title: The effects of different concentrations of phenanthrene on FHM liver

status: Public on Aug 27 2013

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

country: USA

institute: UF

summary: FHMs were exposed to three concentrations of phenanthrene (average measured 29, 287, 1006 ng/L) and fish were sampled after 48hr.

overall_design:
There were 20 samples analyzed  5) control liver tissues  5) 29 ng/L phenanthrene exposed liver tissues 5) 287 ng/L phenanthrene exposed liver tissues 5)1006 ng/L phenanthrene exposed liver tissues. There was a total of 20 microarrays processed.
In this study, gene expression to a 'dose-response' was investigated after in vivo exposure of fish to phenanthrene.

first: Jennifer

middle: R

last: Loughery

first: Chris

middle: J


title: A defect in ATP-citrate lyase links acetyl-CoA production, virulence factor elaboration and virulence in Cryptococcus neoformans

status: Public on Aug 15 2013

city: Vancouver

first: Emma

last: Griffiths

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

summary:
The interaction of Cryptococcus neoformans with phagocytic cells of the innate immune system is a key step in disseminated disease leading to meningoencephalitis in immunocompromised individuals.  Transcriptional profiling of cryptococcal cells harvested from cell culture medium or from macrophages found differential expression of metabolic and other functions during fungal adaptation to the intracellular environment by SAGE analysis. We focused on the ACL1 gene for ATP-citrate lyase, which converts citrate to acetyl-CoA, because this gene showed elevated transcript levels in macrophages and because of the importance of acetyl-CoA as a central metabolite.  Mutants lacking ACL1 showed delayed growth on medium containing glucose, reduced cellular levels of acetyl-CoA, defective production of virulence factors, increased susceptibility to the antifungal drug fluconazole and decreased survival within macrophages. Importantly, acl1 mutants were unabl  e to cause disease in a murine inhalation model, a phenotype that was more extreme than other mutants with defects in acetyl-CoA production (e.g., an acetyl-CoA synthetase mutant). Loss of virulence is likely due to perturbation of critical physiological interconnections between virulence factor expression and metabolism in C. neoformans.  Phylogenetic analysis and structural modeling of cryptococcal Acl1 identified three indels unique to fungal protein sequences; these differences may provide opportunities for the development of pathogen-specific inhibitors.

SAGE analysis of C. neoformans cells isolated from macrophages The murine macrophage-like cell line J774A.1 was maintained at 37°C in 10% CO2 in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% heat-inactivated fetal calf serum (FBS), 1% nonessential amino acids, 100 µg mL-1 penicillin-streptomycin, and 4 mM L-glutamine (Invitrogen). Cryptococcus cells were opsonized with monoclonal antibody 18B7 against capsule (1 µg mL-1), and macrophages were treated with recombinant mouse gamma interferon (IFN-gamma) (50 U mL-1) and lipopolysaccharide (LPS) (0.3 µg mL-1) prior to co-incubation at a multiplicity of infection (MOI) of 1:1. Macrophages were inoculated with H99 cells and washed after 1 h of inoculation to remove unattached, extracellular fungal cells. After 6 h of incubation, sterile, ice-cold distilled H2O was applied to each well to lyse the macrophages, and the fungal cells (4 x 107) were harvested by centrifugation. H99 control cells were prepared by growth under the same condition but without macrophages, and 108 cell  s were harvested.

overall_design: SAGE library construction, sequencing and analysis SAGE library construction, sequencing and analysis were as previously described (Hu et al., 2007; Hu et al., 2008; Steen et al., 2002; Steen et al., 2003). Briefly, RNA was isolated from lyophilized cells by vortexing with glass beads (3.0 mm, acid-washed and RNase-free) for 15 min in 15 mL of TRIZOL extraction buffer (Invitrogen, Carlsbad, CA, USA). The mixture was incubated for 15 min at room temperature and total RNA was isolated according to the manufacturer's instructions. Total RNA was used directly for SAGE library construction as described by Velculescu et al. (1995) using the I-Long SAGE kit (Invitrogen). The tagging enzyme for cDNA digestion was NlaIII and 29 PCR cycles were performed to amplify the ditags during library construction. Colonies were screened by PCR (M13F and M13R primers) to assess the average clone insert size and the percentage of recombinants. Clones from the libraries were sequenced by BigDye primer cycle sequencing on an ABI PRISM 3700 DNA analy  zer. Sequence chromatograms were processed using PHRED (Ewing et al., 1998), and vector sequence was detected using Cross_match (Gordon et al., 1998). Fourteen-base-pair tags were extracted from the vector-clipped sequence, and an overall quality score for each tag was derived based on the cumulative PHRED score. Duplicate ditags and linker sequences were removed as described previously (Steen et al., 2002). Only tags with a predicted accuracy of 99% were used, and statistical differences between tag abundance in different libraries were determined as described (Audic and Claverie, 1997). The libraries yielded 23,904 tags from cells grown in media without macrophages for 6hr and 38,5444 tags from cells grown in media with macrophages for 6hr. An overview of the abundance classes for both SAGE libraries is presented in Table S1 in the supplementary material, with both the number of different tag sequences and the total number of tags present in each class for the cells from th  e 6h infection and the control. All libraries were normalized to 23,904 to allow direct comparisons, and the tags that appeared less than once in any given library were removed. The EST database available for strain H99 at the University of Oklahoma's Advanced Center for Genome Technology http://www.genome.ou.edu/cneo.html) was used for the preliminary assignment of tags to genes. When an EST sequence could not be identified for a particular tag, the genomic sequence for H99 at the Duke University Center for Genome Technology (http://cgt.genetics.duke.edu/data/index.html) and the Broad Institute (http://cneo.genetics.duke.edu/) was used to identify contigs with unambiguous tag assignments. Note that a limitation of the SAGE approach is that some transcripts are not detected because of low abundance and/or the absence of an NlaIII site for transcript processing. The control (fungal cells alone) and cryptococcal-macrophage interaction SAGE datasets were deposited to the NCBI under accession number GSM986206 and GSM986207 respectively.


title: Expression data from LoVo and GP5d CRC cell lines

status: Public on Aug 16 2013

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: TF binding clusters in promoter correlate well with gene expression. We used ChIP-seq to map binding sites of the majority of highly expressed TFs in the cell. The size of clusters of TFs in the promoters of genes were found to correlate well with gene expression.

overall_design:
CRC cell lines were grown on plastic

This submission reprsents transcriptome component of study.

first: Enge

last: Martin

first: Jian

last: Yan


title: DCP5, a highly conserved P-body-nucleating protein, regulates multiple small RNA-mediated silencing pathways in Arabidopsis (RNA-seq)

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

type: Expression profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) negatively regulate their targets by 1) repressing translation, 2) endonucleolytic RNA cleavage, or 3) DNA methylation resulting in transcriptional silencing. P-body/decapping components are likely required for translational repression, but are not known to function in other posttranscriptional regulatory pathways or to affect smRNA levels. Here, we show that the P-body/decapping protein DCP5 is required for miRNA-mediated translational repression but not cleavage, and to regulate the transcription of specific miRNAs. We find that this protein also affects the abundance of tRNA-derived smRNAs. Significantly, DCP5 is required for the transcriptional silencing and DNA methylation of numerous transposable/repetitive elements and imprinted genes, indicating that it is a novel component of the RNA-directed DNA methylation pathway. Our results demonstrate that DCP5 and likely the P-body itself are required for multiple smRNA-mediated silencing pathways and provide the first evidence for the spatial separation of translational inhibition and cleavage by miRNAs.

overall_design: total RNA expression comparison with between wildtype (Col-0) and dcp5 mutant plants in Arabidopsis

first: Matthew

middle: W

last: Endres

first: Isabelle

last: Dragomir

first: Li

last: Yang

first: Ross

last: Weber

first: Ian

middle: M

last: Silverman

first: R

middle: S

last: Poethig

first: Brian

middle: D

last: Gregory


title: Transcriptional profile of tomato roots exhibiting Bacillus thuringiensis-induced resistance to Ralstonia solanacearum

status: Public on Aug 29 2013

city: Sendai

first: Hideki

last: Takahashi

address: 1-1 Tsutsumidori-Amamiyamachi

country: Japan

institute: Tohoku University

summary: Bacillus thuringiensis, a well-known and effective bio-insecticide, has attracted considerable attention as a potential biological control agent for the suppression of plant diseases. Treatment of tomato roots with a filter-sterilized cell-free filtrate (CF) of B. thuringiensis systemically suppresses bacterial wilt caused by Ralstonia solanacearum through systemic activation of the plant defense system. Comparative analysis of the expression of the Pathogenesis-Related 1(P6) [PR-1(P6)] gene, a marker for induced resistance to pathogens, in various tissues of tomato plants treated with CF on their roots suggested that the B. thuringiensis-induced defense system was activated in the leaf, stem, and main root tissues, but not in the lateral root tissue. At the same time, the growth of R. solanacearum was significantly suppressed in the CF-treated main root tissue but not in the CF-treated lateral root tissue. This distinct activation of the defense reaction and suppression of R. solanacearum were reflected by the differences in the transcriptional profiles of the main and lateral tissues in response to the CF. In the CF-treated main root tissue, but not CF-treated lateral root tissue, the expression of several salicylic acid (SA)-responsive defense-related genes was specifically induced, whereas jasmonic acid (JA)-related gene expression was either down-regulated or not induced in response to the CF. On the other hand, genes encoding ethylene (ET)-related proteins were induced equally in both the main and lateral root tissues. Taken together, the co-activation of SA-dependent signaling pathway with ET-dependent signaling pathway and suppression of JA-dependent signaling pathway may play key roles in B. thuringiensis-induced resistance to R. solanacearum in tomato plants.

overall_design: Gene expression was measured in main and lateral root tissues of tomato treated with Bacillus thuringiensis or distilled water-treated control at 48 hours after treatment.  Two independent experiments were performed at each tissue (main root or lateral root tissue) for each treatment (Bacillus thuringiensis or distilled water control).


