title: LSD1, EDS1 and PAD4 Conditionally Regulate Cellular Signaling Homeostasis, Photosynthesis, Water Use Efficiency and Seed Yield in Arabidopsis

status: Public on Feb 07 2013

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: There is growing evidence that for a comprehensive insight into the function of plant genes it is crucial to assess their functionalities under a wide range of conditions. In this study we examined the role of LESION SIMULATING DISEASE1 (LSD1), ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) in the regulation of photosynthesis, water use efficiency (WUE), ROS/hormonal homeostasis and seed yield in Arabidopsis thaliana grown in the laboratory and in the field. We demonstrate that the LSD1 null mutant (lsd1), which is known to exhibit a runaway cell death in non-permissive conditions, proves to be more tolerant to combined drought and high-light stress than the wild type. Moreover, depending on growing conditions, it shows variations in WUE, salicylic acid and hydrogen peroxide concentrations, photosystem II maximum efficiency and in transcription profiles. However, despite these changes, lsd1 demonstrates similar seed yield under all tested conditions. All of these traits depend on EDS1 and PAD4. The differences in the pathways prevailing in the lsd1 in various growing environments are manifested by the significantly smaller number of transcripts deregulated in the field compared to the laboratory, with only 43 commonly regulated genes. Our data indicate that LSD1, EDS1 and PAD4 participate in the regulation of various molecular and physiological processes that influence Arabidopsis fitness. On the basis of these results we emphasize that the function of such important regulators as LSD1, EDS1 and PAD4 should be studied not only under stable laboratory conditions, but also in the environment abounding in multiple stresses.

overall_design: Six genotypes x two conditions experiment including five-week-old WT (Ws), lsd1, pad4, eds1, eds1lsd1, and pad4lsd1 plants grown in laboratory or field conditions, hybridized in two loop-designs (lab and field). Two biological replicates. In total, 2 x 12 samples were hybridized on 24 Arabidopsis Gene Expression microarrays V4 (Agilent, two-color array) including color swap of replicate samples.

first: W

last: Wituszyńska

first: I

last: Ślesak

first: S

last: Vanderauwera

first: M

last: Szechyńska-Hebda

first: A

last: Kornaś

first: B

last: Karpińska

first: F

last: Van Breusegem

last: Karpiński

first: P

last: Mühlenbock

last: Maćkowski

first: K

last: Van Der Kelen


title: Response to low R/FR light ratio in wt and brc1 mutant Arabidopsis axillary buds

status: Public on Feb 28 2013

city: Campus de Cantoblanco

first: Pilar

last: Cubas

state: Madrid

address: Darwin 3

department: Plant Molecular Genetics

country: Spain

institute: CNB-CSIC

summary: To study the transcriptomic profile of wt and brc1 mutant axillary buds during the shade avoidance response, we simulated a canopy shade with a low R/FR light ratio. We treated plants with white light supplemented with far-red light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 146 μeinstein · m-2 seg-1) for 8 hours. Control plants were left for 8 hours in white light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 2.2 μeinstein · m-2 seg-1) .

overall_design: Six biological replicates of 7-8 plants were collected for each genotype and condition (wt WL, wt FR, brc1 WL, brc1 FR). Samples were compared wt WL vs wt FR and brc1 WL vs brc1 FR.

first: Eduardo

last: González-Grandío


title: Expression profiles of primary bone marrow derived mouse macrophages – untreated and treated with LPS or LPS+PGE

status: Public on Feb 06 2013

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

summary:
The polarization of macrophages into an anti-inflammatory or regulatory phenotype plays an important role in resolving inflammation.  PGE2 regulates macrophage polarization via a PKA dependent pathway.  PKA phosphorylates SIKs, inhibiting their ability to phosphorylate CRTC3 in cells.  This in turn allows CRTC3 to translocate to the nucleus where it acts as a co-activator with the transcription factor CREB to induce IL-10 transcription.   In line with this we find that either genetic or pharmacological inhibition of SIKs mimics the effect of PGE2 on IL-10 production.
We show here that PGE2, in combination with LPS, is able to promote a regulatory like phenotype in macrophages characterized by high expression of IL-10 as well as the regulatory markers SPHK1 and LIGHT.

overall_design: Gene expression profiles of primary bone marrow derived mouse macrophages treated with LPS or LPS+PGE and untreated controls were generated using Affymetrix mouse gene 1.1 ST arrays. In total, 12 arrays were generated from the three groups (LPS, LPS+PGE and control) with 4-replicates in each group. One sample from LPS group was removed due to QC issues and the remaining 11 that were used in our analyses are submitted here.

first: Simon

middle: J

last: Arthur

middle: A

first: Geoffrey

last: Barton

first: Suzzane

last: Elcombe

first: Kirsty

last: MacKenzie


title: PYR/PYL receptors play a major role for regulation of transcriptional response to abscisic acid

status: Public on Nov 30 2012

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

institute: IBMCP (UPV-CSIC)

summary: Abscisic acid (ABA) is a key hormone for plant growth, development and stress adaptation. Perception of ABA through four types of receptors has been reported. We show here that impairment of ABA perception through the PYR/PYL/RCAR branch reduces vegetative growth and seed production, and leads to a severely open stomata and dramatic ABA insensitive phenotype, even though other branches for ABA perception remain functional. Arabidopsis sextuple mutant impaired in 6 PYR/PYL receptors, namely PYR1, PYL1, PYL2, PYL4, PYL5 and PYL8, was able to germinate and grow even on 100 mM ABA. Whole-rosette stomatal conductance (Gst) measurements revealed that leaf transpiration in the sextuple pyr/pyl mutant was higher than in the ABA-deficient aba3-1 or ABA-insensitive snrk2.6 mutants. The gradually increasing Gst values of plants lacking three, four, five and six PYR/PYLs indicate quantitative regulation of stomatal aperture by this family of receptors. The sextuple mutant lacked ABA-mediated activation of SnRK2s and ABA-responsive gene expression was dramatically impaired as was reported in snrk2.2/2.3/2.6. In summary, these results show that ABA perception by PYR/PYLs plays a major role to regulate seed germination and establishment, basal ABA signaling required for vegetative and reproductive growth, stomatal aperture and transcriptional response to the hormone.

overall_design: Four biological replicates were generated for the 3 genotypes, pyr1pyl1pyl2pyl4pyl5pyl8 sextuple mutant, snrk2.2/2.3/2.6 triple mutant, and Col-0. All the samples were treated with ABA for 3 hours before harvesting. The four Col-0 samples were mix to create an unique reference Col-0 sample. Two comparasion were made, fisrt one, PYR/PYL sextuple mutant versus Col-0 reference sample and second one, SnRK2 triple mutant versus Col-0 reference sample. In each comparasion four biological replicates were made. Replicas number 1 and 2 were labeled with Cy5 for the mutant sample and Cy3 for the Col-0 reference sample, while the other two replicas,#3 and #4, were reversed-labeled.

first: Miguel

last: Gonzalez-Guzman

first: Gaston

last: Pizzio

first: Regina

last: Antoni

first: Ebe

last: Merilo

first: George

middle: W

last: Bassel

first: Maria

last: Fernandez

first: Michael

last: Holdsworth

last: Perez-Amador

first: Hannes

last: Kollist

first: Pedro

middle: L

last: Rodriguez


title: Agilent data from Arabidopsis thaliana enriched guard cell tissue and leafs.

status: Public on Jan 14 2013

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

summary: To identify genes of the guard cell transcriptome of Arabidopsis thaliana enriched guard cell samples were compared with total leaf tissue. Genes of the abscisic acid and humidity response of Arabidopsis thaliana guard cells were identified by treatment with ABA-Spray and low humidity.

overall_design: total samples analysed are 24: 4 biological independent replicates of: total leaf (COL-0) vs. enriched guard cells (COL-0); ABA-sprayed enriched guard cells (gl1-1) vs. control-sprayed enriched guard cells (gl1-1); low humidity (20%rh) treated enriched guard cells (COL-0) vs. high humidity (80%) treated enriched guard cells (COL-0)

first: Hubert

last: Bauer

first: Peter

last: Ache

first: Silke

last: Lautner

first: Jörg

last: Fromm

first: Wolfram

last: Hartung

first: Khaled

last: Al-Rasheid

first: Sophia

last: Sonnewald

first: Uwe

first: Nicole

last: Lachmann

first: Ralf-Rainer

last: Mendel

first: Florian

last: Bittner

first: Alistair

last: Hetherington

first: Rainer

last: Hedrich


title: Alterations in cardiac DNA methylation in human dilated cardiomyopathy

status: Public on Dec 18 2012

city: Heidelberg

first: Benjamin

last: Meder

state: Baden-Württemberg

address: Im Neuenheimer Feld 350

department: Internal Medicine III

institute: University Heidelberg

summary: This project analyzes genome-wide cardiac DNA methylation in patients with idopathic DCM and control individuals

overall_design: Given are datafiles from n = 8 controls (patients after Htx) and n = 9 patients with idopathic DCM. The datasets have been normalized together with other beadchip files not subject to this study. Methylation profiles were generated from human left ventricular myocardium DNA.

first: Jan

last: Haas

first: Karen

middle: S

last: Frese

first: Yoon

last: Park

first: Andreas

last: Keller

first: Britta

last: Vogel

first: Anders

middle: M

last: Lindroth

first: Dieter

last: Weichenhan

first: Jennifer

last: Franke

first: Simon

last: Fischer

first: Andrea

first: Sabine

last: Marquart

first: Farbod

last: Sedaghat-Hamedani

first: Elham

last: Kayvanpour

first: Doreen

last: Köhler

first: Nadine

last: Wolf

first: Sarah

last: Hassel

first: Rouven

last: Nietsch

first: Thomas

last: Wieland

first: Philipp

last: Ehlermann

first: Jobst-Hendrik

last: Schultz

last: Dösch

first: Derliz

last: Mereles

first: Stefan

last: Hardt

first: Johannes

last: Backs

middle: D

last: Hoheisel

first: Christoph

last: Plass

first: Hugo

last: Katus


title: Dietary heme alters microbiota and mucosa of mouse colon without functional changes in host-microbe cross-talk.

status: Public on Dec 19 2012

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Colon cancer is a major cause of cancer deaths in Western countries and is associated with diets high in red meat. Heme, the iron-porphyrin pigment of red meat, induces cytotoxicity of gut contents which injures surface cells leading to compensatory hyperproliferation of crypt cells. This hyperproliferation results in epithelial hyperplasia which increases the risk of colon cancer. In humans, a high red-meat diet increases Bacteroides spp in feces. Therefore, we simultaneously investigated the effects of dietary heme on colonic microbiota and on the host mucosa of mice. Whole genome microarrays showed that heme injured the colonic surface epithelium and induced hyperproliferation by changing the surface to crypt signaling. Using 16S rRNA phylogenetic microarrays, we investigated whether bacteria play a role in this changed signaling. Heme increased Bacteroidetes and decreased Firmicutes in colonic contents. This shift was most likely caused by a selective susceptibility of Gram-positive bacteria to heme cytotoxic fecal water, which is not observed for Gram-negative bacteria, allowing expansion of the Gram-negative community. The increased amount of Gram-negative bacteria most probably increased LPS exposure to colonocytes, however, there is no appreciable immune response detected in the heme-fed mice. There was no functional change in the sensing of the bacteria by the mucosa, as changes in inflammation pathways and Toll- like receptor signaling were not detected. This unaltered host-microbe cross-talk indicates that the changes in microbiota did not play a causal role in the observed hyperproliferation and hyperplasia.

