title: Comparison of gene regulation by Gcn5 under KCl stress in S. cerevisiae and S. pombe

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

summary:
This is parallel comparison of gene regulation by Gcn5 in evolutionarily divergent yeasts S. pombe and S. cerevisiae. Our study showed Gcn5 is required for a similar spectrum of stress responses in both organisms, including the response to KCl. This DNA microarray studies is to find conserved or diverged gene regulation pattern under KCl stress condition in the two yeasts.  There are 6 subsets in total, 3 subsets in each evolutionarily divergent yeasts including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment,  3 wild type strains under KCl treatment compared to wild type without treatment.
Keywords: stress response, Gcn5, Comparative genomics, Transcriptional co-activator

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Gene expression profiling experiment in which gene expression in logarithmically growing cultures of test groups was compared to that of the control groups in rich medium at 25C. There are 6 subsets in total, 3 subsets in each yeast including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment, 3 wild type strains under KCl treatment compared to wild type without treatment.  RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004). Independent RNA preparations were used to hybridize to microarray slides with dye swap. Data normalized with 'Lowess' per chip per spot normalization.

first: Yongtao

last: Xue-Franzen

first: Anna

last: Johnsson


title: HBX-HepG2 versus Control-HepG2

status: Public on Dec 31 2009

city: Singapore

first: Yu

last: Wang

address: 11 Hospital Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: Mature microRNA expression profiling of HBx-expressing HepG2 cells versus Control cells under UV stress

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The mature microRNA expression profile of HBx-expressing HepG2 cells versus control cells in three independent biological repeated experiments.  This study focuses only on human sequences. The complete data matrix is linked below as a supplementary file.

first: Caroline

last: Lee


title: pCMV-FAK vs pCMV in R5

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

country: Switzerland

institute: University of Berne

summary: CMV-driven FAK overexpression in soleus muscle was compared vs empty transfection in contralateral muscle after 5 day of reloading

overall_design: paired comparison in contralateral leg

last: Flueck


title: pCMV-FRNK/pCMV-FAK vs pCMV-FAK in CTL

summary: CMV-driven inhibition of FAK in soleus muscle was compared vs contralateral muscle


title: pCMV-FAK vs pCMV in HU

summary: CMV-driven FAK overexpression in soleus muscle was compared vs empty transfection in contralateral muscle after unloading


title: Virally infected LSEC trigger CD8 T cell immunity

city: Bonn

first: Michaela

last: Kern

address: Sigmund-Freud-Str. 25

country: Germany

institute: University of Bonn

summary: Dendritic cell activation through ligation of pattern recognition receptors leading to full functional maturation causes induction of CD8 T cell immunity instead of tolerance through increased delivery of co-stimulatory signals. Here we investigate whether a prototypic organ-resident antigen-presenting cells, i.e. liver sinusoidal endothelial cells (LSEC), also switch from tolerogenic to immunogenic CD8 T cell activation upon such activation. We demonstrate by gene expression analysis that LSEC expressed numerous pattern recognition receptors that attributed sentinel function, but ligand-induced activation of these receptors was not sufficient to overcome tolerance induction of CD8 T cells. However, viral infection caused functional maturation of antigen-presenting LSEC and was sufficient to promote antigen-specific differentiation into fully functional effector CD8 T cells in the absence of dendritic cells. Thus, we identify a novel principle of inducing CD8 T cell immunity by virally infected organ-resident antigen-presenting cells employing distinct mechanisms compared to dendritic cells.

overall_design: Transcriptional profiles of untreated liver sinusoidal endothelial cells (LSEC) and LSEC, stimulated with either LPS (100ng/ml) or infected with MCMV-GFP (MOI=0.1) were compared on Illumina Mouse WG-6 BeadChip microarray platform. All samples represent biological replicates and were processed separately throughout the experiment.

first: Alexey

last: Popov

first: Joachim

middle: L

last: Schultze

first: Percy

middle: A

last: Knolle


title: pCMV-FAK vs pCMV in CTL

summary: CMV-driven FAK overexpression in soleus muscle was compared vs empty transfection in contralateral muscle


title: pCMV-FAK vs pCMV in R1

summary: CMV-driven FAK overexpression in soleus muscle was compared vs empty transfection in contralateral muscle after 1 day of reloading


title: Oxidative stress transcriptome of japonica rice

city: Orono

first: Benildo

middle: G

last: de los Reyes

state: ME

address: 5735 Hitchner Hall

department: School of Biology and Ecology

country: USA

institute: University of Maine

summary:
Regulation of gene expression by reactive oxygen species (ROS) is an important component of abiotic stress signal transduction mechanisms.  Previous genome-wide analysis of chilling-induced changes in gene expression suggested a potential role of H2O2 and other ROS as key signals in the induction of early response genes in japonica rice (cv. Nipponbare). Candidate regulators including bZIP-, Myb- or WRKY-types of transcription factors that were responsive to both chilling (10oC) and exogenous H2O2, and their probable target clusters (as1/ocs/TGA1-like, MybR-like element containing genes) were inferred by integrative analysis of qPCR expression profiles and ab initio promoter motif data.  In an effort to define the composition and hierarchical organization of the ROS-mediated chilling response regulatory networks, we examined the effect of exogenous H2O2 (6 hours in 4mM H2O2 at 28oC and then 6 hours of recovery in water at 28oC) on the transcriptome of Nipponbare in a genome-wide scale and compared them with the chilling stress transcriptome.  Results of this study were consistent with our earlier model that a ROSbZIP-as1/ocs/TGA1 regulatory module is a direct consequence of chilling-induced elevation of intracellular ROS during the initial 24 hours.
Keywords: time course (response to exogenous H2O2)

overall_design:
This experiment describes the analysis of the temporal changes in gene expression in response to exogenous H2O2 in Nipponbare rice. A total of 5 treatment regimes were examined (1, 3, and 6 hours at 4 mM H2O2 and then 3 and 6 hours of recovery in water after 6 hours of exposure to H2O2).

The microarray platform used in this study was the 45K oligonucleotide microarray (www.ricearray.org) which comes in pairs of slides A and B (each containing about 50% of the total number of features). The data described in this series include all hybridizations with slide A and with slide B. All experiments were performed with two independent biological replicates (R1 and R2) for each time point.

first: Myoung-Ryoul

last: Park

first: Kil-Young

last: Yun

first: Venura

last: Herath

first: Bijayalaxmi

last: Mohanty

first: Song-Joong


title: Preadipocytes of T2DM patients display an intrinsic gene expression profile of decreased differentiation capacity

city: Maastricht

first: Florence

last: van Tienen

address: Universiteitssingel 50

department: Genetics and Cell biology

country: Netherlands

institute: Maastricht University

summary: Insulin resistance and Type 2 Diabetes Mellitus (T2DM) are associated with increased adipocyte size, altered secretory pattern and decreased differentiation of preadipocytes. To identify the underlying molecular processes in preadipocytes of T2DM patients that are a characteristic of the development of T2DM, preadipocyte cell cultures were prepared from subcutaneous fat biopsies of T2DM patients and compared with age- and BMI matched control subjects.  Gene expression profiling showed changed expression of transcription factors involved in adipogenesis and in extracellular matrix remodeling, actin cytoskeleton and integrin signaling genes, which indicated decreased capacity to differentiate. Additionally, genes involved in insulin signaling and lipid metabolism were down-regulated, and inflammation/apoptosis was up-regulated in T2DM preadipocytes. The down-regulation of genes involved in differentiation can provide a molecular basis for the reduced adipogenesis of preadipocytes of T2DM subjects, leading to reduced formation of adipocytes in subcutaneous fat depots, and ultimately leading to ectopic fat storage.

overall_design: 7 T2DM preadipocyte samples and 9 age- and BMI-matched control samples were hybridized using 70-mer oligonucleotide microarrays. Samples were labeled with either Cy3 or Cy5. A total of 20 arrays were used including dye swop. Per array, a T2DM sample was hybridized with a control sample of the same gender and matched based on age and BMI. To ensure hybridization of two samples with the same gender, three T2DM (5064, 5128, 5395) and one control sample (5616) were used twice and listed as technical replicates.

middle: H

first: Carla

middle: J

last: van der Kallen

first: Patrick

last: Lindsey

first: Marleen

middle: M

last: van Greevenbroek

first: Ronald

last: Wanders

first: Hubert

last: Smeets


title: Macrophages heterogeneity in human atherosclerotic plaques

status: Public on Dec 30 2009

city: Paris

first: Seraya

last: Maouche

state: Paris

address: 91 Bd de l'Hôpital

department: Cardiovascular Genomics

country: France

institute: INSERM U937

summary: This study aims to characterize the transcriptional profile of Granulocyte-macrophage colony-stimulating factor induced macrophages (GM-MØ) and M-CSF macrophages (M-MØ) and to investigate in situ a subset of genes and their products specific to each phenotype in human atherosclerosis plaques

overall_design: 18 RNG/MRC two-colour oligonucleotide microarrays (Le Brigand et al. 2006) were used to generate global mRNA expression profiles for GM-CSF-induced, M-CSF-induced, and peritoneal macrophages. The microarray experiments were conducted either as a common reference (peritoneal-like macrophages) design or using a direct design by hybridizing Granulocyte-macrophage colony-stimulating factor (GM-CSF)-induced human monocyte-derived macrophage (GM-MØ) and CSF-induced human monocyte-derived macrophages(M-MØ) on the same arrays

first: Isabelle

last: Brochériou

first: Hervé

last: Durand

first: Vincent

last: Braunersreuther

first: Gilles

last: Le Naour

first: Julia

last: Kzhyshkowska

first: Fabien

last: Koskas

first: François

last: Mach

last: Cambien

first: Ewa

last: Ninio


title: CGH analysis of Candida albicans strains after in vitro evolution in the presence or absence of Fluconazole

city: Boston

first: Anna

last: Selmecki

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: Here we provide, for the first time, a longitudinal study of the prevalence, dynamics, and fixation of gross chromosomal rearrangements, including aneuploidy, in the presence and absence of fluconazole during a well-controlled in vitro evolution experiment.  While no aneuploidy was detected in any of the no-drug control populations, in all fluconazole-treated populations analyzed, isochromosome 5L [i(5L)] appeared soon after drug exposure, was associated with increased fitness in the presence of drug, and became fixed in independent populations. In two separate cases, larger supernumerary chromosomes composed of i(5L) attached to other chromosome fragments appeared and were later lost during exposure to the drug. Other aneuploidies, particularly trisomies of the smaller chromosomes (Chr3-7), appeared throughout the evolution experiment, and the rapid accumulation of multiple aneuploid chromosomes per cell coincided with the highest resistance to fluconazole.

