title: Identification of new therapeutic targets by genome-wide analysis of gene expression in the ipsilateral cortex of aged rats after stroke

status: Public on Apr 22 2014

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

country: Germany

institute: University Hospital Würzburg

summary:
Because most human stroke victims are elderly, studies of experimental stroke in the aged rather than the young rat model may be optimal for identifying clinically relevant cellular responses, as well for pinpointing beneficial interventions.
We employed the Affymetrix platform to analyze the whole-gene transcriptome following temporary ligation of the middle cerebral artery in aged and young rats.

overall_design: Expression profiling of periinfarcted brain areas of young and aged rats, as well as healthy tissue from naive animals.

first: Ana

middle: M

last: Buga

middle: J

first: Aurel

last: Popa-Wagner


title: Cumulus High Vs. Low Potential

status: Public on Apr 30 2014

city: Québec

first: Audrey

last: BUNEL

state: Québec

address: 2425, Rue de l'agriculture

department: Sciences Animales

country: Canada

institute: Université Laval

summary: Differences between high- and low-potential COCs were examined by transcriptomic analysis of CC biopsies obtained from COCs of 2-6mm follicles from slaughterhouse ovaries before individual in vitro maturation, fertilization and culture until day 8 post-fertilization. Each COC was individually tracked and categorized based on his fate: embryo at blastocyst stage (CC-Blast) or embryo arrested at 2- to 8-cell stage (CC-2-8-cells). Average blastocyst rates were 27.7% for individual culture, and 31.2% for group control (not significantly different). Five cumulus biopsies per replicate were pooled for each fate. Three CC replicates underwent transcriptomic analysis using RNA microarray assay.

overall_design: Each cumulus cell sample is composed of 5 COC biopsies, 3 samples or biological replicates for each fate (CC-blast or CC-2-8-cells) were analysed by microarray. CC-2-8-cells condition was used as reference.

first: A

last: Bunel

first: E

middle: P

last: Jorssen

last: Merckx

first: J

middle: L

last: Leroy

first: P

middle: E

last: Bols

first: M

last: Sirard


title: miRNA in adult T-cell leukemia/lymphoma

status: Public on Apr 12 2014

city: Padova

first: Alberto

last: Corradin

state: PD

address: via Tiepolo

department: Dipertimento di Ingegneria dell'Informazione

country: Italy

institute: Università degli Studi di Padova

summary: miRNA expression was investigated in ATLL samples and in normal CD4 T-cells (resting and in vitro-stimulated).

overall_design: Total RNA was isolated from ATLL samples and normal T-cell controls. miRNA expression was measured using Agilent miRNA arrays.

first: Katia

last: Ruggero

first: Marta

last: Biasiolo

first: Stefania

last: Bortoluzzi

first: Cynthia

middle: A

last: Pise-Masison

first: Vincenzo

last: Ciminale

first: Donna

last: D'Agostino


title: Effects of dietary obesity in fathers on gene expression of fat in the female offspring

city: Wallace Wurth Building, Sydney

first: Margaret

last: Morris

state: NSW

address: University of New South Wales

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

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

overall_design: Refer to individual Series


title: Intestine-adapted bacterial symbiont response to polysaccharide rich and polysaccharide deficient diets in mice lacking fucosyltransferase-2

status: Public on Apr 21 2014

city: Stanford

first: Angela

last: Marcobal

state: California

address: 299 Campus Drive

department: Microbiology and Immunology

country: USA

institute: Stanford University

summary: Analysis of Bacteroides thetaiotaomicron (BT) from the ceca of ex-germ free Fut2+ or Fut2- mice on polysaccharide rich or glucose rich polysaccharide deficient diet. BT is involved in the breakdown of plant polysaccharides and is also efficiently utilizes host glycans. BT-colonized mice represent a human gut ecosystem model. Results identify genes that may endow flexibility in adapting to dietary changes by mucosal foraging depending on host fucosylation status

platform_organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum

overall_design: In vitro transcriptional profiles of Bacteroides thetaiotaomicron obtained from ceca of ex-germ free Fut2+ or Fut2- mice on polysaccharide rich or glucose rich polysaccharide deficient diet.

first: Purna

last: Kashyap

first: Justin

last: Sonnenburg


title: Identification of Sleep Regulatory Genes in Flies Mutant for the Clock Gene cycle

status: Public on Apr 15 2014

city: St Louis

first: Paul

last: Shaw

state: MO

address: 660 S Euclid

department: Anatomy

institute: Washington University School of Medicine

summary:
Extended periods of waking result in physiological impairments in humans, rats, and flies. Sleep homeostasis, the increase in sleep observed following sleep loss, is believed to counter the negative effects of prolonged waking by restoring vital biological processes that are degraded during sleep deprivation. Sleep homeostasis, as with other behaviors, is influenced by both genes and environment. We report here that during periods of starvation, flies remain spontaneously awake but, in contrast to sleep deprivation, do not accrue any of the negative consequences of prolonged waking. Specifically, the homeostatic response and learning impairments that are a characteristic of sleep loss are not observed following prolonged waking induced by starvation. To identify the genes responsible for the protective effects of starvation we conducted transcription profiling of sleep deprived flies that accrue sleep debt compared to starved siblings that do not.
Genes involved in lipid metabolism were highly enriched in our dataset of 84 differentially regulated transcripts. Follow up genetic studies established that 6 genes involved in lipid metabolism strongly influence sleep homeostasis. Two of these genes, brummer (bmm) and Lipid storage droplet 2 (Lsd2), are in the same lipolysis pathway but exert antagonistic effects on lipid storage.  bmm mutant flies have excess fat stores and display a large homeostatic response following sleep deprivation.  In contrast, Lsd2 mutant flies, which phenocopy aspects of starvation as measured by low triglyceride stores, do not exhibit a homeostatic response following sleep loss.  Importantly, Lsd2 mutant flies are not learning impaired after sleep deprivation.  These results provide the first genetic evidence, to our knowledge, that lipid metabolism plays an important role in regulating the homeostatic response and can protect against neuronal impairments induced by prolonged waking.

overall_design: Two-condition experiments: sleep deprived vs starved.  RNA from 8 biological replicates for each condition was pooled in groups of 2 to create 4 samples.  Each of the 4 samples is run in duplicate with untreated circadian matched controls.

first: Matthew

last: Thimgan


title: Gene expression profile analysis of human keratinocyte HaCaT cells treated with obacunone

status: Public on Apr 29 2014

city: Seoul

first: Jong Min

last: Kim

address: 209, Neungdong-ro, Gwangjin-gu

department: Bioscience and Biotechnology

country: South Korea

institute: Sejong University

summary: Obacunone treatment upregulates gene expression of cholesterol and lipid metabolism-associated genes in HaCaT cells

overall_design: Total RNA obtained from HaCaT cells treated with 10, 50, or 100 uM obacunoe for 4 h was compared to that of vehicle control cells.

first: Jong

middle: G

last: Lee


title: Dietary flaxseed- and radiation-sensitive microRNAs in murine lung

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: MD

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: Murine lung miRNAs were profiled by rodent TaqMan OpenArray after flaxseed feeding and/or radiation exposure

overall_design: Lung tissue was obtained 48 hours after radiation or no exposure from three animals each: flaxseed/no radiation, flaxseed/radiation, control diet/no radiation, control diet/radiation. miRNA profiles were determined by OpenArray.

first: Melpo

last: Christofidou-Solomidou

first: Melissa

last: McAlexander

first: Ralph

last: Pietrofesa

first: Evguenia

last: Arguiri


title: Ctk1 + CTD mutants

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

summary: Transcription termination in Saccharomyces cerevisiae can be performed by at least two distinct pathways and is directed by the phosphorylation status of the carboxy-terminal domain (CTD) of RNA polymerase II (Pol II). Late termination of mRNAs is performed by the CPF/CF complex and requires CTD-Ser2 phosphorylation. Early termination of shorter cryptic unstable transcripts (CUTs) and small nucleolar RNAs (snoRNAs) is preformed by the Nrd1 complex, and requires CTD-Ser5 phosphorylation. In this study, mutants of the different termination pathways were compared by genome-wide expression analysis. Surprisingly, the expression changes observed upon loss of the CTD-Ser2 kinase Ctk1 are more similar to loss of a subunit of the Ser5P binding Nrd1-complex, than to loss of Ser2P binding factors. Tiling array analysis of ctk1Δ reveals readthrough at several hundred sites, including snoRNAs, as reported previously, but also many cryptic unstable transcripts, stable untranslated transcripts (SUTs) and other transcripts. Surprisingly, neither loss of CTK1 nor a Pol II CTD-Ser2 substitution mutant results in a global defect in termination of mRNAs, indicating that Ser2P is not essential for proper termination of most mRNAs. At snoRNA, Nrd1 location is shifted downstream in ctk1∆, indicating defective release rather than recruitment of Nrd1. Weakening the interaction between Nrd1 and Pol II rescues the readthrough in ctk1∆, likely by facilitating Nrd1 release. The termination defect is kinase activity dependent, but cannot be completely explained by loss of CTD-Ser2 phosphorylation , a major substrate of Ctk1, suggesting the involvement of an additional substrate. Mutant alleles of the elongation factor Spt5 rescue ctk1∆-dependent readthrough, indicating a role for Spt5 in this process, perhaps as a substrate of Ctk1. The results show that Ctk1 is more intimately involved in termination of small non-coding RNAs than was previously assumed and lead to a model in which Ctk1 influences Spt5 activity to achieve this.

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

first: Tineke

last: Lenstra

first: Agnieszka

last: Tudek

first: Domenico

last: Libri

first: Frank

last: Holstege


title: DksA Guards Elongating RNA Polymerase Against Ribosome-Stalling-Induced Arrest

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 600 16th Street

institute: UC San Francisco

type: Genome binding/occupancy profiling by genome tiling array

summary: In bacteria, translation-transcription coupling inhibits RNA polymerase (RNAP) stalling. We present evidence suggesting that, upon amino acid starvation, inactive ribosomes promote rather than inhibit RNAP stalling. We developed an algorithm to evaluate genome-wide polymerase progression independently of local noise, and used it to reveal that the transcription factor DksA inhibits promoter-proximal pausing and increases RNAP elongation when uncoupled from translation by depletion of charged tRNAs. DksA has minimal effect on RNAP elongation in vitro and on untranslated RNAs in vivo. In these cases, transcripts can form RNA structures that prevent backtracking. Thus, the effect of DksA on transcript elongation may occur primarily upon ribosome slowing/stalling or at promoter-proximal locations that limit the potential for RNA structure. We propose that inactive ribosomes prevent formation of backtrackblocking mRNA structures and that, in this circumstance, DksA acts as a transcription elongation factor in vivo.

