title: Canine Cutaneous Peripheral Nerve Sheath Tumours versus Fibrosarcomas can be Differentiated by Neuroectodermal Marker Genes in their Transcriptome.

status: Public on Oct 30 2012

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

country: Germany

institute: Charité-Universitätsmedizin Berlin

summary: The diagnostic differentiation of canine fibrosarcomas and peripheral nerve sheath tumors (PNST) is mainly based on their histopathologic phenotype. Histologic differentiation of these tumors can, however, be difficult and there is a lack of immunohistochemical markers to prove their histogenic origin. To identify possible PNST markers and to further investigate the histogenic origin of the two tumor types, we compared histologically defined canine fibrosarcomas and peripheral nerve sheath tumors by microarray analysis.   Forty-five annotated gene products were significantly differentially expressed in both tumor types. Seven of these gene products, known to be specifically expressed in neuroectodermal tissues, showed higher expression in peripheral nerve sheath tumors: FMN2, KIF1B, GLI1, ROBO1, NMUR2, DOK4 and HMG20B. Furthermore, eight genes associated with carcinogenesis were up-regulated in fibrosarcomas: FHL2, PLAGL1, FNBP1L, BAG2, HK1, CSK and Cox5A. Comparison of the fibrosarcoma and PNST transcriptome therefore identified PNST phenotype-associated genes involved in neuroectodermal differentiation which may be potential PNST markers. Furthermore, the identified fibrosarcoma phenotype-associated genes may be potential markers to differentiate fibrosarcomas from other tumor types and may be involved in their pathogenesis.

overall_design: The aim of the present study was to examine the differences in global gene expression of histologically prototypic fibrosarcomas and PNST. To this end, complete transcriptome microarray analyses were used to quantify differences in gene expression activity in both tumor types.

first: Robert

last: Klopfleisch

first: Anja

last: Meyer

first: Michael

last: Hummel

first: Achim

middle: D

last: Gruber


title: Rhesus monkey cumulus cells revert to a mural granulosa cell state following an ovulatory stimulus

status: Public on Oct 04 2012

city: Philadelphia

first: Young

middle: Shin

last: Lee

state: PA

address: 3307 N. Broad Street AHB 557

department: Fels Institute for Cancer Research and Molecular Biology

country: USA

institute: Temple University

summary: Follicular somatic cells (mural granulosa cells and cumulus cells) and the oocyte communicate through paracrine interactions and through direct gap junctions between oocyte and cumulus cells. Considering that mural and cumulus cells arise through a common developmental pathway and that their differentiation is essential to reproductive success, understanding how these cells differ is a key aspect to understanding their critical functions. Changes in global gene expression before and after an ovulatory stimulus were compared between cumulus and mural granulosa cells to test the hypothesis that mural and cumulus cells are highly differentiated at the time of an ovulatory stimulus and further differentiate during the periovulatory interval. The transcriptomes of the two cell types were markedly different (>1500 genes) before an ovulatory hCG bolus but converged after ovulation to become completely overlapping. The predominant transition was for the cumulus cells to become more like mural cells after hCG. This indicates that the differentiated phenotype of the cumulus cell is not stable and irreversibly established but may rather be an ongoing physiological response to the oocyte.

overall_design: We compared transcriptomes of mural granulosa cells isolated from the follicles before (PM-GC) and after (VVM-GC) an ovulatory stimulus.  These data were analyzed with previously published cumulus cells data to compare transitions in granulosa cell state before and after an ovulatory stimulus with transitions in cumulus cells.

middle: S

first: Charles

middle: L

last: Chaffin

first: Catherine

middle: A

last: VandeVoort

first: Bela

middle: G

last: Patel

first: Keith

middle: E

last: Latham


title: Comparison of Darinaparsin and Arsenic Trioxide effect on HI-LAPC-4, human prostatic cancer cell line

status: Public on Oct 13 2012

city: Stanford

first: Junqiang

last: Tian

state: CA

address: 300 Pasteur Drive

department: Department of Urology

institute: Stanford University

summary: Darinaparsin (DPS) is an arsenic cytotoxin with a more favorable toxicity profile than the established anti-leukemic drug, arsenic trioxide (ATO). Here we report effects of DPS on a variety of solid tumor cell lines under normoxia as well as hypoxia, the latter an important characteristic of the tumor microenvironment. Using MTT and clonogenic assays, we demonstrated that DPS had potent cytotoxic activities under both normoxia and hypoxia, with IC50??s ~ 2- to 3-fold lower than ATO. Xenograft studies using tumor cell lines as well as patient-derived tumor tissues implanted under the renal capsule in mice confirmed the anti-tumor activity of DPS in vivo. DPS was also a more potent radiosensitizer under hypoxia than ATO in vitro, and sensitized solid tumors to radiation in vivo at doses that had no systemic toxicities. Interestingly, in contrast to previous reports of DPS effects on leukemic cells under normoxia, DPS-induced killing of hypoxic solid tumor cells was not dependent on ROS generation and oxidative damage. Instead, cDNA microarray analysis suggested that DPS inhibited oncogene- (such as RAS and MYC) associated gene expression. In fact, compared to normal mouse embryonic fibroblasts (MEFs), oncogene (RAS/E1A) transformed MEFs were markedly more sensitive to DPS-induced apoptosis under both normoxia and hypoxia. Altogether, these results demonstrate that DPS has significant and preferential cytotoxicity against solid tumor as compared with normal cells, and is an effective radiosensitizer. Since DPS is in early clinical development as a single agent, these findings have near term translational potential.


title: Xanthomonas campestris pv. campestris 8004: wild type vs. ravA (or ravS or ravR) mutant

status: Public on Oct 10 2012

city: Beijing

first: jun

last: tao

address: Beichen west road

country: China

institute: institute of microbiology, Chinese academy of sciences

summary:
Transcriptional profiling of Xanthomonas campestris pv. campestris 8004 comparing control wild type strain with ravA  (or ravS or ravR) mutant
The effects of mutating ravS, ravR and ravA on EPS synthesis, biofilm production and motility were very different , the factors responsible for these differences are not clear. With comparative analysis of the regualtion pathways by RavS, RavR and RavA, we can indentify different genes regulated by these three genes and maybe explain the different phenotypes caused by these genes mutations.

overall_design:
Comparative analysis of the regualtion pathways by RavS, RavR and RavA
Two-condition experiment, wild type vs. mutants. Biological replicates were independently grown and harvested. One replicate per array

first: Jun

last: Tao

first: Chaozu

last: He


title: Growth factor independence 1 (Gfi1) as a new target for leukemia therapy

status: Public on Oct 03 2012

city: Montréal

first: Lothar

last: Vassen

state: Quebec

address: 110, avenue des Pins Ouest

department: Hematopoiesis and Cancer

country: Canada

institute: IRCM

summary:
Using (conditional) Gfi1 knock-out mice we show that ablation of the transcriptional repressor Gfi1 cures mice from lymphoid leukemia and reduces the expansion of primary human T-ALL xenografts in mice. We find that Gfi1 alters the p53 dependent transcriptional activation of a substantial subset of known p53 target genes and thus sets a threshold for cell death.
We used Affymetrix mouse Gene-1.0-ST arrays to define the changes in the gene expression pattern of wt or Gfi1-KO thymocytes (Gfi1-fl/fl X MX-CRE, induced by pIpC) that were either untreated (WT, GfiKO thymocytes), irradiated (WT_irr, Gfi1KO_irr), ENU transformed (WT_Tum, Gfi1KO_Tum), or transformed by Notch1-CT and ENU-induced to enhance tumorigenesis (WT_Notch_Tum, Gfi1KO_Notch_Tum).

overall_design: The study should determine how loss of Gfi1 alters the gene expression pattern in irradiated or tumor derived thymocytes

first: Cyrus

last: Khandanpour

first: James

last: Phelan

first: Judith

last: Schütte

first: Rivan

last: Chen

first: Shane

middle: R

last: Horman

first: Marie

middle: C

last: Gaudreau

first: Joseph

last: Krongold

first: Jinfang

last: Zhu

first: William

last: Paul

first: Ulrich

last: Dührsen

first: Bertie

last: Göttgens

first: H

last: Grimes

first: Tarik

last: Möröy


title: Differential expression in response to water deficit in diploid leaves of sweet orange scion grafted alternatively on a diploid or auto-tetraploid Rangpur lime rootstock: data concerning the scion grafted onto tetraploid rootstock

status: Public on Oct 05 2012

city: Seville

first: Jose

middle: M.

last: Colmenero-Flores

address: Av. Reina Mercedes 10

department: Plant Biotechnology

country: Spain

institute: IRNAS (CSIC)

summary: Whole-genome duplication, or polyploidy, is common in many plant species and often leads to better adaptation to adverse environmental condition. However, little is known about the physiological and molecular determinants underlying adaptation. We examined the drought tolerance in diploid (2x) and autotetraploid (4x) clones of Rangpur lime (Citrus limonia) rootstocks grafted with 2x Valencia Delta sweet orange (Citrus sinensis) scions, named V/2xRL and V/4xRL, respectively. Physiological experiments to study root-shoot communication associated with gene expression studies in roots and leaves were performed. V/4xRL was much more tolerant to water deficit than V/2xRL. Gene expression analysis in leaves and roots showed that more genes related to the response to water stress were differentially expressed in V/2xRL than in V/4xRL. Prior to the stress, when comparing V/4xRL to V/2xRL, V/4xRL leaves had lower stomatal conductance and greater abscisic acid (ABA) content. In roots, ABA content was higher in V/4xRL and was associated to a greater expression of drought responsive genes, including CsNCED1, a pivotal regulatory gene of ABA biosynthesis. We conclude that tetraploidy modifies the expression of genes in citrus roots to regulate long-distance ABA signaling and adaptation to stress.