title: Expression analysis of Drosophila S2R+ cells depleted of M1BP by RNAi

status: Public on Aug 13 2013

city: University Park

first: David

middle: Scott

last: Gilmour

state: Pennsylvania

address: 465 North Frear

department: Biochemistry and Molecular Biology

institute: Penn State University

summary:
Microarray analysis of gene expression profiles in control and M1BP-depleted Drosophila S2R+ cells.
The results of this analyses are reported in Li, J. and D.S. Gilmour (2013) The newly identified transcription factor M1BP ad GAGA factor orchestrate distinct mechanisms of transcriptional regulation on paused genes. The EMBO J, in press.

overall_design: Four biological replicates comparing total RNA isolated from M1BP-RNAi treated and LacZ-RNAi treated cells.

last: Li


title: The role of the Cj0440c gene in Campylobacter jejuni

city: wuhan

first: Xia

last: Fang

state: hubei

address: Shizishan Street

country: China

institute: Huazhong Agricultural University

summary:
Cj0440c encodes a putative transcriptional regulator. To determine the role of Cj0440c in C.jejuni, we knocked out Cj0440c in the wild-type strain (S) to obtain the Cj0440c mutants (SM). Then we compared the transcriptome of the Cj0440c mutant with that of the parent strain using DNA microarray. These comparisons identified 19 genes that showed a≥2-fold change in expression in SM. The differentially expressed genes in SM encode proteins involved in flagellar biosynthesis, O-linked glycosylation and hypothetical proteins with unknown fuctions. Cj0440c may regulate flagellar structural element expression or as a compenent of flagellar complex co-expressed with other flagellar genes. Subsequent experiments demonstrated that inactivation of Cj0440c affected corresponding phenotypes of C.jejuni, including broken flagella, weaker motility and reduced colonization ability in chickens.
These findings indicate that Cj0440c governs the expression of multiple genes related to flagellar biosynthesis and O-linked glycosylation. This study provides favorable evidence for completing the information of the Campylobacter jejuni genome.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: An eight chip study using total RNA recoverd from four separate wild-type cultures of Campylobacter jejuni NCTC111168 (S) and four separate cultures of a mutant strain, Campylobacter jejuni NCTC11168 delta- Cj0440c (SM), in which Cj0440c is deleted. Each chip measures the expression level of 1634 genes from Campylobacter jejuni NCTC11168.

first: Haihong

last: Hao

first: Zonghui

last: Yuan


title: The role of the Cj0440c gene in erythromycin-resistant (Eryr) Campylobacter jejuni

summary:
Cj0440c, a putative transcriptional regulator, was over-expressed in the high-level erythromycin-resistant (Eryr) Campylobacter jejuni strains. To determine the role of Cj0440c on the development and fitness of erythromycin resistance in C. jejuni, we knocked out Cj0440c in Eryr strain (R) to obtain the Cj0440c mutants (RM). Then we compared the transcriptome of the Cj0440c mutant with that of the parent strain using DNA microarray. These comparisons identified 9 genes that showed a ≥2-fold change in expression in RM. The differentially expressed genes in RM are related to flagellar biosynthesis and unknown functions. What's more, katA, encoding catalase, down-regulated in RM. Cj0440c may progress flagellar genes expression, help to escape drug pressure and disseminate and colonize smoothly, and Cj0440c in Eryr Campylobacter may protect bacteria from harmful oxygen stress from the host immune system, other microorganism in host intestinal and its own products.
These findings indicate that Cj0440c is essential for the fitness (growth) of resistant C. jejuni by controlling the expression of several genes involved in flagellar assembly and catalase, enhancing cell motility for colonization and invasion under the pressure of drug. This study widened our understanding on the molecular mechanism of resistance and provides scientific reference for drug research and application.

platform_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

overall_design: An eight-chip study using total RNA recoverd from four separate resistant-type cultures of Erythrocin-resistant Campylobacter jejuni NCTC 111168 (R) and four separate cultures of a mutant strain, erythrocin-resistant Campylobacter jejuni NCTC 11168 delta- Cj0440c (RM), in which Cj0440c is deleted. Each chip measures the expression level of 1634 genes from Campylobacter jejuni NCTC 11168.


title: Applied Biosystems Human TaqMan Low Density Array (TLDA) in plasma samples from EOC cases and controls

status: Public on Aug 30 2013

city: Tianjin

first: Lina

last: Zhang

address: HuanHuXi Road

department: Breast Oncology

institute: Tianjin Medical Univercity Cancer Institute and Hospital

summary: Most (70%) epithelial ovarian cancers (EOCs) are diagnosed late. Non-invasive biomarkers that facilitate disease detection and predict outcome are needed. The microRNAs (miRNAs) represent a new class of biomarkers. This study was to identify and validate plasma miRNAs as biomarkers in EOC. We evaluated plasma samples of 360 EOC patients and 200 healthy controls from two institutions. All samples were grouped into screening, training and validation sets. We scanned the circulating plasma miRNAs by TaqMan low-density array in the screening set and identified/validated miRNA markers by real-time polymerase chain reaction assay in the training set. Receiver operating characteristic and logistic regression analyses established the diagnostic miRNA panel, which were confirmed in the validationsets. We found higher plasma miR-205 and lower let-7f expression in cases than in controls. MiR-205 and let-7f together provided high diagnostic accuracy for EOC, especially in patients with stage I disease. The combination of these two miRNAs and carbohydrate antigen-125 (CA-125) further improved the accuracy of detection. MiR-483-5p expression was elevated in stages III and IV compared with in stages I and II, which was consistent with its expression pattern in tumor tissues. Furthermore, lower levels of let-7f were predictive of poor prognosis in EOC patients. Our findings indicate that plasma miR-205 and let-7f are biomarkers for ovarian cancer detection that complement CA-125; let-7f may be predictive of ovarian cancer prognosis.

overall_design: We designed a multi-stage, retrospective, nested case-control study to determine whether serum miRNA profiles can be used to predict EOC development. All samples were grouped into screening, training, and validation sets. A total of 560 plasma samples (360 cases and 200 controls) were obtained from Tianjin Medical University Cancer Institute and Hospital (TCIH) and Cancer Center of Nanjing Medical University. The cases and controls were well matched for age. The International Federation of Gynaecology and Obstetrics (FIGO) staging system was used to stage cases. All patients and controls were genetically unrelated, ethnic Han Chinese women who were permanent residents of the urban area of Tianjin and Nanjing. Controls with cardiovascular, respiratory, digestive, urinary, reproductive, and endocrine diseases were excluded. The study protocols were approved by the Tianjin and Nanjing Center review committees. In screening set, to detect generalizable miRNA signatures, we pooled serum samples of 10 early-stage cases (stage I), 10 late-stage cases (stage IIIc-IV), and 10 healthy controls, respectively, and analyzed these three pool samples using a TaqMan low-density array (TLDA set 2.0, Applied Biosystems) chip screening in the discovery stage. In training set, the miRNAs identified in the screening set were validated using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on individual plasma samples of 76 EOC patients and 30 normal controls. In validation set, the validation set comprised a two-phase process. Promising associations from the screening and training set were evaluated in the validation phase I set, comprising 134 cases and 70 controls from Tianjin Center. The validation phase II set included samples of 77 EOC cases and 50 normal controls were from Tianjin Center and 73 EOC cases and 50 normal controls were from Nanjing Center.

first: Kexin

last: Chen


title: Antenatal maternal long-term hypoxia: acclimatization responses with altered gene expression in ovine fetal carotid arteries

city: TUCSON

first: Ravi

last: Goyal

state: Arizona

address: 1501 N. Campbell Ave

institute: University of Arizona

summary: In humans and other species, Longlong-term hypoxia (LTH) during pregnancy can lead to intrauterine growth restriction with reduced body/brain weight, dysregulation of cerebral blood flow (CBF), and other problems in humans and rodents. In contrast, sheep appear to undergo relatively successful acclimatization, not demonstrating any of the above-mentioned problems except at extremely high altitude. To identify the signal transduction genetic pathways and those critical molecules, which may be involved in acclimatization to high altitude LTH, we conducted microarray with advanced bioinformatic analysis on carotid arteries (CA) from the normoxic near-term ovine fetus at sea-level and those acclimatized to high altitude for 110+ days during gestation. In response to LTH acclimatization, in fetal CA we identified, mRNA from 38 genes upregulated (> 2 fFold; (P < 0.05) and 9 genes downregulated (> 2-f Fold; (P < 0.05). The major genes with upregulated mRNA were SLC1A3, Insulin-like growth factor (IGF) binding protein 3, IGF type 2 receptor, transforming growth factor (TGF) Beta-3, and genes involved in the AKT and BCL2 signal transduction networks. The majority of genes with upregulated mRNA have a common motif for Pbx/Knotted homeobox in the promoter region, and Sox family binding sites in the 3’ un -translated region (UTR). Genes with downregulated mRNA included those involved in the P53 pathway and 5-lipoxygenase activating proteins. The promoter region of all genes with downregulated mRNA, had a common 49 bp region, with a binding site for DOT6 and TOD6, components of the RPD3 histone deacetylase complex RPD3C(L). We also identified miRNA complementary to a number of the altered genes. Thus, the present study identified molecules in the ovine fetus, which may help it to play a role in the acclimatizatione successfully response to high-altitude associated LTH.

overall_design: In these series of experiments we examined changes in gene expression in sheep carotids. Pregnant sheep and non-pregnant adult sheep were exposed to 110 days of hypoxia at 3801 meters of altitude.   Carotid arteries from fetuses from non-pregnant adult from sea-level controls and those from high-altitude were compared by Agilent ovine custom array


title: Investigating the changes in gene expression of liver tissue exposed to phenanthrene over 72hr

first: Christopher

last: Martyniuk

summary: FHM were exposed to 29ng/L phenanthrene. Fish were euthanized and samples taken after 24, 48 and 72hr.

overall_design: There were 28 samples analyzed; control liver tissues at 24hr (n=4) 5) phen treated liver tissues at 24hr 5) control liver tissues at 48hr 5) phen treated liver tissues at 48hr 5)control liver tissues at 72hr 4)phen treated liver tissues at 72hrs. There was a total of 28 microarrays processed.

