, Efg1. Here, we determine that despite morphological and regulatory differences, inhibition of Hsp90 induces a transcriptional profile similar to that induced by other filamentation cues, and does so in a manner that is independent of Efg1. Further, we identify Hms1 as a transcriptional regulator required for morphogenesis induced by elevated temperature or compromise of Hsp90 function. Hms1 functions downstream of the cyclin Pcl, and the cyclin-dependent kinase Pho85, both of which are required for temperature-dependent filamentation. Upon Hsp90 inhibition, Hms1 binds to DNA elements involved in filamentous growth, including UME6 and RBT5, and regulates their expression, providing a mechanism through which Pho85, Pcl1, and Hms1 govern morphogenesis. Consistent with the importance of morphogenetic flexibility with virulence, deletion of C. albicans HMS1 attenuates virulence in a metazoan model of infection. Thus, we establish a new mechanism through which Hsp90 orchestrates C. albicans morphogenesis, and define novel regulatory circuitry governing a temperature-dependent developmental program, with broad implications for temperature sensing and virulence of microbial pathogens.

overall_design: Genome-wide occupancy experiments (Chip-CHIP) of FLAG-tagged Hms1p from cells grown in the presence or absence of geldanamycin (GldA). Co-precipitating genomic DNA was labelled and hybridized to whole-genome tiling arrays.

first: Rebecca

middle: S

last: Shapiro

first: Adnane

last: Sellam

first: Malcolm

last: Whiteway

first: Leah

last: Cowen


title: A set of 72 differentially expressed miRNAs provide a molecular signature for pancreatic cancer

status: Public on Mar 31 2012

city: Tampere

first: Eeva

middle: M

last: Laurila

address: Biokatu 6-8

department: Institute of Biomedical Technology

country: Finland

institute: University of Tampere

summary: MicroRNAs (miRNAs) are short single-stranded RNA molecules that have a critical role in the regulation of gene expression. Alterations in miRNA expression levels have been observed in multiple tumor types and there is clear evidence on their active involvement in cancer development. Here, a comprehensive miRNA expression profiling in 16 pancreatic cancer cell lines and four normal pancreatic samples provided a specific molecular signature for pancreatic cancer and enabled us to identify 72 differentially expressed miRNAs with approximately half of them being up- and half downregulated in cancer cells as compared to normal samples. Of these, miR-31 was selected for further functional analyses based on its interesting “on-off” type expression profile, i.e. very low or even absent expression in normal pancreas and in six of the pancreatic cancer samples but extremely high expression in the remaining ten cell lines. Quite unexpectedly, both the inhibition of miR-31 in AsPC-1 and HPAF-II pancreatic cancer cells with high endogenous expression and forced expression of miR-31 in MIA PaCa-2 with low endogenous levels led to reduced cell proliferation, migration and invasion. More importantly, in AsPC-1 cells further enhancement of miR-31 also resulted in reduced cell migration and invasion, implicating that the level of miR-31 is critical for these phenotypes. We also identified novel miR-31 target genes, APBB2 and RSBN1, that might contribute to cancer pathogenesis. This study highlights a specific miRNA expression pattern in pancreatic cancer and reveals that manipulation of miR-31 expression leads to reduced cell migration and invasion in pancreatic cancer.

overall_design: 16 pancreatic cancer cell lines and 4 normal pancreatic RNA samples were hybridized on Agilent vs1 miRNA microarrays. Pool of four normal samples was hybridized on each slide to allow normalization between slides.

first: Saana

last: Sandstrom

first: Laura

last: Rantanen

first: Reija

last: Autio

first: Anne

last: Kallioniemi


title: Gene expression changes in anti-diabetic treated Zucker diabetic rats

city: Seoul

first: Seong

last: Je kyung

country: South Korea

institute: Seoul National University

summary: Transcriptional profiling of insulin-sensitive tissues comparing control untreated ZDF rat with ZDF rat treated with three different anti-diabetic drugs and ZLC rat.

overall_design: Four-condition experiment, ZDF vs. anti-diabetic drug treated ZDF and ZLC rat. Biological replicates: 3 control, 3 treated, One replicate per array.

first: Je

middle: K

last: Seong

first: Sanghyuk

last: Lee


title: Influence of oxygen limitation, absence of the cytochrome bc1 complex and low pH on global gene expression in Gluconobacter oxydans 621H using DNA microarray technology

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

summary: The genome-wide transcriptional responses of the strictly aerobic -proteobacterium Gluconobacter oxydans 621H to oxygen limitation, to the absence of the cytochrome bc1 complex, and to low pH were studied using DNA microarray analyses. Oxygen limitation caused expression changes of 486 genes, representing 20% of the chromosomal genes. Genes with an increased mRNA level included those for terminal oxidases, the cytochrome bc1 complex, transhydrogenase, two alcohol dehydrogenases, heme biosynthesis, PTS proteins, proteins involved in cyclic diGMP synthesis and degradation, two sigma factors, flagella and chemotaxis proteins, several stress proteins, and a putative exporter protein. The downregulated genes comprised those for respiratory dehydrogenases, enzymes of central metabolism, PQQ biosynthesis, outer membrane receptors, Sec proteins, and proteins involved in transcription and translation. A ΔqrcABC mutant of G. oxydans showed a growth defect during cultivation on mannitol at pH 4 under oxygen saturation. Comparison of the transcriptomes of this mutant versus the wild type under these conditions revealed 51 differentially expressed genes. Interestingly, almost all of the 45 genes with increased expression in the ΔqrcABC mutant at pH 4 were also upregulated in the wild type grown at pH 6 under oxygen limitation. These results support an active role of the cytochrome bc1 complex in G. oxydans respiration. The transcriptome comparison of G. oxydans wild type at pH 4 versus pH 6 in mannitol medium under oxygen-saturated conditions uncovered only 72 differentially expressed genes. The 35 upregulated genes included those for cytochrome bd oxidase, major polyol dehydrogenase, iron storage and oxidative stress proteins. Among the 37 downregulated genes were some encoding enzymes dealing with carbon dioxide, such as biotin carboxylase, biotin carboxyl carrier protein, and carboanhydrase. These results give first insights into global transcriptional responses of G. oxydans.

overall_design: DNA microarray experiments were repeated independently three times for G. oxydans ΔqrcABC versus wild type and G. oxydans grown at pH 4 versus pH 6 and four times for G. oxydans grown at oxygen limitation versus pH oxygen saturation in biological replicates.

first: Tanja

last: Hanke

first: Janine

last: Richhardt

first: Hermann

last: Sahm

first: Stephanie

last: Bringer

first: Michael

last: Bott


title: Deciphering regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa

status: Public on Mar 26 2012

city: Tianjin Airport Economic Area

first: Chaoguang

last: Tian

state: Tianjin

address: Xiqi Dao 32

institute: Tianjin Institute of Industrial Biotechnology, CAS

summary: Hemicellulose, the second most abundant plant biomass fraction after cellulose, is widely viewed as a potential feedstock for the production of liquid fuels and other value-added materials. Degradation of hemicellulose by filamentous fungi requires production of many different enzymes, which are induced by biopolymers or its derivatives and regulated mainly at the transcriptional level through transcription factors (TFs). Neurospora crassa has been shown to express and secrete plant cell wall associated enzymes. To better understand genes specifically associated with degradation of hemicellulose, we identified 353 genes by transcriptome analysis of N. crassa wild type strain grown on beechwood xylan. Exposure to xylan induces 9 of the 19 predicted hemicellulase genes. The xylanolytic phenotype of strains with deletions in genes identified from the secretome and transcriptome analysis of wild type showed that none were essential for growth on beechwood xylan. The transcription factor XlnR/Xyr1 in Aspergillus and Trichoderma species is considered to be the major transcriptional regulator of genes encoding both cellulases and hemicellulases. We identified a xlnR/xyr1 homolog in N. crassa, NCU06971, termed xlr-1 (xylanase regulator 1). Deletion of xlr-1 in N. crassa abolishes the growth on xylan and xylose, but growth on cellulose was indistinguishable from wild type. To determine regulatory mechanisms associated with hemicellulose degradation, we explored the transcriptional regulon of XLR-1 under xylose and xylanolytic versus cellulolytic conditions. XLR-1 regulated only some predicted hemicellulase genes in N. crassa and was required for a full induction of several cellulase genes. Hemicellulase gene expression was induced by a combination of release from carbon catabolite repression (CCR) and induction. However, in N. crassa, xlr-1 is subject to non-CRE-1 mediated CCR.  This systematic analysis provides the similarities and differences of hemicellulose degradation and regulation mechanisms used by N. crassa in comparison to other filamentous fungi.

overall_design: Four-condition experiments (minimal medium, xylan medium,xylose and Avicel medium) of mutant strain(xlr-1) compared to wild type strain; Cy3 and Cy5 dye swap

first: N

middle: L

last: Glass


title: RNA polymerase inhibitor

status: Public on Mar 21 2012

city: Beijing

first: Hua

last: Fu

address: 6#, Rongjing East Street

institute: Institute of pathogen biology

summary: Global transcriptional responses of shigella flexneri to RNA poly merase inhibitor

overall_design: We used two drugs with two concentration. At each concentration, there 3 time points.