Keywords: Expression profiling by array

overall_design: Mice were fed a Westernized high fat control diet, or the same diet supplemented with 0.5 µmol heme/g diet. After 14 days of intervention, mice were killed and gene expression was profiled in colon.

first: Noortje

last: IJssennagger

first: Anneke

last: Rijnierse

first: Michael

last: Müller

first: Roelof

last: van der Meer


title: Transcriptional Responses to Sleep in Peripheral Tissues (Heart)

status: Public on Nov 17 2012

city: Sao Paulo

first: Renata

last: Pellegrino

address: Rua NApoleao de Barros 925

country: Brazil

institute: UNIFESP

summary: Molecular profiles in sleep and sleep deprivation in peripheral tissues using microarrays

overall_design: Time point study. Mice were sacrificed by cervical dislocaton following 3, 6, 9, and 12 h of total sleep deprivation (n = 8 or 9 at each time point). Deprivation was initiated at lights-on and performed through gentle handling.

first: Ron

last: Anafi

first: Keith

middle: R

last: Shockley

first: Micah

last: Romer

first: Sergio

last: Tufik

first: Allan

middle: I

last: Pack


title: Transcriptional Responses to Sleep in Peripheral Tissues (Lung)


title: Expression data from obese children (boys)

status: Public on Oct 12 2012

city: Pamplona

first: Tara

last: Rendo-Urteaga

state: Navarra

address: irunlarrea sn

department: Food Science, physiology and toxicology

institute: University of Navarra

summary: The aim of this study was to analyze gene response to a 10-week dietary intervention for weight loss in peripheral blood mononuclear cells of overweight/obese male children.

overall_design: PBMCs were obtained from 12 overweight/obese boys for RNA extraction and hybridization on Affymetrix microarrays. We performed the microarray analysis at baseline and after a weight loss intervention program in a total of 24 samples. They were distributed by dietary response as high and low responders.

first: Amelia

last: Marti

first: Sonia

last: García-Calzón

first: Pedro

last: Gonzalez-Muniesa

first: Fermín

last: Milagro

first: Maria

last: Chueca

first: Mirentxu

last: Oyarzabal

middle: C

last: Azcona-Sanjulian

first: J

last: Martínez


title: Lgr5+ve stem cells in nephrogenesis

status: Public on Sep 04 2012

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary: Multipotent stem cells and their lineage-restricted progeny drive nephron formation within the developing kidney. Validated markers of these early stem/progenitor populations are essential for deciphering their in vivo function and for evaluating their clinical potential for treating adult kidney disease. Here, we document expression of the adult stem cell marker Lgr5 in the developing kidney and assess the stem/progenitor identity of Lgr5+ve cells via in vivo lineage tracing. The appearance and localization of Lgr5+ve cells coincided with that of the S-shaped body around E14. Lgr5 expression remained restricted to cell clusters within developing nephrons in the cortex until P7, when expression was permanently silenced. In vivo lineage tracing identified Lgr5 as a marker of a novel progenitor population within nascent nephrons dedicated to generating the thick ascending limb of Henle's loop and distal convoluted tubule. The Lgr5 surface marker and experimental models described here will be invaluable for deciphering the contribution of early nephron stem cells to developmental defects and for isolating human nephron progenitors as a prerequisite to evaluating their therapeutic potential.

overall_design: Metanephric kidneys of timed pregnancies of ~14 days of gestation were harvested and cultured for ~10 days. Lgr5-EGFP-Ires-CreERT2-positive embryonic kidneys were identified by fluorescence microscopy and enzymatically digested to a single cell solution. GFPhi and GFPneg cells were sorted by flow cytometry (MoFlo; Dako). RNA, isolated using RNeasy (Qiagen), was analyzed using the Affymetrix platform.

first: Maarten

last: Rookmaaker

first: Nick

last: Barker

first: Marc

last: van de Wetering

first: Hans

last: Clevers


title: Transcriptional Responses to Sleep in Peripheral Tissues

first: Renata

last: Pellegrino

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

overall_design: Refer to individual Series


title: Expression data from mouse embryonic stem cells and ES cell-derived definitive endoderm and early hepatic cells

status: Public on Aug 03 2012

city: Beijing

first: Chenhuan

last: Xu

address: 1 Beichen West Road

country: China

institute: Beijing Institute of Genomics

summary: Foxa2 is required for endoderm differentiation into the hepatic lineage. The mechanism of activation for Foxa2 during this developmental process has not been elucidated yet. We established an in vitro system to guide ES cells differentiating into definitive endoderm (DE) cells and the following DE cells to early hepatic cells. ChIP-seq assays have been successfully performed to assess the Foxa2 binding profile. Over 50% of Foxa2 target genes in DE cells were found to be activated in hepatic cells which were at a stage later than the DE stage. Therefore, our finding at the genome-wide level proved Foxa2 serves as a pioneer factor at the DE stage. Furthermore, Foxa2 could specifically induce H3K4me2 modifications to the promoter/enhancer regions of many hepatic genes to pre-mark the chromatin, and determine the hepatic lineage differentiation competence. Our study illustrated the wide existence of Foxa2's pioneer factor function and uncovered the correlation between pioneer factor and chromatin pre-mark. These findings will be helpful for understanding the developmental process of hepatogenesis and efficiently controlling Foxa2 during hepatic induction for generating functional hepatocytes.

overall_design: To further gain a genome-wide view of Foxa2's effects on its target gene expression, 3 representative time points from the ES cell differentiation process to hepatic cells were selected for cDNA microarray analysis: 1) Day 0, representing ES cells, where there was no Foxa2 expression; 2) Day 5, representing DE cells; and 3) Day 7, representing early hepatic cells.

first: Xiaowen

last: Lyu

first: Eric

middle: Z

last: Chen

first: Zhiying

last: He

first: Borjigin

last: Uyunbilig

first: Guangpeng

last: Li

first: Yue

last: Ma

first: Lijian

last: Hui

first: Bin

last: Xie

first: Yuan

last: Gao

first: Xiaoyan

last: Ding

first: Yiping

last: Hu

first: Ping

first: Jing-Dong

last: Han

first: Xin

last: Wang


title: Gene Expression profiling of transgenic mice expressing the genetically encoded calcium indicator TN-XXL in muscle and brain tissues

status: Public on Jul 26 2012

city: Martinsried

first: Stephan

last: Direnberger

address: Grosshaderner Str. 2

institute: Ludwig-Maximilians University

summary:
Engineering of genetically encoded calcium indicators predominantly focused on optimizing fluorescence changes, but effects of indicator expression on host organisms have largely not been addressed. Here, we report biocompatibility and wide-spread functional expression of the genetically encoded calcium indicator TN-XXL in a transgenic mouse model. To validate the model and to characterize potential effects of indicator expression we assessed both indicator function and a variety of host parameters such as anatomy, physiology, behavior and gene expression profiles in these mice. We also demonstrate the usefulness of primary cell types and organ explants prepared from these mice for imaging applications. While we do find mild signatures of indicator expression that may guide further indicator development the “green” indicator mice generated provide a well characterized resource of primary cells and tissues for in vitro and in vivo calcium imaging applications.
Using expression profiling we could detect a number of transcripts regulated predominantly in heart and skeletal muscle of TN-XXL transgenic mice but only very few showed a level of regulation of a factor of two or higher and thus the majority of these changes were considered physiologically irrelevant. Remarkably this regulation occurred in skeletal and cardiac muscle, but not in brain. This suggests that skeletal muscle TnC as calcium sensing moiety within the indicator may be bio-orthogonal in brain but may lose some of this advantage in muscle tissue where it is derived from.

overall_design: Factorial design comparing transgenic mice with wild type littermates in three different tissues (hippocampus, skeletal and heart muscle)

first: Oliver

last: Griesbeck


title: Gene expression analysis in skeletal muscle and heart of 11 days-old TK2 knockout mice

status: Public on Jul 31 2012

city: Huddinge

first: João

middle: Amorim

last: Paredes

state: Stockholm

address: Karolinska Universitetssjukhuset Huddinge, F68

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

summary:
TK2 deficiency causes severe mtDNA depeltion in several tissues, including skeletal muscle and heart. TK2 knockout mice grow slower and their skeletal muscles appeared significantly underdeveloped, whereas heart was close to normal size.
We used microarrays in order to compare the transcriptomes in skeletal muscle and heart tissue of 11 days-old TK2 knockout pups with the sames tissues of wild-type pups at the same age.

overall_design: We collected skeletal muscle from the hind limb and hearts of three 11 days-old TK2 knockout and three wild-type pups and extracted total RNA. These RNA samples were used for hybridization in Affymetrix arrays.

first: Anna

last: Karlsson


title: Gene expression data from differentiated 3T3-L1 preadipocytes treated with Palmitic Acid, Stearic Acid, Palmitoleic Acid, or Oleic Acid

status: Public on Nov 13 2012

city: Guelph

first: David

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

country: Canada

institute: University of Guelph

summary:
Saturated fatty acids (SFA) are widely thought to induce inflammation in adipose tissue (AT), while monounsaturated fatty acids (MUFA) are purported to have the opposite effect; however, it is unclear if individual SFA and MUFA behave similarly. Our goal was to examine adipocyte transcriptional networks regulated by individual SFA (palmitic acid, PA; stearic acid, SA) and MUFA (palmitoleic acid, PMA; oleic acid, OA).
Global gene expression was examined in differentiated preadipocytes treated with either 250 μM PA, SA, PMA, or OA for 48 hrs.
Individual fatty acid treatments had significant effects on adipocyte gene expression. Functional analyses revealed that PA induced the TLR signalling pathway, while PMA had the opposite effect. SA and OA had similar effects, with increases in key metabolic pathways including mTOR and PPAR signalling, and a reduction in TLR signalling. Ccl5 was validated as a candidate gene that may mediate the differential inflammatory effects of SFA and MUFA in AT.
Individual SFA and MUFA trigger distinct transcriptional responses in differentiated preadipocytes, with inflammatory and metabolic pathways particularly sensitive to these fatty acids.

