title: A comparison between egg trancriptomes of cod and salmon reveals species specific traits in eggs for each species

status: Public on Aug 31 2014

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

summary: Fish in use in aquaculture display large variation in gamete biology. To reach better understanding around this issue, this study aims at identifying if “egg life history traits” can be hidden in egg transcriptomes. To pursue this, salmon and cod eggs were selected due to their largely differencing phenotypes (size, robustness, fresh/marine). An oligo microarray analysis was performed on ovulated eggs from cod (~23 000 genes, n=8) and salmon (~44 000 genes, n=7). The arrays were normalized to a similar spectrum for both arrays. Both arrays were re-annotated based on official gene symbol to retrieve an orthologous KEGG annotation, in salmon and cod arrays this represented 14009 and 7437 genes respectively. The probe linked to the highest gene expression for that particular KEGG annotation was used to compare expression between species. Differential expression was calculated for genes that had an annotation with score > 300, resulting in a total of 2354 KEGG annotations (genes) being differently expressed between the species. The most differentially expressed genes in salmon and cod (FD≥2), were used to reveal pathways that were overrepresented in the eggs of each species. This analysis revealed that immune, signal transduction, and excretory related pathways were overrepresented in salmon compared to cod. The most overrepresented pathways in cod were related to regulation of genetic information processing and metabolism. To conclude this analysis clearly point at some distinct transcriptome repertoires for cod and salmon and that these differences may explain some of the species-specific biological features for salmon and cod eggs.

overall_design: 16 samples

first: Anna

last: Wargelius

first: Tomasz

last: Furmanek

first: Jérôme

last: Montfort

first: Aurélie

last: Le Cam

first: Lene

last: Kleppe

first: Rolf

middle: B

last: Edvardsen

first: Geir

middle: L

last: Taranger


title: Transcriptome evaluation of gene expression changes during carotenoid accumulation in the storage root of carrot (Daucus carota)

status: Public on Aug 13 2014

city: Madison

first: Megan

last: Bowman

state: WI

address: 1575 Linden Drive

department: Plant Breeding and Plant Genetics

country: USA

institute: University of Wisconsin-Madison

summary: In this study, a cross species hybridization (CSH) approach was used to evaluate whole transcriptome changes during carotenoid accumulation in the storage root of carrot (Daucus carota). Carotenoids are isoprenoid compounds providing red, yellow and orange color to plants. Previous gene expression analyses of carotenoid accumulation in non-model plant species have primarily used a candidate gene approach. Since global transcriptome analyses require extensive genome sequence, in the absence of these genomic resources an alternate approach uses platforms developed for model plant species. To assess transcriptome patterns associated with carotenoid pigmentation in carrot storage root, two carrot sibling inbred lines, B8788, true breeding for orange color and B8750, true breeding for white root color, were hybridized to the Medicago Affymetrix GeneChip microarray.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Near isogenic recombinant inbred lines B8788 and B8750, derived from a cross between white rooted wild carrot (QAL) and orange-rooted B493 were used for comparative analyzes to minimize background genetic differences. B8788 is true breeding for orange color whereas B8750 is true breeding for white storage root color. Carrots were grown in three pots for each genotype under greenhouse conditions and carrots were selected arbitrarily from these pots for harvest. Roots were harvested at approximately 11 weeks post planting when carotenoid accumulation becomes apparent in the storage root. Storage root tissue from sixteen individual carrot roots was pooled into three one-gram tissue pools of four carrots for each genotype.

middle: J

first: Philipp

middle: W

last: Simon


title: Switching on antibiotic resistance in Staphylococcus aureus – Contribution of WalK and VraS histidine kinases in the development of vancomycin and daptomycin resistance

status: Public on Aug 18 2014

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

summary: Staphylococcus aureus is a notorious bacterial pathogen that causes a broad range of human diseases, and isolates that are resistant to several antibiotic classes including last resort antibiotics like vancomycin and daptomycin complicate the situation. We characterized S. aureus VC40, a strain that shows full resistance to vancomycin (MIC of 64 µg/ml) and daptomycin (MIC of 4 µg/ml) as well as a decreased susceptibility to further cell wall active agents. Genome sequencing revealed mutations in genes encoding the histidine kinases WalK and VraS that control cell envelope related processes and gene expression profiling indicated the induction of the respective regulons in strain VC40. Reconstitution of the mutations in walK or vraS into the susceptible S. aureus NCTC 8325 background resulted in a considerably increased resistance to vancomycin and daptomycin with MICs surpassing the clinical breakpoints for these antibiotics, thereby generating vancomycin-intermediate S. aureus (VISA) strains. As observed for S. aureus VC40, the walKwalk and vraS mutations also led to an increased expression of the respective regulons in the NCTC 8325 background. Phenotypic studies showed that S. aureus VC40 as well as the walKwalk and vraS mutants of strain NCTC 8325 were characterized by a significantly thickened cell wall, a decreased growth rate, a reduced autolytic activity and an increased resistance to lysostaphin-induced lysis. These results demonstrate that the WalK and VraS histidine kinases act as major switches which allow S. aureus to rapidly develop vancomycin resistance up to the VISA level via mutation of one single gene locus and concomitantly contribute to cross-resistance to other antibiotics including the last resort antibiotic daptomycin.

sample_organism: Staphylococcus aureus subsp. aureus VC40

overall_design: Microarray was used to evaluate alteration in the transcriptome of mutS mutant and compared to the parental strain VC40

first: Anne

last: Berscheid

first: Patrice

last: Francois

first: Axel

last: Strittmatter

first: Gerhard

last: Gottschalk

first: Jacques

last: Schrenzel

first: Peter

last: Sass

first: Gabriele

last: Bierbaum


title: Gene signaling pathways in liver of largemouth bass by a sub-chronic dietary exposure to EE2

city: Gainesville

first: Reyna

middle: Cristina

last: Colli-Dula

state: Florida

address: Mowry Drive 471

department: CEHT

institute: University of Florida

summary: The objective of this study was to investigate pathway signatures altered in the livers of female largemouth bass (LMB) and their potential links with biological responses by dietary exposure to 0.2 mg EE2/Kg (1% of their body weight) over two months using a transcriptomics approach.

overall_design: A high concentration of dietary 17alpha-ethinylestradiol (EE2) can activate key signaling pathways in response to oxidative damage may occur regardless of tumorigenesis and cancer. Female LMB received about 1.2g EE2/day/fish (from EE2-laced feed containing 0.2 mg EE2/Kg) for 60 days.

middle: C

first: Kevin

last: Kroll

first: Marianne

last: Kozuch

first: David

middle: S

last: Barber

first: Nancy

last: Denslow


title: Circadian regulation of EGF-receptor signaling by glucocorticoids

status: Public on Aug 30 2014

city: Rehovot

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

country: Israel

institute: Weizmann Institute of Science

summary: Transcriptional responses to stimuli are regulated by tuning rates of transcript production and degradation. Here we show that stimulation-induced changes in transcript production and degradation rates can be inferred from simultaneously measured precursor mRNA (pre-mRNA) and mature mRNA profiles. Our studies on the transcriptome-wide responses to extracellular stimuli in different cellular model systems revealed hitherto unanticipated dynamics of transcript production and degradation rates. Intriguingly, genes with similar mRNA profiles often exhibit marked differences in the amplitude and onset of their production. Moreover, we identify a group of genes, which take advantage of the unexpectedly large dynamic range of production rates to expedite their induction by a transient production overshoot. These findings provide an unprecedented quantitative view on processes governing transcriptional responses, and may have broad implications for understanding their regulation at the transcriptional and post-transcriptional levels.

overall_design: MCF10A cells stimulated with EGF, DEX, and their combination

first: Mattia

last: Lauriola

first: Eytan

last: Domany

first: Yosef

last: Yarden


title: Targeted inhibition of human breast cancer cell lines selected as model systems of ERBB2-positive/EGFR high breast cancer [RPPA-Longterm-HCC1954-SKBR3]

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

country: Germany

institute: German Cancer Research Center

summary:
EGFR-inhibition is required for targeted therapies of ERBB2-positive/EGFR high breast cancer.
Approximately 30% of human ERBB2-positive breast tumors also express EGFR.

overall_design: Three therapeutics were analyzed in five combinations plus control. Each experiment was performed in three biological replicates. This resulted in 180 samples. Exceptionally, time point 18 has just two biological replicates, and time point 48 just one. A dilution series of control lysated was included as control.

first: Frauke

last: Henjes

first: Christian

last: Bender

first: Silvia

last: von der Heyde

first: Lisa

last: Braun

first: Heiko

middle: A

last: Mannsperger

last: Schmidt

first: Stefan

last: Wiemann

first: Max

last: Hasmann

first: Sebastian

last: Aulmann

first: Tim

last: Beissbarth


title: TP53 mutational status is a potential marker for risk stratification in Wilms tumour with diffuse anaplasia [expression]

city: London

first: Richard

middle: Dafydd

last: Williams

address: 30 Guilford Street

department: Developmental Biology and Cancer

country: United Kingdom

institute: UCL Institute of Child Health

summary: The presence of diffuse anaplasia in Wilms tumours (DAWT) is associated with TP53 mutations and poor outcome. As patients receive intensified treatment, we sought to identify whether TP53 mutational status confers additional prognostic information. We studied 40 patients with DAWT with anaplasia in the tissue from which DNA was extracted and analysed for TP53 mutations and 17p loss. The majority of cases were profiled by copy number (n=32) and gene expression (n=36) arrays. TP53 mutational status was correlated with patient event-free and overall survival, genomic copy number instability and gene expression profiling. From the 40 cases, 22 (55%) had TP53 mutations (2 detected only after deep-sequencing), 20 of which also had 17p loss (91%); 18 (45%) cases had no detectable mutation but three had 17p loss. Tumours with TP53 mutations and/or 17p loss (n=25) had an increased risk of recurrence as a first event (p=0.03, hazard ratio (HR), 3.89; 95% confidence interval (CI), 1.26-16.0) and death (p=0.04, HR, 4.95; 95% CI, 1.36-31.7) compared to tumours lacking TP53 abnormalities. DAWT carrying TP53 mutations showed increased copy number alterations compared to those with wild-type, suggesting a more unstable genome (p=0.03). These tumours showed deregulation of genes associated with cell cycle and DNA repair biological processes. This study provides evidence that TP53 mutational analysis improves risk stratification in DAWT. This requires validation in an independent cohort before clinical use as a biomarker.

overall_design: 36 tumour samples were expression profiled in 2-colour hybridisations with Stratagene Universal Human Reference RNA in the reference channel. There were no replicates.

middle: D


title: TP53 mutational status is a potential marker for risk stratification in Wilms tumour with diffuse anaplasia