title: Rat primary chondrocyte: Control vs. IL-1beta treated

city: Shanghai

first: Jing

last: Li

address: South Chongqing Road

institute: Institue of Health Sciences

summary: microRNA expression profilings of chondrocytes comparing control untreated cells with cells treated with IL-1beta. Three timepoints included are 6h,12h and 24h. Many microRNAs change their expression patterns owing to IL-1beta stimulation. Some of them are chosen for further investigation.

overall_design: time series,including three time points and one control.Five replicates per array.


title: Transcriptional responses of human monocyte-derived macrophages (HMDM) to lipopolysaccharide (LPS)

city: Brisbane

first: Kate

last: Schroder

state: QLD

address: University of Queensland, St Lucia

country: Australia

institute: Institute for Molecular Bioscience

summary: Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing inter-species differences in the transcriptional responses of primary human and mouse macrophages to the TLR4 agonist, LPS. Using a custom platform permitting cross-species interrogation coupled with deep sequencing of mRNA 5’ ends, we identified extensive divergence in LPS-regulated orthologous gene expression between humans and mice (24% of orthologs, http://www.macgate.qfab.org). Divergently regulated (DR) orthologs were enriched for genes encoding cellular “inputs” such as cell surface receptors (e.g. TLR6, IL-7Rα), and functional “outputs” such as inflammatory cytokines/chemokines (e.g. CCL20, CXCL13). Conversely, intracellular signaling components linking inputs to outputs were typically concordantly regulated. DR genes were associated with a large dynamic range of gene expression, and specific promoter architectural features (TATA box enrichment, CpG island depletion). Surprisingly, regulatory divergence was also associated with enhanced inter-species promoter conservation. Thus, the genes controlled by complex, highly conserved promoters that facilitate dynamic regulation are also the most susceptible to evolutionary change.

overall_design: Human monocyte-derived macrophages (HMDM) were stimulated with the TLR4 agonist, lipopolysaccharide, over a time course (0, 2, 6, 24h) and analysed in biological quadruplicate (each of which represents a pool of two independent blood donors), in total representing 8 macrophage preparations from independent blood donors, on a custom-designed, focused microarray.

first: Katharine

last: Irvine

first: Matthew

middle: J

last: Sweet


title: Gene expression during early stages of arbuscular mycorrhizal root formation in Medicago truncatula.

status: Public on Mar 28 2012

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

summary:
Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression during early stages of Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on mycorrhizal root fragments enriched for early fungal infection stages.
We used Medicago GeneChips to detail the global programme of gene expression in response to early stages of colonization by arbuscular mycorrhizal fungi and identified genes differentially expressed during these early stages.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Medicago truncatula GFP-HDEL hairy roots (genotypes A17 and DMI3) were grown in vertically-oriented petri dishes, incubated at 26°C and inoculated with 8 Gigaspora margarita spores, which were positioned between the lateral roots. G.margarita spores germinated in 2 to 4 days. Hyphopodia were observed after 5-6 days. Root fragments which reacted to the fungal contact were collected and frozen. Non-inoculated control root fragments were harvested at a comparable age.

first: Giuseppe

last: Ortu

first: Raffaella

last: Balestrini

first: Patricia

middle: A

last: Pereira

first: Jörg

middle: D

last: Becker

first: Paola

last: Bonfante


title: Comparison Gene Expression and Biochemical Profile of Escherichia coli K12 and O157:H7 Interaction with Lettuce Rhizosphere

city: st. paul

first: zhe

last: hou

state: MN

address: 1334 Eckles Ave

department: Food Science and nutrition

institute: University of Minnesota

summary: Leafy green vegetables, such as lettuce, have been increasingly implicated in outbreaks of foodborne illnesses due to contamination by Escherichia coli O157:H7. While E. coli can survive in soils, colonize plants, and survive on produce, very little is known about the interaction of E. coli with the roots of growing lettuce plants. In these studies, a combination of microarray analyses and surface enhanced Raman spectroscopy (SERS) were used to gain a comprehensive understanding of bacterial genes involved in the colonization and growth of E. coli O157:H7 on lettuce roots and compared to E. coli K12 using a hydroponic system (HS) which we have reported in the previous studies.    Using microarray, after three days of interaction with lettuce roots, 94 and 109 genes of E. coli O157:H7 were significantly up-regulated and down-regulated at least 1.5 fold, respectively. Only 8 genes were also found in the E. coli K12 up-regulated genes. No genes were found in the down-regulated genes clusters between those two strains. For E. coli O157:H7, forty out of the 94 up-regulated genes (43%) were involved in protein synthesis and were highly repressed compared to 40 out of 193 (23%) E. coli K12 up-regulated genes associated with protein synthesis.    The wildtype of E.coli O157:H7 colonized two log CFU per root less compared to E. coli K12. Genes involved in biofilm modulation (bhsA and ybiM) were significantly up-regulated in E. coli O157:H7 and curli production (crl and csgA) were found important for E. coli K12 to attach to lettuce roots in the previous studies. BhsA mutant of E. coli O157:H7 was impaired in the colonization of lettuce roots.     The SERS spectra of E. coli K12 and O157 controls (cells without interacting with roots) were very similar. The spectra of E. coli K12 and O157 exposed to the hydroponic system (HS) showed some differences in the nucleic acid, protein, and lipid regions compared with controls. The spectra of E. coli K12 HS cells exhibited significant differences compared to spectra from E. coli O157 HS cells in the RNA and protein regions. The overall band intensity of amide regions declined for E. coli O157 HS cells, while it increased for E. coli K12 HS cells. The intensity of the RNA bands of E. coli K12 HS cells were also found much higher than those of E. coli O157 HS cells. These findings were in agreement to our Microarray data.    Our microarray and SERS data showed that E. coli K12 and O157:H7 behavior dramatically differently in colonizing on lettuce roots. Compared to K12, E. coli O157:H7 colonized less efficiently on lettuce roots.

overall_design: Escherichia coli O157:H7 strains were grown in the lettuce rhizosphere for three days. Transcriptional profiling of E. coli was compared between cells grown with and without rhizosphere . Three biological replicates of each treatment were prepared, and six microarray slides were used.

first: Zhe

last: Hou

first: Francisco

last: Diez-Gonzalez

last: Sadowsky


title: Genome-wide prediction and validation of σ70 promoters in Lactobacillus plantarum WCFS1

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

type: Expression profiling by genome tiling array

summary:
Background: In prokaryotes, sigma factors are essential for the targeting of the transcription machinery to promoters. Various sigma factors have been described that recognize and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor σ70 is commonly involved in transcription of the cell's general housekeeping genes, which is mediated by the conserved σ70 promoter sequence motifs. This study detects and predicts the general σ70-promoter sequences in Lactobacillus plantarum WCFS1 using genome-wide analysis. The accuracy of the transcriptionally-active part of this promoter prediction was subsequently evaluated by correlating locations of predicted promoters with experimentally detected transcription starts sites (TSSs) using high-resolution tiling array transcriptome datasets.

Results: To identify σ70-related promoter sequences, we performed a genome-wide sequence motif scan of the L. plantarum WCFS1 genome focusing on the regions upstream of protein-encoding genes. We obtained several highly conserved motifs including those resembling the conserved σ70-promoter consensus. Position weight matrices-based models of the recovered σ70-promoter sequence motif were employed to identify 4746 motifs with significant similarity (p-value < 10-4) to the model-motif in the L. plantarum genome. Genome-wide transcription start site information deduced from whole genome tiling-array transcriptome datasets revealed 936 TSSs that were employed to validate the transcriptionally active fraction of these predicted promoters. In total, 578 predicted promoters were found in proximity (≤ 100 nucleotides) of the identified TSSs, showing a highly significant co-occurrence of predicted promoter and measured TSS (p-value < 10-23). An additional 224 predicted promoters was validated when the significant similarity to the model-motif was applied less strictly (10-4 ≤ p-value < 10-3).

