title: Identification of active microRNA/transcription factor feed-forward loops during human adipogenesis (mRNA)

status: Public on Dec 20 2011

city: Padova

first: Federica

last: Eduati

state: Italy

address: Via G. Gradenigo 6/B

institute: University of Padova

summary: Post-transcriptional regulation of gene expression accomplished by microRNAs (miRNAs) importantly affects the complex gene regulatory network. In particular, miRNAs are known to be involved in recurrent motifs named miRNA-mediated feed forward loops (FFLs) where a transcription factor (TF) regulates a miRNA and they both regulate the expression level of a target RNA. Here, we focus on the identification of active FFLs during adipogenic differentiation. A list of putative feed-forward loops was generated based on sequence analysis of conserved and overrepresented motifs in the regulatory regions. Since this approach is not specific for adipogenesis and is known to generate false positive feed-forward loops, an experiment was designed to select active ones based on their dynamics using a model-based approach. Microarray time series of gene and miRNA expression data were collected at seven time points on human multipotent adipose-derived stem (hMADS) cells upon adipogenic differentiation. Three different dynamic models, sharing the same FFL topology but incorporating descriptions of increasing complexity of miRNA and mRNA dynamics, are identified on miRNA and mRNA expression data and compared based on identification criteria, namely: goodness of fit, precision of the estimates and comparison with submodels. 24 FFLs, able to properly reproduce data, are selected as active out of the 329 putative ones. This method considerably reduces the search space for new interactions between TFs, miRNAs and mRNAs and provides interesting biological results identifying genes known from the literature to be regulators in adipogenesis and adipocyte-related functions that can be interpreted as positive control of the validity of the apporoach. Therefore, the genes in the selected FFLs that are not yet known to be involved in this context are potential novel players in this regulatory network of adipogenesis and adipocyte function.

overall_design: Two independent cell culture experiments were performed as biological replicates during adipogenic differentiation of human mesenchymal stem cell. Cells where harvested at the pre-confluent stage as reference (day -3) and at seven subsequent time points during human adipogenic differentiation: day -2 and 0 before, and 1, 2, 5, 10, 15 days after induction of differentiation. All hybridizations were repeated with reversed dye assignment (dye-swap).

first: Barbara

last: Di Camillo

first: Michael

last: Karbiener

first: Marcel

last: Scheideler

first: Davide

last: Corà

first: Michele

last: Caselle

first: Gianna

last: Toffolo


title: Identification of active microRNA/transcription factor feed-forward loops during human adipogenesis (miRNA)

country: Italy


title: Identification of common lupus-disease related microRNA expression pattern in three different murine models of lupus

status: Public on Dec 17 2011

city: blacksburg

first: rujuan

last: dai

state: VA

address: 1410 price fork RD

department: CMMID

country: USA

institute: virginia Tech

summary: In this study, miRNA expression in splenic lymphocytes from three genetically disparate lupus-prone mouse models (MRL-lpr, B6-lpr and NZB/WF1) were profiled. 49 miRNAs were found to be differentially expressed in MRL-lpr mice compared to MRL mice; and 24 miRNAs were differentially expressed in B6-lpr mice compared to B6 mice. Among these dysregulated miRNAs, we noted that 15 miRNAs were common to both lpr strains.  Interestingly, microarray analysis of NZB/W and NZW at 3 months of age, an age when overt lupus disease is not evident in NZB/W mice, revealed that only one miRNA, miR-148a was significantly upregulated in NZB/W mice.

overall_design: The aim of this porject is to determine the common miRNA expression changes in splenocytes from different strains of murine lupus models. The splenocytes were prepared from genetically lupus-prone female mice including MRL/MpJ-Faslpr/J (MRL-lpr), NZBWF1/J  (NZB/W), B6.MRL-Faslpr/J (B6-lpr) and their control mice MRL/MpJ (MRL), NZW/LacJ (NZW) and C57BL/6J (B6) mice (The Jackson laboratory, ME).  Total RNAs, containing miRNAs were isolated from whole splenocytes using mirVana miRNA isolation kits (Ambion) following manufactory’s instructions and  sent to LC Sciences (http://www.lcsciences.com/) for the microarray assay. The mouse miRNA array chips (Chip ID miRMouse 12.0 version), which included 617 unique, mature, mouse miRNA, based on the Sanger miRBase Release 12.0, were used in the assay.

first: Rujuan

last: Dai

first: S

middle: A

last: Ahmed


title: The Enterococcus faecalis V583 transcriptional profile during survival within macrophages

status: Public on Dec 21 2011

city: Norman

first: Scott

middle: M

last: Maddox

state: OK

address: 101 David L. Boren Blvd.

department: Botany and Microbiology

institute: University of Oklahoma

summary:
Transcriptional profiling of E. faecalis V583 during intracellular survival compared to V583 grown to mid-log phase (OD 600 = 0.05) in THB + 1% glucose.
In this study we report the complete intracellular E. faecalis V583 transcriptome following infection of RAW264.7 macrophages.  During intracellular survival, approximately 45% of the V583 genome was differentially regulated including numerous genes involved in the oxidative stress, heat shock and SOS responses.  We observed that the E. faecalis-containing phagosome was limited for glycolytic substrates, nucleotides, amino acids and numerous ions necessary for growth and protein function.   Approximately 35% of the genes differentially regulated during survival within macrophages were of hypothetical/unknown function, suggesting that the V583 response to phagocytosis involves many previously unstudied loci.  Here, we provide the first comprehensive study elucidating the transcriptional response of E. faecalis to phagocytosis, which may provide new targets for future studies.

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

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

overall_design: Bacterial RNA was obtained from RAW264.7 macrophage infected with E. faecalis V583 4, 8 and 12 h post-infection and compared to E. faecalis V583 RNA extracted from mid log growth (OD 600 = 0.05).  Control cultures were grown in Todd-Hewett Broth supplemented with 1% glucose.

first: Tyrrell

last: Conway

first: Joe

last: Grissom


title: Gastric cancer: cancer vs. normal, chemoresistance signature that correlates with time to progression of disease

status: Public on Dec 16 2011

city: Bethesda

first: Jeffrey

middle: E

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

institute: NCI

summary:
microRNA profiling of gastric cancer vs. normal, pre-/-post CF (cisplatin/fluorouracil) chemotherapy.
Biopsy samples were collected prior to chemotherapy from 90 gastric cancer patients treated with CF and from 34 healthy volunteers.  At the time of disease progression, post-treatment samples were collected from 8 clinical responders. miRNA expression was determined using a custom-designed Agilent microarray.  In order to identify an miRNA signature for chemotherapy resistance, we correlated miRNA expression levels with the time to progression (TTP) after CF.

overall_design: 90 pre-treatment gastric cancer samples, 34 healthy volunteers, 8 post-treatment samples.

first: Chang

middle: H

last: Kim

first: Hark

middle: K

first: R

middle: L

last: Rettig

first: Joseph

first: Il

middle: J

last: Choi

first: David

last: Munroe


title: Influence of 17β-estradiol on Gene Expression of Paracoccidioides During Mycelia-to-Yeast Transition

status: Public on Dec 14 2011

city: San Jose

first: Jata

last: Shankar

state: CA

address: 2260 Clove Drive

department: Division of Infectious Diseases and Geographic Medicine

institute: Stanford University

summary:
Background: Paracoccidioides is the causative agent of paracoccidioidomycosis, a systemic mycosis endemic to Latin America. Infection is initiated by inhalation of conidia (C) or mycelial (M) fragments, which subsequently differentiate into yeast (Y). Epidemiological studies show a striking predominance of paracoccidioidomycosis in adult men compared to premenopausal women. In vitro and in vivo studies suggest that the female hormone (17β-estradiol, E2) regulates or inhibits M-or-C-to-Y transition. In this study we have profiled transcript expression to understand the molecular mechanism of how E2 inhibits M-to-Y transition.
Methodology: We assessed temporal gene expression in strain Pb01 in the presence or absence of E2 at various time points through 9 days of the M-to-Y transition using an 11,000 element random-shear genomic DNA microarray and verified the results using quantitative real time-PCR. E2-regulated clones were sequenced to identify genes and biological function.
Principal findings: E2-treatment affected gene expression of 550 array elements, with 331 showing up-regulation and 219 showing down-regulation at one or more time points (p ≤ 0.001).  Genes with low expression after 4 or 12 h exposure to E2 belonged to pathways involved in heat shock response (hsp90 and hsp70), energy metabolism, and several retrotransposable elements. Y-related genes, α-1,3-glucan synthase, mannosyltransferase and Y20, demonstrated low or delayed expression in E2-treated cultures. Genes potentially involved in signaling, such as palmitoyltransferase (erf2), small GTPase RhoA, phosphatidylinositol-4-kinase, and protein kinase (serine/threonine) showed low expression in the presence of E2, whereas a gene encoding for an arrestin domain-containing protein showed high expression. Genes related to ubiquitin-mediated protein degradation, and oxidative stress response genes were up-regulated by E2.
Conclusion: This study characterizes the effect of E2 at the molecular level on the inhibition of the M-to-Y transition and is indicative that the inhibitory actions of E2 may be working through signaling genes that regulate dimorphism.

overall_design: Two-condition experiment, Controls  vs. 17β-estradiol (E2) treated Paracoccidioides Pb01 cells (at 0, 4, 12 24, 72, 144 or 216 h time points). Biological replicates: 4 controls (2 untreated(C) + 2 ethanol (OH) treated control), 2 (E2)treated at each time points, independently grown and harvested. Two array from each biological samples.

first: Thomas

middle: D

last: Wu

first: Karl

middle: V

last: Clemons

first: Jomar

middle: P

last: Monteiro

first: Laurence

middle: F

last: Mirels

last: Stevens


title: Genomic aberrations in distant fields from oral potentially malignant lesions by high resolution DNA flow cytometry and array-CGH