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

overall_design: Chromatin immunoprecipitation (ChIP) experiments were performed by using antibodies against RNA polymerase b subunit in wild-type and DdksA cells treated with 0.5mg/ml serine hydroxamate (SHX) or untreated. DksA and s70 enrichments were compared to RNAP enrichment by ChIP experiments using antibodies against s70 and DksA in wild-type cells (also in DdksA cells as a negative control for DksA ChIP-chip). Differentially labeled ChIP DNA and genomic DNA were competitively hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~12bp spacing across the entire genome. The series contains 19 datasets.

first: Rachel

last: Mooney

first: Jeffrey

last: Grass

first: Priya

last: Sivaramakrishnan

first: Christophe

last: Herman

first: Robert

last: Landick

first: Jue

middle: D

last: Wang


title: Murine bone marrow cells: Wild-type vs. PU.1 knockdown

status: Public on Apr 24 2014

city: Heidelberg

first: Miriam

last: Sonnet

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

type: Methylation profiling by genome tiling array

summary: Genome-wide screen for aberrant DNA methylation in bone marrow of PU.1 knockdown mice compared to control wildtype animals in three stages

overall_design: 7 age and gender matched mice pairs in the preleukemic stage, 5 pairs in the early leukemic stage and 7 pairs in the late leukemic stage

first: Rainer

last: Claus


title: High-throughput sequencing of small RNAs in Petunia

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

institute: University of Udine

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Petunia x hybrida tissues (including leaves and flowers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

overall_design: Small RNA libraries were derived from leaves and flowers (see Series GSE13764) of Petunia x hybrida. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank  Ana Dorantes-Acosta and Richard A. Jorgensen for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

first: Monica

last: Accerbi

first: Pamela

last: Green

first: Blake

middle: C

last: Meyers


title: Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation [Affymetrix]

status: Public on Apr 20 2014

city: Boston

first: David

last: Weinstock

state: MA

address: 450 Brookline Ave

institute: DFCI

summary: Children with Down syndrome (DS) have a 20-fold increased risk of developing B cell acute lymphoblastic leukemia (B-ALL). Polysomy 21 (i.e., extra copies of chr.21) is also the most frequent somatic aneuploidy among all B-ALLs. Additional B-ALLs harbor intrachromosomal amplifications of chr.21q22 (iAMP21). Yet, the mechanistic links between chr.21q22 triplication and B-ALL remain undefined. Here we show that germline triplication of only 31 genes orthologous to human chr.21q22 is sufficient to confer murine B cell self-renewal in vitro, B cell maturation defects in vivo, and B-ALL in concert with either BCR-ABL or CRLF2 with activated JAK2. Chr.21q22 triplication suppresses H3K27me3 in murine progenitor B cells and B-ALLs, and “bivalent” genes with both H3K27me3 and H3K4me3 at their promoters in wild-type progenitor B cells are preferentially overexpressed in triplicated cells. Strikingly, human B-ALLs with polysomy 21 are distinguished by their overexpression of genes known to be marked with H3K27me3 in multiple cell types. Finally, overexpression of HMGN1, a nucleosome remodeling protein encoded on chr.21q22, suppresses H3K27me3 and promotes both B cell proliferation in vitro and B-ALL in vivo. These data implicate HMGN1 overexpression and loss of H3K27me3 in progenitor B cell transformation and suggest strategies to target leukemias with polysomy 21.

overall_design: Gene expression analysis of 8 samples, 4 wild-type and 4 HMGN1 overexpressing transgenic B cells

first: Andrew

last: Lane


title: BCLAF1 Chip-chip control (siGFP) and BRCA1 depleted (siBRCA1) 293T cells in the absense or presense of Etoposide

status: Public on Apr 25 2014

city: Belfast

first: Kienan

last: Savage

address: 97 Lisburn Rd

department: Centre for Cancer Research and Cell Biology

country: United Kingdom

institute: Queen's University Belfast

summary: BCLAF1 is a serine-arginine (SR) protein implicated in transcriptional regulation and mRNA splicing.  We have recently identified BCLAF1 as part of a novel mRNA splicing complex that is recruited to different genetic promoters by the breast cancer susceptiblity protein, BRCA1 in response to DNA damage. This ChIP-chip study was designed to identify genes/promoters regulated by the BRCA1/BCLAG1 mRNA splicing complex by identifying promoters bound by BCLAF1 in the absense and presense of BRCA1 in control cells and cells treated with etoposide to induce DNA damage.  This study includes tripicate BCLAF1 ChIP-chip experiments in untreated and etoposide treated (1uM 16 hours) control cells (siGFP) and cells depleted of BRCA1 (siBRCA1).

overall_design: Chromatin Immunoprecipitaitons were performed in triplicate with BCLAF1 antibodies in control 293T cells transfected with siGFP siRNAs and BRCA1 siRNAs (siBRCA1 to deplete BRCA1).  Immunoprecipitated genomic DNA was labelled with Cy3 and Input genomic DNA was labelled with Cy5 and hybridized to NimbleGen human 3x720k RefSeq promoter arrays to identify BCLAF1 boundgenomic DNA regions.

middle: I

first: D

last: Harkin


title: Open lung approach with low tidal volume mechanical ventilation attenuates lung injury in rats with massive brain damage

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary:
Introduction: The ideal ventilation strategy for patients with massive brain damage requires better elucidation. We hypothesized that in the presence of massive brain injury, a ventilation strategy using low (6 mL/kg) tidal volume (VT) ventilation with open lung positive end-expiratory pressure set according to the minimal static elastance of the respiratory system (LVT/OLPEEP), attenuate the impact of massive brain damage on gas-exchange, respiratory mechanics, lung histology and whole genome alterations compared with high (12 mL/kg) VT and low PEEP ventilation (HVT/LPEEP).

Methods: Twenty-eight adult male Wistar rats were randomly assigned to one of four groups: 1) no brain damage (NBD) with LVT/OLPEEP; 2) NBD with HVT/LPEEP; 3) brain damage (BD) with LVT/OLPEEP; and 4) BD with HVT/LPEEP. All animals were mechanically ventilated for six hours. Brain damage was induced by an inflated balloon catheter into the epidural space. Hemodynamics was recorded and blood gas analysis was performed hourly. At the end of the experiment, respiratory system mechanics and lung histology were analysed. Whole genome analysis was performed using Affimetrix gene chips and confirmatory real-time PCR.

Results: In NBD, both LVT/OLPEEP and HVT/LPEEP did not affect arterial blood gases, as well as whole genome expression changes and real-time PCR. In BD, LVT/OLPEEP, compared to HVT/LPEEP, reduced lung damage according to histology, genome analysis and real-time PCR with decreased interleukin (IL-6), cytokine-induced neutrophil chemoattractant (CINC)-1 and angiopoietin-4 expressions. LVT/OLPEEP compared to HVT/LPEEP improved overall survival.

Conclusions: In BD, LVT/OLPEEP minimizes lung morpho-functional changes and inflammation compared to HVT/LPEEP.  LVT/OLPEEP might represent a suitable ventilatory strategy in massive brain damage.

overall_design:
24 Wistar rats -  lung samples, 4 groups,
1. non-braindamaged/braindead high tidal volume ventilation,
2. non-braindamaged/braindead best PEEP ventilation,
3. Braindamaged/braindead high tidal volume ventilation,
4. Braindamaged/braindead  best PEEP ventilation

first: Joerg

last: Krebs

first: Charalambos

last: Tsagogiorgas

first: Paolo

last: Pelosi

first: Patricia

middle: R

last: Rocco

first: Maximilia

last: Hottenrott

first: Benito

last: Yard

first: Thomas

last: Luecke


title: Prospective molecular profiling of canine cancers provides a clinically relevant comparative model for evaluating precision medicine (PMed) trials

status: Public on Apr 28 2014

city: Grand Rapids

last: Cherba

state: MI

address: 333 Bostwick Ave

department: Bioinformatics and Biostatistic Core

institute: Van Andel Institute

summary: Feasibility trial to examine the ability to conduct molecular guided therapy in a geographically distributed systems within strict time constraints

overall_design: Canine patients were enrolled across a broad panel of tumor types where tumor samples were acquired and processed to preserve RNA quality for genomic analysis at distributed locations to predict possible effective therapies.  Genomic driven therapy suggestion derived using a collection of algorithms based on tumor expression levels.