first: Jennifer

last: Loughery

first: Chris


title: Gene expression data for mock and 5-Aza-CdR treated colorectal cancer (CRC) cell lines SW480, HCT116 and RKO

city: BALTIMORE

first: hari

last: easwaran

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

summary: DNA hypermethylated genes undergo silencing and show re-expression in response to 5-Aza-CdR treatment. Agilent arrays were used to determine the genes that get reactivated in response to the drug treatment.

overall_design: To determine expression levels of genes in SW480, HCT116 and RKO.

first: H

middle: P

last: Easwaran

first: S

middle: B

last: Baylin


title: The transcriptome of erythromycin-resistant Campylobacter jejuni strain selected from NCTC 11168

summary: Campylobacter, a major foodborne pathogen, is increasingly resistant to macrolide antibibotics. Previous findings suggested that development of macrolide resistance in Campylobacter requires a multi-step process, but the molecular mechanisms involved in the process are not known. In our study, erythromycin-resistant C. jejuni mutant (R) was selected in vitro by stepwise exposure of C. jejuni NCTC11168(S) to increasing concentrations of erythromycin.The resistant were subjected to microarray and the the global transcriptional profile was analyzed. In this series, DNA microarray was used to compare the gene expression profiles of the macrolide-resistant strain with its parent wild-type strain NCTC11168. A large number of gene showed significant changes in R. The up-regulated genes in the resistant strains are involved in miscellaneous periplasmic proteins, efflux protein and putative aminotransferase, while the majority of the down-regulated genes are involved in electron transport, lipoprotein, heat shock protein and unknown function proteins. The over-expression of efflux pump and periplasmic protein was involved in the development of resistance to macrolide in C. jejuni.

overall_design: An eight chip study using total RNA recovered from four separate resistant-type cultures of Erythrocin-resistant Campylobacter jejuni NCTC111168 (R) and four separate cultures of Campylobacter jejuni NCTC111168 (S). Each chip measures the expression level of 1634 genes from Campylobacter jejuni NCTC11168.


title: Genome-enabled studies of anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

city: Livermore

first: Anu

last: Chakicherla

state: CA

address: 7000 East Avenue, Mail Stop: L-446

institute: Lawrence Livermore National Lab

summary: Investigation of whole genome gene expression level changes in anaerobic, nitrate-dependent Fe(II) oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

overall_design: Here we report on a study to identify genes associated with nitrate-dependent Fe(II) oxidation by whole-genome transcriptional (microarray) assays including the use of FeCO3, Fe2+, and U(IV) oxides as electron donors under denitrifying conditions.  A 25 chip study using total RNA recovered from wild-type T. denitrificans was cultivated at 30oC under strictly anaerobic conditions with growth medium that contained 20 mM thiosulfate, 20 mM nitrate, and 30 mM bicarbonate (pH ~7) and exposed to 8 treatments.  Each chip measures the expression level of 2832 ORFs with N 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Harry

last: Beller

first: Peng

last: Zhou

first: Tina

last: Legler

first: Staci

last: Kane

first: Tracy

last: Letain

first: Peggy

last: O'Day


title: Parasite gene expression differences between RH-ERP, RH-JSR and GT1 of Toxoplasma gondii.

status: Public on Aug 20 2013

city: Cambridge

first: Ninghan

last: Yang

state: Massachusetts

address: 77 Massachusetts Ave, 68-270

department: Biology

institute: MIT

summary: Parasite gene expression differences have been reported previously between RH-ERP, RH-JSR and GT1. To independently confirm these gene expression differences, we examined the parasite gene expression profiles of RH-ERP, RH-JSR and GT1 through microarray.

overall_design: Three type I strains of Toxoplasma gondii were compared with one array each, and these were used to verify data from previous studies.

first: Jeroen

last: Saeij


title: Response of Rhodospirillum rubrum S1H to three pharmaceuticals

status: Public on Aug 23 2013

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary:
The present study explores the potential of compound-specific gene-upregulation profiles in the ubiquitous purple nonsulfur bacterium Rhodospirillum rubrum S1H as biomarkers for exposure to surface water contaminants, i.e. high production-volume pharmaceuticals. Even though the pharmaceuticals [i.e., acetylsalicylic acid (ASA), diclofenac (DCF), and 17α-ethinylestradiol (EE2)] did not affect the bacterial growth kinetics at environmentally-relevant concentrations (86nM), whole-genome microarray analyses revealed the upregulation of 128, 49, and 47 genes upon exposure to DCF, ASA, and EE2, respectively. A strong overlap (27-48%) was observed between transcriptional responses, but a total of 93 genes were found to be upregulated in a compound-specific manner. Hence, we were able to identify 74 and 15 potential biomarker genes for DCF and ASA, respectively. DCF specifically induced genes involved mainly in stress response, signal transduction, response regulation, the electron transport chain, and transcription, while ASA specifically induced genes predominantly involved in signal transduction, response regulation, and trans-membrane translocation. Moreover, our findings validated triclosan-specific biomarker genes that were identified previously. As only 4 genes were specifically-upregulated for EE2, no representative biomarker profile was identified. This study illustrates that a pollutant-specific molecular response can be generated in R. rubrum S1H, which could become a relevant model-microorganism to screen for the ecological impact of surface water contaminants in situ.
KEYWORDS: environmental impact studies, risk assessment, biosensor, wastewater, micropollutant, aspirin

overall_design: Two-condition experiments. Comparing samples after induction of three pharmaceuticals each with a non-induced samples. Biological triplicate. Each array contains 3 technical replicates.

first: Benny

middle: F

last: Pycke

first: Pieter

last: Monsieurs

first: Hilda

last: Witters

first: Heleen

last: De Wever

first: Natalie

last: Leys

first: Willy

last: Verstraete


title: Bacterial Adaptation Through Loss of Function

city: Princeton

first: Alison

last: Hottes

state: NJ

address: 220 Carl Icahn Lab Washington Road

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Transcriptional profiling of mutants with beneficial in-frame null mutations.  The goal of the study is to understand how expression of the mutants and their parental strain differs in conditions where the mutations are beneficial.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: For each of two conditions (media with either glutamine or alanine as the sole carbon source) four mutants were compared with the parental strain.  Two biological replicates were done for each comparison.  A total of 16 arrays were used.

middle: K

first: Peter

middle: L

last: Freddolino

first: Anupama

last: Khare

first: Zachary

middle: N

last: Donnell

first: Julia

middle: C

last: Liu

first: Saeed

last: Tavazoie


title: Mouse placenta irradiaion

city: PITTSBURGH

first: Yoel

last: Sadovsky

address: 204 Craft Ave

department: Obstetrics and Gynecology

institute: MAGEE WOMENS RESEARCH INSTITUTE

summary: External ionizing Irradiation of pregnant mice at E13.5 4 Gy, gene expression at E17.5

overall_design: On E13.5, female C57Bl/6HN mice were irradiated (total body) at 0 Gy (sham) or 4 Gy using a Gamma Cell cesium irradiator (JL Shepherd, San Fernando, CA), with a dose rate of 70 cGy/min. The mice were monitored for 4 days, and on E17.5, they were sacrificed, and placentas were procured and processed for RNA extrtaction.


title: Genome heterogeneity in Lactobacillus helveticus: Rethinking a “niche specialist”*

city: Logan

first: Jeff

last: Broadbent

state: UT

department: NFS

institute: Utah State University

summary: Lactobacillus helveticus is a rod-shaped lactic acid bacterium that is widely used in the manufacture of fermented dairy foods and for production of bioactive peptides from milk proteins.  Although L. helveticus is commonly associated with milk environments, phylogenetic studies show it is closely related to an intestinal species, Lactobacillus acidophilus, which has been shown to impart probiotic health benefits to humans.  This relationship has fueled a prevailing hypothesis that L. helveticus is a highly specialized derivative of L. acidophilus which has adapted to acidified whey.  However, L. helveticus has also been sporadically recovered from non-dairy environments, which argues the species may not be as highly specialized as is widely believed.  This study employed genome sequence analysis and comparative genome hybridizations to investigate genomic diversity among L. helveticus strains collected from cheese, whey, and whiskey malt, as well as commercial cultures used in manufacture of cheese or bioactive dairy foods.  Results revealed considerable variability in gene content between some L. helveticus strains, and indicated the species should not be viewed as a strict dairy-niche specialist.  In addition, comparative genomic analyses provided new insight on several industrially and ecologically important attributes of L. helveticus that may facilitate commercial strain selection.

platform_organism:
Lactobacillus helveticus
Lacticaseibacillus paracasei ATCC 334

overall_design: 42 samples were hybridized to the microarray chip, which contains probe sequences from L. helveticus CNRZ32.  CNRZ32 was also hybridized and used as the reference sample. Data from the microarray was statistically analyzed using the R software. Samples were compared to the reference (CNRZ32) to investigate genome diversity amoung L. helveticus strains,

first: Hui

last: Cai

first: Joanne

last: Hughes

first: Rebecca

last: Larsen

first: Dennis

last: Welker

first: Vanessa

last: de Carvalho

first: Thomas

last: Tompkins

first: Guillaume

last: Barreau

first: Marcin

last: Swiatek

first: James

last: Steele

first: Ylva

last: Ardö

first: Finn

last: Vogensen

first: Angela

last: De Lorentiis

first: Monica

last: Gatti

first: Erasmo

last: Neviani


title: Mutation of the RNA polymerase β-subunit gene promotes hetero-to-homo conversion of ß-lactam resistance of methicillin-resistant Staphylococcus aureus

city: Bunkyo-Ku

first: tomomi

last: hishinuma

state: Tokyo

institute: juntendo university

summary: Three types of phenotypic expression of ß-lactam resistance has been reported in MRSA: heterogeneous-, homogeneous-, and Eagle-type resistance. Heterogeneous to homogeneous (hetero-to-homo) conversion of ß-lactam resistance is postulated to be caused by a chromosomal mutation (chr*) together with mecA-gene expression. The Eagle-type resistance is a special pattern of chr* expression in the pre-MRSA strain N315 under the strong mecI-gene mediated repression of mecA gene transcription. Here, for the identification of chr*, experiments were conducted using an in-vitro derived homogeneously imipenem-resistant MRSA strain N315∆IPH5 (∆IPH5). The strain was selected with imipenem 8 mg/L from the heterogeneously imipenem-resistant MRSA strain N315∆IP (∆IP). The whole genome sequencing of ∆IPH5 revealed the presence of a unique mutation in the rpoB gene, rpoB(N967I), causing the amino-acid (AA) substitution of Asp by Ile at the 967th AA position of the RNA polymerase ß subunit. The effect of the mutation on the phenotypic change was confirmed by constructing and studying the phenotype of the strains H5rpoB(I967N), a ∆IPH5-derived strain cured of the rpoB mutation, and N315rpoB(N967I), a N315-derived strain introduced with the mutated rpoB gene. H5rpoB(I967N) regained the hetero-MRSA phenotype, and the mutant strain N315rpoB(N967I) showed an Eagle-type phenotype similar to that of N315h4. Furthermore, subsequent whole genome sequencing revealed that N315h4 also had a missense mutation in the rpoB gene rpoB(R644H). The rpoB mutations caused decreased autolysis, prolonged doubling-time, and tolerance to bactericidal concentrations of methicillin. We concluded that the certain rpoB mutations are chr* responsible for the hetero-to-homo phenotypic conversion of MRSA.