overall_design: Transcriptional profiling of sweet orange (Citrus sinensis) scion leaves comparing control untreated with water deficit conditions. We examined the drought tolerance in diploid (2x) and autotetraploid (4x) clones of Rangpur lime (Citrus limonia) rootstocks grafted with 2x Valencia Delta sweet orange (Citrus sinensis) scions, named V/2xRL and V/4xRL, respectively. Physiological studies showed that V/4xRL was much more tolerant to water deficit than V/2xRL. Global gene expression changes induced by water deficit were monitored in the leaves of V/2xRL and V/4xRL by microarray hybridization. The Citrus genome-wide cDNA microarray was used, which includes 21,081 putative unigenes described in Martinez-Godoy et al. (2008). Two independent microarray hybridization experiments with leaves of the 2x Valencia Delta orange alternatively grafted onto 2x or 4x RL rootstocks were respectively performed. For each experiment, the Cy-labelled cDNA of control leaves was hybridized with labelled cDNA from water-stressed samples. To avoid Cy3 and CY5 dye-related artefacts, control and water-stressed cDNA samples were dye-swapped and used to hybridize four slides corresponding to different combinations of the four biological replicates obtained from every treatment. The microarray hybridizations were performed according to Allario et al. (2011). A GenePix 4000B microarray scanner (Axon Instruments, Inc.) and the GenePix Pro 4.1 acquisition software were used to scan the chips at 5-10 µm resolution. Photomultiplier gains for the two channels were adjusted so that the ratio of total intensities was approximately 1 and the percentage of saturated spots was about 1%. High-resolution tiff images were generated and used for quantification of gene expression data. Spot positions were identified on the colour images and quality flags were assigned to individual spots both automatic and manually. Only spots with background-subtracted foreground intensity greater than two in at least one channel were used, and only microarrays with optimal hybridization data were pre-processed and normalized for further analyses. Raw data were imported into the R computing environment for pre-processing, visualization, and statistical analysis. To identify probes showing significant differential gene expression between samples, the Linear Models in Microarrays (LIMMA; Smyth, 2005) software package was used. Pre-processing and normalization of two-color microarray data including signal intensity, background correction, uniformity of the expression ratio over the chip surface (within-array normalization), and normality of M-value distributions were evaluated according to Smyth and Speed (2003). M-value was defined as the logarithm in base-2 of water-deficit versus control expression ratio. Reproducibility between replicates that were assessed indicated that the experimental system provided consistent signals in spots corresponding to the same gene and acceptable low variability between biological replicates (not shown). P-values associated to the statistical analysis of differential expression obtained from Limma analysis are corrected for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) procedure (Benjamini & Hochberg, 1995). Differences in gene expression were considered to be significant when the M-value was higher than 0.7 (absolute value) andthe FDR-adjusted P-value was smaller than 0.05.

first: Thierry

last: Allario

first: Javier

last: Brumos

middle: M

first: Domingo

middle: J

last: Iglesias

last: Pina

first: Luis

last: Navarro

first: Manuel

last: Talon

first: Patrick

last: Ollitrault

first: Raphaël

last: Morillon


title: Identification of gonadotropin-responsive genes in fish testis

status: Public on Oct 22 2012

city: Rennes

first: Elisabeth

last: Sambroni

address: Bat 16A Campus de Beaulieu

department: PHASE

country: France

institute: INRA

summary: In all vertebrates, the dual function of testis (production of sexual steroids and production of gametes) is mainly regulated by two gonadotropic pituitary hormones, FSH and LH. However, in fish the biological activities of the two hormones are not still clearly delineated and moreover, their molecular mechanisms are yet poorly understood. In this study we investigated the effects of FSH and LH on testicular gene expression, in the rainbow trout, at two developmental stages I-II and III (I: spermatogonia only, II: active spermatogonia proliferation, III: meiosis onset with the appearance of spermatocytes and round spermatids).

overall_design: Testes were collected from all-male population rainbow trout and incubated in six replicates for 96 hours, at 12°C, in the absence or presence of purified salmonid gonadotropins, FSH and LH (500 ng/mL).

first: Antoine

last: Rolland

first: Jean-Jacques

last: Lareyre

first: Florence

last: Le Gac


title: Comparison of the expression profiles of 630E JIR8094 strain and a ccpA mutant after 10h of growth in TY.

status: Public on Oct 02 2012

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: Transcriptionnal profiling of C. difficile 630E JIR8094 strain vs a ccpA mutant after 10h of growth in TY

overall_design: two-conditions experiments, WT strain vs ccpA mutant strain, 4 biological replicates for each condition, in an indirect design using a 8h TY RNA preparation as Reference

first: Frederic

last: Barbut

first: Ana

last: Antunes

first: Marc

last: Monot


title: Clostridium difficile CD630E JIR8094: growth 10h with 0.5% glucose in TY vs growth 10h in TY

summary: transcriptionnal profiling of a C. difficile strain JIR8094 comparing growth 10h in 0.5% TY medium with growth 10h in TY medium

overall_design: two-conditions experiments, 0.5% glucose TY for 10h vs TY for 10h, 4 biological replicates for each condition, in an indirect design using a 8h TY RNA preparation as Reference


title: Differential expression in response to water deficit in diploid leaves of sweet orange scion grafted alternatively on a diploid or auto-tetraploid Rangpur lime rootstock: data concerning the scion grafted onto diploid rootstock.

last: Colmenero-Flores

overall_design: Transcriptional profiling of sweet orange (Citrus sinensis) scion leaves comparing control untreated with water deficit conditions. We examined the drought tolerance in diploid (2x) and autotetraploid (4x) clones of Rangpur lime (Citrus limonia) rootstocks grafted with 2x Valencia Delta sweet orange (Citrus sinensis) scions, named V/2xRL and V/4xRL, respectively. Physiological studies showed that V/4xRL was much more tolerant to water deficit than V/2xRL. Global gene expression changes induced by water deficit were monitored in the leaves of V/2xRL and V/4xRL by microarray hybridization. The Citrus genome-wide cDNA microarray was used, which includes 21,081 putative unigenes described in Martinez-Godoy et al. (2008). Two independent microarray hybridization experiments with leaves of the 2x Valencia Delta orange alternatively grafted onto 2x or 4x RL rootstocks were respectively performed. For each experiment, the Cy-labelled cDNA of control leaves was hybridized with labelled cDNA from water-stressed samples. To avoid Cy3 and CY5 dye-related artefacts, control and water-stressed cDNA samples were dye-swapped and used to hybridize four slides corresponding to different combinations of the four biological replicates obtained from every treatment. The microarray hybridizations were performed according to Allario et al. (2011). A GenePix 4000B microarray scanner (Axon Instruments, Inc.) and the GenePix Pro 4.1 acquisition software were used to scan the chips at 5-10 µm resolution. Photomultiplier gains for the two channels were adjusted so that the ratio of total intensities was approximately 1 and the percentage of saturated spots was about 1%. High-resolution tiff images were generated and used for quantification of gene expression data. Spot positions were identified on the colour images and quality flags were assigned to individual spots both automatic and manually. Only spots with background-subtracted foreground intensity greater than two in at least one channel were used, and only microarrays with optimal hybridization data were pre-processed and normalized for further analyses. Raw data were imported into the R computing environment for pre-processing, visualization, and statistical analysis. To identify probes showing significant differential gene expression between samples, the Linear Models in Microarrays (LIMMA; Smyth, 2005) software package was used. Pre-processing and normalization of two-color microarray data including signal intensity, background correction, uniformity of the expression ratio over the chip surface (within-array normalization), and normality of M-value distributions were evaluated according to Smyth and Speed (2003). M-value was defined as the logarithm in base-2 of water-deficit versus control expression ratio. Reproducibility between replicates that were assessed indicated that the experimental system provided consistent signals in spots corresponding to the same gene and acceptable low variability between biological replicates (not shown). P-values associated to the statistical analysis of differential expression obtained from Limma analysis are corrected for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) procedure (Benjamini & Hochberg, 1995). Differences in gene expression were considered to be significant when the M-value was higher than 0.7 (absolute value) and the FDR-adjusted P-value was smaller than 0.05.


title: Gene profiling in arbuscular mycorrhizal symbiosis between the actinorhizal tree Casuarina glauca and the fungus Glomus intraradices.

city: MONTPELLIER CDX 5

first: Valérie

last: HOCHER

address: 911 av. Agropolis BP64501

department: DIADE

institute: IRD

summary: Casuarina glauca belongs to a family of angiosperms called actinorhizal plants because they can develop nitrogen-fixing nodules in association with the soil bacteria Frankia.  They can also develop arbuscular mycorrhizae (AM) while associated with Glomeromycota fungi. The aim of this transcriptomic study was to get a global view of the plant symbiotic genetic program in AM and to identify new key plant genes involved in endosymbioses.

overall_design:
C. glauca plants were grown in hydroponics  then transferred to pots with or without spores of Glomus intraradices and watered with low phosphate solution to enhance mycorrhization. For this study we considered two stages:  -  a stage where plants were inoculated with G. intraradices, roots were harvested 8 weeks after inoculation with the G. intraradices. AM structures were present.   - a stage where plants were not inoculated, roots were harvested at the same time as the inoculated roots , this is our control condition. AM structures were absent.   Three biological replicates were used for each condition.
Microarrays were designed by Imaxio (Clermont Ferrand, France ; http://www.imaxio.com/index.php) which has been accredited by Agilent Technologies (Palo Alto, CA, USA; http://www.home.agilent.com/agilent/home.jspx) as a certified service provider for microarray technologies. Based on 14327 annotated unigenes for C. glauca, 60mers probes were designed using eArray software (1 probe per unigene) and custom 8 x 15K Oligo Microarrays were manufactured by Agilent.

last: Hocher

first: Sergio

last: Svistoonoff


title: Functional divergence of PP2Cs encoding genes in Brassica oleracea and Arabidopsis thaliana

status: Public on Oct 28 2012

city: Poznan

first: Agnieszka

middle: Wioletta

last: Ludwików

address: Umultowska 89

department: Biotechnology

country: Poland

institute: Adam Mickiewicz University

summary: We investigated the expression profiles and genomic organization of PP2Cs-encoding genes in Brassica oleracea. Analysis of cDNA macroarray transcription profiles for Brassica oleracea and Arabidopsis thaliana revealed significant differences in the expression of a gene encoding protein phosphatase 2C, ABI1, a member of the group A PP2C. To gain insight into the ABA signaling network conservation in a model plant and its crop relatives group A PP2C genes in B. oleracea have been identified and functionally characterized. Twenty homologous sequences were identified as putative members of the group A PP2Cs (BolC.PP2Cs). Phylogenetic analysis revealed that the B. oleracea homologues are closely related to the particular members of the A. thaliana PP2C family. The genetic analysis has corroborated the presence of 2 to 3 copies for almost all of the PP2Cs examined, which corresponded to the unique genes in the A. thaliana genome. Gene expression analyses showed that among 15 PP2Cs-encoding genes studied in B.oleracea, BolC.ABI2, BolC.HAB1, BolC.HAB2.a-c, and BolC.PP2CA.a were drought-induced. However, in contrary to AtPP2Cs, only BolC.ABI1.a-b, BolC.ABI2 and BolC.PP2CA.a were ABA-responsive at the time points tested. Our results indicate that in B. oleracea PP2C-based drought stress signaling has evolved distinctly in comparison to A. thaliana. It is hypothesized that different reactions of particular B. oleracea PP2C genes to the water stress and ABA treatment may indicate lower conservation of their specificity in stress-induced reversible phosphorylation-based protein network operating in B. oleracea and A. thaliana.