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: Loss of BTG1 function promotes ETV6-RUNX1-mediated leukemic transformation by upregulation of BCL6

status: Public on Aug 22 2014

city: Nijmegen

first: Frank

middle: N

last: van Leeuwen

address: PO BOX 9101 route 412

department: Pediatrics

country: Netherlands

institute: Radboudumc

summary: Analysis of gene signatures in WT+Ctrl vs WT+ETV6-RUNX1, Btg1-/- and Btg1-/-+ETV6-RUNX1 in cKit+Ter119- fetal liver-derived hematopoietic progenitor cells (FL-HPCs). The Btg1-/-+ETV6-RUNX1 FL-HPCs display a strong increase in proliferation compared to WT+ETV6-RUNX1.

overall_design: Total RNA otained from WT+Ctrl, WT+ETV6-RUNX1, Btg1-/-+Ctrl and Btg1-/-+ETV6-RUNX1 FL-HPCs cells that were cultured for 12 days in expansion medium.

first: Esther

last: Tijchon

first: Liesbeth

last: van Emst

first: Laurensia

last: Yuniati

first: Dorette

last: van Ingen Schenau

first: Mylène

last: Gerritsen

first: Simone

middle: R

last: de Rijk

first: Laurens

middle: T

last: van der Meer

first: Owen

first: Peter

middle: M

last: Hoogerbrugge

first: Blanca

last: Scheijen


title: T-C cell mouse microarray

status: Public on Aug 21 2014

city: Galveston

first: QiQi

last: Zhou

state: TX

address: 301 University Blvd

department: Internal Medicine

institute: UTMB

type: Non-coding RNA profiling by high throughput sequencing

summary: Small molecules that mimic or inhibit miRNA based mechanisms may readily available

overall_design: treated T-C cell with TB-CF

first: L

last: Yang

first: Q

last: zhou

first: S

last: Patric


title: Comparison of gene expression profile of muscle samples from growth promoters-treated and control cows.

status: Public on Aug 28 2014

city: legnaro

first: sara

last: pegolo

address: viale dell'università 16

country: Italy

institute: university of padua

summary: A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from twenty-four (24) muscle samples from growth promoters-treated cows and thirteen (13) from control animals. Two-factor ANOVA was performed using age and treatment as independent categorical variables and 958, 2695 and 2482 genes were found significantly regulated by the treatment for Finaplix, Revalor and Revalor plus dexamethasone, respectively.

overall_design: In this study, we analyzed thirty-seven (37) bovine biceps brachii samples, twenty-four (24) from growth promoters treated cows and thirteen (13) from control animals. Gene expression profiling was performed using the Agilent-015354 Bos taurus Oligo Microarray platform (GPL7053) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Sara

last: Pegolo

first: Luca

last: Bargelloni


title: microRNA profiling in mantle cell lymphoma cell lines before and after 5-azadC treatment

city: Hong Kong

first: Chor Sang

last: Chim

address: Queen Mary Hospital

department: Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: Mantle cell lymphoma (MCL) is an aggressive B-cell non-Hodgkin’s lymphoma (NHL). In cancers, tumour suppressive microRNAs may be silenced by DNA hypermethylation. By microRNA profiling, miR-155-3p was significantly upregulated upon demethylation treatment of MCL cell lines with 5-aza-2’-deoxycytidine (5-azadC). Methylation-specific PCR, verified by pyrosequencing, showed complete methylation of miR-155-3p in one MCL cell line (REC-1). 5-azadC treatment of REC-1 led to demethylation and re-expression of miR-155-3p. Over-expression of miR-155-3p led to increased sub-G1 apoptotic cells and reduced cellular viability, demonstrating its tumour suppressive properties. By luciferase assay, lymphotoxin-beta (LT-β) was validated as a miR-155-3p target. In 31 primary MCL, miR-155-3p was found hypermethylated in 6(19%) cases. To test if methylation of miR-155-3p was MCL-specific, miR-155-3p methylation was tested in an additional 191 B-cell, T-cell and NK-cell NHLs, yielding miR-155-3p methylation in 66(34.6%) including 36(27%) non-MCL B-cell, 24(53%) T-cell and 6(46%) of NK-cell lymphoma. Moreover, in 72 primary NHL samples with RNA, miR-155-3p methylation correlated with miR-155-3p downregulation (p=0.030), and LT-β upregulation (p=0.004). Collectively, miR-155-3p is tumour suppressive microRNA hypermethylated in MCL and other NHL subtypes. As miR-155-3p targets LT-β, which is an upstream activator of the non-canonical NF-kB signalling, miR-155-3p methylation is potentially important in lymphomagenesis

overall_design: Total RNA isolated from MINO and JEKO-1 before and after 5-azadC treatment were converted into cDNA by MegaplexTM RT Primers and TaqMan® MicroRNA Reverse Transcription Kit. cDNA was pre-amplified using MegaplexTM PreAmp Primer and loaded onto 384-well format Taqman® human microRNA array A V2.0 & B V3.0. Real-time PCR was performed on 7900HT Real-Time PCR system and raw data were analyzed normalizing to mean of three endogenous controls (U6snRNA, RNU44 and RNU48). Relative microRNA levels were determined by ΔΔCt using endogenous controls and untreated controls using SDS 2.4 and RQ manager 1.2. All experimental procedures and analyses were performed according to manufacturer’s instruction, using reagents, system and softwares acquired from Applied Biosystems (Foster City, USA).

first: Rita

middle: H

last: Yim

first: Chor-Sang


title: Human Esophageal Squamous Cell Cancer Cell line: Control vs. mir203 expression vector Transfected

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Transcriptional profiling of  Human Esophageal Squamous Cell Cancer Cell line (KYSE520) comparing mock transfectant (KYSE520 Mock②) with cells transfected with a mir203 expression vector (KYSE520 miR203⑥)

overall_design: KYSE520 Mock② VS KYSE520 miR203⑥

first: Tomoyuki

last: Okumura


title: Epigenetic regulation of gene expression is instructed by promoter sequence and refined by developmental progression [genomic]

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

type: Methylation profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

summary: A large body of literature suggests that local features of chromatin are crucial in determining functional properties of underlying DNA.  The extent to which DNA sequence plays an active role in the establishment and maintenance of patterns of histone and DNA modification at promoters in cells and tissues in an adult animal remains poorly understood.  Likewise, whether passage through development is required for refinement of transcriptional states and chromatin marks characteristic of fully differentiated adult cells remains unclear.  Here we undertook analysis of gene expression along with the genomic distribution of DNA methylation and a set of histone marks in primary tissues derived from different primordial germ layers in adult mice.  We find that promoter CpG content correlated strongly with specific repressive mechanisms.  Likewise, RNA polymerase II occupancy and active histone marks were omnipresent on CpG rich promoters regardless of transcriptional output and of cell type.  However, these same chromatin features cleanly demarcate transcriptional activity on promoters with low CpG content.  While these observations imply an instructive role for DNA sequence in establishment and maintenance of epigenetic states, experimental evidence presented here also suggests an additional role for development in refining these features at individual promoters.

overall_design: DNA methylation and a set of histone marks (H3K4me3, H3K9me2 and H3K27me3) were examined in B cells and liver using Nimblegen mouse promoter arrays.

first: Ruifang

last: Li

first: Paul

last: Wade

first: Ruchir

last: Shah


title: NAD+ and PPAR-modifying drugs in a C. elegans model of respiratory chain complex I deficiency

city: Philadelphia

first: Shana

middle: Erin

last: McCormack

state: PA

address: 34th and Civic Center Boulevard, Suite 11NW30

department: Pediatrics, Division of Diabetes and Endocrinology

institute: Children's Hospital of Philadelphia

summary: The gas-1(fc21) mutation affects the 49 kD subunit of complex I, decreasing the rate of complex I-dependent oxidative phosphorylation. This is a model for human mitochondrial respiratory chain disease. NAD+ and PPAR-modifying drugs may confer benefits with respect to lifespan in these short-lived mutant worms. Analysis of gas-1(fc21) electron transport chain complex I mutants treated either starting in development or in young adulthood only with nicotinic acid (1 mM), resveratrol (50 microM), rosiglitazone (5 mM) or fenofibrate (14 microM) is presented. The goal is to detect transcriptional changes in clusters of genes using gene set enrichment analysis to explain treament effects in these mutant worms.

overall_design: Four biological replicates were performed for each treatment condition (nicotinic acid, resveratrol, rosiglitazone, and fenofibrate) for each drug beginning either in development or in young adulthood for gas-1 mutant worms, i.e., 8 treated samples in total. At most one outlier was excluded from each analysis. Untreated N2 and gas-1 in each of the control solvents (S-basal, for nicotinic acid, and 1% DMSO, for resveratrol, rosiglitazone, and fenofibrate) were also analyzed; at least 3 replicates of each were included. These were used as sources of total RNA, each for hybridization to a single Affymetrix whole-genome microarray. Analysis was performed to reveal transcriptional changes related to mutantion and/or drug treatment effects.

first: Z

last: Zhang

middle: E

first: M

last: Falk


title: Differential Immunomodulatory Impact of Bacillus subtilis Spores and Vegetative Cells on a Human Colonic Epithelial Cell-Line Model

status: Public on Aug 14 2014

city: Montreal

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

country: Canada

institute: Lallemand Health Solutions Inc.

summary: Bacillus subtilis strain R0179 is found in a number of commercially-available probiotic products. The mechanism(s) of action of B. subtilis in the host are poorly understood, but may involve the immune system response to switching between spore and vegetative forms. In order to help elucidate this mechanism, we challenged the immune response of a human colonic epithelial HT-29 cell model for 3 hours with the two forms of B. subtilis. The cellular response was evaluated using a custom-designed two-color expression microarray targeting 1354 genes of the human immune system. The data obtained in this study indicates that the vegetative cell form of the strain moderately induced TH1 pro-inflammatory response through IL-17C and TNF signaling pathway while down-regulating anti-inflammatory response genes IL-10 and TGFβ-2. The spore form had an opposite effect and acted primarily by down-regulating the Mitogen-Activated Protein Kinase pathway.

overall_design: The overall design consisted of 2 samples of HT-29 cells treated with Bacillus subtilis R0179 spores or vegetative states versus unchallenged HT-29 cells. A minimum of four dye-swap hybridizations (4 biological replicates) were performed for each of the 2 samples analyzed. Unchallenged HT-29 cells were controls and challenged HT-29 cells with Bacillus subtilis R0179 spores or vegetative were treated samples.