overall_design: We compared the gene expression profiles of the wild-type strain and rpoB mutant (N967I) using a 60mer oligo array.

first: yoshifumi

last: aiba

first: yuki

last: katayama

first: hiroko

last: murakami-kuroda

first: longzhu

last: cui

first: keiichi

last: hiramatsu


title: Metabolism of four α-glycosidic linkage-containing oligosaccharides by Bifidobacterium breve UCC2003

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: Members of the genus Bifidobacterium are common inhabitants of the gastrointestinal tract of humans and other mammals, where they ferment many diet-derived carbohydrates that cannot be digested by their host. To extend our understanding of bifidobacterial carbohydrate utilisation, we investigated the molecular mechanisms by which various strains of Bifidobacterium breve metabolize four distinct α-glucose and/or α-galactose-containing oligosaccharides, namely raffinose, stachyose, melibiose and melezitose. Here we demonstrate that all B. breve strains examined possess the ability to utilise raffinose, stachyose and melibiose. However, the ability to metabolize melezitose was not ubiquitous for all tested B. breve strains. Transcriptomic and functional genomic approaches identified a gene cluster dedicated to the metabolism of α-galactose-containing carbohydrates, while an adjacent gene cluster, dedicated to the metabolism of α-glucose-containing melezitose, was identified, yet being present only in those B. breve strains that were able to support growth on this carbohydrate.

sample_organism:
Bifidobacterium breve
Bifidobacterium breve UCC2003

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003  (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Kerry

last: O'Connell


title: Hydrodynamic conditions shape ammonia-oxidizer communities in the central Baltic Sea water column

status: Public on Aug 24 2013

first: Bess

last: Ward

address: Washington Road

department: Geosciences

summary: The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone.

sample_organism:
artificial sequences
aquatic metagenome

overall_design: Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype).  Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array.  Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

first: B

last: Bess

first: H

last: Jantti

first: S

last: Heitanen


title: Genome-wide expression of transcriptomes under waterlogging stress condition in subtropical maize

status: Public on Aug 14 2013

city: new delhi

first: Nepolean

last: Thirunavukkarasu

state: Delhi

address: IARI PUSA

department: Division of Genetics

country: India

institute: Indian Agricultural Research Institute

summary:
Genome-wide transcriptome analysis was performed to understand the expression pattern of transcriptomes in tolerant and susceptible subtropical maize genotypes under waterlogging stress condition.

Waterlogging stress causes yield reduction in maize (Zea mays). It is important to dissect the genetic circuits that underlie the plant responses to waterlogging. So, the experiment was designed with the following objectives: to understand the expression pattern of transcriptomes in the tolerant and the susceptible genotypes under waterlogging stress; to identify DEGs functioning in important pathways underlying adaptive traits; to co-map bin locations of the transcriptomes with already known QTLs for waterlogging and find synteny with other species; and to generate gene co-expression networks to study cohorts of genes expressed together in modules and functional cluster, while comparing the two genotypes.

overall_design: Two tropical maize (Zea mays L.) inbred lines, HKI1105 (tolerant) and V-372 (susceptible), were used for our experiment. The genotypes were sown in plastic pots filled with loam soil with sandy texture. The plants were watered daily to soil capacity until the application of stress at 28 days after sowing. To impose waterlogging condition, the perforation in the bottom of the pots (35 cm in height) was sealed and the stress treatment was given by watering the pots (5 cm standing water) for seven continuous days. To allow for recovery from stress, the perforations of the pots were unsealed for proper drainage of excess water. The root samples from both genotypes were collected on the 28th, 32nd, 35th and 42nd day after sowing, which represented control, moderate stress, severe stress and post-stress recovery stages, respectively. Two biological replications were used for each comparison.


title: High-density genome-wide copy number variation (CNV) in human head and neck paragangliomas.

status: Public on Aug 21 2013

city: Chieti Scalo

first: Renato

last: Mariani-Costantini

state: CH

address: Via Colle dell'Ara

department: Ageing Research Center (CeSI)

country: Italy

institute: "G. d'Annunzio" University Foundation

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Gene-centric CNV analysis of 24 individual paraganglioma cases identified a list of 104 genes most significantly targeted by tumor-associated alterations. The NOTCH signaling pathway was the most significantly enriched term in the list. Overexpression of the relevant NOTCH pathway proteins in sustentacular (glial), chief (neuroendocrine) and endothelial cells was confirmed by immunomorphological studies in 47 paragangliomas, including CNV-tested cases.  NOTCH upregulation was observed also in cases with no evidence of CNVs at NOTCH signaling genes, suggesting altered epigenetic modulation of the pathway. Notably, this was confirmed by microRNA expression analysis, that showed tumor-associated downregulation of the miR-200s and miR-34s families, correlated to NOTCH signaling and directly targeting NOTCH1.

overall_design: Total DNA from paraganglioma sample compared to total DNA from paired blood sample.

first: Annalisa

last: Morgano

first: Andria

last: D'Orazio


title: Lost miRNA surveillance of NOTCH, IGFR pathway-road to sarcomagenesis [Exiqon]

status: Public on Aug 28 2013

city: Silver Spring

first: BIJU

last: ISSAC

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

summary: The goal of this study was comparative analysis of differentially expressed miRNA and their targets in human chondrosarcoma JJ012 and chondrocytes C28 cell line (control) to elucidate the major signal transduction pathways deregulation in sarcomagenesis. Total RNA extraction was followed by the analysis of RNA quality and integrity, Exiqon human miRNA panel of 743 unique miRNA assays,  Illumina microarray HT12 platform and qRT-PCR verification of targets were performed. 189 downregulated and 147 upregulated miRNAs were detected when comparing chondrosarcoma cell line to control C 28 chondrocytes cell line using human Exiqon arrays with biological triplicates. 3045 target genes in total were detected with 587 common and 2458 unique target genes between up and downregulated miRNAs.The upregulated miRNAs were linked to the promotion of aggressive phenotype and the majority of the downregulated miRNAs were oncosuppressors. Among upregulated targtes for upregulated miRNAS were the cluster of cancer testis antigen (CTA) genes, located on X chromosome the major signal transduction pathways leading to sarcomagenesis.

overall_design: Comparison in triplicates the miRNA expression profile with Exiqon between human JJ012 chondrosarcoma cell line and C28 control chondrocytes

first: Karina

last: Galoian

first: Toumy

last: Guettouche

first: Biju

last: Issac

first: Loida

last: Navarro

last: Temple


title: Gene signature of adult mammary stem cells and mammary cancer stem cells (RT_PCR)

city: Rotterdam

first: Claudia

last: Gaspar

address: Dr. Molenwaterplein 40, PO Box 2040

department: Experimental Pathology

country: Netherlands

institute: ErasmusMC

summary: The Wnt/beta-catenin signalling pathway plays a central role in mammary stem cell homeostasis and in breast cancer. We employed the CD29hiCD24+ cell surface antigens to identify a subpopulation of mammary CSCs from Apc1572T/+, a mouse model for metaplastic breast adenocarcinoma, a subtype of triple-negative breast cancer in man. The MaCSCs are capable of recapitulating tumorigenesis when transplanted at low multiplicities in vivo, and of forming self-renewing organoids in vitro. Expression profiling of the different subpopulations sorted from normal and neoplastic mammary tissues revealed that the normal stem cell compartment is more similar to tumor cells than to their own differentiated progenies. Accordingly, Wnt signaling was found to be activated in the subpopulation encompassing normal mammary stem cells, though to a lesser degree than in the tumor cells. By comparing normal with cancer mouse mammary compartments, we were able to derive a MaCSC-specific signature composed of human orthologous genes able to predict poor survival, relapse and distant metastasis in human breast cancer. Finally, upon intravenous injection, only MaCSCs among the different tumor cell subpopulations are able to form metastatic lesions in a broad spectrum of anatomical sites. Overall, our data indicate that constitutive Wnt signaling activation interferes with mammary stem cell homeostasis leading to metaplasia and basal-like adenocarcinomas.

overall_design: The objective was to compare the: i) expression profiles between normal adult  mammary stem cells and tumor cancer stem cells identified by Lin-CD29hiCD24+; ii) expression profile between adult stem cells and their differentiated counterparts both in normal and in tumor tissue to generate a cancer stem cell signature that can be used to compare with mammary human tumor expression data to predict survival and prognosis. To this aim five independent mammary adenocarcinomas from C57BL6/J Apc+/1572T mice and three independently isolated pools of mammary glands from C57BL6/J Apc+/+ mice were employed to sort 10,000 cells of each of the following populations: Lin-, Lin-CD29+CD24+ and Lin-CD29hiCD24+.