Conclusions: High-resolution tiling arrays provide a suitable source for TSS detection at a genome-wide level, and allow experimental verification of in silico-predicted promoter sequence motifs.

overall_design: Triplicate hybridizations (technical replicates) of two L. plantarum WCFS1 samples (biological replicates) gathered from a fermentation run at OD600 of 1. Dye swap applied to one of the three technical replicates.

first: Tilman

last: Todt

first: Roger

last: Bongers

first: Roland

last: Siezen

first: Sacha

last: van Hijum

last: Kleerebezem


title: Epigenome analysis of newborn placenta and cord blood samples

city: Philadelphia

first: Nahid

last: Turan

state: PA

address: 3307 North Broad Street, AHB

department: Fels Institute

institute: Temple University School of Medicine

summary: DNA methylation profiling of placenta and cord blood samples. The Illumina GoldenGate methylation assay was used to obtain DNA methylation profiles across approximately 1,536 CpGs in 23 placenta and 23 cord blood samples.

overall_design: Bisulphite converted DNA from the 46 samples were hybridised to the Illumina GoldenGate Methylation assay

first: Carmen

last: Sapienza


title: Transcriptional characterization of tomato roots response to iron deficiency

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

summary: Iron (Fe) deficiency is a yield-limiting factor for a variety of field crops across the world and generally results from the interaction of limited soil Fe bioavailability and susceptible genotype cultivation. Tomato, a Strategy I, model plant for Fe deficiency, is an important economical crop. Tomato responses in order to improve Fe uptake are based on acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells.

overall_design:
Transcriptional profile obtained by roots (27-d) of 21-d-old tomato plants starved of iron for an additional week was compared with the transcriptional profile obtained for roots (27-d) of 21-d-old tomato plants grown for an additional week at 100 μM Fe. Tomato plants were hydroponically grown in both cases.
Three different biological replicates were used for each sample repeating the experiment three times.
All samples were obtained pooling roots of six plants (27-d-old).

first: Zamboni

last: Anita

first: Laura

last: Zanin

first: Tomasi

last: Nicola

first: Pezzotti

last: Mario

first: Pinton

last: Roberto

first: Varanini

last: Zeno

first: Cesco

last: Stefano


title: Transcriptional responses of mouse BMM and TEPM to lipopolysaccharide (LPS)

first: Kate

last: Schroder

overall_design: Mouse macrophages (bone marrow-derived macrophages, BMM and thioglycollate-elicited peritoneal macrophages, TEPM) were stimulated with the TLR4 agonist, lipopolysaccharide, over a time course (0, 2, 6, 24h) and analysed in biological triplicate on a custom-designed, focused microarray.

first: Katharine

last: Irvine

first: Matthew

last: Sweet


title: Transcriptional responses of mouse bone marrow-derived macrophages (BMM) to lipopolysaccharide (LPS) - Illumina arrays

summary: These microarrays were performed for use in a genome-wide scan for LPS-regulated genes in mouse macrophages, in order to construct a list of LPS-regulated genes for detailed interrogation on custom microarrays (see GSE19490 for custom array analysis).

overall_design: Mouse macrophages (bone marrow-derived macrophages, BMM) were stimulated with the TLR4 agonist, lipopolysaccharide, over a time course (0, 0.5, 2, 6, 24h) and analysed in biological duplicate by commercial Illumina microarray.


title: Network-based analysis of carbohydrate-active gene transcription in Aspergillus niger

city: Kgs. Lyngby

first: Mikael

middle: R

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

summary: Transcriptomics was performed on batch cultivations of A. niger grown on three monosaccharides and three complex carbohydrates with defined compositions as to allow the detection of cross-induction if present, and for demonstration of how enzyme interaction graphics can be used to visualize the global transcription response.

platform_organism:
Aspergillus niger
Aspergillus oryzae
Aspergillus nidulans

overall_design: Batch cultivations of A. niger were grown in shake-flasks on one of three monosaccharides (arabinose, glucose, xylose) or one of three complex carbohydrates (arabinan, starch, xylan). Three replicates were performed for each monosaccharide and complex carbohydrate, except for starch, where two replicates were performed.

first: Malene

middle: G

last: Jakobsen

first: Ronald

middle: P

last: de Vries

first: Jens

last: Nielsen


title: camv treatment-Gene profiling durinig CaMV infection.

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

institute: INRA

summary: rs06-06-mirna_camv_treatment - camv treatment - Which genes (including miRNA genes) are differentially regulated by CaMV? Requirement of 21nt, 22nt, 24nt virus-derived siRNAs in this differential gene regulation?  - 4/5 weeks old seedlings (Col-0, dcl2/dcl3, dcl2/dcl4, dcl3/dcl4, dcl2/dcl3/dcl4) infected with CaMV and harvested 21 days post infection.

overall_design: 7 dye-swap - gene knock out,normal vs disease comparison

first: Olivier

last: Voinnet

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: cRNA hybridizations of 18 accessions of Arabidopsis thaliana under well-watered and mild soil drying

status: Public on Mar 12 2012

city: Austin

first: David

middle: Lee

last: Des Marais

state: TX

address: 1 University Station C0930

department: Integrative Biology

institute: The University of Texas at Austin

summary:
These data provide a basis for exploration of gene expression differences between physiologically diverse accessions of Arabidopsis thaliana.
Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range.  Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin.  These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance.  Therefore we studied the physiology, genome content and gene expression of 18 physiologically diverse accessions. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.

overall_design: The basic experimental design involves 18 accessions crossed with two environmental levels (well-watered soil and mild soil drying) and 3 biological replicates per accession/treatment combination.

first: Thomas

last: Juenger


title: Effect of rosiglitazone on adipose gene expression in HSL knockout mice with different diet treatment

status: Public on Mar 18 2012

city: Palo Alto

first: Wen-Jun

last: Shen

state: CA

address: 3801 Miranda Avenue

department: Medicine

institute: Stanford University

summary: To test whether HSL is required for the supply of intrinsic ligands for PPARg for normal adipose differentiation, HSL-/- and wild type (WT) littermates were fed normal chow (NC) and high fat (HF) diets supplemented with or without rosiglitazone (200 mg/kg) for 16 weeks. The expression of diabetes related genes in the WAT of the animals was analyzed using Oligo GEArray Mouse Diabetes Microarrays (OMM-023, SABiosciences, Frederick, MD). Together with other biochemical and physiological data, our results suggest that one of the mechanisms by which HSL modulates adipose metabolism is by providing intrinsic ligands for PPARg.

overall_design: To examine the changes in gene expression in WAT of WT and HSL-/- mice with rosiglitazone and diet treatment, RNA isolated from 4 animals of each group were used for studies of gene expression profiles using Oligo GEArray Mouse Diabetes Microarrays (OMM-023, SABiosciences, Frederick, MD). Data were analyzed using GEArray Expression Analysis Suite (SABiosciences, Frederick, MD) and SAM programs to comprehensively evaluate the differential gene expression of the various samples.

first: Zaixin

last: Yu

first: Shailja

last: Patel

first: Dyron

last: Jue

first: Li-Fen

last: Liu

first: Fredric

middle: B

last: Kraemer


title: Early life growth and gene profile changes during childhood

status: Public on Mar 14 2012

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

summary:
To compare early life exposures to see if they are associated with persistent molecular changes at the transcriptional level.
Subjects were drawn from the Newcastle Pre-Term Birth Growth Study.  A randomised, controlled trial to look at the effect on growth of dietary manipulation after hospital discharge.

overall_design: 23 chips with 4 conditions with factors sex and growth status (slow/rapid).  Each condition has 6 replicates except for {male, rapid growth} which has 5 replicates.

first: Alix

last: Groom

first: Daniel

middle: C

last: Swan


title: Gene expression profiling of C57BL/6 mouse lung tissue with various treatments using the MA11 array

first: Floyd

last: Dukes

address: 3615 Civic Center Boulevard

institute: University of Pennsylvania

summary: Flaxseed (FS), a nutritional supplement consisting mainly of omega-3 fatty acids and lignan phenolics, has potent anti-inflammatory, anti-fibrotic and antioxidant properties. We have shown that dietary FS supplementation ameliorates oxidative stress and inflammation in experimental models of acute and chronic lung injury in mice resulting from diverse toxicants. The development of lung tissue damage in response to direct or indirect oxidant stress is a complex process, associated with changes in expression levels of a number of genes. We therefore postulated that flaxseed may modulate gene expression of vital signaling pathways, thus interfering with the development of tissue injury. We evaluated gene expression in lungs of flaxseed-fed (10% FS) mice under unchallenged, control conditions and 48hrs post-radiation treatment (13.5 Gy). Gene expression levels in lung tissues were analyzed using three arrays for each sample, whereby a total of 28,800 genes were evaluated.

overall_design: C57BL/6 black mice were fed a 10% flaxseed diet for 21 days and/or given 13.5Gy thoracic radiation and sacrificed 48hrs post radiation.