first: Chad

last: MacPherson

first: Pierre

last: Burguière


title: BP001-002: The genomic landscape of compensatory evolution

status: Public on Aug 27 2014

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

summary: Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations. However, deleterious mutations may also have an important role by promoting adaptive genetic changes that are otherwise inaccessible. Here we study the capacity of the baker’s yeast genome to compensate the complete loss of genes during evolution, and explore the long-term consequences of this process. We initiated laboratory evolutionary experiments with over 180 haploid yeast genotypes, all of which initially displayed slow growth due to the deletion of a single gene. Compensatory adaptation was rapid and pervasive, and it promoted the genomic divergence of parallel evolving populations. The accumulated mutations did not restore wild type genomic expression states and generated diverse growth phenotypes across environments. Taken together, gene loss initiates genomic changes that can influence evolutionary potential upon environmental change.

overall_design: Evolved yeast-lines were generated by growing strains for 400 doublings during 104 days on YPD medium in 96 wells plates, 8 evolved lines were selected for microarray analysis. Two independent colonies of the wild type control, evolved and corresponding ancestor knock-out strains were grown to early midlog and used for transcription profiling by dual channel array against a common reference.

first: Bela

last: Szamec

first: Gabor

last: Boross

first: Dorottya

last: Kalapis

first: Karoly

last: Kovacs

first: Zoltan

last: Farkas

first: Viktoria

last: Lazar

first: Monika

last: Hrtyan

first: Patrick

last: Kemmeren

first: Frank

last: Holstege

first: Edit

last: Rutkai

first: Balazs

last: Papp

first: Csaba

last: Pal


title: Targeted inhibition of human breast cancer cell line selected as model system of ERBB2-positive/EGFR high breast cancer [RPPA-Shortterm-SKBR3]

first: Ulrike

last: Korf

overall_design: Three targeted therapeutics (erlotinib, pertuzumab, trastuzumab) and two ligands (EGF, HRG) were analyzed in all possible combinations. Each experiment involving inhibition with targeted drugs was performed in three, and measurements without inhibitors were performed in five biological replicates. This resulted in 780 samples. HRG stimulated cells under the triple drug combination exceptionally have two biological replicates. Incubation with therapeutics only and dilution series of control lysated were included as controls.

first: Frauke

last: Henjes

first: Christian

last: Bender

first: Silvia

last: von der Heyde

first: Lisa

last: Braun

first: Heiko

last: Mannsperger

last: Schmidt

first: Stefan

last: Wiemann

first: Max

last: Hasmann

first: Sebastian

last: Aulmann

first: Tim

last: Beissbarth


title: The synthetic glucocorticoids prednisolone and dexamethasone regulate the same genes in acute lymphoblastic leukemia cells [Set 2]

status: Public on Aug 12 2014

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

summary:
Background: Glucocorticoids (GCs) cause apoptosis in malignant cells of lymphoid lineage by transcriptionally regulating a plethora of genes.  As a result, GCs are included in almost all treatment protocols for lymphoid malignancies, particularly childhood acute lymphoblastic leukemia (chALL). The most commonly used synthetic GCs in the clinical setting are prednisolone and dexamethasone. While the latter has a higher activity and more effectively reduces the tumor load in patients, it is also accompanied by more serious adverse effects than the former. Whether this difference might be explained by regulation of different genes by the two GCs has never been addressed.
Results: Using a recently developed GC bioassay based on a GC-responsive reporter construct in human Jurkat T-ALL cells, we found ~7-fold higher biological activity with dexamethasone than prednisolone. Similarly, 1.0e-7M dexamethasone and 7.0e-7M prednisolone triggered similar cell death rates in CCRF-CEM-C7H2 T-chALL cells after 72 hours of treatment. Using microarray-based whole genome expression profiling and a variety of statistical and other approaches, we compared the transcriptional response of chALL cells to 6 hour exposure to both synthetic GCs at the above concentrations. Our experiments did not detect any gene whose regulation by dexamethasone differed significantly from that by prednisolone.
Conclusions: Our findings suggest that the reported differences in treatment efficacy and cytotoxicity of dexamethasone and prednisolone are not caused by inherent differences of the 2 drugs to regulate the expression of certain genes, but rather result either from applying them in biologically in-equivalent concentrations and/or from differences in their pharmacokinetics and - dynamics resulting in different bioactivities in tumor cells and normal tissues.

overall_design: CCRF-CEM-C7H2 childhood T-ALL cells were treated with 1.0e-7M dexamethasone (DEX), 7.0e-7M prednisolone (PRED) or 0.1% ethanol (empty carrier control) in three independent experiments. RNA was extracted after 6 hours of treatment and subjected to gene expression profiling using Affymetrix HuGene 1.0 ST microarrays. Differences in transcriptional responses was determined by comparing DEX against PRED treated samples, GC-regulated genes for each synthetic GC by comparing DEX or PRED against ethanol treated samples. Significance for differential regulation or expression was determined using the moderated t-test from Bioconductor's limma package. Resulting p-values were adjusted for multiple hypothesis testing using the method from Benjamini and Hochberg.

first: Daniel

last: Bindreither

first: Simone

last: Ecker

first: Reinhard

last: Kofler


title: Identification of a microRNA regulator for axon guidance in the olfactory bulb of adult mice

city: Hangzhou

first: Ting

middle: ting

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Neuroscience and Anatomy

country: China

institute: Zhejiang University School of Medicine

summary: Using the highly sensitive miRNA array, we screened 40 microRNAs abundant in the olfactory bulb and we explored the functions of these miRNAs in the olfactory bulb by Gene Ontology and Kyoto Encyclopedia of Genes annotation. The enrichment results indicated that these miRNAs mainly participated in the axon guidance process. Furthermore, the quantitative real-time polymerase chain reaction, immunohistochemistry, and dual luciferase reporter assay results showed that miR-30c is a specific regulator of semaphorin-3A, which will give new insights in disclosing the mechanism of functional maintenance and sexual-specific differentiation of the olfactory bulb.

overall_design: In this study, three samples from steady-state mice were used to acquire the miRNA expression profiling and the function of the abudant miRNAs in the olfactory bulb were analyzed by bioinformatic methods.Finally, miR-30c was experimentally validated to be a regulator of semaphorin-3A, an important axon guidance cue in the nervous system.

first: Shu

last: Ling


title: TP53 mutational status is a potential marker for risk stratification in Wilms tumour with diffuse anaplasia [aCGH]

first: Richard

last: Williams

overall_design: 32 tumour samples were profiled by aCGH, in 2-colour hybridisations with common pooled unrelated normal genomic DNA in the reference channel. There were no replicates.


title: Comparative genomics reveals new molecular targets for accelerated strain improvement of rifamycin B-producing strains

status: Public on Aug 26 2014

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary: In the present study, we have used a genomic approach to understand how the classical mutate-and-screen method actually generated an improved rifamycin B producer. Compared with the reference strains Amycolatopsis mediterranei S699 (rifamycin B producer) and U32 (rifamycin SV producer), a total of 250 variations affecting a total of 227 coding sequences (CDS) were found in rifamycin B overproducing strain HP-130. One hundred nine CDS variations were specific to HP-130 as they were absent in both S699 and U32. A lot of variations affected genes coding for fatty acid (an lipid) metabolism, which is tightly interconnected with rifamycin biosynthesis by common metabolic precursors (malonyl-CoA, methylmalonyl-CoA). Interestingly, a nonsense mutation was mapped within mutB coding for methylmalonyl-CoA mutase suggesting the importance of metabolic re-direction of carbon flow toward rifamycin biosynthesis in the over-producing phenotype of HP-130. Other key mutations were: i.) a missense mutation affecting ppk, which encodes a polyphosphate kinase and was previously shown to play a negative role in the control of antibiotic biosynthesis in Streptomyces lividans; ii.) a missense mutation in argS2 affecting one of the two arginyl tRNA synthetases of A. mediterranei; iii.) a missense mutation in rifN coding for a protein belonging to the ROK family of transcriptional regulators with kanosamine kinase activity. Microarray analysis of the transcriptome of HP-130 as compared to that of S699 was useful to understand the effects of several mutations on global gene expression profile. Genomic and transcriptomic data were used to improve rifamycin B production in S699 by genetic engineering thus proving the causative effect of the above-mentioned mutations on the overproducing phenotype.

overall_design: In this study by using comparative genomic analysis we have identified all genetic changes that have occurred during development of a rifamycin B overproducer (HP-130), which was obtained by the traditional mutate-and-screen method. To gain insight about the mechanisms underlying improved rifamycin B production in HP-130, DNA microarray of A. mediterranei were manufactured and used for comparative analysis of the gene expression profile in HP-130 and S699. In DNA microarray experiments the two strains were cultivated under standard batch-culture conditions in modified RFB 2244 fermentation medium, and samples were collected at different time points (24-72 h) for RNA extraction. Gene expression data were analyzed to identify transcripts modulated during the growth curve. Amycolatopsis mediterranei S699 (WT) and the  improved rifamycin B producer (HP-130) were profiled at 5 time points. For each time point two biological replicates are provided.

first: Clelia

last: Peano

first: Giorgio

last: Corti

first: Adelfia

last: Talà

first: Carla

last: Palumbo

first: Luisa

last: Siculella

first: Fabrizio

last: Damiano

first: Mattia

last: Forcato

first: Guidantonio

last: Malagoli Tagliazucchi

first: Daniela

last: Pasanisi

first: Fabio

last: Fuligni

first: Alessandro

last: Pietrelli

first: Gianluca

last: De Bellis

first: Pietro

last: Alifano


title: Small RNA sequencing identifies miRNA roles in ovule and fiber development

status: Public on Aug 16 2014

city: Greenville

first: Baohong

last: Zhang

address: 562 Science and Technology Building

department: Biology

institute: East Carolina University

summary: To dissect the roles of miRNAs in fiber development, we sequenced small RNAs from ovules -1 to +1 day post anthesis (DPA) and young leaves. A series of conserved and novel miRNA were identified from cotton EST database and the genome of G.raimondii, many of which were shown to be expressed differentially between ovule and leaf, indicating their potential roles in fiber development or leaf development.

overall_design: Cotton (Gossypium Hirsutum L.) cultivar TM-1 were grown in the greenhouse. Cotton ovules -1 to +1 day post anthesis (DPA) and young leaves were harvested for five biological replicates and immediately frozen in liquid nitrogen. They were then stored at -80°C following RNA extraction. Totals RNAs were extracted from each tissue sample using the mirVana miRNA isolation kit (Ambion, Austin, TX) according to the manufacturer’s protocol. The small RNA samples extracted from the five biological replicates were pooled together for leaf and ovule, respectively. Finally, the construction of pooled small RNA libraries and sequenced were performed by LC Sciences (Houston, TX) using Illumina high-throughput sequencing platform.

