title: UV-C dose and time range finding study on Mouse Embryonic Fibroblasts (MEFs)

summary:
In molecular biology, the design of mechanistic experiments has to be optimized by considering statistical and biological principles. In contrast to statistical principles, biological principles of experimental design are not universally formulated. In an attempt to pinpoint generally acceptable rules, we investigated the importance of determining the optimal ranges of scale of i.e. dose and time in gene expression experiments.
We propose a protocol for executing small scale, genome wide, range finding studies, covering a wide range of the potentially relevant part of the design space to find the optimal ranges of experimentation. This protocol is executed and a proof-of-concept is presented, where this approach is tested for both an in-vitro and an in-vivo study that aim to unravel DNA repair mechanisms provoked after UV radiation. We identified four challenges of range finding studies in omics experimentation; (1) the modularity of biological processes, (2) their dynamics, (3) the extent to which end-points indicate biological processes, and (4) the costs associated with the assays, which are all addressed by our approach.

overall_design: 48 MEF samples having various combinations of 9 timepoints and 6 UV-C Doses without replication were used


title: Neisseria meningitidis elicits a pro-inflammatory response involving IκBζ in a human blood-cerebrospinal fluid barrier model.

status: Public on Sep 16 2014

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: The human-specific, Gram-negative bacterium Neisseria meningitidis (Nm) is a leading cause of bacterial meningitis world-wide. It has been described that Nm can enter the central nervous system via the blood-cerebrospinal fluid barrier (BCSFB), which is constituted by the epithelial cells of the choroid plexus. Using a recently established in vitro model of the human BCSFB based on human malignant choroid plexus papilloma (HIBCPP) cells we investigated the cellular response of HIBCPP cells challenged with the meningitis-causing Nm strain MC58. In comparison we analysed the answer to the closely related unencapsulated carrier isolate Nm α14. Transcriptome analysis revealed a stronger transcriptional response after infection with strain MC58, in particular with its capsule deficient mutant MC58siaD-, which correlated with bacterial invasion levels. Expression evaluation and Gene Set Enrichment Analysis pointed to a NF-κB-mediated pro-inflammatory immune response involving up-regulation of the transcription factor IκBζ. Consistent with this, infected cells secreted significant levels of pro-inflammatory chemokines and cytokines, among others, IL8, CXCL1-3 and the IκBζ target gene product IL6. Expression profile of pattern recognition receptors in HIBCPP cells and the response to specific agonists indicates that TLR2 rather than TLR4 is involved in the cellular reaction following Nm infection.

overall_design: Human malignant choroid plexus papilloma (HIBCPP) cells were infected from the basolateral side with the meningitis-causing Neisseria meningitidis disease isolate MC58, its non-capsulated mutant MC58siaD- and the Neisseria meningitidis carrier isolate α14 for 4 h.The transcriptional response of HIBCPP cells to the different Neisseria meningitidis strains was evaluated by microarray analysis. Untreated HIBCPP cells served as control. Three replicates of each condition were analysed.

first: Julia

last: Borkowski

first: Li

last: Li

first: Ulrike

last: Steinmann

first: Natascha

last: Quednau

first: Carolin

last: Stump

first: Peter

last: Findeisen

first: Norbert

last: Gretz

first: Hiroshi

last: Ishikawa

first: Tobias

last: Tenenbaum

first: Horst

last: Schroten

first: Christian

last: Schwerk


title: Gene expression profiling in leaf and panicles of non-transgenic and HMB4 over-expression line.

status: Public on Sep 01 2014

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

type: Expression profiling by genome tiling array

summary:
The profiling was conducted with the Rice 3'-Tiling 135k Microarray designed from 31,439 genes deposited at IRGSP, RAP2 database (http://rapdb.lab.nig.ac.jp).
In this research, an array of 31,439 rice genes was used to elucidate gene expression in leaf and panicles of non-transgenic and HMB4 over-expression line. The analyses show that transgenic rice induces early flowering due to an enhancement of stress response.

overall_design: A total of 20 chips were used for microarray. Total RNAs were extracted from rice leaf and panicle. Experiments were duplicated.

first: P

middle: T

last: Thu

first: B

middle: H

last: Nahm

first: Y


title: UV-B dose and time range finding study on mouse biopsy skin samples

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

overall_design: 57 skin biopt samples taken from 12 individual mice on 8 timepionts and for 6 different UV-B doses. Per mouse 5 skin biopts were samples in time

first: Wendy

last: Rodenburg

first: Conny

last: van Oostrum

first: Martijs

middle: J

last: Jonker

first: Mark

last: de Jong

first: Rob

last: Dekker

first: Han

last: Rauwerda

first: Wim

middle: A

last: Ensink

first: Annemieke

last: de Vries

first: Timo

middle: M

last: Breit


title: Aldosterone regulated genes in distal colon surface cells

city: Rehovot

first: Haim

last: Garty

address: Hertzel 234

department: Biological Chemistry

country: Israel

institute: The Weizmann Institute of Science

summary: Effects of aldosterone on the transcriptome in distal colon.

overall_design: Expression of genes was studied in distal colon surface cells from aldosterone treated vs. vehicle treated rats.