first: Joana

last: Monteiro

first: Wilfrid

last: Richer

first: Patrick

last: Franken

first: Andrea

last: Sacchetti

first: Rosalie

last: Joosten

first: Anouar

last: Idali

last: Brandao

first: Charles

last: Decraene

first: Riccardo

last: Fodde


title: Expression data from laser capture microdissected human atherosclerotic plaque, rich or void of plasmacytoid dendritic cells

status: Public on Aug 26 2013

city: Maastricht

first: Marco

last: Manca

state: Limburg

address: P. Debyelaan 25

department: CARIM

institute: University of Maastricht

summary:
Plasmacytoid dendritic cells (pDCs) are scarcely present in the inflamed human atherosclerotic plaque, where they are presumed to exert pro-inflammatory functions through release of type I interferons. However, the precise role of pDCs in human atherosclerosis yet remains to be established.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: We investigated the impact of human plaque pDCs on its local context, applying state of the art transcriptomics analysis on Laser Capture Microdissected fractions of human atherosclerotic plaques, distinctively enriched in pDCs, or pDCs-void.

first: Anette

last: Christ


title: Differential gene expression during Exobasidium vexans and Pestalotiopsis theae infection in tea by DNA Microarray

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

institute: Genotypic Technology

summary: Microarray analysis is being performed with cultivated selections using custom designed arrays. Custom designed arrays include the design of microarray probes using clearly described bioinformatics methods. We have used the sequence data related to fungal resistance from Camellia Sp. and Arabidopsis thaliana available in the biological databases, to design these arrays. Results of this work will help us to understand the genes expressed during the blister blight and grey blight infection.

overall_design: Camellia sinensis 4x44k Microarray  designed by Genotypic Technology Private  Limited. (AMADID:043117)

first: K

last: Chandrashekara

first: Raj

last: Kumar

first: Mohamed

last: Aiyaz


title: A Parallel Study of mRNA and MicroRNA Profiling of Peripheral Blood in Young Adult Women (MicroRNA Profiling)

city: Chicago

first: Samantha

last: Gadd

state: IL

address: 2430 N Halsted St

department: Pathology

institute: Children's Memorial Research Center

summary: The goal of this study is to identify aging-related biomarkers to improve our understanding of complex physiological changes, thereby providing a means to investigate the mechanism by which aging influences various diseases.

overall_design: Global microRNA expression patterns from peripheral blood of two groups of healthy young adult women, among which 13 were aged 22-25 and 9 were aged 36-39 years old, were compared to determine changes in microRNA expression that are associated with aging.

first: Chiang-Ching

last: Huang


title: A Parallel Study of mRNA and MicroRNA Profiling of Peripheral Blood in Young Adult Women (mRNA Profiling)

overall_design: Global gene expression patterns from peripheral blood of two groups of healthy young adult women, among which 13 were aged 22-25 and 9 were aged 36-39 years old, were compared to determine changes in gene expression that are associated with aging.


title: Gene Expression differences in Hepatic Parenchyma and Portal Tracts in Hepatitis C Virus Infected Subjects with High and Low Fibrosis

city: Baltimore

first: Supriya

last: Munshaw

address: 855 N. Wolfe St, Suite 530

department: Medicine

summary: Background & Aims:  Chronic hepatitis C virus (HCV) infection is complicated by hepatic fibrosis.  Hypothesizing that fibrogenic signals may originate in cells susceptible to HCV infection, gene expression of hepatocytes was analyzed from persons with chronic HCV at different stages of liver fibrosis.    Methods:  HCV-infected subjects with significant liver fibrosis (Ishak fibrosis ≥3) were matched for age, race, and gender to subjects with minimal fibrosis (Ishak fibrosis 0-1). RNA from portal tracts and hepatic parenchyma was isolated from biopsies by laser capture and transcriptome profiling was performed using hybridization arrays.  Results:  Portal tracts from both groups were enriched for immune related genes when compared to hepatocytes but high fibrosis subjects showed a loss of this enrichment.  Hepatocytes from persons with high fibrosis were depleted for genes involved in small molecule and drug metabolism, especially butyrylcholinesterase (BCHE), a gene involved in the metabolism of drugs of abuse.  Differential expression of BCHE was validated in the same tissues using qPCR.  Cross-sectional and longitudinal testing in an expanded cohort of HCV-infected individuals showed that serum BCHE activity decreased in advance of progression to fibrosis.  Conclusion: Chronic HCV  infection is associated with a loss of hepatocyte metabolic function, decreased enrichment of immune-related genes in portal tracts and downregulation of BCHE in hepatocytes.  Our results indicate that BCHE may be involved in the progression of fibrosis during HCV infection among injection drug users and may serve as a useful marker for fibrosis progression.

overall_design: Liver tissues were chosen from five subjects with chronic HCV infection and Ishak fibrosis stage 3-5 who had sufficient tissue stored in OCT and no HIV infection.  Tissues that were stored in Trizol® or other lysis buffers were excluded to avoid homogenization of transcriptomes between cellular constituents.  Five control tissues were selected from persons of the same race and gender with chronic HCV infection estimated to be of similar duration (by age matching) but whose baseline Ishak fibrosis score was 0-1.  One high fibrosis case was later excluded because the subject was found to be HBsAg positive, leaving a total of nine subjects.

first: Hyon

last: Hwang

first: Michael

last: Torbenson

first: Jeffrey

last: Quinn

first: Kasper

last: Hansen

first: Jacquie

last: Astemborski

first: Shruti

middle: H

last: Mehta

first: Stuart

last: Ray

first: David

last: Thomas

first: Ashwin

last: Balagopal


title: Effect of light on gene expression in Schizophyllum commune

status: Public on Aug 12 2013

city: Utrecht

last: Wösten

address: Padualaan 8

institute: Utrecht University

summary: In order to study the effect of light on gene expression in Schizophyllum commune, genome wide gene expression was analysed in 4-day-old monokaryotic and dikaryotic wild type colonies, grown either in light or in darkness.

overall_design:
4 samples:
- monokaryon, grown for 4 days in the light
- monokaryon, grown for 4 days in the dark
- dikaryon, grown for 4 days in the light
- dikaryon, grown for 4 days in the dark
RNA was obtained from 3 biological replicates and pooled

last: Ohm

last: Lugones

last: Wosten


title: Dissolved and particulate copper exposure induce differing gene expression profiles in a deposit feeding amphipod

status: Public on Aug 10 2013

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

country: Australia

institute: CSIRO

summary: The southeastern Australian epibenthic amphipod Melita plumulosa was exposed to copper via different routes of exposure for 48 hours.

overall_design: RNA from exposed animals (10 individuals, pooled) was hybridised against reference RNA from unexposed animals.  Each treatment was replicated 5 times.  Alternate arrays were dye swapped.  Data are presented (exposed/ unexposed).

middle: E

first: Hannah

last: Osborn

first: Lisa

middle: A

last: Golding

last: Spadaro

last: Simpson


title: Effect of sc3 and sc4 on aerial hypha formation

summary:
In order to study changes in gene expression during mushroom development in Schizophyllum commune, genome wide gene expression was analysed in 4 developmental stages: vegetative mycelium, stage I aggregates, stage II primordia and mature mushrooms.
In order to study the effects of absence of expression of sc3 and sc4, genome-wide expression was analysed in a dikaryon in which those genes have been inactivated by targeted gene deletion.

overall_design:
5 samples:
- vegetative mycelium
- stage I aggregates
- stage II primordia
- mature mushrooms
- deltaSC3 deltaSC4 dikaryon
RNA was obtained from 3 biological replicates and pooled

last: de Jong


title: Development of Helicobacter pylori microarrays to test pathogenicity of clinical isolates

status: Public on Aug 05 2013

city: Cambridge

first: Alexander

last: Sheh

state: ma

address: 77 Massachusetts ave 16-828

department: Biological Engineering

summary: To distinguish between Helicobacter pylori isolates that may cause greater disease in patients, we used whole genome expression profiling as a platform to study host-pathogen interactions and identify gene signatures associated with isolates from patients with higher cancer risk.

platform_organism:
Helicobacter pylori 26695
Helicobacter pylori J99
Helicobacter pylori HPAG1
Helicobacter pylori Shi470
Helicobacter pylori G27
Helicobacter pylori P12
Helicobacter pylori B38

overall_design: Expression profiles were studied for 3 clinical isolates from a region of high gastric cancer incidence (PZ5056, PZ5080, PZ5086) in Colombia and 3 isolates from a region with low gastric cancer incidence in Colombia (PZ5004, PZ5024, PZ5026).  Each experiment was done in triplicate by infecting monolayers of gastric epithelial cells for 1 hour with the isolates.

first: Rupesh

last: Chaturvedi

first: D

last: Merrell

first: Pelayo

last: Correa

first: Keith

middle: T

last: Wilson

first: James

middle: G

last: Fox


title: Eisenia andrei exposed to different 2-phenylethyl isothiocyanate concentrations in soil

status: Public on Aug 11 2013

city: Amsterdam

first: Elaine

last: van Ommen Kloeke

address: De Boelelaan 1085

department: Ecological Science

institute: VU University Amsterdam

summary: Background: Earthworms are essential for a healthy soil ecosystem, performing key functions such as bioturbation. The soil ecosystem can be challenged by natural toxins such as isothiocyanates (ITC), secondary metabolites produced by many commercial crops. This study investigated the effects of the natural toxin, 2-phenylethyl isothiocyanate on the earthworm Eisenia andrei using an ecotoxicogenomics approach that combined standardised ecotoxicological testing with gene expression analyses.  Results and discussion: Exposure to 2-Phenylethyl ITC reduced both survival and reproduction of E. andrei in a dose-dependent manner, with an EC50 (reproduction) value of 556 nmol/g soil. Cross-species comparative genomic hybridisation validated the applicability of an existing 4x44k E. fetida microarray to E. andrei. Gene expression profiles revealed the importance of metallothionein (mt) as an early warning signal when E. andrei is exposed to low concentrations of 2-phenylethyl ITC. Allignment of these mt genes with the mt-2 gene of Lumbricus rubellus showed that there must at least have 2 mt genes in the Eisenia sp. genome. At high exposure concentrations of 2-phenylethyl ITC gene expression was mainly affected by inhibiting chitinase activities, inducing an oxidative stress response, and stimulating energy metabolism. KEGG pathway analysis, furthermore, implied that the high concentration may cause impaired light sensitivity, angiogenesis (e.g. wound healing), olfactory perception (olfaction), learning and memory.  Conclusions:  Increased levels of isothiocyanates may be found in the field in the near future. Risks of such compounds should be carefully investigated before allowing them to enter the soil on a large scale. This is the first study to investigate the effects of an isothiocyanate on an earthworm both on the ecotoxicological and genomic level.