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

institute: "San Martino" Hospital

type: Genome variation profiling by genome tiling array

summary:
The aim of the study was to address the concept of field cancerization in oral cancer. The presence of genomic aberrations, indicative of chromosomal instability (CIN), in oral distant fields (ODFs) of visually normal and non-dysplastic mucosa at the mirror image from concomitant oral potentially malignant lesions (OPMLs) was investigated.
This pilot study comprised 16 OPMLs (8 without dysplasia, nd-OPMLs; 8 with dysplasia, d-OPMLs) and 16 ODFs. DNA diploid (DNA Index, DI=1) and aneuploid (DI≠1) sublines were detected by high resolution DNA-flow cytometry (FCM) at (hr DNA-FCM) using DAPI stained nuclei suspensions. Nuclei with different DIs were FCM-sorted in order to enrich the epithelial component and to obtain genomic DNA for high resolution oligonucleotide array-Comparative Genomic Hybridization (a-CGH) analysis to provide a genome-wide measurement of DNA copy number aberrations (CNAs).
The frequencies of DNA aneuploidy in ODFs and OPMLs were 6.2% and 43.8%, respectively (p=0.037). ODFs and nd-OPMLs were all near-diploid (DI≠1 and DI≤1.4), while d-OPMLs were also high-aneuploid (DI>1.4). CNA averages were 2.3 in ODFs (1.5 for nd-OPMLs and 3.1 for d-OPMLs), and 7.325 in OPMLs (3.0 in nd-OPMLs; 11.6 in d-OPMLs). CNAs were present in the DNA diploid sublines and often the same CNAs were observed in both ODFs and corresponding OPMLs
DNA aneuploid sublines and CNAs in the present series of 16 ODFs are likely to represent early events of the natural history of oral carcinogenesis and to indicate an early onset of the field effect cancerization. Moreover, gains within 20q13.33-qter, 7p22.2-pter and 16p13.3-pter chromosomal regions in ODFs and in the relative OPMLs suggest that specific genes localized in these regions (RTEL1, MAD1L1 and TEL2) might contribute to the ODF/d-OPML transition.

overall_design: We analyzed: 8 samples of oral potentially malignant lesions with dysplasia, 8 samples of oral potentially malignant lesions without dysplasia and for each patient a corresponding  oral distant field of visually normal mucosa.

first: Paola

last: Scaruffi

first: Simona

last: Coco

first: GianPaolo

last: Tonini

first: Massimo

last: Maffei

first: Alessandra

last: Donadini

first: Walter

last: Giaretti


title: Genome wide analysis of Histone H3 acetylation patterns in AML identifies PRDX2 as an epigenetically silenced tumor suppressor gene

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

institute: Columbia University Medical Center

type: Genome binding/occupancy profiling by array

summary: Epigenetic deregulation plays a critical role in the pathogenesis of Acute Myeloid Leukemia. But changes in histone modification patterns at the epigenome level still remain largely unknown. Here, we analyzed alterations of histone H3 acetylation patterns in a large number of patients with AML compared to CD34+ progenitor cells. Using ChIP-Chip assays, we demonstrate that AML blasts exhibit significant changes in Histone H3 acetylation levels at more than 1000 genomic loci. Importantly, at core promoter regions losses of H3 acetlyation levels prevailed which suggested that a large number of genes is epigenetically silenced in AML. The validation of identified genes led to the discovery of Peroxiredoxin 2 (PRDX2) as a potential tumor suppressor gene in AML. Peroxiredoxin-2 (PRDX2) was silenced in most AML patients by decreased Histone H3 acetylation and in almost 20% by promoter DNA hypermethylation. Low protein expression of the antioxidant PRDX2 gene was clinically associated with a poor prognosis in AML patients. Functionally, PRDX2 acted as an inhibitor of myeloid cell growth by reducing levels of reactive oxygen species generated in response to cytokines. A high level of PRDX2 expression inhibited myc-induced murine leukemogenesis  whereas loss of PRDX2 increased myeloid cell proliferation and accelerated myc-induced leukemogenesis. Taken together, we identify widespread loss of Histone H3 acetylation at core promoter regions as a signature of AML blasts. Epigenome wide analyses of histone H3 acetylation led to the identification of PRDX2 as an epigenetically silenced growth suppressor that contributed to the malignant phenotype in AML.

overall_design: Blasts from patients with AML (n=72) were obtained at the time of diagnosis (in a few cases at first relapse). CD34+ progenitor cells (n=17) and white blood cells (n=16) were used as control samples. Immunoprecipitations were performed for anti-acetylated Histone H3. Chromatin-IPs were amplified using ligation mediated PCR and labeled using Cy3 coupled to incorporated amino-allyl-UTP. Common reference DNA consisting of a mixture of genomic DNA from AML patients was prepared, amplified and labeled in a similar way with Cy5.

first: Shuchi

last: Agrawal-Singh

first: Fabienne

last: Isken

first: Konstantin

last: Agelopoulos

first: Nils

last: Thoennissen

first: Gabriele

last: Koehler

first: Antje

last: Hascher

first: Nicole

last: Bäumer

first: Wolfgang

last: Berdel

first: Christian

last: Thiede

first: Gerhard

last: Ehninger

first: Anke

last: Becker

first: Peter

last: Schlenke

first: Yipeng

last: Wang

first: Michael

last: McClelland

first: Utz

last: Krug

first: Steffen

last: Koschmieder

last: Büchner

first: Dae-Yeul

last: Yu

first: Shailendra

last: Singh

first: Klaus

last: Hansen

first: Hubert

last: Serve

first: Martin

last: Dugas

first: Carsten

last: Müller-Tidow


title: Indirect expression microarray from 5 pairs of tissues from colorectal cancer patients

status: Public on Dec 27 2011

city: Daejeon

first: sunwoo

last: Lee

address: 829 tamnip-dong, yuseong-gu

country: South Korea

institute: Genomictree,Inc.

summary: 5 colorectal cancer (CRC) tissues and 5 paired non-tumor tissues from CRC patients were indirectly compared using a 17K cDNA microarray.

overall_design: The total RNA from each tissue was labeled with Cy5, and the total RNAs from 11 human cell lines were labeled with Cy3 as the reference.

first: Sunwwo

first: Taejeong

last: Oh


title: Ceratitis capitata gene expression related to sexual maturation in females

status: Public on Dec 25 2011

city: Pavia

first: Ludvik

middle: Marcus

last: Gomulski

state: PV

address: Piazza Botta 9

department: Biologia Animale

institute: University of Pavia

overall_design: This analysis compares gene expression between 1 day old and 4 day old virgin medfly, Ceratitis capitata females. Samples where made from the heads of the females.

first: L


title: Effect of salicylic acid on Fusarium graminearum, the major causal agent of fusarium head blight in wheat

status: Public on Dec 15 2011

city: Ottawa

first: Linda

last: Harris

state: Ontario

address: 960 Carling Ave.

department: Eastern Cereal & Oilseed Research Centre

country: Canada

institute: Agriculture & Agri-Food Canada (AAFC)

summary: Salicylic acid (SA) is one of the key signal molecules in regulating plant resistance to diverse pathogens. It is predominantly associated with resistance against biotrophic and hemibiotrophic pathogens, and triggering systemic acquired resistance (SAR) in Arabidopsis. However, whether and how SA directly affects Fusarium graminearum and how SA influences the defence efficiency of wheat against fusarium head blight (FHB) are still poorly understood. Previous experiments have shown that the growth of F. graminearum mycelia and the germination of spores were significantly inhibited, and eventually stopped by increasing amounts of SA in both liquid and solid media cultures. Co-inoculation of SA and Fg spores has led to reduced FHB symptoms in the very susceptible Triticum aestivum cultivar ‘Roblin’. To better understand the effect of SA on F. graminearum mycelial growth, we have compared the expression profiles of SA-treated and untreated F. graminearum liquid cultures after 8 and 24 h of treatment, using an F. graminearum custom-commercial microarray.  The microarray analysis suggests that F. graminearum can metabolize SA through two pathways, the gentisate and catechol pathways that are present in many fungal species. Additional experiments have confirmed the capacity of F. graminearum to metabolize SA. Our results demonstrate that, although F. graminearum has the capacity to metabolize SA, SA has a significant and direct impact on F. graminearum through a reduction in efficiency of germination and growth at higher concentrations.

overall_design: Untreated and Salicylic Acid (SA) treated liquid cultures of F. graminearum at 8h and 24h collection times. Three biological replicates per time point and treatment, 2 technical replicates (dye flips) per sample.

first: Peng-Fei

last: Qi

first: You-Liang

last: Zheng

first: Thérèse

last: Ouellet

first: Anne

last: Johnston


title: A pilot study of circulating miRNAs as potiential biomarkers in patients with  system lupus erythematosus

status: Public on Dec 13 2011

city: Shenzhen

first: Honglei

last: Wang

state: Guangdong

address: No 1017, dongmen north road

department: Clinical Medical Research Center of The Second Clinical Medical College (Shenzhen People’s Hospital)

country: China

institute: Jinan Univesity

summary:
The gole of this study was to determine whether circulaitng miRNAs could be used as candidate miRNAs of SLE .
In this study a miRNA profile was used to determine aberrant expressed circulating miRNAs in patients with system lupus erythematosus (SLE), compared with rheumatoid arthritis (RA) and healthy control (HCs). To further confirm these microarray data, we identify 8 miRNAs (miR-126, miR-21, miR-451, miR-223, miR-16, miR-125a-3p,miR-155,miR-146a) by real-time quantitative PCR in 20 healthy controls and in 55 cases, of whom 30 were diagnosed with SLE and 25 were diagnosed RA.

overall_design: Using microarray-based expression profiling follwed by real-time quantitative polymerase Cycle Reaction (RT-qPCR)validation, we compared the levels of circulating miRNAs in plasma sample from SLE patients, RA patients, and healthy controls

first: Yong

last: Dai


title: Profiling of antibodies against prostate cancer xenograft-released proteins

city: Rotterdam

first: Guido

last: Jenster

department: Urology

country: Netherlands

institute: Erasmus MC

summary: The present study describes a novel xenograft-based biomarker discovery platform and proves its usefulness in the discovery of novel serum markers for prostate cancer (PCa). By immunizing immuno-competent mice with serum from nude mice bearing PCa xenografts, an antibody response against xenograft-derived antigens was elicited. By probing protein microarrays with serum from immunized mice, several PCa-derived antigens were identified, of which a subset was successfully retrieved in serum from mice bearing PCa xenografts and validated in human serum samples of PCa patients. In conclusion, this novel method allows for the identification of low abundant cancer-derived serum proteins, circumventing dynamic range and host-response issues in standard patient cohort proteomics comparisons.