first: Ekaterina

last: Petrovich


title: Toxicogenomics of Eohaustorius estuarius following pyrethroid and ammonia exposure

city: Moncton

first: Paula

last: Jackman

state: NB

address: 443 University ave

country: Canada

institute: Environment Canada

summary: A variety of contaminants find their way to the marine sediments from different sources, and these contaminants can pose serious risks to the natural marine flora and fauna. For example, pyrethroids, which are a potent pesticide family, are often used in agriculture fields worldwide, and these find their way into the marine environment through run off. Further, pyrethroids are used in farmed Atlantic salmon cages in Chile, Great Britain and Norway. Ammonia is another contaminant that is used in agriculture in form of ammonia-rich fertilizer and can be carried during run-offs to localized rivers and streams.  Ammonia is also detectable after emission of effluents from sewage treatment plants and industrial plants like oil refineries and meat processing plants.  Contaminants may have short and long term effects on non-target organisms living in the water column or in the marine sediment. Importantly, the sediment ecosystem houses a variety of plants, animals and crustaceans, including the American lobster Homarus americanus.  Lobster is the most fished crustacean in New Brunswick and Quebec and its resale and exportation produced over $1.6 billion in 2011.  Due to its economic and environmental importance, it is essential to study the effects of contaminants present in its ecosystem.  Sediment samples are often used as pollution markers during toxicity testing due to their tendency to accumulate hydrophobic contaminants.  To better understand the possible effects of contaminants in sediment, a total gene expression study was developed using the marine amphipod Eohaustorius estuarius.  A 10 day spike-in exposure was performed using ammonia and two pyrethroids, namely cypermethrin and deltamethrin. As pyrethroids and ammonia are known to have vastly different mechanisms of action in living organisms, we compared global gene expression patterns following exposure to ammonia against the patterns observed following exposure to pyrethroids. Total gene expression was measured by oligonucleotide microarray.  The expression of five genes of interest involved in different biological processes such as metabolism, transcription, translation, immunity and stress, which were found to be differently expressed by microarray, was validated by RT-qPCR.  A set of genes was identified that showed differential expression levels in a treatment-dependent manner, thus further highlighting the different mechanisms of action of ammonia and pyrethroids in the marine sediment.  This study provides a proof of concept for the use of DNA microarrays with model crustaceans for the study of marine sediment contaminants.

overall_design: This specific study is aimed at evaluating the effect of ammonia and pyrethroid exposure on E.estuarius and to identify possible biomarkers of these exposures.

first: Valérie

last: Béchard

first: Pier

last: Jr Morin

last: Laflamme

first: Steven

last: Bay

first: Chris

last: Vulpe


title: Evaluation of the robustness of classification of carcinogen-modified transcriptomic responses in HepaRG cells and the interlaboratory reproducibility of the model

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

country: Belgium

institute: VUB

summary: Efforts to develop alternatives which can at least partially replace some of the currently used in vivo tests are ongoing. The recently ended FP6 European project carcinoGENOMICS had the goal to use the combination of toxicogenomics and in vitro cell culture models for identification of genotoxic- and non-genotoxic carcinogen-specific gene signatures. In this study is presented a part of the outcome of the project and in particular the performance of the gene classifier derived after exposure of the HepaRG cell line to prototypical hepatocarcinogens. Upon analyzing the data at a gene and a pathway level by using diverse biostatistical approaches, a clear-cut separation of the genotoxic from the non-genotoxic hepatocarcinogens and non-carcinogens was achieved (up to 88% correct prediction). The most characteristic pathway for genotoxic exposure was DNA damage. Further to show the robustness of the HepaRG model, the interlaboratory reproducibility of 3 blindly tested compounds was assessed. The results showed between 20% and 35% reproducibility. The subsequent classification of the 3 blindly tested compounds resulted in correct prediction of the genotoxicant, whereas the other two compounds were misclassified. In conclusion, the combination of transcriptomics and HepaRG in vitro cell model provides a solid basis for the detection of the genotoxic potential of unknown chemicals.

overall_design:
HepaRG cells were exposed to 15 selected compounds for 72 hours, i.e. 5 GTX (N-nitrosomorpholine, NMP; Hydroquinone, HQO; Hydrazine dihydrochloride, HHC; 2-acetylaminofluorene, TAF; 2-amino-3-methylimidazo(4,5-f)quinoline, AMQ), 5 NGTX (Fumonisin B1, FMB; Cyclosporine A, CsA; Acetamide, ACE; Diethylhexyl Phthalate, DHP; Ethanol, ETH), 5 NC (4-acetylaminofluorene, FAF; D,L-Menthol, DLM; Benzoin, BEN; Benzyl Alcohol, BEA; Triclosan, TRI). The IC10 concentrations (reducing cell viability by 10%) were determined by a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide test (MTT test)  (number of replicates n=3). Further RNA samples were generated by exposure of the HepaRG cells to the MTT-determined IC10 for a period of 24h and 72h. Complementary RNA targets were prepared and hybridized according to the manufacturer's procedures on high-density oligonucleotide microarrays (i.e. Affymetrix U133 Plus 2.0 GeneChip). Finally,alaysis was performed at a gene and pathway level.
In the analysis, control (DMSO) samples were re-normalized with several sample groups and new processed data were created for each analysis.  Thus, some of the Samples in this Series represent a re-analysis of other Samples and CEL files are identical.

