title: Effects of dietary curcumin on the colon proteome and transcriptome in the Mdr1a-/- mouse model of inflammatory bowel disease

status: Public on Oct 02 2014

city: Palmerston North

first: Helge

last: Dzierzon

address: Bachelar Road

department: Bioinformatics

institute: Plant and Food Research Ltd.

summary:
This study assessed gene expression changes associated with inflammation in the colon tissue of multi-drug resistance targeted mutation (Mdr1a-/-) mice, a model of human IBD. It also tested the anti-inflammatory potential of curcumin in the colon of these mice with a particular focus on the proteome.
A colonic histological injury score was determined for each mouse to assess the level of colon inflammation in Mdr1a-/- mice, and to establish the effect of curcumin on inflammation. Insights into mechanisms of colonic inflammation in the Mdr1a-/- mice were gained using transcriptome (microarray) and proteome (2-D gel electrophoresis and LCMS protein identification) analyses. These data were compared to changes in the colon proteome in response to curcumin, and to previously described transcriptomic analyses [Nones et al, PMID: 18761777; GSE10684] in response to curcumin, in this model.

overall_design: A total of 24 male Mdr1a-/- mice, and 24 male FVB/N mice, purchased from Taconic (Hudson, NY, USA) at 4-5 weeks of age, were used for this study. 12 mice were randomly assigned to each of two different dietary groups: control (AIN-76A powdered diet), or curcumin (AIN-76A + 0.2% curcumin). At 21 and 24 weeks of age, mice were euthanized and colon samples taken for histological, microarray, and proteomics analyses. The total histology score (HIS) in the colon was determined according to previously described criteria. Total RNA was isolated using TRIzol® reagent. Colon RNA from four Mdr1a-/- mice (with high HIS) on the control diet (i.e. AIN-76A powdered diet) was compared with colon RNA from four FVB/N mice with low HIS also on the control diet (i.e. AIN-76A powdered diet). All individual RNA samples were hybridized against a common reference RNA on separate slides. The reference RNA was prepared using equimolar RNA extracts from small intestine, colon, kidney and liver of normal healthy growing Swiss mice plus RNA extracts from Swiss mouse fetuses. These data were compared with previously reported transcriptomics analysis of colon RNA from the same four Mdr1a-/- mice on the AIN-76A diet (with high HIS) compared with colon RNA from four Mdr1a-/- mice on the curcumin diet (with low HIS; Nones et al 2009, PMID: 18761777)

first: Janine

last: Cooney

first: Matthew

middle: P

last: Barnett

first: Yvonne

middle: E

last: Dommels

first: Diane

middle: T

last: Brewster

first: Christine

last: Butts

first: Warren

last: McNabb

first: William

last: Laing

first: Nicole

last: Roy


title: oxi1 transcriptome-Transcriptomic analysis on the effect of oxi1 mutation under high light.

status: Public on Oct 01 2014

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: cea13-01_oxi1 - oxi1 transcriptome - Transcriptomic analysis on the effect of oxi1 mutation under high light stress? - 5 weeks old mutannt (M) and wild type (WT) plants were exposed to high light and low temperature (1300-1350 µmol photons m-2s-1, 7°C/14°C day/night and 380ppm CO2) for 25 hours. ~100 mg fresh weight leaves were harvested, and total RNA prepared from them. For control experiments, leaves were harvested directly from the phytotron (No light stress). Three microarray comparisons were made: Mcontrol/WTcontrol, Mstress/WTstress and Mstress/Mcontrol . For each comparison, 2 biological replicates are performed.

overall_design: 6 dye-swap - genotype comparaison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Michel-

last: Havaux

first: Marie-Laure

last: Martin-Magniette


title: Comparative gene expression analysis in Artemisia annua (cv. CIM-Arogya) seedling and mature leaf tissues having contrasting artemisinin content

status: Public on Dec 31 2014

city: Lucknow

first: Ajit

middle: K.

last: Shasany

state: Uttar Pradesh

address: P.O. CIMAP

department: Biotechnology Division

country: India

institute: CSIR-Central Institute of Medicinal and Aromatic Plants

summary: Artemisia annua is known to produce the antimalarial phytomolecule artemisinin. The seedling and mature leaf of the plant represent two contrasting tissues in terms of their artemisinin content. The major objective of the present study was to use a small-scale (750 target genes) microarray of A. annua for identification of genes that are differentially expressed in the seedling and mature leaf tissues of the plant.

overall_design: The experiment aimed at studying the expression levels of target genes in A. annua. A dual channel procedure with dye-swap arrangement was adopted in the study on two samples - Seedling and Mature Leaf. The interest was to compare the expression levels of target genes in Seedling against Mature Leaf. The expression data was generated on 1,569 probes, in which each probe was replicated twice.

first: Priya

last: Nair

first: Amita

last: Misra

first: Ashutosh

middle: K

last: Shukla

first: Suman

last: Khanuja


title: Expression profiles of 186-gene signature in Italian hepatitis C virus (HCV)-related liver cirrhosis

status: Public on Aug 22 2014

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

summary:
OBJECTIVE: The number of patients with HCV-related cirrhosis is increasing, leading to a rising risk of complications and death. Prognostic stratification in patients with early-stage cirrhosis is still challenging. We aimed to develop and validate a clinically useful prognostic index based on genomic and clinical variables to identify patients at high risk of disease progression.