overall_design: To perform a large-scale identification of antibodies generated against human PCa-derived proteins in the serum of immunized mice, sera from mice immunized with either depleted serum, full serum or both from PC346 and PC339-bearing mice as well as preimmune serum and serum from mice immunized with normal mouse serum were incubated onto ProtoArrays. These ProtoArrays contain approximately 8,000 partial and full-length human proteins, expressed as N-terminal glutathione S-transferase (GST) fusion proteins. To detect antibodies bound to spotted proteins, ProtoArrays were developed using a fluorescent labeled secondary antibody. Before being used for immunization, serum from xenografted mice was not treated (full) or depleted for most abundant proteins (depleted). Two arrays were hybridized with pre-immune serum and one array with serum from an immune competent mouse that was immunized with serum from a nude mouse. Six arrays were performed using serum from immune competent mice that were immunized with serum from xenograft-bearing nude mice.

first: Flip

last: Jansen

first: Angelique

last: van Rijswijk

first: Wilma

last: Teubel

first: Frank

last: Staal

first: Wytske

last: van Weerden


title: MicroRNAs and their isomiRs function cooperatively to target common biological pathways (Agilent miRNA array)

city: Brisbane

first: Nic

last: Waddell

address: St Lucia

country: Australia

institute: Queensland Centre for Medical Genomics

summary: This data set is part of a larger study: Variants of microRNAs, (isomiRs) are commonly reported in deep-sequencing studies; however the functional significance of these variants remains controversial. To assess their biological relevance, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline (miRNA-MATE) to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. We isolated polyribosome-associated mRNA, and captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Together, these results find isomiRs to be biologically relevant and functionally synergistic partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur with predominantly non-specific miRNA-mRNA interactions.

overall_design:
6 samples submitted, all replicates of Human Placenta total RNA, Ambion

The miRNA-Seq data have been submitted to the short read archive under SRA number SRP006043: http://www.ncbi.nlm.nih.gov/sra?term= SRP006043

first: Nicole

last: Cloonan


title: Discovering novel bile protection systems in Bifidobacterium breve UCC2003 through functional genomics

city: Utrecht

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

institute: Utrecht University

summary:
Tolerance of gut commensals to bile salt exposure is an important feature for their survival in and colonization of the intestinal environment. A transcriptomic approach was employed to study the response of Bifidobacterium breve UCC2003 to bile, allowing the identification of a number of bile-induced genes with a range of predicted functions.
The potential role of a selection of these bile-inducible genes in bile protection was determined by heterologous expression in Lactococcus lactis with subsequent characterization of the recombinant strains. Genes coding for three transport systems belonging to the MFS superfamily, Bbr_0838, Bbr_0832 and Bbr_1756, and three ABC-type transporters, Bbr_0406-0407, Bbr_1804-1805 and Bbr_1826-1827, along with the dps gene Bbr_0016, were thus analyzed.
L. lactis cells expressing selected transporters exhibited enhanced resistance and survival to bile. In addition, L. lactis cells expressing the Dps protein also demonstrated a higher resistance to bile.
This work significantly improves our understanding as to how bifidobacteria respond to and survives bile exposure.

overall_design: In order to investigate differences in global gene expression upon growth or exposure of B. breve UCC2003 to cholic acid and ox-gall compared to normal growing cells, DNA microarray experiments were performed. Total RNA was isolated from B. breve UCC2003 cultures under normal conditions and cultures grown on or exposed to cholic acid and ox-gall. All experiments were performed as single experiments and targets where confirmed with QRT-PCR.

first: Lorena

last: Ruiz

first: Mary

last: O'Connell-Motherway

first: Douwe

last: van Sinderen

first: Abelardo

last: Margolles


title: Transcriptomic profiling of Salmonella during lag, exponential and stationary phases of growth

city: Western Bank

first: Matthew

last: Rolfe

state: Sheffield

address: Firth Court

department: Department of Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

summary: Transcriptional profiles during all phases of growth of Salmonella Typhimurium SL1344 were obtained and used to investigate growth phase-dependent alterations in gene expression. Viable count growth curve analysis of the growth system showed a culture lag time of 2.09 hours, and profiles at 4, 20, 40, 60, 90 and 120 minutes were measured accordingly. For comparison, profiles of the inoculum (0 min), mid-exponential (380 min), late-exponential (630 min), early-stationary (900 min) and late-stationary phase (2880 min) were also obtained. Large-scale gene-expression changes were seen, with substantial changes within 4 minutes of inoculation, indicating the speed and sophistication at which Salmonella senses its new environment during lag phase.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. DT104

platform_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: Timecourse; 46 samples (11 timepoints, each with two biological replicates and at least two technical replicates); each sample hybridised in a two-channel hybridization against Salmonella genomic DNA as the comparator/reference, which also acted as a control for spot quality.

first: M

first: C

last: Rice

first: S

last: Lucchini

last: Pin

first: A

last: Thompson

last: Cameron

last: Alston

last: Stringer

first: R

last: Betts

first: J

last: Baranyi

middle: W

last: Peck

middle: C

last: Hinton


title: MicroRNA profiling in primary prostate cancer

status: Public on Dec 10 2011

city: Detroit

first: Fazlul

middle: H.

last: Sarkar

state: MI

address: 4100 John R

department: Pathology

institute: Wayne State University School of Medicine

summary: Deregulated expression of miRNAs contributes to prostate cancer progression. This study is aimed to identify which miRNA(S) is (are) asociated with prostate cancer aggressiveness.

overall_design: Prostate cancer tissues and matched adjacent normal tissue were used to isolate total RNA. miRNA expressions were analyzed by miRNA Microarray assay.

first: Dejuan

last: Kong


title: Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

city: Boston

first: Kevin

last: Murphy

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

summary:
Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae transcription factors but a comprehensive evaluation of their data has been lacking.

Results: We analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae transcription factors. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8 bp sequences. Included in this database is DNA binding specificity data for 27 TFs independently generated by PBM analysis in this current study. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHR transcription factor families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR transcription factors, newly characterized by protein binding microarrays in this study, recognize bZIP like DNA motifs, while the bZIP transcription factor Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) transcription factors. We identified several transcription factors with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo transcription factor binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific transcription factors.

overall_design: 27 Protein binding microarray (PBM) experiments of Saccharomyces cerevisiae transcription factors were performed. Briefly, the PBMs involved binding GST-tagged yeast transcription factors to double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006 (PMID 16998473). A key feature is that the microarrays are composed of de Bruijn sequences that contain each 10-base sequence once and only once, providing an evenly balanced sequence distribution. Individual de Bruijn sequences have different properties, including representation of gapped patterns. The array probe sequences on the custom array design used in this study were reported previously in Berger et al., Cell 2008 (PMID 18585359) and are available via an academic research use license.  Here we provide the data transformed into median signal intensities (after normalization and detrending of the original array data) for all 32,896 8-base sequences, Z-scores for these intensities, and E-scores. E-scores are a modified version of AUC and describe how well each 8-mer ranks the intensities of the spots. In general, the E-scores are slightly more reproducible than Z-scores, but contain less information about relative binding affinity. Additional experimental details are found in Berger et al., Nature Biotechnology 2006, Gordan et al., Genome Biology (in press), and the accompanying Supplementary information.

first: Raluca

last: Gordan

first: Rachel

last: McCord

first: Cong

last: Zhu

first: Anastasia

last: Vedenko

first: Martha

last: Bulyk


title: ATM kinase inhibition in glial cells activates the innate immune response and causes neurodegeneration in Drosophila

city: Madison

first: Andrew

middle: Jay

last: Petersen

state: WI

address: 1300 University Avenue, 379MSC

department: Department of Cellular and Regenerative Biology

institute: University of Wisconsin-Madison

summary: Analysis of the effects of ATM loss on gene expression to identify causes of neurodegeneration.  ATM levels were reduced ubiquitously via the temperature-sensitive ATM^8 allele, or via tissue-specific RNAi of ATM (ATMi) using the Gal4/UAS expression system in neurons (Elav-GAL4 and ElavC155-GAL4) or glial cells (Repo-GAL4).

overall_design: A 20-chip study using total RNA representing 2 replicates of 3 control genotypes (ATM^8/+, Repo-GAL4, and ElavC155-GAL4) and 3 experimental genotypes (ATM^8/ATM^8, Repo-ATMi, ElavC155-ATMi), and 4 replicates each of a control (Elav-GAL4) and experimental (Elav-ATMi) genotype

first: David

last: Wassarman


title: Transcriptional analysis of physiological pathways in a generalist herbivore: responses to different host plants and plant structures by the cotton bollworm (CBW) Helicoverpa armigera [DifferentHost]

status: Public on Dec 12 2011

city: Stockholm

first: Maria de la Paz

last: Celorio-Mancera

address: Svante Arrheniusväg 18 B

department: Zoology

country: Sweden

institute: Stockholm University

summary:
Transcriptional profiling comparing gut tissue from fifth instar larvae exposed to six different diets, namely cotton fruit or boll (B), tobacco flower bud (TFB), bean pod (BP), chick pea fruit (CKPF), pinto bean-based artificial diet (PB) and wheat-based artificial Lepidoptera diet (BIO).
The generalist lepidopteran herbivore Helicoverpa armigera can feed on more than 87 plant species belonging to 48 families. However, life table studies on different crops have revealed that cotton and corn are the most suitable hosts of this pest and tomato, hot pepper and tobacco are suboptimal.  It is believed that generalists owe their success to the deployment of various members of multigene families of detoxicative and digestive enzymes, a strategy that may also be responsible for rapid evolution of insecticide resistance.  However studies of generalist adaptations have been limited to specific genes or gene families, and an overview of how these adaptations are orchestrated at the transcriptional level is lacking. We compared the transcript profiles of larval guts in response to differentially suitable hosts and towards two different artificial diets commonly used for laboratory rearing of this species, using a two-color alternating loop design microarray experiment.

overall_design: Two-color alternating loop design. Biological replicates: 4 (10 individuals per replicate). 24 samples total.