overall_design: All experimental strains were compared to the same reference control - sequenced strain SC5314.  Some replicates are included and titled 'slide 2' for a given strain.  Whole genomic DNA was used for all samples except the array labeled 'CHEFband' where we isolated DNA from a single CHEF gel band, labeled it, and hybridized it to the array.

first: Judith

last: Berman

first: James

last: Anderson

first: Leah

last: Cowen


title: Growth of Cupriavidus metallidurans CH34 in the presence of basalt

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

country: Belgium

summary: The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Yet the genetics of biological rock weathering are unknown. For the first time, we apply a DNA microarray to investigate the genes involved in weathering by the heavy metal resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium sequesters iron in the ferrous state (FeII); therefore, not requiring siderophores. Instead an energy efficient process involving upregulation of large porins is employed concomitantly with genes associated with biofilm formation. We hypothesise that rock weathering is induced by changes in chemical equilibrium at the microbe-mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal resistant genes. Volcanic environments are analogous to some of the earliest environments on Earth. These results not only elucidate the mechanisms by which microorganisms might have sequestered nutrients on the early Earth but they also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity.

overall_design: Cultures of Cupriavidus metallidurans CH34 were grown in Tris buffered medium MM284 media (with iron), MM284 without iron and MM284 without iron with sterilized basalt at 25 rpm, 30°C until mid-log phase. RNA was extracted from the cells. Three biological replicates of both samples were differentially labeled (resp. Cy3 and Cy5) and hybridized to three CH34 60-mer oligonucleotide glass-spotted microarray carrying three technical repeats.

first: Karen

last: Olsson

first: Rob

last: Van Houdt

first: Max

last: Mergeay

first: Charles

middle: S

last: Cockell


title: Expression data from RNA half-life experiments in Prochlorococcus

city: Freiburg

first: Claudia

last: Steglich

address: Schaenzlestr. 1

department: Biology

institute: University of Freiburg

summary:
RNA decay was measured in Prochlorococcus after inhibition of transcription by rifampicin using customized Affymetrix gene expression arrays.
RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, a relatively slow-growing marine cyanobacterium doubling approximately once a day, which is extremely abundant in the oceans. Using a combination of microarrays, quantitative RT-PCR and a new algorithm for determining RNA decay rates, we found a median half-life of 2.4 min and a median decay rate of 2.6 min for expressed genes – two-fold faster than that reported for any organism. The shortest transcript half-life (33 seconds) was for a gene of unknown function, while some of the longest (ca. 18 min) were for highly expressed genes. Genes organized in operons displayed intriguing mRNA decay patterns, such as increased stability, and delayed onset of decay with greater distance from the transcriptional start site. The same phenomenon was observed on a single probe resolution for genes greater than 2 kb. We hypothesize that the fast turnover relative to generation time in Prochlorococcus may enable a swift response to environmental changes through rapid recycling of nucleotides, which could be advantageous in nutrient poor oceans. Our growing understanding of RNA half-lives will inform on the modelling of cell processes and help interpret the growing bank of metatranscriptomic studies of wild populations of Prochlorococcus. The surprisingly complex decay patterns of large transcripts reported here, and the method developed to describe them, will open new avenues for the investigation and understanding of RNA decay for all organisms.

sample_organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

overall_design: Prochlorococcus cells were treated with rifampicin, which prevents initiation of new transcripts. Cells were harvested at 0 min (before rifampicin addition), 2.5 min, 5 min, 10 min, 20 min, 40 min and 60 min after rifampicin addition.

first: Matthias

last: Futschik

first: Debbie

last: Lindell

first: Trent

last: Rector

first: Robert

last: Steen

first: Sallie

middle: W

last: Chisholm


title: Differential expression of Aedes aegypti salivary gland transcriptome upon blood feeding

city: Galveston

first: Saravanan

last: Thangamani

state: TX

address: 301 University Blvd

department: Pathology

institute: University of Texas Medical Branch

summary: We have developed an oligoGEArray with 434 genes from Ae. aegypti salivary gland. OligoGEArray was customized with the salivary gland genes chosen from the transcriptome source published by Ribeiro et al (2007). Oligonucleotides (60bp) were designed and array were manufactured by SABiosciences.  Using this OligoGEArray, we analyzed the differential expression of salivary trancritptome upon blood feeding.

overall_design: Salivary glands were dissected from 1, 3, 24 and 48 hours post fed (hpf) and unfed Ae. aegypti. Total RNA were extracted and the differential expression of transcriptome were analysed.  Quantitative Real-Time PCR was performed on selected genes to validate the OligoGEArray data.

first: Stephen

last: Wikel


title: Gene Expression Changes in Campylobacter jejuni triggered by exposure to Novobiocin

status: Public on Dec 28 2009

city: Ames

first: Yang

last: Wang

state: IA

address: 1113 Vet Med

department: VMPM

institute: Iowa State University

summary: In order to investigate the gene experssion changes in Campylobacter jejuni triggered by exposure to Novobiocin.

overall_design: DNA microarray was used to identify genes that were differentially expressed in C. jejuni 11168 treated with Novobiocin. For RNA extraction, Campylobacter cells were grown 4 hrs in MH broth to the mid exponential phase (OD600=0.4-0.5) with shaking rates 180rpm at 42°C, and then split into two equal portions, one of which was treated with subinhibitory dose of Novobiocin (256ug/ml, 0.25 MIC) and the other served as a non-treated control, all of these samples were incubated at 42°C for 30 min under microaerobic conditions, RNA samples were extracted from 4 independent treatments and 4 non-treated controls. Then cDNA was synthesized using aminoallyl-dNTP and RNA samples according to the manufacturer’s instruction. After purification, aminoallyl labeled cDNA was fluorescently labeled with Cy-3/Cy-5 mono-Reactive Dye Pack.

first: Jianzhong

last: Shen

first: Jing

last: Han

first: Zhangqi

first: Qijing

last: Zhang


title: Epigenetic Control of Light-Regulated Gene Expression in Arabidopsis

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

type: Genome binding/occupancy profiling by genome tiling array

summary: Although landscapes of several epigenetic marks are now available for Arabidopsis and rice, such profiles remain static and do not provide information about dynamic changes of plant epigenomes in response to developmental or environmental cues. Here we analyzed the effects of light regulation on four epigenetic histone modifications (H3K9ac, H3K9me3, H3K27ac, H3K27me3). Our genome-wide profiling of H3K9ac and H3K27ac revealed that these modifications are gene-specific. In contrast, we found that H3K9me3 and H3K27me3 target genes, but also intergenic-regions and transposable elements. Specific light conditions affected the number of epigenetically modified regions, as well as the overall correlation strength between the presence of specific epigenetic modifications and transcription. Futhermore, we observed that acetylation is an important contributor to light-regulated genome expression not only through its activating action on HY5 and HYH but also on their downstream targets. We found that dynamic acetylation changes in response to light have a major role in the active regulation of photosynthetic gene expression, while H3K27ac and H3K27me3 are major contributors to light regulation of the gibberellin metabolism. We also identified distinct epigenetic patterns in the epigenome of the photomorphogenic mutant cop1-4, suggesting that COP1 might have a role in the establishment of specific epigenetic modifications. Thus, this work provides a dynamic portrait of the variations in histone modifications in response to the plant’s changing light environment and strengthens the concept that epigenetic modifications represent another layer of control for light-regulated genes involved in photomorphogenesis.

overall_design: Arabidopsis ecotype Columbia (Col-0) was the genetic background used for this study. Seeds were stratified for two days at 4°C, then germinated and grown for five days at 22°C in continuous darkness (D). Six hours before harvest, a number of plates were transferred to continuous white light (D to L). The cop1-4 mutant was also used in this study. Seedlings from the different conditions and genotypes were harvested at the same time of day. Chromatin was immunoprecipitated, washed, reverse crosslinked, amplified and hybridized according to Affymetrix’ Chromatin Immunoprecipitation Assay Protocol Rev.3. Three μl of the following antibodies were used: anti-H3K9ac (Upstate 06-942), anti-H3K9me3 (Upstate 07-442), anti-H3K27ac (Upstate 07-360), anti-H3K27me3 (Upstate 07-449), and anti-H3 (Upstate 07-690). Four biological replicates were hybridized to tiling arrays.

first: Jean-Benoit

middle: F

last: Charron.

first: Axel

last: Elling

first: XingWang

last: Deng


title: Streptococcus mutans UA159 vs. spx mutant strains

status: Public on Dec 25 2009

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: Transcriptional profiling to investigate the regulatory roles of SpxA and SpxB of S. mutans.

sample_organism:
Streptococcus mutans
Streptococcus mutans UA159

overall_design: RNA was extracted from four replicate samples of each strain of interest (spxA mutant, spxB mutant, spxAB double-mutant, UA159 wild type) and labeled with Cy3.  For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cells grown to mid-log.

first: Jacqueline

last: Abranches

first: Jose

last: Lemos


title: Microarray analysis of mRNAs enriched in the vegetal cortex of Xenopus oocytes

city: Iowa City

first: Douglas

middle: W.

last: Houston

department: Department of Biology

institute: The University of Iowa

summary: RNA localization is a fundamental mechanism for controlling the spatial regulation of protein synthesis within cells, as well as differential cell fates during early development. Localized RNAs are known to control critical aspects of early Xenopus development, but few have been studied in detail. We set out to identify novel transcripts localized to the vegetal cortex of Xenopus oocytes, one of the best-studied examples of RNA localization. We identified over 400 transcripts enriched in the vegetal cortex, compared with whole oocytes. Included were many novel genes, as well as known genes not thought to undergo RNA localization. These data suggest that the role of RNA localization in early development is extensive and will provide a resource for identifying candidate regulatory genes for early developmental processes.

overall_design: RNA was extracted from isolated vegetal cortices and compared with whole oocytes. Two biological replicates were used, each from a different donor female.


title: Analysis of PHOTOPERIOD SENSITIVITY5 Sheds Light on the Role of Phytochromes in Photoperiodic Flowering in Rice

city: Cologne

first: Fernando

last: Andres

address: Carl von Linne 10

department: Plant Developmental Biology

institute: Max Planck Institute for Plant Breeding Research

summary: A great majority of plants synchronize flowering with day length. In rice, the most important environmental cue that triggers flowering is the photoperiod. Here, we show that the s73 mutant, identified in a gamma irradiated Bahia collection, displays early flowering and photoperiodic insensitivity due to a null mutation in the SE5 gene, which encodes an enzyme implicated in phytochrome chromophore biosynthesis. s73 mutant plants showed a number of alterations in the characteristic diurnal expression patterns of master genes involved in photoperiodic control of flowering, resulting in up-regulation of Hd3a, the most important floral integrator. Ehd1, an additional rice floral activator, was also highly expressed in the s73 mutant, suggesting that SE5 represses Ehd1 in wild-type plants. Silencing of Ehd1 in both Bahia and s73 backgrounds implies that SE5 regulates Ehd1 expression. The data also indicate that SE5 confers photoperiodic sensitivity through regulation of Hd1. These results provide direct evidence that phytochromes inhibit flowering affecting both Hd1 and Ehd1  flowering pathways.

overall_design:
Four biological replicates from each genotype (s73 mutant and Bahia wt) were labelled with Cy3 and Cy5 alternatively (2+2) following a dye-swap design. In total, 4 microarrays were hybridized.