overall_design: Three-exposure experiment; Acetone control vs.EC10 vs.EC50 exposed animals. Biological replicates: 4 replicates for each exposure. Technical replicates: 2 replicates for each exposure

first: Ping

last: Gong

first: Jacintha

last: Ellers

first: Dick

last: Roelofs


title: A Parallel Study of mRNA and MicroRNA Profiling of Peripheral Blood in Young Adult Women

first: Samantha

last: Gadd

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

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

overall_design: Refer to individual Series


title: Comparative transcriptional analysis of Acinetobacter baumannii strain ATCC 17978 and strain 17978hm

city: Adelaide

first: Bart

last: Eijkelkamp

state: SA

address: North Tce

institute: University of Adelaide

summary: In this study the transcriptomes of Acinetobacter baumannii strains ATCC 17978 and 17978hm were compared. Strain 17978hm is a hns knockout derivative of strain ATCC 17978. Strain 17978hm displays a hyper-motile phenotype on semi-solid Mueller-Hinton (MH) media (0.25% agar). ATCC 17978 and 17978hm from an 37C overnight culture were transferred to the centre of the semi-solid MH plate and incubated at 37C for 8 hours. Only 17978hm cells displayed a motile phenotype and covered the complete surface of the plate. These motile 17978hm cells and the non-motile wild-type ATCC 17978 cells were harvested and RNA was isolated. The comparative transcriptome analysis was performed using the FairPlay labeling kit and a custom made Agilent MicroArray with probes designed to coding regions of the ATCC 17978 genome. The data was analyzed using Agilent GeneSpring GX9 and the significance analysis of microarray MS Excel add-on.

overall_design: The motile 17978hm cells and the non-motile wild-type ATCC 17978 cells were harvested and RNA was isolated. The comparative transcriptome analysis was performedThe probes on the microarray cover all predicted open reading frames (at least 4 per ORF) and additional replicates of housekeeping genes of the A. baumannii ATCC 17978 genome .

first: Uwe

last: Stroeher

first: Karl

last: Hassan

first: Liam

last: Elbourne

first: Ian

last: Paulsen

first: Melissa

last: Brown


title: Transcriptome analysis of A661 leaves

status: Public on Aug 02 2013

city: Pontevedra

first: Victor

middle: M

last: Rodriguez

address: Apartado 28

department: Plant Genetics and Breeding

country: Spain

institute: Mision Biologica de Galicia (CSIC)

summary: The maize inbred line A661 shows a characteristic phenotype when grown at suboptimal temperatures for three weeks and then is exposed to optimal temperatures for one extra week. After this period the third leaf showed two well defined sections: distal (chlorophyll-less; CL) and proximal (chlorophyll-containing; CC) sections. To further investigate the performance of the inbred line A661 under cold conditions a gene expression profiling analysis was conducted using large scale maize microarrays. A total of 1002 transcripts change their expression between both leaf sections and the majority of these codify for proteins located to the chloroplast.

overall_design: Three biological replicates of each leaf sections were analysed. The CC section was used as control.

first: Víctor

last: Rodríguez

first: Pablo

last: Velasco

first: Pedro

last: Revilla

first: Ana

last: Butrón


title: Predicting HMX bioavailability using microarray gene expression data and regression modeling

city: Vicksburg

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

summary: Motivation: Monitoring, assessment and prediction of environmental risks that chemicals pose demand rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT, RDX and HMX. One important goal of microarray experiments is to discover novel biomarker genes for quantitative phenotypic prediction. We have developed an earthworm microarray containing 15,208 unique oligo probes. Our objective was to identify biomarker genes that can be used to quantitatively predict earthworm tissue residues of the explosives compounds that they were exposed to and took in from the HMX-spiked soil.  Results: We collected a large microarray gene expression and earthworm tissue residue dataset. First, differentially expressed genes were identified for each exposure duration (4, 14 and 28 days). These genes were used in multivariate regression modeling for HMX residue prediction. Eighteen different regression models were tested and compared. The best performing model was able to achieve very high prediction accuracies with R2 values of 0.715, 0.728 and 0.822 for 4 days, 14 days and 28 days exposures, separately.  Conclusions: This study demonstrated that multivariate regression coupled with high throughput microarray gene expression was a promising approach to quantitative phenotypic prediction.

overall_design: Adult earthworms (Eisenia fetida) were exposed in soil spiked with HMX (0, 8, 16, 32, 64, or 128 mg/kg) for 4, 14 or 28 days. Each treatment originally had 10 replicate worms with all 10 worms survived at the end of exposure. Total RNA was isolated from the surviving worms. A total of 120 worm RNA samples were hybridized to a custom-designed oligo array using Agilent’s one-color Low RNA Input Linear Amplification Kit. The array contains 15,208 non-redundant 60-mer probes, each targeting a unique E. fetida transcript. After hybridization and scanning, gene expression data were acquired using Agilent’s Feature Extraction Software (v.9.1.3). The 120-array dataset consists of three exposure groups (4 day, 14 day and 28 day) with each group having the following 8 treatments: day 0 control, blank control, solvent control, 8, 16, 32, 64, and 128 mg HMX/g soil. Each treatment had 5 biological replicates (i.e., five individual worms).

first: Natalie

last: Barker


title: Positive emotion-specific changes in gene expression profile in hypothalamus of the tickled rats

city: Tsurumi-ku, Yokohama

first: Katsuyuki

last: Hayashi

state: Kanagawa

address: 1-1-43, Suehiro-cho

department: Business Development

institute: DNA Chip Research Inc

summary:
The changes of mRNA expression levels were analyzed in the hypothalamus of the juvenile rat stimulated by tickling for 4 weeks as a positive stimulation. The genes involved in feeding regulation were up-regulated by positive stimulation compared with light-touch stimulation, and the genes related to the stress hormone were down-regulated compared with control (no stimulus).
Keywords: Stress response

overall_design:
Twenty-one-day-old male Wistar rats　after weaning were used. All rats were separately maintained in the standard cages which were shielded with screens not to see each other during the study. The rats were then subjected to the following three conditions; tickling, light touch, and no stimulus. The stimulation was given to the rats once every weekday (Monday to Friday) for 4 weeks. Tickling stimulation was used as a mimic of the rough-and-tumble play of rats which induced a positive emotional response [50 kHz ultrasonic vocalization (USV)]. Light touch was a discriminative stimulation to tickling, and neither the rat with light touch nor with no stimulus showed such a response in general. Gene expression changes in hypothalamus of the tickled rats were comprehensively analyzed comparing with light touched and no stimulated rats using microarray techniques.
Biological replicates: 4 animals each condition. One replicate per array.

first: Miyo

last: Hori

first: Takashi


title: Transcriptome analysis of Thermotoga maritima under multiple growth conditions [tiling array]

city: La Jolla

first: Haythem

last: Latif

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

type: Expression profiling by genome tiling array

summary:
Investigation of transcripts (boundary, level, etc.) across the entire T. maritima genome in mulitple growth conditions, including logphase, late exponential, heat shock and hydrogen inhibited conditions.

The new genome annotation has been approved by Genbank [CP004077, pending release of the manuscript].

overall_design: A fourteen array expression profiling study was performed using total RNA from four distinct growth conditions collected under maltose minimal media.

first: Joshua

last: Lerman

first: Vasiliy

last: Portnoy

first: Yekaterina

last: Tarasova

first: Harish

last: Nagarajan

first: Alexandra

last: Schrimpe-Rutledge

first: Richard

last: Smith

last: Adkins

first: Dae-Hee

last: Lee

first: Yu

last: Qiu

first: Bernhard

middle: O

last: Palsson

first: Karsten

last: Zengler


title: Identification of global copy number variations among diverse pig breeds by a CGH array

status: Public on Aug 09 2013

city: Wuhan

first: Fenge

last: Li

state: Hubei

address: Shizishan Street

institute: Huazhong Agricultural University

type: Genome variation profiling by genome tiling array

summary:
A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH).
We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0).

overall_design: In this study, a custom-made tiling oligo-nucleotide 720k array was used with a median probe spacing of 2506 bp for screening 12 pigs with a female Duroc as the reference. WD: White Duroc (♀); YX: Yangxin (♂); EH: Erhualian (♀); TC: Tongcheng (♀); LW: Large White (♀); PT: Pietrain (♂); LD1: Landrace × DIV pig 1 (♂); LD2: Landrace × DIV pig 2 (♀); DIV1: Chinese new pig line DIV 1 (♀); DIV2: Chinese new pig line DIV 2 (♀); L1: Landrace 1 (♂); L2: Landrace 2 (♂).

first: Yan


title: JMJD2A ChIP-chip from HEK293T cells

status: Public on Aug 01 2013

city: Charlestown

first: Johnathan

last: Whestine

state: MA

address: RM7103 Bldg 149 13th Street

department: Cancer Center

institute: MGH

type: Genome binding/occupancy profiling by genome tiling array

summary:
JMJD2A was chromatin immunoprecipitated from HEK293T cells overexpressing GFP-JMJD2A.
From Van Rechem et al. 2011 JBC

overall_design: Determination of JMJD2A binding sites by MA2C analysis

last: Whetstine

last: Black


title: Slx5_Slx8_Genome_Stability

status: Public on Aug 06 2013

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: The Saccharomyces cerevisiae Slx5/8 complex is the founding member of a recently defined class of ubiquitin ligases (STUbLs) that target sumoylated substrates. Slx5/8 has been implicated in genome stability and transcription, but the precise contribution to these processes is not clear. To characterize Slx5/8 function, we determined genome-wide changes in gene expression upon loss of either subunit. The majority of mRNA changes are part of a general stress response, also exhibited by mutants of other genome integrity pathways and therefore indicative of an indirect effect on transcription. Genome-wide binding analysis reveals a uniquely centromeric location for Slx5. Detailed phenotype analyses of slx5D and slx8D mutants show severe mitotic defects that include aneuploidy, spindle mispositioning, fish hook spindles and aberrant spindle kinetics. This is associated with accumulation of the PP2A regulatory subunit Rts1 at centromeres prior to entry into anaphase. Knockdown of the human STUbL orthologue RNF4 also results in chromosome segregation defects due to formation of chromosome bridges. The study shows that STUbLs have a conserved role in maintenance of chromosomal stability and the results link SUMO-dependent ubiquitination to a centromere-specific function during mitosis.