DESIGN: We developed a prognostic index, comprised of a 186-gene signature validated in our previous genome-wide profiling study, bilirubin (>1 mg/dL) and platelet count (<100 000/mm3), in an Italian HCV cirrhosis cohort (training cohort, n=216, median follow-up 10 years). The gene signature test was implemented using a digital transcript counting (nCounter) assay specifically developed for clinical use and the prognostic index was evaluated using archived specimens from an independent cohort of HCV-related cirrhosis in the USA (validation cohort, n=145, median follow-up 8 years).

RESULTS: In the training cohort, the prognostic index was associated with hepatic decompensation (HR=2.71, p=0.003), overall death (HR=6.00, p<0.001), hepatocellular carcinoma (HR=3.31, p=0.001) and progression of Child-Turcotte-Pugh class (HR=6.70, p<0.001). The patients in the validation cohort were stratified into high-risk (16%), intermediate-risk (42%) or low-risk (42%) groups by the prognostic index. The high-risk group had a significantly increased risk of hepatic decompensation (HR=7.36, p<0.001), overall death (HR=3.57, p=0.002), liver-related death (HR=6.49, p<0.001) and all liver-related adverse events (HR=4.98, p<0.001).

CONCLUSIONS: A genomic and clinical prognostic index readily available for clinical use was successfully validated, warranting further clinical evaluation for prognostic prediction and clinical trial stratification and enrichment for preventive interventions.

overall_design: 90 liver tissue needle biopsy specimens from patients with histologically proven cirrhosis lacking evidence and a history of hepatic decompensation or HCC.

first: Lindsay

last: King

first: Claudia

last: Canasto-Chibuque

first: Kara

last: Johnson

first: Shun

last: Yip

first: Xintong

last: Chen

first: Kensuke

last: Kojima

first: Manjeet

last: Deshmukh

first: Anu

last: Venkatesh

first: Poh

middle: S

last: Tan

first: Augusto

last: Villanueva

first: Angelo

last: Sangiovanni

first: Venugopalan

first: Milind

last: Mahajan

first: Masahiro

last: Kobayashi

first: Hiromitsu

last: Kumada

first: Massimo

last: Iavarone

last: Colombo

first: Scott

middle: L

last: Friedman

first: Josep

middle: M

last: Llovet

first: Raymond

last: Chung


title: A. baumannii Cells: oleanolic acid (OA) tretment vs. ethanol treatment (OA solvent)

status: Public on Aug 09 2014

city: seoul

first: BORA

last: SHIN

state: 성북구 안암로

country: South Korea

institute: Korea university

summary: Transcriptional profiling of Acinetobacter baumannii ATCC17978 cells comparing treated ethanol cells with oleanolic acid treated. Based on the gene expression, we performed experiments to confirm the therapeutic effect and mechanism of OA in A. baumannii.

overall_design: We performed a transcriptome anaylsis of 2 samples that are OA and ethanol treatment, respectively.

first: Bora

last: Shin

first: Park

last: Woojun


title: Transcript data affected by constitutive expression of VvMYBPAR in Arabidopsis

status: Public on Jun 03 2014

city: Higashi-Hiroshima

first: Kazuya

last: Koyama

state: Hiroshima

address: 3-7-1, Kagamiyama

department: Fundamental Reesearch Division

country: Japan

institute: National Research Institute of Brewing

summary: Constitutive expression of VvMYBPAR in Arabidopsis was found to accumulate proanthocyanidins when the plants were grown on sucrose-supplemented media to induce anthocyanins. To identify the putative targets of VvMYBPAR, the transcriptome analysis of the transgenic lines which highly express VvMYBPAR was carried out using NimbleGen microarray.

overall_design: Three transgenic lines in which VvMYBPAR were constitutively expressed under the control of 35S promoter vs. empty vector transformants were compared.

first: Nobukazu

last: Tanaka


title: MiRNA-expression based, individualized outcome prediction for the cardiovascular disease patients

status: Public on May 04 2014

city: Jinan

first: Xi

last: Li

state: Shandong

address: 44 Wen Hua West Road

department: School of Medicine

country: China

institute: Shandong University

summary: Individualized outcome prediction classifiers were successfully constructed through expression profiling of a total of 2,500 miRNAs in 13 cardiovascular disease patients and 5 healthy controls

overall_design: In the study presented here, a well-defined cohort of 13 cardiovascular disease cases and 5 healthy controls was used to acquire expression profiles of a total of 2,500 unique genes.

first: Li

last: Xi


title: Gene expression analysis of jmj30 jmj32 mutant grown at 29°C under long day conditions

status: Public on Aug 31 2014

city: Singapore

first: Toshiro

last: Ito

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary:
Analysis of loss-of-function mutants of JUMONJI30 (JMJ30) and JMJ32 in Arabidopsis thaliana (Col). JMJ30 and JMJ32 encode the histone demethylases that contain the catalytic JmjC domain.
The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. Here, we show that JMJ30 and JMJ32 encode H3K27me3 demethylases, and genes down-regulated in jmj30 jmj32 mutant are enriched for H3K27me3 targets.

overall_design: Columbia wild-type (Col WT) and jmj30 jmj32 mutant were grown at 29°C, and seedling samples were collected at 13 day-after-germination (DAG). Two independent sets of WT and jmj30 jmj32 seedling mRNA samples were used for this array.