first: Melpo

last: Christofidou-Solomidou


title: Birdsong "Transcriptomics": Neurochemical Specializations of the Oscine Song System

status: Public on Mar 15 2012

city: Urbana

first: Kirstin

last: Replogle

address: 1206 W Gregory Drive

institute: University of Illinois

summary:
Background: Vocal learning is a rare and complex behavioral trait that serves as a basis for the acquisition of human spoken language. In songbirds, vocal learning and production depend on a set of specialized brain nuclei known as the song system.
Methodology/Principal Findings: Using high-throughput functional genomics we have identified, 200 novel molecular markers of adult zebra finch HVC Vocal, a key node of the song system. These markers clearly differentiate HVC from the general pallial region to which HVC belongs, and thus represent molecular specializations of this song nucleus. Bioinformatics analysis reveals that several major neuronal cell functions and specific biochemical pathways are the targets of transcriptional regulation in HVC, including: 1) cell-cell and cell-substrate interactions (e.g., cadherin/catenin-mediated adherens junctions, collagen-mediated focal adhesions, and semaphorin-neuropilin/plexin axon guidance pathways); 2) cell excitability (e.g., potassium channel subfamilies, cholinergic and serotonergic receptors, neuropeptides and neuropeptide receptors); 3) signal transduction (e.g., calcium regulatory proteins, regulators of G-protein-related signaling); 4) cell proliferation/death, migration and differentiation (e.g., TGF-beta/BMP and p53 pathways); and 5) regulation of gene expression (candidate retinoid and steroid targets, modulators of chromatin/nucleolar organization). The overall direction of regulation suggest that processes related to cell stability are enhanced, whereas proliferation, growth and plasticity are largely suppressed in adult HVC, consistent with the observation that song in this songbird species is mostly stable in adulthood.
Conclusions/Significance: Our study represents one of the most comprehensive molecular genetic characterizations of a brain nucleus involved in a complex learned behavior in a vertebrate. The data indicate numerous targets for pharmacological and genetic manipulations of the song system, and provide novel insights into mechanisms that might play a role in the regulation of song behavior and/or vocal learning.

overall_design: Comparison of HVC and shelf regions from adult male zebra finches, 6 biological replicates per group. Each sample was hybridized against the SoNG universal reference RNA pool.

first: Peter

middle: V

last: Lovell

last: Clayton

first: Claudio

last: Mello


title: Synthetic circuit identifies subpopulations with sustained memory of DNA damage

status: Public on Mar 02 2012

city: Boston

first: Pamela

last: Silver

state: MA

address: 200 Longwood Avenue WAB 536

department: Systems Biology

institute: Harvard Medical School

summary: Differential responses to stimuli can affect how cells succumb to disease. In yeast, DNA damage can create heterogeneous responses. To delineate how a response contributes to a cell's future behavior, we constructed a transcription-based memory circuit that detects DNA repair to isolate subpopulations with heritable damage responses. Strongly responsive cells show multigenerational effects, including growth defects and iron-associated gene expression. Less-responsive cells exhibit increased mutation frequencies but resume wild-type behavior. These two subpopulations remain distinct for multiple generations, indicating a transmissible memory of damage. Collectively, this work demonstrates the efficacy of using synthetic biology to define how environmental exposure contributes to distinct cell fates.

overall_design: Cells containing the HUG1 memory device (Burrill, 2011) were exposed to 0.3% EMS for 24 h and recovered for 36 h, at which point cells were sorted based on YFP expression, i.e. memory and non-memory cells. These two sorted populations were then grown for another 12 h, at which point transcriptional profiling was performed.

first: Devin

last: Burrill


title: miRNA expression in LNCaP, PC3, Du-145 and RWPE-1 cell lines

status: Public on Mar 08 2012

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary: MiRNAs are small non-coding RNAs that regulate the expression of specific mRNA targets mainly by translational repression, mRNA deadenylation or cleavage. This series is meant to identify miRNAs deregulated in prostate cancer (PCa) by comparing the PCa cell lines LNCaP, PC3 and Du-145 to the normal prostate epithelial cell line RWPE-1.

overall_design: We analyzed three arrays each for LNCaP, PC3, Du-145 and RWPE-1 cell lines

first: Kerstin

last: Boll

first: Nora

last: Mörbt

first: Antje

last: Kretzschmar

first: Katharina

last: Schutt

first: Janina

last: Tomm

first: Gerald

last: Verhaegh

first: Jack

last: Schalken

first: Martin

last: v Bergen

first: Friedemann

last: Horn

first: Jörg

last: Hackermüller


title: Gene expression profiling of C57BL/6 mouse lung tissue with various treatments using the MA07 array

first: Floyd

last: Dukes

first: Melpo

last: Christofidou-Solomidou


title: Expression analysis of abiotic stress-treated rice

status: Public on Mar 01 2012

city: Yongin

first: Jin

middle: Seo

last: Jeong

state: Gyeonggido

address: San 38-2 Namdong, Cheoin-gu

institute: Myongji University

summary: For identification of genes up-regulated in abiotic stress (drought, high salinity, low temperature and ABA) treated rice, total RNA (100 μg) was prepared from root tissues of 14-d-old rice seedlings (Oryza sativa cv Nakdong) grown under normal growth conditions.  For the high salinity and ABA treatments, the 14-d-old seedlings were transferred to a nutrient solution containing 400 mM NaCl or 100 μM ABA for 2 h in the greenhouse under continuous light of approximately 1000 μmol m-2 s -1. For drought treatment, 14-d-old seedlings were air-dried for 2 h also under continuous light of approximately 1000 μmol m-2 s -1. For low temperature treatments, 14-d-old seedlings were exposed at 4°C in a cold chamber for 6 h under continuous light of 150 μmol m-2 s -1.

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 abiotic stress treated rice. Cy3-labeled target cDNA fragments were synthesized 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.

first: Se-Jun

last: Oh

first: Ju-Kon

last: Kim


title: Gene expression analysis in pre- and early post-anthesis stage ovules of Citrus sinensis

city: New Delhi

first: Vajinder

last: Kumar

state: Delhi

address: LBS Builduing, Pusa Campus IARI

country: India

institute: National Research Center on Plant Biotechnology

summary: Nucellar embryony is a form of apomixis found in citrus where somatic nucellar cells differentiate into embryos and are included in the seed resulting from the normal sexual process.  The nucellar cells giving rise to adventive embryo start proliferating prior to anthesis and fully differentiate obtaining nourishment from sexually derived endosperm.  To identify transcripts differentially expressed during nucellar embryo initiation we have taken RNA samplesfrom different developing stages of ovules from polyembryonic (cv. Vaniglia Sanguigno) and monoembryonic (cv. Temple) cultivars. We used microarray for a detailed analysis of global gene expression during nucellar embryony initiation and development. We have further validated the differentially expressed genes using qRT-PCR.

overall_design: Citrus ovules were harvested from the excised ovaries of different flower developmental stages. These developing stages were decided on the basis of morphological and histological characteristics of flower and female gametophyte, respectively. We selected, Pre anthesis, post anthesis, and initial fruit set stage of flower to excise ovules from Polyembryonic cultivar Vaniglia Sanguigno and  Monoembryonic cultivar Temple. Leaf tissue of Vaniglia Sanguigno was used to check the overall transcriptome level differences between leaf and ovule tissues. For each sample,  three technical replicates were used.

first: Surendra

last: Malik

first: Digvender

last: Pal

first: Ramamurthy

last: Srinivasan

first: Shripad

last: Bhat


status: Public on Mar 05 2012

city: Shanghai

first: Yanxun

last: Xia

address: 3 Lane 345,Shilong Road

institute: Shanghai Institute of Domestic Animal Parasitology,Chinese Academy of Agricultural Sciences

summary:
Suppression subtractive hybridization(SSH) libraries of Schistosoma japanicum female and male worms were constructed by using Clontech  PCR-selectTM  cDNA subtraction kit. S.japonicum cDNA microarrays were fabricated using female and male cDNA clones originating from SSH libraries. female-associated and Male-associated differentially expressed gene clones were obtained, Analysis of gender-associated differentially expressed genes helps to determine which genes are important to sexual maturation of schistosome and better understand schistosome biology and host-parasite relationship, facilitate the discovery of novel gene products that could represent targets for the development of new drugs and vaccines to control chitosomiasis.
Keywords: gender-associated

overall_design: Four  Samples were analyzed about Schistosoma japonicum gender-associated differentially expressed genes

first: Jiaojiao

last: Lin

first: Chunxiu

last: Yuan

first: Guoqing

last: Li


title: Temperature dependent gene expression levels at  28°C and 37°C for  Pseudomonas aeruginosa PAO1

first: daqiang

last: wu

address: 800 Dongchuan Road

department: School of life science and biotechnology

institute: Shanghaijiaotong University

summary: To further understand the gene expression characteristics of Pseudomonas aeruginosa PAO1, we have applied whole genome microarray expression profiling as a discovery platform to specify the temperature dependent expression of PAO1 genome at soil and human body temperature. We selected 28°C as temperature representative of the soil niche and 37°C for human body. The results from the temperature dependent transcriptome analysis are consistent to our previous published data that the phzM, ptsP and lasI genes expression is upregulated at 37°C [11]. The comparison analysis of the M18 genome expressional profiles at 28°C and 37°C indicated a total of 596 genes expressed in a temperature dependent manner over two fold.

overall_design: Cells were grown to OD600=5.0-6.0 (late exponential phase) in LB medium at 28℃ and 37℃, respectively. Three independent experiments were performed at each time.