first: Fuliang

last: Xie


title: gravity-Gravitational signature of synchronized cell cultures in particular cell cycle stages

status: Public on Aug 23 2014

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

summary: au13-11_gravity - gravity - Cell cycle and cell proliferation are decoupled under altered gravity conditions. We have previously shown that semisolid cell cultures of Arabidopsis suffer overall genome changes in response to altered gravity and also that cell cycle stages duration is altered. By using synchronized cell cultures we will demonstrate the precise alterations in cell cycle duration and also the transcriptional signature in any of them. - Experiments consists on exposures of Arabidopsis cell cultures to 1g control/simulated microgravity (RPM) conditions. Asynchronous cells exposed for 14 h + Syncronous populations choosen to have an enrichment of cell cycle phases were used (being T7/T10 samples on G2 phase, T14/T16 samples on G1 phase).

overall_design: 6 dye-swap - time course,treated vs untreated comparison

first: Sandrine

last: Balzergue

first: Ludivine

last: Taconnat

first: Raul-

last: Herranz

first: Marie-Laure

last: Martin-Magniette


title: Targeted inhibition of human breast cancer cell line selected as model system of ERBB2-positive breast cancer [RPPA-Longterm-BT474]

first: Ulrike

last: Korf

summary:
EGFR-inhibition is required for targeted therapies of ERBB2-positive/EGFR high breast cancer.
Approximately 30% of human ERBB2-positive breast tumors also express EGFR.

overall_design: Three therapeutics were analyzed in five combinations plus control. Each experiment was performed in three biological replicates. This resulted in 180 samples. Exceptionally, time point 18 has just two biological replicates, and time point 48 just one. A dilution series of control lysated was included as control.

first: Frauke

last: Henjes

first: Christian

last: Bender

first: Silvia

last: von der Heyde

first: Lisa

last: Braun

first: Heiko

last: Mannsperger

last: Schmidt

first: Stefan

last: Wiemann

first: Max

last: Hasmann

first: Sebastian

last: Aulmann

first: Tim

last: Beissbarth


title: Targeted inhibition of human breast cancer cell line selected as model system of ERBB2-positive/EGFR high breast cancer [RPPA-Shortterm-HCC1954]

overall_design: Three targeted therapeutics (erlotinib, pertuzumab, trastuzumab) and two ligands (EGF, HRG) were analyzed in all possible combinations. Each experiment involving inhibition with targeted drugs was performed in three, and measurements without inhibitors were performed in five biological replicates. This resulted in 780 samples. Incubation with therapeutics only and dilution series of control lysated were included as controls.


title: Mouse Tracheal Epithelial Cell Air-Liquid Interface Primary Culture Time Course (ALI d0, d2, d7)

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

summary:
Mouse tracheal epithelial cells were cultured at air-liquid interface (ALI), RNA was harvested at days 0, 2, and 7 post-ALI, and hybridized to two-channel MEEBO arrays.
The experiment was designed to allow investigators to identify genes differentially expressed during airway epithelial cell differentiation and development, including ciliogenesis.

first: Jie-hong

last: Pan

first: Tracy

middle: L

last: Adair-Kirk

first: Tao

last: Huang

first: Nicholas

last: Yozamp

first: Jian

last: Xu

first: E

middle: P

last: Reddy

first: Derek

last: Byers

first: Richard

last: Pierce

first: Michael

middle: J

last: Holtzman

first: Steven

last: Brody


title: Comparison of Expression Profiles for Agrobacterium tumefaciens visR mutant to wild-type strain.

city: Bloomington

first: Jason

middle: Eugene

last: Heindl

state: IN

address: 1001 E. 3rd St., Jordan Hall 142

institute: Indiana University

summary: Many bacteria colonize surfaces and transition to a sessile mode of growth. The plant pathogen Agrobacterium tumefaciens produces a unipolar polysaccharide (UPP) adhesin at single cell poles that contact surfaces. Here we report that elevated levels of the intracellular signal cyclic diguanosine monophosphate (c-di-GMP) lead to surface-contact-independent UPP production and a red colony phenotype due to production of UPP and the exopolysaccharide cellulose, when A. tumefaciens is incubated with the polysaccharide stain Congo Red. Transposon mutations with elevated Congo Red staining identified presumptive UPP-negative regulators, mutants for which were hyperadherent, producing UPP irrespective of surface contact. Multiple independent mutations were obtained in visN and visR, activators of flagellar motility in A. tumefaciens, now found to inhibit UPP and cellulose production. Expression analysis in a visR mutant and isolation of suppressor mutations, identified three diguanylate cyclases inhibited by VisR. Null mutations for two of these genes decrease attachment and UPP production, but do not alter cellular c-di-GMP levels. However, analysis of catalytic site mutants revealed their GGDEF motifs are required to increase UPP production and surface attachment. Mutations in a specific presumptive c-di-GMP phosphodiesterase also elevate UPP production and attachment, consistent with c-di-GMP activation of surface-dependent adhesin deployment.

overall_design: Three biological replicates, independent RNA preparations, one dye swap.

first: Jing

first: Jinwoo

last: Kim

first: Benjamin

last: Koestler

first: Jeong-Hyeon

last: Choi

first: Christopher

last: Waters

first: Clay

last: Fuqua


title: The synthetic glucocorticoids prednisolone and dexamethasone regulate the same genes in acute lymphoblastic leukemia cells

first: Johannes

last: Rainer

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

overall_design: Refer to individual Series; GSE55877 contains the main microarray data set presented in the publication, GSE55876 provides additional data for cells treated with water soluble prednisolone.


title: Targeted inhibition of human breast cancer cell line selected as model system of ERBB2-positive breast cancer [RPPA-Shortterm-BT474]

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

institute: German Cancer Research Center

first: Frauke

last: Henjes

first: Christian

last: Bender

first: Silvia

last: von der Heyde

first: Lisa

last: Braun

first: Heiko

middle: A

last: Mannsperger

last: Schmidt

first: Stefan

last: Wiemann

first: Max

last: Hasmann

first: Sebastian

last: Aulmann

first: Tim

last: Beissbarth


summary:
Background: Glucocorticoids (GCs) cause apoptosis in malignant cells of lymphoid lineage by transcriptionally regulating a plethora of genes.  As a result, GCs are included in almost all treatment protocols for lymphoid malignancies, particularly childhood acute lymphoblastic leukemia (chALL). The most commonly used synthetic GCs in the clinical setting are prednisolone and dexamethasone. While the latter has a higher activity and more effectively reduces the tumor load in patients, it is also accompanied by more serious adverse effects than the former. Whether this difference might be explained by regulation of different genes by the two GCs has never been addressed.
Results: Using a recently developed GC bioassay based on a GC-responsive reporter construct in human Jurkat T-ALL cells, we found ~7-fold higher biological activity with dexamethasone than prednisolone. Similarly, 1.0e-7M dexamethasone and 7.0e-7M prednisolone triggered similar cell death rates in CCRF-CEM-C7H2 T-chALL cells after 72 hours of treatment. Using microarray-based whole genome expression profiling and a variety of statistical and other approaches, we compared the transcriptional response of chALL cells to 6 hour exposure to both synthetic GCs at the above concentrations. Our experiments did not detect any gene whose regulation by dexamethasone differed significantly from that by prednisolone.
Conclusions: Our findings suggest that the reported differences in treatment efficacy and cytotoxicity of dexamethasone and prednisolone are not caused by inherent differences of the 2 drugs to regulate the expression of certain genes, but rather result either from applying them in biologically in-equivalent concentrations and/or from differences in their pharmacokinetics and - dynamics resulting in different bioactivities in tumor cells and normal tissues.

Additional microarray data set with RNA from CCRF-CEM-C7H2 cells treated with 1.0e-7M dexamethasone, 4.0 and 8.0 e-6M Solu-dacortin (prednisolone 21-(sodium succinate), a water soluble prednisolone) and 0.1% ethanol.

overall_design: CCRF-CEM-C7H2 childhood T-ALL cells were treated with 1.0e-7M dexamethasone (DEX), 4.0 and 8.0 e-6M Solu-dacortin (SD, prednisolone 21-(sodium succinate), a water soluble prednisolone) or 0.1% ethanol (empty carrier control) in three independent experiments. RNA was extracted after 6 hours of treatment and subjected to gene expression profiling using Affymetrix HuGene 1.0 ST microarrays. Differences in transcriptional responses was determined by comparing DEX against SD treated samples, GC-regulated genes for each synthetic GC by comparing DEX or SD against ethanol treated samples. Significance for differential regulation or expression was determined using the moderated t-test from Bioconductor's limma package. Resulting p-values were adjusted for multiple hypothesis testing using the method from Benjamini and Hochberg.

first: Daniel

last: Bindreither

first: Simone

last: Ecker

first: Reinhard

last: Kofler


title: Homo sapiens foetal mesenchymal stem cell miRNA transcriptome

status: Public on Aug 06 2014

city: London

first: Nicholas

middle: John

last: Dibb

address: Du Cane Road

department: Surgery and Cancer

institute: Imperial College London

summary: We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional.  Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro.  This result was confirmed by the use of isomiR-specific sponges.  Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution.  This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes

overall_design:
Sequence library of miRNAs from a single sample of human foetal mesenchymal stem cells.  Results tested and confirmed by northern blotting.
Please note that only raw data files are available for the embryonic and neual samples and thus, directly submitted to SRA (SRX547311, SRX548700, respectively under SRP042115/PRJNA247767)

first: Nick

last: Fisk


title: Inhalation exposure of hexanal in rats (miRNA)

status: Public on Aug 08 2014

city: Seoul

first: Yoon

last: Cho

address: hwarang-ro 14

country: South Korea

institute: KIST

summary: To further development of insight into the mechanism of toxicity, it is important to employ whole genome microarray expression profiling to identify and characterize miRNAs profiles as a discovery platform relevant for toxicologic mechanisms of hexanal. miRNAs have prominent role in cell cycle control, apoptosis, cancer development and proliferation-related processes. However, few reports have described the effect of hexanal on miRNA expression profiles using animal model. In this respect, we studied the expression profiles of miRNAs in hexanal-exposed in rats by miRNA microarray analysis.

overall_design: To evaluate the miRNA expression in lung tissue of rats after exposure of hexanal, Fischer-344 rats were inhaled to three concentrations (600, 1000, 1500 mg/m3) for 5 weeks. miRNA expression analysis was conducted using Rat miRNA 8 x 15K microarray v19.0 (Agilent Technologies, USA).