overall_design: A total of 4 microarrays were run for each FA treatment. We experienced difficulties with the cRNA amplification for one replicate from the OA treated cells; therefore this treatment group only had an n=3. For each sample, 100 ng of total RNA was prepared for hybridization to Affymetrix Mouse Gene 1.1 ST array strips, according to the manufacturer’s instructions (Affymetrix Inc., Fremont, CA, USA).

first: Wong

last: Monica HT

first: Shaw

last: Brittany

first: Lambert

last: Sam

first: Mutch

last: David M


title: CD1d-restricted NKT cell function prevents insulin resistance in lean mice, and is regulated by adipocytes  and is regulated by adipocytes

status: Public on Aug 07 2012

first: Guido

last: Hooiveld

summary: Lipid overload and adipocyte dysfunction are key to the development of insulin resistance and can be induced by a high-fat diet. CD1d-restricted invariant natural killer T (iNKT) cells have been proposed as mediators between lipid overload and insulin resistance, but recent studies found decreased iNKT cell numbers and marginal effects of iNKT cell depletion on insulin resistance under high-fat diet conditions. Here, we focused on the role of iNKT cells under normal conditions. We showed that iNKT cell–deficient mice on a low-fat diet, considered a normal diet for mice, displayed a distinctive insulin resistance phenotype without overt adipose tissue inflammation. Insulin resistance was characterized by adipocyte dysfunction, including adipocyte hypertrophy, increased leptin, and decreased adiponectin levels. The lack of liver abnormalities in CD1d-null mice together with the enrichment of CD1d-restricted iNKT cells in both mouse and human adipose tissue indicated a specific role for adipose tissue–resident iNKT cells in the development of insulin resistance. Strikingly, iNKT cell function was directly modulated by adipocytes, which acted as lipid antigen-presenting cells in a CD1d-mediated fashion. Based on these findings, we propose that, especially under low-fat diet conditions, adipose tissue–resident iNKT cells maintain healthy adipose tissue through direct interplay with adipocytes and prevent insulin resistance.

overall_design: four samples

first: Henk

last: Schipper

first: Maryam

last: Rakhshandehroo

first: Stan

middle: F

last: van de Graaf

first: Koen

last: Venken

first: Arjen

last: Koppen

first: Rinke

last: Stienstra

first: Serge

last: Prop

first: Jenny

last: Meerding

first: Nicole

last: Hamers

first: Gurdyal

last: Besra

first: Louis

last: Boon

first: Edward

middle: E

last: Nieuwenhuis

first: Dirk

last: Elewaut

first: Berent

last: Prakken

first: Sander

last: Kersten

first: Marianne

last: Boes

first: Eric

last: Kalkhoven


title: Identification of the core gene-regulatory network that governs the dynamic adaptation of intestinal homeostasis during conventionalization in mice

status: Public on Jul 11 2012

first: Guido

last: Hooiveld

summary: Molecular adaptation of the intestinal mucosa occurs during microbial conventionalization to maintain a balanced immune response. However, the genetic regulation of such adaptation is obscure. Here, combined analysis of germ free and conventionalized mice revealed that the major molecular adaptations were initiated at day 4 of conventionalization with a strong induction of innate immune functions followed by stimulation of adaptive immune functions. We identified central regulatory genes and reconstructed a common regulatory network that appeared to be sufficient to regulate the dynamic adaptation of the intestinal mucosa to the colonizing microbiota. The majority of the genes within this regulatory network play roles in mucosal inflammatory diseases in mouse and human. We propose that the identified central regulatory network may serve as a genetic signature for control of intestinal homeostasis in healthy mice and may help to unravel the genetic basis of pathway dysregulation in human intestinal inflammatory diseases.

overall_design: Expression profiling of jejunum, ileum, and colon tissue from germ-free and colonized mice at day 1,2,4,8,16 and 30.

first: Sahar

last: El Aidy

first: Peter

last: van Baarlen

first: Michiel

last: Kleerebezem


title: Transcript profiling of different Arabidopsis thaliana ecotypes in response to Tobacco etch potyvirus infection

status: Public on Jul 04 2012

first: Julia

last: Hillung

state: Valencia

address: Ingeniero Fausto Elio s/n

department: IBMCP

institute: CSIC-UPV

summary: We have used a strain of Tobacco etch potyvirus (TEV) experimentally adapted to Arabidopsis thaliana ecotype Ler-0 to infect a set of seven A. thaliana plant ecotypes(Col-0, Ei-2, Wt-1, ler-0, Oy-0, St-0). Each ecotype was inoculated with the same amount of the virus.  Using commercial microarrays containing probes Arabidopsis thaliana ssp. Col-0 plant transcripts, we explored the effect of viral infection in the plant transcriptome

overall_design: This microarray can be useful to study gene activity of Arabidopsis thaliana associated with response to virus infection. For ecotypes ST-0, Wt-1, Ler-0, Di-2 there are five biological replicates and for ecotype Oy-0 there are three. As control we used four technical replicates of each ecotype, but five for Ler-0. Rows and columns are numbered as scanned by a GenePix Scanner (barcode on the bottom, DNA on the front surface).

first: José

last: Cuevas

first: Santiago

last: Elena


title: Dietary heme mediated PPARα activation does not affect the heme-induced epithelial hyperproliferation and hyperplasia in mouse colon

status: Public on Aug 22 2012

summary: Red meat consumption is associated with an increased colon cancer risk. Heme, present in red meat, injures the colon surface epithelium by luminal cytotoxicity and reactive oxygen species. This surface injury is overcompensated by hyperproliferation and hyperplasia of crypt cells. Transcriptome analysis of mucosa of heme-fed mice showed, besides stress- and proliferation-related genes, many upregulated lipid metabolism-related PPARα target genes. The aim of this study was to investigate the role of PPARα in heme-induced hyperproliferation and hyperplasia. Male PPARα KO and WT mice received a purified diet with or without heme. As PPARα is proposed to protect against oxidative stress and lipid peroxidation, we hypothesized that the absence of PPARα leads to more surface injury and crypt hyperproliferation in the colon upon heme-feeding. Heme induced luminal cytotoxicity and lipid peroxidation and colonic hyperproliferation and hyperplasia to the same extent in WT and KO mice. Transcriptome analysis of colonic mucosa confirmed similar heme-induced hyperproliferation in WT and KO mice. Stainings for alkaline phosphatase activity and expression levels of Vanin-1 and Nrf2-targets indicated a compromised antioxidant defense in heme-fed KO mice. Our results suggest that the protective role of PPARα in antioxidant defense involves the Nrf2-inhibitor Fosl1, which is upregulated by heme in PPARα KO mice. We conclude that PPARα plays a protective role in colon against oxidative stress, but PPARα does not mediate heme-induced hyperproliferation. This implies that oxidative stress of surface cells is not the main determinant of heme-induced hyperproliferation and hyperplasia.

overall_design: Wild type and peroxisome proliferator-activated receptor alpha (PPARα) knockout mice were fed a Westernized high fat diet, or the same diet supplemented with 0.5 µmol heme/g diet. After 14 days of intervention, mice were killed and gene expression was profiled in colon.

first: Noortje

last: IJssennagger

last: de Wit

first: Michael

last: Müller

first: Roelof

last: van der Meer


title: Arabidopsis thaliana: auxin-treated seedlings versus control seedlings

status: Public on May 10 2012

city: Fuchu

first: Naoya

last: Wasano

state: Tokyo

address: Saiwai-cho 3-5-8

country: Japan

institute: Tokyo University of Agriculture & Technology

summary: Transcriptional profiling of Arabidopsis thaliana seedlings treated with auxin (indole-3-acetic acid),  highlighting to the physiological function of auxin by observing early response of gene expressions in Arabidopsis seedlings.

overall_design: Two-condition experiment,  auxin-treated seedlings vs. control seedlings. Biological replicates:2 control replicates, 2 auxin-treated.


title: Arabidopsis thaliana: cis-cinnamic acid-treated seedlings versus control seedlings

status: Public on Jul 01 2012

summary: Transcriptional profiling of Arabidopsis thaliana seedlings treated with cis-cinnamic acid.

overall_design: Two-condition experiment, cis-cinnamic acid-treated seedlings vs. control seedlings. Biological replicates: 2 control replicates, 2 cis-cinnamic acid treated.


title: Transcriptome analysis of Arabidopsis plants that overexpress green fluorescent protein (GFP) and GFP-LOV kelch protein 2 (GFP-LKP2)

status: Public on Apr 25 2012

city: Tokyo

first: Yuji

last: Miyazaki

address: 1-5-1, mejiro, Toshima-ku

department: Graduate School of Science

institute: Gakushuin University

summary: LKP2 belongs to a group of blue light receptors in Arabidopsis thaliana. We performed DNA microarray analysis to identify genes whose expression levels are altered in LKP2-overexpressing plants. Agilent's Whole Arabidopsis Genome Oligo Microarray (G2519F, V4, 4x44K) was used.

overall_design: Comparison between 35S:GFP overexpressing- and 35S:GFP-LKP2 overexpressing- plants (Yasuhara et al. 2004) was performed.

first: Hiroshi

last: Abe

first: Tomohiro

last: Kiyosue


title: Activation of natural killer T cells promotes M2 macrophage polarization in adipose tissue and improves systemic glucose tolerance via the IL-4/STAT6 signaling axis in obesity

status: Public on Apr 13 2012

summary: Natural killer T (NKT) cells are important therapeutic targets in various disease models and under clinical trials for cancer patients. However, their function in obesity and type 2 diabetes remains unclear. Our data show that adipose tissues of both mice and humans contain a population of type-1 NKT cells, whose abundance decreases with increased adiposity and insulin resistance. Although loss-of-function of NKT cells had no effect on glucose tolerance in animals with prolonged high-fat diet (HFD) feeding, activation of NKT cells by lipid agonist α-galactosylceramide (αGalCer) enhances alternative macrophage polarization in adipose tissue and improves glucose homeostasis in animals at different stages of obesity. Furthermore, the effect of NKT cells is largely mediated by the IL-4/STAT6 signaling axis in obese adipose tissue. Thus, our data identifies a novel therapeutic target for the treatment of obesity-associated inflammation and type-2 diabetes.