first: Eng-Seng

last: Gan


title: Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) liver tissues from hepatocellular carcinoma patients

status: Public on Jan 31 2014

first: Yujin

last: Hoshida

summary: Background and Aims  Formalin-fixed, paraffin-embedded (FFPE) tissue is the most commonly available form of archived clinical specimens, which are often stored as thin sections on glass slides. RNA isolated from such archived section (AS) of FFPE tissue is more degraded compared to freshly cut (FC) FFPE section because of prolonged air exposure. In this study, we evaluated performance of transcriptome profiling-based disease classification in AS-FFPE tissue.  Methods  Genome-wide gene-expression profiles of 5-year-old AS-FFPE tissues of 83 hepatocellular carcinoma (HCC) and 47 liver cirrhosis samples were generated by using whole-genome DASL assay (Illumina), and compared with the profiles previously produced by using FC tissue sections from the same FFPE blocks. Previously reported 186-gene liver signature of poor prognosis was also analyzed by digital transcript counting technology (nCounter assay, NanoString). Quality of the profiles and performance of gene signature-based class prediction were systematically evaluated.  Results  RNA quality and assay reproducibility of AS-FFPE RNA were comparable to intermediate ~ poor quality FC-FFPE samples (R2 as high as 0.93). Gene-expression signal was detected in lower number of probes in AS FFPE samples compared to FC-FFPE samples (proportion of probes with present signal (%P-call): 10-60% and 70-90% in AS- and FC-FFPE profiles, respectively). Based on %P-call quality threshold of 20%, 64/88 (77%) HCC and 37/48 (77%) liver profiles were judged as having relatively good quality data with comparable inter-sample correlation. Inter-sample correlation coefficient, as a measure to detect outlier profiles due to poor RNA quality, was also lower in AS-FFPE (0.4-0.9) compared to FC-FFPE (0.6-1.0).  In the genome-wide profiling analysis, previously identified molecular subclasses of HCC tumors were reproduced in 67/83 (81%) samples, which was improved to 43/48 (90%) samples when we focused on statistically confident predictions (p<0.05). A 186-gene prognostic signature in liver cirrhosis was reproduced in 32/47 (68%) samples, which was slightly improved to 11/16 (69%) when focused on statistically significant predictions. Switch of prediction to another subclass was observed in 6% or less of the patients. nCounter assay yielded highly confident prediction: p<0.05 in 20/24 samples (83%). Switch of the prediction was observed in 2/24 samples (8%).  Conclusions  We observed decay of genome-wide transcriptional profiles in AS-FFPE tissues in a quantitative manner. However, disease classification was still possible, which suggests potential of AS-FFPE material for clinical diagnosis and prognosis. Digital transcript counting is a promising option to measure gene-expression signatures in AS-FFPE tissue.

overall_design: FFPE tissue sections (10 micron-thick) sliced from 5~16-year-old FFPE blocks and archived for 6~7 years on glass slide

first: Xintong

last: Chen


title: Gene-expression profiles of archived section of formalin-fixed paraffin-embedded (AS-FFPE) liver and tumor tissues from hepatocellular carcinoma patients (Illumina and Nanostring)

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

overall_design: Refer to individual Series


title: Adaptation of Bacillus subtilis carbon core metabolism to simultaneous nutrient limitation and osmotic challenge

status: Public on Mar 31 2014

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

summary: Here, we investigated for the first time the systems-wide response of B. subtilis to different simultaneous stresses, i.e. nutrient limitation and high osmolarity. To address the anticipated complexity of the cellular response networks, we combined chemostat experiments under conditions of carbon limitation, salt stress and osmoprotection with multi-omics analyses at the transcriptome, proteome, metabolome and fluxome levels. Our results indicate that the flux through central carbon and energy metabolism is very robust under all conditions studied. The key to achieve this robustness is the adjustment of the biocatalytic machinery to compensate for solvent-induced impairment of enzymatic activities during osmotic stress. The accumulation of the exogenously provided osmoprotectant glycine betaine helps the cell to rescue enzyme activities in the presence of high salt. A major effort of the cell during osmotic stress is the production of the compatible solute proline. This is achieved by the concerted adjustment of multiple reactions around the 2-oxoglutarate node, which drives metabolism towards the proline precursor glutamate. The fine-tuning of the transcriptional and metabolic networks involves functional modules that overarch the individual pathways.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
We applied transcriptomic, mass spectrometry-based protein, metabolite and 13C-metabolic flux analysis techniques to B. subtilis cells grown under well-controlled conditions in a glucose-limited chemostat at a growth rate of 0.1 h-1 under i) reference conditions, ii) in the presence of 1.2 M NaCl, and iii) in the presence of 1.2 M NaCl and 1 mM GB.
Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all 9 samples was labeled with Cy3.

first: Michael

last: Kohlstedt

first: Judith

last: Becker

first: Praveen

last: Sappa

first: Jörg

last: Stülke

first: Erhard

last: Bremer

first: Uwe

last: Völker

first: Christoph

last: Wittmann


title: Examination of genome-wide methylation changes in lung cancer cell lines A549 (A) and HTB56 (H) [HumanMethylation27 BeadChip experiments]

status: Public on Dec 18 2013

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

summary: Cancer cell phenotypes are partially determined by epigenetic specifications such as DNA methylation. Metastasis development is a late event in cancerogenesis and might be associated with epigenetic alterations. Here, we analyzed genome wide DNA methylation changes that were associated with pro-metastatic phenotypes in non-small cell lung cancer using the Illumina HumanMethylation27 BeadChip platform.

overall_design: We studied genome-wide methylation changes in lung cancer cell lines A549 (A) and HTB56 (H). We generated NSCLC lines with highly increased propensity to form tumor nodules in murine lungs after intravenous injections. In addition to the normal cell lines (0R) we analyzed the methylome of the the cell lines after three rounds of in vivo selection towards a highly metastatic phenotype (3R).