first: Jae-Chun

last: Ryu


title: The microRNA bantam regulates a developmental transition in epithelial cells that restricts sensory dendrite growth

status: Public on Aug 04 2014

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

institute: University of California, San Francisco

summary: Microarray profiling of GFP-marked epithelial cells isolated by FACS from 1st and 3rd instar wild type and mutant Drosophila larvae.

overall_design: Multiple independent replicates collected for each population/timepoint combination.  RNA isolated and amplified from FACS-sorted populations.  Hybridized as two-color experiment against a common pooled reference.

first: Charles

middle: C

last: Jiang

first: Peter

last: Soba

first: Edward

last: Parker

first: Jay

middle: Z

last: Parrish


title: Effect of 10 or 25 days cortisol treatment on late gestation fetal septum

status: Public on Aug 07 2014

city: Gainesville

first: Maureen

last: Keller-Wood

state: FL

department: Pharmacodynamics

institute: University of Florida

summary: We have previously shown in sheep that 10 days of modest chronic increase in maternal cortisol result in fetal heart enlargement and Purkinje cell apoptosis. In subsequent studies in which we extended the duration of cortisol infusion (1mg/kg/d) to term, we found a dramatic incidence of stillbirth in the pregnancies with chronically increased cortisol and associated maternal hyperglycemia. To investigate the effects on the heart, transcriptomic analyses were performed on the septa using ovine microarrays and Webgestalt and Cytoscape programs for pathway inference. Analyses of the effects of 10 days of maternal cortisol infusion (130d-cortisol vs 130d control), ~25 days (term at ~140d-cortisol vs 140d control), normal maturation (140d-control vs 130d control) were performed.  In all analyses gene ontology (GO) terms related to immune function and cytokine actions were significantly over-represented.  After 10 days of cortisol, growth factor and muscle cell apoptosis pathways were significantly over-represented, consistent with our previous findings.  We found significantly differentially regulated genes in the term fetuses (ie after ~25 days of cortisol) in pathways consistent with altered metabolism in the heart, particularly in mitochondria, associated with responses to hypoxia and to nutrient.  Analysis of mitochondrial number by quantitative real-time PCR confirmed a significant decrease. These pathways were different from those modeled following the normal increase in cortisol in late gestation which contributes to normal maturation of the heart, and thus may be indicative of the fetal heart pathophysiologies seen in pregnancies complicated by diabetes, Cushing’s disease and chronic stress.

overall_design: 2 cohorts of  singleton sheep fetuses at 129-131d gestation or 139-144d gestation (approximately term)  were used. The first cohort received maternal cortisol infusion of 1mg/kg/day or vehicle for 10 days until approximately  day 130 of gestation (n=6/group), the second cohort received the same dose of cortisol for approximately 25 days until near term (n=7, cortisol; n=7ewes, n=8 fetuses due to one set of twins, control)

first: Elaine

last: Richards

last: Wood

first: Maria

middle: B

last: Rabaglino

first: Andrew

last: Antolic


title: MicroRNAs differentially present in the plasma of HIV elite controllers

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

summary: Elite controllers maintain HIV-1 viral loads below the limit of detection. The mechanisms responsible for this phenomenon are poorly understood. As microRNAs (miRNAs) are regulators of gene expression and some of them modulate HIV infection, we have studied the miRNA profile in plasma from HIV elite controllers and chronically infected individuals and compared against healthy donors. Several miRNAs correlate with CD4+ T cell count or with the known time of infection. No significant differences were observed between elite controllers and healthy donors; however, 16 miRNAs were different in the plasma of chronic infected versus healthy donors. In addition, levels of hsa-miR-29b-3p, hsa-miR-33a-5p and hsa-miR-146a-5p were higher in plasma from elite controllers than chronic infected and hsa-miR-29b-3p and hsa-miR-33a-5p overexpression significantly reduced the viral production in MT2 cells. Therefore, levels of circulating miRNAs might be of diagnostic and/or prognostic value for HIV infection. Additionally, hsa-miR-29b-3p and miR-33a-5p may be used in therapeutic strategies.

overall_design: An exploratory cross-sectional study of microRNA levels in EDTA plasma samples. Plasma samples were obtained from 24 subjects and were classified in 3 groups, 9 Elite Controllers (defined as individuals with plasma viral load (PVL) < 50 copies/ml, CD4 count >350/ml), 9 chronic HIV patients (CH) under anti-retroviral treatment and 6 healthy HIV negative donors (HD). This study was approved by the Huésped Foundation Ethics Committee and informed consent was obtained from all subjects.

first: Rita

last: Reynoso

first: Natalia

last: Laufer

first: Susanna

last: Skalicky

first: Rosella

last: Monteforte

first: Gabriela

last: Turk

first: Mauricio

last: Carobene

first: Jorge

last: Quarleri

first: Pedro

last: Cahn

first: Roland

last: Werner

first: Heribert

last: Stoiber

first: Regina

last: Grillari-Voglauer

first: Johannes

last: Grillari


title: Association of microRNAs with colon tumor metastases

status: Public on Aug 01 2014

city: Bethesda

first: Aaron

last: Schetter

state: MD

address: 37 Convent Drive, Building 37, Room 3050

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary:
We compared the expression of microRNAs in primary colon tumors with their paired liver metastases using the Nanostring human microRNA assays version 1
23 microRNAs were found to be differentially expressed between colon primary tumors and their paired metastases

overall_design: Total mRNA was extracted from flash frozen primary colon tumors and paired metastases. 18 tissues from 9 donors were used for this study.  100 ng of RNA was hybridized to Nanostring Human 0microRNA assays version 1.0.  Data was normalized according to manufacterer's recommendation.  This included background substraction and normalizing to the geometric mean of the highest 75 microRNAs.

first: Curtis

last: Harris


title: Genetic lineage analysis in intramucosal gland-forming gastric neoplasms

city: Otsu

first: Takahisa

last: Nakayama

state: Shiga

address: Seta Tsukinowa-cho

department: Pathology 1

institute: Shiga University of Medical Science

type: Genome variation profiling by genome tiling array

summary: To predict the progression risk of non-invasive gland-forming gastric neoplasms to invasive carcinoma, we assessed lineage continuity or discontinuity between the non-invasive and invasive neoplasms by applying hierarchical clustering analysis to the gene copy-number profiles of individual tumours.

overall_design: array-based Comparative Genomic Hybridization. Samples are including of 7 tumours of Vienna category 3, 12 tumours of Vienna category 4, 8 intramucosal cancers (Vienna category 5), 16 intramucosal lesions and 16 invasive parts (Vienna category 5); 40 reference for control, 19 control replicates

first: Diem

middle: T

last: Vo


title: Expression profile of Arabidopsis thaliana seedlings subjected to hypoxia

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

institute: University of Bayreuth

summary: Arabidopsis thaliana (Col-0) seedlings were grown on vertically oriented agar plates and subjected to hypoxia (0.2% oxygen, 99.8% nitrogen) for 30 to 240 minutes.

overall_design: Five independent samples were analysed: three samples were subjected to hypoxia treatment and two samples were kept at ambient conditions;


title: Detect circulating miRNA Expression change after exposure to hexavalent chromium (an carcinogen) among occuaptional workers

city: Beijing

first: Yang

last: Li

state: Beijing

address: 38 Xueyuan Road, Beijing 100191, China

department: Department of Occupational and Environmental Health Science School of Public Health

institute: Peking University

summary: We profiled plasma miRNA expression in workers exposed to Cr(VI), and assessed genetic damage on chromosome and DNA to compare the sensitivity between epigenetic changes and genetic damage for biomarkers

overall_design: We screened differently expressed plasma miRNAs between high and low Cr(VI) exposed workers using Agilent miRNA microarray. low exposure : <5.49 ng/ml; high exposure >5.49 ng/ml

first: Li

last: Yang

first: Jia

last: Guang


title: S. aureus gene expression of WT (USA300) vs fakAKO

city: Memphis

first: Matthew

middle: Wilmer

last: Frank

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St Jude Children's Research Hospital

summary:
S. aureus response to fakA deletion
Gene expression profiles were generated by microarray analysis of S. aureus WT (USA300) or fakAKO

overall_design: S. aureus was grown in LB to an OD600nm of 0.45, and RNA was extracted to look at the gobal gene expression.

first: Pam

last: Jackson

first: Josh

last: Parsons

first: Charles

middle: O

last: Rock


title: Identification of miRNAs regulated by TGF-b in human CD8+ T cells (expression)

city: Würzburg

first: Anoop

last: Chandran P

address: Josef-schneiderstrasse

institute: University of Würzburg

summary: The goal of the current study was to identify miRNAs regulated by TGF-b in human CD8+ T cells and analyze the function of these miRNAs in shaping the immunomodulatory effect of TGF-b in these cells. We identified the miR-23a cluster to be upregulated and found that this cluster could target key molecules (IFN-g and LAMP1) involved in immune response by CD8+ T cells.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: CD8+ T cells were isolated and purified from healthy human peripheral blood of 5 donors and were activated using beads coupled to anti-CD2, anti-CD3 and anti-CD24. They were then treated with 5ng/ml TGF-b, with 1µM SD-208 or left untreated. RNA from these cells were then isolated and used for generating miRNA microarrays.

last: Chandran

first: Silvia

last: Rüberg

first: Jörg

last: Wischhusen


title: Transcriptomics of the Fetal Hypothalamic Response to Brachiocephalic Occusion and Estradiol Treatment

status: Public on Jul 01 2014

city: GAINESVILLE

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

summary: Estradiol (E2) is a well-known modulator of fetal neuroendocrine activity, and has been proposed as a critical endocrine signal readying the fetus for birth and postnatal life.  To investigate the modulatory role of E2 on fetal stress responsiveness and the response of the fetal brain to asphyxic stress, we subjected chronically catheterized fetal sheep to a transient (10 min) brachiocephalic occlusion or sham occlusion.  Half of the fetuses received subcutaneous pellets that released E2 (5 days@~250 μg/day, increasing plasma E2 from 62±6 to 102±12 pg/mL).  Hypothalamic mRNA was analyzed using the Agilent 8x15k ovine array (019921), processed and annotated as previously reported by our laboratory.  Analysis of the data by ANOVA revealed that E2 differentially regulated (DR) 561 genes, and BCO DR 894 genes compared to control and estradiol+BCO DR 1153 genes compared to BCO alone (all p<0.05).  E2 upregulated epigenetic pathways and downregulated local steroid biosynthesis, but did not significantly involve genes known to directly respond to the estrogen receptor (ie.,  contain ERE sequences).  BCO upregulated kinase pathways as well as genes associated with lymphocyte infiltration into the brain, and downregulated neuropeptide synthesis.  E2 upregulated immune- and apopotosis- related pathways after BCO, and reduced kinase and epigenetic pathway responses to the BCO.  We conclude that array results are consistent with the results of more limited hypotheses previously published from these experiments.