overall_design: Wild type and CD1d1 antigen (CD1d) knockout mice were fed a high fat diet for 4 days. On day 0 and 2 mice were injected intraperitoneally with α-galactosylceramide (αGalCer) or vehicle. On day 4 mice were killed and gene expression was profiled in epididymal adipose tissue.

first: Yewei

last: Ji

first: Shengyi

last: Sun

first: Aimin

last: Xu

first: Liu

last: Yang

first: Prerna

last: Bhargava

first: Karen

last: Lam

first: Bin

last: Gao

first: Chih-Hao

last: Lee

first: Sander

last: Kersten

first: Ling

last: Qi


title: The ATP-P2X7 signaling axis is dispensable for obesity-associated inflammasome activation in adipose tissue

status: Public on Feb 24 2012

first: Guido

last: Hooiveld

summary: Inflammasome activation in adipose tissue has been implicated in obesity-associated insulin resistance and type 2 diabetes. However, when and how inflammasome is activated in adipose tissue remains speculative. Here we test the hypothesis that extracellular ATP, a potent stimulus of inflammasome in macrophages via purinergic receptor P2X, ligand-gated ion channel, 7 (P2X7), may play a role in inflammasome activation in adipose tissue in obesity. Our data show that inflammasome is activated in adipose tissue upon 8-week feeding of 60% HFD, coinciding with the onset of hyperglycemia and hyperinsulinemia as well as the induction of P2X7 in adipose tissue. Unexpectedly, P2X7-deficient animals on HFD exhibit no changes in metabolic phenotypes, nor in inflammatory responses or inflammasome activation when compared to the wildtype controls. Similar observations have been obtained in hematopoietic cell-specific P2X7-deficient animals generated by bone marrow transplantation. Thus, we conclude that inflammasome activation in adipose tissue in obesity coincides with the onset of hyperglycemia and hyperinsulinemia, but unexpectedly, is not mediated by the ATP-P2X7 signaling axis. The nature of the inflammasome-activating danger signal(s) in adipose tissue in obesity remains to be characterized.

overall_design: Wild type and P2X7 knockout mice were fed a low fat diet (chow) or high fat diet for 12 weeks. After the diet intervention period, the animals were killed and epididymal white adipose tissue was removed. Total RNA was isolated and subjected to gene expression profiling.

first: Sheng

last: Xia


title: Expression data from HDAC1 and HDAC2 knocked-out mouse oocyte

status: Public on Dec 31 2011

city: Philadelphia

first: Hua

last: Pan

state: PA

address: 415 S University Avenue

department: Department of Biology

country: USA

institute: University of Pennsylvania

summary:
Dramatic changes in chromatin structure and histone modification occur during oocyte growth, as well as a global cessation of transcription. The role of histone modifications in these processes is poorly understood. We report the effect of conditionally deleting Hdac1 and Hdac2 on oocyte development. Deleting either gene has little or no effect on oocyte development, whereas deleting both genes results in follicle development arrest at the secondary follicle stage. This developmental arrest is accompanied by substantial perturbation of the transcriptome and a global reduction in transcription even though histone acetylation is markedly increased. There is no apparent change in histone repressive marks but there is a pronounced decrease in histone H3K4 methylation, an activating mark. The decrease in H3K4 methylation is likely due to increased expression of Kdm5b because RNAi-mediated targeting of Kdm5b in double mutant oocytes results in an increase in H3K4 methylation. An increase in TRP53 acetylation also occurs in mutant oocytes and may contribute to the observed increased incidence of apoptosis. Taken together, these results suggest seminal roles of acetylation of histone and non-histone proteins in oocyte development.
We used microarrays to detail the global programme of gene expression underlying oocyte development and identified distinct classes of regulated genes during this process.

overall_design: Total RNA was extracted from 80 oocytes isolated from mice 12 days-of-age using the PicoPure RNA kit (Arcturus), amplified with the Ovation Pico WTA system (NuGen), and then fragmented and labeled with the FL-OvationTM cDNA Biotin Module V2 (NuGen). Four independent biological replicates were hybridized to Affymetrix GeneChip Mouse 1.1 ST microarrays (http://www.affymetrix.com/). Raw microarray data were analyzed as previously described using MAS5, GeneSpring v7, SAM and EASE software (56). A 1.4-fold cutoff was used for EASE analysis; four biological replicates provide sufficient statistical power and confidence to detect a 1.4-fold change in transcript abundance

first: Pengpeng

last: Ma

first: Rusty

last: Montgomery

first: Eric

middle: N

last: Olson

first: Richard

last: Schultz


title: Role of 9-Lipoxygenase and α-Dioxygenase oxylipin pathways as modulators of local and systemic defense

status: Public on Dec 02 2011

city: Madrid

first: Jorge

last: Vicente

address: Darwin

institute: CSIC

summary: Plant 9-lipoxygenases (9-LOX) and α-dioxygenases (α-DOX) initiate the synthesis of oxylipins after bacterial infection. Here, the role of these enzymes in plant’s defense was investigated using individual Arabidopsis thaliana lox1 and dox1 mutants and a double lox1 dox1 mutant. Studies with Pseudomonas syringae pv tomato (Pst) revealed the enhanced susceptibility of lox1 to the  virulent strain Pst DC3000 and the partial impairment of lox1 and dox1 mutants to activate systemic acquired resistance. Notably, both defects were enhanced in the lox1 dox1 plants as compared with individual mutants. We found that pre-treatment with 9-LOX- and α-DOX-generated oxylipins protected plant tissues against bacterial infection. The strongest effect in this respect was exerted by 9-ketooctadecatrienoic acid (9-KOT), which is produced from linolenic acid by 9-LOX. Quantification of 9-KOT revealed its accumulation after bacterial infection. The levels were reduced in lox1 and lox1 dox1 plants but strongly increased in the dox1 mutant due to metabolic interaction of the two pathways. Transcriptional analyses indicated that 9-KOT pre-treatment modifies hormone homeostasis during bacterial infection. The nature of the changes detected suggested that 9-KOT interfers the hormonal changes caused by bacterial effectors. This notion was substantiated by the finding that 9-KOT failed to reduce the growth of PstDC3000hrpA, a mutant compromised in effector secretion, and of the avirulent strain Pst DC3000 avrRpm1. Further support to the action of the 9-LOX- and α-DOX-oxylipin pathways as modulators of hormone homeostasis was the observation that lox1 dox1 seedlings are hypersensitive to the growth-inhibitory effect of ABA and showed enhanced activation of ABA-inducible marker genes.

overall_design: Two experiments, Col-0 treated with 9-KOT vs. Col-0 treated with water and Col-0 treated with 9-KOT vs. Col-0 treated with water after treatment with Pst DC3000. Biological replicates: 4 control replicates treated , 4 9-KOT treated replicates; 4 control treated and Pst DC3000 replicates and 4 9-KOT treated and Pst DC3000 replicates

first: Tomás

last: Cascón

first: Begonya

last: Vicedo

first: Pilar

last: García-Agustín

first: Mats

last: Hamberg

first: Carmen

last: Castresana


title: Arabidopsis thaliana seedlings:early light regulated gene expression in Ler wildtype versus eid3 mutant

status: Public on Jan 01 2012

city: Freiburg

first: Cornelia

last: Klose

address: Schänzlestr. 1

department: Institute for Biology 2/ Botany

institute: Albert-Ludwigs-University Freiburg

summary: Transcriptional profiling of Arabidopsis thaliana Ler wildtype and eid3 (empfindlicher im dunkelroten Licht 3) mutant seedlings in darkness and 45 min after a red-light pulse.

overall_design: Arabidopsis thaliana Ler wildtype and eid3 mutant seedlings were grown on 1/2 MS Agar plates covered with filter paper for 4 days in darkness after induction of germination with 2 h red light. Samples were either treated with 2 min red light (30 µmol/m2s) or kept in darkness and harvested after additional 45 min in darkness. 3 biological replicas were used for each of the 4 experimental conditions.

first: Thomas

last: Kretsch


title: MYB46-related transcriptome analysis in Arabidopsis thaliana

status: Public on Nov 21 2011

first: Pablo

last: Vera

email: vera@ibmcp.upv.es, oliveros@cnb.csic.es

address: Camino de Vera s/n

institute: Instituto de Biología Molecular y Celular de Plantas (IBMCP) UPV-CSIC

summary: In this study we show that the Arabidopsis transcription factor MYB46, previously described to regulate secondary cell wall biosynthesis in the vascular tissue of the stem, is pivotal for mediating disease susceptibility to the fungal pathogen Botrytis cinerea. We identified MYB46 by its ability to bind to a new cis element located in the 5´ promoter region of the pathogen-induced Ep5C gene which encodes a type III cell wall-bound peroxidase. We present genetic and molecular evidence indicating that MYB46 modulates the magnitude of Ep5C gene induction following pathogenic insults. Moreover, we demonstrate that different myb46 knock-down mutant plants exhibit increased disease resistance to B. cinerea, a phenotype that is accompanied by selective transcriptional reprogramming of a set of genes encoding cell wall proteins and enzymes, of which extracellular type III peroxidases are conspicuous. In essence our results substantiates that defense-related signaling pathways and cell wall integrity are interconnected, and MYB46 likely functions as a disease susceptibility modulator to B. cinerea through the integration of cell wall remodeling and downstream activation of secondary lines of defense.

overall_design: 10-15 days-old plants were collected, frozen in liquid nitrogen and stored at -80ºC. Independent replicates from 3 different experiments (separated in time) were used in the analysis. Samples from Col-0 and myb46-2 were compared.

first: Vicente

last: Ramirez

first: Astrid

last: Agorio

first: Alberto

last: Coego

first: Javier

last: García-Andrade

first: María

last: Hernández

first: Begoña

last: Balaguer

first: Pieter

middle: B

last: Ouwekerk

first: Ignacio

last: Zarra


title: To establish specific structural evidence that glycans are indeed blunted/altered from the glycan profiling of glycan moieties on the surface of leukocytes

status: Public on Oct 03 2011

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: We want to characterize the glycan moieties on the surface of leukocytes treated with fluorinated analogs of glucosamine.  Since these metabolic inhibitors compete with natural-occuring glucosamine used in oligosaccharide chain formation, these compounds have been shown to be effective in lowering Type 2 lactosamine and sialylated Lewis antigens, which results in altered selectin ligand functions.