The supplementary file 'GSE16796_stat_analysis.txt' contains the final statistical analysis of study GSE16796.

first: David

last: Galbraith

first: Manuel

last: Talon

first: Concha

last: Domingo


title: Chilling stress transcriptional regulatory networks of japonica rice

first: Benildo

last: de los Reyes

summary:
The central role of transcriptional regulation in integrating various low temperature response mechanisms has been established in Arabidopsis, where the CBF/DREB regulon plays a prominent role during acclimation. Rice is sensitive to chilling but many japonica cultivars can survive continuous exposure to as low as 10oC for up to 7 days during the most critical stage of seedling establishment better than most indica cultivars. The transcriptional regulatory networks that define this variation have not been studied in detail as cold acclimation has been scrutinized in Arabidopsis. Towards the comparison of the compositional complexity of low temperature response regulons of rice and Arabidopsis, we used the cultivar Nipponbare for genome-wide survey of regulatory clusters by integrative analysis of promoter architectures and temporal expression profiles during exposure to 10oC at narrow time intervals.
Temporal profiles revealed major clusters of genes that were induced within the initial 24 hours. These clusters were further defined by common features of having either CRT/DRE-like elements, as1/ocs-like elements or both in their promoters. Genes containing as1/ocs-like elements with or without CRT/DRE, but not those containing only CRT/DRE-like elements were induced by exogenous H2O2 but not by ABA at ambient temperature, suggesting that they belong to a potential regulon (ROS-bZIP – as1/ocs module) that responds to elevated levels of reactive oxygen species (ROS) during the initial stages of stress.  Parallel analysis of transcription factors during the initial 12 hours revealed candidate regulator(s) of this putative early response regulon. Cultivar-specific expression signatures of selected members of this regulatory cluster were also positively correlated with genotypic variation in chilling tolerance. We hypothesized that the ROS-bZIP – as1/ocs cluster has important roles in configuring the transcriptome of rice seedlings during the early stages of chilling stress and it appears to be independent of ABA and functions in parallel to the CBF/DREB regulon.
Keywords: time course (response to low temperature)

overall_design: This experiment describes the analysis of the temporal changes in gene expression in response to chilling temperature in Nipponbare rice. A total of 10 stress time points, i.e., 0.5, 2, 4, 6, 12, 18, 24, 36, 48, and 96 hrs after exposure to 10C in a growth chamber and one recovery time point, i.e., 96 hrs at 10C and then 24 hrs (24R) at ambient or control temperature (29C), were profiled with reference to a corresponding control, which was exposed to ambient temperature (29C) for the same length of time under cold stress (each stress time point has a corresponding control sample).  Control and cold stress samples were labeled with Cy5 and Cy3, respectively. No dye swap replicate was performed in this experiment. The microarray platform used in this study was the 45K oligonucleotide microarray (www.ricearray.org) which comes in pairs of slides A and B (each containing about 50% of the total number of features). The data described in this series include all hybridizations with slide A and with slide B. All experiments were performed with two independent biological replicates (R1 and R2) for each time point.

first: Kil-Young

last: Yun

first: Myoung-Ryoul

last: Park

first: Bijayalaxmi

last: Mohanty

first: Richard

last: Bruskiewich


title: Genetic Influences on Asthma Susceptibility in Developing Lung

first: Alvin

middle: T.

last: Kho

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

summary: Whole transcriptome assay of whole lung of rat from 3 genetic strains (Lewis, Fisher, Brown Norway) at 3 postnatal time points (postnatal days 1, 7, 14).

overall_design: Total RNA obtained from whole lung of rat from 3 genetic strains and 3 postnatal time points in (mainly) quadruplicate measurements per strain and time point.

middle: T

first: Andre

last: Ponton

first: Jen-Hwa

last: Chu

first: Feige

last: Kaplan


title: Growth and Transcriptional Response of Salmonella Typhimurium LT2 to Glucose-Lysine-Based Maillard Reaction Products

city: Fayetteville

first: Arunachalam

last: Muthaiyan

state: AR

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

summary: Glucose-lysine based Maillard reaction products (MRPs) are introduced to the human body via food ingestion or are synthesized in vivo. Depending on reaction conditions, they represent a mixture of compounds with diverse chemical structures and physiological properties. MRPs may also be a potential nutrient source for Salmonella, a major foodborne gastrointestinal pathogen. This study was designed to determine the growth and transcriptional responses of S. Typhimurium LT2 to MRPs generated at low water activity to simulate the reaction occurring during food processing and storage. Maillard reactions between N-α-acetyl-lysine and glucose were varied in time (4, 23, and 143 h) to generate sub-samples with prevailing Amadori compound, advanced glycation end products (AGEs), or melanoidines respectively. The addition of MRP up to 5 mg mL-1 to defined media with 0.4% glucose had no effect on S. Typhimurium LT2 growth. In media, where the MRP sub-samples (4 and 23 h) served as the only carbon source, MRP assimilation by S. Typhimurium LT2 was observed as secondary logarithmic growth phases (0.063 h-1 and 0.072 h-1) after the growth on glucose available in the MRP  reaction mixtures (0.479 h-1). The MRPs sub-sample with the highest concentration of melanoidines (143 h) also supported S. Typhimurium LT2 growth (0.368 h-1). Of the three MRPs sub-samples, the Amadori compound was the preferred carbon source for S. Typhimurium LT2 as evidenced by its almost complete disappearance (98%). Decreases in AGEs (37%) and melanoidines (15%), when incubated with S. Typhimurium LT2, also occurred. Transcription profiles of the cells grown on the MRPs fractions revealed predominant up-regulation of genes associated with the functional groups of energy metabolism, fatty and phospholipid metabolism, cellular process, and regulatory functions, and general down-regulation of the genes in the groups of amino acid biosynthesis, protein synthesis and transcription, transport and binding proteins, and DNA metabolism. The carbon flow in tricarboxylic acid (TCA) cycle partitioned by the glyoxylate cycle appeared to play an essential role in the assimilation of glucose-lysine-derived MRPs. The high expression level of numerous genes encoding hypothetical proteins or proteins with unknown function suggested the presence of genes whose role in glucose-lysine MRPs catabolism in Salmonella remains to be determined.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design:
This study was designed to determine the growth and transcriptional responses of S. Typhimurium LT2 to MRPs generated at low water activity to simulate the reaction occurring during food processing and storage. Maillard reactions between N-α-acetyl-lysine and glucose were varied in time (4, 23, and 143 h) to generate sub-samples with prevailing Amadori compound, advanced glycation end products (AGEs), or melanoidines respectively. Total bacterial RNA was isolated as previously described and the RNA samples were then converted to fluorescently-labeled cDNA and hybridized to S. Typhimurium microarrays version 5 (NIAID's Pathogen Functional Genomics Resource Center). Real-time PCR and physiological experiments were performed to validate the microarray data.

In all supplementary files channel A = Cy3, channel B = Cy5.

first: Vesela

middle: I

last: Chalova

first: Oswaldo

last: Hernández

first: Sujata

last: Sirsat

first: María

last: Sanz

first: Javier

last: Moreno

first: Steven

middle: C

last: Ricke


title: The effect of negative energy balance on bovine blood PMN gene expression

city: Tjele

first: Kasey

last: Moyes

address: Blichers Allé 20, P.O. BOX 50

department: Animal Health, Welfare, and Disease

country: Denmark

institute: University of Aarhus

summary: Our objectives were to compare gene expression profiles in neutrophils (PMN) during a Streptococcus uberis mastitis challenge between lactating cows subjected to feed restriction to induce negative energy balance (NEB; n = 5) and cows fed ad libitum to maintain positive energy balance (PEB; n = 5).  The NEB cows were feed-restricted to 60% of calculated net energy for lactation requirements for 7 d, whereas PEB cows were fed the same diet for ad libitum intake.  After 5 d of feed restriction, one rear mammary quarter of each cow was inoculated with 5,000 cfu of Streptococcus uberis (strain O140J).  Blood PMN were isolated at 24 h post-inoculation from all cows for RNA extraction and microarray analysis.  NEB resulted in 94 differentially expressed genes compared with PEB.  Of these, 51 genes were down-regulated, including genes involved with antigen presentation (HLADRA and HLAA), respiratory burst (SOD1), and the pro-inflammatory response (TNFA and IRAK-1).  The most affected genes up-regulated by NEB (n = 43) included IL1R2 and IL6, toll-like receptors (TLR2 and TLR4), and THY1. Network analysis by Ingenuity Pathway Analysis ® revealed that TNFA was associated with the expression of numerous differentially expressed genes involved with immune response in NEB cows compared with PEB cows.  Energy balance alters PMN expression of several genes involved with immune response, which provides new information on transcriptomic mechanisms associated with post-partal NEB and immune response during early lactation.