overall_design: Chronically catheterized fetal sheep; 4 groups: control (no treatment); estradiol treatment (250 ug/day x 5 days); brachiocephalic occlusion of fetal sheep (BCO, 10 min, no other treatment); BCO plus estradiol (combination of estradiol treatment and BCO).  All fetuses had blood drawn from chronically implanted catheters at 0, 5, 10, and 30 min after start of BCO or sham-BCO period.  Fetal sheep 124-128 days gestation (term=147 days) at the time of study.  Fetuses euthanized and fetal hypothalami collected for gene array studies 1 hour after first blood sample drawn (and start of BCO or sham-BCO period).

middle: E

first: Maria

last: Rabaglino

first: Elaine

last: Richards

first: Nancy

last: Denslow

first: Miguel

last: Zarate

first: Eileen

middle: I

last: Chang

first: Maureen

last: Keller-Wood


title: Bone Morphogenetic Protein Receptor Antagonists Inhibit Growth and Survival of Lung Cancer Cells Expressing Stem Cell Markers Oct4 or Nestin

status: Public on Jul 30 2014

city: New Brunswick

first: John

last: Langenfeld

state: NJ

address: One Robert Wood Johnson Place

department: Surgery

institute: Rutgers-RWJMS

summary:
H1299 cells were stably transfected with the Oct4 promoter/GFP or Nestin promoter/GFP reporter vectors. By FACS, 106 cells expressing high levels of GFP were isolated and placed into cell culture for twenty-four hours. Total RNA was used.
Bone morphogenetic proteins (BMP) are aberrantly expressed in most lung carcinomas. BMPs mediate cell fate decisions and self-renewal of stem cells. Inhibition of BMP signaling decreases the growth and induces cell death of lung cancer cells lines. It is not known whether the BMP signaling cascade is growth promoting in lung cancer cells expressing the stem cell markers Oct4 and/or nestin. Lung cancer cells expressing Oct4 or nestin were isolated from lung cancer cell lines by stably transfecting the Oct4 promoter or Nestin promoter expression vectors that activate the green fluorescent protein reporter. Our studies support that lung cancer cells activating the Oct4 or nestin promoter are different cell populations. Microarray and quantitative RT-PCR demonstrated that the expression levels of specific stem cell markers were different between the isolated Oct4 and nestin cells. Both the Oct4 and nestin populations were more tumorigenic that controls but histologically they were quite different. The isolated Oct4 and nestin cells also responded differently to inhibition of BMP signaling. Blockade of BMP signaling with the BMP receptor antagonist DMH2 caused significant growth inhibition in both the Oct4 and nestin cell populations but only increased cell death in the nestin population. DMH2 also induced the expression of nestin in the Oct4 population but not in the nestin cells. We also show that BMP signaling is an important regulator of the inhibitor differentiation proteins Id1 and Id3 in Oct4 and nestin cell populations

overall_design: Lung cancer cells expressing Oct4 or nestin were isolated and transfected with Oct4 or Nestin promoter expression vectors that activate the green fluorescent protein reporter. Microarray and quantitative RT-PCR were performed to study the differentially expressed genes. BMPs mediate cell fate decisions and self-renewal of stem cells were investigated.

first: Malik

last: Deen

first: Emmanuel

last: Zachariah


title: Tbx2 and Tbx3 impose nodal phenotype and induce cushion formation in the atrioventricular canal

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

institute: Leiden University Medical Center

summary:
Rationale: A critical step in heart development is the coordinated formation of nodal myocardium and cushion tissue from the atrioventricular canal (AVC). After its specification, the myocardium of the AVC aligns the chambers, forms the AV node, and induces the formation of the mesenchymal AV cushions, primordia of valves and septa, while it resists working myocardial differentiation.

Objective: To assess what roles Tbx2 and Tbx3, two closely related T-box transcription factors expressed in the AVC, play in these processes.

Methods and Results: We analyzed mice ectopically expressing Tbx3 in the atrial myocardium by genome-wide microarray and expression analysis. We found a prominent role for Tbx3 in defining the nodal phenotype by repressing working myocardial genes (sarcomeric, mitochondrial, fast conduction) and cell proliferation regulators, and in inducing node-associated genes. Moreover, there was a striking induction of genes associated with endocardial cushions and mesenchyme. Using gain-of-function models, we found that in the developing heart both Tbx2 and Tbx3 induce ectopic Bmp2 and Tgfb2 expression and endocardial cushion formation. Analysis of compound Tbx2/Tbx3 mutant embryos revealed that upon loss of more than two functional alleles, expansion of the AV myocardium does not occur and AV cushions fail to form.

Conclusions: Tbx2 and Tbx3 locally stimulate development of the AVC myocardium, induce the AV nodal phenotype therein and trigger AV cushion formation from the overlying AV endocardium, providing a mechanism for the colocalization and coordination of these two important processes in heart development.

overall_design:
Nppa-Cre4 (Cre4) mice were crossed with CT mice to obtain efficient activation of Tbx3 in atria of double transgenic Cre4-CT mice, as previously described (Hoogaars et al., 2007). To investigate the gene expression profile of atria of Cre4-CT mice, we performed whole genome microarray analysis using Sentrix Mouse-6 oligonucleotide beadchips.

We compared the atrial gene expression profiles of six male double transgenic Cre4-CT mice and six male Cre4 control mice.

first: Willem

middle: M

last: Hoogaars

first: Danielle

last: Clout

first: Antoon

middle: F

last: Moorman

first: Peter-Bram

last: 't Hoen

first: Vincent

last: Christoffels


title: Expression data of chronic lymphocytic leukemia patient samples from the REACH study

city: South San Francisco

first: Ru-Fang

last: Yeh

address: 1 DNA Way

institute: Genentech

summary:
We assessed genome-wide expression of available pretreatment specimens from CLL patients enrolled in REACH, a study of fludarabine and cyclophosphamide FC or R-FC (addition of rituximab to FC) in relapsed CLL, to understand the disease heterogeneity and explore genes that may be prognostic or predictive of benefit from R-FC treatment. REACH (NCT00090051) was registered at www.clinicaltrials.gov.
This dataset supports the manuscript "PTK2 expression and immunochemotherapy outcome in chronic lymphocytic leukemia" by Weisser et al.

overall_design:
300 available pretreatment specimens from patients enrolled in REACH trial were analyzed.
Additional contributers: REACH study investigators and patients

first: Martin

last: Weisser

first: Guillemette

last: Duchateau-Nguyen

first: Giuseppe

last: Palermo

first: Tri

last: Nguyen

first: Xiaoyan

last: Shi

first: Susanna

middle: Y

last: Stinson

last: Yu

first: Annika

last: Dufour

first: Tadeusz

last: Robak

first: Sergey

last: Moiseev

first: Anna

last: Dmoszynska

first: Philippe

last: Solal-Celigny

first: Boris

middle: V

last: Afanasiev

first: Loree

last: Larratt

first: Viktor

last: Rossiev

first: Isabelle

last: Bence-Bruckler

first: Christian

middle: H

last: Geisler

first: Marco

last: Montillo

last: Valente

first: Michael

middle: K

last: Wenger

first: David

last: Dornan


title: Evolutionary conserved mutations in PhoPR attenuate the virulence of animal-adapted tuberculosis strains for humans

status: Public on Jul 07 2014

city: Paris

first: Alexandre

last: Pawlik

address: 28 rue du Dr. Roux

institute: Institut Pasteur

summary: By genome comparison of 30 MTBC strains, we identified three SNPs affecting the phoPR genes of members of the animal and M. africanum lineages that were not seen in the M. tuberculosis sensu-stricto genomes. The genes phoPR encode a two component regulatory system that is known for its strong impact on virulence and immunogenicity of M. tuberculosis due to its key role in the regulation of genes involved in lipid synthesis and secretion of the 6 kDa secreted antigenic target ESAT-6. To explore whether these SNPs affect the expression of the PhoP regulon, we compared the transcriptome of M. tuberculosis mutants lacking the endogenous phoPR genes (ΔphoPR) and their complemented derivatives expressing either the M. bovis or M. tuberculosis allele of phoPR (phoPR-bovis and phoPR-TB respectively). These comparisons were performed in parallel in two M. tuberculosis strains from distinct genetic backgrounds, i.e. strain GC1237 from lineage 2 (also named East-Asia or Beijing cluster) and the H37Rv reference strain from lineage 4 (also named Euro-American cluster).

overall_design: To perform the transcriptomic comparison of the different M. tuberculosis variants (ΔphoPR, complemented and wt) from the two distinct genetic background, a customized micro-array has been designed then manufactured by Agilent (8 x 15k format). The design of oligonucleotides covering all protein coding sequences was done using OligoArray version 2.1 on the basis of the 3924 predicted coding sequences composing the entire M. tuberculosis H37Rv reference genome. The experimental data for each of the comparison consisted of 4 hybridizations (2 biological replicates with dye-swap); 16 in the end for each genetic background.

first: Jesùs

last: Gonzalo-Asensio

first: Wladimir

last: Malaga

first: Catherine

last: Astarie-Dequeker

first: Charlotte

last: Passemar

first: Flavie

last: Moreau

first: Françoise

last: Laval

first: Mamadou

last: Daffé

first: Carlos

last: Martin

first: Roland

last: Brosch

first: Christophe

last: Guilhot


title: Gene expression of mantle cell lymphoma-initiating cells from primary tumor samples

status: Public on Aug 02 2014

city: Houston

first: Rohit

last: Mathur

state: Texas

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma and Myeloma

institute: M.D. Anderson cancer center

summary: In this study we compared the expression of 30215 genes in mantle cell lymphoma-initiating cells (MCL-ICs) with mantle cell lymphoma-non-initiating cells (MCL-non-ICs) and B-cells from healthy donor

overall_design:
Three samples each of MCL-ICs and MCL-non-ICs were isolated from aphresis of 3 mantle cell lymphoma primary patient samples and 2 samples of CD19+ Bcells isolated from buffy coats of healthy donor
Microarray include both coding and non-coding transcripts but only mRNA coding transcript were included in this study.