sample_organism:
Arabidopsis thaliana
Brassica oleracea

overall_design: For each genotype 7 samples were analysed; 4 controls and 3 samples extracted from drought-treated plants. The reliability and reproducibility of the macroarray analyses were ensured by using biological replicates in the experiment.

first: Danuta

last: Babula-Skowrońska

first: Witold

last: Nowak


title: Genomic and epigenomic analysis of taurine and indicine cattle

city: College Station

first: Ryan

last: Doan

state: Texas

address: 4467 TAMU

institute: Texas A&M University

type: Genome variation profiling by genome tiling array

summary: Custom aCGH analysis of copy number across taurin and indicine subspecies

overall_design: All  samples were compared to a single Angus reference

first: Scott

last: Dindot


title: Clostridium difficile mutant ccpA CD630E JIR8094: growth 10h with 0.5% glucose in TY vs growth 10h in TY

summary: transcriptionnal profiling of a ccpA mutant of C. difficile strain JIR8094 comparing growth 10h in 0.5% TY medium with growth 10h in TY medium


title: Transcriptional profiling of cumulus cells differentiation throughout oocyte competence acquisition in the bovine ovarian follicles.

status: Public on Oct 14 2012

first: Julien

last: Bobe

address: Campus de Beaulieu

institute: Institut National de la Recherche Agronomique

summary:
Somatic cells surrounding the oocyte were sampled at the following stages: developmentally incompetent or poorly competent prophase I oocytes (NC1 oocytes), developmentally competent prophase I oocytes (C1 oocytes), and developmentally competent metaphase II oocytes (C2 oocytes).
NC1 cumulus cells (CC) were sampled from immature calf oocytes, C1 samples from immature cow oocytes, and C2 samples from in vivo matured cow oocytes.

overall_design: Global transcriptional profiling was performed using cumulus cells collected from bovine ovarian follicles during in vivo oocyte developmental competence acquisition. Cumulus cells were collected at 3 stages: early stage follicles (prophase I arrested oocytes, meiotically competent but developmentally incompetent, n=6), late stage follicles (prophase I arrested oocytes, meiotically competent and developmentally competent, n=6) and ovulatory follicles collected by ovum pick-up (OPU) in vivo (metaphase II arrested oocytes, developmentally fully competent, n=5).

first: Cathy

last: Charlier

first: Svetlana

last: Uzbekova

first: Franck

last: Chesnel


title: The midgut of domestic silkworm: Control vs. phoxim treated

city: Suzhou

first: Zhi

middle: Ya

last: Gu

address: Renai Road

department: School of Basic Medicine and Biological Sciences

institute: Soochow University

summary: Transcriptional characteristics of genes in the midgut of domestic silkworms after 24 h exposure to phoxim through whole-genome oligonucleotide microarray.

overall_design: Transcription profiling experiments, phoxim-treated midgut (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and control samples labeled by Cy3. Three Biological replicate. No dye-swaps.

first: Z

middle: Y

first: S

last: Sun


title: Expression analysis of C. elegans genes daf-9 and daf-12 mutant

status: Public on Oct 18 2012

city: kunming

first: yi

middle: cheng

last: ma

state: Yunnan

address: No.2 North Cuihu Road

institute: Lab for Conservation and Utilization of Bio-Resources

summary:
Investigation of whole genome gene expression level changes in C. elegans genes daf-9 and daf-12 mutant,compared to the wild-type strain
NimbleScan software’s implementation of RMA offers quantile normalization and background correction. There are three steps of RMA: Firstly, background subtraction was performed using a local background estimator. Secondly, quantile normalization (Bioinformatics 2003; 19:185) at probe level was done to make the expression distributions the same for all arrays. Last, probe set summarization was performed using Robust Multichip Average (RMA) algorithm as described by Irizarry, et al. (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249).

overall_design: A nine chip study using total RNA recovered from three separate wild-type cultures of C.elegans and three separate cultures of daf-9 mutant，three separate cultures of daf-12 mutant.The C. elegans 12 x 135K Gene Expression Array was manufactured by Roche NimbleGen. This array enables you to conveniently and simultaneously hybridize 12 samples on each slide. About 13,187 genes are collected from the authoritative data source including Wormbase.

first: Yi

last: Ma

first: Jun

last: Tao

first: Cheng

last: Zou


title: Transcriptional effects of TNF-α and TGF-β1 on human umbilical vein endothelial cells

status: Public on Oct 31 2012

city: Westmead

first: Catherine

last: Emmanuel

state: NSW

address: Westmead Centre for Oral Health, Westmead Hospital

department: Oral Pathology

country: Australia

institute: University of Sydney

summary: Transcriptional profiling of human umbilical vein endothelial cells following stimulation with tumour necrosis factor alpha and transforming growth factor beta singly or combined for 8 hr

overall_design: All stimulations were for 8 hr - TNF-α vs no cytokine; TGF-β1 vs no cytokine; TNF-α & TGF-β1 vs TNF-α alone; TNF-α & TGF-β1 vs TGF-β1 alone

first: C

first: H

last: Zoellner


title: Gene expression in phagocytic and non-phagocytic Entamoeba histolytica populations

status: Public on Oct 16 2012

city: Burlington

first: Adam

last: Sateriale

state: VT

address: 320 Stafford Hall

department: Medicine

institute: University of Vermont

summary:
The ability of Entamoeba histolytica to phagocytose host cells correlates to observed virulence in vivo. To better understand the mechanism of phagocytosis we used paramagnetic beads coated with host ligand and sorted trophozoites based on phagocytic ability. Gene expression was then measured in both the sorted phagocytic and non-phagocytic populations using a custom Affymetrix chip for E. histolytica.
Feed forward regulation of phagocytosis by Entamoeba histolytica. Infection and Immunity. PMID 23045476

overall_design:
M280 Streptavidin Dynabeads (Invitrogen) were labeled with 20ug/mL biotinylated Human C1q (Quidel). Entamoeba histolytica (strain HM1) were washed twice with PBS then resuspended with the labeled beads at a 10:1 ratio of beads to trophozoites. Samples were  incubated at 37°C for 45 minutes, washed twice with agitation to remove adherent beads, then resuspended in MACS buffer. Samples were loaded into magnetic columns (Miltenyi Biotec) and trophozoites were seperated according to manufacturer's protocols.
phagocytic vs. non-phagocytic Entamoeba histolytica populations

first: Archana

last: Vaithilingam

first: Liam

last: Donnelly

first: Peter

last: Miller

first: Christopher

last: Huston


title: Aspergillus nidulans: Control (Wt) vs. ypkA induction or repression (alcAypkA)

city: Ribeirão Preto

first: Ana

middle: Cristina

last: Colabardini

state: São Paulo

address: Av do Café s/n Cidade Universitária

department: Ciências Farmacêuticas

country: Brazil

institute: FCFRP-USP

summary: Transcriptional profiling of A. nidulans comparing the mutant strain alcAypkA grown on inducing or repressing conditions. The main objective was to identifiy genes related to ypkA gene function. The experiment was further validated by real-time PCR and enzymatic assay.

overall_design: Four-condition experiment: A. nidulans strains grown during 16 and 24 h at 37°C in glucose 4% or glycerol 2% threonine 100mM.


title: Understanding the molecular events underpinning cultivar differences in physiological performance and heat tolerance

status: Public on Oct 20 2012

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary: Plants were acclimated for 4 d at optimal conditions (32/25 oC day/night) in the growth cabinet before initiation of the temperature treatment. For the control (32 oC), cabinet conditions were left unchanged during the treatment period. Due to limited growth cabinet space, plants of a comparative physiological age were transferred to the controlled environment growth cabinet after the control plants had been removed. Well-watered plants were exposed to heat stress by increasing the ambient air temperature to 42 oC (67% RH) during the photoperiod and 25 oC (40 % RH) during the dark period.  The third youngest fully expanded leaf of plants at the first square physiological age was sampled for all experiments. Three leaf tissue samples were collected for each genotype under the ambient or hot growth cabinet (12 samples total) at 0.5, 1, 3, and 7 h after initiation of the high temperature stress, where the time 0.5 samples were collected at 0930 h which equated to 3.5 h into the photoperiod. For RNA preparations, whole leaves were excised at the junction of the lamina and petiole, immediately snap frozen in liquid nitrogen and stored at -80oC. Leaves were ground to a fine powder in liquid nitrogen and a 0.1 g sub-sample was taken and total RNA was extracted using a hot borate buffer.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Nicole Cottee.  The equivalent experiment is GO12 at PLEXdb.]

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: temperature: 32 C - cultivar: Sicala 45(3-replications);  temperature: 32 C - cultivar: Sicot 53(3-replications);  temperature: 42 - cultivar: Sicala 45(3-replications);  temperature: 42 - cultivar: Sicot 53(3-replications)

first: Nicole

last: Cottee

first: Michael

middle: P

last: Bange


title: DNA copy number analysis from mice with radiation-induced acute myeloid leukemia

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Certain mouse strains such as CBA, C3H and RFM, have high incidence of radiation-induced acute myeloid leukemia (AML). The data in this serie was generated by using spleen DNA from CBA mice which were irraidated with either gamma-rays or heavy ion (HZE) particles. Spleen DNA with radiation-induced AML was compared with DNA from normal CBA mice.

overall_design: Comparison of spleen DNA from CBA mice with radiation-induced AML vs genomic DNA from normal CBA mice

first: Liang-Hao

last: Story

last: Weil


title: Transcriptional profiling of somatic cells differentiation throughout oocyte competence acquisition in rainbow trout ovarian follicles.

first: Julien

last: Bobe

summary:
Somatic cells surrounding the oocyte were sampled at the following stages: developmentally incompetent or poorly competent prophase I oocytes (NC1 oocytes), developmentally competent prophase I oocytes (C1 oocytes), and developmentally competent metaphase II oocytes (C2 oocytes).
NC1 samples were collected from late vitellogenic females (LV), C1 samples from post-vitellogenic females (PV), and C2 samples from females undergoing meiotic maturation (Germinal Vesicle Breakdown)

overall_design: Global transcriptional profiling was performed using somatic cells collected from rainbow trout ovarian follicles during in vivo oocyte developmental competence acquisition. Somatic cells were collected at 3 stages of oogenesis: NC1 stage follicles (LV, late vitellogenic, prophase I arrested oocytes, meiotically incompetent and developmentally incompetent, n=6), C1 stage follicles (PV, post-vitellogenic, prophase I arrested oocytes, meiotically competent and developmentally competent, n=16). Ovulatory follicles were also collected during oocyte maturation after in vivo induction (metaphase II arrested oocytes, developmentally fully competent, n=6).