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Using the Erlenmeyer growth protocol up to five deletion strains were grown on a single day. In the tecan platereader, up to eleven deletion strains could be grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.

first: Loes

last: van de Pasch

first: Antony

middle: J

last: Miles

first: Wilco

last: Nijenhuis

first: Nathalie

last: Brabers

first: Dik

last: van Leenen

first: Philip

last: Lijnzaad

first: Markus

last: Brown

first: Jimmy

last: Ouellet

first: Yves

last: Barral

first: Geert

last: Kops

first: Frank

last: Holstege


title: Down regulation of qptgene in arabidopsis-Regulation of NAD biosynthesis in Arabidopsis : role of quinolinate phosphoribosyltransferase.

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: rs11-08_nad2 - down regulation of qptgene in arabidopsis - Study of the biosynthesis of NAD in Arabidopsis. Involvment of QPTgene using the knock out Salk mutant N575260. - Study of the biosynthesis of NAD in Arabidopsis. Involvment of QPTgene using the knock out Salk mutant N575260.

overall_design: 2 dye-swap - normal vs transgenic comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Bertrand

last: Gakière

first: Marie-Laure

last: Martin-Magniette


title: H. salinarum TrmB dynamics

status: Public on Aug 07 2013

city: Durham

first: Horia

last: Todor

state: North Carolina

address: 125 Science Drive

department: Biology

institute: Duke University

summary: Previous work characterized TrmB as a global glucose responsive metabolic transcription factor in archaeal extremophiles. However, it remains unclear how TrmB dynamically regulates its ~100 metabolic enzyme-coding genes. Using a dynamic perturbation approach, we elucidate the topology of the metabolic GRN in Halobacterium salinarum. We assayed gene expression in a wild-type and trmB knockout strain before and immedeatly following glucose perturbation. Clustering dynamic gene expression patterns reveals that TrmB functions alone to regulate central metabolic enzyme-coding genes, but cooperates with various regulators to control peripheral metabolic pathways.

overall_design: Gene expression of 100 genes was assayed in two strains - a wild-type and a trmB knockout. Two biological replicates of each strain were performed. Gene expression was assayed 240, 60, and 0 minutes prior to glucose addition and 5,10,20,45,90,180,360 minutes after.

first: Amy

last: Schmid


title: Coordination in the transcriptome and proteome of the diatom Thalassiosira pseudonana reveals  a diverse phosphorus stress response

status: Public on Aug 03 2013

city: Woods Hole

first: Sonya

last: Dyhrman

address: 266 Woods Hole Road

institute: Woods Hole Oceanographic Institution

summary: Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem structure and function in the ocean. Diatoms are an abundant and widespread functional group of phytoplankton that are responsible for significant amounts of primary production in the ocean, however there has not been a comprehensive study of diatom physiological responses to P deficiency. Here, we coupled deep sequencing of transcript tags and quantitative proteomic analysis from the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. The reads (tags) were mapped to the T. pseudonana genome sequence, confirming expression of 91% of the modeled gene set.  A total of 318 genes were differentially regulated with a false discovery rate of p<0.05.  A total of 1264 proteins were detected, and of those 136 were differentially expressed with a false discovery rate of p<0.05.  Significant changes in the abundance of transcripts and proteins were observed and these changes were coordinated for glycolysis, translation, and multiple biochemical responses to P deficiency. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P (DOP) through increased production of alkaline phosphatase metalloenzymes and a diesterase, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to rapidly respond to variations in environmental P availability.

overall_design: T. pseudonana (Strain 1335 from the Provosoli-Guillard National Center for the Culture of Marine Phytoplankton (CCMP)) was grown in a modified f/2 medium made from Sargasso Sea water. Macronutrients and vitamin B12, biotin, and thiamine solutions were treated with prepared Chelex-100 resin to remove trace metal contaminants followed by trace-metal clean syringe sterilization to yield final nutrient concentrations of 882 μM NaNO3 and 106 μM Na2SiO3, and vitamin concentrations of 75 pM, 400 pM, and 60 nM, respectively. The Fe concentration was also modified from f/2 to 400 nM. All conditions were run in triplicate at 14 ºC, in constant light (120 µmol photons m-2 s-1).  Cells were grown with f/2 phosphorus concentrations (P-replete; 36 µM PO4) and with low phosphorus concentrations (P-deficient; 0.4 µM PO4). Growth was monitored daily with cell counts. Duplicate P-replete treatments were pooled and harvested in mid log phase, and triplicate P-deficient treatments were pooled, and also quickly harvested onto 2 µm filters at the onset of P depletion.  All RNA samples were snap frozen in liquid nitrogen.  Replicate P-deficient cultures were refed to 36 µM phosphate at the onset of P depletion, and subsequently resumed growth. Additional growth studies were performed as described above substituting glycerolphosphate and adenosine monophosphate at 36 µM, for the phosphate in the medium.

first: Bethany

middle: D

last: Jenkins

first: Tatiana

last: Rynearson

first: Mak

last: Saito

first: Melissa

last: Mercier

first: Harriet

last: Alexander

first: LeAnn

last: Whitney

first: Andrea

last: Drzewianowski

first: Vladimir

middle: V

last: Bulygin

first: Erin

last: Bertrand

first: Zhijin

last: Wu

first: Claudia

last: Benitez-Nelson

first: Abigail

last: Heithoff


title: Kaplan2013: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

first: Marian

last: Groot Koerkamp

summary: Dynamic control of gene expression is crucial for most aspects of cell physiology and at its core is RNA polymerase II (RNAPII).  Using 53 RNAPII point mutants, we generated a point mutant epistatic miniarray profile (pE-MAP) comprising ~60,000 quantitative genetic interactions in Saccharomyces cerevisiae.  This enabled functional assignment of RNAPII sub-domains, including connections to protein complexes.  Using splicing microarrays and point mutants altering elongation rates in vitro, we found an inverse relationship between RNAPII speed and in vivo splicing efficiency.  Furthermore, the pE-MAP classified groups of fast and slow mutants that favor upstream and downstream start site selection, respectively.  Finally, the pE-MAP identified Sub1 as a positive transcription factor regulating start site selection and splicing.  These data reveal striking coordination of polymerization rate with transcription initiation and splicing, suggesting transcription rate is tuned to coordinate multiple gene expression steps.  The pE-MAP approach provides a powerful strategy to understand other multi-functional machines at amino acid resolution.

overall_design: Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Using the Erlenmeyer growth protocol up to five deletion strains were grown on a single day. In the tecan platereader, up to eleven deletion strains could be grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance. Strains with point mutations in either rpb1, rpb2 or rpb7 subunits of RNA polymerase II (RNAPII) examined under normal growth conditions. The mutated RNAPII subunit is present on URA3 or LEU2 marked CEN plasmid, and the corresponding genomic RNAPII subunit deleted. Strains labeled as wildtype also have the relevant genomic RNAPII subunit deleted, but complemented with wildtype RNAPII subunit on CEN plasmid.

first: Hannes

last: Braberg

first: Huiyan

last: Jin

first: Erica

last: Moehle

first: Yujia

last: Chan

first: Shuyi

last: Wang

first: Michael

last: Shales

first: Joris

last: Benschop

first: John

last: Morris

first: James

middle: S

last: Fraser

first: Fuqu

last: Hu

first: Leung

last: Tang

first: Frank

last: Holstege

first: Philip

last: Hieter

first: Christine

last: Guthrie

first: Craig

last: Kaplan

first: Nevan

last: Krogan


city: Suwon

first: Sang Rim

last: Kang

address: San 94-6,Iui-dong

department: Department of biological engineering

country: South Korea

institute: Kyonggi University

summary:
Transcriptional profiling of  E.coli SE15 comparing wild type E.coli SE15 with Autoindecur 2 synthesis gene LuxS mutnat E.coli SE15. E.coli SE15 is isolated from indwelling catheter of urinary tract infected patient.
Examine change of quorum sensing related gene by deleting autoinducer 2 synthesis gene LuxS in E.coli

overall_design: One array: Wild type E.coli SE15 vs. LuxS mutant E.coli SE15

first: Sang-Rim

first: Sang-Seob

last: Lee


title: Comparison of gene expression in three strains of Spodoptera Frugiperda (Insecta: Lepidoptera: Noctuidae)

city: Harpenden

first: Chris

last: Bass

state: Hertfordshire

address: West Common

department: Biological Chemistry

country: United Kingdom

institute: Rothamsted Research

summary:
The aim of this experiment was to compare the transciptome of the fall armyworm (Spodoptera frugiperda) strain SUS (a laboratory insecticide-susceptible standard) with organophosphate (OP) and pyrethroid (PYR) resistant strains were collected in cornfields located in Minas Gerais and Mato Grosso States, Brazil, in 2008 and maintained in the laboratory under selection with chlorpyrifos (at increasing discriminating doses from 100 up to 400 µg of insecticide/g of insect in a topical bioassay) or lambda-cyhalothrin (from  8.4 up to 27 µg of insecticide/g of insect) respectively
The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies). A SurePrint HD (8×15k) expression array was designed using  the base composition and the best probe methodologies to design sense orientation 60-mer probes with a 3′ bias. The FAW EST database (SPODOBASE) was used as the reference transcriptome (Negre, Hotelier et al. 2006). These sequences are derived from 8 cDNA libraries as follows: Sf1F: Fat body, Sf1H: Hemocyte, Sf1M: Midgut, Sf1P: Pool of various tissues, Sf2H: Immune Challenged hemocytes, Sf2L: Sf21 Cell lines sequences, Sf2M: Xenobiotic Induced Midgut and Sf9L: Sf9 cell lines sequences. All assembled contigs and singlets were kindly sent by the website maintainers. The BLAST2GO software v.2.3.1 (http://www.blast2go.org) was used to annotate the EST database. 60-mer probes were designed for all 7,552 assembled contigs and 5,519 annotated singlets (BlastX), totaling 13,071 sequences. For contigs encoding detoxification enzymes (P450s, GSTs and CEs) three probes were designed. Additional probe groups for 15 control genes were also included. For reference all sequences are included in the zip file with array data. References: Negre, V., T. Hotelier, et al. (2006). "SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera." BMC Bioinformatics 7: 322.