first: Heiko

last: Vogel

first: Maria


title: Identification of Six Potential Markers for the Detection of Circulating Canine Mammary Tumor Cells in the Peripheral Blood

city: Berlin

first: Dido

last: Lenze

address: Hindenburgdamm 30

department: Pathologie, Campus Benjamin Franklin

country: Germany

institute: Charité-Universitätsmedizin Berlin

summary: Circulating tumor cells in the peripheral have proven to be independent prognostic factors for overall survival the monitoring of therapeutic success of human breast cancer patients. Postmortem morphologic evidence also points towards the presence of circulating tumor cells in the peripheral blood of dogs with metastatic canine mammary tumors. However, the existence of these cells has not been verified in canines in vivo and they have not been isolated and characterized due to the lack of appropriate and canine specific detection methods. In the present study a panel of 73 genes with high expression levels in canine mammary carcinoma cells and but not in peripheral blood leukocytes were identified using microarray analysis. From this panel, six mRNA markers, AGR2, ATP8B1, CRYAB, F3 and IRX3, were expressed in canine mammary carcinoma cells but not in the peripheral blood of dogs. All six RT-PCR assays, were sensitive enough detect one carcinoma cell admixed in 106 or more peripheral blood leukocytes, a common concentration of circulating tumor cells in the peripheral blood of human breast cancer patients. These five mRNA markers may therefore be used to detect canine mammary circulating tumor cells and to study their spatio-temporal presence in the peripheral blood of canine patients.

overall_design: Two canine mammary carcinoma cell lines, CMM115 and CMM26, and peripheral blood samples of 3 healthy dog donors were used for microarray analysis. All blood donors were female, showed no signs of infectious or inflammatory disease and did not have mammary gland tumors or any other identifiable tumors at the time of collection. Furthermore, blood cell count and blood chemistry were unremarkable in all dogs.

last: da Costa

first: Michael

last: Hummel

first: B

last: Kohn

first: Achim

last: Gruber

first: Robert

last: Klopfleisch


title: Salmonella Typhimurium: Wild type SL1344 Vs. ∆relA, ∆spoT (ppGpp0) strain grown under SPI1-inducing conditions

status: Public on Dec 09 2011

city: Norwich

first: Neil

last: Shearer

state: Norfolk

address: Colney Lane

department: Gut Health and Food Safety

institute: Institute of Food Research

summary: Transcriptional profiling of early stationary phase S. Typhimurium, comparing wild type SL1344 with an isogenic ∆relA,∆spoT strain (JH3370).

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91

overall_design: Each array used labelled cDNA against a common genomic DNA reference. The wild type strain was arrayed in triplicate and the ∆relA,∆spoT strain in quadruplicate using RNA isolated from biologically independent cultures.

first: Arthur

last: Thompson

first: Vinoy

last: Ramachandran


title: Transcriptional analysis of physiological pathways in a generalist herbivore: responses to different host plants and plant structures by the cotton bollworm (CBW) Helicoverpa armigera [CottonStructures]

summary:
Transcriptional profiling comparing gut tissue from fifth instar larvae exposed to five different diets, namely cotton fruit or boll (B), cotton flower bud or square (SQ), cotton leaf (L), pinto bean-based artificial diet (PB) and wheat-based artificial Lepidoptera diet (BIO).
The generalist lepidopteran herbivore Helicoverpa armigera can consume host plants in more than 40 plant families, and often utilizes several different tissues on the same plant.  It is believed that generalists owe their success to the deployment of various members of multigene families of detoxicative and digestive enzymes, a strategy that may also be responsible for rapid evolution of insecticide resistance.  However studies of generalist adaptations have been limited to specific genes or gene families, and an overview of how these adaptations are orchestrated at the transcriptional level is lacking.  To investigate the previously-shown CBW preferences for different cotton plant structures, we measured net weight gain of larvae that fed on different cotton organs and compared the transcript profiles of larval guts in response to these organs and towards two different artificial diets commonly used for laboratory rearing of this species, using a two-color alternating loop design microarray experiment.

overall_design: Two-color alternating loop design. Biological replicates: 4 (10 individuals per replicate). 20 samples total.


title: DNA binding factors shape the mouse methylome at distal regulatory regions [ChIP_chip]

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: To gain insights into the interplay between DNA methylation and gene regulation we generated a basepair resolution reference map of the mouse methylome in stem cells and neurons. High genome coverage allowed for a novel quantitative analysis of local methylation states, which identified Low Methylated Regions (LMR) with an average methylation of 30%. These regions are evolutionary conserved, reside outside of CpG islands and distal to promoters. They represent regulatory regions evidenced by their DNaseI hypersensitivity and chromatin marks of enhancer elements. LMRs are occupied by transcription factors (TF) and their reduced methylation requires TF binding while introduction of TF binding sites creates LMRs de novo. This dependency on TF activity is further evident when comparing the methylomes of embryonic stem cells and derived neuronal cells. LMRs present in both cell types are occupied by broadly expressed factors, while LMRs present at only one state are occupied by cell-type specific TFs. Methylome data can thus enhance the prediction of occupied TF binding sites and identification of active regulatory regions genome-wide. Our study provides reference methylomes for the mouse at two cell states, identifies a novel and highly dynamic feature of the epigenome that defines distal regulatory elements and shows that transcription factor binding dynamically shapes mammalian methylomes.

overall_design: Whole genome shotgun bisulfite sequencing of mouse embryonic stem (ES) cells and derived neuronal progenitors (NP). CTCF ChIP sequencing in mouse ES and Dnmt1/3a/3b triple knock-out ES (TKO) cells. H3K4me1, H3K4me2 and H3K27me3 ChIP sequencing in mouse SE cells. Pax6 ChIP-chip in mouse NP cells.

middle: B

last: Stadler

first: Rabih

last: Murr

first: Lukas

last: Burger

last: Ivanek

first: Florian

last: Lienert

first: Anne

last: Scholer

first: Edward

last: Oakeley

first: Dimos

last: Gaidatzis

first: Vijay

last: Tiwari

last: Schubeler


title: MicroRNA expression in chronic rhinosinusitis

status: Public on Dec 08 2011

city: Wuhan

first: zhang

last: xinhao

address: 1095 Jiefang Avenue

institute: Tongji Hospital

summary: Increasing evidence suggests that CRS is a heterogeneous group of sinus disorders involving overlapping but distinct disease entities.The factors leading to different CRS phenotypes remain enigmatic. The role of miRNAs in the regulation of immunological and inflammatory processes is beginning to emerge.Thus, we examined microRNAs expression profiles  in eosinophilic CRSwNP adn CRSsNP. Compared with controls, 31 differentially expressed miRNAs (30 downregulated and 1 upregulated miRNAs) in eosinophilic CRSwNP and 4 differentially expressed miRNAs (2 downregulated and 2 upregulated miRNAs) in CRSsNP were indentified. Real time RT-PCR was subsequently performed to verify the miRNA microarray result.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Examination of miRNAs expression in eosinophilic CRSwNP and CRSsNP

first: Xin-Hao

last: Zhang


title: nitrogen starvation -New developments towards a genetic and diagnosis use of plant mircoarrays

city: EVRY CEDEX

first: Elftieh

last: Samira

address: 2 rue Gaston Crémieux, CP 5708

department: Unité de Recherche en Génomique Végétale

country: France

institute: INRA

summary: gnp06-01_agriarray - nitrogen starvation  - Several factors affect today a more extended use of microarrays for research and as a diagnosis tool. These factors are the experimental cost, the reproducibility of the measurements and the format of the analyses. This project aims at bringing solutions in these three domains by optimizing multiplexed analyses in order to reduce cost and enhance the number of samples treated simultaneously; by proposing new couples flurophores / slide surface in order to increase the signal precision and by developing new applications such as Comparative Genomic Hybridization (GGH) or Promoter Arrays to bring the plant microarray beyond transcriptome analyses. Altogether, these approaches will allow us to construct an optimized diagnostic tool based on 96 well microplate microarrays. This multidisciplinary project bring together biologists, chemists, physicists and mathematicians to develop innovative solutions for future application of DNA microarrays. - Dual-target hybridization microarray experiment.

overall_design: 2 dye-swap - time course,tissue comparison

first: Samira

last: Elftieh

first: Jean-Pierre

last: Renou

first: Jean-Christophe

last: Avarre

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Transduction signaling signature of Wilms tumor revealed by parallel analysis of kidney differentiation

status: Public on Dec 07 2011

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary: Precise regulation of transduction signaling pathways genes is crucial for correct differentiation of kidney cells and perturbation may lead to tumor onset. Wilms tumors (WT), or nephroblastoma, originates from the metanephric blastema cells, which were unable to complete the differentiation, resulting in a triphasic tumor composed by distinct cell types, blastemal, epithelial and stromal, where the former harbor molecular characteristics similar to cells of the earliest stages of kidney development.  In this study, to identify key early events involved in the disruption of correct cell signaling during kidney differentiation that can drive WT, we developed a cDNA platform containing genes from signaling transduction pathways. By using bioinformatics tools, we defined high conserved regions between human and mouse orthologous genes and assessed the gene modulation in blastemal cells captured from WT and differentiated kidneys (DK) in human and from four temporal stages of kidney differentiation in mouse. We found 18 genes, whose transcriptional level of the earliest phases of blastemal cell differentiation was recapitulated in WT. PAX2, FZD10, SHPK, WNT5B, FZD2, CRABP2, FRZB, GRK7, TESK1, HDGF and IGF2 were up- and MAPK9, PIK3CA, FRAT2, ITPR3, CDH6, HIPK1 and TIMP3 were down-regulated in WT respectively. Hierarchical clustering based on the expression of this gene set grouped DK from both species, human and mouse, and discriminated them from fetal kidney and WT in human, and the earliest kidney stages in mouse, validating the model proposed by this study and reveling a transduction signaling signature of WT. High robustness of this data was detected since expression level was tested by quantitative RT-PCR in the initial and independent sample set, with 75 and 56% of agreement. Agreement of 62% was also observed in protein level assessing blastemal component of an independent group of 137 WT. Protein expression of CRABP2, IGF2, GRK7, TESK1, HDGF, WNT5B, FZD2 and TIMP3 was also characterized in human fetal kidneys revealing interesting aspects of kidney differentiation. This study identified key genes modulated during kidney differentiation which may play a determinant role for WT onset. As far as we know, FZD10, FRZB, HDGF, MAPK9, FRAT2, SHPK, WNT5B, GRK7, TESK1, HDGF, PIK3CA, ITPR3, HIPK1 and TIMP3 were not previously associated to WT.