first: Antje

last: Hascher

first: Carsten

last: Müller-Tidow


title: affy_rose_2012_06: RhDiF1 knockdown

status: Public on Sep 12 2013

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

summary: affy_rose_2012_06 - affy_rose_2012_06 - - Study of rose perfume by comparing a wild-tpe rose with one in which the expression of a scent gene has been altered.-Study of rose perfume by comparing a wild-tpe rose with one in which the expression of a scent gene has been altered.

overall_design: 8 arrays - rose; normal vs rnai mutant comparaison

first: Stephanie

last: Huguet

first: Sylvie

last: Baudino

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis

status: Public on Apr 01 2012

summary: Reversible protein phosphorylation is an important and ubiquitous protein modification in all living cells. We report that protein arginine phosphorylation plays a physiological significant role for the regulation of protein activity. We detected 121 arginine phospho-sites for 87 proteins in the Gram-positive model organism Bacillus subtilis in vivo. Moreover, we provide evidences that arginine phosphorylations are involved in the fine-tuned signal transduction of many critical cellular processes, such as protein degradation, motility, competence, stringent and stress response. Our results suggest that in B. subtilis the activity of a protein arginine phosphatase allows a fast regulation of protein activity by protein arginine kinases and that protein arginine phosphorylations play an important role as a reversible post-translational modification in bacteria.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design:
Cells were grown under vigorous agitation at 37 °C in a defined medium  (Stülke et al., 1993, J Gen Microbiol 139, 2041-2045). Samples were taken at OD500 0.4 and 1h upon entry into stationary phase.
Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all 10 samples was labeled with Cy3.

first: Alexander

last: Elsholz

first: Stephan

last: Michalik

first: Turgay

last: Kürsad

last: Hecker

first: Ulf

last: Gerth


title: The Pitx2:miR-200c/141:noggin pathway regulates BMP signaling and ameloblast differentiation

status: Public on Jul 09 2013

city: Iowa City

first: Brad

last: Amendt

state: Iowa

address: 100 Bowen Science Building

department: Anatomy and Cell Biology

institute: University of Iowa

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: The mouse incisor is a remarkable tooth that grows throughout the animal’s lifetime. This continuous renewal is fueled by epithelial stem cells that give rise to ameloblasts, which generate enamel, and little is known about the function of specific miRNAs in this process. Here we describe the role of a novel Pitx2:miR-200c/141:Noggin regulatory pathway in dental epithelial cell differentiation. miR-200c repressed noggin, an antagonist of Bmp signaling. Pitx2 expression caused an up-regulation of miR-200c and chromatin immunoprecipitation (ChIP) assays revealed endogenous Pitx2 binding to the miR-200c/141 promoter. A positive feedback loop was discovered between miR-200c and Bmp signaling. miR-200c/141 induced expression of E-cadherin and the dental epithelial cell differentiation marker, amelogenin. In addition, miR-203 expression was activated by endogenous Pitx2 and targeted the Bmp antagonist Bmper to further regulate Bmp signaling. miR-200c/141 knockout mice showed defects in enamel formation with decreased E-cadherin and amelogenin expression and increased noggin expression. Our in vivo and in vitro studies reveal a multistep transcriptional program involving the Pitx2:miR-200c/141:Noggin regulatory pathway that is important in epithelial cell differentiation and tooth development.

overall_design: Lower incisors of 3-5 P0 WT and Pitx2-Cre;Dicer1 cKO mices from same litter were dissected and combined for RNA extraction. Two different litters were analyzed. For mRNA microarray, CodeLink Mouse Whole Genome chips (Applied Microarrays) were used according to manufacturer’s instruction (done at Genomics Core of TAMU). miRNA from P0 Lower Incisor ameloblast and cervical loops.

first: Huojun

last: Cao

first: Andrew

last: Jheon

first: Xiao

last: Li

first: Zhao

last: Sun

first: Jianbo

last: Wang

first: Sergio

last: Florez

first: Zichao

last: Zhang

first: Michael

last: McManus

first: Ophir

middle: D

last: Klein

middle: A


title: affy_infection_medicago-Comparison of plant responses upon Aphanomyces euteiches infection in wild type (A17) line and in the Mtnf-ya1-1 mutant

status: Public on Nov 01 2011

first: stephanie

last: huguet

summary: affy_infection_medicago - affy_infection_medicago - MtNF-YA1 is a transcription factor involved in the regulation of nitrogen fixing nodule organogenesis. Mtnf-ya1-1 mutant has been shown to be more resistant to Aphanomyces euteiches (Ae), a root pathogen, than the A17 wild type (WT) line. In this study we want to compare both WT and mutant plant responses, 1 and 6 days post inoculation (dpi) between WT and the Mtnf-ya1-1 mutant, in order to identify MtNF-YA1-dependent gene networks during infection. Data about non inoculated A17 control plants and infected A17 at 1 dpi have been already obtained in another experiment in which the conditions of in vitro culture of M. truncatula plants and ofA.euteiches(Ae) inoculation were exactly the same than the ones used in these experiments.-Fifteen-day-old A17 or Mtnf-ya1-1 plants were grown in vitro on M medium. The entire roots were then inoculated (or not = controls) with a A. euteiches zoospores (105/ml) and harvested one or six days after inoculation. Three independent repeats were performed.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 12 arrays - Medicago; normal vs disease comparison,normal vs ems mutant comparison,time course

first: Christophe

last: Jacquet

first: Stephanie

last: Huguet

first: Andreas

last: NIEBEL

last: Balzergue


title: MeDIP for ten early passage melanoma cell cultures

status: Public on May 28 2014

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

type: Methylation profiling by genome tiling array

summary: Malignant melanoma is the most fatal skin cancer with a high degree of genetic and epigenetic aberrations. To investigate the role of DNA methylation on melanoma heterogeneity, we performed methylated DNA immunoprecipitation (MeDIP) microarray analysis of 10 primary melanoma cell cultures.