overall_design:
We need to establish specific structural evidence that glycans are indeed blunted/altered.
Current research efforts include investigations on how circulating leukocytes traffic to inflamed tissues, how circulating solid tumor cells interact with endothelial linings to enhance metastatic potential, and how treatment with analogs of glucosamine disrupt leukocyte trafficking mechanisms and/or influence effector/regulatory function of T cells.

first: Charles

last: Dimitroff

first: Alex

middle: T

last: Moffit


title: To investigate how the glycosylation of podocyte proteins changes during diabetic kidney disease

summary: Podocytes are cells of the visceral epithelium in the kidneys and form a crucial component of the glomerular filtration barrier, contributing to size selectivity and maintaining a massive filtration surface.

overall_design:
We are interested in pursuing a microarray analysis to identify the glycosylation-related genes that are modulated in podocytes during insulin and glucose stimulation. As such, we propose to isolate RNA from cultured AB 8/13 human podocyte cell line in their normal state and treated with different concentrations of insulin and glucose.
Initially, we would like to analyze 12 samples (Normal control, 2 Starved controls, Insulin experiments 1-4, and glucose experiments 1-5). These experiments would give us information on the gene regulation changes in different healthy and diabetic conditions. In addition to providing possible identification of the unknown proteins involved with diabetic nephropathy, such analysis would provide novel information about early responses by podocytes in response to insulin and glucose level changes in vitro. The results from this analysis will be utilized to focus our research with regard to glycosylation of the proteins in the podocyte slit diaphragm.

first: Harry

last: Holthofer


title: To better understand the molecular basis for modulation of glycosaminoglycans (GAGs) and proteoglycans post-UV exposure

summary: UV irradiation is a major environmental effector of skin damage and aging. Elevated levels of glycosaminoglycans (GAGs), as measured by Hale’s stain, are seen following cutaneous photodamage.  Preliminary data from our lab indicates that this is a complex response involving differential regulation of both GAGs and proteoglycans.  Recently, different GAG species have been shown to have distinct effects on the recruitment and activation of immune cells and stimulation of cytokine production (Taylor and Gallo, FASEB, 2006; 20: 9-22).  We speculate that the elevated GAGs and proteoglycans observed after ultraviolet B (UVB) irradiation are involved in the inflammatory and healing responses to photodamage.

overall_design:
Chondroitin sulfate synthases (CSSs) are not increased by UVB in mice or in cultured human fibroblasts.  To determine whether genomic upregulation of CSSs is responsible for the post-UVB CS increase, we measured the dermal expression of CSS1 and CSS3 mRNA in C57Bl6 mice after 5 days of UV-B exposure.  Irradiation caused no change in either CSS1 or CSS3 mRNA expression.  We also studied CSS RNA expression in cultured human fibroblasts.  We compared control cells to cells treated with 30 mJ/cm2 UVB, cells treated with 1 ng/mL IL-1α, and cells co-stimulated with UVB and IL-1α.  In vivo, UV-B induces IL-1α production by keratinocytes and inflammatory cells, and this IL-1α interacts with fibroblasts.  Co-stimulation with IL-1α + UVB induces TNF-α production by the fibroblasts, mirroring the in vivo interaction.  CSS1 mRNA was suppressed 60% and CSS3 mRNA expression dropped 87% relative to sham at 24 hours post-treatment (p<0.001, Dunnet q’).
Since CS is not upregulated by its synthases, we postulated an alternative mode of induction whereby one or more CS proteoglycans are transcriptionally increased and bind more CS in the dermis.  We used the N-13 goat monoclonal anti-serglycin antibody to visualize changes in cutaneous serglycin content following acute UV-B exposure.  Serglycin is one example of CS-binding dermal proteoglycans that is induced by UVB, and there are likely others. Diffuse upper-dermal serglycin staining, like upper-dermal CS, was induced continuously at 24, 48, and 72 hours after irradiation.  Serglycin-expressing inflammatory cells are recruited to the dermis following irradiation, peaking at 48 hours post-exposure.  A statistically significant 1.70 fold increase in serglycin mRNA was measured in cultured human fibroblasts 6 hours after co-stimulation with UVB and IL-1α.  Realtime PCR also revealed a significant 2.04 fold upregulation at 24 hours after co-stimulation, and serglycin was increased 4.63 times 6 hours after Il-1α treatment alone.

first: Victoria

last: Werth


title: To compare the levels of expression of the different glycosyltransferases in order to explain the exclusive detection of LeX in the neurons

summary: Human NT2- cells differentiate in vitro into NT2N neurons in the presence of retinoic acid, and culture in the presence of mitosis inhibitors. We have previously observed the presence of the Lewisx determinant exclusively in NT2N neurons but not in NT2- cells. We also obtained evidence that Lex is synthesized in these cells by FUT9 (Brito,...,Costa (2007) J. Neurosci. Res. 85, 1260).

overall_design:
We would like to compare the levels of expression of the different glycosyltransferases, particularly, fucosyltransferases and sialyltransferases to explain the exclusive detection of Lex in the neurons.
In addition, we would like to know if there are some Lex-binding proteins that may act as binding partners of Lex in the neurons.

first: Julia

last: Costa


title: An environment with strong gravitational and magnetic field alterations synergizes to promote variations in Arabidopsis thaliana callus global transcriptional state

first: Raúl

last: Herranz

address: Ramiro de Maeztu 9

department: Plant Cell Nucleolus, proliferation and microgravity

institute: Centro Investigaciones Biológicas

summary: Using diamagnetic levitation, we have exposed A. thaliana in vitro callus cultures to five environments with different levels of effective gravity (from levitation i.e. simulated mg* to 2g*) and magnetic fields (10.1 to 16.5 Tesla) and we have compared the results with those of similar experiments done in a Random Position Machine (simulated micro g) and a Large Diameter Centrifuge (2g) free of high magnetic fields. Microarray analysis indicates that there are changes in overall gene expression of the cultured cells exposed to these unusual environments but also that gravitational and magnetic field produce synergic variations in the steady state of the transcriptional profile of A. thaliana. Significant changes in the expression of structural, abiotic stress and secondary metabolism genes were observed into the magnet field. These results confirm that the strong magnetic field, both at micro g* or 2g*, has a significant effect on the expression of these genes but subtle gravitational effects are still observable. These subtle responses to microgravity environments are opposite to the ones observed in a hypergravity one.

overall_design: seven-condition experiment, MM2D Arabidopsis culture callus control vs.  Treatment (altered gravity simulation, GBF). Three GBF were used (LDC (2g) + control, RPM (mg) + control and Magnet (mg*, 0.1g*, 1g*, 1.9g*, 2g*) + control). Biological replicates: 3  replicates in all conditions and controls except 1.9g* (2 replicates)

first: Ana

last: Manzano

first: Jack

middle: J

last: van Loon

first: Peter

last: Christianen

first: Juana

last: Gonzalez-Rubio

first: F

last: Medina

first: Raul


title: To identify glycosylation-specific targets contributing to the interferon gamma-dependent upregulation of sialylated CD44v6 in certain types of intestinal epithelial cells

status: Public on Sep 06 2011

summary: This project was done in collaboration with Dr. Richard Cummings to examine sialylation of CD44v6 and its role in clearance of neutrophils from inflamed intestinal epithelium.  Specifically, we have employed a functional approach using membrane preparations from interferon gamma-stimulated intestinal epithelial cells to generate a monoclonal antibody, designated GM35, which blocks neutrophil transepithelial migration through the promotion of neutrophil adhesion at the apical surface of the intestinal epithelium.  Protein biochemistry, sequencing, confocal microscopic analysis, and immunoprecipitation studies all identify the protein ligand for this antibody as CD44v6.  However, selective inhibition of O- or N-linked glycosylation reveal that the antibody is specific for an O-linked glycotope and glycoarray analysis of the GM35 antibody by Core H of the Consortium for Functional Glycomics reveal that this antibody binds with high affinity and specificity to a carbohydrate epitope consistent in structure with sLeA.  Inhibition of O-linked glycosylation attenuated both GM35 binding and its functional effects as did specific cleavage of sialic acid residues from the cell surface, using neuraminidase, although the functional effects of cleavage were smaller and harder to assess.

overall_design:
CD44v6 has previously been studied as a marker of inflammation in Inflammatory Bowel Disease, and GM35 staining is clearly upregulated by interferon gamma in T84 and HT29 intestinal epithelial cells.  The specific enzymes governing the sialylation of CD44v6 in intestinal epithelium have yet to be determined.  Analysis of a panel of intestinal epithelial cells including T84, HT29, and Caco-2 cells revealed that cell-type specific regulation of both splicing and glycosylation is essential for the regulation of the expression of the GM35 epitope.  And, forcible expression of CD44 in Caco-2 cells, which are negative for CD44v6 at baseline, results only in upregulation of previously expressed isoforms of CD44, but not in GM35 expression.
Based on western blot and immunofluorescent staining, GM35 expression is greatest in interferon gamma-treated T84 cells.  Thus, we analyzed RNA samples for  the expression of glycosylation specific genes in interferon gamma-stimulated T84 cells relative to that of both non-stimulated T84 cells and GM35-negative Caco-2 cells in order to identify glycosylation-specific targets contributing to the interferon gamma-dependent upregulation of sialylated CD44v6 in intestinal epithelial cells.

first: Nancy

middle: A

last: Louis


title: Two types of estrogen receptor-positive (ER+) and -negative (ER-) breast cancer will be compared with glycan structure analyses

status: Public on Sep 26 2011

summary: ER+ve and ER-ve breast cancers tend to show different patterns of metastasis, with ER+ve tumours having a propensity to metastasize to the bone while ER-ve tumours tend to induce visceral metastasis. Glycans can play an important role in metastasis through their interactions with glycan binding proteins. Moreover we, and others have also shown that expression of particular tumor-associated glycoforms of the mucin MUC1, allows it to interact with lectins of the immune system. We now have data showing differences in the level of expression of some glycosyltransferases in ER+ve and ER-ve of breast cancer suggesting the expression of different O-linked glycoforms.