first: Samaniego

last: Felipe

first: Mathur

last: Rohit


title: Copy number alteration burden predicts prostate cancer relapse: Agilent 1M aCGH data for human primary prostate cancer samples

status: Public on Jun 30 2014

city: New York

first: Nikolaus

last: Schultz

state: NY

address: 1275 York Ave, Box 460

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

summary: Prostate cancer is the most common malignancy in men.  Yet, the modest benefit of treatment highlights the unmet need for prognostic biomarkers in prostate cancer (1).  Few large prostate oncogenome resources currently exist that combine the molecular and clinical outcome data necessary for prognostic discovery. To determine the extent to which genomic aberrations reflect the risk of prostate cancer-specific outcomes, we profiled more than 100 primary prostate cancers with long-term follow-up for genome-wide copy number alterations (CNA). We also updated the long-term clinical outcome (median 8 years) of an additional independent cohort of 181 primary prostate cancers that we previously profiled for CNA and expression changes (2). Together, we found that CNA burden across the genome, defined as the percent of the tumor genome affected by CNA, is prognostic for recurrence and metastasis in these two cohorts.  This prognostic significance of CNA is independent of Gleason grade, a major existing histopathological prognostic variable in prostate cancer. Moreover, in intermediate-risk Gleason 7 prostate cancers that show a wide range of outcomes, CNA burden is also prognostic for biochemical recurrence, independent of prostate-specific antigen or nomogram score.  CNA burden therefore has the potential to stratify patients by their risk of recurrence in an otherwise intermediate risk subpopulation.  We further demonstrate that CNA burden can be established in diagnostic FFPE needle biopsies using low-input whole genome sequencing. Together, this work highlights the potential of oncogenomics to identify useful and clinically amenable prognostic factors that may inform prostate cancer outcome and treatment.

overall_design: Human prostate samples were profiled on Agilent 1M aCGH arrays per manufacturer's instructions. A pooled reference normal DNA was used as the reference.

first: Haley

last: Hieronymus

first: Barry

middle: S

last: Taylor

first: Charles

middle: L

last: Sawyers


title: Determining the M. smegmatis DosR regulon

status: Public on Jul 10 2014

city: Bronx

first: Michael

last: Berney

address: 1301 Morris Park Avenue

department: Department of Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary: DosR is the regulator of a two-component system in mycobacteria that senses oxygen concentration and the redox state of the cells.

overall_design:
To determine the DosR regulon, the transcriptomes of M. smegmatis mc2155 and the ΔdosR cells were compared by microarray at 10 hours following induction of oxygen-limitation in serum vials.
4 biological replicates  incl. 2 dye swaps. 3 technical replicates per array


title: Time course and dose response analysis of gene expression in BCR or CD40-stimulated DT40 B cell

city: Yokohama

first: Hisaaki

last: Shinohara

address: 1-7-22 Suehiro-cho

institute: RIKEN IMS

summary:
Gene Expression dynamics is important information. To know IKK- or ERK-dependent B cell receptor- or CD40-induced gene expression dynamics,
we performed the time course and dose response analysis in wild type or MEK inhibitor treated or IKKbeta inactive DT40 B cells.

overall_design: Two replicated samples were analysed. Unstimulated cells (T0) were control. WT cells or MEK Inh. (MEK inhibitor;U0126 5mM, 30min pretreated) or IKKbetaSA (S176/181A knock-in) Cells were stimulated with 0.1, 1, 10 µg/ml of anti-IgM (M4) or 1, 3, 6  µg/ml of CD40ligand (CD40L) for 0, 15, 30, 45, 60 or 90min.


title: Serum miRNA profiling by quantitative RT PCR [RT-PCR Array 1]

status: Public on Jun 27 2014

city: Hamamatsu

first: Mahesh

last: Mundalil Vasu

state: Shizuoka

address: 1-20-1 Handayama, Higashi Ward

department: Department of Psychiatry

institute: Hamamatsu University School of Medicine

summary:
Initial screening, the expression of 125 mature miRNA was compared between pooled control and autism samples by two microarray analysis. The differential expression of 14 miRNA was further validated by SYBR green quantitative PCR of Individual samples. Thirteen miRNAs were differetially expressed in autistic individuals compared to the controls (8 upregulated and 5 down regulated).
miR-151a-3p, miR-181b-5p, miR-320a, miR-328, miR-433, miR-489, miR-572, and miR-663a were downregulated, while miR-101-3p, miR-106b-5p, miR-130a-3p, miR-195-5p, and miR-19b-3p were upregulated. We have identified a set of serum miRNAs that could be used as non-invasive biomarkers for autism.

overall_design: RNA from age- and gender- matched control (n=40) and autism (n=40) serum samples were pooled separately to generate four pools per group, with each pool consisting of 10 samples. miRNAs were detected and quantified using SYBR Green real-time quantitative PCR performed on ABI PRISM 7900 Sequence Detection System (SDS) [Applied Biosystems (ABI), Foster City, CA, USA]. This observed an altered expression of 14 miRNAs in the autism samples compared to that of healthy controls.


title: Expression data from Thermus thermophilus HB8 wild type and TTHA1559 disrupted

status: Public on Aug 03 2014

city: Bunkyo-ku, Tokyo

first: Naoki

last: IWANAGA

address: 1-1, Yayoi

institute: The university of Tokyo

summary: We observed the expression profile of the total mRNA of wild-type and TTHA1559 disrupted Thermus thermophilus HB8 strain at 70°C.

overall_design: Wild-type and TTHA1559 disrupted T. thermophilus HB8 strains were pre-cultured at 70°C in 10 ml of synthetic medium. The cells (0.1 ml) were inoculated into 10 ml of the same medium and then cultivated at 70°C. Cells were collected after 5h, and then crude RNA was extracted. The expression of each mRNA was analyzed on a GeneChip.

first: Kaori

last: IDE

first: Makoto

last: NISHIYAMA


title: Differential Expression of Stress and Immune Response Pathway Transcripts and miRNAs in Normal Human Endothelial Cells Subjected to Fractionated or Single-Dose Radiation [miRNA]

city: Northbrook

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

summary: While modern radiotherapy technologies can precisely deliver higher doses of radiation to tumors; thus, reducing overall radiation exposure to normal tissues, moderate dose and normal tissue toxicity still remains a significant limitation. The present study profiled the global effects on transcript and miR expression in Human Coronary Artery Endothelial Cells (HCAECs) using single-dose irradiation (SD, 10Gy) or multi-fractionated irradiation (MF, 2Gy x 5) regimens. Longitudinal timepoints were collected after a SD or final dose of MF irradiation for analysis using Agilent Human Gene Expression and miRNA microarray platforms. Compared to SD, the exposure to MF resulted in robust transcript and miR expression changes in terms of the number and magnitude. For data analysis, statistically significant mRNAs (2-fold) and miRs (1.5-fold) were processed by Ingenuity Pathway Analysis (IPA) to uncover miRs associated with target transcripts from several cellular pathways post-irradiation. Interestingly, MF radiation induced a cohort of mRNAs and miRs that coordinate the induction of immune response pathway under tight regulation. Additionally, mRNAs and miRs associated with DNA replication, recombination and repair, apoptosis, cardiovascular events and angiogenesis were revealed.

overall_design: Human Coronary Artery Endothelial Cells (HCAECs) were irradiated in a PANTAK high frequency X-ray generator (Precision X-ray Inc., N. Bedford, CT), operated at 300kV and 10MA. The dose rate was 1.6 Gy per min. Cells were plated into T75cm2 flasks (1-1.5 x 10^6 for single dose radiation and 0.6-0.8 x 10^6 for fractionated radiation). After 24h, cells were exposed to a total of 10 Gy radiation administered either as a single-dose radiation (SD), or as multi-fractionated radiation of 2 Gy x 5 (MF). These non-isoeffective doses were selected to simulate clinical hypofractionated and conventionally fractionated radiotherapy regimens. For the MF protocol, cells were exposed to 2 Gy radiation twice a day, at 6h interval. The cells were approximately 90% confluent at the time of harvesting. For both protocols, radiation-induced changes were analyzed at 6h and 24h after a SD and 6h and 24h after the final dose of fractionated irradiation. Separate controls were maintained for SD and MF radiation protocols.

first: Sanjeewani

last: Palayoor

first: Molykutty

last: John-Aryankalayil

first: Adeola

last: Makinde

first: Scott

last: Magnuson

first: C

middle: N

last: Coleman


title: Genome-wide microarray analysis of Atlantic cod (Gadus morhua) oocyte and embryo

status: Public on Jun 12 2014

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Microarray analyses  were performed to assess temporal profiles of maternal and zygotic transcripts and their developmental roles. Results revealed the presence of multiple transcripts involved in patterning and development of tissues and organs long before activation of the zygotic genome. The switch from maternal to zygotic developmental programs is associated with large-scale modification of chromosomes.

overall_design: Analyses included unfertilized and newly fertilized oocytes, mid blastulas and embryos at different stages of segmentation. Pooled organs of adult cod were used as common reference.

first: Krasnov

last: Aleksei

first: Skugor

last: Adrijana


title: Transcript profiling in Paoenia ostii during chilling induced endo-dormancy release

city: Qingdao

first: Shu-Peng

last: Gai

state: Shandong Province

address: Changcheng Road 700

department: College of Life Science

institute: Qingdao Agricultural University

summary: To better understanding the genetic and physiological changes behind the dormancy process in tree peony, we performed customized cDNA microarray to investigate gene expression profiling in tree peony ‘Feng Dan Bai’ buds during chilling induced dormancy release. Endo-dormant tree peony plants were exposed to 0-4°C from 5 November to 30 December 2009 in Qingdao, Shandong, China. Buds were collected after 0 d, 6 d, 12 d, 15 d, 18 d and 24 d chilling endured. DNA microarrays were customized using Agilent eArray 5.0 program, containing spots with 14,957 gene-specific 60-mer oligonucleotides representing 14,957 non abundant ESTs obtained from 454 sequencing normalized cDNA of tree peony buds during chilling duration (TSA, 65,217). Total 3,174 significantly differentially-expressed genes (P<0.05) were observed through endo-dormancy release, and the number of up-regulated (1,611) and that of down-regulated (1,563) was almost same. Expression of differentially-expressed genes associated with GA biosynthesis and signaling, cell growth and development was confirmed by quantitative RT-PCR, which displayed similar trends pattern in expression.

overall_design: Transcript profiling of tree peony was measured during chilling (0-4°C) induced dormancy release. Mixed buds, three buds for each individual, were collected after 0, 6, 12, 15, 18 (endo-dormancy release), 24 days (eco-dormancy) chilling requirement fulfilling. Three replications (3 plants/ replication) were harvested between November and December.