first: Yuquan

last: Xu

first: Daqiang

last: Wu


title: Pho85, Pcl1, and Hms1 Signaling Governs Candida albicans Morphogenesis Induced by Elevated Temperature or Hsp90 Compromise [mRNA]

city: Montreal

first: Andre

last: Nantel

address: 6100 Royalmount

institute: National Research Council of Canada

summary: The capacity to sense and transduce temperature signals pervades all aspects of biology, and temperature exerts powerful control over the development and virulence of diverse pathogens. In the leading fungal pathogen of humans, Candida albicans, temperature has a profound impact on morphogenesis, a key virulence trait.  Many cues that induce the transition from yeast to filamentous growth are contingent on a minimum temperature of 37ºC, while further elevatation to 39ºC serves as an independent inducing cue.  The molecular chaperone Hsp90 is a key regulator of C. albicans temperature-dependent morphogenesis, as induction of filamentous growth requires relief from Hsp90-mediated repression of the morphogenetic program. Compromise of Hsp90 function genetically, pharmacologically, or by elevated temperature induces filamentation in a manner that depends on protein kinase A (PKA) signaling, but is independent of the terminal transcription factor, Efg1. Here, we determine that despite morphological and regulatory differences, inhibition of Hsp90 induces a transcriptional profile similar to that induced by other filamentation cues, and does so in a manner that is independent of Efg1. Further, we identify Hms1 as a transcriptional regulator required for morphogenesis induced by elevated temperature or compromise of Hsp90 function. Hms1 functions downstream of the cyclin Pcl, and the cyclin-dependent kinase Pho85, both of which are required for temperature-dependent filamentation. Upon Hsp90 inhibition, Hms1 binds to DNA elements involved in filamentous growth, including UME6 and RBT5, and regulates their expression, providing a mechanism through which Pho85, Pcl1, and Hms1 govern morphogenesis. Consistent with the importance of morphogenetic flexibility with virulence, deletion of C. albicans HMS1 attenuates virulence in a metazoan model of infection. Thus, we establish a new mechanism through which Hsp90 orchestrates C. albicans morphogenesis, and define novel regulatory circuitry governing a temperature-dependent developmental program, with broad implications for temperature sensing and virulence of microbial pathogens.

overall_design: Two-color experimental design testing the effect of geldanamycin on wild type of delta-efg1 cells. RNA from each replicate came from independent cultures.

first: Rebecca

last: Shapiro

first: Adnane

last: Sellam

first: Malcolm

last: Whiteway

first: Leah

last: Cowen


title: Gene expression profiling of C57BL/6 mouse lung tissue with various treatments using the MA10 array

first: Floyd

last: Dukes

first: Melpo

last: Christofidou-Solomidou


title: Target-gene mediated activation of phosphatase activity of sensor kinase in the SaeRS two-component system of Staphylococcus aureus

status: Public on Mar 09 2012

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary: In bacterial two-component regulatory systems (TCSs), dephosphorylation of phosphorylated response regulator is essential for resetting the activated systems to the pre-activation state. However, in the SaeRS TCS, a major virulence TCS of Staphylococcus aureus, the mechanism for dephosphorylation of the response regulator SaeR has not been identified. Here we report that two auxiliary proteins from the sae operon, SaeP and SaeQ, form a ternary complex with the sensor kinase SaeS and activate the sensor kinase’s phosphatase activity. Efficient activation of the phosphatase activity of SaeS required the presence of both SaeP and SaeQ. When SaeP and SaeQ were expressed, the expression of coagulase, a sae target with low affinity to phosphorylated SaeR, was greatly reduced, while the expression of alpha-hemolysin, a sae target with high affinity to phosphorylated SaeR, was not, demonstrating a differential effect of SaePQ on sae target gene expression. When expression of SaePQ was abolished, most sae target genes were induced at an elevated level. Since the expression of SaeP and SaeQ is induced by SaeRS TCS, these results suggest that the SaeRS TCS returns to pre-activation state by a negative feedback mechanism.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: To examine the global effect of SaePQ on sae target gene expression, we treated the wild type strain of USA300-P23 and its P1 promoter mutant with HNP-1 and analyzed the transcription of sae target genes by microarray assays. WT and P1 cells were compared against a each other at the same time point and against a T=0 reference.

first: Marcus

last: Jones

first: Taeok

last: Bae

first: Scott

middle: N

last: Peterson


title: Transcriptional Profile of the Shigella flexneri Response to Berberine

status: Public on Mar 10 2012

city: Beijing

first: Hua

last: Fu

address: 6#, Rongjing East Street

institute: Institute of pathogen biology

summary: Berberine is a natural isoquinoline alkaloid found in Chinese medicinal herbs which is active against a variety of microbial infections. To examine the potential effects of berberine on Shigella flexneri, a whole-genome DNA microarray was constructed and transcriptome analysis of the cellular responses of S.flexneri when exposed to Berberine Chloride (BC) was performed.

overall_design:
When cultures were grown to early exponential growth phase, drug was added. Meanwhile, DMSO solution without BC was added to control cultures to the same final concentration. At 30 min after treatment, samples were collected and washed twice with phosphate buffered saline at 25°C for subsequent RNA isolation. To prepare biological replicates for RNA isolation, each experiment was independently performed three times. After drug treatment, total RNA was extracted using SV RNA Isolation System (Promega). Reverse transcription of 20 ug RNA from each sample was performed with Superscript II system (Invitrogen) to prepare cDNA. According to the manufacturer's instructions, the cDNA was labeled with incorporation of fluorescent dyes (Amersham). Cy3-dCTP monofunctional dye was selected for control cDNA samples and Cy5-dCTP was used for drug-treated samples. Each pair of labeled cDNA was mixed and dried by vacuum centrifugation. The pairs of the labeled cDNA samples were hybridized to the DNA microarrays following the protocol available at http://www.ifr.ac.uk/safety/microarrays/.

The slides were scanned by using a GenePix 4100A scanner. Fluorescent spots and local background intensities were quantified using GenePix Pro 6.0 software (Axon). Signal intensities were corrected by subtracting the local background value. The data set was filtered so that spots flagged as "not found," "bad," and "empty" were excluded from further analysis. Moreover, spots either with signal-to-noise ratio below the detection limit of 3 or containing less than 55% of pixels two standard deviations above background in both channels were discarded from the data set. Lowess normalization was performed with the fluorescent signal ratios (Cy5/Cy3) using MIDAS software (http://www.tigr.org/software/tm4) with a 0.33 smooth parameter.


title: Expression analysis of RCc3:OsNAC6 and GOS2:OsNAC6 transgenic rice plants

first: Jin

last: Jeong

summary: For identification of genes up-regulated in RCc3:OsNAC6, GOS2:OsNAC6 plants, total RNA (100 μg) was prepared from root tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions.

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 85C. 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 RCc3:OsNAC6, GOS2:OsNAC6 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized 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.

first: Youn

last: Kim

first: Harin

last: Jung

first: Mark

last: Redillas

first: Yang

last: Choi

first: Christophe

last: Reuzeau

first: Ju-Kon


title: How post-translational modification of nitrogenase is circumvented in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

summary: Characterization of post-translational modification of nitrogenase in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively.

overall_design: To characterize the effect of yeast extract as nitrogen source on gene expression under nitrogen fixing conditions, expression profiles of wild-type cells grown on either NF plus yeast extract and succinate and PM plus ammonium sulfate and succinate were compared using Affymetrix GeneChip. Using NF plus yeast extract and succinate media, transcriptome profiles of various mutants and wild-type cells were compared using glass spotted microarrays.

first: Erin

last: Heiniger

first: Sudip

last: Samanta

first: Caroline

last: Harwood


title: Gene expression profiling of soft and firm Atlantic salmon fillet

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Microarray analyses  revealed strong correlations between firmness of fillet (most important quality parameter) and a large number of genes. Highly similar expression profiles were observed in several functional groups. Positive regression was found between firmness and genes encoding proteasome components (41 genes) and mitochondrial proteins (129 genes), proteins involved in stress responses (12 genes) and lipid metabolism (30 genes). A weaker though highly significant negative regression was seen in sugar metabolism (26 genes) and myofiber proteins (42 genes). Among individual genes that showed a strong association with firmness, there were extracellular matrix proteins (negative correlation), immune genes and intracellular proteases (positive correlation). Several genes can be regarded as candidate markers of flesh quality (coiled-coil transcriptional coactivator b, AMP deaminase 3 and oligopeptide transporter 15) though their functional roles are unclear.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Fillet firmness in a population of farmed Atlantic salmon with known pedigree. Sixteen individuals were chosen to cover the normal range of this trait.