overall_design:
RNA will be isolated from ER+ve and ER-ve primary breast cancers supplied by the Guy’s and St Thomas’ Research Breast Tissue Bank. Tumor tissue will be macro-dissected from thick cryostat sections by visual comparison with a representative H&E section. We will verify the level of expression of ER and document the expression of ST3Gal-I and ST6GalNAc-II by RT-qPCR. We have already isolated RNA from a number of tumours and shown we can obtain RNA of good quality with a RNA integrity number, as measured with an Agilent Bioanalyser, of >4.5
Since there is likely to be variability among primary tumors, ideally we analyzed of 10 ER negative and 9 ER positive tumours.

first: Joy

last: Burchell


title: To examine the expression of Sulf1 and Sulf2, as well as other glycan-related genes, in human Idiopathic pulmonary fibrosis (IPF) lungs compared to normal lung samples

summary:
Microarray analysis to examine glycan-related gene expression in idiopathic pulmonary fibrosis
Heparan sulfate 6-O-endosulfatases (Sulf1 and Sulf2) remove 6-O sulfate groups from heparan sulfate intra-chain sites on the cell surface and in the extracellular matrix, and modulate the functions of many growth factors and morphogens including FGF, Wnt and TGF-beta. Works from our laboratory have shown that TGF-beta 1 induces Sulf1 and Sulf2 expression in a cell-type specific manner in the lung, specifically Sulf1 in lung fibroblasts and Sulf2 in type II alveolar epithelial cells. Interestingly TGF-beta 1-induced Sulf1 and Sulf2 in turn modulate TGF-beta 1 function in culture.

overall_design: The aim of this study is to examine the expression of Sulf1 and Sulf2 as well as other glycan-related genes (heparan biosynthetic enzymes, TGF-beta, FGF and Wnt signaling pathway components) in human idiopathic pulmonary fibrosis (IPF) lungs compared to normal lung samples. We will examine gene expression in triplicate samples from RNA of total lung homogenates from IPF and control (normal) lungs

first: Xinping

last: Yue


title: To determine the changes in the expression of human colon cancer cells (HCT-15) untreated and treated with 5-aza-2''-deoxycytidine

overall_design:
Human colon cancer cells (HCT-15) treated with 5-aza-2'-deoxycytidine greatly enhanced sialyl Lewis X epitope, which correlated with increased binding of these cells to immobilized E-selectin in a parallel plate dynamic flow binding assay.
The sialyl Lewis x epitope resides at a 250 Kd protein band as assessed following immunoprecipitation. We would like to know changes in the expression of glycogenes following 5-aza-2'-deoxycytidine treatment.

first: Pi-Wan

last: Cheng


title: To understand how glycosylation on human B cells is regulated during differentiation and activation

first: Steven

summary: Our goal is to understand how glycosylation on human B cells is regulated during the differentiation and activation. Accumulating evidences have indicated that functions of immune cells are regulated in a glycan-dependent manner. One of well-known examples is B cell regulation by CD22 through its association with sialylated glycans. While recent studies uncovered that B cell activation leads to loss of high affinity glycan ligands for human CD22 (Neu5Ac-a2,6-Gal-B1,4-GlcNAc(6-sulfo)), the gene expression profile of human B cells before and after activation is unknown. Therefore we would like to perform gene expression analysis of human B cells before and after activation. We already have published the glycan profiling and gene expression of mouse B cells before and after activation done in collaboration with the CFG. This study revealed programmed changes in glycosylation relevant to regulation of B cell signaling by CD22. Since the ligands of human CD22 differ in several respects from that of mouse CD22, these experiments are relevant to the evolution of siglec ligands and their conserved functions in B cell biology.

overall_design:
In brief, the experimental protocol is as follows: human peripheral B cells are isolated from human peripheral blood of healthy donors and stimulated for 0, 24, 48 and 72 hrs.
Human B cells were isolated from human peripheral blood of healthy donors by the negative selection kit (Miltenyi). For the resting B cell samples, isolated B cells were immediately shock-frozen in the liquid N2 and kept at -80˚C until the RNA extraction. For the activated B cell samples, the cells were activated in the RPMI medium (Invitrogen) supplemented with 10% heat-inactivated FCS, 2 mM glutamine, 100 U/mL penicillin, 100 ug/mL streptomycin, 1 mM non-essential amino acid, 1 mM sodium pyruvate, and 50 uM 2-melcaptoethanol, 10 ug/mL anti-human IgA, G, M (Jackson Immunoresearch), and 50 nM CpG ODN 2006 (Invivogen) for 3 days. Total RNA was isolated using the TRIzol reagent (Invitrogen).

first: James

last: Paulson


title: To identify the deficient enzyme(s) in the glycosylation pathway that yield incomplete maturation of (uPAR) protein

last: Head

summary: We previously demonstrated plasticity in urokinase receptor (u-PAR) display in clonal colon cancer cells (Cancer Research 66: 7957-7967 (2006)). Thus, u-PAR display oscillates 10 fold between high and low density at the cell surface. We have determined that this oscillation in u-PAR display is posttranslational in nature. Thus, while clonal cell populations with high and low u-PAR density synthesize u-PAR at the same rate, the protein is inefficiently glycosylated in cells down-shifted for u-PAR display and subsequently degraded.

overall_design:
The objective of this study is to identify the deficient enzyme(s) in the glycosylation pathway that yield incomplete maturation of the u-PAR protein and hence its premature degradation.
We will compare a clonal population of the RKO colon cancer cell line (designated RKO C2) with a population derived (by FACS sorting for low u-PAR) from RKO C2 (designated RKO C2 F3).

first: Douglas

last: Boyd

first: Alex


title: Mechanism of lacritin-dependent production of the important dry eye mucin 'MUC16'

summary: Lacritin targets its coreceptor 'syndecan-1' in lacritin-dependent production of the important dry eye mucin 'MUC16'.  Real-time PCR analysis suggests that this effect is post-transcriptional.  In contrast, serum stimulation of MUC16 by these cells is transcriptionally dependent.  Our goal is to determine whether this regulation is global to other heavily O-glycosylated proteins, and if so, if it is dependent on transcription of a Golgi glycosyltransferases.  If not, the mechanism might be microRNA dependent.

overall_design:
Among other glycogenes, expression of heparanases, sulfotransferases and epimerase are also of interest.  Heparanase is required for lacritin binding to its co-receptor syndecan-1 and this binding site may require a sulfated iduronic acid.  In request 1705, we recently asked core D whether they could generate this sulfate iduronic acid-containing glycan (iduronic acid (2-O-sulfated)-N-acetylglucosamine-glucuronic acid-N-acetylglucosamine-[glucuronic acid-N-acetylglucosamine]5-glucuronic acid-galactose-galactose-SERINE) to test as a competitive inhibitor in binding studies.
Our experiment is to compare Glyco-gene expression by human corneal epithelial cells in response to cell communication glycoprotein 'lacritin' versus negative control deletion construct 'C-25 lacritin' and versus positive control serum.

first: Gordon

middle: W

last: Laurie

last: Moffit


title: Gene microarray of human embryonic stem cells, differentiated at three development stages, to investigate changes in the genomic transcripts associated with their glycome.

summary:
We are interested in investigating changes in both the glycome and transcriptome of human embryonic stem cells upon differentiation. We have chosen as a model system to differentiate human ES cells into neural spheres using a published protocol by Zhang, S.C. et al. (2001; Nat Biotech. 19: 1129-33).
Based on the information provided by microarray analysis, proteins of interest can be further investigated to associate a particular glycosyltransferase, for example, with production of a specific glycan structure at  a particular stage. Techniques such as the use of RNAi for the knock-down or transfection of hESCs to effect the overexpression of the transcript, followed by subsequent analysis of the glycan structures can be employed.

overall_design: Three developmental stages will be investigated: Stage 1: undifferentiated stem cells; Stage 2: differentiation into embryoid bodies; Stage 3: differentiation into neural spheres. In addition to characterizing the cell surface for glycomic “fingerprints” we want to characterize the genomic transcripts associated with the glycome.

first: Carolyn

last: Bertozzi


title: Interferon-gamma/TNF-treated human corneal epithelial cells

summary: Our experiment is to compare Glyco-gene expression by interferon-gamma/TNF-treated human corneal epithelial cells also treated either with cell communication glycoprotein 'lacritin' or negative control deletion construct 'C-25 lacritin'.  In a newly developing story, lacritin but not C-25 protects human corneal epithelial cells from INFG/TNF-induced cell death.  This expression array will help work out the mechanism of protection to complement phosphoblotting and shRNA approaches currently underway.

overall_design:
Lacritin targets its coreceptor 'syndecan-1' in lacritin-dependent cell proliferation and secretion.
Lacritin appears to be important in human 'dry eye' and in promoting corneal epithelial cell survival in the presence of inflammatory cytokines.


title: To study colon cell line, HCT116, transfected with a candidate microsatellite instability (MSI) gene at one time point after induction

summary: Colorectal cancer, one of the most frequent types of malignancy in the Western world, develops through a multi-step process. The main pathways establishing transformation of normal mucosa to invasive carcinoma include chromosomal instability (CIN), microsatellite instability (MSI) or epigenetic silencing through the CpG Island Methylator Phenotype (CIMP). These pathways have distinct clinical, pathological and genetic characteristics. In general, altered cell surface glycosylation has been linked to colorectal cancer progression, however the impact of MSI-specific pathways on the glycosylation machinery of MSI colon cancer cells has not been investigated yet. In a recent study (Patsos et al., 2009) we have shown that MSI-specific mutations induce marked alterations in cell surface glycosylation, indicating specific changes in the expression of glyco-genes. Therefore the purpose of our experiment is to define these changes by glyco-gene chip analysis.

overall_design:
Biallelic mutational inactivation of MSI target genes is believed to drive MSI tumorigenesis. TGFBR2, ACVR2 and AIM2 are among the most frequently mutated genes in MSI colorectal adenomas and carcinomas and functional studies indicate their contribution to MSI-carcinogenesis. A first general screening approach by lectin FACS analysis indicated a correlation between functional inactivation of these genes and cell surface glycosylation of the MSI colon cell line HCT116 (Patsos et al., 2009). For detailed analysis of the altered glycosylation pattern and the underlying molecular mechanisms we have established HCT116 double stable transfectants that allow doxycycline-inducible expression of the three MSI target genes TGFBR2, ACVR2 and AIM2 in a reversible manner. Thus we can experimentally control the expression of the MSI-genes and analyze short and long-term effects on different cell functions, including glycosylation. From the application of the glyco-gene chip for analysis of the transfectants we expect to gain seminal information on the influence of MSI-target genes on glycan expression and function in MSI tumor cells.
Correlating loss-of-function of MSI target genes not yet linked with glycosylation to the regulation of the glycophenotype is a novel approach to investigate the glycobiology of tumor cells. In addition it is also suitable to detect new MSI-(glyco)markers for clinical applications, including diagnostic tumor markers and specific targets for immunotherapies.