first: Melissa

last: Paoloni

first: Craig

last: Webb

first: Christina

last: Mazcko

first: Susan

last: Lana

last: Ehrhart

first: Brad

last: Charles

first: Heather

last: Fehling

first: Leena

last: Kumar

last: Vail

first: Michael

last: Henson

last: Childress

first: Barbara

last: Kitchell

first: Christopher

last: Kingsley

first: Seungchan

last: Kim

first: Mark

last: Neff

last: Davis

first: Chand

first: Jeffrey

last: Trent


title: Differential gene expression in Xylella fastidiosa 9a5c during co-cultivation with the endophytic bacteria Methylobacterium mesophilicum SR1.6/6

status: Public on Apr 18 2014

city: São Paulo

first: Manuella

middle: Nóbrega

last: Dourado

state: São Paulo

address: Av. Prof. Lineu Prestes, 1374 - Ed. Biomédicas II

country: Brazil

institute: University of São Paulo

summary: Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa, is an important citrus disease that produces chlorotic injuries on leaves and reduced fruit size. This bacterium colonizes plant xylem, thereby interrupting sap flow. Other disease symptoms depend on environmental factors, since asymptomatic and symptomatic CVC plants may be genetically similar. The endophytic microbiome comprises many microbial species that may interact with pathogens, reducing disease symptoms and improving plant growth. However, the genetic and physiological mechanisms that underlie this interaction are largely unknown. In this study, the citrus endophytic bacterium Methylobacterium mesophilicum SR1.6/6 was isolated from healthy plants. This bacterium was able to colonize citrus xylem and could be transferred from plant to plant by Bucephalogonia xanthopis (Insecta), suggesting that this endophytic bacterium may interact with X. fastidiosa in planta, as a result of co-transmission by the same insect vector. To better understand how X. fastidiosa genetic responds to the presence of M. mesophilicum in the same environment, we used microarrays to evaluate the transcriptional profile of X. fastidiosa, after in vitro co-cultivation with M. mesophilicum SR1.6/6. The results showed that during co-cultivation with M. mesophilicum, X. fastidiosa downregulated genes related to growth, while genes related to energy production (cellular respiration) and transport were upregulated. Moreover, X. fastidiosa modulates genes associated with molecular recognition, nutrient competition and the stress response, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium

overall_design: To evaluate and compare the Xylella fastidiosa 9a5c transcriptome profiles from bacteria cultured in PW and in co-cultive with Methylobacterium mesophilicum SR1.6/6, bacterial cultures were harvested for total RNA extraction after 24h of inoculation. Samples from the resulting RNAs were then used in competitive hybridizations against Xf microarrays. Replicated experiments were performed with RNA preparations from cells in each treatment and since each microarray carried two replicas of each spotted gene, we ended up with a series of 4 independent readings for each gene present in the microarrays. Images were analyzed with the TIGR Spotfinder program (v.2.2.4). All spots with median values lower than the median local background plus two Standard Deviations have been flagged and excluded from further analyses. Replicated experiments were performed with two independent RNA preparations from cells cultivated in each medium. For each pair of RNA preparations, two independent hybridizations were performed, with dye swaps within each pair. The results from each hybridization were submitted to a series of mathematical transformations with the aid of the software TIGR MIDAS v.2.19. These included filtering out all spots whose integrated intensities were below 10,000 a/d units, normalization between the two channels with the aid of the Lowess algorithm and SD regularization of the Cy5/Cy3 ratios across all sectors (blocks) of the array. Finally, the results from each individual experiment were loaded into the software TIGR Multi-Experiment Viewer (TMEV), v.3.01. Experiments were then normalized and genes that displayed statistically significant modulation were identified with the aid of the one-class option of the Significance Analysis of Microarrays (SAM) test, described by Tusher et al. (2001). The δ factor of the SAM test was adjusted to guarantee a False Discovery Rate (FDR) < 1.

first: Daiene

last: Santos

first: Luiz

last: Nunes

first: Regina

last: de Oliveira

first: Marcus

first: Welington

last: Araújo


title: Identification of potential miRNAs and their targets in Vriesea carinata (Poales, Bromeliaceae) [small RNA-seq]

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

institute: Universidade Federal do Rio Grande do Sul

summary: miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Bromeliaceae family is an example of a large and well described adaptive radiation of plant families in the Neotropics. This family is composed of terrestrial xerophytes and both facultative and obligatory epiphytes, occurring in a wide range of habitats. Bromeliads have different habits, varying from terrestrial to epiphytical, and are found from sea level to altitudes above 4,000 m, in both desert and humid regions, as well as in soils subject to regular floods and in places with very little or great luminosity. This huge habitat plasticity makes bromeliads an interesting model to study the expression of miRNAs in different natural conditions and the first step is to identify miRNAs and its targets. For this purpose, we used a high-throughput sequencing analysis (Solexa technology) of small RNAs (sRNAs) from the endemic South American species Vriesea carinata.

overall_design: microRNA profiles in 1 leaf library of Vriesea carinata by deep sequencing (Illumina HiSeq2000)

first: Frank

middle: F

last: Guzman

first: Mauricio

last: Almerao

first: Rogério


title: Serum Inflammatory Mediators as Markers of Human Lyme Disease Activity

first: William

last: Robinson

address: 269 Campus Dr

summary: Chemokines and cytokines are key signaling molecules that orchestrate the trafficking of immune cells, direct them to sites of tissue injury and inflammation and modulate their states of activation and effector cell function. We have measured, using a multiplex-based approach, the levels of 58 immune mediators and 7 acute phase markers in sera derived from of a cohort of patients diagnosed with acute Lyme disease and matched controls. This analysis identified a cytokine signature associated with the early stages of infection and allowed us to identify two subsets (mediator-high and mediator-low) of acute Lyme patients with distinct cytokine signatures that also differed significantly (p<0.0005) in symptom presentation. In particular, the T cell chemokines CXCL9 (MIG), CXCL10 (IP-10) and CCL19 (MIP3B) were coordinately increased in the mediator-high group and levels of these chemokines could be associated with seroconversion status and elevated liver function tests (p=0.027 and p=0.021 respectively). There was also upregulation of acute phase proteins including CRP and serum amyloid A. Consistent with the role of CXCL9/CXCL10 in attracting immune cells to the site of infection, CXCR3+ CD4 T cells are reduced in the blood of early acute Lyme disease (p=0.01) and the decrease correlates with chemokine levels (p=0.0375). The levels of CXCL9/10 did not relate to the size or number of skin lesions but elevated levels of serum CXCL9/CXCL10 were associated with elevated liver enzymes levels. Collectively these results indicate that the levels of serum chemokines and the levels of expression of their respective chemokine receptors on T cell subsets may prove to be informative biomarkers for Lyme disease and related to specific disease manifestations.

overall_design: A total of 65 immune and inflammatory mediators were profiled in serum samples derived from early Lyme disease patients and age- and sex-matched controls. These samples have been generated as part of a prospective cohort study that includes a well-defined cohort of patients with acute Lyme disease enrolled from a Lyme endemic area of the mid-Atlantic United States. Only patients with untreated, confirmed early Lyme disease manifesting an active EM skin lesion at the time of enrollment, as defined by CDC case criteria are eligible. Patients with a history of prior Lyme disease or the presence of confounding preexisting medical conditions associated with prolonged fatigue, pain or neurocognitive symptoms are excluded. Controls are nonhospitalized age- and sex-matched and have no prior history of Lyme disease or any exclusionary medical conditions including lack of inflammatory disorders.

last: Soloski

first: Lauren

last: Crowder

last: Lahey

first: Catriona

last: Wagner

middle: H

first: John

middle: N

last: Aucott


title: Key Role of MicroRNA in the Regulation of Granulocyte Macrophage Colony-stimulating Factor Expression in Murine Alveolar Epithelial Cells (AEC) during Oxidative Stress

status: Public on Apr 11 2014

city: Salt Lake City

first: Jesse

middle: Worth

last: Rowley

state: Ut

department: Medicine

institute: University of Utah

summary: A genome wide microarray identified 19 candidate miRNA altered in primary AEC during oxidative stress with reversal by treatment with GM-CSF. Three of these microRNA (miR 133a, miR133a* and miR133b) are also predicited to bind the GM-CSF 3 UTR.

overall_design: 4 samples. Primary murine alveolar epithelial cells were isolated and subjected to room air or 80% oxygen in the presence or absence of recombinant murine GM-CSF (20 ng/ml).  Total RNA was extracted and quality checked (260/280>2 and 260/230 > 1.6).  Mouse genome microRNA analysis (MAM3200) was performed by SABioscience.

first: Anne

last: Sturrock

first: Mustafa

last: Mir-Kasimov

first: Jessica

last: Baker

first: Robert

last: Paine


title: Unravelling osmotololerance in Escherichia coli using a pseudosexual model system

status: Public on Apr 16 2014

city: College Station

first: James

last: Winkler

state: TX

address: 3122 TAMU

institute: Texas A&M University

summary: Transcriptional analysis of mutants evolved for tolerance to excess sodium chloride (up to 0.75 M)

sample_organism:
Escherichia coli
Escherichia coli BW25113

overall_design: Mutant compared to parental reference during sustained exponential growth in 0.55 M NaCl, two biological replicates per sample, reference is unevolved parent strain for each mutant

first: Katy

last: Kao


title: The impact of calorie restriction and diet-induced obesity on microRNA expression

city: Columbus

first: Susan

middle: Elizabeth

last: Olivo-Marston

state: OH

address: 1841 Neil Avenue

department: Epidemiology

institute: The Ohio State University

summary:
We analyzed the impact of calorie restriction and diet-induced obesity on expression of microRNAs in the mouse colon.  For this analysis, data was LOESS normalized in R.  Data was then imported into BRB Array for analysis.
We identified microRNAs that were altered in response to calorie-restriction and diet-induced obesity

platform_organism:
Homo sapiens
Mus musculus

overall_design: Total mRNA was extracted from mouse colon tissue that was flash frozen immediately after euthaniasia.  A total of 6 colons per the three groups were used for microarray analysis.  Briefly, 5 ug of RNA were biotin labeled and hybridized to OSU-CCC microRNA microarrays version 4.0.  We then analyzed differences in expression with BRB Array.

first: Aaron

last: Schetter

first: Mohammed

last: Khan

first: Curtis

last: Harris


title: Transcriptome analysis of Pichia pastoris fermentation process

city: Changchun

first: chongyang

last: Liang

state: Jilin

address: No.1266, Fujin Road

department: Pharmaceutical Sciences

country: China

institute: JiLin University

summary: Over the past three decades, due to the universal application of Pichia yeast in the fermentation industry as well as the establishment of Pichia pastoris fermentation process for more than 30 years, the technology of the whole process has become very mature and has now reached a stagnated period of growth. However, studies and research conducted on the genomics of the classic fermentation process and the uncovering of the biological phenomena in the fermentation process from the point of view of high-throughput gene or protein is still in its early stages, and there is still insufficient data within this field. First, in collaboration with Agilent Company, we designed and prepared an expression microarray that could be used for the detection of Pichia pastoris transcriptomics. The transcriptomic changes in the five key technology steps (time points), during the fermentation process of Pichia pastoris would then be detected with the aid of an expression microarray. The five key steps of technology described above formed two important biological processes, namely, the limiting carbon source replacement and secondly, the fermentative production of exogenous proteins. The biological phenomena involved in these two processes were displayed and analyzed at the transcriptional level. In addition to this, with regard to the most important function in the fermentation process of Pichia pastoris, oxid-reduction, the metabolic drift process was analyzed and the important genes that might dominate the changes in the metabolic flux were discovered creatively by using the function tree method in this paper. This study was undertaken from the point of view of the transcriptome and the biological phenomena in the fermemntation process of Pichia pastoris. Both of which, were thoroughly explained during this study. The hope is for many more researchers to optimize the strain fermentation process, to produce proteins at the genetic level, as well as providing and obtaining new perspectives and detailed scientific data for the continued development within this field.