sample_organism:
Homo sapiens
Mus musculus

overall_design: The strong connection between nephrogenesis and WT highlights the importance of a detailed characterization of modulated genes belonged to signal transduction. Identification of gene expression involved in kidney differentiation arresting might be imperative to point out early alterations that drive WT onset and consequently are potential candidate as molecular marker. Here, we characterized expression pattern of genes belonged to transduction signaling pathways in blastemal cells during kidney development stages in mouse and WT in human. For that, we established a model of inter- and intra-specific hybridization to assess gene expression modulation to identify key events that drive WT onset. Dye-swap was performed for each sample as control for dye bias and used as replicate. In total, 24 frozen favorable histology WT and differentiated kidney samples were laser microdisscted for blastemal cells. Three kidneys from CD1 lineage from Mus Musculus were isolated from embryos (E) and postnatal animals (P) at ages E15.5, E17.5, P1.5 and P7.5 for laser microdissection of the blastemal cells in all stages of kidney differentiation. NA were purified with PicoPure™ RNA Isolation kit (Arcturus Engineering #KT0204) and treated with RNase-Free DNase Set (Qiagen #79254; Qiagen-Germantown MD USA).

first: Mariana

last: Maschietto

first: Adriana

last: Trape

first: Silvia

last: Lourenço

first: Pedro

last: Galante

first: Fernando

last: Soares

first: Beatriz

last: Camargo

first: Helena

last: Brentani

first: Dirce

last: Carraro


title: Identification of sigB inhibitors in L. monocytogenes

status: Public on Dec 06 2011

city: Ithaca

first: M.

middle: Elizabeth

last: Palmer

address: 415 Stocking Hall

department: Food Science

institute: Cornell University

summary: The extensively studied intracellular pathogen, L. monocytogenes, is an ideal model for identifying small-molecule agents for treating bacterial infections. By selecting specific biological targets in L. monocytogenes, which are common to Gram-positive pathogens, we could extrapolate drug discovery information derived from this well-studied bacterium. Attenuating the pathogen’s virulence and stress response attributes without killing it, eliminates selective pressure caused by disruption of essential gene functions (as done by current antibiotics) and reduces the likelihood of developing microbes that are impervious to the effects of antibiotics. To this end, we have assessed multiple libraries of small organic compounds to identify inhibitors of L. monocytogenes σB, the alternative sigma factor common to several clinically relevant Gram-positive pathogens, such as Staphylococcus aureus, Bacillus cereus, and Bacillus anthracis. The role of σB as a transcriptional regulator of stress response and virulence makes it an ideal, well conserved target for chemotherapeutic development.

platform_organism:
Listeria monocytogenes
Listeria innocua

overall_design: Independent RNA isolations were performed for each growth experiment (log phase cells exposed to BHI+0.3M NaCl and BHI+0.3M NaCl + CMPD). Four biological replicates were used in competitive whole-genome microarray experiments. For the hybridizations, RNA from the wildtype parent strain L. monocytogenes 10403S were hybridized to RNA from the wildtype parent strain 10403S treated with CMPD.

first: M

first: Soraya

last: Chaturongakul

first: Martin

last: Wiedmann

first: Kathyrn

last: Boor


title: Gene expression study after 3 days of salt exposure in a Solanum tuberosum cultivar called Desirée

status: Public on Dec 03 2011

city: Belvaux

first: Danièle

last: Evers

address: 41, rue du Brill

department: EVA

country: Luxembourg

institute: CRP-Gabriel Lippmann

summary: The molecular response to salt exposure was studied in the leaves of an S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed, whereas cell rescue and transcription factor-related genes were mostly up-regulated. A strong down-regulation of several functional categories including primary metabolism, detoxication apparatus and signal transduction was also observed.

overall_design: Gene expression has been followed three days after salinity treatment (150 mM NaCl). For each condition, 4 independent biological replicates were sampled. Dye-swaps were performed.

first: Sylvain

last: Legay

first: Jean-François

last: Hausman

first: Lucien

last: Hoffmann

first: Jenny

last: Renaut


title: Expression analysis of gene silenced barley to identify the function of a novel LRR-RLK (leucine-rich repeat receptor-like kinase)

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

summary: VIGS (virus-induced gene silencing) was used to silence a putative LRR-RLK, Affy ID Rbaal9i05_at, in barley. Expression patterns in leaves were compared between untreated control leaves, virus treated leaves, VIGS-Rbaal knockdown leaves and VIGS-Rbaal/PDS (phytoene desaturase) co-silenced leaves.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  David L Parrott.  The equivalent experiment is BB108 at PLEXdb.]

overall_design: treatment: Untreated Control(3-replications);  treatment: Empty Virus (no inserted plant sequences)(3-replications);  treatment: Rbaal VIGS(3-replications);  treatment: Co-silencing (Rbaal + PDS)(3-replications)

first: David

last: Parrott

first: Andreas

middle: M

last: Fischer


title: Gene expression study after 3 days of cold exposure in a Solanum tuberosum cultivar called Desirée

summary: The molecular response to cold exposure was studied in the leaves of an S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon cold exposure in Desirée leaves were observed in the photosynthesis-related genes, which were down-regulated, whereas cell rescue, detoxication and transcription factor-related genes were mostly up-regulated. We also observed an increased expression of polyamine and proline synthesis-related genes, as well as some carbohydrate-related genes such as sucrose synthase and trehalose-6-phosphate synthase.

overall_design: Gene expression was followed at day 3 after the beginning of the treatment: cold (4°C) and control conditions. For each condition, 4 independent biological replicates were sampled.


title: Lemon_acidity

summary: Samples from fruit juice vesicle tissue from three lemon genotypes (Frost Lisbon, Faris "sour" and Faris "sweet") differing in fruit acidity were compared at two developmental timepoints (immature, mature). Faris lemon appears to be a graft chimera with the L2 layer derived from normal acid lemon and layer L1 from Millsweet limetta or a closely related genotype. Fruit of Faris sour and Faris sweet grew on different branches of the same tree, with sour fruit developing on branches with L1 and L2 from acid lemon.

overall_design:
genotype: Faris sweet lemon - developmental stage: PO:0007009 FF.01 fruit size 30%,(3-replications);  genotype: Faris sweet lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening,(3-replications);  genotype: Faris acid lemon - developmental stage: PO:0007009 FF.01 fruit size 30%,(3-replications);  genotype: Faris acid lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening,(3-replications);  genotype: Frost Lisbon lemon - developmental stage: PO:0007009 FF.01 fruit size 30%,(3-replications);  genotype: Frost Lisbon lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening,(3-replications)

PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Mikeal L. Roose. The equivalent experiment is CT1 at PLEXdb.

first: Mikeal

last: Roose


title: A methyl-deviator epigenotype of estrogen-receptor-positive breast carcinoma is associated with malignant biology

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

summary: We broadly profiled DNA methylation in breast cancers (n=351) and benign parenchyma (n=47) for correspondence with disease phenotype using formalin-fixed paraffin-embedded (FFPE) diagnostic surgical pathology specimens. Exploratory analysis revealed a distinctive primary invasive carcinoma subclass featuring extreme global methylation deviation. Subsequently we tested the correlation between methylation remodeling pervasiveness and malignant biology. A methyl deviation index (MDI) was calculated for each lesion relative to terminal ductal-lobular unit (TDLU) baseline, and group comparisons revealed that high-grade, short-survival ER+ cancers manifest significantly higher MDI than low-grade, long-survival ER+ cancers. In contrast, ER- cancers display significantly lower MDI, revealing a striking epigenomic distinction between cancer hormone receptor subtypes. Kaplan-Meier survival curves of MDI-based risk classes showed significant divergence between low- and high-risk groups. MDI showed superior prognostic performance to crude methylation levels, and MDI retained prognostic significance (p<0.01) in Cox multivariate analysis including clinical stage and pathologic grade. Most MDI targets individually are significant markers of ER+ cancer survival. Lymphoid and mesenchymal indices were not substantially different between ER+ and ER- groups, and do not explain MDI dichotomy. However, mesenchymal index was associated with ER+ cancer survival, and high lymphoid indices with medullary carcinoma. Finally, comparison between metastases and primaries suggests methylation patterns are established early and maintained through disease progression for both ER+ and ER- tumors.

overall_design: Bisulfite-converted DNA from 397 lesions were analyzed with the Illumina GoldenGate Methylation Cancer Panel I array.

first: J

middle: K

last: Killian

first: Sven

last: Bilke

first: Sean

last: Davis

first: Robert

last: Walker

first: Erich

last: Jaeger

middle: S

first: Joshua

last: Waterfall

first: Marina

last: Bibikova

first: Jian-Bing

last: Fan

first: William

middle: I

last: Smith Jr

first: Paul

last: Meltzer


title: Histone protein and peptide reactivity within patients with systemic lupus erythematosus (SLE) from the ABCoN cohort

status: Public on Dec 02 2011

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

summary:
The aim of the study was to test the hypothesis that IFN high SLE patient sera is more reactive to whole histone proteins and post-translationally modified histone peptides than IFN low patient sera.
We diluted patient sera 1:250 and incubated dilutions on a nitrocellulose-platform array printed with whole protein and peptide histone antigens.

platform_organism:
Gallus gallus
Homo sapiens
Bos taurus

overall_design: In this study, serum from 30 patients subsetted into high and low interferon signature categories were profiled for IgG autoantibody reactivity to whole histone proteins, unmodified and post-translationally modified histone peptides. IFN high patient sera was found using the significance analysis of microarrays (SAM) algorithm to be significantly more reactive with whole histone and modified histone peptide antigens.

middle: V

first: Stephanie

last: Tangsombatvisit

first: Guangyu

last: Xu

first: Dan

last: Levy

first: Emily

last: Baechler

first: Or

last: Gozani

first: Madoo

last: Varma

middle: J

last: Utz

first: Chih

middle: L

last: Liu


title: Patterns of histone H3 Lysine 27 monomethylation and erythroid cell-type specific gene expression [ChIP-chip]