overall_design: Briefly, 10 multiparous Holstein cows in PEB and past peak lactation were used for this study. The NEB cows were feed-restricted to 60% of calculated NEL requirements for 7 d, whereas PEB cows were fed the same diet for ad libitum intake. After 5 d of feed restriction, one rear mammary quarter of each cow was inoculated with 5,000 cfu of Streptococcus uberis (strain O140J). Blood PMN were isolated at 24 h post-inoculation from all cows. A 13,257-oligonucleotide (70-mers) array was used for transcript profiling. Cy3- and Cy5 labelled cDNA from PMN and a reference standard were used for hybridizations. All samples were hybridized to duplicate slides with reverse labeling (20 microarrays total).

first: James

last: Drackley

first: Dawn

middle: E

last: Morin

first: Massimo

last: Bionaz

first: Sandra

last: Rodriguez-Zas

first: Robin

last: Everts

first: Harris

last: Lewin

first: Juan

last: Loor


title: Comparative Genomic Hybridizations of Mycoplasma gallisepticum Vaccine strains and strain Rlow

status: Public on Dec 24 2009

city: Storrs

middle: J.

last: Geary

address: 61 N. Eagleville Rd

department: Pathobiology and Veterinary Science

institute: University of Connecticut

summary: Genomic content of Vaccine strains were probed against the known sequence of the virulent strain Rlow of M. gallisepticum to identify divergent or absent genes in the attenuated strains.

overall_design: Genomic DNA was extracted from in vitro grown cultures of M. gallisepticum strains Rlow, F, ts-11, and 6/85 and three samples from each were selected for hybirdization to oligonucleotide microarrays using standard methods from the Bioprime CGH kit.  All samples were labeled with Cy3 dye and scanned at a PMT gain of 700 using a GenePix 4000B scanner.  Features are duplicated on the slides and data were averaged between duplicate features on each slide.  Median signal intensities were averaged between samples of the same strain and each feature from each vaccine strain was compared to Rlow.  Features exhibiting four-fold or less hybridization in the vaccine strains were considered divergent or absent.

first: T

last: Gorton

first: S

last: Szczepanek


title: Influence of Microbial and Host Cell Sublethal Heat Stress on S. Typhimurium Gene Expression

first: Arunachalam

last: Muthaiyan

summary: Environmental stress contributes to the outcome of infection by impacting both microbial virulence and host susceptibility to infection.  Thermal processing, commonly used for decontamination of poultry in the food industry, may elicit sublethal stress on resistant serovars of Salmonella. We employed traditional heat shock temperatures (42 and 48ºC), similar to avian body temperature and poultry processing conditions, to study gene expression of Salmonella enterica serovar Typhimurium. Microarray analysis indicated that thermal shock at 42°C and 48°C induced expression of SPI-2 and SPI-5 genes, whose products are required for adhesion and survival.   However, SPI-1 genes, responsible for invasion of Salmonella into host cells, were down-regulated following exposure to 42°C and 48°C.  Bacterial adhesion assays showed greater adhesion of heat-stressed S. Typhimurium to Caco-2 cells compared to non-stressed bacteria.  In addition, subjecting Caco-2 cells to mild heat shock (39°C), which is similar to human fever, enhanced host cell susceptibility to bacterial adhesion.  Data indicate that thermal stress enhances bacterial colonization and host cell susceptibility to adhesion during S. Typhimurium infection.

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

overall_design: Several different hurdles methods are used in the food industry to combat foodborne pathogens on meat surfaces. One of these methods is thermal treatment. The objective of our study was to test the effect of heat stress on the gene expression of Salmonella. We tested traditional heat shock temperatures (42 and 48ºC), similar to avian body temperature and poultry processing conditions for this study. We grew the Salmonella at 30 ºC overnight. After this, we transferred to fresh media and grew the cells to mid-log phase.  The cells were then subjected to heat shock and gene expression analysis using microarrays was carried out. We found an induced gene expression profile of genes involved in adhesion and repression in genes involved in invasion. We followed up this study by tissue culture analysis to test if heat stressed Salmonella adhere better to intestinal Caco-2 cells and found that there was increased adhesion but decreased invasion.

first: Kristin

last: Burkholder

first: Scot

last: Dowd

first: Arun

last: Bhunia


title: Gene expression profiles of mono- and biallelic CEBPA mutations in cytogenetically normal AML

city: Munich

first: Klaus

last: Metzeler

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University of Munich

summary:
Purpose: CEBPA mutations are found as either biallelic (biCEBPA) or monoallelic (moCEBPA). We set out to explore whether the kind of CEBPA mutation is of prognostic relevance in cytogenetically normal AML (CN-AML).
Patients and Methods: 467 homogeneously treated CN-AML patients were subdivided into moCEBPA, biCEBPA and wildtype (wt) CEBPA patients. The subgroups were analyzed for clinical parameters and for additional mutations in the NPM1, FLT3 and MLL genes. Furthermore, we obtained gene expression profiles (GEP) for a subgroup of 61 patients using oligonucleotide microarrays.

overall_design: 61 bone-marrow samples from CN-AML patients were analyzed using Affymetrix HG-U133 oligonucleotide microarrays (Affymetrix, Santa Clara, CA). Sample preparation, hybridization and image acquisition were performed according to standard Affymetrix protocols. Custom chip definition files based on the GeneAnnot database were used for data analysis (Ferrari et al, BMC Bioinformatics 8:446). The twilight algorithm was used to comapre gene expression profiles of patients with wildtype CEBPA and mono- and biallelic CEBPA mutations.

first: Manuela

last: Hummel

first: Ulrich

last: Mansmann

first: Wolfgang

last: Hiddemann

first: Annika

last: Dufour

first: Karsten

last: Spiekermann


title: Goat mammary gland differentiation during pregnancy

status: Public on Dec 23 2009

city: Jouy en Josas

first: Felicie

last: Faucon

address: Domaine de Vivert Bat 221

department: Genetique Animale

institute: INRA Jouy en Josas

summary:
Development of mammary secretory epithelium and its functional differentiation occur during pregnancy under combined actions of ovarian steroids, pituitary hormones and growth factors. If the effect of these molecules is relatively well known, effect of differentiation factors expressed locally is not enough characterized. To understand local regulation of mammary tissue development and differentiation we realized transcriptional analysis on 5 physiological stages (4 during pregnancy and 1 during lactation). An appropriate experimental design was drawn to follow gene expression profiles during differentiation of mammary tissue. Results showed that at mid-pregnancy, mammary tissue was enough defferentiated into secretory epithelium to express milk protein genes and genes of the immune response system actors. But the secretoty activation of mammary epithelium was done only after parturition and wwas characterized by the expression of lipidogenesis genes.

Keywords: time course, mammary gland differentiation, goat, pregnancy

overall_design: 18 samples, loop design

first: Emmanuelle

last: Rebours

first: Jean

last: Helbing

first: Julie

last: Aubert

first: Claudia

last: Bevilacqua

first: Samira

last: Makhzami

first: Marie

last: Martin-Magniette

first: Stephane

last: Robin

first: Patrice

last: Martin


title: Promoter hypermethylation in MLL-r leukemia: biology and therapeutic targeting

status: Public on Dec 29 2009

city: Baltimore

first: Eric

middle: Stephen

last: Schafer

state: MD

address: CRB1, Room 252a, 1650 Orleans St.

department: Pediatrics and Oncology

institute: Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins

type: Methylation profiling by genome tiling array

summary:
MLL-r infant acute lymphoblastic leukemia (ALL) has largely unclear oncogenesis.  It has been shown unrelated to copy number change or mutations in the tyrosine kinome.  We therefore, explored the possible role of genome wide CpG island hypermethylation in MLL-r infant ALL.  We employed the HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to examine MLL-r infant leukemia samples (n=5), other common childhood ALL (n=5) and normals (n=5).  We then investigated biological correlation and the therapeutic potential of 5-aza-2’-deoxycytidine (decitabine).  Analysis of the HELP assay showed both tight clustering of samples into their biological groups and that MLL-r infant leukemia was globally and comparatively hypermethylated.  Further, a majority of genes chosen for analysis from the HELP assay were silenced or under-expressed.  MLL-r cell lines showed dose and time-dependent cell kill when treated with decitabine and most down-regulated genes showed increase in expression.  This was not seen in the MLL-wt cell line.  For the re-expressed genes, methylation specific PCR confirmed preferential promoter methylation in MLL-r samples.  Together, this suggests that methylation signatures are unique in pediatric ALL, that promoter hypermethylation may play a significant role in MLL-r infant leukemogenesis, that this can be reversed and demethylating agents may be a potential new therapeutic option in infant leukemia.

Keywords: DNA methylation profiling

overall_design: Direct comparison of DNA methylation in leukemic blasts from 5 infants with MLL-r ALL with 5 children with other common types of ALL and 5 normal samples consisting of CD34+ selected cord blood cells (n=3) and CD19+ selected cord blood cells (n=2)

first: Maria

last: Figueroa

first: Ari

last: Melnick

first: Patrick

last: Brown


title: microRNA expression in rat lung receiving chemopreventive agents and attenuation of cigarette smoke-induced alterations

status: Public on Dec 21 2009

city: Genoa

first: Alberto

last: Izzotti

address: A. Pastore, 1

department: Dept. of Health Sciences

country: Italy

institute: University of Genoa

summary:
We previously showed that exposure of rats to environmental cigarette smoke (ECS) causes extensive downregulation of microRNA expression in the lung, resulting in overexpression of multiple genes and proteins.  In the present study, we evaluated by microarray the expression of 484 microRNAs in the lung of rats receiving orally chemopreventive agents, including N-acetylcysteine, oltipraz, indole-3-carbinol, 5,6-benzoflavone and phenethyl isothiocyanate, or combinations thereof.  Scatterplot, hierarchical cluster, and principal component analyses showed that none of the above chemopreventive regimens appreciably affected the baseline microRNA expression, while all of them attenuated ECS-induced alterations but to a variable extent.  Thus, mirnome analysis provides a new tool for predicting both safety and efficacy of cancer chemopreventive agents at early carcinogenesis stages.