first: Cathy

last: Charlier

first: Svetlana

last: Uzbekova

first: Franck

last: Chesnel


title: Gene Expression Profiles in Skeletal Muscle and Liver of Type 2 Diabetes Rats

status: Public on Oct 27 2012

city: Nanchang

first: xl

last: tang

address: Xuefu road

institute: Nanchang university

summary: Analyzing changes in gene expression in liver and skeletal muscle from streptozotocin-diabetic rats. From the 9,929 expressed genes across the genome, 1,305 and 997 differentially expressed genes (DEGs, P < 0.01) were identified in comparisons of skeletal muscle and liver, respectively. Interestingly, large numbers of DEGs (200) were common to both comparisons, which was clearly more than the predicted number (131 genes, P < 10−4). Further interpretation of gene ontology used three over-representation analysis software (WebGestalt, Expander and GATHER). All the tools detected one KEGG pathway (MAPK signaling) and two GO biological processes (response to stress and cell death), with enrichment of DEGs in both tissues. In addition, PPI (protein-protein interaction) networks constructed using human homologs not only revealed the tendency of DEGs to form a highly connected module, but also suggested a “hub” role of MAPK related genes (such as MAPK14) in the pathogenesis of T2D.

overall_design: Total RNA obtained from liver and skeletal muscle of streptozotocin-diabetic rats and controls, respectivly.

first: Xiaoli

last: Tang

first: Libin

last: Deng


title: Development of  gene expression profile on different sampling sites of the Ebro River

city: Barcelona

first: Anna

last: Navarro Cuenca

state: Barcelona

address: C/Jordi Girona 18-26

department: Environmental Toxicology

institute: IDAEA-CSIC

summary: The zebra mussel is present in Spain since early 2000,s, when it was discovered in the lower part of the Ebro river. To study the gene expression pattern of different populations of zebra mussel a long the Ebro River we use a custom microarray developed in our laboratory, using 4057 publicly available DNA sequences from Dreissena polymorpha and other related genera. Also it was used an external sampling site located in Sitjar Dam, about 200km form the Ebro river. Transcriptome profiles were analysed using the gills of individuals collected in the same period (20-23 March) to diminish seasonal effects. A total of 755 transcripts changed significantly their mRNA levels among the sites of the study (ANOVA p<0.01, fc ±1.5). Genes encoding for xenobiotic, energetic and calcium metabolism and cell proliferation were those showing the highest differences among populations. Geographical origin appeared as the major driver of the differences among the studied populations, as the transcriptomic profiles from four populations collected within a radius of few km around the Flix factory clustered together and separated from those from other distant populations both upstream the Ebro River or in the Sitjar dam.

overall_design: Differences on gene expression pattern were measure in gills of Dreissena polymorpha in different populations in five populations along the Ebro river and one population in Sitjar dam. The collection of samples were done during Srping (March). For the microarray it was used 2 replicates of each sites of the study.

first: Bueno

last: Campos


title: Photoinduction of the Vibrio campbellii Type III Secretion System

status: Public on Oct 09 2012

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

summary: Although many members of the genus Vibrio are known to inhabit the marine photic zone, an understanding of the influence of light on the molecular physiology of Vibrio spp. has largely been neglected. To begin to characterize the photophysiology of one such Vibrio sp. (Vibrio campbellii ATCC strain BAA-1116) we used microarray-based expression profiling to compare the transcriptomes of illuminated versus dark cell cultures. Specficially, we compared the transcriptomes of wild type V. campbellii (STR) cells that were cultured in M9 minimal salts medium plus glucose under two conditions: (i) after 24 hours of continuous dark and (ii) after a 12 hour dark:12 hour light cycle (white light illumination at 54 µmol photons s-1 m-2). The results revealed a large photostimulon (differential expression of ~20% of the V. campbellii genome; adjusted p value < 0.0001) that surprisingly included ~75% of the type III secretion system (T3SS) genes which were found to be 1.6 – 5.4X more abundant in illuminated cultures. These findings, which were confirmed by quantitative reverse transcription PCR and quantitative membrane proteomics, strongly suggest that the photostimulon of strain BAA-1116 includes the T3SS.

sample_organism: Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920

overall_design: Five biological replicates of V. campbellii BAA-1116 (STR) were grown to log phase (200 rpm, 30°C, 25 mL M9 minimal salts medium plus glucose in 125 mL baffled Erlenmeyer flasks) under continuous dark for 24 hours or under a 12 hour dark:12 hour light cycle (white light illumination at 54 µmol photons s-1 m-2) and total RNA was extracted from 1.0E+9 cells. Messenger RNA was isolated from the total RNA extracts treated with DNase, labeled with biotin, fragmented and hybridized to V. campbellii BAA-1116 whole genome microarrays (520694F, Affymetrix).

first: Dagmar

middle: H

last: Leary

first: Zheng

last: Wang

first: Robert

last: Rubin

first: Gary

last: Vora


title: Effects of the nutritional background and parasite infection on the intestine transcriptome of gilthead sea bream, Sparus aurata

city: Castellón

first: Josep

last: Calduch-Giner

address: Ribera de Cabanes

institute: Institute of Aquaculture Torre de la Sal (CSIC)

summary: Gilthead sea bream fed plant-protein based diets with either fish oil or vegetable oil as the most iportant source of dietary lipids were experimentally exposed to the intestinal parasite Enteromyxum leei by water effluent. A specific gilthead sea bream oligo-microarray was used to determine the intestine transcriptomic response.

overall_design: 41 samples from six experimental groups (2 diets x 3 infective status) in a single-color hybridization

first: Jaume

last: Pérez-Sánchez


title: The rectal cancer microRNAome - a comprehensive comparative analysis of microRNA expression in rectal cancer and matched normal mucosa

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

summary:
Purpose: MicroRNAs play a prominent role in a variety of physiological and pathological biological processes, including cancer. For rectal cancers, only limited data are available on microRNA expression profiles, while the underlying genomic and transcriptomic aberrations have been firmly established. We therefore aimed to comprehensively map the microRNA expression patterns of this disease.

Experimental design: Tumor biopsies and corresponding matched mucosa samples were prospectively collected from 72 patients (68 tumors and 70 normal mucosa) with locally advanced rectal cancers. Total RNA was extracted, and tumor and mucosa microRNA expression profiles were subsequently established for all patients. The expression of selected microRNAs was validated using semi-quantitative real-time PCR.

Results: Forty-nine microRNAs were significantly differentially expressed (log2-fold difference >0.5 and P<0.001) between rectal cancer and normal rectal mucosa. The predicted targets for the identified microRNAs were enriched for the following KEGG pathways: Wnt, TGF-beta, mTOR, insulin, MAPK, and ErbB signaling. Between rectal tumor and normal tissue, miR-492, miR-542-5p, miR-584, miR-483-5p, miR-144, miR-2110, miR-652*, miR-375, miR-147b, miR-148a, miR-190, miR-26a/b, and miR-338-3p were found to be differentially expressed. Of clinical impact, miR-135b expression correlated significantly with overall survival that could be validated in a larger multicenter patient set (n=94).

Conclusion: The comprehensive analysis of the rectal cancer microRNAome uncovered novel microRNAs and pathways associated with rectal cancer. This information contributes to a detailed view of rectal cancer. The identification and validation of miR-135b will help to identify novel molecular targets and pathways for therapeutic exploitation.

overall_design: Paired samples from rectal tumor and matched normal samples. Included are also 2 technical replicates.

first: Jochen

last: Gaedcke

first: Marian

last: Grade

first: Jordi

last: Camps

first: Bogumil

last: Kaczkowski

first: Aaron

last: Schetter

first: Michael

last: Difilippantonio

first: Curtis

last: Harris

last: Ghadim

first: Søren

last: Møller

first: Tim

last: Beissbarth

first: Thomas

last: Ried

last: Litman


title: Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat

city: Hamilton

first: Elizabeth

last: Weretilnyk

state: Ontario

address: 1280 Main Street West

department: Biology

institute: McMaster University

summary:
Background: Thellungiella salsuginea is an important model plant due to its natural tolerance to abiotic stresses including salt, cold, and water deficits.  Microarray and metabolite profiling have shown that Thellungiella undergoes stress-responsive changes in transcript and organic solute abundance when grown under controlled environmental conditions.  However, few reports assess the capacity of plants to display stress-responsive traits in natural habitats where concurrent stresses are the norm.

Results:  To determine whether stress-responsive changes observed in cabinet-grown plants are recapitulated in the field, we analyzed leaf transcript and metabolic profiles of Thellungiella growing in its native Yukon habitat during two years of contrasting meteorological conditions.  We found 673 genes showing differential expression between field and unstressed, chamber-grown plants.  There were comparatively few overlaps between genes expressed under field and cabinet treatment-specific conditions.  Only 20 of 99 drought-responsive genes were expressed both in the field during a year of low precipitation and in plants subjected to drought treatments in cabinets.  There was also a general pattern of lower abundance among metabolites found in field plants relative to control or stress-treated plants in growth cabinets.  Nutrient availability may explain some of the observed differences.  For example, proline accumulated to high levels in cold and salt-stressed cabinet-grown plants but proline content was, by comparison, negligible in plants at a saline Yukon field site.  We show that proline accumulated in a stress-responsive manner in Thellungiella plants salinized in growth cabinets and in salt-stressed seedlings when nitrogen was provided at 1.0 mM.  In seedlings grown on 0.1 mM nitrogen medium, the proline content was low while carbohydrates increased.  The relatively higher content of sugar-like compounds in field plants and seedlings on low nitrogen media suggests that Thellungiella shows metabolic plasticity in response to environmental stress and that resource availability can influence the expression of stress tolerance traits under field conditions.