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

type: Genome binding/occupancy profiling by genome tiling array

summary: Post-translational histone modifications, acting alone or in a context-dependent manner, influence numerous cellular processes via their regulation of gene expression. Monomethylation of histone H3 lysine 27 (K27me1) is a poorly understood histone modification. Some reports describe depletion of K27Me1 at promoters and transcription start sites (TSS), implying its depletion at TSS is necessary for active transcription, while others have associated enrichment of H3K27me1 at TSS with increased levels of mRNA expression. Tissue- and gene-specific patterns of H3K27me1 enrichment and their correlation with gene expression were determined via chromatin immunoprecipitation on chip microarray (ChIP-chip) and human mRNA expression array analyses. Results from erythroid cells were compared to those in neural and muscle cells. H3K27me1 enrichment varied depending on levels of cell-type specific gene expression, with highest enrichment over transcriptionally active genes. Over individual genes, the highest levels of H3K27me1 enrichment were found over the gene bodies of highly expressed genes. In contrast to H3K4me3, which was highly enriched at the TSS of actively transcribing genes, H3K27me1 was selectively depleted at the TSS of actively transcribed genes. There was markedly decreased to no H3K27me1 enrichment in genes with low expression. At some locations, H3K27 monomethylation was also found to be associated with chromatin signatures of gene enhancers.

overall_design: The Histone H3K4Me3 and H3K27me1 binding profiles in a panel of red cell related genes were examined using chip-chip.   Human cell lines SY5Y, RD and K562 were examined using custom Nimblegen microarrays.

first: Laurie

middle: A

last: Steiner

first: Vincent

middle: P

first: Yelena

last: Maksimova

first: Clara

last: Wong

first: Patrick

middle: G

last: Gallagher


title: Tiling microarray expression analysis of Heliconius butterfly pupal forewing sections across the genomic interval controlling red color pattern

city: San Juan

first: Riccardo

last: Papa

address: Avenida Barbosa

department: Biology

country: Puerto Rico

institute: University of Puerto Rico

type: Expression profiling by genome tiling array

summary: We investigated gene expression levels in Heliconius erato butterflies with divergent wing patterns across a 656KB genomic interval linked to the red color pattern wing polymorphism. This included comparison of expression between two H. erato color pattern populations (H. e. petiverana and a H.e. etylus x H. himera hybrid) across three sections of the forewing that differed in pigmentation (the basal, mid, and distal wing sections) and five different stages of pupal development (Day 1, 3, 5 pupae and ommochrome and melanin pigmentation stages). These results allowed us to determine whether certain genes in this interval were differentially expressed between the wing pattern elements, and, therefore, potentially responsible for adaptive color pattern variation in these butterflies.

sample_organism: Heliconius erato etylus x Heliconius himera

overall_design: Forewings from a total of 29 individuals, covering three biological replicates of five developmental time points for each of the two H. erato distinct phenotypes were dissected, with the only exception being that there were only two replicates of the day 1 hybrid phenotype. Individuals were reared at 25˚C and dissected at the following stages: a) day 1 = 12 hr after pupation; b) day 3 = 60 hr after pupation; c) day 5 = 108 hr after pupation; d) early ommochrome = ~ 156 hr after pupation when red scales in forewing partially mature, showing a pale orange color; and e) early melanin = ~ 180 hr after pupation melanic scales begin to turn black and are present primarily at the center of the wing.  Using wing veins as landmarks, each forewing was cut into three sections corresponding to the color pattern boundaries: basal (F1), middle (F2), and apical (F3). A eight custom-designed Roche NimbleGen 12x135K format microarrays with probes spanning a 656,307bp genomic region (Roche NimbleGen Inc., Madison, Wisconsin, United States) were used to hybridize double stranded cDNA from 87 tissue samples. Repetitive sequence elements found more than five times across all currently available H. erato genomic sequences, including the probed region as well as additional genomic BAC sequences, were masked from the tiling region. The remaining unmasked non-repetitive genomic sequences were tiled using 60 bp probes staggered every 13 bp on average, with slight modifications to ensure probe quality, for a total of 48,547 probes. Microarry design and printing was performed by Roche NimbleGen. cDNA labeling, hybridization, and array scanning was performed by the City of Hope Microarray Facility (Duarte, California, United States). In addition to the probes from the red color pattern intervals, the arrays also include 40,763 probes across two other genomic intervals not addressed in this study, 45,046 probes representing 12450 transcripts from a recent transcriptome assembly at 1-6X coverage, and 3248 random probes. Results from the transcriptome and other color pattern intervals will be published separately, however, we analyzed all probes together for array normalization and quality control.

first: Heather

last: Hines

first: Robert

middle: D

last: Reed

first: W

middle: O

last: McMillan


title: Marking of the genome by H3K4 methylation prior to embryonic gene activation

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Early zebrafish embryo development proceeds first from a maternally transcribed and stored mRNAs, and zygotic gene activation (ZGA) is initiated at the mid-blastula transition (MBT; 1000-cell stage), 3.3 h post-fertilization.  Very little is known on how the zygotic genome is programmed  for transcriptional activation at the MBT. To start addressing this issue, we have mapped by ChIP-chip genome-wide promoter histone methylation (H3K4me3, H3K9me3, H3K27me3, H3K36me3) and RNA Pol II profiles before ZGA (256-cell stage; 2.5 hpf), during ZGA (MBT; 3.5 hpf)) and after ZGA (Post-MBT; 5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. Peak detection was done using MA2C with P=10e-4 as cutoff.

overall_design: ChIP-chip experiments were performed from  chromatin prepared by sonication after formaldehyde cross-linking, from embryos are the indicated developmental stages and ChIP DNA was hybridized onto the aforementioned Nimbegen promoter arrays.

first: P

first: A

middle: H

last: Reiner


title: Propionibacterium freudenreichii transcriptomic response during cold storage

status: Public on Dec 01 2011

city: Fermoy

first: Marion

last: Dalmasso

address: Moorepark

department: Food Safety

country: Ireland

institute: Teagasc

summary: Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It produces flavor compounds over the whole ripening period. During cheese ripening, P. freudenreichii is exposed to a temperature downshift, especially when cheeses are transferred from warm temperature (about 24°C) to cold temperature (about 4°C). The aim of this study was to investigate the adaptation of P. freudenreichii at cold temperature by means of the first global gene expression profile for this species. The temporal transcriptomic response of P. freudenreichii was analyzed at five times of growth, during growth at 30°C then for 9 days at 4°C, in the constant presence of lactate as the main carbon source. P. freudenreichii response was also investigated by RT-qPCR for 30 genes, by proteomics and metabolomics (main metabolites quantified in culture supernatant). Microarray analysis revealed that 565 genes (25% of the protein-coding sequences of P. freudenreichii genome) were differentially expressed during transition from warm to cold temperature (P < 0.05 and |fold change| > 1). Most of the down-expressed genes were involved in cell machinery (cell division, protein turnover, translation, transcription and DNA replication). During incubation at cold temperature, P. freudenreichii accumulated carbon supplies by up-regulating genes involved in lactate, alanine and serine conversion to pyruvate, in gluconeogenesis and in glycogen synthesis. Interestingly, some genes involved in the formation of important flavor compounds of cheese, coding for an extracellular lipolytic esterases and enzymes of the pathways of formation of branched-chain compounds, were not significantly affected by cold. In conclusion, P. freudenreichii is metabolically active at cold temperature and induces pathways to maintain its long-term viability, which could explain its contribution to cheese ripening even at low temperature.

sample_organism: Propionibacterium freudenreichii subsp. shermanii

overall_design: Gene expression was measured in the middle of exponential growth phase at 30°C (20 h, OD650 ≈ 0.5), at the end of exponential growth phase (40 h, OD650 ≈ 2), and after 3, 6 and 9 days of incubation at 4°C. Three independent biological experiments were performed at each time (20h, 40h, 3, 6 and 9 days) and labelled A, B, C. One technical repetition was performed using the  RNA of the 20HA sample ; This technical repetition was labelled 20HAbis.

first: Julie

last: Aubert

first: Valérie

last: Briard-Bion

first: Victoria

last: Chuat

first: Stéphanie-Marie

last: Deutsch

first: Sergine

last: Even

first: Hélène

last: Falentin

first: Gwenaël

last: Jan

first: Julien

last: Jardin

first: Marie-Bernadette

last: Maillard

first: Sandrine

last: Parayre

first: Michel

last: Piot

first: Jarna

last: Tanskanen

first: Anne

last: Thierry


title: Global gene expression of B. abortus-infected bovine macrophages

status: Public on Dec 05 2011

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

summary:
In a time course study, we characterized global gene expression profile of B. abortus-infected macrophages from cattle naturally resistant (R) and susceptible (S) to brucellosis. B. abortus infection causes early down-regulation of transcript levels in Mø from R cattle at 4 h p.i. (22 up- and 126 down-regulated genes) which is reversed by 12 h post-infection (31 up- and 25 down-regulated genes), compared to uninfected control. On the other hand, B. abortus-infected S bovine macrophages exhibited a down-regulated expression profile at 4 (45 up- and 65 down-regulated genes) and 12 h p.i. (47 up- and 193 down-regulated genes).  The analysis of the results indicates that B. abortus – infected Mø from cattle naturally R and S to brucellosis display different transcriptional profiles. Specific genes and biological processes identified in this study will further help elucidate how different macrophages from resistant and susceptible animals interact with Brucella during the early infectious process.