Keywords: cancer chemoprevention, microRNA, environmental cigarete smoke (ECS), 5,6-benzoflavone (BF), Indole 3-carbinol (I3C),N-acetylcysteine (NAC), oltipraz (OPZ), Phenethyl isothiocyanate (PEITC).

platform_organism:
Arabidopsis thaliana
Homo sapiens
Mus musculus

overall_design: Adult male Sprague-Dawley rats (Harlan Italy, Correzzana, Milan, Italy), weighing 315-320 g, were divided into 16 groups, each composed of 8 animals.  Half of them were exposed to ECS for 28 consecutive days, as previously described (Izzotti et al., 2005), while the remaining rats (Sham-exposed) were kept for the same period of time in filtered air.  The rats belonging to 14 groups were treated with chemopreventive agents, starting 3 days before exposure to ECS.

first: George

middle: A

last: Calin

first: Vernon

last: Steele

first: Cristina

last: Cartiglia

first: Mariagrazia

last: Longobardi

first: Carlo

last: Croce

first: Silvio

last: De Flora


title: Comparison of Invasive TAM sub-population to General TAM population

status: Public on Dec 26 2009

city: Bronx

first: Laureen

last: Ojalvo

state: NY

address: Chanin 607, 1300 Morris Park Avenue

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

summary: The tumor microenvironment modifies the malignancy of tumors. In solid tumors this environment is populated by many macrophages (tumor-associated macrophages; TAMs) that in genetic studies that depleted these cells from mouse models of breast cancer were shown to promote tumor progression to malignancy and increase metastatic potential. Mechanistic studies showed that these effects are through the stimulation of tumor cell migration, invasion, intravasation as well as an enhancement of angiogenesis. Using an in vivo invasion assay it was demonstrated that invasive carcinoma cells are a unique sub-population of tumor cells whose invasion and chemotaxis is dependent upon the co-migration of TAMs with obligate reciprocal signaling through an EGF/CSF-1 paracrine loop. In this study these invasion-promoting macrophages were isolated and subjected to analysis of their transcriptome in comparison to TAMs isolated indiscriminately to function using established macrophage markers by flow cytometry.

overall_design: Five biological replicates for each population (Invasive and General TAM) were used.

first: Charles

last: Whittaker

first: John

last: Condeelis

first: Jeffrey

last: Pollard


title: Comparative ChIP-chip analysis of  general transcription factor TFIIB and negative cofactor NC2 in human B cells

status: Public on Dec 19 2009

city: Muenster

first: Thomas

middle: Karl

last: Albert

address: Robert-Koch-Strasse 43

department: IMTB - Institute of Molecular Tumor Biology

institute: University Muenster

summary: A comparative ChIP-chip analysis of TFIIB and NC2 in human B cells reveals that basal core promoter architectures control the equilibrium between NC2 and preinitiation complexes. We conducted a comparative ChIP-chip and gene expression analysis of TFIIB in human B cells and analyze associated core promoter architectures. TFIIB occupancy relates well to gene expression, with the vast majority of promoters being GC-rich and lacking defined core promoter elements. TATA consensus and TATA-like motifs but not the previously in vitro defined TFIIB recognition elements (BREs) are enriched in approximately 5% of the genes. Further insight was obtained by performing a parallel ChIP-chip analysis of the TFIIB antagonist NC2. The latter identifies a highly related target gene set. Nonetheless, subpopulations show strong variations in TFIIB/NC2 ratios, with high NC2/TFIIB ratios correlating to promoters that show dispersed transcription start site patterns and lacking defined core elements. Conversely, high TFIIB/NC2 ratios select for conserved core promoter elements that include TATA and INR (initiator), the upstream TFIIB recognition element (BREu) and the downstream promoter element (DPE).

overall_design: Two biological samples from LCL 721 lymphoblastoid human B cells  were subjected to ChIP-chip analysis of TFIIB and NC2 using a Nimblegen human promoter array (based on the HG17 genome build) covering 1.5 kb DNA around transcription start sites.

first: Korbinian

last: Grote

first: Stefan

last: Boeing

first: Michael

last: Meisterernst


title: Functional enhancers at the gene-poor 8q24 cancer-linked locus

city: Rehovot

first: Gilad

last: Landan

address: PO Box 26

department: Applied Math & Computer Science, Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

type: Expression profiling by genome tiling array

summary: Multiple discrete regions at 8q24 were recently shown to contain alleles that predispose to many cancers including prostate, breast, and colon. These regions are far from any annotated gene and their biological activities have been unknown. Here we profiled a 5-megabase chromatin segment encompassing all the risk regions for RNA expression, histone modifications, and locations occupied by RNA polymerase II and androgen receptor (AR). This led to the identification of several transcriptional enhancers, which were verified using reporter assays. Two enhancers in one risk region were occupied by AR and responded to androgen treatment; one contained a single nucleotide polymorphism (rs11986220) that resides within a FoxA1 binding site, with the prostate cancer risk allele facilitating both stronger FoxA1 binding and stronger androgen responsiveness. The study reported here exemplifies an approach that may be applied to any risk-associated allele in non-protein coding regions as it emerges from genome-wide association studies to better understand the genetic predisposition of complex diseases.

overall_design: 20 Normal Prostate cDNA samples (no replicates), 4 cell line cDNA samples (each cell line in duplicate), 4 cell line Acetylated H3 ChIP (each line in duplicate), 2 cell line various histone modification and protein ChIPs (6 Abs LNCaP, 5 Abs PC3, each in duplicate). All samples were hybridized with matching genomic DNA as reference.

first: Li

last: Jia

first: Mark

last: Pomerantz

first: Rami

last: Jaschek

first: Paula

last: Herman

first: David

last: Reich

first: Chunli

last: Yan

first: Omar

last: Khalid

first: Phil

last: Kantoff

first: William

last: Oh

first: J

middle: R

last: Manak

first: Benjamin

middle: P

last: Berman

first: Brian

last: Henderson

first: Baruch

last: Frenkel

first: Cristopher

last: Haiman

first: Matthew

last: Freedman

first: Amos

last: Tanay

first: Gerhard

last: Coetzee


title: Csac growth on model substrates found in lignocellulose

city: Raleigh

first: Amy

last: VanFossen

state: NC

address: 840 Main Campus Dr.  Rm3305

department: Chemical and Biomolecular Engineering

institute: NC State Unversity

summary: The co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait for in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on oligosaccharides (composed of glucose and xylose) compared to monosaccharides. Based on the whole-genome transcriptional response analysis and comparative genomics, carbohydrate specificities for transport systems could be proposed for a number of the 24 putative carbohydrate ATP-binding cassette (ABC) transporters in the C. saccharolyticus genome. Transcriptome analysis showed different transporters were utilized for uptake of oligosaccharides than those used for monosaccharides uptake. No evidence for catabolite repression was noted for either growth on multi-sugar mixtures or in the corresponding transcriptomes.

overall_design: C. saccharolyticus was subcultured (overnight) seven times on the substrate of interest in modified DSMZ 640 medium before inoculating a 1-liter batch containing 0.5 gram substrate per liter. Cells were grown at 70 °C until mid-logarithmic phase (3-5*107) and harvested by rapid cooling to 4 °C and centrifugation and then stored at -80 °C. To elucidate the transporters plus the central carbon metabolic pathways and their regulation utilized on the different sugars, transcriptome analysis was performed after growth on xylan (oat spelt), xyloglucan, xylogluco-oligosaccharides, glucose and xylose.

middle: L


title: Gene expression in the Schistosoma japonicum infected spleen

status: Public on Dec 18 2009

city: Herston

first: Melissa

middle: Louise

last: Burke

state: QLD

address: 300 Herston Road

department: Division of Infectious Diseases and Immunology

country: Australia

institute: Queensland Institute of Medical Research

summary: Determining the molecular events induced in the spleen during schistosome infection is an essential step in better understanding the immunopathogenesis of schistosomiasis and the mechanisms by which schistosomes modulate the host immune response.    The present study defines the transcriptional and cellular events occurring in the murine spleen during the progression of Schistosoma japonicum infection. Additionally, we compared and contrasted these results with those we have previously reported for the liver. Microarray analysis combined with flow cytometry and histochemistry demonstrated that transcriptional changes occurring in the spleen were closely related to changes in cellular composition. Additionally, the presence of alternatively activated macrophages, as indicated by up-regulation of Chi3l3 and Chi3l4 and expansion of F4/80+ macrophages, together with enhanced expression of the immunoregulatory genes ANXA1 and CAMP suggests the spleen may be an important site for the control of S. japonicum-induced immune responses.     The most striking difference between the transcriptional profiles of the infected liver and spleen was the contrasting expression of chemokines and cell adhesion molecules. Lymphocyte chemokines including the homeostatic chemokines, CXCL13, CCL19 and CCL21, were significantly down-regulated in the spleen but up-regulated in the liver. Eosinophil (CCL11, CCL24), neutrophil (CXCL1) and monocyte (CXCL14, CCL12) chemokines and the cell adhesion molecules VCAM1, NCAM1, PECAM1 were up-regulated in the liver but unchanged in the spleen. Chemokines up-regulated in both organs were expressed at significantly higher levels in the liver. Co-ordinated expression of these genes probably contributes to the development of a chemotactic signalling gradient that promotes recruitment of effector cells to the liver, thereby facilitating the development of hepatic granulomas and fibrosis.    Together these data provide, for the first time, a comprehensive overview of the molecular events occurring in the spleen during schistosomiasis and will substantially further our understanding of the local and systemic mechanisms driving the immunopathogenesis of this disease.

overall_design: The gene expression profile of the murine spleen were examined at 4, 6 and 7 weeks post infection with Schistosoma japonicum in comparison to that of uninfected controls. Microarray analysis was performed on pooled RNA from 4 mice per group. Two technical replicates were performed for each cRNA sample.

first: Donald

last: McManus

first: Grant

last: Ramm

first: Mary

last: Duke

first: Yuesheng

last: Li

first: Malcolm

last: Jones

first: Geoffrey

middle: N

last: Gobert


title: Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans

status: Public on Dec 17 2009

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

type: Genome variation profiling by genome tiling array

summary:
Background:
Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain.
Results:
We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314).  Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains.
Conclusion:
Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers.

overall_design: Twelve C. elegans natural isolate samples were studied. There were no replicates or dye-swap hybridizations.

first: Jason

middle: S

last: Maydan

first: Adam

last: Lorch

first: Mark

last: Edgley

middle: G

last: Moerman


city: Chongqing

first: yi

last: qing

state: Chongqing

address: No.10 Changjiangzhi Rd

department: Daping Hospital and Research Institute of Surgery

country: China

institute: Third Military Medical University

summary:
[original title] Microarray analysis of DNA damage repair gene expression profiles in cervical cancer cells radioresistant to 252Cf neutron and X-rays.