first: P

middle: F


title: Mnase-seq for six histone mutants and two wild-types in S. cerevisiae

status: Public on Dec 05 2012

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown.   Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4.   Histone residues grouped by expression change similarity displayed overall structural relevance.  This regulatory functional map of the core histones led to novel findings.   First, the residues specific to each histone family tend to be more influential than those commonly found among different histones.   Second, unlike histone acetylations, H3K4 trimethylation does not appear to be prerequisite for gene activation.   Third, H3Q5 has been newly identified for its putative interactions with many chromatin regulators for transcription control.   Lastly, the nucleosome lateral surface seems to play a key role through interactions with the surrounding DNA. Remarkably, we discovered a novel role for H3K56 in chromatin dynamics.   The deletion of this residue, but not the alteration of acetylation states, caused a genome-wide decrease in nucleosome mobility and stabilized nucleosome positioning near transcription start and end sites.   Occupying the DNA entry/exit site, H3K56 is thought to modulate nucleosome sliding along DNA.   Taken together, genomics approaches such as microarray and deep sequencing prove valuable for mapping the function of histone residues.
SUBMITTER_CITATION: Global Mapping of the Regulatory Interactions of Histone Residues, Epigenomics Keystone Symposium, January 21th (2012).

overall_design: Performing Mnase-seq for six histone mutants and two wild-types in Saccharomyces cerevisiae

first: Jungkyoon

last: Choi


title: Comparison of Apis mellifera workers and queens hind leg development at prepupal stages

status: Public on Feb 15 2012

city: Piracicaba

first: Ana

middle: Durvalina

last: Bomtorin

state: São Paulo

address: R Ajudante Albano 847

country: Brazil

institute: Universidade de Sao Paulo

summary: In Apis mellifera, the female eggs can develop into workers or queen depending on the diet offered during early development. The outputs of the developed honeybee females are two morphs with particular morphological traits and related physiology. Among the specialized structures in workers the hind tibia forms the corbicula or the pollen basket, a smooth region surrounded by a row of a long scopal hairs, used for carrying pollen and other materials to the nest. This morphological trait and the respective behaviour are absent in queens. Herein we show details of the initial steps of hind legs morphogenesis in honeybee castes. Using results from the hybridization of whole genome-based oligonucleotide arrays with RNA samples from hind leg imaginal discs of pre-pupa honeybees of both castes we present a list of differentially expressed genes.

overall_design: Analysis used one dye-swap combination to compare workers and queens hind leg development at prepupal stages when juvenile hormone titers is much higher in queens

first: Angel

middle: R

last: Barchuk

first: Zila

last: Simoes


title: Transcriptome analysis of Bacillus subtilis in response to air plasma treatment

status: Public on Aug 22 2013

first: Ulrike

last: Mäder

summary:
In this study, we present a follow up investigation on the effects of argon plasma on vegetative growing Bacillus subtilis 168 (see GSE27113). A growth chamber system suitable for low temperature gas plasma treatment of bacteria in liquid medium enabled a first glimpse on the
complex cellular response. In order to gain further knowledge, a second kind of plasma treatment was applied and combined proteomic and transcriptomic analyses were used to investigate the specific stress response of B. subtilis cells to treatment with not only argon but also
air plasma. Besides similar cellular responses, due to both argon and air plasma treatment, a variety of different responses such as growth retardation and morphological changes were observed. Furthermore, we analyzed the specific response to DNA damages and oxidative stress.
The biological findings such as oxidative stress responses were supported by the detection of reactive plasma species by OES and FTIR measurements.

overall_design:
Cells were grown in LB medium. At OD540 of 0.5, air plasma treatment was set for 15 min with a discharge power of 7.4 W. Samples for mircroarray analysis were taken 5 min after the 15 min plasma treatment.
Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all samples was labeled with Cy3.

first: Theresa

last: Winter

first: Jörg

last: Bernhardt

first: Jörn

first: Rabea

last: Sietmann

first: Klaus-Dieter

last: Weltmann

last: Hecker

first: Harald

last: Kusch


title: Structural mapping of regulatory function of histone H3 and H4 residues


title: Transcriptome analysis of Bacillus subtilis in response to physical plasma treatment

status: Public on Jun 01 2011

summary:
In this study, we introduce for the first time a growth chamber system suitable for physical plasma treatment of bacteria in liquid medium. Bacillus subtilis 168 cells were treated with argon plasma in order to investigate their specific stress response usong a proteomic and
transcriptomic approach. The treatment with three different discharge voltages revealed not only growth differences, but also clear cellular stress responses. B. subtilis faces severe cell wall stress, which was made visible alsoelectron microscopy, DNA damages and oxidative
stress. The biological findings could be supported by the reactive plasma species, found by plasma diagnostics, i.e. optical emission spectroscopy (OES) and Fourier transformed infrared spectroscopy (FTIR).

overall_design:
Cells were grown in LB medium. At OD540 of 0.5, argon plasma treatment was set for 15 min with a discharge power of 5 W. Samples for mircroarray analysis were taken 5 min after the 15 min plasma treatment.
Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all samples was labeled with Cy3.