Keywords: Expression profiling by microarray

overall_design: Microarrays were used to examine the transcriptional profiles of monocytes-derived macrophages from cattle naturally resistant or susceptible to brucellosis that were infected with wild type Brucella abortus S2308.  The gene expression of infected macrophages at two time points (4 and 12 hours) was compared with gene expression from non-infected macrophages treated similarly. Experiments were performed in triplicate, generating a total of 24 arrays. Bovine ORFs were double spotted on each microarray. Each replicate was normalized against labeled bovine reference RNA.

first: Carlos

last: Rossetti

first: Cristi

last: Galindo

first: Robin

middle: E

last: Everts

first: Harris

last: Lewin

first: Harold

middle: R

last: Garner

first: L


title: A Pooled RNAi Screening Strategy Reveals Novel Regulators for EpCAM

city: Huntsvilee

first: Kruti

last: Patel

state: AL

address: 601 Genome Way, Suite 2100

institute: Thermo Fisher Scientific

summary: The cell surface receptor, Epithelial Cell Adhesion Molecule (EpCAM), is overexpressed in a variety of cancers and has been carefully examined for its functional role in carcinogenesis and its potential as a therapeutic target.  However, little is known about the upstream molecular pathways that regulate EpCAM expression.  To elucidate the mechanisms by which EpCAM expression is controlled, we designed a combinatorial screening strategy that utilized pooled shRNA gene knockdown with  magnetically-activated cell separation for selection of cells with reduced EpCAM protein expression on the cell surface.  The pooled RNAi screen was analyzed by comparing EpCAM-enriched and EpCAM-depleted cell populations for shRNA abundance using competitive hybridization to microarrays.   Our RNAi screen and further validation efforts revealed that at least four genes (GRM1, SLITRK5, EFNA5, and IL23A) are important for EpCAM expression in the ovarian cancer cell line OVCAR8.  Further investigations into the ephrin ligand, EFNA5, suggest that its activation by the Eph receptor, EPHA4, contributes to the regulation of EpCAM expression via a reverse signaling mechanism.  Our screening strategy revealed novel mechanisms for the regulation of EpCAM expression and provides insight into the biology of this cancer-associated gene.  Importantly, this study also demonstrates the utility of pooled RNAi screening in the identification of genes required for the regulation of cell surface protein expression.

overall_design: Two condition experiment; EpCAM-Bound or EpCAM-Unbound OVCAR8 cells vs Reference population of transduced cells without phenotypic selection; biological triplicate

middle: M

first: Katie

last: Spayd


title: Comparison of aCGH profiles from KB1C61GP, KB1P and KP mouse mammary tumors

city: Amsterdam

first: Rinske

last: Drost

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

summary: While BRCA-related cancers respond well to double-strand break (DSB) inducing agents, resistance is a serious clinical problem. One mechanism of resistance is reversion of the BRCA1 mutation, suggesting that BRCA1 function is required for resistance. Here we show that secondary Brca1 mutations are not always necessary, since residual activity of the mutant BRCA1 protein can be sufficient for tumor cells to withstand treatment. Genomic profiling and RAD51 foci formation are currently seen as potential biomarkers to stratify patients for therapies targeting homologous recombination deficiency (HRD). However, we show that while mouse mammary tumors with different Brca1 mutations have identical genomic profiles, they respond considerably different to HRD targeted therapy. It may therefore be useful to stratify patients according to functional assays and the underlying BRCA1 mutation.

overall_design: We performed aCGH on mammary tumor DNA from KB1C61GP (n=20), littermate KB1P (n=18) and KP mice (n=19). Spleen DNA of the same animal was used as control material.

first: Peter

last: Bouwman

first: Sven

last: Rottenberg

first: Ute

last: Boon

first: Eva

last: Schut-Kregel

first: Sjoerd

last: Klarenbeek

first: Christiaan

last: Klijn

first: Ingrid

last: van der Heijden

first: Hanneke

last: van der Gulden

first: Ellen

last: Wientjens

first: Mark

last: Pieterse

first: Aurelie

last: Catteau

first: Pete

last: Green

last: Solomon

first: Joanna

last: Morris

first: Jos

last: Jonkers


title: Yap1/Birc, c-Met and N-ras DNA amplifications are mutually exclusive in mouse mammary tumors.

city: South San Francisco

middle: Nicolaas

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

summary: Tumors acquire somatic DNA copy number aberrations, leading to activation of oncogenes and inactivation of tumor suppressors. Many studies have focused on the analysis of single copy number aberrations and associated driver genes, but few studies have performed combinatorial analyses. We propose a genome-wide scoring framework to find mutually exclusive gains and losses. Mutually exclusive copy number aberrations can identify genes whose oncogenic function is redundant, either by functioning in the same pathway or in a parallel pathway. As one gene is aberrated the selective pressure for its partner is alleviated which leads to a mutually exclusive perturbation pattern. In a dataset of mouse models for invasive lobular carcinoma we found three mutually exclusive DNA amplifications, containing several well-known oncogenes: the Met proto-oncogene on chromosome 6, the cluster of Birc2, Birc3 and Yap1 genes on chromosome 9, and Nras on chromosome 3. Furthermore, gene expression or protein expression of these genes correlates very well with copy number data indicating that they are the target of the amplification.   Although homologous amplifications in human tumors are rare, the mutual exclusivity of MET, BIRC/YAP1 and NRAS is maintained in a variety of cancer types. This suggests a novel function for YAP1 in the mitogen-activated signaling pathway by association with MET and NRAS, known players in this pathway. This function is independent to the propensity of YAP1 to cause Epithelial-to-Mesenchymal transition.

overall_design: aCGH data of 67 mouse mammary tumors from K14-Cre and WAP-Cre driven P53-F/F;Cdh1-F/F animals - tumor DNA hybridized against same-animal splenic DNA

first: Jan

last: Bot

first: Tanya

last: Braumuller

first: Marcel

last: Reinders

first: Lodewyk

middle: F

last: Wessels


title: High IGFBP2 Expression Correlates with Tumor Severity in Pediatric Rhabdomyosarcoma.

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: Rhabdomyosarcoma (RMS) is the most common childhood sarcoma and is identified as either the embryonal or alveolar (ARMS) subtype. In approximately 75% of cases, ARMSs are characterized by specific chromosomal translocations that involve PAX and FKHR genes. ARMS gene expression signatures vary, depending on the presence or absence of the translocations. Insulin-like growth factor-binding protein 2 (IGFBP2) is strongly overexpressed in translocation-negative RMS. Because IGFBP2 is associated with tumorigenesis, we investigated its functional role in RMS. An analysis of IGFBP2 distribution in RMS cell lines revealed a strong accumulation in the Golgi complex, in which morphological characteristics appeared peculiarly modified. After silencing IGFBP2 expression, our microarray analysis revealed mostly cell cycle and actin cytoskeleton gene modulations. In parallel, IGFBP2-silenced cells showed reduced cell cycle and rates of invasion and decreased seeding in the lungs after tail vein injections in immunodeficient mice. An analysis of IGFBP2 mRNA and protein localization in human tumors showed abnormal protein accumulation in the Golgi complex, mostly in PAX/FKHR-negative RMS. Moreover, an analysis of patients with RMS revealed the presence of conspicuous circulating levels of IGFBP2 proteins in children with highly aggressive RMS tumors. Taken together, our data provide evidence that IGFBP2 contributes to tumor progression and that it could be used as a marker to better classify clinical and biological risks in RMS.

overall_design:
Three independent silencing experiments on RH36, an embryonal rhabdomyosarcoma  cell line, were performed to study the role of IGFBP2 oncogene in this childhood tumor.
Each of 3 biological replicates has its own control which is represented by cell culture treated with a non-targeting siRNA (siCONTROL). 3 controls were used to produce a “control pool” that has been used as reference in all microarray experiments.
Each microarray experiment consists of a competitive hybridization between test and reference RNA (e.g. silenced cells vs. control), labelled with Cy3 or Cy5.
Two microarray experiments were performed for each of three silencing experiment (technical replicate).
Each slide was scanned and the data was normalized and analyzed.

first: Lucia

last: Tombolan

first: Silvia

last: Casara

first: Cristiano

last: De Pittà

first: Francesca

last: Orso

first: Angelica

last: Zin

first: Vincenza

last: Guzzardo

first: Chiara

last: Romualdi

first: Rita

last: Alaggio

first: Daniela

last: Taverna

first: Angelo

last: Rosolen


title: Implication of Nos2 inactivation on the transcriptome of developing cerebellum and Ptch1+/- medulloblastomas  (mRNA)

city: Stanford

first: Daniel

last: Haag

state: Santa Clara

address: 265 Campus Drive

department: ISCBRM

country: USA

institute: Stanford School of Medicine

summary: The Ptch1+/-  strain constitues an established mouse model for the Shh-driven type of medulloblastoma. Combined Ptch1+/- Nos2-/- mice show a two-fold increased incidence for this tumor. Here, the impact of Nos2 inactivation on medulloblastoma development was investigated by gene expression profiling of tumor samples as well as healthy cerebellum at different ages and genotypes.

overall_design: Medulloblastoma samples from three Ptch1+/- and six combined Ptch1+/- Nos2-/- mice were analyzed. Healthy cerebellum taken from mice at postnatal day nine, six weeks after birth, and about 1 year of age were analyzed for wildtype animals and the genotypes Ptch1+/-, Ptch1+/- Nos2-/-, and Nos2-/-. The cerebellar developmental stages at six weeks and one year were measured in three biological replicates, while samples taken at postnatal day six consisted of pooled individual specimen. These were measured in three replicates being amplified and labelled in separate reactions. All samples were subjected to two-color hybridizations against Universal Reference RNA (Stratagene) with color-switch experiments yielding two technical replicates, respectively.

first: Petra

last: Zipper


title: Quorum sensing and silencing in Vibrio parahaemolyticus

city: Iowa City

first: Linda

last: McCarter

state: Iowa

address: 3-401 BSB  51 Newton Rd

department: Microbiology

institute: University of Iowa

summary: The quorum regulatory cascade is poorly characterized in Vibrio parahaemolyticus, in part because swarming and pathogenicity - the hallmark traits of the organism - are repressed by this scheme of gene control. As a consequence, many isolates appear silenced for quorum sensing via phase variation. In these studies, we examine a swarm proficient, virulent strain and find an altered function allele of the central quorum regulator luxO. We use this allele, which produces a constitutively active LuxO, to probe the upstream elements of the pathway and demonstrate their functionality for the first time. We find that the state of luxO affects expression of three small regulatory RNAS (Qrrs) and the activity of a translational fusion in opaR, the central output regulator. We use microarray profiling to determine the OpaR regulon, which was found to encompass ~5.2% of the genome. The quorum sensing proficient strain seems adapted for a sessile, community lifestyle; it is competent to uptake DNA, produces much capsular polysaccharide, has a high level of c-di-GMP, and strongly expresses one type six secretion system. Expressing the entire surface sensing regulon and numerous methyl accepting chemotaxis proteins, the quorum-disrupted cell type seems prepared for a mobile lifestyle. It is also cytotoxic to host cells in co-culture and expresses distinct type six as well as type three secretion systems. Thus, the scope and nature of the genes in the OpaR regulon provide many clues to the distinguishing traits of this Vibrio species as well as to the quite divergent survival strategies of the quorum ON/OFF phase variants

overall_design: The gene expression profiles of different strains of Vibrio parahaemolyticus cells grown on rich medium and compared using Affymetrix custom microarrays.