first: Thomas

last: Larsson


title: Transcriptional profiling of Aspergillus fumigatus in response to RBL-2H3 mast cells

first: Natalie

last: Fedorova

department: Infectious Disease

institute: JCVI

summary: In patients with chronic pulmonary disease colonization with the mold Aspergillus fumigatus is associated with declining pulmonary function and obstructive airway disease.  One potential effector of this inflammatory response is the pulmonary mast cell.  In vitro studies have demonstrated that A. fumigatus contact induces IgE-independent mast cell degranulation. Conversely, the Aspergillus secondary metabolite gliotoxin has been shown to suppress mast cell activation. These contradictory results emphasize the need for a better understanding of the interactions between A. fumigatus and mast cells. Thus, the objective of this work was to identify A. fumigatus genes that are differentially regulated upon exposure to mast cells. Transcriptional profiling experiments indicated that, in addition to genes encoding for iron acquisition systems, allergens and putative virulence factors, genes from the gliotoxin biosynthesis cluster were significantly down-regulated upon exposure to mast cells. Globally, the results from this study provide insight into the A. fumigatus response to mast cells and suggest that one mechanism by which the host may circumvent the effects of gliotoxin is via the suppression of fungal gliotoxin synthesis by mast cells.

overall_design: Aspergillus fumigatus hyphae were exposed either to RBL-2H3 mast cells or culture medium for 1.5hr or 3hrs. Hybridizations were performed with biological replicates and flip-dye pairs.

first: Donald

last: Sheppard

first: Ghyslaine

last: Vanier

first: Dan

last: Chen

first: William

last: Nierman


title: MeDIP-chip of zdp mutant

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

type: Methylation profiling by genome tiling array

summary: Using meDIP-chip to provide methylation profile in zdp mutant and identify hypermethylated regions comparing to wild type Arabidopsis plants.

overall_design: Examination of zdp mutant's methylome. 4 samples(1 mutant, 1 WT, each has two biological replicates)

first: María

middle: I

last: Martínez-Macías

first: Weiqiang

last: Qian

first: Daisuke

last: Miki

first: Kai

last: Tang

first: Renyi

last: Liu

first: Teresa

last: Roldán-Arjona


title: Novel targets of microRNA miR-142 in cardiac myocytes

status: Public on Mar 07 2012

city: Miami

first: Salil

last: Sharma

state: Florida

address: 1600 NW 10th Ave

department: Molecular and Cellular Pharmacology

institute: University of Miami

summary: The nuclear acetyltransferase p300 is a dose-dependent and limiting regulator of cardiac hypertrophy. p300 regulates hypertrophy by controlling the expression of specific microRNAs.The objective of this study was to dissect the role of miR-142 during p300 regulated hypertophic growth in vitro and in vivo and to verify its targets.

overall_design: MiR142  and a non target control were overexpressed using lentivirus in primary culture of neonatal cardiac myocytes. Overexpression was checked 48 hour post transfection. Samples include miR142 OE and non target from three different experiments.

first: Nanette

middle: H

last: Bishopric


title: A cost-effective method for double stranded cDNA synthesis for microarray analysis

city: Espinardo

first: Daniel

last: Gonzalez-Ibeas

state: Murcia

address: Campus de Espinardo s/n

department: Biologia Estres y Patologia Vegetal

country: Spain

institute: CEBAS-CSIC

summary: DNA microarrays are two-dimensional arrangements of specific probes deposited on a substrate that have been widely used in gene expression analysis by measuring mRNA accumulation. The use of this type of microarrays involves the synthesis of cDNA, which has to be double stranded (ds) if the microarray probes are of the positive strand. We have used a custom-synthesized non-commercial NimbleGen microarray from melon to evaluate an alternative method of ds cDNA synthesis, which differs substantially in its economical cost relative to a widely recommended method. The results suggested that both methods produce cDNA representative of the melon transcriptome to a similar extent, indicating that the alternative technique provides a cheaper method of ds cDNA synthesis for microarray gene expression assays.

overall_design: Recently, we have analyzed the transcriptome of melon in response to WMV infection. Cotyledons of two genotypes of melon were virus inoculated and transcriptomic responses to the infection were analyzed by comparing infected and mock inoculated samples at 1, 3, and 7 days post-inoculation (dpi). Three biological replicates were performed for each sample. Double stranded cDNA was obtained with the Double stranded cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA), based on the nick translation approach (Mol. Cell. Biol (1982) 2:161-170; Gene (1983) 25:263-269). Raw and processed microarray data are freely available from GEO database under the accession number GSE30111. By using this set of microarray hybridizations as a reference, RNA corresponding to infected cotyledons replicate 3 at 1 dpi (A1) and replicate 1 at 3 dpi (A2) (GEO accession numbers GSM745566 and GSM745567) were used to perform cDNA synthesis by the alternative method (samples B1 and B2, respectively), based on the SMART approach (BioTechniques (2001) 30:892-897), and microarray data were compared.

first: Jose

last: Blanca

first: Joaquin

last: Cañizares

first: Veronica

last: Truniger

first: Miguel

last: Aranda


title: Autoantibody profile timecourse of UNK

status: Public on Mar 16 2012

city: Stanford

first: Hogune

last: Im

address: 300 Pasteur Dr. Alway M308

department: Genetics

institute: Stanford

summary: We have determined the whole genome sequence of an individual at high accuracy and performed an integrated analysis of omics profiles over a 1.5 year period that included healthy and two virally infected states. Omics profiling of transcriptomes, proteomes, cytokines, metabolomes and autoantibodyomes from blood components have revealed extensive, dynamic and broad changes in diverse molecular components and biological pathways that occurred during healthy and disease states. Many changes were associated with allele- and edit-specific expression at the RNA and protein levels, which may contribute to personalized responses. Importantly, genomic information was also used to predict medical risks, including Type II Diabetes (T2D), whose onset was observed during the course of our study using standard clinical tests and molecular profiles, and whose disease progression was monitored and subsequently partially managed. Our study demonstrates that longitudinal personal omics profiling can relate genomic information to global functional omics activity for physiological and medical interpretation of healthy and disease states.

overall_design: Plasma and serum from  a virus infected timepoint (in triplicate) and 34 healthy contorl samples were collected and used to probe Invitrogen human protoarray v5.0.

first: Rui

first: George

last: Mias

first: Jennifer

last: Li-Pook-Than

first: Hugo

last: Lam

first: Lihua

last: Jiang

first: Rong

first: Elana

last: Miriami

first: Konrad

last: Karczewski

first: Manoj

last: Hariharan

first: Frederick

last: Dewey

first: Shin

last: Lin

first: Lukas

last: Habegger

first: Michael

last: Clark

first: Sugnthi

last: Balasubramanian

first: Yong

last: Cheng

first: Maeve

last: O'Huallachain

first: Joel

last: Dudley

first: Sara

last: Hillemenyer

first: Rajini

last: Haraksingh

first: Donald

last: Sharon

first: Ghia

last: Euskirchen

first: Phil

last: Lacroute

first: Keith

last: Bettinger

first: Scott

last: Seki

first: Marco

last: Garcia

first: Michelle

last: Whirl-Carrillo

first: Mercedes

last: Gallardo

first: Maria

last: Blasco

first: Peter

last: Greenberg

first: Phyllis

last: Snyder

first: Teri

middle: E

last: Klein

first: Russ

last: Altman

first: Atul

last: Butte

first: Euan

last: Ashley

first: Kari

last: Nadeau

first: Mark

last: Gerstein

first: Hua


title: Transcriptome Response of Leukocytes from Chickens Infected with Avian Pathogenic Escherichia coli Identifies Pathways Associated with Resistance

city: Ames

first: Susan

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

summary: Gene expression profiling of peripheral blood leukocytes in male broiler chickens exposed to APEC O1.  Comparisons were made between Day 1 and Day 5 of all treatment groups, between differences in pathology and effect of vaccine on spleen gene expression.  The goal was to determine expression differences that could convey genetic resistance to APEC O1.

overall_design: Chickens were either challenged or non-challenged with APEC, vaccinated or non-vaccinated, with blood collected 1 or 5 days post challenge.  The non-vaccinated, challenged group was further subdivided into mild and severe pathologay based on internal lesion scores.  This created 10 groups, done in 4 replicates.  The non-vaccinated, non-challenged, day 1 group was used as the reference for all other samples.  Peripheral blood leukocytes were isolated from whole blood for analysis.

first: Erin

last: Sandford

first: Megan

last: Orr

first: Mandy

last: Shelby

first: Xianyao

last: Li

first: Huaijun

last: Zhou

first: Timothy

last: Johnson

first: Subhashinie

last: Kariyawasam

first: Peng

last: Liu

first: Lisa

middle: K

last: Nolan


title: Salmonella Enteritidis strains from poultry show differential responses to stress and survival in the egg albumen

city: Pullman

first: Devendra

last: Shah

address: 100 Dairy Rd

department: Veterinary Microbiology and Pathology

institute: Washington State University

summary: Salmonella Enteritidis is the major food-borne pathogen primarily causing human infection through contaminated chicken meat and eggs. We recently demonstrated that S. Enteritidis strains from poultry differ in their ability to invade human intestinal cells and cause disease in orally challenged mice. Here we hypothesized that the differential pathogenicity of S. Enteritidis strains is due to the differential fitness in the adverse environments that may be encountered during infection in the host. The response of a panel of six S. Enteritidis strains to acid stress, oxidative stress, survival in egg albumen and the ability to cause infection in chickens were analyzed. This analysis allowed classification of strains into two categories: stress- sensitive and stress- resistant, with the former showing significantly (P<0.05) reduced survival in acidic (gastric phase of infection) and oxidative (intestinal and systemic phase of infection) stress. Stress-sensitive strains also showed impaired intestinal colonization and systemic dissemination in orally inoculated chickens and failed to survive/grow in egg albumen. Comparative genomic hybridization microarray analysis revealed no differences at the discriminatory level of the whole gene content between stress-sensitive and stress-resistant strains. However, sequencing of rpoS, a stress-regulatory gene, revealed that one of the three stress-sensitive strains carried an insertion mutation in the rpoS resulting in truncation of σS. Finding that one of the stress-sensitive strains carried an easily identifiable small polymorphism within a stress-response gene suggests that the other strains may also have small polymorphisms elsewhere in the genome, which likely impact regulation of stress or virulence associated genes in some manner.