first: Martin

last: Polak

first: Kathrin

last: Ehlbeck

first: Michael

first: Sacha

last: van Hijum


title: S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics

status: Public on Jul 04 2011

summary: Protein S-thiolation is a post-translational thiol-modification that controls redox-sensing transcription factors and protects active site cysteine residues against irreversible oxidation. In Bacillus subtilis the MarR-type repressor OhrR was shown to sense organic hydroperoxides via formation of mixed disulfides with the redox buffer bacillithiol (Cys-GlcN-Malate, BSH), termed as S-bacillithiolation. Here, we have studied changes in the transcriptome and redox proteome caused by the strong oxidant hypochloric acid in B. subtilis. The expression profile of NaOCl stress is indiciative of disulfide stess as shown by the induction of the thiol- and oxidative stress-specific Spx, CtsR and PerR regulons. Thiol redox proteomics identified only few cytoplasmic proteins with reversible thiol-oxidations in response to NaOCl stress that include GapA and MetE. Shotgun-LC-MS/MS analyses revealed that GapA, Spx and PerR are oxidized to intramolecular disulfides by NaOCl stress. Furthermore, we identified six S-bacillithiolated proteins in NaOCl-treated cells, including the OhrR repressor, two methionine synthases MetE and YxjG, the inorganic pyrophosphatase PpaC, the 3-D-phophoglycerate dehydrogenase SerA and the putative bacilliredoxin YphP. S-bacillithiolation of the OhrR repressor leads to up-regulation of the OhrA peroxiredoxin that confers together with BSH specific protection against NaOCl. S-bacillithiolation of MetE, YxjG, PpaC and SerA causes hypochlorite-induced methionine starvation as supported by the induction of the S-box regulon. The mechanism of S-glutathionylation of MetE has been described in Escherichia coli also leading to enzyme inactivation and methionine auxotrophy. In summary, our studies discover an important role of the BSH redox buffer in protection against hypochloric acid by S-bacillithiolation of the redox-sensing regulator OhrR and of four enzymes of the methionine biosynthesis pathway.

overall_design: The B. subtilis 168 wild type strain was grown in minimal medium to OD500 of 0.4 and harvested before and 10 minutes after exposure to 50 µM NaOCl. Microarray hybridizations were performed in triplicate using RNA isolated from independent cultures.

first: Bui

last: Chi

first: Katrin

last: Gronau

first: Bernd

last: Hessling

first: Dörte

last: Becher

first: Haike

last: Antelmann


title: Gene expression changes upon the mutation of individual residues of histone H3 and H4

first: Inkyung

last: Jung

summary:
Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown.  Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4. Histone residues grouped by expression change similarity displayed overall structural relevance.  This regulatory functional map of the core histones led to novel findings.  First, the residues specific to each histone family tend to be more influential than those commonly found among different histones. Second, unlike histone acetylations, H3K4 trimethylation does not appear to be prerequisite for gene activation.  Third, H3Q5 has been newly identified for its putative interactions with many chromatin regulators for transcription control. Lastly, the nucleosome lateral surface seems to play a key role through interactions with the surrounding DNA. Remarkably, we discovered a novel role for H3K56 in chromatin dynamics.  The deletion of this residue, but not the alteration of acetylation states, caused a genome-wide decrease in nucleosome mobility and stabilized nucleosome positioning near transcription start and end sites. Occupying the DNA entry/exit site, H3K56 is thought to modulate nucleosome sliding along DNA. Taken together, genomics approaches such as microarray and deep sequencing prove valuable for mapping the function of histone residues.
SUBMITTER_CITATION: Global Mapping of the Regulatory Interactions of Histone Residues, Epigenomics Keystone Symposium, January 21th (2012).

overall_design: Microarray analysis was performed for 123 histone mutants and four wild-types as two reaplications of H3 and H4 of Saccharomyces ceravisiae.

first: Jung

last: Choi


title: Phenotype Enhancement Screen of a Regulatory spx Mutant Unveils a Role for the ytpQ Gene in the Control of Iron Homeostasis.

status: Public on Oct 25 2011

first: Ulrike

last: Mäder

summary: Spx is a global regulator of genes that are induced by disulfide stress in Bacillus subtilis. Most of the Spx-regulated genes (SRGs) are of unknown function, but many encode products conserved in low %GC Gram positive bacteria. Using a gene-disruption library of B. subtilis genomic mutations, the SRGs were screened for phenotypes related to Spx-controlled activities, such as growth in minimal medium and sensitivity to methylglyoxal, but nearly all of the SRG mutations showed little if any phenotype. To uncover SRG function, the mutations were rescreened in an spx mutant background to determine which mutant SRG allele would enhance the spx mutant phenotype. One of the SRGs, ytpQ, was the site of a mutation that, when combined with an spx null mutation, elevated the severity of the Spx mutant phenotype, as shown by reduced growth in a minimal medium and by hypersensitivity to methylglyoxal. Proteomic and transcriptomic data indicated that the ytpQ mutation caused the derepression of the Fur and PerR regulons, as well as heightened LexA-controlled gene expression. Our study suggests that the ytpQ gene, encoding a conserved DUF1444 protein, functions directly or indirectly in repairing or stabilizing Fe-bearing proteins, which are sensitive to thiol reactive agents and, therefore, likely influenced by Spx-controlled genes.