The aim of the study was to obtain stable radioresistant sub-lines from the human cervical cancer cell line HeLa by prolonged exposure to 252Cf neutron and X-rays.
Radioresistance mechanisms were investigated in the resulting cells using SuperArray Oligo GEArray® Human DNA Damage Signaling Pathway Microarray.

overall_design: HeLa cells were treated with fractionated 252Cf neutron and X-rays, with a cumulative dose of 75 Gy each, over 8 months, yielding the sub-lines HeLaNR and HeLaXR.Gene expression patterns of the radioresistant sub-lines were studied through microarray analysis

first: Qing

last: Yi

first: Wang

last: Dong


title: Illumina GoldenGate Methylation array data for X-CGD patients and healthy controls

city: Heidelberg

first: Rongxi

last: Yang

address: Im Neuenheimer Feld 580

institute: German Cancer Research Center

summary: We report on the molecular and cellular events observed in two patients treated by gene therapy in 2004. After the initial resolution of bacterial and fungal infections, both patients exhibited silencing of transgene expression due to methylation of the viral promoter, and myelodysplasia with monosomy 7 as a result of insertional activation of EVI1. In line with this observation, a genome wide methylation analysis of 807 cancer related genes revealed a DNA methylation pattern characteristic of MDS and AML patients.

overall_design: Genomic DNA was prepared from peripheral blood cells of patient 1 (d 0 and month 27) and 25 healthy controls including 12 males and 13 females. The GoldenGate Methylation Cancer Panel I array was used to compare methylation degree in 1.505 CpG sites from promoter regions or the first exon of 807 mostly cancer related genes between the patient 1 (d 0 and month 27) and 25 healthy controls.


title: Small fish comp tox FHM haloperidol 96 h ovary

status: Public on Dec 22 2009

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

summary: This experiment was conducted as part of an overall study aimed at examining effects of a dopamine receptor antagonist on reproduction, behavior, and gene expression in cyprinid fish. Relative to gene expression, we hypothesized that if haloperidol disrupted normal regulation of the HPG axis, there may be robust transcriptional alterations in the ovary of exposed females that might serve as useful markers of exposure and/or effects. For the purposes of this study, robust transcriptional alterations were defined as those detected in two separate fish species (fathead minnow and zebrafish), exposed to the same concentration of haloperidol for the same duration. There is a companion zebrafish microarray experiment (GSE14861) that these data are compared to. Transcriptional responses in the ovary of the two species are compared in terms of differentially expressed genes, enriched gene ontology categories they represent, and associated pathways.

overall_design:
Fathead minnow and zebrafish microarray experiment
Samples for microarray analysis were generated in a separate, 96 h, continuous flow-through experiment. Nominal treatment concentrations for the microarray experiment were 0 and 50 μg haloperidol/L. Chemical (or control water) delivery was initiated 24 h prior to adding fish to the tanks. To start the experiment, fathead minnows (4 males, 4 females per tank) were added to each of three tanks per treatment group, while zebrafish (6 males, 6 females per tank) were added to each of two tanks per group. The time of fish addition was staggered by replicate within each treatment such that all samples from a given exposure tank could be collected within 60 min of the intended 96 h exposure duration. After 96 h, male and female zebrafish and female fathead minnows were anesthetized in buffered MS-222 and weighed. Whole gonads were removed, weighed, and preserved in RNAlater.

Total RNA was isolated from fathead minnow ovary samples using RNeasy kits (Qiagen). RNA quality was assessed with a Agilent 2100 Bioanalyzer and quantity was determined using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). Aliquots of six fathead minnow ovary RNA samples per treatment group (two from each replicate per treatment) were prepared for microarray analysis.

first: Natalia

last: Garcia-Reyero

first: Dalma

last: Martinovic

first: Nathaniel

middle: D

last: Mueller

first: Jenna

last: Cavallin

first: Elizabeth

middle: J

last: Durhan

first: Kathleen

middle: M

last: Jensen

first: Michael

last: Kahl

last: Makynen

first: Lindsey

last: Blake

first: Edward

last: Perkins

first: Gerald

last: Ankley


title: Light activation of the sigmaB-mediated general stress-response of Bacillus subtilis

city: Zeist

first: Remco

last: Kort

address: Utrechtseweg 48

department: Microbiology

institute: TNO

summary:
The sigma(B)-dependent general stress response in the common soil bacterium Bacillus subtilis can be elicited by a range of stress factors, such as starvation or an ethanol-, salt-, or heat-shock, via a complex upstream signaling cascade. Additionally, sigma(B) can be activated by blue light, via the phototropin homologue YtvA, a component of the environmental branch of the signaling cascade.
The genome-wide transcriptomes of B. subtilis reported here show that sigma(B) can activated by blue as well as red light via RsbP/RspQ, the energy branch of sigma(B) upstream signaling cascade.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: A 16 chip genome-wide expression study using RNA recovered from B.subtilis strain PB565/pYtvA under light and dark conditions before and after induction with IPTG, and from B.subtilis strain PB565 under light and dark conditions. Each B.subtilis subsp. subtilis strain 168 NC_000964 chip measures the expression level of 4,104 genes in two-fold from with eight 60-mer probe pairs (PM/MM) per gene.

first: Alie

last: de Kat Angelino-Bart

first: Michel

last: Ossendrijver

first: Marcela

last: Perez


title: Mycobacterium bovis transcriptional response to nitric oxide

city: Valdivia

first: Germán

last: Rehren

state: Valdivia

address: Campus Isla Teja

department: Biochemistry

country: Chile

institute: Universidad Austral de Chile

summary: We used microarray hybridization to analyze the expression pattern of M. bovis after exposure to nitric oxide. In M. tuberculosis, this treatment has been shown to induce a response similar to the hypoxic stress. Results showed the up-regulation of 51 genes belonging to the DosR regulon. The most remarkable difference with M. tuberculosis was the lack of expression of narX and narK2 in M. bovis, both genes related to survival during hypoxic stress. We further confirm this by qRT-PCR and also explore differential activity at promoter level.

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: Four independent biological replicates were analyzed for each condition, and two dye-swap experiments were included.

first: German

first: Ana

last: Zarraga


title: A novel hybrid kinase is essential for regulating the σB-mediated stress response of Bacillus cereus.

city: Wageningen

first: Mark

middle: de

last: Been

address: Bomenweg 2

department: Agrotechnology and Food Sciences Group

institute: Wageningen UR

summary:
A common bacterial strategy for monitoring environmental challenges is to use two-component systems, which consist of a sensor histidine kinase (HK) and a response regulator (RR). In the food-borne pathogen Bacillus cereus, the alternative sigma factor σB is activated by the RR RsbY. Here we present strong indications that the PP2C-type phosphatase RsbY receives its input from the multi-sensor hybrid kinase BC1008 (renamed RsbK). Genome analyses revealed that, across bacilli, rsbY and rsbK are located in a conserved gene cluster. A B. cereus rsbK deletion strain was shown to be incapable of inducing σB upon stress conditions and was impaired in its heat adaptive response. Comparison of the wild-type and rsbK mutant transcriptomes upon heat shock revealed that RsbK was primarily involved in the activation of the σB-mediated stress response. Truncation of the RsbK RR receiver domain demonstrated the importance of
this domain for σB induction upon stress. The domain architecture of RsbK suggests that in the B. cereus group and in other bacilli, environmental and intracellular stress signalling routes are combined into one single protein. This strategy is markedly different from the σB activation pathway in other low-GC Grampositives.

overall_design:
Two different comparisons were performed (both in duplo and Cy5-Cy3 dye-swapped):
(1) B. cereus WT 30°C versus B. cereus WT 42°C (10 min heat shock)
(2) B. cereus WT 42°C versus B. cereus FM1404 42°C

Data from comparisons (2) were subsequently compared with transcriptome data obtained previously by Van Schaik et al., 2007

last: de Been

first: Marcel

middle: H

last: Tempelaars

first: Willem

last: van Schaik

first: Roy

last: Moezelaar

first: Roland

last: Siezen

first: Tjakko

last: Abee


title: Human primary and secondary glioblastoma vs. non-neoplastic adult brain tissue

city: Lecce

first: Oscar

middle: Fernando

last: D'Urso

state: Lecce

address: provinciale Monteroni

department: Department of biological science

institute: Salento University

summary:
MicroRNAs (miRNAs) are small (21-25 nucleotide in length) non-coding RNA molecules that negatively regulate protein expression. They are linked to cancer development and maintenance. In this work, studying gene expression profiles of 340 mammalian miRNAs with DNA microarrays, we selected 10 miRNAs gene features able to distinguish primary from secondary glioblastoma type; furthermore we verified that miR-21 and miR-155 up-regulatation seems to characterize the glioblastoma tumour state since it was found up-regulated in all samples analyzed compared to adult brain noneoplastic tissue. Since miR-21 function in glioblastoma cells was addressed previously we concentrated our efforts on miR-155 function. We found that miR-155 levels were markedly elevated both in primary and secondary glioblastomas tumours, in glioblastoma cell cultures and in 4 glioblastoma cell lines (U87, A172, LN229, and LN308) compared with adult brain tissue, CHP212-neuroblastoma cell lines and DAOY-1-medulloblastoma cell line.  Since one of the miR-155 target was gamma-aminobutyric acid (GABA) A receptor (GABRA1) we verified if there was a relation between miR-155 up-regulation and GABRA1 expression. We  demonstrated that, in cultured glioblastoma cells, knockdown of miR-155, which lower miR-155 expression to normal level, restore the normal expression of the gamma-aminobutyric acid (GABA) A receptor (GABRA1), making glioblastoma cells responsive to GABA cell cycle inhibiting signals. Our data suggest that aberrantly over-expressed miR-155 contribute to the malignant phenotype of the glioblastoma cells, promoting their unlimited growth.