first: Juergen

last: Kopitz


title: To detect the heparan sulfate proteoglycans (HSGP) core proteins that are expressed in these cell lines, so that candidates for the Sulf-2 substrate can be identified

summary: We are requesting a gene microarray analysis for 10 cell lines that are pertinent to human non-small lung cancer.  A main focus of ours has been the role that Sulf-2 plays in non-small cell lung cancer (NSCLC).  Sulf-2 is an extracellular sulfatase that acts on internal glucosamine-6-sulfates within heparan sulfate chains.  Sulf-2 can activate Wnt signaling, as well as modulate other signaling pathways.  Our recent work (Oncogene 29:635, 2010) has shown that Sulf-2 is required for the malignant phenotype of five human NSCLC cell lines (increased migration, increased growth, growth in soft agar, and tumorigenecity in nude mice).

overall_design:
Because Sulf-2  acts on HSPGs to regulate signaling, we are interesting in the HSGP core proteins that are expressed in these cell lines, so that candidates for the Sulf-2 substrate can be identified.  In addition we would like to define the expression of heparan sulfate 6-O-sulfatransferase (3 genes) to see whether these genes are upregulated in cells that depend on Sulf-2 for their malignant phenotype.  Finally, gene profiling will define which Wnt ligands and Wnt receptors (Frizzled''s) are expressed in the cells.
We are asking for gene profiling on the 5 Sulf-2 expressing NSCLC lines previously studied (H292, H460, P-ST, B-ST, and Calu-6), 3 Sulf-2 negative NSCLC lines (H1299, H1703, H1975) and two normal bronchial epithelial cell populations (B-C, P-C).  All of the cells are human in origin.  There are a total of 10 cell types.  With 3 repicates for each, the request is for 30 arrays.

last: Rosen


title: Arabidopsis thaliana young flowers: Wild type vs. sdg2-1 mutant

status: Public on Oct 06 2010

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

summary: Transcriptional profiling in young flowers (stage 8) of Arabidopsis wild type control plants and sdg2-1 mutant is performed using Aligent’s Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K). A significant number of genes involved in gametophyte development are found differentially regulated in the sdg2-1 mutant.

overall_design: Two-condition experiment, young flowers of wild type control vs. young flowers of sdg2-1 mutant. Two biological replicates: 2 control, 2 mutant, independently grown and harvested. One replicate per array.

first: Alexandre

last: Berr

first: Rozenn

last: Ménard

first: Aiwu

last: Dong


title: To study gene expression differences in various dermal equivalents prepared by the individual's laboratory

summary: We have prepared tissue engineered self assembled dermal equivalents with high similarity to the human dermis (skin).

overall_design:
We have manipulated the culture conditions to prepare dermal equivalents with varying amounts of hyaluronic acid and potentially other glycosaminoglycans (GAGs).
We are interested in using array technology to determine which genes responsible for carbohydrate and GAG (and if available protein/glycoprotein) synthesis are being either up-or down-regulated in these constructs as compared to a Normal base construct.

first: Tara

last: Pouyani


title: Identification of natural diterpenes as inducers of resistance to bacterial wilt disease in tobacco, tomato, and Arabidopsis

status: Public on Aug 19 2011

city: Tsukuba

first: Shigemi

last: Seo

state: Ibaraki

address: 2-1-2 Kannondai

department: Plant and Microbial Research Unit, Division of Plant and Microbial Sciences

institute: National Institute of Agrobiological Sciences

summary: The soil-borne bacterial pathogen Ralstonia solanacearum invades a broad range of plants through roots, resulting in wilting of the plant, but no effective protection against this disease has been developed. Two R. solanacearum resistance-inducing compounds were biochemically isolated from tobacco and identified as sclareol and cis-abienol, diterpenes. When exogenously applied to their roots, these diterpenes induced resistance to R. solanacearum in tobacco, tomato, and Arabidopsis plants without exhibiting any antimicrobial activity. Structure-activity correlation analysis of sclareol-related compounds revealed that the hydroxyl group at the eighth carbon position is responsible for the activity for inducing resistance. Microarray analysis identified many sclareol-responsive Arabidopsis genes, such as those encoding or with role in ABC transporters, biosynthesis and signaling of defense-related signal molecules, and mitogen-activated protein kinase (MAPK) cascades. Sclareol-induced R. solanacearum resistance was partially compromised in Arabidopsis mutants defective in the ABC transporter AtPDR12, the MAPK MPK3, and ethylene and abscisic acid signaling pathways. Transgenic tobacco plants in which NtPDR1, a tobacco homolog of AtPDR12, was silenced exhibited also reduced resistance. These results suggest that multiple host factors are involved in resistance to R. solanacearum induced by sclareol and its related compounds and that these compounds can be used to protect crops from bacterial wilt disease.

overall_design: Genes that were preferentially expressed in Arabidopsis roots 2 hours after treatment with sclareol were explored. The microarray analysis was performed in triplicate.

first: Seo

last: Shigemi


title: Expression data in Arabidopsis hda6 mutant axe1-5 and its parental line DR5 under cold and control conditions.

status: Public on Jan 27 2011

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

institute: RIKEN CSRS

summary: To understand the role of Arabidopsis histone deacetylase HDA6 in plant cold acclimation, we have employed transcriptional profiling of the hda6 mutant and its parental line under cold and control conditions to identify genes differentially expressed in the hda6 mutant under cold and control conditions. Aligent’s Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K) were used.

overall_design: Arabidopsis hda6 mutant axe1-5 and its parental line DR5 were grown in MS agar plates for 2 weeks (16 hours light / 8 hours dark). For cold treated sample, the plants were subjected for cold treatment at 2˚C for 3 days (12 hours light / 12 hours dark). Then total RNA was prepared and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.

first: Taiko

middle: K

last: To

first: Kentaro

last: Nakaminami

first: Jong

last: Kim

first: Taeko

last: Morosawa

first: Junko

last: Ishida

first: Maho

last: Tanaka

first: Kazuo

last: Shinozaki


title: A mechanism for triggering cell differentiation in Arabidopsis

status: Public on Jul 09 2011

city: MADRID

first: MAITE

last: SANMARTIN

address: CALLE DARWIN 3

institute: CNB-CSIC

summary: To determine whether IYO is not only necessary but also sufficient to activate transcription of developmental programs, we compared the transcriptome of shoot apices from 35S::IYO-GFP plants to that of 35S::GFP plants at the time of inflorescence emergence. Our results strongly suggest that IYO activates the transcription of key developmental regulators driving differentiation.

overall_design: Shoot apices RNA sample is a pool from RNAs from four independent experiments, and the RNA from each experiment was a pool of RNAs extracted from 12 individuals  Arabidopsis 35S:IYO-GFP or 35S:GFP plants.

first: Maite

last: Sanmartín

first: Michael

last: Sauer

first: Alfonso

last: Muñoz

first: Jan

last: Zouhar

first: Angel

last: Ordóñez

first: Wilhelmina

last: van de Ven

first: Elena

last: Caro

first: María

last: de la Paz Sánchez

first: Natasha

middle: V

last: Raikhel

first: Crisanto

last: Gutiérrez

first: José

last: Sánchez-Serrano


title: Arabidopsis thaliana growth time series

status: Public on Jul 07 2011

city: Dummerstorf

first: Dirk

last: Repsilber

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology

summary:
Transcriptional profiling of A. thaliana seedlings (early development) at 7 time points
We investigate biomass heterosis by scoring partial correlations of transcriptional profiles.

overall_design: We compare 4 genotypes: Col-0 (homozygous parental line), C24 (homozygous parental line), Col-0xC24 and C24xCol-0 (crossings) using 2-4 replicates each

first: Sandra

last: Andorf

first: Hanna

last: Witucka-Wall

first: Thomas

last: Altmann

first: Rhonda

last: Meyer

first: Kathrin

last: Poos

first: Joachim

last: Selbig


title: NINJA connects JAZ proteins to the co-repressor TOPLESS

status: Public on Apr 05 2010

first: Gloria

middle: Garcia

last: Casado

address: C/Darwin 3

department: Genomica

summary: NINJA (At4g28910)  and TOPLESS proteins function as negative regulators of jasmonate responses. Our results point to TPL proteins as general co-repressors that affect multiple signalling pathways through the interaction with specific adaptor proteins. This new insight reveals how stress- and growth-related signalling cascades use common molecular mechanisms to regulate gene expression in plants.

overall_design: Two-condition experiment, Col-0 vs. plants silencing NINJA (RNAi-NINJA) and both Col-0  vs RNAi NINJA treated with coronatine  . Biological replicates: 4 control replicates untreated , 4 RNAi NINJA untreated replicates, 4 control treated replicates and 4 RNAi NINJA treated replicates

first: Laurens

last: Pauwels

first: Gemma

last: Barbero

last: Geerinck

first: Sofie

last: Tilleman

first: Wim

last: Grunewald

first: Amparo

last: Pérez

middle: M

last: Chico

first: Robin

last: Vanden Bossche

first: Jared

last: Sewell

first: Eduardo

last: Gil

last: García-Casado

first: Erwin

last: Witters

last: Inzé

first: Jeff

last: Long

first: Geert

last: De Jaeger

first: Roberto

last: Solano

first: Alain

last: Goossens


title: Identification of putative H2O2 regulated genes during the establishment of the Sinorhizobi...

status: Public on Jan 01 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary:
The involvement of ROS in the legume – Rhizobium symbiotic interaction has been highlighted (Santos et al., 2001; Rubio et al., 2004). This interaction is characterized by the formation of a new organ on the root, the nodule and by the penetration, in parallel, of the bacteria into the root tissue via an infection thread (IT) (Parniske and Downie, 2003; Gage, 2004). H2O2 production has been shown in ITs during the Medicago – Sinorhizobium meliloti interaction (Santos et al., 2001). Moreover, S. meliloti mutants impaired in H2O2 detoxification mechanism possess in planta symbiotic phenotypes. As H2O2 production is known to orchestrate plant gene expression, our goal is focused on identifying the H2O2 regulated genes in the symbiotic process. We focus our analysis in the M. truncatula transcriptome as we are characterising the S. meliloti H2O2 transcriptome. -M. truncatula seedlings were grown in axenic condition on modified Fahraeus medium during seven days. Then they were transferred on new plates supplemented either with dimethyl sulfoxide (DMSO, mock treatement) or diphenylene iodonium (DPI, 10 µM). Twenty four hours later, they were inoculated either with water (mock inoculation; DMSO-H2O and DPI-H2O) or wild type S. meliloti 2011 strain (DMSO-INOC and DPI-INOC). Roots without apexes were harvested 48 hours after inoculation. After RNA extraction (Trizol), quality of the treatment was verified by RT-PCR (ENOD11: inoculation efficiency; GSHS1: DNA contamination; MTC27: constitutive)