overall_design: The wild type parent, ytpQ and spx mutants were grown in a glucose minimal medium, with and without 2.8 mM methylglyoxal, to mid-log phase. Cells were harvested and RNA was extracted for microarray hybridization analysis to determine if any changes in the transcriptome could be detected that were attributable to the ytpQ mutation. Microarray hybridizations were performed with RNA from three biological replicates.

first: Shefali

last: Chauhan

first: Praseeda

last: Pilaka

first: Michiko

last: Nakano

first: Sairam

last: Gurumoorthy

first: Peter

last: Zuber


title: Genes involved in thoracic exoskeleton formation during the pupal-to-adult molt of a social insect model, Apis mellifera

status: Public on Dec 29 2012

city: Ribeirão Preto

first: Michelle

middle: Prioli Miranda

last: Soares

address: Bandeirantes avenue, 3900

department: Genetics

institute: USP

summary: The exoskeleton gives to insects its shape, waterproofing and a range of other roles, besides serving as means of locomotion, the motor function being accomplished by the attachment of somatic muscles. Exoskeleton is renewed every time the insect molts under the control of ecdysteroid hormones. The last molt, which in the holometabolous transforms pupae in adults, involves biosynthesis of the definitive exoskeleton by the subjacent epidemis, followed by progressive differentiation. We used whole genome-based oligonucleotide microarray hybridization and RNA extracted from the honey bee thoracic dorsum, at three time-points of the pupal-to-adult molt, as a strategy to screen genes involved in exoskeleton formation. Gene ontology analysis separated the differentially expressed genes (DEGs) in distinct Biological Processes and Molecular Functions dependently on the time-point approached, thus revealing the functional categories required for adult exoskeleton formation.  Approximately 546 of a list of 1253 unique DEGs were up-regulated in the thoracic dorsum during adult cuticle formation, including 23 among the 24 identified cuticle protein (CP) genes, and 29 muscle-related genes. Conserved sequence motifs allowed to include the CP genes in the CPR, Tweedle, Apidermin, CPF, CPLCP1 and Analogous-to-Peritrophins families. Two genes, which do not pertain to any known CP families, were abundantly expressed in the epidermis during adult cuticle formation as shown by in situ hybridization, thus strongly suggesting that they are genuine CP genes. The search for cis-regulatory motifs in the 5’untranslated region of the DEGs revealed potential binding sites for known transcript factors. Several of them were shared by CP genes and thoracic muscle genes, thus allowing to infer that they are co-regulated during differentiation of the thoracic exoskeleton. Together, these data add new information on molecular aspects of exoskeleton formation in the context of the ecdysteroid-coordinated pupal-to-adult molt.

overall_design: The microarray experiments compared differential gene expression in the thoracic integuments of newly-ecdysed pupae (Pw phase), pupae-in-apolysis (Pp phase) and pharate-adults (Pbl phase) collected at the same time from a single honey bee colony. Two separate pools of 10 thoracic integuments each were prepared for each developmental phase (Pw, Pp and Pbl). Dye swaps were done for each comparison and two slides were used to evaluate the differential expression.

first: Angel

last: Barchuk

first: Ana

middle: C

last: Simões

first: Márcia

last: Bitondi


title: RNA processing in Bacillus subtilis: Identification of targets of the essential RNase Y

status: Public on Sep 01 2011

summary: RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other Gram-positive bacteria. Recently, the essential endoribonuclease RNase Y has been discovered in B. subtilis. This RNase is involved in the degradation of bulk mRNA suggesting a major role in mRNA metabolism. However, only a few targets of RNase Y have been identified so far. In order to assess the global impact of RNase Y, we compared the transcriptomes of strains expressing RNase Y or depleted for RNase Y. Our results indicate that processing by RNase Y results in accumulation of about 80 mRNAs. Some of these targets were substantially stabilized by RNase Y depletion, resulting in half-lives in the range of an hour. Moreover, about 40 mRNAs were less abundant when RNase Y was depleted among them the mRNAs of the operons required for biofilm formation. Interestingly, overexpression of RNase Y was sufficient to induce biofilm formation. The results emphasize the importance of RNase Y for B. subtilis and are in support of the idea that RNase Y is the functional equivalent of RNase E.

overall_design: To study the global function of RNase Y, a microarray analysis was performed with a B. subtilis strain allowing controlled depletion of RNase Y. Strain GP193 (Commichau et al., 2009, Mol. Cell. Proteomics 8: 1350-1360) expressing the rny gene under the control of a xylose-inducible promoter was cultivated in CSE minimal medium in the presence or absence of the inducer xylose. The transcriptomes of the two cultures (i.e. expressing RNase Y and depleted for RNase Y) were compared at a timepoint at which the reduced RNase Y amounts already affected the mRNA turnover whereas the growth rates of the two cultures were still almost identical.

first: Martin

last: Lehnik-Habrink

first: Marc

last: Schaffer

first: Christine

last: Diethmaier

first: Fabian

last: Rothe

first: Christina

last: Herzberg

first: Jörg

last: Stülke


title: Transcriptome analysis of glucose starved Bacillus subtilis cells

status: Public on Dec 01 2010

summary: In this study, temporal changes in the proteome, transcriptome and extracellular metabolome of B. subtilis caused by glucose starvation were monitored. For proteomic profiling, a combination of in vivo metabolic labeling and shot gun mass spectrometric analysis was carried out for five different proteomic subfractions (i. cytosolic, ii. extracellular, iii. membrane, iv. integral membrane, and v. surface proteome fraction) leading to the identification of about 52% of the predicted proteome of B. subtilis. Acquired proteomic and transcriptomic data were analyzed using Voronoi treemaps which link functional classifications and relative expression changes of gene products according to their fate in the stationary phase. The data obtained enables for in-depth analysis of major physiological processes including protein degradation and is the first comprehensive profiling of changes in the membrane subfraction.