Conclusion: Comparisons between Thellungiella plants responding to stress in cabinets and in their natural habitats showed differences but also overlap between transcript and metabolite profiles.  The traits in common offer potential targets for improving crops that must respond appropriately to multiple, concurrent stresses.

overall_design: A custom cDNA mcroarray was used for transcript profiling. Cauline leaves from individual plants collected at a Yukon, Canada field site were used in this study.  Three samples were obtained in 2003 (Field 2003 A, B and C) and three harvested in 2005 (Field 2005 A, B and D).  Cauline leaves from 12 week old  chamber grown plants served as controls.  For each microarray experiment a technical replicate (dye swap) was performed resulting in a total of 12 hybridizations.

first: David

last: Guevara

first: Marc

last: Champigny

first: Ashley

last: Tattersal

first: Jeff

last: Dedrick

first: Chui

last: Wong

first: Y

last: Li

first: Aurelie

last: Labbe

first: Chien-Lu

last: Ping

first: Yanxiang

last: Wang

first: Paulo

last: Nuin

first: G

middle: B

last: Golding

first: Brian

last: McCarry

first: Peter

middle: S

last: Summers

first: Barbara

last: Moffatt


title: VIPR HMM: A hidden Markov model for detecting recombination with microbial detection arrays

city: St. Louis

first: Adam

middle: F

last: Allred

state: MO

address: 660 S. Euclid

institute: Washington University in St. Louis, School of Medicine

summary: In previous work, we developed a novel algorithm, VIPR, for analyzing diagnostic microarray data using a training set of empirical hybridizations of infected and uninfected samples. We have expanded up our previous implementation by incorporating a hidden Markov model (HMM) to detect recombination. We trained our HMM on a set of nonrecombinant parental viruses and applied our method to 11 recombinant alphaviruses and 4 recombinant flaviviruses hybridized to a diagnostic microarray in order to evaluate performance of the HMM. VIPR HMM identified 95% of the 62 inter-species recombinant breakpoints in the validation set and only two false positive breakpoints were predicted. This study represents the first description and validation of an algorithm capable of identifying recombination in viruses based on diagnostic microarray hybridization patterns.

sample_organism:
Chlorocebus aethiops
Alphavirus
Flavivirus

overall_design: In this study, 30 viruses including recombinant and nonrecombinant alphaviruses and flaviviruses were grown in culture and hybridized to 105 microarrays.  In addition, 9 uninfected samples were hybridized (114 total hybridizations).  These hybridizations were used to train and test a novel algorithm for detecting recombination using diagnostic microarrays.

first: Wang

last: David


title: Effect of fludioxonil treatment on candida albicans SC5314

status: Public on Oct 01 2012

city: Braunschweig

first: Anna

last: Buschart

address: Inhoffenstr. 7

department: BiSA

institute: Helmholtz-Centre for Infection Research

summary: Comparison of Candida albicans SC5314 treated with fludioxonil for 30 min and untreated controls under hyphae-inducing conditions

overall_design: 3 biologically independent replicates of a reference sample (U30) and fludioxonil treatment (F30) each

first: Robert

last: Geffers


title: Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis (time series)

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

summary: A novel experimental design strategy (A Mead et al, in preparation), based on the principle of the “loop design”, was developed to enable efficient extraction of information about key sample comparisons using a two-colour hybridisation experimental system. With 192 distinct samples (four biological replicates at each of 24 time points in mock and treated conditions) to be compared, the experimental design included 288 two-colour microarray slides, allowing four technical replicates of each sample to be observed. One third of the slides were devoted to assessment of changes in gene expression between time points, using a simple loop design to link samples from time points across the 24 sampled times, directly comparing samples collected on adjacent sampling times (i.e. 2 hrs post-infection with 4 hrs post-infection, 4 hrs post-infection with 6 hrs post-infection, etc.). With the remaining slides, four separate loops were constructed comparing treatments, biological replicates and samplling times.

overall_design: infected vs. mock, 24 time points, randomized loop, 576 Imagene files

first: Oliver

last: Windram

first: Priyadharshini

last: Madhou

first: Stuart

last: McHattie

first: Claire

last: Hill

first: Richard

last: Hickman

first: Emma

last: Cooke

first: Dafyd

last: Jenkins

first: Christopher

last: Penfold

first: Laura

last: Baxter

first: Emily

last: Breeze

first: Steven

last: Kiddle

first: Johanna

last: Rhodes

first: Susanna

last: Atwell

first: Dan

last: Kliebenstein

first: Youn-sung

last: Kim

last: Stegle

first: Karsten

last: Borgwardt

first: Cunjin

last: Zhang

first: Alex

last: Tabrett

first: Roxane

last: Legaie

first: Bärbel

last: Finkenstädt

first: David

middle: L

last: Wild

first: Andrew

last: Mead

last: Rand

first: Jim

last: Beynon

first: Sascha

last: Ott

first: Vicky

last: Buchanan-Wollaston

first: Katherine

last: Denby


title: Modulation of activation-associated host cell gene expression by the apicomplexan parasite Theileria annulata

city: Glasgow

first: William

last: Weir

address: Room 220, Henry Wellcome Building, Garscube Campus, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

summary:
The experiment investigates bovine gene expression in response to LPS in uninfected and Theileria annulata-infected cell cultures
A subset of genes are identified which are activated in response to LPS stimulation with further modulation due to parasite infection.

sample_organism:
Theileria annulata
Bos taurus

platform_organism:
Theileria annulata
Bos taurus

overall_design: Six experimental conditions with three replicates per condition. Total RNA prepared from cell cultures. BL20 (uninfected bovine lymphosarcoma cell line), BL20 4 hours post-LPS stimulation, BL20 18 hours post-LPS, TBL (T. annulata infected bovine cell line), TBL 4 hours post-LPS, TBL 18 hours post-LPS. Each hydridisation represents bovine and parasite gene expression on a single channel and 2 technical replicates of each probeset are represented on the chip.

first: Zeeshan

last: Durrani

first: Sreerekha

last: Pillai

first: Jane

last: Kinnaird

first: Brian

last: Shiels


title: Development of oligonucleotide microarray to study global gene expression profile in guinea pigs in response to tuberculosis infection

city: New Delhi

first: Anil

middle: K

last: Tyagi

state: Delhi

address: Benito Juarez Road

department: Biochemistry

country: India

institute: University of Delhi South Campus

summary: In this study we developed a guinea pig oligonucleotide microarray (GPOM) comprising of a total number of 45,220 features including 43,803 valid features from different mammalian species. These features are inclusive of 2971 newly annotated probes corresponding to 344 unique genes of guinea pig. As a case study, we utilized this array to examine the gene expression profile in guinea pig lungs in response to infection with Mycobacterium tuberculosis. Studying the global gene expression profile in guinea pigs allowed identification of the disease signature of pulmonary TB infection represented by several unique genes that are differentially regulated in this model. While, 1344 unique genes exhibited marked up regulation, 1856 genes were significantly down regulated. The newly developed tool not only finds its utility in studying the global gene expression profile associated with vaccination and/or M. tuberculosis infection in this highly useful animal model but would also be immensely useful in identification of new drug targets, testing of therapies, molecular genetic analysis for diseases other than tuberculosis as well.

overall_design: Genotypic Technology designed Custom Cavia porcellus 4x44k Gene Expression Array (Agilent-AMADID-019424) * In order to validate the GPOM developed in this study, we compared the gene expression profile of guinea pig lungs at 10 weeks post- M. tuberculosis infection with respect to that obtained from normal uninfected animals. To address this, guinea pigs were aerosol infected with M. tuberculosis, lungs were harvested at 10 weeks post-infection and RNA obtained from infected lungs was employed for cDNA synthesis and microarray hybridization. The gene expression was compared with the RNA sample obtained from the lungs of normal uninfected guinea pigs.

first: Ruchi

last: Jain

first: Bappaditya

last: Dey


title: Effects of fzr1 knockdown on senescence-associated gene expression in human diploid fibroblasts.

status: Public on Aug 01 2012

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Analysis of gene expression profile in Ras-induced senescent human diploid fibroblasts with or without depletion of fzr1/cdh1.  Results provide insight into the effect on fzr1/cdh1 on the regulation of senescence-associated gene expression in human diploid fibroblasts.

overall_design: IMR-90-ER:Ras cells were cultured for 6 days with or without 4-hydroxytamoxifen (OHT) and were subsequently subjected to transfection with siRNA oligos against fzr1/cdh1 or control for three times (at 2 day intervals).  Total RNA was isolated using Trizol reagent and were analyzed using the human 3D-Gene DNA chip (Toray) which that contains 25000 genes. The genome wide transcriptional response of proliferating cells (IMR si control2) and fzr1/cdh1 depleted senescent cells (IMR+OHT si cdh1) were compared to that of senescent cells (IMR+OHT si control).

first: Akiko

last: Takahashi

first: Eiji

last: Hara


title: Sinus Microbiome Plays a Primary Role in Rhinosinusitis

city: San Francisco

first: Susan

last: Lynch

address: 513 Parnassus Ave, S357D

institute: University of California at San Francisco

summary: Persistent mucosal inflammation and microbial infection are characteristic of Chronic Rhinosinusitis (CRS). Though mucosal microbiota dysbiosis is a characteristic feature of other chronic inflammatory diseases, the relationship between sinus microbiota composition and CRS is unknown. Here we demonstrate, using comparative microbiome profiling of a cohort of CRS patients and healthy subjects, that the sinus microbiota of CRS patients exhibit significantly reduced bacterial diversity. Characteristic of this community collapse is the depletion of multiple, phylogenetically distinct, Lactic Acid Bacteria and the concomitant increase in relative abundance of a single species, Corynebacterium tuberculostearicum. Recapitulating the conditions observed in our human cohort in a murine model confirmed the pathogenic potential of C. tuberculostearicum and the critical necessity for a replete mucosal microbiota to protect against this species. Moreover, we provide evidence that Lactobacillus sakei, identified from our comparative microbiome analyses as a potentially protective species, affords defense against C. tuberculostearicum sinus infection, even in the context of a depleted sinus bacterial community. These studies demonstrate that sinus mucosal health is highly dependent on the composition of the resident microbiota, and identifies a new sino-pathogen and a strong bacterial candidate for therapeutic intervention.

platform_organism: Bacteria Archaea

overall_design: A total of 14 samples were profiled for microbiome composition: 7 from non-sinusitis patients, and 7 from patients with clinically diagnosed chronic sinusitis.

first: Nicole

middle: A

last: Abreu

first: Nabeetha

last: Nagalingam

first: Yuanlin

last: Song

first: Frederick

middle: C

last: Roediger

first: Steven

middle: D

last: Pletcher

middle: N

last: Goldberg

middle: V


title: Lack of microRNA-101 causes E-cadherin expression and function deregulation through EZH2 up-regulation in gastric cancer

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

country: Portugal

institute: University of Aveiro

summary: Background & Aims: E-cadherin expression disruption is commonly observed in epithelial cancers and metastasis. Such event is also recognized as a crucial step in gastric cancer (GC) initiation and progression. As aberrant expression of microRNAs often perturb the normal expression and function of pivotal cancer-related genes, we characterized and dissected a pathway initiated by loss of microRNA-101 that causes E-cadherin dysfunction through upregulation of EZH2 expression in GC.  Methods: Microarrays were used to profile the expression of microRNAs in human GC. Array-CGH revealed DNA copy number changes that were validated by genomic quantitative PCR and Snapshot. Expression levels of microRNAs, mRNA and protein were determined by quantitative-real time PCR and western-blot/co-immunofluorescence. CDH1 inactivating mechanisms were analyzed. Gain and loss of function experiments were done in KatoIII cells. E-cadherin functionality was assessed by immunofluorescence and flow cytometry.    Results: MiR-101 expression was significantly decreased in tumors in comparison with normal gastric mucosas (P<.0001). In 65% of the analyzed GC cases, miR-101 downregulation was caused by deletions and/or microdeletions at miR-101-2 locus. EZH2 overexpression and consequent loss/aberrant E-cadherin expression was found in concomitance with miR-101 downregulation in 41% of the analyzed GC cases. This occurred preferentially in cases retaining allele(s) untargeted by classical CDH1 inactivating mechanisms. MiR-101 gain of function experiments or direct inhibition of EZH2, led to a strong depletion of endogenous EZH2 protein and consequent rescue of functional E-cadherin at the cell membrane, mimicking results obtained with clinical GC samples.   Conclusions:   Deletions and/or microdeletions at miR-101-2 locus underlying mature miR-101 downregulation and consequent EZH2 overexpression represented a novel cascade of genetic events leading to E-cadherin disruption, preferentially affecting the intestinal-type of GC.