Keywords: miRNA expression profile

overall_design: We studied the expression profiles of 340 miRNAs in 97 glioblastoma tissues, of which 66 were primary glioblastomas and 27 were secondary glioblastomas. We have 66 replicates of primary glioblastoma and 27 replicates of secondary glioblastoma, each hybridized with the respective adult non-neoplastic brain tissue as a control.

middle: F

first: Pietro

middle: I

first: Pasqualino

last: Ciappetta


title: Maize gene expression during infection with Fusarium moniliforme

status: Public on Dec 16 2009

city: Ya'an

first: Guangsheng

last: Yuan

state: Sichuan Province

address: Xinkang Road 46

department: Maize Research Institute

institute: Sichuan Agricultural University

summary:
The fungal pathogen Fusarium moniliforme causes ear rot in maize. Ear rot in maize is a destructive disease globally caused by Fusarium moniliforme , due to decrease of grain yield and increase of risks in raising livestock by mycotoxins production. Plants have developed various defense pathways to cope with pathogens.
We used microarrays to detail the global programme of gene expression during the infection process of Fusarium moniliforme in its host plant to get insights into the defense programs and the host processes potentially involved in plant defense against this pathogen.

overall_design: In two compared independent experiments plants were infected with the Fusarium moniliforme. Samples from infected bracts of resistant maize (Bt-1) as well as susceptible maize (Ye478) were taken at 4 days post infection. Samples from uninfected control plants were taken at the same time points. For example: R0 (control)  and RT (treat) in Bt-1 and S0 (control) and ST (treat) in Ye478.

first: Guangtang

last: Pan


title: Bifidobacterium longum mutants and resistance to Heat-Shock

city: Lausanne 26

first: Bernard

last: Berger

address: Vers-Chez-Les-Blanc

department: Nutrition & Health

institute: Nestlé Research Center

summary:
Transcriptional profiling of Bifidobacterium longum mutants versus wt strain in exponentional phase, with or without heat-shock treatment, and in stationary phase

Keywords: Characterization of natural mutants

overall_design: Two B. longum mutants (NCC2912 and NCC2913) were analysed versus the wt strain NCC2705 in three conditions : exponential phase 37°, exponential phase with 7 min 50° heat shock, stationary phase. Two biologic replicates and 2 technical replicates

first: Deborah

last: Moine


title: DLBCL Patients

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary:
Genomic profiles of DLBCL (Diffuse Large B-cell Lymphoma) patients
20 DLBCL patients were selected for detection of genomic aberrations

overall_design: Patient's DNA were hybridized against Promega control on Agilent G4410B arrays and scanned with the Agilent G2505B scanner.

first: Frederic

last: Lepretre

first: Fabrice

last: Jardin


title: Global gene expression analysis of waterlogging stressed Cotton root and leaf tissue

city: Acton

first: Jed

last: Christianson

state: ACT

address: Clunies Ross Road

institute: CSIRO Plant Industry

summary:
Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants.
Waterlogging stress causes yield reductions in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging causes significant reductions in stem elongation, shoot mass, root mass, and leaf number. At the global gene expression level waterlogging significantly alters the expression of 1012 genes (4.2% of genes assayed) in root tissue as early as 4h after flooding. Many of these genes are associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global leaf gene expression, significantly changing the expression of 1305 genes (5.4% of genes assayed) after 24h of flooding. Genes associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism were affected in leaf tissues of waterlogged plants. Implications of these results for the development of waterlogging tolerant cotton are discussed.

Keywords: Stress Response

platform_organism:
Gossypium barbadense
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii

overall_design: Plants of cotton cultivar Sicot 71 were grown to the two-leaf stage in tubs. For stress treatments plants were either watered as normal or flooded with water to completely submerge the root system. At four and twenty-four hours post-flooding samples of root or leaf tissue were taken from control and flooded plants. Total RNA was extracted from each tissue sample and assayed on cotton Affymetrix chips. Two biological replications were used for each comparison.

middle: A

first: Iain

middle: W

last: Wilson

first: Danny

last: Llewellyn

first: Elizabeth

last: Dennis


title: CLL Patients

summary:
Genomic profiles of CLL (Chronic Lymphocytic Leukemia) patients.
11 CLL patients were selected for detection of genomic aberrations, 8 patients with atypical CLL and 3 patients with typical CLL.

overall_design: Patient's DNA were hybridized against Promega control on Agilent G4410A arrays and scanned with the Agilent G2505B scanner.

first: Xavier

last: Troussard


title: High-resolution array comparative genomic hybridization of genetic deficiencies on chromosome V in C. elegans

first: Martin

middle: Richard

last: Jones

address: Room 419 NCE Building 2125 East Mall

department: Medical Genetics

summary:
We have extended our array-CGH analysis of genetic deficiencies in Caenorhabditis elegans to a set on LGV (left) balanced by the reciprocal translocation eT1. This set includes 20 deletions and a single duplication.

Keywords: C.elegans Deficiencies CGH

overall_design: 20 test samples from heterozygous deficiency containing strains individually hybridized to reference DNA from BC2842 (eT1 balanced strain), BC1999 (sDf72), BC3470 (sDf40) or BC3957 (sDf74)

middle: R

first: David

last: Baillie

first: Bob

middle: C

last: Johnsen

first: Nigel

last: O'Neil

first: Shuyi

last: Chua

first: Ann

last: Rose


title: Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit

city: Florence

first: Monica

last: Berta

address: Via Maragliano 77

department: Agricultural Biotechnology

institute: University of Florence

summary: A transcriptome analysis of P. alba cambial zone was performed with the aim to unravel the gene network underlying the response to water deficit within the cambium and the differentiating derivatives cambial cells. Water stress was induced on one-year-old plant of Populus alba by withholding water for 9 days. At that time, leaf Ψpd fell down to -0,8 MPa resulting in a significant reduction of the stomatal conductance, CO2 assimilation, consistent increment of stem shrinkage and cessation of the radial growth. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected a few functional categories as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit.

platform_organism:
Populus trichocarpa x Populus deltoides
Populus euphratica
Populus tremula x Populus alba

overall_design: Three-condition experiment, Stress vs. Control, Re-hydrated vs. Stress and Re-hydrated vs Control. Each sample consists of a pool of two plants independently grown and harvested. Two technical replicates are performed for each of the three treatments. One swap replicate per array.

first: Alessio

last: Giovannelli

first: Federico

last: Sebastiani

first: Alessandro

last: Camussi

first: Milvia

middle: L

last: Racchi


title: Folic acid supplementation normalizes the endothelial progenitor cell transcriptome of patients with type 1 diabetes

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

institute: Health e-genomics

summary: Background: Endothelial progenitor cells play an important role in vascular wall repair. Patients with type 1 diabetes have reduced levels of endothelial progenitor cells of which their functional capacity is impaired. Reduced nitric oxide bioavailability and increased oxidative stress play a role in endothelial progenitor cell dysfunction in these patients. Folic acid, a B-vitamin with anti-oxidant properties, may be able to improve endothelial progenitor cell function. In this study, we investigated the gene expression profiles of endothelial progenitor cells from patients with type 1 diabetes compared to endothelial progenitor cells from healthy subjects. Furthermore, we studied the effect of folic acid on gene expression profiles of endothelial progenitor cells from patients with type 1 diabetes. Methods: We used microarray analysis to investigate the gene expression profiles of endothelial progenitor cells from type 1 diabetes patients before (n=11) and after a four week period of folic acid supplementation (n=10) compared to the gene expression profiles of endothelial progenitor cells from healthy subjects (n=11). The probability of genes being differentially expressed among the classes was computed using a random-variance t-test. A multivariate permutation test was used to identify genes that were differentially expressed among the two classes. Functional classification of differentially expressed genes was performed using the biological process ontology in the Gene Ontology database.   Results: Type 1 diabetes significantly modulated the expression of 1591 genes compared to healthy controls. These genes were found to be involved in processes regulating development, cell communication, cell adhesion and localization. After folic acid treatment, endothelial progenitor cell gene expression profiles from diabetic patients were similar to those from healthy controls. Genes that were normalized by folic acid played a prominent role in development, such as the transcription factors ID1 and MAFF. Few oxidative-stress related genes were affected by folic acid. Conclusion: Folic acid normalizes endothelial progenitor cell gene expression profiles of patients with type 1 diabetes. Signaling pathways modulated by folic acid may be potential therapeutic targets to improve endothelial progenitor cell function.

first: Olivia

last: van Oostrom

first: Dominique

middle: P

last: de Kleijn

first: Joost

middle: O

last: Fledderus

first: Andrew

last: Stubbs

first: Attie

last: Tuinenburg

first: Sai-Kiang

last: Lim

first: Marianne

last: Verhaar


title: Comparative gene expression in floral whorls of the basal eu-dicot Aquilegia formosa

status: Public on Dec 15 2009

city: Palmerston North

first: Claudia

last: Voelckel

address: Riddet Road

department: Allan Wilson Centre for Molecular Ecology and Evolution

country: New Zealand

institute: Massey University

summary: Investigation of genome-wide gene expression in sepals, petals, stamens, staminodia and carpels in pre-anthesis Aquilegia flowers. One goal was to identify transcriptional signatures associated with petaloidy by comparing gene expression in petals and petaloid sepals. Other goals were to study the evolutionary origin and ecological function of staminodia by comparing a) expression patterns in stamens, staminodia and carpels, b) identifying transcriptional regulators expressed in staminodia and c) using gene set enrichment analysis to identify biological processes operating in staminodia.

overall_design: A 15 chip study using total RNA from the five floral tissues from three replicate natural populations with each sample representing tissue pooled from 60 flowers.

first: Justin

last: Borevitz

first: Scott

last: Hodges


title: miR-193b represses cell proliferation and regulates cyclin D1 in melanoma: benign nevi and metastatic melanoma

status: Public on Dec 20 2009

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

institute: Queen's University

summary: Cutaneous melanoma is an increasingly common form of skin cancer. The molecular mechanisms regulating melanoma progression are not completely understood. We speculated that specific miRNAs may be involved in melanoma development. We compared the miRNA expression profiles of benign nevi and metastatic melanomas. Unsupervised hierarchical clustering demonstrated a distinct miRNA expression pattern in metastatic melanomas compared to nevi. We identified miRNAs that were differentially expressed in melanoma. Notably, miR-193b was significantly down-regulated in the melanoma tissue examined. Using functional studies we demonstrated that over-expression of miR-193b significantly reduced melanoma cell proliferation, and arrested cell at G1 phase. Further gene expression analysis revealed that miR-193b regulated targets involved in cell cycle. Cyclin D1 was down-regulated by miR-193b at both  the mRNA and protein level. This is the first study to show that the miR-193b may reduce cell proliferation by directly repressing cyclin D1. Overall, our study suggests that miRNAs are dysregulated in metastatic melanoma, and that miR-193b may play an important role in melanoma.