first: Chongyang


title: The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1 [NimbleGen]

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: We use a metabolic labeling strategy for directly measuring nucleosome turnover to determine the role of chromatin remodeler Chd1 on chromatin dynamics in mouse embryonic fibroblasts expressing with wildtype-Chd1 and dominant negative K510R-Chd1. We find that expression of K510R-Chd1 decreases nucleosome turnover at the promoter and increases turnover within the gene body.

overall_design: 10 Illumina sequencing samples and 4 Nimblegen array samples

first: Peter

middle: J

last: Skene

last: Hernandez

first: Mark

last: Groudine

first: Steven


title: Global DNA Methylation: Uncommon Event in Oral Lichenoid Disease [Illumina GoldenGate Methylation Cancer Panel I array]

city: Adelaide

first: Naiara

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

institute: The University of Adelaide

summary:
Purpose: Accumulating evidence indicates aberrant DNA methylation is closely related to oral carcinogenesis, and it has been shown that methylation changes might be used as prognostic biomarker in oral squamous cell carcinoma. Oral lichenoid disease (OLD) is the most common oral potentially malignant disorder in our region. In this study, we have performed a wide DNA methylation study of a series of oral lichenoid disease in order to assess the relevance of DNA methylation changes in this premalignant disorder.
Experimental Design: Discovery phase utilized the Illumina Golden Gate Cancer Panel I in 51 OLD and 6 control samples. The differently methylated loci and the global DNA methylation surrogate LINE-1, were further validated in an independent sample set consisting in 160 OLD and 65 controls.
Results: DNA methylation profiles of the OLD showed only minor significant differences when compared to controls.
Conclusions: In summary, our data indicates that the frequency of aberrant DNA alteration is very low in OLD, which support the low rate of malignization of this oral potentially malignant disorder.

overall_design: Bisulphite-converted DNA from the 51 oral lichenoid disease samples and 6 control samples were hybridised to the Illumina GoldenGate Methylation Cancer Panel I.

first: Jose

middle: M

last: Aguirre-Urizar

first: Amelia

last: Acha-Sagredo


title: Endothelin-1 driven proliferation of PASMC is c-fos dependent

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary:
Background: Pulmonary hypertension is a rare disease characterized by pulmonary artery smooth muscle cell (PASMC) proliferation leading to vascularremodeling. Multiple factors have been associated with the vessel wall thickening. However, the responsible mechanisms are not fully understood.
Aim: In this study we aim to decipher the role ofc-fos and c-jun transcription factors in the vascular remodeling process.
Methods and Results: Expression and immunohistochemical analyses revealed high expression of c-fos and c-jun transcription factors in the vessel wall of lungs from human IPAH samples, hypoxia exposed mice and monocrotaline treated rats. Microarray study from hypoxic lung homogenates revealed MAP kinase asthe most differentially regulated pathway. Additionally, ET-1 and CTGF were the most up-regulated genes. Consequently, ET-1 but not CTGF stimulation of human PASMCs increased DNA synthesis and expression of proliferative markers such as Ki67 and cell cycle regulator, cyclin D1. Moreover, ET-1 treatment elevated ERK-dependent c-fos expression and phosphorylation of c-fos and c-jun. Silencing of c-fos with siRNA abrogated the ET-1-induced proliferation of PASMC.
Conclusion: This finding shed light on the involvement of c-fos/c-jun in vascular remodeling as well as on the molecular mechanisms regulating the proliferative response of PASMCs to ET-1.

overall_design: 36 mice were divided into 2 groups and kept either under normoxic (Nox) or under hypoxic conditions (Hox.3h). RNA from 3 animals was pooled to get 6 pools per group. Each pool was subjected to microarray hybridization (Nox vs. Hox.3h) in a balanced dye-swap design, giving a total of 6 dual-color hybridizations.


title: Expression profile of a parent and ∆lstC strain in regular and high salt conditions

city: Laurel

first: Atin

last: Datta

address: 8301 Muirkirk Rd

department: CFSAN/DVA

institute: FDA

summary:
Microarray analysis of the expression profiles of a parent and its derived ∆lstC mutant in normal and high salt conditions.
The analysis was performed to determine which genes were altered in the mutant when grown in high salt conditions relative to the parent strain.

overall_design: Cultures were performed in triplicate and collected during mid-log phase growth in normal and high salt conditions. RNA was extracted for Affymetrix microarray analysis and compared to identify genes significantly altered in their expression using R and Bioconductor.

first: Laurel

last: Burall

first: Pongpan

last: Laksanalamai


title: Genomic analysis of hESC pedigrees enables identification of de novo genetic alterations and determination of the timing and origin of mutational events

city: La Jolla

first: Francesca

last: Boscolo

address: 9500 Gilman Drive

department: Reproductive Medicine

institute: UCSD

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

summary: Given the association between mutational load and cancer, the observation that genetic aberrations are frequently found in human pluripotent stem cells (hPSCs) is of concern. Prior studies in hiPSCs have shown that deletions and regions of loss-of-heterozygosity (LOH) tend to arise during reprogramming and early culture, while duplications more frequently occur during long-term culture. For the corresponding experiments in hESCs, we studied two sets of hESC lines: one including the corresponding parental DNA; and the other generated from single blastomeres from four sibling embryos. Here, we show for the first time that genetic aberrations observed in hESCs can originate during preimplantation embryo development and/or early derivation. These early aberrations are mainly deletions and LOH, while aberrations arising during long-term culture of hESCs are more frequently duplications. Our results highlight the importance of close monitoring of genomic integrity and the development of improved methods for derivation and culture of hPSCs.

overall_design: Total DNA extracted at from human embryonic stem cells originated independently

first: Dalit

last: Ben-Yosef

middle: S

first: Hadar

last: Amir

first: Mira

last: Malcov

first: Ami

last: Amit

first: Louise

last: Laurent


title: Inhibition of endogenous MTF-1 signaling in zebrafish embryos identifies novel roles for MTF-1 in development

city: Hamilton

first: Andrew

middle: G.

last: McArthur

state: Ontario

address: 1280 Main Street West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

summary: The MTF-1 transcription factor is considered to be a master regulator of zinc homoestasis. We previously characterized a constitutively nuclear, dominant-negative zebrafish MTF-1/eGFP fusion protein (dnMTF-1). In this study, in vitro transcribed dnMTF-1 mRNA was microinjected into zebrafish embryos (2-cell stage), with controls consisting of zebrafish embryos (2-cell stage) microinjected with in vitro transcribed enhanced green fluorescent protein (eGFP) mRNA. Transcriptomic profiling was performed using an Agilent 4 x 44K array on 4 replicate pools of thirty 28- and 36-hpf embryos for each treatment.

overall_design: The role of MTF-1 signaling in zebrafish embryos was examined by injection of in vitro transcribed dnMTF-1 mRNA into zebrafish embryos (2-cell stage), with controls consisting of zebrafish embryos (2-cell stage) microinjected with in vitro transcribed enhanced green fluorescent protein (eGFP) mRNA. Transcriptomic profiling was performed using an Agilent 4 x 44K array on 4 replicate pools of thirty 28- and 36-hpf embryos for each treatment. A Narishige IM-300 microinjector was used to microinject 1-2 cell embryos with ~100 pg of dnMTF-1 IVT mRNA (~2.1 nL microinjection volume with a concentration 50 ng/µL IVT mRNA), or ~100 pg of enhanced green fluorescent protein (eGFP) IVT mRNA. Immediately after microinjection, embryos from each treatment were divided into 4 replicates of 30 pooled embryos and held in 25 mL of 0.3X Danieau’s at 28.5°C under a 14 hour light/10 hour dark cycle. eGFP positive embryos (dnMTF-1 and eGFP) were collected at 28 and 36 hpf and flash frozen in liquid nitrogen for future RNA isolation and microarray hybridization. Total RNA was prepared using the RNA STAT60 protocol (Tel-Test, Inc., TX). RNA was quantified using a Nanodrop 2000C spectrophotometer and assessed for quality using an Agilent 2100 Bioanalyzer Lab-on-chip system. Only samples with RNA integrity number (RIN) between 9.8-10 were used for microarray analysis. For each RNA sample, a single microarray was hybridized with 750 ng Cy3 labeled cDNA using Agilent’s standard conditions for single-color microarrays. The samples were hybridized to a the Agilent 4x44K feature zebrafish microarray using the Agilent In situ Hybridization Kit Plus by the Genome Technology Core at the Whitehead Institute for Biomedical Research (Cambridge, MA). Post-hybridization, microarray slides were washed as per the Agilent In situ Hybridization Kit Plus and scanned with an Agilent DNA Microarray Scanner. Extraction of raw microarray results was performed using Agilent’s Feature Extraction software with background detrending (spatial and multiplicative). The data were normalized using a non-linear scaling method based on rank invariant probes. Cy3 signal saturated probes and probes not above background in all replicated were then removed prior to statistical analysis. Statistical tests were performed using the MeV microarray analysis suite. All data were log transformed and median centered for each probe. A two-factor ANOVA was performed for time (28 vs. 36 hpf), treatment (dnMTF-1 vs. eGPF), and their interaction with p-value based on 1000 permutations of the data and alpha of 0.01. For post-hoc analyses to find biologically relevant results, the probes significant for treatment and time-treatment interaction were secondarily examined using Rank Product (RP) analysis. Rank product analysis was performed to provide lists of probes up- and down-regulated between GFP control and MTF-1 for each time point. For each test, a two-class unpaired RP analysis was performed using 1000 permutation of the data with a false discovery rate (FDR) not exceeding 5%.

first: Matthew

last: Jenny

first: Britton

last: O'Shields

first: Martin

last: Kamper

last: Holowiecki

first: J

last: Tapley


title: Expression profiling of 376 wildtypes to assess day-to-day variance

city: Utrecht

first: Patrick

last: Kemmeren

address: Universiteitsweg 100

institute: UMC Utrecht

summary: A collection of budding yeast wild types grown in parallel to 1,484 budding yeast deletion mutants to assess day-to-day variance. Related to series GSE42526 and GSE42527.