overall_design: In the present study,  37 primary GCs and a pool of 10 normal gastric mucosas were used to acquire the expression of 703 known human mature miRNAs deposited in the Sanger miRBase Sequence Database, Release 10.0 (http://microrna.sanger.ac.uk), as well as 393 novel human miRNAs discovered through deep sequencing and validated by qRT-PCR and array profiling (NCode™ Human miRNA microarray probe set V3 from Invitrogen). The 10 normal gastric mucosa RNA samples were pooled to obtain the normal gastric reference sample, which was labelled and hybridised four times to check arrays' reproducibility.

first: Joana

last: Carvalho

first: Raquel

last: Seruca

last: van Grieken

first: Patricia

middle: M

first: Sónia

last: Sousa

first: Marianne

last: Tijssen

first: Tineke

middle: E

last: Buffart

first: Begoña

last: Diosdado

first: Heike

last: Grabsch

first: Manuel

last: Santos

first: Gerrit

last: Meijer

first: Beatriz

first: Carla

last: Oliveira


title: Comparison of Zmiz1-induced keratoancanthoma and normal skin

city: Iowa City

first: Adam

last: Dupuy

address: 51 Newton Road

institute: University of Iowa

summary:
Transgenic mice expressing a truncated form of Zmiz1 in the skin develop spontaneous keratoacanthomas.
In this experiment, a Cre-inducible transgene expressing a truncated form of Zmiz1 was introduced into mice.  Activation of the transgene in these mice was achieved by breeding to K14-Cre transgenic animals.  Double transgenic mice formed spontaenous keratoacanthomas with short latency.

overall_design: In this experiment, we generated gene expression profiles for five Zmiz1-induced keratoacanthomas and six normal skin samples.

middle: J


title: Comparative analysis of Calanus finmarchicus collected from surface and deep waters in Gulf of Maine

city: Groton

first: Ebru

last: Unal

state: CT

address: 1080 Shennecossett Road

department: Department of Marine Sciences

institute: University of Connecticut

summary: The marine copepod Calanus finmarchicus is the most abundant zooplankton species in the northern regions of the Atlantic Ocean and the Barents Sea. Very little is known about the molecular mechanisms underlying critical processes associated with this species’ complex life history (e.g., ontogenetic development, reproduction, molting, diapause) and physiology (e.g., digestion, neural processes, and membrane physiology). This study analyzed patterns of gene expression of C. finmarchicus samples collected from the Gulf of Maine (Northwest Atlantic Ocean) using a 1,000 expressed sequence tag (EST) microarray designed to assay genes of known physiological function and hypothesized ecological importance for C. finmarchicus. Replicate analyses compared adult females and final-stage juveniles (Copepodite-5) collected from surface (0-30m) and deep (130-170m) layers. Environmental data include detailed characterization of biological, chemical, and physical oceanographic parameters in the sampled water packets. All data were screened for artifacts, normalized and selected using a fold-change filter prior to analysis. Replicate comparisons were analyzed by Significance Analysis of Microarrays (SAM; Stanford University Labs) with a control for False Discovery Rate (FDR) and with Principle Component Analysis with evaluation of significance by one- or two-sample t-test in Acuity Microarray Informatics Software (Molecular Devices, Inc.). Gene Ontology Enrichment Analysis was carried out using GOEAST (http://omicslab.genetics.ac.cn/GOEAST/index.php) to assess functional relationships of selected genes and/or proteins. The results indicated: up-regulation of genes involved in cell division, protein synthesis and mating in deep females and juveniles; up-regulation of genes related to cellular homeostasis, circadian behavior and nervous system development in surface females; and up-regulation of genes related to muscle development and protein catabolism in deep juveniles versus deep females. KEGG pathway analysis using the Blast2GO suite (http://www.blast2go.org/) indicated: up-regulation of genes encoding enzymes related to the citrate cycle and anaerobic metabolism in deep females and juveniles; and up-regulation of genes encoding enzymes related to energy metabolism and osmoregulation in surface females.

overall_design:
Two comparisons were performed using deep females, deep CVs and surface females of C. finmarchicus.
Comparison A: Deep females versus surface females (5 replicates)
Comparison B: Deep CVs versus surface females (5 replicates)

first: Ann

last: Bucklin

first: Petra

last: Lenz

first: David

middle: W

last: Towle


title: Comparative transcriptomics of wild-type (UCD 153) and patN-deletion strains (UCD 524) of Nostoc punctiforme ATCC 29133

city: Davis

first: Douglas

last: Risser

state: California

address: One Shields Ave

department: Microbiology

institute: UC Davis

summary:
Heterocysts, cells specialized for nitrogen fixation in certain filamentous cyanobacteria, appear singly in a nonrandom spacing pattern along the chain of vegetative cells. A two-stage, biased initiation and competitive resolution model has been proposed to explain the establishment of this spacing pattern. There is substantial evidence that competitive resolution of a subset of cells initiating differentiation occurs by interactions between a self enhancing activator, HetR, and a diffusible inhibitor PatS-5 (RGSGR).
Results presented here show that the absence of a unique membrane protein, PatN, in Nostoc punctiforme strain ATCC 29133 leads to a threefold increase in heterocyst frequency and a fourfold decrease in the vegetative cell interval between heterocysts. A PatN-GFP translational fusion shows a pattern of biased inheritance in daughter vegetative cells of ammonium-grown cultures. Inactivation of another heterocyst patterning gene, patA, is epistatic to inactivation of patN, and transcription of patA increases in a patN- deletion strain, implying that patN may function by modulating levels of patA. The presence of PatN is hypothesized to decrease the competency of a vegetative cell to initiate heterocyst differentiation, and the cellular concentration of PatN is dependent on cell division that results in cells transiently depleted of PatN. We suggest that biased inheritance of cell-fate determinants is a phylogenetic domain- spanning paradigm in the development of biological patterns.

overall_design:
Change in gene expression for a wild-type (UCD 153) and patN-deletion strain, (UCD 524) of Nostoc punctiforme ATCC 29133 over the time course of heterocyst developments.

Total RNA from 3 biological replicates at each time point from 0 to 120 hours after removal of combined nitrogen (Nitrogen step-down) was converted to cDNA, dye-labled and hybridized to nimblegen 12x135k array slides.

first: Francis

last: Wong

first: John

last: Meeks


title: Targeting EWSR1-FLI1 oncogene induced protein kinase C beta abolishes Ewing sarcoma growth in vivo

status: Public on Jul 01 2012

city: Paris

first: Franck

last: Tirode

address: 26 Rue d'Ulm

department: Inserm U830

institute: Institut Curie

summary: Identification of druggable targets is a prerequisite for developing targeted therapies against Ewing sarcoma. We report the identification of Protein Kinase C Beta (PRKCB) as a protein specifically and highly expressed in Ewing sarcoma as compared to other pediatric cancers. Its transcriptional activation is directly regulated by the EWSR1-FLI1 oncogene. Getting insights in PRKCB activity we show that, together with PRKCA, it is responsible for the phosphorylation of histone H3T6, allowing global maintenance of H3K4 trimethylation on a variety of gene promoters. In the long term, PRKCB RNA interference induces apoptosis in vitro. More importantly, in xenograft mice models, complete impairment of tumor engraftment and even tumor regression were observed upon PRKCB inhibition, highlighting PRKCB as a most valuable therapeutic target. Deciphering PRKCB roles in Ewing sarcoma using expression profiling, we found a strong overlap with genes modulated by EWSR1-FLI1 and an involvement of RPKCB in regulating crucial signaling pathways. Altogether, we show that PRKCB may have two important independent functions and should be considered as highly valuable for understanding Ewing sarcoma biology and as a promising target for new therapeutic approaches in Ewing sarcoma.

overall_design: A673 Ewing cell line was treated for 72 hours by either control siRNA or siRNA directed against PRKCB or EWSR1-FLI1. Total RNAs were extracted and hybridized on HuGene1.1STv1 Affymetrix Arrays. Normalisation was performed using specific Brainarray Enrtez gene CDF file (v14.1).

first: Didier

last: Surdez

first: Olivier

last: Delattre


title: The relationship between inhibition of gastric acid secretion and eradication of Helicobacter pylori

status: Public on Sep 30 2012

city: Los Angeles

last: Scott

state: CA

address: 11301 Wilshire Blvd

institute: UCLA/VA GLAHS

summary: Background: Penicillins inhibit cell wall synthesis; therefore, H. pylori must be dividing for these antibiotics to be effective. Identifying growth responses to varying medium pH may allow design of more effective treatment regimens. Aim: To determine the effect of acidity on bacterial growth and the bactericidal efficacy of ampicillin. Methods: H. pylori were incubated in dialysis chambers suspended in 1.5L of media at various pHs with 5mM urea, with or without ampicillin, for 4, 8 or 16 hours, thus mimicking unbuffered gastric juice. Changes in gene expression, viability and survival were determined. The bacterial load of H. pylori infected gerbils was determined with and without profound acid inhibition. Results: At pH 3.0, but not at pH 4.5 or 7.4, there was decreased expression of ~400 genes, including many cell envelope biosynthesis, cell division genes and penicillin-binding proteins. In the presence of ampicillin, viability and survival declined at pH 4.5 and 7.4 but not at pH 3.0. Profound acid inhibition of H. pylori infected gerbils increased the antral bacterial load >3 fold, showing that elevation of intragastric pH stimulated growth. Conclusions: Ampicillin is bactericidal at pH 4.5 and 7.4, but not at pH 3.0, due to decreased expression of cell envelope and division genes at pH 3.0. Therefore, at pH 3.0, the pH at the gastric surface, the bacteria are non-dividing and persist with ampicillin treatment. A more effective inhibitor of acid secretion that maintains gastric pH near neutrality for 24 hours/day should enhance the efficacy of triple therapy and of amoxicillin, even allowing dual therapy for H. pylori eradication.