overall_design: 8 benign nevi and 8 metastatic melanoma tissue samples were profiled by Agilent MicroRNA Microarray (V1.5).

first: Jiamin

last: Chen

first: Xiao

last: Zhang

first: Victor

last: Tron


title: Potential mechanisms of low salt diet induced cardiac diseases

city: Valhalla

first: Caroline

last: Ojaimi

institute: New York Medical College

summary: We hypothesized that a LS intake leads to a cascade of events involving increases in plasma AII, the AT1 receptor, NADPH oxidase and O2˙ production and ultimately to reduced NO bioactivity. This reduced NO bioactivity results in altered control of the coronary circulation and cardiac metabolism. This study was undertaken to determine the global changes in cardiac gene expression in dogs fed LS diet (0.5% NaCl) for two weeks. Cardiac RNA was extracted from the control and LS fed groups (n=4). Statistical significance (P≤0.05; fold change of ±2) showed that there were 443 genes that changed, 110 decreasing and 333 increasing. All of the differentially expressed genes were grouped into functional categories based on their Gene Ontology.

overall_design: Adult male mongrel dogs (n=10, BW;25-28kg) were put on LS which contains 0.5% sodium chloride for two weeks. RNA was isolated using Trizol reagent. RNA from each sample was used to generate a high fidelity cDNA using the labeling protocols for sample preparation recommended by Affymetrix. Data and statistical analysis were performed in Genetraffic using a t-test and with variance stabilization. Differences were considered statistically significant at a nominal significance of p≤0.05 and at least ±2 fold change in expression between control (n=3), and LS dogs (n=4).

first: Nobuhiro

last: Suematsu

first: caroline

first: Zipping

last: Wang

first: Xiaobin

last: Xu

first: Suhua

first: Fabio

last: Recchia

first: Pawel

last: Kaminski

first: Dong

last: Sun

first: Michael

middle: S

last: Wolin

first: Gabor

last: Kaley

first: Thomas

last: Hintze


title: HTCC1062 glucose versus no carbon log phase

city: Madison

last: Schwalbach

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin-Madison

summary:
The primary goal of this experiment is to examine the transcription profiles of HTCC1062 when grown in the presence or absence of D-glucose (30uM final concentration).
Experiment confirmed activity of predicted glycolysis operon.

platform_organism:
Candidatus Pelagibacter ubique HTCC1002
Candidatus Pelagibacter ubique HTCC1062
Candidatus Pelagibacter sp. HTCC7211

overall_design: Three biological replicates of HTCC1062 grown on glucose (30uM final conc) were compared to three biological replicate control treatments of HTCC1062 grown without glucose in the media.

first: M

first: L

last: Steindler

first: S

last: Giovannoni


title: Transcriptional analysis of RelE family toxin overexpression in Mycobacterium tuberculosis

city: Rockville

first: Helena

last: Boshoff

address: 12441 Parklawn Drive

department: LIG

institute: NIAID/ NIH

summary: To understand the mechanism of action of the RelE family of toxins on metabolism of Mycobacterium tuberculosis. To this effect, toxin expression was induced under control of a tetracycline regulatable promoter and transcriptional profiles compared during overexpression of the three RelE toxin family members. Profiles were also compared to previously published profiles of drugs of known mechanism of action against this organism.

overall_design: For the design, RNA isolated from cells where toxin expression was induced with anhydrotetracycline was converted to Cy5-labeled cDNA whereas RNA derived from cells in which toxin expression was not induced (treated with ethanol solvent only) was converted to Cy3-labeled cDNA. Time points were taken for each overexpression condition. Treatments were performed indepedently a minimum of two times to give independent biological replicates.


title: The profile of cellular and KSHV microRNAs in KSHV infected lymphatic endothelial cells (6 and 72 hours post infection)

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

country: United Kingdom

institute: UCL

summary: Kaposi sarcoma is the most common cancer in AIDS patients and is typified by red skin lesions. The disease is caused by the KSHV virus (HHV8) and is recognizable by its distinctive red skin lesions. The lesions are KSHV infected spindle cells, most commonly the lymphatic endothelial and blood vessel endothelial cells (LEC and BEC), plus surrounding stroma. The effects of KSHV infection of LECs were assayed using Affymetrix hgu133plus2 chips at 6 and 72 hours post infection.

overall_design: There were n=4 each of lymphatic endothelial cells (LEC) following 6 hours of culture, LEC following 6 hours post KSHV infection, LEC following 72 hours of culture, and LEC following 72 hours post KSHV infection.

first: Dimitrios

last: Lagos

first: Chris


title: DNA methylation distinguishes pathologically normal human tissues

status: Public on Dec 12 2009

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

summary:
Epigenetic control of gene transcription is critical for normal human development and cellular differentiation. While alterations of epigenetic marks such as DNA methylation have been linked to cancers and many other human diseases, interindividual epigenetic variation in normal tissues due to aging, environmental factors, or innate susceptibility are poorly characterized. The plasticity, tissue-specific nature, and variability of gene expression are related to epigenomic states that vary across individuals. Thus, population-based investigations are needed to further our understanding of the fundamental dynamics of normal individual epigenomes. We analyzed 217 non-pathologic human tissues from 10 anatomic sites at 1413 autosomal CpG loci associated with 773 genes to investigate tissue-specific differences in DNA methylation, and to discern how aging and exposures contribute to normal variation in methylation. Methylation profile classes derived from unsupervised modeling were significantly associated with age (P < 0.0001), and were significant predictors of tissue origin (P < 0.0001).  In solid tissues (n=119) we found striking, highly significant CpG island dependent correlations between age and methylation; loci in CpG islands gained methylation with age, loci not in CpG islands lost methylation with age (P < 0.001), and this pattern was consistent across tissues and in an analysis of blood-derived DNA. Our data clearly demonstrate age and exposure related differences in tissue-specific methylation, and significant age associated methylation patterns which are CpG island context dependent. This work provides novel insight into the role of aging and the environment in susceptibility to diseases such as cancer, and critically informs the field of epigenomics by providing evidence of epigenetic dysregulation by age-related methylation alterations. Collectively we reveal key issues to consider both in the construction of reference.

The causes and extent of tissue-specific interindividual variation in human epigenomes are underappreciated and hence, poorly characterized. We surveyed over 200 carefully annotated human tissue samples from ten anatomic sites at 1413 CpGs for methylation alterations to appraise the nature of phenotypically, and hence potentially clinically important epigenomic alterations. Within tissue types, across individuals, we found variation in methylation that was significantly related to aging and environmental exposures such as tobacco smoking. Individual variation in age and exposure-related methylation may significantly contribute to increased susceptibility to several diseases. As the NIH-funded HapMap project is critically contributing to annotating the human reference genome defining normal genetic variability, our work raises key issues to consider in the construction of reference epigenomes. It is well recognized that understanding genetic variation is essential to understanding disease. Our work, and the known interplay of epigenetics and genetics, makes it equally clear that a more complete characterization of epigenetic variation and its sources must be accomplished to reach the goal of a complete understanding of disease. Additional research is absolutely necessary to define the mechanisms controlling epigenomic variation. We have begun to lay the foundations for essential normal tissue controls for comparison to diseased tissue, which will allow the identification of the most crucial disease-related alterations and provide more robust targets for novel treatments.

overall_design: Normal human tissues were assembled by a collaborative, multi-institutional network of investigators conducting molecular epidemiologic studies of human cancer. Tissues were obtained through Institutional Review Board approved studies already underway at these institutions, or were obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA). Briefly, normal brain tissues (n=12) were contributed by the Wiencke lab at UCSF through the San Francisco Adult Glioma Study (Wiemels JL, Int J Ca 2002). Normal lung tissues (n=49) were obtained from adjacent non-tumor portions of lung in patients treated for NSCLC (Wiencke JK, Ca Res, 1995) or from the NDRI from non-diseased individuals at autopsy (n=4). Peripheral blood DNA was obtained from controls enrolled in a study of bladder cancer (n=15) (Karagas MR, Env Health Persp 1998), controls enrolled in a study of head and neck cancer (n=15) (Peters ES, CEBP 2005, 14:476-82), and newborn infants (n=55) (Urayama KY, CEBP, 2007, 16:1172). Non-tumorigenic pleural samples (n=18) were obtained from grossly disease-uninvolved regions of incident mesothelioma (Christensen BC, Carcinogenesis 2008). Head and neck anatomic sites (n=11), bladder (n=5), kidney (n=6), and small intestine (n=5) were obtained from the NDRI, all from individuals with no gross diseases or tumors of the obtained tissues. Non-pathologic placenta samples (n=19) were obtained as residual tissues from control infant term births as part of an ongoing hospital-based case-control study of intrauterine growth restriction at Women and Infants Hospital in Providence RI. All tissues obtained from patients with disease (lung, pleura) were histologically confirmed as normal by independent study pathologist review of tissue samples prior to DNA extraction.

first: Karl

middle: T

last: Kelsey


title: Profile of microRNA during adipogenesis regulating by microRNA and WNT signaling

status: Public on Dec 11 2009

city: Guangzhou

first: Qin

last: Limei

address: North Third road

institute: SunYatsen University

summary: To investigate miRNAs that implicate the process of adipogenesis by interacting with canonical Wnt/β-catenin signaling pathway, we constructed two cell models at first, and then investigated the expression profile of microRNAs by using Microarray. Based on the data of high throughput microarray, we identified 18 miRNAs which might promote adipogenesis by repressing WNT signaling, including mir-210, mir-148a, mir-194, mir-322 etc. On the other hand, we also identified 29 miRNAs which might repress adipogenesis by activation of WNT signaling, including mir-344, mir-27, and mir-181. The target genes involved in WNT signaling pathway of these identified miRNAs were also predicted through online tools.

overall_design: Two cell models of 3T3-L1, i.e. activation and suppression of WNT signaling including four samples, i.e. preadipocytes, mature adipocytes (MDI induction), Lithium treated preadipocytes, MDI induction of Lithium treated preadipocytes. Each sample was replicated in triplicate.

first: Y

middle: N

last: Niu

first: D

last: Mo

first: W

middle: Q

last: Chen

first: Q

last: Xiao

last: Xie

first: A

last: Li

first: J

first: X

last: Zhao

first: Z

middle: Y

last: He