overall_design: Cells were grown in a minimal medium with glucose and L-malate (0.05 % each) to induce glucose starvation after growth to an OD500 of 1.0. Samples were taken at different time points along the growth curve (exponential growth, transition phase, transition phase +30, +60 and +120 minutes). Microarray hybridizations were performed with RNA from two biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all 10 samples was labeled with Cy3.

first: Andreas

last: Otto

last: Bernhardt

first: Hanna

last: Meyer

first: Florian

last: Herbst

first: Juliane

last: Siebourg

first: Michael

last: Lalk

last: Hecker

first: Dörte

last: Becher


title: Confirmation of the gene expression pattern in Mxi1-deficient mouse (time course)

status: Public on Mar 31 2008

city: Seoul

first: Min Joo

last: Lee

address: Hyochangwon-gil 52, Yongsan-ku

department: Department of Biological Science

institute: Sookmyung Women's University

summary:
For final aim to completes network map between gene that is concerned in cystogenesis, verifies meaning genes connected with cyst formation analyzing gene pattern in time-dependent Mxi1 KO mouse that have phenotype of polycystic kidney disease. Monitoring meaning genes through microarray analysis, and confirm the function of these genes. Also, find pathway including meaning genes and new pathway related with PKD. Completes network map concerned in time-dependent cystogenesis through integrates knowing pathway and predicting pathway. Develope diagnostic of cyst disease and cure target through such completed network map, and wish to clear new role of cyst formation connection gene through in vivo model and examine closely control system of cyst formation mechanism.
Keywords: time course

overall_design: Use 1 mouse at each time experiment and control(total 12 mice). Indirect labeling of 10g cRNA, using bacterial control mRNA.

first: M

first: K

last: Yoo

first: J

last: Park


title: Molecular evidence and gene expression profiles implicating involvement of Human Papilloma Virus in human retinoblastoma

status: Public on May 21 2008

city: Mexico City

first: Martha

middle: Veronica

last: Ponce-Castañeda

address: Av. Cuauhtemoc 330

department: Hospital de Pediatría, CMN SXXI

country: Mexico

institute: Instituto Mexicano del Seguro Social IMSS

summary: Bilateral retinoblastoma has served as a critical model for studying genetic predisposition to cancer, however international incidence of unilateral retinoblastoma is variable across populations suggesting the involvement of environmental factors. DNA from Human Papilloma Virus (HPV) has been found in human retinoblastoma tissue through polymerase chain reaction based methods in several independent reports. To search for HPV oncoproteins and characterize transcriptional profiles in retinoblastoma, we analyzed tumor tissue obtained after enucleation and cultured for one week from 13 previously untreated Mexican children with retinoblastoma.  We identified the presence of E7 HPV oncoproteins using western blot analysis in HPV positive tumors, and using non-supervised methods of classification on gene expression microarrays data, tumors clustered according to the presence or absence of HPV DNA identified by PCR. These methods were unable to discriminate retinoblastoma tissues by laterality. 2,404 genes were differentially expressed between HPV positive and HPV negative retinoblastoma, including a group of genes involved in a transcriptional response to viral infection. This molecular evidence supports the hypothesis that HPV is involved in the molecular pathogenesis of these tumors.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design:
The 13 children and tumors examined here, are incident cases participating in a larger case-control study at two Pediatric Hospitals of third level of medical attention in Mexico City, that form part of the public health system.
Nine different tumors positive and four negative to HPV by PCR were included in the experimental design. From these, seven are unilateral and six are bilateral and are considered biological replicas. Two unilateral and two bilateral cases were chosen to make technical replicas.
From the surgical specimens, two tumor portions were obtained, one was frozen, DNA was extracted from it, and HPV status was assigned using MY09 and MY11 primers by PCR. Another portion of tumor tissue was used to grow in culture, separating viable cells from non viable cells through a ficoll gradient. In the eye, retinoblastoma usually grows into the vitreous which has no cells, and thus the tissue obtained is predominantly formed by tumor cells and few endothelial cells from capillaries in the tumor. Retinoblastoma  grow in culture as non adherent cells, and when adherent cells were also present, cell suspension was moved to a new dish to keep retinoblastoma cells as the main or only cellular type as possible.
We used a two channel platform with in house spotted microarrays. Since retinoblastoma has known classes: uni and bilateral, we sought to verify these classes or discover new, we used a class discovery approach and a reference experimental design. As the reference sample we used RNA form exponentially growing Saccharomyces cerevisiae because major signaling pathways and basic cellular processes among Saccharomyces cerevisiae and mammalian cells including cell cycle control and DNA repair mechanisms have a high degree of conservation. Also because yeast is easy to grow, and thus a reliable and robust source of reference RNA.

first: Verónica

first: Juan

last: Burgueño-Ferreira

first: J.

last: Bravo

first: G.

last: Ramón

first: A.

last: Hernández-Angeles

first: K.

last: Fernández-Hernánddez

first: D.

last: León García

first: V.

last: Bautista-DeLucio

first: M.

last: Ramírez-Ortiz

last: Cabrera-Muñoz

first: S.

last: Sadowinsky-Pine

last: Ramírez

last: Coello

first: F.

last: López-Casillas

last: Orjuela