sample_organism: Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093

overall_design: There were a total of three biological replicates, each containing one control (incubated at pH 7.4) and one acidic (pH 3.0) sample, whose RNA were extracted on different dates. Microarray studies performed on these six samples were done in triplicate. One of the triplicates for two of the biological control triplicates were removed from the data set due to poor hybridization

first: Elizabeth

last: Marcus

first: George

last: Sachs

first: Glenn

middle: T

last: Nagami

first: Nobuhiro

last: Inatomi

middle: R


title: Changes in gene expressions associated with egg diapause in multivoltine silkworm Bombyx mori

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

overall_design: Agilent one-color experiment, Agilent-Custom : Bombyx mori 4x44k designed by Genotypic Technology Pvt. Ltd. (AMADID: 034793) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0444)

first: Kangayam

last: Ponnuvel

first: Sirigineedi

last: Sasibhushan


title: Transcriptome and proteome analysis of tyrosine kinase treated canine mast cell tumour cells identifies potentially KIT signalling-dependent genes

status: Public on Jul 25 2012

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

institute: Charité-Universitätsmedizin Berlin

summary: Canine mast cell tumour proliferation depends to a large extent on the activity of KIT, a tyrosine kinase receptor. Inhibitors of the KIT tyrosine kinase have recently been introduced and successfully applied as a therapeutic agent for this tumour type. However, little is known on the downstream target genes of this signalling pathway and molecular changes after inhibition. Transcriptome analysis of the canine mast cell tumour cell line C2 treated for up to 72 hours with the tyrosine kinase inhibitor masitinib identified significant changes in the expression levels of approximately 3500 genes representing 16% of the canine genome. Approximately 40% of these genes had increased mRNA expression levels including genes associated with the pro-proliferative pathways of B- and T-cell receptors, chemokine receptors, steroid hormone receptors and EPO-, RAS and MAP kinase signalling. Proteome analysis of C2 cells treated for 72 hours identified 24 proteins with changed expression levels, most of which being involved in gene transcription, e.g. EIA3, EIA4, TARDBP, protein folding, e.g. HSP90, UCHL3, PDIA3 and protection from oxidative stress, GSTT3, SELENBP1. Transcriptome and proteome analysis of neoplastic canine mast cells treated with masitinib confirmed the strong important and complex role of KIT in these cells. Approximately 16% of the total canine genome and thus the majority of the active genes were significantly transcriptionally regulated. Most of these changes were associated with reduced proliferation and metabolism of treated cells. Interestingly, several pro-proliferative pathways were up-regulated which may represent attempts of masitinib treated cells to activate alternative pro-proliferative pathways. These pathways may contain hypothetical targets for a combination therapy with masitinib to further improve its therapeutic effect.

overall_design: The present study aimed at identifying the transcriptional and translational responses of neoplastic canine mast cells to the tyrosine kinase inhibitor masitinib. To this end, C2 cells, a cell line with a tandem duplication in the juxtamembrane unit and thus constitutively activated KIT, were treated with masitinib and changes in the global mRNA and protein expression levels were characterized.

first: Robert

last: Klopfleisch

first: Anja

last: Meyer

first: Patricia

last: Schlieben

first: Angelika

last: Bondzio

first: Chris

last: Weise

first: Michael

last: Hummel

first: Ralf

last: Einspanier

first: Achim

last: Gruber


title: Biomarker genes highlight intraspecific and interspecific variations in the responses of Pinus taeda L. and Pinus radiata D. Don to Sirex noctilio F. acid gland secretions

status: Public on Aug 10 2012

city: Athens

first: Adam

middle: W.

last: Barb

state: GA

address: 180 E. Green Street

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: Sirex noctilio F., a Eurasian horntail woodwasp recently introduced into North America, oviposits in pines and other conifers and in the process spreads a phytopathogenic fungus that serves as a food source for its larvae.  During oviposition the woodwasp also deposits a mucus produced in its acid (venom) gland that alters pine defense responses and facilitates infection by the fungus.  A 26,496-feature loblolly pine cDNA microarray was used to survey gene expression of pine tissue responding to S. noctilio venom.  Six genes were selected for further assessment by qRT-PCR, including one that encoded an apparent PR-4 protein and another that encoded a thaumatin-like protein. Expression of both was strongly induced in response to venom, while expression of an apparent actin gene (ACT1) was stable in response to the venom.  The pattern of gene response was similar in Pinus taeda L. and P. radiata D. Don, but the magnitude of response in P. radiata was significantly stronger for each of the induced genes.  The magnitude of biomarker gene response to venom also varied according to genotype within these two species.  The qRT-PCR assay was used to demonstrate that the primary bioactive component in S. noctilio venom is a polypeptide.

overall_design: Reference design.  Two condition experiment, two time points each compared to a common reference. Two biological replicates, two technical replicates, 12 slides total, duplicate/re-scanned images submitted for each slide.

first: John

last: Bordeaux

first: W

last: Lorenz

first: Jeffrey

last: Dean


title: IL-1 Exposure Significantly increases gene expression of BDNF, NTF3 and NRP2 as well as NGF Production in Human Annulus Cells

status: Public on Jun 27 2012

city: Charlotte

first: Helen

state: NC

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

summary:
Although the degenerating disc is considered to be the key source of pain in patients with low back pain, the relationship between disc cells, nerves, and pain production is poorly understood.  Neurotrophins are signaling molecules involved in the survival, differentiation, migration, and neurite outgrowth of central and peripheral neurons.  Neurotrophins are now known to be expressed in non-neuronal tissues, including the intervertebral disc. We hypothesize that the inflammatory cytokine interleukin-1 (IL-1beta), which is produced by disc cells during degeneration, is a key element in the cascade of events involving neurotrophins.  To test this, we used an in vitro experimental design which challenged 3D-cultured human annulus cells with IL-1beta and utilized microarray analysis to evaluate neurotrophin- and nerve-related gene expression profiles in treated vs. control cells.  Analysis of nerve growth factor levels in conditioned media was also performed.
Findings presented here support the hypothesis that proinflammatory cytokines (which are produced by disc cells during degeneration) are involved with a significant increase in the expression of neurotrophins and other nerve-related genes.  Findings expand previous data on expression of neurotrophins in the degenerating disc, and provide the first documentation of expression of neurotrophin 3 and neuropilin 2.  These results have direct translational relevance because they address the primary clinical issue with disc degeneration (low back pain) and open the possibility of novel analgesic therapies based on development of specific small-molecular antagonists to neurotrophins.

overall_design: Human disc tissue samples were obtained from surgical disc procedures performed on patients with herniated discs and degenerative disc disease. Cultured annulus cells were grown in a 3D collagen construct with or without 10 2 pM IL-1 for a total of 14 days. Following homogenization in TRIzol reagent, total RNA was isolated and analyzed via mircoarray.

first: Gretchen

last: Hoelscher

first: Synthea

last: Bethea

first: Edward

last: Hanley Jr


title: RNase Y of Staphylococcus aureus and its role in the activation of virulence genes

status: Public on Jun 21 2012

first: Gabriella

last: Marincola

address: Elfriede Auhlornstr. 6

institute: IMIT - Interfaculty Institute for Microbiology and Infection Medicine

summary: RNase Y of Bacillus subtilis is a key member of the degradosome and important for bulk mRNA turnover. In contrast to B. subtilis, the RNase Y homologue (rny/cvfA) of Staphylococcus aureus is not essential for growth. Here we found that RNase Y plays a major role in virulence gene regulation. Accordingly, rny deletion mutants demonstrated impaired virulence in a murine bacteraemia model. RNase Y is important for the processing and stabilisation of the immature transcript of the global virulence regulator system SaePQRS. Moreover, RNase Y is involved in the activation of virulence gene expression at the promoter level. This control is independent of both the virulence regulator agr and the saePQRS processing and may be mediated by small RNAs some of which were shown to be degraded by RNase Y. Besides this regulatory effect, mRNA levels of several operons were significantly increased in the rny mutant and the half-life of one of these operons was shown to be extremely extended. However, the half-life of many mRNA species was not significantly altered. Thus, RNase Y in S. aureus influences mRNA expression in a tightly controlled regulatory manner and is essential for coordinated activation of virulence genes.

overall_design: Three biological replicates of both wild type and rny (cvfA) mutant bacteria were grown in complex medium until the late exponential phase at which point RNA was prepared for microarray analysis on GeneChip S. aureus Genome Array (Affymetrix). Preliminary results indicated that during the late exponential growth phase, the most prominent differences between wild type and rny mutants were observed when selected gene expression was analysed by Northern hybridisation.

first: Tina

last: Schäfer

first: Juliane

last: Behler

first: Jörg

last: Bernhardt

first: Knut

last: Ohlsen

first: Christiane

last: Goerke

last: Wolz


title: Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy

status: Public on Jul 18 2012

city: San Diego

first: Eric

last: Scott

address: 9500 Gilman Dr.

department: School of Medicine

institute: UC San Diego

summary: Autism is present in 1% of the population, yet treatments are extremely limited. We identified homozygous inactivating mutations in the BCKDK gene in families presenting with autism and epilepsy. The encoded branched chain ketoacid dehydrogenase kinase protein is responsible for phosphorylation-mediated inactivation of the E1-alpha subunit of branched chain ketoacid dehydrogenase, itself mutated in Maple Syrup Urine Disease (MSUD). Patients with homozygous BCKDK mutations display reductions in BCKDK mRNA and protein, E1-alpha phosphorylation and serum branched chain amino acids (BCAAs). Bckdk knockout mice show abnormal brain amino acids profiles and neurobehavioral defects, which are largely corrected by dietary BCAA supplementation. Thus autism presenting with epilepsy due to BCKDK mutations represent a new and potentially treatable disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A 51 chip study that includes both human and mouse samples to investigate the expression changes that result in a mutation or knockout of the BCKDK gene. Starting with human fibroblasts from three affecteds and two controls, cells were converted into IPSs, then NPCs, and finally Neurons. Each of these cell types were used to view the expression changes between a cells with a BCKDK mutation versus controls. Finally, a mouse knockout was performed to verify consistency of the expression pattern differences between the BCKCK knockout and wild-type.  Samples are labeled as Affected if the sample came from a patient with a BCKDK mutation and WildType otherwise. Samples were usually replicated once.

first: Gaia

last: Novarino

first: Joe

middle: G

last: Gleeson


title: Transcriptome analysis of the uninjured Muller glia (MG) and MG derived retinal progenitors at 4 day post injured zebrafish retina

city: Ann Arbor

first: Rajesh

last: Ramachandran

state: Michigan

address: 109 Zina Pitcher Place

department: Molecular and Behavioral Neuroscience Institute

institute: University of Michigan

summary: The study was aimed at comparing the transcriptome of MG cells of the retina with the progenitors derived from them after an injury. This information will help in the identification of factors that are responsible for the retinal regeneration.