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

first: Katrin

last: Sameith

first: Loes

last: van de Pasch

first: Frank

last: Holstege


title: Gene expression profile of oncogenic Ras-induced senescence in normal human diploid fibroblasts.

status: Public on Apr 10 2014

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 normal human diploid fibroblasts(TIG-3) comparing empty vector transducted cells with RasV12 transducted cells.

overall_design: TIG-3 cells were subjected to infection with retrovirus encoding RasV12 or empty vector. Total RNA was isolated using TRIzol reagent and were analyzed using the human 3D-Gene DNA chip (Toray) that contains 25000 genes. The genome wide transcriptional resp

first: Yoshinori

last: Imai

first: Eiji

last: Hara


title: Effects of DP1 knockdown on E2F target gene expression in normal human diploid fibroblasts.

summary: Transcriptional profiling of normal human diploid fibroblasts(TIG-3) infected with retrovirous encoding DP1-shRNA or control-shRNA.

overall_design: TIG-3 cells were subjected to infection with retrovirus encoding DP1-shRNA or control-shRNA. Total RNA was isolated using TRIzol reagent and were analyzed using the human 3D-Gene DNA chip (Toray) that contains 25000 genes. The genome wide transcriptional


title: A family of nonclassical class I MHC genes contributes to ultrasensitive chemodetection by mouse vomeronasal sensory neurons

status: Public on Apr 09 2014

city: Frankfurt

first: Peter

last: Mombaerts

address: Max-von-Laue-Str. 3

institute: Max Planck Research Unit for Neurogenetics

summary: We applied the NanoString gene expression platform to total RNA isolated from the vomeronasal mucosa of mice of a strain (∆H2Mv) in which we had excised with chromosome engineering a 530 kb genomic region that encompasses nine non-classical class I MHC genes that are expressed specifically in vomeronasal sensory neurons. At three weeks of age, there is no difference of expression for all Vmn2r genes tested; and at eight weeks of age, there is no difference of expression for the majority of Vmn2r genes.

overall_design: We designed NanoString probes for one third of the mouse Vmn2r gene repertoire, based on the reference C57BL/6 genome sequence. CodeSet Chanel includes probes for 46 Vmn2r genes and nine non-classical class I MHC H2-Mv genes that are expressed specifically in mouse vomeronasal sensory neurons. Results were analyzed with tTREAT.

first: Tomohiro

last: Ishii

first: Sachiko

last: Akiyoshi

first: Mona

last: Khan

first: Evelien

last: Vaes


title: Gene expression profile of p16-induced senescence in normal human diploid fibroblasts.

summary: Transcriptional profiling of p16-induced senescent human diploid fibroblasts compared with proliferating cells.

overall_design: TIG-3 ER-p16 cells (primary normal human diploid fibroblasts expressing a 4-hydroxytamoxifen(4-OHT) regulatable form of human p16) were cultured for 7 days  with or without 4-OHT. Total RNA was isolated using TRIzol reagent and were analyzed using the hum


title: Pituitary Tumors cDNA SAGE Libraries

city: Ribeirao Preto

first: Leandro

middle: Machado

last: Colli

state: SP

address: Av Bandeirantes 3900

department: Department of Internal Medicine

institute: School of Medicine of Ribeirao Preto

summary: Despite a considerable literature concerning the molecular pathogenesis of pituitary tumors, the mechanisms of pituitary tumors development and progression remain unknown. Four SAGE cDNA libraries were constructed using a pool of mRNA obtained from five GH-, two ACTH-secreting, and four non secreting pituitary tumors (NS), and three normal pituitaries from patients who had accidental death, using I-SAGE kit (Invitrogen). The aim of this study was to evaluate the differential gene expression profile by SAGE genes in different subtypes of pituitary tumors to contribute for understanding of pituitary tumorigenesis.

overall_design: Comparative analysis of gene expression profiles in subtypes of pituitary tumores.

first: Paixao

last: Beatriz

first: Amaral

last: Fernando

first: Deison

last: Lima

first: Wilson

middle: A

last: Silva

first: Ayrton

last: Moreira

first: Sonir

last: Antonini

first: Ricardo

middle: Z

last: Vêncio

first: Margaret

last: Castro


title: Global hepatic gene expression patterns associated with reproductive success of fathead minnows and environmental variables in streams across varying landscapes

city: Riverside

first: Jordan

last: Crago

address: Science Lab 1

institute: University California-Riverside

summary: The goal of this study was to use global gene expression as a diagnostic tool to compare hepatic gene expression patterns in both male and female FHM in streams with the lowest and highest reproductive success, and potentially identify a suite of mRNA transcripts indicative of reproduction in a population

overall_design: The goal of this study was to compare differences in hepatic mRNA expression between gender at high and low egg-producing streams, not differences between individual streams.  A k-means cluster analysis was performed using eggs/pair/day on the original 17 streams to delineate 3 clusters: high, medium and low. From that analysis, FHM from 6 of the original 17-streams used in Crago et al. (2010) were chosen for the microarray experiment (Fig. 1, Table 1). In this study the experimental condition is reproductive success; High versus Low reproductive success. The streams grouped into High Reproductive Success were Oak Creek-2007 (2313 eggs), Point Creek (1277 eggs), Meeme Creek (1164 eggs) and Baird Creek (967 eggs). The streams grouped into Low Reproductive Success were: Ashwaubenon Creek (0 eggs), Devils Creek (541 eggs) and Oak Creek-2006 (642 eggs). Multiple regression analysis using the 22 sediment and water quality characteristics measured in the 6 streams with the highest (n = 4 and lowest (n = 3) streams demonstrated that there were no differences amongst the streams in regards to measure sediment and water variables. .5 One array was run for each gender from each stream.  So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth.  There were 14 arrays used in this study, 7 for males, 7 for females from individual rivers.  So that Males from Point Creek were pooled and run on one array, males from Ashwaubenon Creek were run on a separate array, and so forth.  In the case of Oak Creek, which was sampled in both years, there was a large difference in egg production between two years. Therefore separate arrays were run for Oak Creek 2006 and Oak Creek 2007. All streams chosen had overall survival rates of at least 80% through the 21-day sampling period, except Devils River. The survival rate for Devils River was at 100% until four days prior to the end of the experiment when six fish died or escaped.

first: Rebecca

last: Klaper

first: Steven

last: Corsi


title: Negative energy balance and hepatic gene expression patterns in high yielding dairy cows during the early postpartum period [liver]

status: Public on Apr 08 2014

city: Athenry

first: Dermot

middle: G

last: Morris

state: Co. Galway

address: Animal & Grassland Research and Innovation Centre, Mellows Campus

department: Animal Bioscience Research Department

country: Ireland

institute: Teagasc

summary: In high yielding dairy cows the liver undergoes extensive physiological and biochemical changes during the early postpartum period in an effort to re-establish metabolic homeostasis and to counteract the adverse effects of negative energy balance (NEB). These adaptations are likely to be mediated by significant alterations in hepatic gene expression. To gain new insights into these events an EB model was created using differential feeding and milking regimes to produce two groups of cows with either a mild (MNEB)  (n=5) or severe NEB (SNEB) (n=6) status. Cows were slaughtered and liver tissues collected on days 6-7 of the first follicular wave postpartum. Using an Affymetrix® 23k oligonucleotide bovine array to determine global gene expression in hepatic tissue of these cows, a total of 416 genes (189 up- and 227 down-regulated) were found to be altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with widespread changes in gene expression classified into 36 gene networks including those associated with lipid metabolism, connective tissue development and function, cell signalling, cell cycle and metabolic diseases. Severe NEB cows displayed reduced expression of transcription activators and signal transducers that regulate the expression of genes and gene networks associated with cell signalling and tissue repair. These alterations are linked with increased expression of abnormal cell cycle and cellular proliferation associated pathways. This study provides new information and insights on the effect of SNEB on gene expression in high yielding Holstein Friesian dairy cows in the early postpartum period.

overall_design: Multiparous Holstein-Friesian cows (n=24) were blocked 2 weeks prior to expected calving date according to parity, body condition score, and previous lactation yield (average lactation 6477±354kg) and randomly allocated to mild (MNEB; n=12) or severe (SNEB; n=12) NEB groups. MNEB cows were fed ad lib grass silage and 8 kg day-1 concentrates and milked once daily; SNEB cows were fed 25 kg day-1 silage and 4kg day-1 concentrate and milked three times daily. Measurements of body condition score and EB were used to select cows which showed extremes in EB from each group (MNEB, n=5; SNEB, n=6). Cows were slaughtered on days 6-7 of the first follicular wave after calving (mean number of days post-partum: MNEB mean 13.6 ± 0.75, range 11–15; SNEB mean 14.3 ± 0.56, range 13–16), based on daily transrectal ultrasonography.The entire liver was removed within 15 to 30 min after slaughter and weighed. Samples weighing approximately 1 g were dissected, rinsed in RNase free phosphate buffer, snap frozen in liquid nitrogen and stored at -80ºC.

first: S

middle: D

last: McCarthy

last: Waters

first: D

last: Kenny

first: M

last: Diskin

first: R

last: Fitzpatrick

first: J

last: Patton

last: Wathes


title: Expression analysis in anaerobic Hanford 100H aquifer flow-through columns receiving lactate and chromate

city: Berkeley

first: Ulas

last: Karaoz

address: 1 Cyclotron Rd.

institute: LBNL

summary: Columns containing Hanford 100H aquifer sediment continuously infused with 5 mM lactate, 5 uM Cr(VI), and either 7.5 mM sulfate or 12 mM nitrate as an electron acceptor.

overall_design: A two-chip study using total RNA extracted from unfiltered effluent from columns (nitrate or sulfate infused).