first: Shupeng

first: Yuxi

last: Zhang

first: Guosheng

last: Zheng


title: Dehydration-induced endodormancy in crown buds of leafy spurge highlights roles for an RVE1-like homolog and hormone signaling cross-talk

status: Public on May 31 2014

city: Fargo

first: Munevver

last: Dogramaci

state: ND

address: 1605 Albrecht Blvd N

institute: USDA-ARS

summary: New shoot growth from underground adventitious buds of leafy spurge is critical for survival of this invasive perennial weed after episodes of severe abiotic stress. Because global climate change is expected to increase abiotic stress, such as dehydration, objectives of this study include examining the impact that dehydration stress has on molecular mechanisms associated with vegetative reproduction. Greenhouse plants were exposed to mild- (3-day), intermediate- (7-day), severe- (14-day) and extended- (21-day) dehydration treatments, prior to decapitation of aerial tissue and rehydration of soil to induce new vegetative shoot growth. Compared to well-watered control plants, mild-dehydration accelerated new vegetative shoot growth but intermediate- and severe-dehydration treatments both delayed and reduced shoot growth, and 21-day dehydration treatment inhibited initiation of new vegetative shoots and was considered a lethal treatment. Overall, transcriptome profiles revealed that 2109 genes were differentially-expressed (P<0.05) in crown buds in response to the various dehydration treatments. Sub-network enrichment analyses identified central hubs of over-represented genes involved in processes such as hormone responses and signaling (e.g., ABA, auxin, ethylene, GA, and JA), response to abiotic stress (DREB1A/2A) and light (PIF3), phosphorylation (CLV1, MPK3/4/6, SOS2), gene silencing (miRNA156/172a), circadian regulation (CRY2, LHY, PHYA/B), and flowering (AGL8/20, AP2, FLC).  Further, results from this and previous studies highlight HY5, MAF3, MYB-like/RVE1 and RD22 as molecular markers for endodormancy in crown buds of leafy spurge. Early response to dehydration also highlighted involvement of upstream ethylene and jasmonate signaling, whereas longer-term dehydration impacted ABA signaling. The identification of conserved ABRE- and MYC-consensus, cis-acting elements in the promoter of a leafy spurge gene similar to Arabidopsis MYB-like/RVE1 (AT5G17300) implicates a potential role for ABA signaling in its dehydration-induced expression. Response of these molecular mechanisms to dehydration-stress provides insights on the ability of invasive perennial weeds to adapt and survive under harsh environments, which provide new insights for addressing future management practices.

platform_organism:
Manihot esculenta
Euphorbia esula

overall_design: Changes in transcript abundance for underground adventitious buds of leafy spurge which were exposed various levels of dehydration stress  (Day-3, -7, -14, -16, -21) are analysed relative to controls (Day-0).


title: PhyloChip-based characterization of wastewater reactors

status: Public on Jun 06 2014

city: Berkeley

first: Yvette

last: Piceno

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

institute: LBNL

summary: We developed a laboratory-scale model to improve our understanding and capacity to assess the biological risks of genetically engineered bacteria and their genetic elements in the natural environment.  Our hypothetical scenario concerns an industrial bioreactor failure resulting in the introduction of genetically engineered bacteria to a downstream municipal wastewater treatment plant (MWWTP). As the first step towards developing a model for this scenario, we sampled microbial communities from the aeration basin of a MWWTP at three seasonal time points. Having established a baseline for community composition, we investigated how the community changed when propagated in the laboratory, including cell culture media conditions that could provide selective pressure in future studies. Specifically, using PhyloChip 16S rRNA gene-targeting microarrays, we compared the compositions of sampled communities to those of inoculates propagated in the laboratory in simulated wastewater conditionally amended with various carbon sources (glucose, chloroacetate, D-threonine) or the ionic liquid 1-ethyl-3-methylimidazolium chloride ([C2mim]Cl). Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in aeration basin and laboratory-cultured populations. Laboratory-cultured populations were enriched in Gammaproteobacteria. Enterobacteriaceae and Aeromonadaceae were enriched by glucose, Pseudomonadaceae by chloroacetate and D-threonine, and Burkholderiaceae by high (50 mM) concentrations of chloroacetate. Microbial populations cultured with chloroacetate and D-threonine were more similar to sampled populations than thoes cultured with glucose or [C2mim]Cl. Although observed relative richness in operational taxonomic units was lower for laboratory cultures than for sampled populations, both flask and reactor systems cultured phylogenetically diverse communities. These results importantly provide a foundation for laboratory models of industrial bioreactor failure scenarios.

overall_design: 46 samples, flask and reactor experiments were conducted in triplicate with two exceptions: [C2mim]Cl_flask and No-Carbon_flask treatments had only one sample (no replicates).

first: Sangwon

last: Lee

first: Jil

last: Geller

first: Tamas

last: Torok

first: Cindy

last: Wu

first: Mary

last: Singer

first: Francine

middle: C

last: Reid

first: Daniel

last: Tarjan

first: Terry

last: Hazen

first: Adam

middle: P

last: Arkin

first: Nathan

middle: J

last: Hillson


title: Characterization of the miRNA Landscape in an Inner Medullary Collecting Duct Cell Line

city: Palo Altp

first: Mollie

middle: Elizabeth

last: Jacobs

address: 3801 Miranda AVE

department: Medicine

institute: Stanford University

summary: The affect of aldosterone on the miRNA landscape in mIMCD-3 cells was determined

overall_design: In the study presented here, the affect of aldosterone was examined on the miRNA content in a murine inner medullary collecting duct cell line


title: Loss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons [fibroblasts]

status: Public on Jun 01 2014

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary:
Aims: Loss of nuclear TDP-43 characterises sporadic and most familial forms of amyotrophic lateral sclerosis (ALS). TDP-43 (encoded by TARDBP) has multiple roles in RNA processing. We aimed to determine whether 1) RNA splicing dysregulation is present in lower motor neurons in ALS and in a motor neuron-like cell model, and 2) TARDBP mutations (mtTARDBP) are associated with aberrant RNA splicing using patient-derived fibroblasts.
Methods: Affymetrix exon arrays were used to study mRNA expression and splicing in lower motor neurons obtained by laser capture microdissection of autopsy tissue from individuals with sporadic ALS and TDP-43 proteinopathy. Findings were confirmed by qRT-PCR and in NSC34 motor neuronal cells following shRNA-mediated TDP-43 depletion. Exon arrays and immunohistochemistry were used to study mRNA splicing and TDP-43 expression in fibroblasts from patients with mtTARDBP-associated, sporadic and mutant SOD1-associated ALS.
Results: We found altered expression of spliceosome components in motor neurons and widespread aberrations of mRNA splicing that specifically affected genes involved in ribonucleotide binding. This was confirmed in TDP-43 depleted NSC34 cells. Fibroblasts with mtTARDBP showed loss of nuclear TDP-43 protein and demonstrated similar changes in splicing and gene expression, that were not present in fibroblasts from patients with sporadic or SOD1-related ALS.
Conclusion: Loss of nuclear TDP-43 is associated with RNA processing abnormalities in ALS motor neurons, patient-derived cells with mtTARDBP, and following artificial TDP-43 depletion, suggesting that splicing dysregulation directly contributes to disease pathogenesis. Key functional pathways affected include those central to RNA metabolism.

overall_design: RNA was extracted from fibroblasts grown from neurologically healthy controls (n=6) and 3 groups of patients with ALS:  1) sporadic cases (n=6); 2) cases due to mutations of SOD1 (n=4); 3) cases due to mutations of TARDBP (n=3).  The three ALS groups were compared to the controls.

first: J

middle: R

last: Highley

first: Channa

middle: A

last: Hewamadduma

first: Joeri

last: Jansweijer

first: Janine

last: Kirby

first: Alfredo

last: Kalaitzis

first: Adrian

last: Higginbottom

first: Rohini

last: Raman

first: Laura

last: Ferraiuolo

first: Scott

last: Allen

first: Christopher

last: McDermott

first: Neil

last: Lawrence

first: Jonathan

last: Cooper-Knock

first: Marta

last: Milo

first: Stuart

last: Wilson

middle: G

last: Ince

first: Pamela

last: Shaw


title: Jagged1 regulates miRNA expression profile

status: Public on May 30 2014

city: Buffalo

first: AC

last: CHANG

address: Elm and Carlton

institute: RPCI

summary: miRNA expression profiles of HMECs treated with 40mM Jagged1 (JAG1) or the control peptide for 1 day

overall_design: Genome-wide miRNA PCR array analysis was performed using human miRNA PCR arrays (MIHS216Z, SABiosceinces) acccording to the manufacturer's instructions

first: Chun-Ju

last: Chang


title: Transcriptome profiling of Pinus radiata branches reveals new insights into compression wood formation in response to gravity stress

city: Canberra

first: Xinguo

last: Li

state: ACT

address: Building 602, Black Mountain Laboratories

department: Plant Industry

country: Australia

institute: CSIRO

summary: Compression (CW) and opposite wood (OW) are formed in the uniderside and upperside of conifer branches respectively in response to gravity stress. We investigated genes differentially transcribed between the underside and upside of radiate pine branches using cDNA microarrays with a view to plant gravitropism.

overall_design: Six trees with well-developed branches were selected from a radiata pine commercial plantation (aged 13 years) located at Bondo, NSW, Australia (35º 16' 44.04 S, 148º 26' 54.66 E). The largest branch from each tree was further selected for sampling, including three branches sampled in April 2007 (autumn in Bondo) and three sampled in October 2007 (spring). Bark was removed from the base part (about 10 cm in length) of each branch. Developing xylem tissues were scraped from the exposed upperside and underside surface respectively with a sharp chisel. Samples were immediately placed into 50 ml BD FalconTM tubes filled with liquid nitrogen. Gene expression in the underside and upperside of branches was compared using radiata pine cDNA microarrays.

first: Harry

middle: X

last: Wu


title: Metabolism of sialic acid by Bifidobacterium breve UCC2003

status: Public on May 29 2014

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: Bifidobacteria constitute a specific group of commensal bacteria which inhabit the gastrointestinal tract of humans and other mammals. Bifidobacterium breve UCC2003 has previously been shown to utilise several plant-derived carbohydrates that include cellodextrins, starch and galactan. In the current study, we investigate the ability of this strain to utilise the mucin- and human milk oligosaccharide (HMO)-derived carbohydrate, sialic acid. Using a combination of transcriptomic and functional genomic approaches, we identified a gene cluster dedicated to the uptake and metabolism of sialic acid. Furthermore, we demonstrate that B. breve UCC2003 can cross feed on sialic acid derived from the metabolism of 3’ sialyllactose, a HMO, by Bifidobacterium bifidum PRL2010.

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

first: Muireann

last: Egan


title: SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

city: Ulm

first: Julia

last: Vogt

address: Albert-Einstein Allee 11

department: Institute of Human Genetics

institute: Ulm University

summary: Array CGH analysis in order to determine the size of atypical NF1 deletions under investigation

overall_design: 12 atypical NF1 deletions were investigated with the custom array CGH

first: Hildegard

last: Kehrer-Sawatzki