overall_design: Muller glia were isolated by fluorescent activated cell sorting (FACS) using uninjured retinas from transgenice zebrafish (gfap:gfp) where green florescent protein (GFP) is under the control of the glial fibrillary acidic protein (gfap) promoter. MG-derived retinal progenitors were isolated by FACS at 4 days post retinal injury from 1016 tuba1a:gfp transgenic fish where GFP is driven by the tuba1a promoter which is specifically activated in these progenitors. Total RNA was isolated from these cell populations and subjected to microarray analysis to compare their transcriptomes. Samples were prepared in duplicate.

first: Daniel

last: Goldman


title: Comparative genomic hybridization of Schistosoma japonicum Chinese and Philippine isolates

status: Public on Jul 14 2012

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

institute: QIMR

summary: Chinese and Philippine strains of the blood fluke Schistosoma japonicum present clear and distinctive phenotypes in areas of fecundity, pathology, drug sensitivity and immunology. Despite these differences large scale sequencing efforts have focused solely on Chinese mainland strain of the parasite. We have undertaken a comparative genomic hybridisation (CGH) approach to highlight some of the structural differences in the genome of two of the major geographical isolates of S. japonicum. We identified seven distinct regions of the S. japonicum genome that present differential CGH between Chinese and Philippine strains of the blood fluke Schistosoma japonicum, representing either deletion or duplication regions in the Philippine strain. Within these regions, genes that may be related to phenotypical differences are identified and discussed.

overall_design: Genomic DNA was isolated from adult (7 week post cercarial challenge) Schistosoma japonicum Chinese and Philippine isolates and separate maleand femalesamples comparatively hybridised on an Agilent customn designed oligo microarray.


title: Real time quantitative PCR analysis of murine macrophages

status: Public on Aug 09 2012

city: San Antonio

first: Sarah

last: Hardison

state: Georgia

address: One UTSA Circle

institute: University of Texas at San Antonio

summary: Murine macrophages were isolated from the lungs of mice given a pulmonary challenge with C. neoformans strain H99. Mice were either given a protective (H99γ) or a mock (HKCn) immunization prior to C. neoformans H99 challenge, and macrophages were isolated from the lungs of mice 24 hours, 3 days, or 7 days post-challenge using anti-CD11b microbeads according to the Miltenyi cell sorting system. We used SA Biosciences Toll-like Receptor PCR assay panel to quantitate gene expression of signal transduction factors in total RNA isolated from macrophages derived from immunized mice compared to non-immunized.

overall_design: qPCR gene expression profiling.  Macrophages from 5 mice per group were pooled and assayed as indicated in the summary. Each experiment was performed 3 times and the resulting Ct values of each group from each experiment averaged prior to data analysis. TIme points were analyzed separately

first: S

first: F

last: Wormley


title: Oral Benzo[a]pyrene in Cyp1a1/1b1(-/-) Double-Knockout Mice: Microarray Analysis During Squamous Cell Carcinoma Formation in Preputial Gland Duct

status: Public on Sep 06 2012

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Benzo[a]pyrene (BaP) is a prototypical polycyclic aromatic hydrocarbon (PAH) found in combustion processes. Cytochrome P450 1A1 and 1B1 enzymes (CYP1A1, CYP1B1) and other enzymes can activate PAHs to reactive oxygenated intermediates involved in mutagenesis and tumor initiation; also, CYP1 enzymes can detoxify PAHs. Cyp1(+/+) wild-type (WT) and Cyp1b1(-/-) knockout mice receiving oral BaP (12.5 mg/kg/day) remain healthy for >12 months. In contrast, we found that global knockout of the Cyp1a1 gene (1a1KO) results in proximal small intestine (PSI) adenocarcinoma within 8 to 12 weeks on this BaP regimen; striking compensatory increases in PSI CYP1B1 likely participate in initiation of adenocarcinoma in 1a1KO mice. Cyp1a1/1b1(-/-) double-knockout (DKO) mice on this BaP regimen show no PSI adenocarcinoma, but instead preputial gland duct (PGD) squamous cell carcinoma (SCC) occurs by 12 weeks. Herein we compare microarray expression of PGD genes in WT, 1a1KO and DKO mice at zero, 4, 8, 12, and 16 weeks of oral BaP; about four dozen genes up- or down-regulated during the most critical time-points were further verified by qRT-PCR. In DKO mice, CYP3A59 was unequivocally identified as the BaP-inducible and BaP-metabolizing best candidate responsible for initiation of BaP-induced SCC. Striking increases or decreases were found in 26 cancer-related genes plus eight Serpin genes in DKO, but not in 1a1KO or WT, mice on this BaP regimen; of the 26, eight were RAS-related oncogenes. The mechanism by which cancer-related genes are responsible for SCC tumor progression in the PGD remains to be elucidated.

overall_design: The tissue being tested is preputial gland duct of mice. Three genotypes (WT, Cyp1a1 KO and Cyp1a1/1b1 DKO) were compared with one another, at zero, 4, 8, 12 and 16 weeks of oral BaP. The five time-points within each genotype were also compared.

last: Nebert

first: Marina

last: Galvez-Peralta

first: Zhanquan

last: Shi

first: Jing

last: Chen

first: Marian

last: Miller


title: Gene expression data at 24hrs post-siRNA transfection for HCT116 cultures transfected with either DDX5si2008, DDX5si2053, or EBNA1si1666 siRNA's or mock transfected.

status: Public on Jun 02 2012

city: Cold Spring Harbor

first: Anthony

last: Mazurek

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: HCT116 cells were transfected with two different siRNA's targeting either DDX5, an siRNA targeting EBNA1, or no siRNA (mock). The siRNA targeting EBNA1 is used as a negative control since HCT116 cells do not have the EBNA1 gene. RNA was obtained from cultures at 24hrs post-siRNA transfection using the Qiagen RNeasy Minikit (cat. # 74104) with on-column DNase digestion performed as per the manufacturer's protocol. The RNA samples were isolated at 24hrs post-siRNA transfection since this timepoint precedes an impaired G1-to-S phase cell cycle progression phenotype that is evident at 48hrs post-siRNA transfection and so may reveal gene expression changes occuring before this effect on cell cycle. RNA samples were submitted to the Cold Spring Harbor Laboratory Microarray Faciity where cDNA was prepared, labeled, and hybridized to Affymetrix GeneChip Human Gene 1.0 ST microarrays. Data from the arrays were processed using the RMA method with an up-to-data probe set definition (Biostatistics 4:249-264 and Nucleic Acids Research 33(20):e175. Gene set analysis was performed using generally applicable gene set enrichment (BMC Bioinformatics 10:161). The most differentially regulated gene ontology groups were selected with FDR q-value < 0.1.

overall_design: Expression data from 3 independent HCT116 cutures transfected with either DDX5si2008, DDX5si2053, or EBNA1si1666 and 2 independent cultures transfected with mock conditions (no siRNA) were obtained from RNA samples prepared 24hrs post-siRNA transfection. These cultures were seeded with 200,000 cells per well 24hrs prior to siRNA transfection and were grown in DMEM media supplemented with 10% fetal bovone serum. Transfections were performed using lipofectamine RNAiMAX (Invitrogen 13778-075) and the manufacturer's protocol.

first: Weijun

last: Luo

first: Bruce

last: Stillman


title: NanoString nCounter immune-related gene expression in blood sorted CD14+CD16- monocytes from sALS, fALS and HC subjects

status: Public on Jul 26 2012

city: Boston

first: Oleg

last: Butovsky

state: MA

address: 77 Avenue Louis Pasteur, Office 614

department: Center of Neurologic Diseases

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

summary:
We investigated the innate immune system in the SOD1 ALS model. We found that splenic Ly6CHi monocytes were activated and their progressive recruitment to the spinal cord, but not brain, correlated with neuronal loss. We found a decrease in resident microglia in the spinal cord with disease progression. Two months prior to disease onset, splenic Ly6CHi monocytes had an M1 signature which included increased CCR2. At one month prior to disease onset, microglia expressed increased CCL2 and other chemotaxis-associated molecules. Microglia derived from the spinal cord of SOD1 mice recruited Ly6C+ monocytes to the CNS. Treatment with anti-Ly6C mAb modulated the Ly6CHi monocyte cytokine profile, reduced monocyte recruitment to the spinal cord, diminished neuronal loss and extended survival. In humans with ALS, CD14+/CD16- monocytes (analogue of Ly6CHi monocytes) exhibited an ALS specific microRNA inflammatory signature similar to that observed in the SOD1 mouse providing a direct link between the animal model and the human disease. Thus, the SOD1-like profile of monocytes in ALS subjects may serve as a biomarker for disease stage or progression. Our results suggest that recruitment of inflammatory monocytes plays an important role in disease progression and that modulation of these cells is a potential therapeutic approach
This study used the NanoString nCounter hybridization system and the Nanostring  GX Human Immunology and Nanostring Human Inflammation assays to identify and quantitate immune-related genes in blood CD14+CD16- monocytes from ALS, MS and HC subjects

overall_design: Total RNA was isolated from FACS sorted CD14+CD16- blood-derived monocytes from sporadic sALS (n=10), fALS (n=4) and HC (n=10) subjects. RNA was profiled using the Nanostring  GX Human Immunology and Nanostring Human Inflammation assays


title: eXtreme Array Mapping (XAM) for the low leaf Cd phenotype in Arabidopsis thaliana accession CS28181

status: Public on Jul 31 2012

city: Shanghai

first: Daiyin

last: Chao

address: 300 Fenglin Road

department: Shanghai Institute of Plant Physiology and Ecology

institute: Shanghai Institutes for Biological Sciences

summary: Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5 – 2 μg Cd g-1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids.

overall_design: Genomic DNA from two F2 progeny pools (low leaf Cd pool and high leaf Cd pool) of CS28181 x Col-0 was labelled and hybridized separately to the Affymetrix SNP-tiling array AtSNPtile. The signal intensity difference between the two pools for all probes were analyzed using R scripts that are available at http://ars.usda.gov/mwa/bsasnp .

first: Dai

middle: Y

first: Ivan

last: Baxter

first: Adriano

last: Silva

first: David

last: Salt


title: Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [tiling arrays]

status: Public on Jul 30 2012

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: Investigation of whole genome gene expression level in Klebsiella pneumoniae MGH78578 grown up to mid-exponential phase in M9 minimal media supplemented with 0.2% glucose

sample_organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

overall_design: A two chip study using total RNA recovered from MGH78578 grown up to OD600nm 0.5 (mid-exponential phase) in M9 minimal media supplemented with 0.2% glucose. The high-density oligonucleotide tiling arrays used were consisted of 392,778 oligonucleotide probes spaced 30 bp apart (20-bp overlap between two probes) across the K. pneumoniae main genome and plasmids.

first: Jay

middle: S

last: Hong

first: Bernhard

middle: O

last: Palsson