first: Harry

last: Beller

first: Eoin

middle: L

last: Brodie


title: The 19S proteasome subunit Rpt3 regulates distribution of CENP-A by associating with centromeric chromatin

status: Public on Apr 07 2014

city: Kami

first: Kojiro

last: Ishii

state: Kochi

address: 185 Miyanokuchi, Tosayamada

institute: Kochi University of Technology

summary: CENP-A, a variant of histone H3, is incorporated into centromeric chromatin and plays a role during kinetochore establishment. In fission yeast, the localization of CENP-A is limited to a region spanning 10 to 20 kb of the core domain of the centromere. Here, we report a mutant (rpt3-1) in which this region is expanded to 40 to 70 kb. Likely due to abnormal distribution of CENP-A, this mutant exhibits chromosome instability and enhanced gene silencing. Interestingly, the rpt3+ gene encodes a subunit of the 19S proteasome, which localizes to the nuclear membrane. While Rpt3 associates with centromeric chromatin, the mutant protein has lost this localization. A loss of the cut8+ gene encoding an anchor of the proteasome to the nuclear membrane causes similar phenotypes as observed in the rpt3-1 mutant. Thus, we propose that the proteasome (or its subcomplex) associates with centromeric chromatin and regulates distribution of CENP-A.

overall_design: Chromosomal distributions of differentially expressed centromere protein A in wild-type and a proteasome mutant.

first: Teppei

last: Kitagawa

first: Tomohiro

last: Matsumoto


title: Negative energy balance and splenic gene expression patterns in high yielding dairy cows during the early postpartum period [spleen]

summary: Increased energy demands to support lactation, coupled with lowered feed intake capacity results in negative energy balance (NEB) and is typically  characterized by extensive mobilization of body energy reserves in the early postpartum dairy cow. The catabolism of stored lipid leads to an increase in the systemic concentrations of nonesterified fatty acids (NEFA) and  -hydroxy butyrate (BHB). Oxidation of NEFA in the liver result in the increased production of reactive oxygen species and the onset of oxidative stress and can lead to disruption of normal metabolism and physiology. The immune system is depressed in the peripartum period and early lactation and dairy cows are therefore more vulnerable to bacterial infections causing mastitis and or endometritis at this time. A  bovine Affymetrix oligonucleotide array was used to determine global gene expression in the spleen of dairy cows in the early postpartum period. Spleen tissue was removed post mortem from five severe NEB (SNEB) and five medium NEB (MNEB) cows 15 days postpartum.SNEB increased systemic concentrations of NEFA and BHB, and white blood cell and lymphocyte numbers were decreased in SNEB animals. A total of 545 genes were altered by SNEB. Network analysis using  Ingenuity Pathway Analysis revealed that SNEB was associated with NRF2-mediated oxidative stress, mitochondrial dysfunction, endoplasmic reticulum stress, natural killer cell signaling, p53 signaling, downregulation of IL-15, BCL-2, and IFN- ; upregulation of BAX and CHOP and increased apoptosis with a potential negative impact on innate and adaptive immunity.

overall_design: Multiparous Holstein-Friesian cows (n=24) were blocked 2 weeks prior to expected calving date according to parity, body condition score, and previous lactation yield (average lactation 6477±354kg) and randomly allocated to mild (MNEB; n=12) or severe (SNEB; n=12) NEB groups. MNEB cows were fed ad lib grass silage and 8 kg day-1 concentrates and milked once daily; SNEB cows were fed 25 kg day-1 silage and 4kg day-1 concentrate and milked three times daily. Measurements of body condition score and EB were used to select cows which showed extremes in EB from each group (MNEB, n=5; SNEB, n=5). Cows were slaughtered on days 6-7 of the first follicular wave after calving (mean number of days post-partum: MNEB mean 13.6 ± 0.75, range 11–15; SNEB mean 14.3 ± 0.56, range 13–16), based on daily transrectal ultrasonography.At slaughter the entire spleen was removed and weighed, and samples weighing  1 g were dissected, rinsed in RNase-free phosphate buffer, snap frozen in liquid nitrogen, stored for 4 h in dry ice, and subsequently stored at  80°C.

last: D McCarthy

first: B

last: Earley

last: Murphy

first: A

last: Brass

middle: C


title: Effect of SAOUHSC_02810 deletion in S. aureus NCTC8325

city: He Fei

first: Haipeng

last: Sun

state: An Hui

address: Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: To analyze function of SAOUHSC_02810, we have employed whole genome microarray expression profiling to identify genes transcription changed in mutant strain. SAOUHSC_02810 were replaced by ermB gene.

sample_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: Cells were grown to OD600=2.0, and the RNA level of wild type NCTC8325 and SAOUHSC_02810 mutant were compared.

first: Ting

last: Xue


title: CNV in sexual and apomictic Boechera

city: Gatersleben

first: Timothy

last: Sharbel

address: Corrensstrasse 4

institute: IPK Gatersleben

type: Genome variation profiling by genome tiling array

summary:
The absence of meiosis and sex are expected to lead to mutation accumulation in asexual (apomictic) plants.  We have performed a double-validated analysis of copy number variation (CNV) on 10 biological replicates each of diploid sexual and diploid apomictic Boechera using a high-density (>700K) custom microarray, in order to compare mutation accumulation in the form of CNV between the transcribing regions of their genomes.
The Boechera genome demonstrated higher levels of depleted compared to enriched CNV, irrespective of reproductive mode.  Genome-wide patterns of CNV revealed four divergent lineages, three of which were characterized by both sexual and apomictic genotypes.  Hence genome-wide CNV is reflective of at least 3 independent origins (i.e. expression) of apomixis from different sexual genetic backgrounds.
CNV distributions for different families of transposable elements (TEs) were lineage specific, and a trend for enrichment in LINE/L1 and LTR/Copia elements in lineage 3 apomicts is consistent with sex and meiosis being mechanisms for purging genomic parasites. We hypothesize that significant overrepresentation of specific gene ontology classes (e.g. pollen-pistil interaction) in apomicts implies that gene enrichment could be an adaptive mechanism for genome stability in diploid apomicts by providing a polyploid-like system for buffering the effects of deleterious mutations.

sample_organism:
Boechera stricta
Boechera lignifera
Boechera divaricarpa
Boechera crandallii
Boechera retrofracta
Boechera schistacea
Boechera polyantha
Boechera retrofracta x Boechera stricta
Boechera duchesnensis

platform_organism:
Boechera stricta
Boechera holboellii
Boechera divaricarpa

overall_design: 10 biological replicates each of sexual and apomictic Boechera genotypes, 720K NimbleGen custom CGH array based on 454 sequenced Boechera cDNA, Cy3 and Cy5 dye swap approach

first: Olawale

last: Aliyu

first: Michael

last: Seifert

first: Jose

last: Corral

first: Joerg

last: Fuchs


title: Dose response analysis of monophthalates in the murine embryonic stem cell test

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

institute: Natl. Inst. Public Health & Environment

summary: Three embryotoxic phthalate monoesters, monobutyl phthalate (MBuP), monobenzyl phthalate (MBzP) and mono-(2-ethylhexyl) phthalate (MEHP) and the non-embryotoxic monomethyl phthalate (MMP) were studied for their effects on gene expression at several concentrations that did not induce cytotoxicity.

overall_design: 192 arrays


title: Genome wide expression analysis of genes regulated by SGE1 in Fusarium verticillioides

city: Peoria

first: Daren

middle: W.

last: Brown

state: IL

address: 1815 N. University St.

department: Bacterial Foodborn Pathogens and Mycology Research

institute: USDA-ARS

summary: Investigation of whole genome expression changes induced by SGE1 30 minutes after induction of SGE1 expression in an SGE1 mutant strain of Fusarium verticillioides.  Comparison between wild-type, SGE1 overexpression mutant GMTcp-272 (xlnp:SGE1 in SGE1 mutant background) and sge1 mutant in liquid medium (18 hrs) after induction with xylose.  SGE1 plays a role in pathogenicity and synthesis of secondary metabolism.

overall_design: In this study, total RNA recovered from nine cultures of F. verticillioides (wild-type, sge1 mutant and SGE1 overexpression mutant GMTcp-272, in triplicate) 30 minutes after the addition of xylose was used to identify genes regulated by SGE1.

middle: W


title: E.faecalis regulate immune responses in HCT116 cells

status: Public on Apr 04 2014

city: Singapore

first: Shugui

last: Wang

address: Biopolis Way, Matrix

country: Singapore

institute: Danone Nutricia research

summary: Colonizing commensal bacteria after birth are required for the proper development of the gastrointestinal tract. It is believed that bacterial colonization pattern in neonatal gut affects gut barrier function and immune system maturation. Studies on the development of faecal flora microbiota in infants on various formula feeds showed that the neonatal gut was first colonized with enterococci followed by other flora microbiota such as Bifidobacterium in breast feeding infants. Intriguingly, Bjorksten group Other studies showed that Bbabies who developed allergy were less often colonized with Enterococcus during the first month of life as compared to healthy infants. A lot of Many studies have been done on conducted to elucidate how bifidobacteria or lactobacilli, some of which are considered probiotic, regulate infant gut immunity. However, much fewer studies have been focused on enterococi. In our study, we demonstrate that E. faecalis, isolated from healthy newborns, suppress inflammatory responses activated in vivo and in vitro. We found E. faecalis attenuates proinflammatory cytokine secretions, especially IL-8, through JNK and p38 signaling pathways. This finding shed light on how the first colonizer, E.faecalis, regulate inflammatory responses in the host.

overall_design: Samples are analysed using web-based GEArray Expression Analysis Suite


title: Endogenous Elevation of Homocysteine Induces Retinal Neuron Death in the Cystathionine-b-Synthase Mutant Mice

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

summary: The effects of endogenous elevation of homocysteine on retinal gene expression were screened by microarray analysis, which was performed in triplicate (i.e., three different paired RNA samples) with RNA isolated from neural retinas of cbs+/- HM at 5-weeks after a methionine diet and age-matched wildtype mice. The microarray chips used in this study permitted the screening of 36,212 genes. Of particular interest were those genes in cbs+/- HM mice whose expression levels changed by at least a factor of 2 (increased or decreased expression) compared with the wild-type in each of the replicate experiments. Using these selection criteria, we identified 1219 genes. They were categorized into six functional groups: (1) proapoptosis, (2) antiapoptosis, (3) cell cycle, (4) antioxidant, (5) calcium signaling, and (6) axon growth/guidance, with the remaining genes with marked changes in expression placed in a miscellaneous group. After categorization, relevant genes were further narrowed by SAM analysis; q < 0.06 was considered significant.

overall_design: Microarrays were performed in triplicate as biological repeats and reverse fluoro (i.e., three different paired RNA samples) with RNA isolated from neural retinas of cbs+/- HM at 5-weeks after a methionine diet and age-matched wildtype mice after a methionine diet.

first: Preethi

last: Ganapathy

first: Brent

last: Moister

first: Penny

last: Roon

first: Barbara

last: Mysona

first: Jennifer

last: Duplantier

first: Ying

last: Dun

first: Tracy

middle: K

first: Marlena

last: Farley

first: Puttur

last: Prasad

first: Sylvia

middle: B

last: Smith


title: Expression data from intestinal mucosa of patients with CD under anti-TNF-alpha therapy.