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: To determine if the differential stress response and virulence observed in this study could be due to the differences in the gene content between different strains, we compared the genomes of all the strains using CGH microarray designed based on the genomic information available for the sequenced strain.  All strains (n=6) were hybridized in triplicate.

first: Carol

last: Casavant

first: Quincy

last: Hawley

first: Tarek

last: Addwebi

first: Douglas

last: Call

first: Jean

last: Guard


title: Nuclear Factor Kappa B is central to Marek’s Disease lymphomagenesis

city: College Station

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

summary: Chicken Marek’s disease (MD) is a unique naturally occurring model for human herpesvirus-induced lymphomas that over-express the “Hodgkin’s disease antigen” (TNFRSF-8; CD30) on the lymphoma’s neoplastically-transformed cells. We used transcriptomics, proteomics, computational systems biology and reductionist molecular biology to identify the differences between the CD30(hi) lymphoma cells and the non-transformed CD30(lo) MD lymphoma cells. We propose specific mechanisms of neoplastic transformation, genetic resistance to lymphomagenesis and impact of lymphoma microenvironment on CD30(hi) cell development. We demonstrate that: a) in situ, CD30(lo) cells are pre-neoplastic and we identify the proteome involved in transformation as well as potential mechanisms that may be controlled by MDV oncogene Meq; b) MD herpesvirus, (via its Meq oncogene) can drive a feed forward loop that induces CD30 transcription and overexpression, increased CD30 signaling, which then activates NFκB and, in turn, increases Meq transcription; c) Meq transcriptional repression or activation from the CD30 promoter generally correlates with a polymorphism in the CD30 promoter between MD-resistant and -susceptible chicken genotypes and so a herpesvirus has evolved to utilize NFκB as a direct transcriptional activator for its oncogene.

overall_design: A dual color, balanced design was carried on eight sorted lymphoma cells from white leghorn chickens infected with MDV GA/22 strain. Each of two sample types, CD30(hi) and CD30(lo) cells, includes four biological replicates for total RNA extraction and labeling. A Dye swap was used in four biological repeats of  CD30(hi) to CD30(lo) cells comparison. Background subtracted signal intensities were collected from 4 arrays and normalized for data analysis.

first: S

last: Kumar

first: D

last: Kunec

first: J

last: Buza

first: H

last: Chiang

last: Lakshmi

last: Cheng

last: Burgess


title: cRNA hybridizations of 10 Spring annual accessions of Arabidopsis thaliana under well-watered and mild soil drying

city: Austin

first: David

last: Des Marais

address: 1 University Station C0930

institute: The University of Texas at Austin

summary:
These data provide a basis for exploration of gene expression differences between physiologically diverse Spring annual accessions of Arabidopsis thaliana.
Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range.  Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin.  These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance.  Therefore we studied the physiology, genome content and gene expression of 18 physiologically diverse accessions. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.

overall_design: The basic experimental design involves 10 accessions crossed with two environmental levels (well-watered soil and mild soil drying) and 3 biological replicates per accession/treatment combination.

middle: L

first: Thomas

last: Juenger


title: Lgr4 is required for Paneth cell differentiation and maintenance of intestinal stem cells

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: Gene inactivation of the orphan G protein-coupled receptor Lgr4, a paralog of the epithelial stem cell marker Lgr5, results in 50% decrease of epithelial cell proliferation and 80% reduction in terminal differentiation of Paneth cells in postnatal mouse intestinal crypts. When cultured ex vivo, Lgr4-deficient crypts or progenitors, but not Lgr5-deficient progenitors, die rapidly with dramatic downregulation of stem cell markers and Wnt target genes, including Lgr5. Partial rescue of this phenotype is achieved by LiCl addition to the culture medium, but not by Wnt agonists. Our results identify Lgr4 as a permissive factor of the Wnt pathway in the intestine and, as such, as a potential target for intestinal cancer therapy.

overall_design: Microarray hybridization was performed on LGR4 KO intestinal crypts at day 0, day 0.5 and day 1 versus wild-type crypts. The effects of LiCl treatment on LGR4 KO crypts at day1 versus control cells were investigated. After amplification and labelling, sample pairs were hybridized onto Mouse Exonic Evidence Based Oligonucleotide (MEEBO) arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US). Hybridizations were replicated with dye swap.

first: Roxana

last: Mustata

first: Tom

last: Van Loy

first: Anne

last: Lefort

first: Sandra

last: Strollo

first: Gilbert

last: Vassart

first: Isabelle

last: Garcia


title: Transcription Response by sulfur chemolithoautotroph Thiomicrospira crunogenato dissolved inorganic carbon and ammonia limitation

status: Public on Mar 04 2012

city: Tampa

first: Kathleen

last: Scott

state: FL

address: 4202 E Fowler Ave

country: USA

institute: University of South Florida

summary: The hydrothermal vent gammaproteobacterium Thiomicrospira crunogena inhabits an unstable environment and must endure dramatic sweeps in habitat chemistry. This sulfur chemolithoautotroph responds to changes in dissolved inorganic carbon (DIC; = CO2 + HCO3- + CO3-2) availability with a carbon concentrating mechanism (CCM), in which whole-cell affinity for DIC, as well as the intracellular DIC concentration, increase substantially under DIC-limitation.  To determine whether this CCM is regulated at the level of transcription, cells cultivated under high-DIC conditions in chemostats were resuspended in growth medium with low concentrations of DIC, and CCM development was tracked in the presence and absence of RNA polymerase inhibitor rifampicin.  The induction of the CCM, as measured by silicone oil centrifugation, was hindered in the presence of rifampicin.  Similar results were observed for carboxysome gene transcription and assembly, as assayed by qRT-PCR and transmission electron microscopy, respectively.  Genome-wide transcription patterns, assayed via microarrays, were compared for cells grown under DIC-limitation versus ammonia limitation.  In addition to carboxysome genes, two novel genes (Tcr_1019 and Tcr_1315), present in other organisms including chemolithoautotrophs, but whose function(s) have not been elucidated in any organism, were found to be upregulated under low-DIC conditions.  Likewise, under ammonia limitation, in addition to the expected enhancement of ammonia transporter and PII-gene transcription, the transcription of two novel genes was measurably enhanced (Tcr_0466 and Tcr_2018).  Upregulation of all four genes was verified via qRT-PCR (Tcr_1019: 4-fold; Tcr_1315: ~7-fold; Tcr_0466:  >200-fold; Tcr_2018:  7-fold), suggesting novel components are part of the response to nutrient limitation by this organism.

overall_design: In this study Thiomicrospira crunogena cells were grown under inorganic carbon limitation and ammonia limitation (high inorganic carbon concentrations) to examine genome wide transcription responses

first: Kimberly

last: Dobrinski

first: Steven

last: Enkemann

first: Sean

middle: J

last: Yoder

first: Edward

last: Haller

middle: M


title: Gene expression in Atlantic salmon skin in response to infection with the parasitic copepod Lepeophtheirus salmonis, cortisol implant, and their combination

status: Public on Feb 25 2012

first: Aleksei

last: Krasnov

summary: The salmon louse is an ectoparasitic copepod that causes major economic losses in the aquaculture industry of Atlantic salmon. This host displays a high level of susceptibility to lice which can be accounted for by several factors including stress. In addition, the parasite itself acts as a potent stressor of the host, and outcomes of infection can depend on biotic and abiotic factors that stimulate production of cortisol. Consequently, examination of responses to infection with this parasite, in addition to stress hormone regulation in Atlantic salmon, is vital for better understanding of the host pathogen interaction. Atlantic salmon post smolts were exposed to stress hormone cortisol, lice and their combination. The transcriptomic effects of hormone treatment in salmon skin were significantly greater than lice-infection induced changes. Cortisol stimulated expression of genes involved in metabolism of steroids and amino acids, chaperones, responses to oxidative stress and eicosanoid metabolism and suppressed genes related to antigen presentation, B and T cells, antiviral and inflammatory responses. Cortisol and liceBoth treatments equally down-regulated a large panel of motor proteins that can be important for wound contraction. Cortisol also suppressed multiple genes involved in wound healing, parts of which were activated by the parasite. Down-regulation of collagens and other structural proteins was in parallel with the induction of proteinases that degrade extracellular matrix (MMP9 and MMP13). Cortisol reduced expression of genes encoding proteins involved in formation of various tissue structures, regulators of cell differentiation and growth factors.