overall_design: Two-condition experiment. Slide 1: SUS vs. OP S. fugiperda strains. Slide 2: SUS vs. PYR S. fugiperda strains.  Biological replicates: 4 pools of RNA extracted from four pools of 5 second instar larvae. Technical Replicates: None, the biological replicates incorporated a dye swap. Total replication: four replicates for each strain.


title: Differentiated vs. undifferentiated promyelocytic cell lines (HL-60 and KG-1) and Neutrophiles

city: Riaydh

first: Anason

last: Halees

department: Research Center

country: Saudi Arabia

institute: King Faisal Specialist Hospital & Research Centre

summary: We identify the tetraspanin CD82 as the recognition site for xenogeneic endothelial cells independently of  Gala1,3-gal structures. We demonstrate that in contrast to undifferentiated cells, differentiated promyelocytic cell lines (HL-60, THP-1 and KG-1) are capable of recognizing xenogeneic porcine endothelial cells in a calcium-dependent manner. We used serial analysis of gene expression (SAGE) to identify the differentially expressed transcripts in these cell lines. Interrogation of these transcripts revealed a number of differentially expressed genes that include the Gala1,3-gal-independent recognition moiety(s). Comparing these SAGE transcripts with those expressed in resting human naive neutrophils identified the tetraspanin CD82 as the most likely candidate responsible for xenogeneic recognition. Blocking antibodies to CD82 in human naive neutrophils inhibited the calcium response and abolished the subsequent Reactive Oxygen Metabolite (ROM) production evoked by the xenogeneic encounter of either Gala1,3-gal knockout or wild-type porcine aortic endothelial cells. Our data identify CD82 on innate immune cells as the major recognition moiety of the xenogeneic endothelium, independently of Gala1,3-gal-structures and open new avenues of intervention to making xenotransplantation a clinical reality.

overall_design: We used serial analysis of gene expression (SAGE) to identify the differentially expressed transcripts in promyelocytic cell lines (HL-60, THP-1 and KG-1) upon differentiation. We looked for genes common to the differentiation pathway in these cell lines but absent from the control naiive neutrophiles.

first: Futwan

last: Al-Mohanna

first: Soad

last: Saleh

first: Ranjit

last: Parhar

first: Reem

last: Al-Hejailan

first: Razan

last: Bakheet

first: Hala

last: Khaleel

first: Hanif

last: Khlak

first: Marya

last: Zaidi

first: Brian

last: Meyer

first: Gisella

last: Yung

first: Jörg

last: Seebach

first: Khalid

last: Khabar

first: Kate

last: Collison


title: Transcriptional profiling of Populus leaves with altered SA levels

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

summary: Salicylic acid (SA) has long been implicated in plant responses to oxidative stress.  A direct assessment of SA effects in planta has been difficult, as SA-overproducing Arabidopsis mutants are compromised in growth or other developmental processes.  We now report that transgenic Populus expressing a bacterial bifunctional SA synthase accumulated two to three orders of magnitude more total SA than wild type without affecting growth.  Microarray experiments were performed to gauge the transcriptional responses of young source leaves to SA manipulation and/or heat stress.  Differentially expressed genes due to SA perturbation or temperature treatment were identified. Co-expression network analysis was performed to identify key driver genes in SA-modulated response.

overall_design: Wild-type and transgenic Populus expressing cytosolic Irp9 (Irp9 line I6), plastidic Irp9 (FD-Irp9 lines F10 and F52) or NahG (NahG line N31) genes were maintained in two identical growth chambers at normal (NT, 27°C/17°C, day/night) or high (HT, 35°C/25°C) temperatures.  Young source leaves at leaf plastochron index (LPI) 5 were sampled one week after the start of heat stress.  Two biological replicates were used.

first: Scott

last: Harding

first: Liangjiao

last: Xue

first: Wenbing

last: Guo


title: Global gene expression profile of Japanese encephalitis virus(JEV) infected cytolytic B16F10 and Non-cytolytic JEV resistant B16F10r

city: Bengaluru

last: Rangarajan

state: karnataka

address: New biological science building

department: Biochemistry

institute: Indian Institute of Science

summary: B16F10, a murine melanoma cel line is cytolytic to JEV infection. We have identified a B16F10 cell line variant which is non-cytolytic to JEV infection.  This variant cell line has two types of cells, one which is persistently infected JEV and another which is resistant to JEV infection.  The JEV-resistant cells (B16F10r) were seperated from the presistently infected cells by single cell cloning.   To understand the mechanism of JEV resistance microarray analysis was caried out to Identify and characterize  genes differentially expressed during in uninfected/JEV-infected B16F10 and B16F10r cells.

overall_design: Agilent one-color experiment,Organism: Mus musculus ,Agilent Custom Mouse Whole Genome Mouse 8x60k Gene expression designed by Genotypic Technology Private Limited, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Prakash

last: bhandari

first: A

last: Arvind

first: PN


title: Open Ocean and Coastal Strains of Marine Synechococcus display distinctly different Global Responses to DNA Damaging Agents

city: Sydney

first: Sasha

last: Tetu

address: North Ryde

department: CMBS

institute: Macquarie University

summary: We have looked at the transcriptional response of well characterised Synechococcus open ocean (WH8102) and coastal (CC9311) isolates to two DNA damaging agents, mitomycin C and ethidium bromide, using whole genome expression microarrays.  The coastal strain, which was able to grow on higher concentrations of both chemicals, showed differential regulation of a larger proportion of its genome following ‘toxic shock’ treatment with each agent. Many of the orthologous genes in these strains, including those encoding sensor kinases, showed different transcriptional responses, with the CC9311 genes more likely to show significant changes for each tested treatment. While the overall response of each strain was considerably different, there were distinct transcriptional responses common to both strains observed for each DNA damaging agent, linked to the mode of action of each chemical. In both CC9311 and WH8102 there was evidence of SOS response induction under mitomycin C treatment, with genes encoding recA, the lexA repressor and umuC significantly upregulated in this experiment but not under ethidium bromide treatment. Conversely, ethidium bromide treatment tended to result in upregulation of the DNA-directed RNA polymerase genes, not observed following mitomycin C treatment. Interestingly, a large number of genes residing on putative genomic island regions of each genome also showed significant upregulation under one or both chemical treatments.

sample_organism:
Synechococcus sp. CC9311
Parasynechococcus marenigrum WH 8102

overall_design: In this series four conditions have been analyzed. These are 2 hour incubations (shock treatment) with ethidium bromide (EB, final conc 2ug/mL) and mitomycin C (MC, final conc 0.5 ug/mL) for Synechococcus sp. WH8102 and CC9311. For each slide, an experimental RNA sample was labeled with Cy3 or Cy5 and was hybridized with a reference RNA from a control sample (no addition of chemical agent) labeled with the other Cy dye. There are six slides per condition, each with at least two biological replicates and three technical replicates, including at least one flip-dye comparison. Each slide contains six replicate spots per gene.

first: Daniel

last: Johnson

first: Katherine

last: Phillippy

first: Rhona

last: Stuart

first: Chris

last: Dupont

first: Karl

last: Hassan

first: Brain

last: Palenik

first: Ian

last: Paulsen


title: shoots and roots treated with methotrexate and 5-formyl-thf-Transcriptomic and metabolic changes in Arabidopsis thaliana supplemented with 5-CHO-THF and its relationship with the accumulation and transformation to THF active derivatives

first: Soubigou-Taconnat

last: Ludivine

summary: au11-02_cho-thf - shoots and roots treated with methotrexate and 5-formyl-thf - Folates and 1C metabolism - The objective of this study is to investigate the changes on the plant expression profiles due to 5-CHO-THF assimilation and transformation. Additionally, plants supplemented with methotrexate (MTX) (an inhibitor of folate biosynthesis) will complement the study. Results from this work will serve to better understand the effects of folate accumulation in plants.

overall_design: 12 dye-swap - treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Rocio

last: I. diaz de la garza

first: Marie-Laure

last: Martin-Magniette


title: Systematic profiling of human microRNAs in plasma from nasopharyngeal carcinoma patients reveals candidate biomarkers

city: GuangZhou

first: jinze

last: zheng

address: Dongfeng east road 651#

institute: Sun Yat-Sen University Cancer Center

summary: We used microarrays to perform systematic profiling of human microRNAs in plasma from nasopharyngeal carcinoma (NPC) patients to find potential biomarkers. By comparing the plasma microRNA profiles of the NPC patients and healthy donors, potential biomarkers for NPC were investigated. A total of 39 microRNAs were aberrantly expressed based on 50 Agilent microarrays containing 887 human microRNAs

overall_design: 50 microarrays containing 887 human microRNAs were used to screen for potential biomarkers with significant differential expression levels between 31 NPC patients and 19 healthy donors.

first: XiaoHui

last: Zheng

first: WeiHua

last: Jia


title: Transcriptome comparison of wild type Azoarcus sp. strain BH72 grown under nitrogen fixation (experiment) with cells grown with combined nitrogen (ammonia) as nitrogen source

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

country: Germany

institute: University Bremen

summary: Model endophyte Azoarcus sp. BH72 is known to contribute fixed nitrogen to its host Kallar grass by nitrogen fixation and also expresses nitrogenase genes endophytically in rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. Therefore, we analysed global transcription in response to differences in the nitrogen source. Transcription profiles of cells grown microaerobically (0.6% oxygen) on minimal medium with nitrogen (N2-fixing) versus ammonium (combined nitrogen) were compared using a genome-wide microarray approach and differences in the gene expression profile were monitored.

overall_design: RNA from cells grown on nitrogen-free synthetic medium under nitrogen fixation (experiment) and combined nitrogen source as ammonium chloride (control) was used for two-color whole-genome microarray approach.

first: Abhijit

last: Sarkar