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

summary:
Crohn's Disease (CD) is a chronic inflammatory disease of the intestinal tract.
We performed a whole-genome transcriptional analysis using colonic biopsies from CD patients before and after anti-TNF-α therapy.

overall_design: Involved colonic samples from Crohn's disease patients and healthy colonic samples from non-inflammatory controls were collected for RNA extraction and hybridization on Affymetrix microarrays. Inclusion criteria for CD patients were: age between 18 and 70, diagnosis of CD established at least 4 months before inclusion and exclusion of concomitant infection. Active disease was defined by endoscopic and clinical score: endoscopic active disease was defined as a CD endoscopic index of severity (CDEIS) of 5 or more and the presence of large ulcers (> 0.5 cm diameter) in at least one of the explored segments. Clinical activity was defined as a CD activity index (CDAI) above 150. Finally, a total of 39 biopsies were analyzed: 17 healthy controls, 10 active CD without anti-TNF therapy, 5 active CD with anti-TNF therapy (non-responders) and 7 inactive CD with anti-TNF therapy (responders).

first: Raquel

last: Franco Leal


title: Study of circular RNA in Dictyostelium discoideum

status: Public on Apr 01 2014

city: Stanford

first: Julia

last: Salzman

address: 279 West Campus Drive, MC: 5307

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: RNA-Seq to discover circular RNA expression in Dictyostelium discoidieum with a shallow RNaseR treated RNA-Seq library; our goal was simply to prove existence of these molecules and hence samples were multiplexed with Neurospora Crassa using the same barcode.

overall_design: RNA-Seq on Rnase R treated RNA


title: Negative energy balance and hepatic gene expression patterns in high yielding dairy cows during the early postpartum period

first: Dermot

last: Morris

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

overall_design: Refer to individual Series


title: Distinct expression pattern of miRNAs in Marek’s disease virus infected-chicken splenic tumors and non-tumorous spleen tissues

city: Harbin

first: Zhijie

last: Li

address: No. 427 Maduan St.

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

summary: To gain more insight into the molecular mechanisms of the tumorigenesis of MDV, we used microarrays to screen host and viral miRNAs that were sensitive to infection by MDV. Microarray analysis showed significant differential expression of 79 miRNAs,

overall_design: To determine whether miRNAs were involved in the MDV-induced tumorigenesis, miRNA microarray analysis was performed on GA-infected splenic tumors, GA-infected non-tumorous spleen tissues, and control spleen tissues at 28 dpi.

first: Zhi-jie

first: Chang-jun


title: Rare de novo copy number variants in patients with congenital pulmonary atresia

status: Public on Apr 02 2014

city: Changsha

first: zhiping

last: tan

address: 139 Renmin Road

institute: the Second Xiangya Hospiatl

summary:
Ongoing studies using genomic microarrays and next-generation sequencing have demonstrated that the genetic contributions to cardiovascular diseases have been significantly ignored in the past. The aim of this study was to identify rare copy number variants in individuals with congenital pulmonary atresia (PA).
Based on the hypothesis that rare structural variants encompassing key genes play an important role in heart development in PA patients, we performed high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. CNVs were identified in 17/82 patients (20.7%), and eight of these CNVs (9.8%) are considered potentially pathogenic. Five de novo CNVs occurred at two known congenital heart disease (CHD) loci (16p13.1 and 22q11.2). Two de novo CNVs that may affect folate and vitamin B12 metabolism were identified for the first time. A de novo 1-Mb deletion at 17p13.2 may represent a rare genomic disorder that involves mild intellectual disability and associated facial features.

overall_design:
high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform.
Only 21 samples with potentially pathogenic CNVs are included in this records

first: Zhi-Ping

last: Tan

first: Yi-Feng

last: Yang

first: Jin-Lan

last: Chen

first: Wei-Zhi

last: Zhang

first: Li

last: Xie


title: Determine changes of lncRNAs expression in malignant hepatocytes

city: Xi'an

first: Wei-Hua

last: Xu

state: Shaanxi

address: No. 127 West Changle Road

department: Hepatobiliary Surgery

institute: Xijing Hospital, Fourth Military Medical University

summary: We performed a hybridization-based microarray analysis for lncRNA expression to understand the involvement of lncRNAs in HCC and to investigate differentially expressed lncRNAs in HCC, thereby characterizing their potential roles in tumor growth.

overall_design: The expression profiles of SMMC7721 HepG2 and Huh7 human HCC cell lines and the HL-7702 human immortalized normal hepatocyte cells were performed by the lncRNA microassay. SMMC7721, HepG2 and Huh7 human HCC cell lines were defined as the experimental group and HL-7702 cell line was used as the control.

first: Wei-hua

first: Ke-feng

last: Dou


title: Transcriptome profiling of pig chromosomes regions associated with water holding capacity

city: Dummerstorf

first: Klaus

last: Wimmers

state: Mecklenburg-Vorpommern

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology

type: Expression profiling by genome tiling array


title: Transcriptome profiling of pig chromosomes regions associated with water holding capacity [DuPi]

summary:
To further characterize genomic regions previously identified which are linked with meat quality traits like drip loss, PH, conductivity and etc., we employed a customary regional tiling array experiment for two pig populations. Total RNA were taken from muscle sample of M. longissimus dorsi of pigs selected from two phenotypic groups graded according to high (HI) and low (LO) drip loss. Hybridization were made in batches, 2 to 3 biological replicates for each sample.

DuPi and PiF1 are code names for the two experimental populations.


title: Transcriptome profiling of pig chromosomes regions associated with water holding capacity [PiF1].

overall_design: Total RNA were taken from muscle sample of M. longissimus dorsi of pigs selected from two phenotypic groups graded according to high (HI) and low (LO) drip loss. Hybridization were made in batches, 2 to 3 biological replicates for each sample.


title: Gene expression analysis of nine European maize (Zea mays L.) inbred lines and nine corresponding hybrids

status: Public on Apr 03 2014

city: Hamburg

first: Stefan

last: Scholten

state: Hamburg

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

institute: University of Hamburg

summary: In this study expression levels of 732 genes were analyzed for European maize (Zea mays L.) inbred lines (4 Flint and 5 Dent) and nine corresponding hybrids by microarray analysis. The selection of the 732 genes was based on a previous study (Thiemann et al., Theor Appl Genet 2010, 120:401-413), which sequences were derived from the 46k microarray (platform GPL6438) (University of Arizona, USA). 558 of the 732 genes represented on the microarray were differentially expressed between the original 21 parental inbred lines and were correlated with at least one of the three characteristics MPH (mid-parent heterosis) and/or HP (hybrid performance) of the trait GY (grain yield) and/or HP of the trait grain dry matter content. Some of those correlated genes show overlapping correlations. The residual 174 non-correlated genes belong to the top 6 biological processes that were found to be enriched among the HP for GY-correlated genes (Thiemann et al., Theor Appl Genet 2010, 120:401–413).  The aim of this study was the identification of the hybrid expression pattern of the subset of genes, which mid-parental expression levels were shown to be correlated with MPH for GY or showed no correlation. For the analysis total RNA of 7-day old seedlings was extracted and amino-allyl-labeled RNA was synthesized. The microarrays were scanned (AppliedPrecision ArrayWorx Scanner, Applied Precision Inc., USA) and data were evaluated using the Software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, USA). Hybridizations were conducted between each pair of parental inbred lines and its corresponding hybrids. In total 4 biological replicates per genotype were analyzed. As a result 119 (22.9 %) of the 519 MPH for GY or non-correlated genes showed differential expression in at least one of the nine inbred-hybrid comparisons. These differentially expressed genes were further analyzed for hybrid expression, resulting in a mainly additive expression. Of all differential expression, additive expression of 86.21 % (with 13.79 % non-additive) of the MPH-correlated genes, and a slightly smaller contingent of 79.66 % (with 20.34 % non-additive) of the non-correlated genes was measured.

overall_design: Four biological replicates of each of the nine parental inbred lines (4 Flint: F012, F039, F047, L024; 5 Dent: S028, S036, P024, P033, P048) and of the nine corresponding hybrids (P033xF047, P048xF047, P024xF039, S036xL024, S028xL024, S028xF012, S028xF039, P024xF012, F012xF039) were grown under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 % air humidity) for seven days in a climate chamber. Whole seedlings were frozen in liquid nitrogen and were finely pounded. Total RNA was extracted and then precipitated (4 M LiCl). Residual genomic DNA was hydrolyzed with DNaseI (Fermentas, St. Leon-Rot, Germany) and purified with the “NucleoSpin RNA Clean-up Kit” (Macherey-Nagel, Düren, Germany). For first strand cDNA synthesis, 5 µg of total RNA and the Superscript II from Invitrogen (Life Technologies, Carlsbad, USA) were used. Second strand synthesis was performed using DNA Polymerase I and RNase H followed by a 5 min incubation step of T4 DNA Polymerase (Fermentas, St. Leon-Rot). Residual RNA was hydrolyzed with RNase A. In-vitro transcription was performed with the T7 RNA Polymerase (Fermentas, St. Leon-Rot, Germany) for 4 h to incorporate aminoallyl-labeled UTPs (Fermentas, St. Leon-Rot, Germany). Finally, residual DNA was degraded with DNase I (Fermentas). Synthesized aaRNA was coupled with fluorescence dyes Cy3 or Cy5 (GE Healthcare, Chalfont St. Giles, UK). The RNeasy MinElute Kit (Qiagen, Hilden, Germany) was used for purification and removal of unbound dye. In total 105 hybridizations were realized. The dye used for each biological replicate of each genotype was alternated to reduce systematic bias.