overall_design: Atlantic salmon post smolts were organised into four experimental groups: lice + cortisol, lice + placebo, no lice + cortisol, no lice + placebo. Infection levels were equal in both treatments upon termination of the experiment. Gene expression changes in skin were assessed with 21 k oligonucleotide microarray and qPCR at the chalimus stage 18 days post infection at 9oC.

first: Stanko

last: Skugor


title: Gene expression analysis in microdissected shoot meristems of Brassica napus microspore-derived embryos with altered levels of SHOOTMERISTEMLESS

status: Public on Feb 23 2012

city: Saskatoon

first: Raju

last: Datla

address: 110 Gymnasium Place

institute: NRC-PBI

summary: SHOOTMERISTEMLESS (STM) is a well characterized key regulator of the shoot apical meristem (SAM) activity in diverse plant species.  We used a transgenic approach to investigate how the altered expression of Brassica napus (Bn) STM affects the morphology and behavior of microspore-derived embryos (MDEs).  Down-regulation of BnSTM repressed the formation of the SAM and reduced the number of MDEs able to regenerate viable plants at germination.  This was in contrast to embryos over-expressing BnSTM which displayed enlarged SAMs with an improved regeneration frequency.  To further investigate the regulatory mechanisms underpinning these different responses, global changes in transcript levels were analysed in laser micro dissected SAMs of the transformed MDEs. The induction of BnSTM up-regulated the expression of many transcription factors (TFs) some of which directly involved in the formation of the SAM, i.e. CUPSHAPED COTYLEDON1 and WUSCHEL, and regulatory components ofthe antioxidant response, hormone signalling, and cell wall synthesis and modification. Opposite expression patterns for some of these genes were observed in the SAMs of MDEs down-regulating BnSTM.  These data were interpreted in relation to the ability of BnSTM to modulate the size and functionality of the SAM.  Structural and expression studies were further conducted to confirm the role of BnSTM in mediating the regulatory network of cell wall and lignin synthesis. Besides lowering the transcript levels of early components of cell wall and lignin biosynthetic pathways in the SAM, BnSTM had a remarkable repressing effect on the expression of PHENYLALANINE AMMONIA LYASE2, CINNAMATE 4-4HYDROXYLASE, andCINNAMYL ALCOHOL DEHYDROGENASE.  Since lignin formation is a feature of irreversible cell differentiation, these results suggest that one way in which BnSTM promotes indeterminate cell fate may be by preventing the expression of components of biochemical pathways involved in the accumulation of lignin in the meristematic cells.  Overall these studies provide evidence for a novel function of BnSTM in enhancing the quality of in vitro produced meristems, and propose that this gene can be used as a potential target to improve regeneration of cultured embryos.

overall_design: 2 mutants and 1 wild type

first: M

last: Elhiti

middle: F

last: Belmonte

first: A

last: Chan

first: Y

last: Cao

first: D

last: Xiang

first: R

first: C

last: Stasolla


title: Hypoxia transcriptomic time-series data in three different cancer cell lines

city: Toronto

first: Maud

middle: HW

last: Starmans

state: Ontario

address: 661 University Avenue

department: Informatics and Biocomputing Program

institute: Ontario Institute for Cancer Research (OICR)

summary: Tumour hypoxia exhibits a highly dynamic spatial and temporal distribution and is associated with increased malignancy and poor prognosis. Assessment of time-dependent gene-expression changes in response to hypoxia may thus provide additional biological insights and help with patient prognosis.

overall_design: Transcriptome profiling was performed for 3 cell lines derived from diverse tumour-types after hypoxic exposure at 8 time-points.

first: Kenneth

last: Chu

first: Syed

last: Haider

first: Arek

last: Kasprzyk

first: Renaud

last: Seigneuric

first: Michael

last: Magagnin

first: Marianne

last: Koritzinski

first: Paul

last: Boutros

first: Bradly

last: Wouters

first: P

last: Lambin


title: Phenotypic and transcriptional profiling in Entamoeba histolytica reveal costs to fitness and adaptive responses associated with metronidazole resistance

status: Public on Feb 22 2012

city: Shinjuku-ku

first: Gil

middle: Mallari

last: Penuliar

state: Tokyo

address: Toyama 1-23-1

department: Parasitology

country: Japan

institute: National Institute of Infectious Diseases

summary:
In vitro studies have described metronidazole (MTZ) resistance and the potential mechanisms involved. Costs to fitness and adaptive responses associated with resistance, however, have not been investigated. In this study we generated an HM-1-derived strain resistant to 12 µM MTZ (MTZR). We examined its phenotypic and transcriptional profile to determine the consequences and mRNA level changes associated with MTZ resistance.

The expression profile of 9,230 genes in wild-type and metronidazole-resistant strains was compared. Transcriptome analysis revealed 142 differentially expressed genes in MTZR. In contrast to other MTZ-resistant parasites, MTZR did not down-regulate pyruvate:ferredoxin oxidoreductase, but showed increased expression of genes for a hypothetical protein (HP1) and several iron-sulfur flavoproteins, and the downregulation of genes for leucin-rich proteins. Overexpression of HP1-HA did not confer MTZR level of resistance, but provided a slight advantage in cell survival. Fisher's exact test showed 24 significantly enriched GO terms in MTZR, and a 3-way comparison of modulated genes with MTZR cultured without MTZ and HM-1 cultured with MTZ showed that 88 genes were specific to MTZR.

overall_design: Wild-type and the MTZ-resistant strain MTZR were cultured either in the presence or absence of MTZ. 2 biological replicates per strain/condition.

first: Kumiko

last: Nakada-Tsukui

first: Tomoyoshi

last: Nozaki


title: MicroRNA profiling in colorectal cancer highlights miR-1 involvement in MET-dependent proliferation

city: Milano

first: James

last: Reid

address: Via Adamello, 16

department: Molecular Genetics of Cancer

institute: Fondazione Istituto FIRC di Oncologia Molecolare

summary:
Abstract: Altered expression of microRNAs (miRNAs) is associated with development and progression of various human cancers by regulating the translation of oncogenes and tumor suppressor genes. In colorectal cancer (CRC), these regulators complement the Vogelstein multi-step model of pathogenesis and have the potential of becoming a novel class of tumor biomarkers and therapeutic targets. Using QRT-PCR, we measured the expression of 621 mature miRNAs in 40 CRCs and their paired normal tissues and identified 23 significantly deregulated miRNAs. We subsequently evaluated their association with clinical characteristics of the samples and presence of alterations in the molecular markers of CRC progression. Expression levels of miR-31 were correlated with CA19-9 and miR-18a, miR-21 and miR-31 were associated with mutations in APC gene. To investigate the downstream regulation of the differentially expressed miRNAs identified we integrated putative mRNA target predictions with the results of a meta-analysis of seven public gene expression datasets of normal and tumor samples of CRC patients. Many of the CRC deregulated miRNAs computationally map to targets involved in pathways related to progression. Here one promising candidate pair (miR-1 and MET) was studied and functionally validated. We show that miR-1 can have a tumor suppressor function in CRC by directly down-regulating MET oncogene both at RNA and protein level and that re-expression of miR-1 leads to MET driven reduction of cell proliferation and motility, identifying the miR-1 down-modulation as one of the events that could enhance CRC progression.

Note: Each sample has the following information: Type - tissue type (T : Tumor or N: Normal), Patient - patient identifier, Stage - tumor stage (I - IV), Status - disease status at last check-up (ED: evident disease, NED: non-evident disease), CEA - carcinoembryonic antigen (continuous), CA199 - carbohydrate antigen 19-9 (continuous), APC - mutation status of APC gene (0: wild-type, 1: mutated), KRAS - mutation status of KRAS gene (0: wild-type, 1: mutated), chr18qLOH - LOH status of 18q (0: no LOH, 1: LOH), TP53 - mutation status of TP53 gene (0: wild-type, 1: mutated).

overall_design: Tumor and normal counter-parts of 40 colorectal cancer patients (10 of each Stage I to IV) where profiled using TaqMan(r) Array Human MicroRNA A+B Cards v2.0

first: Viktorija

last: Sokolova

first: Eugenio

last: Zoni

first: Andrea

last: Lampis

first: Sara

last: Pizzamiglio

first: Claudia

last: Bertan

first: Susanna

last: Zanutto

first: Tiziana

last: Camerini

first: Gianfrancesco

last: Gallino

first: Paolo

last: Verderio

first: Ermanno

last: Leo

first: Silvana

last: Pilotti

first: Marco

middle: A

last: Pierotti

first: Manuela

last: Gariboldi