first: Cindy

last: Gode-Potratz


title: Chip-chip from C. glutamicum wild type expressing GlxR tagged with Strep Tag II and cyaB deletion strain expressing GlxR tagged with Strep Tag II.

city: Kyoto

first: Masayuki

last: Inui

address: 9-2 Kizugawadai, Kizugawa

country: Japan

institute: Research institute of Innovative Technology for the Earth (RITE)

summary:
Corynebacterium glutamicum GlxR is a homolog of the cAMP receptor protein. Although over 200 GlxR binding sites in the C. glutamicum genome are predicted in silico, studies on the GlxR physiological function have been hindered by the severe growth defects of a glxR mutant. This study comprehensively identified the GlxR regulon by chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analyses. In total, 209 regions were detected as in vivo GlxR binding sites.
Moreover, ChIP-chip analyses showed that GlxR was still able to interact with its target sites in a deletion mutant of cyaB, the sole adenylate cyclase gene in the genome, even though binding affinity was markedly decreased.

overall_design: To identify the direct GlxR targets, we immunoprecipitated DNA from a strain expressing a Strep-tag II-tagged GlxR-protein using an anti-Strep-tag II antibody. To investigate effect of depletion of cAMP by deletion of the cyaB gene, which encodes the sole adenylate cyclase in C. glutamicum, on GlxR binding in vivo, we immunoprecipitated DNA from a cyaB deletion strain expressing a Strep-tag II-tagged GlxR-protein using an anti-Strep-tag II antibody. Three or more independent biological replicates were generated in both cases.

first: Koichi

last: Toyoda

first: Haruhiko

last: Teramoto

first: Hideaki

last: Yukawa


title: X-QTL performed on wild-type and sup35 (C653R) BY x RM segregants in various growth conditions

city: Princeton

first: Noorossadat

last: Torabi

state: NJ

address: 110 Carl Icahn Lab

department: Molecular Biology

institute: Princeton University

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

summary:
Genotyping pools of wildtype(wt) or sup35-C653R(sup35) BYxRM segregants after growth on YPD (control) or YPD+drug-of-interest(selection)
10 Growth conditions tested are control (YPD alone), and YPD plus the following drugs: Chlorpromazine, CoCl2, Cycloheximide, Diamide, E6berbamine, Ethanol, H2O2, Neomucin, and Tunicamycin.

overall_design: Two-condition experiment, control vs selection. 6 biological replicates for control and two biological replicates for each selection included.

first: Noorssadat


title: Daptomycin-Resistance Mechanisms in Clinically-Derived Staphylococcus aureus Strains Assessed by a Combined Transcriptomics and Proteomics Approach

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

summary:
Objectives: Development of daptomycin resistance (DAPR) in Staphylococcus aureus is associated with clinical treatment failures. Mechanism(s) of such resistance has not been clearly defined.

Methods: We studied an isogenic daptomycin-susceptible (DAPS) and daptomycin-resistant (DAPR) S. aureus strain pair (616; 701) from a patient with relapsing endocarditis during daptomycin treatment, using comparative transcriptomic and proteomic techniques.   Results. Minor differences in genome content were found between strains by DNA hybridization. Transcriptomic analyses identified a number of genes differentially expressed in important functional categories: cell division, metabolism of bacterial envelopes and global regulation. Of note, the DAPR isolate exhibited reduced expression of the major cell wall autolysis gene coincident with upregulation of genes involved in wall teichoic acid production. Using quantitative (q)RT-PCR on gene cadre putatively involved in cationic peptide resistance, we formulated a putative regulatory network compatible with microarray data-sets, mainly implicating bacterial envelopes. Of interest, qRT-PCR of this same gene cadre from two distinct isogenic DAPS/DAPR clinical strain pairs revealed evidence of other strain dependent networks operative in the DAPR phenotype. Comparative proteomics of 616 vs 701 revealed differential abundance of proteins in various functional categories including: cell-wall associated targets and biofilm-formation proteins. Phenotypically, strains 616 and 701 showed major differences in ability to develop bacterial biofilms in presence of the antibacterial lipid, oleic acid.

Conclusions: Compatible with previous in vitro observations, in vivo acquired DAPR in S. aureus is a complex, multistep phenomenon allowing for: i) strain dependent phenotypes; ii) transcriptome adaptation; and iii) modification of lipid and protein content of cellular envelopes.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

platform_organism: Staphylococcus aureus subsp. aureus Mu50

platform_organism: Staphylococcus aureus subsp. aureus N315

platform_organism: Staphylococcus aureus subsp. aureus MRSA252

platform_organism: Staphylococcus aureus subsp. aureus MSSA476

platform_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Daptomycin suceptible strain vs daptomycin non suceptible strain after daptomycin treatment

first: Adrien

last: Fischer

first: Soo-Jin

last: Yang

first: Arnold

middle: S

last: Bayer

first: Ali

last: Vaezzadeh

first: Sébastien

last: Herzig

first: Ludwig

last: Stenz

first: Myriam

last: Girard

first: George

last: Sakoulas

first: Alexander

last: Scherl

first: Michael

last: Yeaman

first: Richard

last: Proctor

first: Jacques

last: Schrenzel

first: Patrice

last: François


title: Epigenetic changes in B lymphocytes associated with house dust mite allergic asthma.

city: PAMPLONA

first: Marien

last: Pascual

state: NAVARRA

address: AVDA. PIO XII, 55, LAB 1.04

department: Hemato-Oncology

country: Spain

institute: CIMA, Universidad de Nacarra

type: Methylation profiling by genome tiling array

summary:
The increase in atopic diseases has occurred in such a short period of time that it becomes difficult to be attributed only to genetic factors, which usually need more prolonged time periods to manifest. In this setting during the last decade, the science of epigenetics has increasingly developed offering new perspectives and opening a new challenging research area.
In this study we aimed to study the epigenetic patterns in B CD19+ Lymphocytes from healthy and allergic patients using the improved version of HELP assay.

overall_design:
Our study focused specifically on DNA methylation in B CD19+ Lymphocytes isolated from whole blood of dust allergic patients (ALLERGY, n=3), aspirin intolerants (ASPIRIN INTOLERANT, n=3) and healthy subjects (CONTROL, n=3).
We utilized a two-stage design involving genome-wide discovery followed by quantitative, single-locus validation. Each microarray consists of a two-color comparison of a methylation-sensitive representation of the genome (HpaII) with an internal methylation-insensitive control/reference (MspI).

first: Masako

last: Suzuki

first: Maria

last: Isidoro-Garcia

first: Juana

last: Padron

first: Terrence

last: Turner

first: Felix

last: Lorente

first: Ignacio

last: Davila

first: John

last: Greally


title: Reactivity of commercial antibodies targeting human histone H2B N-terminal tail on the Intel array platform

first: Jordan

last: Price

summary:
The aim of the study was to test the Intel array platform and map the H2B epitopes bound by commercial antibody reagents.  We also tested the ability of SET7 PKMT to methylate Intel array peptides.
We diluted antibody reagents 1:1000 and incubated dilutions on the silicon-based Intel array platorm.

overall_design: We mapped antibody binding epitopes and SET7 PKMT methylation target peptides using a novel, silicon-based array platform with 8820 individual peptide features comprising every possible contiguous peptide from 1-21 a.a. in length within the 21-mer N-terminal tail of human histone H2B.

first: Stephanie

last: Tangsombatvisit

first: Guangyu

last: Xu

first: Dan

last: Levy

first: Emily

middle: C

last: Baechler

first: Or

last: Gozani

first: Madoo

last: Varma

first: Paul

last: Utz

first: Chih

last: Liu


title: miRNA expression in Tregs from HSCT patients

city: Hannover

first: Sya

last: Ukena

address: Carl-Neuberg-Strasse 1

institute: Hannover Medical School

summary: The aim of the study was to identify the miRNA expression profile of CD4+CD25high Tregs in SCT patients with and without GvHD early and late after transplantation compared to healthy donors.

overall_design: pool of n = 3 patients without GvHD early (< d100) and late (> d100) after SCT, n=3 patients with GvHD early (< d100) and late (> d100) after SCT and n = 3 sex- and age matched healthy donors for every timepoint

middle: N

first: Anke

last: Franzke


title: Angiogenesis gene expression upon Notch activation in human vascular smooth muscle cells

city: La Jolla

first: Sara

last: Weis

state: CA

address: 3855 Health Sciences Drive #0803

institute: Univ of California San Diego

summary: VSMCs were cultured on Jag1 or IgG-coated plates as described above. RNA was extracted using RNA isolation kit (Qiagen). Reverse-transcription PCR was done with RNA-to-cDNA kit (Applied Biosystems). cDNA was run on a TaqMan Low-Density Array, human angiogenesis panel (Applied Biosystems , Cat#4378725), amplified on a 7900 HT Fast Real Time PCR system (Applied Biosystems) according to manufacturer’s instructions.

overall_design: Angiogenesis gene expression was screened for human aortic vascular smooth muscle cells that were plated for 18 hours on either Notch ligands (Jag1 or Jag2) as compared to appropriate IgG controls (IgG1 or IgG2).

first: Lea

last: Scheppke-Smoot

first: David

last: Cheresh


title: Characterization of cell density-regulated gene expression of the grass endophyte Azoarcus sp. BH72

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

institute: University Bremen

summary:
Azoarcus sp. BH72 is able to communicate via cell density-dependent gene regulation. Here, the impact of cell-free conditioned culture supernatants, obtained from stationary phase Azoarcus wild type cultures, on gene expression was investigated determining changes in transcript profiles when early exponential aerobic cultures were incubated with cell-free culture supernatants for one and four hours.

Bacterial communication via quorum sensing (QS) is involved in the regulation of several cellular mechanisms such as metabolic processes, microbe-host interactions or biofilm formation. The nitrogen-fixing model endophyte of grasses Azoarcus sp. strain BH72 shows density-dependent gene regulation in the absence of common hydrophobic autoinducers for pilA encoding the structural protein of type IV pili that are essential for plant colonization. Here, we used a transcriptomic approach to identify target genes differentially regulated under QS conditions in conditioned supernatants in comparison to standard growth conditions.

overall_design: Analysis used RNA from the early exponential growth phase as control samples for comparison to the quorum-sensing condition samples taken at one hour and four hours after incubation with cell-free culture supernatants.

first: Lena

last: Hauberg-Lotte

last: Becker