first: A

last: Thiemann

first: J

last: Fu

first: F

last: Seifert

first: R

middle: T

last: Grant-Downton

first: T

last: Schrag

first: H

last: Pospisil

first: M

last: Frisch

middle: E

last: Melchinger

first: S


title: Transcriptional profiles in rat hair follicles after single wave blasting impact

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: Male Sprague-Dawley (SD) rats (350 - 400 g) were anaesthetized with 3% isoflurane for 3 min in a closed induction chamber.  A helium driven shock tube was used at various shock wave pressures (20 - 30 psi).  The exposure system has been developed so that the animals are exposed head only to a ?primary blast? that being a single pulse shock wave with only minimal concussive and whiplash effects.  After exposure, rats were closely observed for either 1 day or 7 days before being sacrificed.  At the end of the observation period, rat whiskers were quickly pulled and placed in a 1.5 ml micro centrifuge tube containing 0.5 ml of RNAlater.  Samples were then stored at -80C until further analysis.

overall_design: There were 3 control rats and 5 treated rats.

first: Martyniuk

last: Chris

first: Langlois

last: Valerie


title: The transcriptomic response to finasteride in the Silurana tropicalis testis

summary: An ex vivo protocol was optimized to expose testis tissues from juvenile Silurana tropicalis to 5 uM finasteride.  Testis tissues were incubated in L-15 media with (n = 8) and without (n = 8) finasteride for 6 h at 26 °C on top of an orbital shaker. Afterwards, the tissues were flash frozen on dry ice and RNA was isolated using Trizol. The isolated RNA of four control tissue samples and four finasteride exposed tissue samples were then analyzed using a custom microarray for S. tropicalis containing 44,000 probes .

first: Bissegger

last: Sonja


title: Gene modulation during downshift and high temperature stress reduces intracellular replication and virulence of Salmonella enterica serovar Typhimurium: roles of RpoS

city: Bangalore

first: Dipankar

last: Nandi

address: CV Raman Avenue

department: Biochemistry

country: India

institute: Indian Institute of Science

summary: Bacterial pathogens adapt to multiple stress conditions; however, the consequences of these responses on infection are not well understood. Here, the adaptive responses of Salmonella enterica serovar Typhimurium (S. typhimurium) to the combination of nutritional deprivation and high temperature (NDHT) stress were investigated. Microarray analysis revealed extensive modulation of expression of genes involved in several metabolic pathways. Interestingly, the expression of a large number of genes involved in chemotaxis, invasion, motility etc are down regulated. Further studies involved S. typhimurium exposed to high temperature (HT) or grown in minimal media, i.e. nutritional downshift (ND), or the combination, i.e. NDHT. The amounts of secretory proteins reduce greatly during NDHT, but not ND or HT, resulting in lower number of colony forming units (CFU) in different organs post oral infection of mice. The expression of the global regulator, RpoS, is downregulated during NDHT. Deletion of rpoS greatly reduces the amounts of secretory proteins and intracellular replication of S. typhimurium during ND but not HT. Extension of these results to RAW macrophage cells demonstrated lower intracellular replication of S. typhimurium at HT. Overall, this study sheds insights on the adaptive responses of S. typhimurium to a combination of stress conditions, resulting in lower infection.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Agilent one-color experiment,Organism: Salmonella Typhimurium ,Agilent-Custom GeneExpression  8x15k designed by Genotypic Technology Pvt. Ltd. (AMADID: 017809)  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Manoj

last: Bhosale


title: SUDHL-4 cells: suspension vs. co-cultured with HK cells

city: Tampa

first: jianguo

last: tao

address: 12902 Magnolia Dr

institute: H Lee Moffitt Cancer Center

summary: We first performed miRNA analysis on SU-4 cells in suspension, and after 24 and 48 h of HK co-culture. To ensure that no HK cell contamination occurred, SU-4 cells in suspension and after co-culture were purified by CD19-positive magnetic selection, followed by total RNA isolation.

overall_design: Two-condition experiment, S4 vs. S4+HK cells. Biological replicates: 2 suspension controls, 2 co-cultured with HK cells, independently grown and harvested. One replicate per array.

first: Jianhong

last: Lin

first: Tint

last: Lwin

first: Jianguo

last: Tao


title: MicroRNA and mRNA biomarkers for short-term in vivo genotoxic and non-genotoxic carcinogen classification

city: Leiden

first: Joost

last: Melis

address: Postbus 9600

department: Toxicogenetics

institute: Leiden University Medical Center

summary:
Many innovative techniques and scientific improvements are available to tackle societal concerns, like public health safety and confining the risk of cancerous exposure to chemicals, but have not been thoroughly tested and implicated yet. We investigated if microRNA and mRNA transcription profiles can be implemented in a short-term carcinogen classifier assay.  Our study is additionally focusing on the drawbacks of present-day carcinogen screening strategies and also aims to contribute to a more ethical approach towards animal use and welfare within risk assessment.  Since current in vitro and in silico assays are still not able to mimic the in vivo situation accurately we set out to develop an alternative short-term in vivo assay. Five genotoxic, seven non-genotoxic and five non-carcinogen exposure studies were used to investigate if murine hepatic microRNA and mNA profiles after 7-day exposure are suitable tools to classify carcinogens. Classification analyses showed that a small transcript set, consisting of both microRNA and mRNA, is able to classify the genotoxic, non-genotoxic and non-carcinogens tested with 100% accuracy. The results indicate that microRNAs have the potential to be used as transcriptional classifiers and that a short-term transcriptional classifier assay in mice can be a powerful tool in carcinogenicity risk assessment.
Since current in vitro and in silico assays are still not able to mimic the in vivo situation accurately we set out to develop an alternative short-term in vivo assay. Five genotoxic, seven non-genotoxic and five non-carcinogen exposure studies were used to investigate if murine hepatic microRNA and mNA profiles after 7-day exposure are suitable tools to classify carcinogens. Classification analyses showed that a small transcript set, consisting of both microRNA and mRNA, is able to classify the genotoxic, non-genotoxic and non-carcinogens tested with 100% accuracy. The results indicate that microRNAs have the potential to be used as transcriptional classifiers and that a short-term transcriptional classifier assay in mice can be a powerful tool in carcinogenicity risk assessment.

overall_design: [mRNA profling] 96 hepatic samples in total, 8 control untreated samples, replicates per treated group n=4-6

middle: P

first: Kasper

last: Derks

first: Paul

last: Wackers

first: Tessa

last: Pronk

first: Mirjam

middle: M

last: Schaap

first: Edwin

last: Zwart

first: Jeroen

last: Pennings

first: Martijs

last: Jonker

first: Timo

last: Breit

first: Wilfred

middle: F

last: van Ijcken

first: Joris

last: Pothof

first: Harry

last: van Steeg

last: Luijten


title: Shoot and root of barley seeds: Methyl Jasmonate (MeJA) treatment

city: Tsukuba

first: Shingo

last: Nakamura

state: Ibaraki

address: Kannondai 2-1-18

institute: National Institute of Crop Science

summary: Transcriptional profiling  of barley shoot and root with MeJA

overall_design: Time course experiments

first: Takashi

last: Matsumoto


title: A targeted knockdown screen of genes coding for phosphoinositide modulators identifies PIP4K2A as required for acute myeloid leukemia cell proliferation and survival

status: Public on Mar 13 2014

city: Manchester

first: Tim

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

summary: Given the importance of deregulated phosphoinositide (PI) signaling in leukemic hematopoiesis, genes coding for proteins that regulate PI metabolism may have significant and as yet unappreciated roles in leukemia. We performed a targeted knockdown screen of PI modulator genes in human AML cells and identified candidates required to sustain proliferation or prevent apoptosis. One of these, the lipid kinase phosphatidylinositol-5-phosphate 4-kinase, type II, alpha (PIP4K2A) regulates cellular levels of phosphatidylinositol-5-phosphate (PtsIns5P) and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). We found PIP4K2A to be essential for the clonogenic and leukemia-initiating potential of human AML cells, and for the clonogenic potential of murine MLL-AF9 AML cells. Importantly, PIP4K2A is also required for the clonogenic potential of primary human AML cells. Its knockdown results in accumulation of the cyclin-dependent kinase inhibitors CDKN1A and CDKN1B, G1 cell cycle arrest and apoptosis. Both CDKN1A accumulation and apoptosis were partially dependent upon activation of the mTOR pathway. Critically, however, PIP4K2A knockdown in normal hematopoietic stem and progenitor cells, both murine and human, did not adversely impact either clonogenic or multilineage differentiation potential, indicating a selective dependency which we suggest may be the consequence of the regulation of different transcriptional programmes in normal versus malignant cells. Thus, PIP4K2A is a novel candidate therapeutic target in myeloid malignancy.

overall_design:
AIM: to determine the transcriptional consequences of Pip4ka knockdown in murine normal and leukaemic bone marrow stem and progenitor cells.

KIT+ stem and progenitor cells were immunomagnetically recovered from the bone marrow of two female C57/BL6 mice, pooled and cultured in RPMI with 20% FBS supplemented with SCF 300ng/mL, FL 1ng/mL and IL-11 20ng/mL. Next day these cells were spinfected with lentiviral supernatant (shPip4k2a constructs #1, #2 or a non-targeting control). Likewise, the same viral supernatant was used to spinfect (cryopreserved, thawed and overnight cultured) leukemic blasts recovered from the BM of mice with MLL-AF9 AML (initiated using a retroviral transduction and transplantation approach). Cells were FACS purified for GFP expression (the selectable marker) 48h following lentiviral infection and returned to culture. Seventy-two hours following lentiviral infection control and Pip4k2a KD cells were recovered from culture for mRNA extraction.


title: Shoot and root of barley seeds: Aluminum treatment

summary: Transcriptional profiling  of barley shoot and root with AlCl3


title: Mycobacterium tuberculosis: Control Vs db-cAMP treated cells

status: Public on Jan 23 2014

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

institute: Translational Health Science and Technology Institute

summary: Transcriptional profiling of Mycobacterium tuberculosis CDC1551 comparing control butyric acid-treated cells with 20mM db-cAMP treated cells after 2hrs of treatment with shaking at 200rpm at 37C.

overall_design: Two-condition experiment, butyric acid (Control) Vs db-cAMP treated cells (Test). Biological replicates: 3 control, 3 test. One replicate per array.

first: William

last: Bishai