Keywords: treated vs untreated comparison

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 8 arrays - Medicago

first: Sandrine

last: Balzergue

first: Nicolas

last: Pauly


title: Colon biopsies from Crohns patients and healthy controls

status: Public on Jul 19 2010

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary: The aim of this study was to investigate differential intestinal gene expression in patients with Crohn's disease (CD) and controls.  172 biopsies from CD and control subjects were studied.  Endoscopic biopsies were taken at ileocolonoscopy from five specific anatomical locations including the terminal ileum for RNA extraction.

overall_design: Biopsies from one of four anatomic locations, from healthy controls and treated (with non-biologic standard of care) or untreated CD patients.

first: Colin

middle: L

last: Noble

first: Alexander

middle: R

first: Charles

last: Lees

first: Jennine

last: Cornelius

first: Karen

last: Toy

first: Zora

last: Modrusan

first: Hilary

last: Clark

first: Ian

middle: D

last: Arnott

last: Penman

first: Jack

last: Satsangi

first: Lauri

last: Diehl


title: Transcriptome in Arabidopsis yellow variegated 2 (var2)

status: Public on Mar 31 2010

city: Okayama

first: Eiko

last: Miura

address: 2-20-1 Chuo, Kurashiki

department: Research Institute for Bioresources

institute: Okayama University

summary: The yellow variegated2 (var2) mutant in Arabidopsis thaliana has been studied as a typical leaf-variegated mutant whose defect results from the lack of FtsH2 metalloprotease in chloroplasts. The var2 green sectors suffer from photooxidative stress and accumulate high levels of reactive oxygen species (ROS) because of compromised Photosystem II repair. This study investigated and compared microarray-based expression profiles of green and white sectors of var2 leaves. Results suggest that ROS that accumulate in chloroplasts of var2 green sectors do not cause much significant change of the transcriptional profile related to ROS signaling and scavenging. In contrast, transcriptome in white sectors apparently differs from those in green sectors and wild type. Numerous genes related to photosynthesis and chloroplast functions were repressed in white sectors. Furthermore, many genes related to oxidative stress were up-regulated. Among them, we specifically examined ROS scavenging genes, such as Cu/Zn superoxide dismutase 2 (CSD2), that were apparently up-regulated in white but not in green sectors. Up-regulation of CSD2 appears to be partly attributable to the lack of a microRNA (miR398) in white sectors. Together, we concluded that white sectors exhibit response to oxidative and other stresses, including CSD2 up-regulation, which might be commonly found in tissues with abnormal chloroplast differentiation.

overall_design: Arabidopsis thaliana ecotype Columbia (Col), used as the wild-type, and var2-1 (var2) were grown in MS medium supplemented with Gamborg’s vitamins (Sigma-Aldrich). MS medium was supplemented with 1.5% (w/v) sucrose and 0.7% (w/v) agar. Plants were maintained under a 12 h light (70 μmol•m-2•s-1)/12 h dark cycle at 22°C. Green and white sectors, surgically separated and collected from 4-week-old true leaves were subjected to total RNA extraction. We also extracted total RNA from Col. Three biological replicates were performed for each sample.

first: Wataru

last: Sakamoto

first: Yusuke

last: Kato


title: Oligonucleotide microarrays for the detection and identification of viable beer spoilage bacteria

status: Public on May 23 2007

city: Bochum

first: Daniel

middle: Gilbert

last: Weber

address: Bürkle-de-la-Camp Platz 1

department: Molekulare Medizin

institute: IPA

summary:
A prototype oligonucleotide microarray was designed to detect and identify viable bacterial species with the potential to grow of common beer spoilage microorganisms from the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus. Probes targeted the intergenic spacer regions (ISR) between 16S and 23S rRNA, which were amplified in a combination of reverse transcriptase (RT) and polymerase chain reaction (PCR) prior to hybridization. This method allows the detection and discrimination of single bacterial species in a complex sample. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non-growing bacteria. The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage microorganisms within mixed population.
Keywords: microarray, oligonucleotide, species-specific, detection, beer spoilage bacteria

sample_organism:
Pectinatus frisingensis
Levilactobacillus brevis
Lacticaseibacillus casei
Loigolactobacillus coryniformis
Megasphaera cerevisiae
Pediococcus damnosus
Pectinatus cerevisiiphilus
Schleiferilactobacillus perolens
Pediococcus inopinatus

overall_design: Each oligonucleotide species-specific probe was spotted in 70 replicate spots on the microarray. Nine single beer spoilage bacteria species were detected with the developed prototype oligonucleotide microarray and also three mixes of two different beer spoilage bacteria species.

middle: G

first: Kerstin

last: Sahm

first: Tino

last: Polen

first: Volker

last: Wendisch

first: Garabed

last: Antranikian


title: Colon biopsies from UC patients and healthy controls

status: Public on Jun 17 2008

first: Alex

last: Abbas

summary:
Transcriptional profiling of colon epithelial biopsies from ulcerative colitis patients and healthy control donors.
Study aims to survey and analyze variation from disease in different GI regions.
Keywords: disease state analysis

overall_design: Biopsies from a variety of anatomic locations, from patients of various treatment status or healthy controls.

first: Colin

last: Noble

first: Alexander

last: Lees

first: Gwo-Tzer

last: Ho

first: Navneet

last: Pal

first: Fiona

last: Zhong

first: Sreedevi

last: Chalasani

middle: F


title: Deletion of Histone Deacetylase 3 reveals critical roles in S-phase progression and DNA damage control

status: Public on Jul 01 2008

city: salt lake city

first: Srividya

last: Bhaskara

state: Utah

address: 2000 circle of hope

department: University of Utah

institute: University of Utah

summary:
Histone deacetylases (HDAC) are enzymes that modify key residues in histones to regulate chromatin architecture, and play a vital role in cell survival, cell cycle progression, and tumorigenesis. To understand the function of Hdac3, a critical component of the N-CoR/SMRT repression complex, a conditional allele of Hdac3 was engineered. Given the vital role of HDAC3 in normal cells and in the generation and treatment of various cancers, a conditional deletion of Hdac3 was engineered in mice. The deletion of Hdac3 in the germ line yielded very early embryonic lethality. Therefore, mouse embryonic-derived fibroblasts (MEFs) containing the Hdac3 conditional allele were used to examine the function of Hdac3 in cell viability and in cell cycle control. Given the links between Hdac3 and transcriptional repression, we used oligonucleotide micro arrays to examine RNA isolated from control and Cre recombinase expressing MEFs to define the changes in gene expression upon inactivation of Hdac3.  Initially, we compared RNA from Ad-Cre infected Hdac3FL/+ and Hdac3FL/- MEFs and then we extended the analysis to Hdac3FL/- MEFs expressing Cre-ER (tamoxifen responsive Cre-estrogen receptor fusion protein).  When the gene expression of ethanol-treated (vehicle) and tamoxifen-treated MEFs was compared at 72 hr post-induction, 83 genes were induced and 111 genes were down-regulated at least 1.5-fold upon inactivation of Hdac3.  Approximately, 48 genes were up-regulated in both Ad-Cre and tamoxifen-treated MEFs at the 72 hr time point.  The majority of the affected genes were associated with signal transduction and metabolism. Overall, few of the up-regulated genes at the 72hr time point in Ad-Cre and tamoxifen-treated MEFs are associated with apoptosis or with cell cycle control. Thus, these metabolic regulatory genes may be “core” Hdac3-regulated genes, and alterations in gene expression are unlikely to trigger apoptosis.
Keywords: Conditional knock out analysis, genetic modification

overall_design: Initially, we compared RNA from Ad-Cre infected Hdac3FL/+ and Hdac3FL/- MEFs. In this analysis, RNA isolated from 64hr and 72hr post Ad-Cre infection were used. We extended the analysis to Hdac3FL/- MEFs expressing Cre-ER (tamoxifen responsive Cre-estrogen receptor fusion protein). In this analysis, two different MEF preparations (repl1 and repl2), two different time points (64hr and 72hr) were used for array analysis with tamoxifen-treated MEFs. For vehicle (ethanol) treated MEFs, two different MEF preparations (repl1 and repl2), and a single timepoint (64hr) was used.

first: Brenda

last: Chyla

first: Joseph

last: amann

first: Sarah

last: Knutson

first: David

last: Cortez

first: Zu-Wen

last: Sun

first: Scott

last: Hiebert


title: Genes regulated by HEB and E2A during DP stage of thymocyte development

status: Public on Dec 04 2007

city: Durham

first: Mary

middle: Elizabeth

last: Jones

state: NC

address: Jones Bldg, Research Dr.

department: Immunology

institute: Duke University

summary:
To investigate gene targets of the E-proteins HEB and E2A during the CD4+CD8+ double positive (DP) stage of T cell development.  We examined E-protein function by simultaneous removal of both HEB (Tcf12) and E2A (Tcfe2a) genes at the DP stage.  This was done by crossing mice containing HEB floxed and E2A floxed alleles to a CD4Cre background (Tcf12f/fTcfe2af/fCD4Cre mice).  Microarray analysis was used to compare gene expression in HEB and E2A double deficient DP thymocytes (Cre+) to Cre- control DP thymocytes.
Keywords: genetic modification

overall_design: CD4+CD8+ DP cells were sorted from Tcf12f/fTcfe2af/fCD4Cre+ (Cre+) and Tcf12f/fTcfe2af/fCD4Cre- (Cre-) thymus.  The same CD4hiCD8hi gate was used for Cre+ and Cre- sorting, to assure analysis of population expressing similar CD4 and CD8 levels.  Independent sorts from two mice per genotype were done: Cre+ A, Cre+ B, Cre- A, Cre- B.  Total RNA was extracted for array analysis.  Two comparisons were performed: Cre+ to a mouse reference sample and Cre- to this same reference, each done in duplicate (2 biological replicas).

middle: E

first: Yuan

last: Zhuang