middle: Y

first: Reha

last: Yildirimman

first: Liesbeth

last: Ceelen

first: Mireia

last: Vilardell

first: Tamara

last: Vanhaecke

first: Mathieu

last: Vinken

first: Gamze

last: Ates

first: Anja

last: Heymans

first: Hans

last: Gmuender

first: Roque

last: Bort

first: Raffaella

last: Corvi

first: Pascal

last: Phrakonkham

first: Ruoya

last: Li

first: Nicolas

last: Mouchet

first: Christophe

last: Chesne

first: Joost

last: van Delft

first: Jos

last: Kleinjans

first: Jose

last: Castell

first: Ralf

last: Herwig

first: Vera

last: Rogiers


title: Characterisation of Modular Reponse of non-pathogenic E.coli K12 MG1655 Response to acid adaptation, part B

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

summary:
To study the dynamics of acid adaptation in E.coli at pH5.5 as opposed to that at pH7, samples were collected from a steady-state system for transcriptomics.

Keywords: time course

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

overall_design: Single channel hybridisation were carried out using cy5 dye. Samples were collected from steady state system at pH7 and pH5.5 for 2.5h at 0min, 10min, 30min, 1h, 1.5h, 2h, 2.5h

first: Ayesha

last: Rahman

first: Francesco

last: Falciani


title: Human hepatocytes support the hypertrophic but not the hyperplastic response to the murine nongenotoxic hepatocarcinogen sodium phenobarbital in an in vivo study using a chimeric mouse with humanized liver [Rat Liver Experiments]

status: Public on Aug 29 2014

city: Osaka

first: Kayo

last: Sumida

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

department: Environmental Health Science Laboratory

country: Japan

institute: Sumitomo Chemical Co., Ltd.

summary: High doses of sodium phenobarbital (NaPB), a constitutive androstane receptor (CAR) activator, have been shown to produce hepatocellular tumors in rodents by a mitogenic mode of action (MOA) involving CAR activation. The effect of 1 week dietary treatment with NaPB on liver weight and histopathology, hepatic CYP2B enzyme activity and CYP2B/3A mRNA expression, replicative DNA synthesis and  selected genes related to cell proliferation and functional transcriptomic and metabolomic analyses was studied in male CD-1 mice, Wistar Hannover (WH) rats and chimeric mice with human hepatocytes. The treatment of chimeric mice with 1000-1500 ppm NaPB resulted in plasma levels around 3-5 fold higher than those observed in human subjects given therapeutic doses of NaPB. NaPB produced dose-dependent increases in hepatic CYP2B activity and CYP2B/3A mRNA levels in all animal models. Integrated functional metabolomic and transcriptomic analyses demonstrated the responses to NaPB in human liver were clearly different from those in rodents. While NaPB produced a dose-dependent increase in hepatocyte replicative DNA synthesis in CD-1 mice and WH rats, no increase in replicative DNA synthesis was observed in human hepatocyte-originated areas of chimeric mice. In addition, treatment with NaPB had no effect on Ki-67, PCNA, GADD45β, and MDM2 mRNA expression in chimeric mice, whereas significant increases were observed in CD-1 mice and/or WH rats. Thus, while NaPB could activate CAR in rodent and human hepatocytes, NaPB did not increase replicative DNA synthesis in human hepatocytes of chimeric mice, whereas it was mitogenic to rat and mouse hepatocytes. As human hepatocytes are refractory to the mitogenic effects of NaPB, the MOA for NaPB-induced rodent liver tumor formation is thus not relevant for humans.

overall_design: Male WH rats (4 animals/dose) were fed diets containing 0 (control) or 2500 ppm NaPB for 7 days. Liver samples were used for gene expression analysis.

first: Tomoya

last: Yamada

first: Yu

last: Okuda

first: Masahiko

last: Kushida

first: Hayato

last: Takeuchi

first: Hirohisa

last: Nagahori

first: Takako

last: Fukuda

first: Brian

middle: G

last: Lake

first: Samuel

last: Cohen

first: Satoshi

last: Kawamura


title: Characterisation of Modular Reponse of non-pathogenic E.coli K12 MG1655 Response to acid adaptation, part A

overall_design: Single channel hybridisation were carried out using cy5 dye. Samples were collected from steady state system at pH7 and pH5.5 for 1hr every 5min.


title: 12plex_vitis_2011_02_24h

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary:
12plex_vitis_2011-02 - 12plex_vitis_2011_02_24h - Biological question (15 lines max):
Identification of grape genes regulated in response to resistance inducer treatments.
This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.

overall_design: 17 dye-swap - normal vs disease comparison,treated vs untreated comparison

first: Stephanie

last: Huguet

first: Xavier

last: Daire

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Expression profiles of wildtype and SHOX transgenic embryonic mouse limbs

status: Public on Aug 13 2014

first: Carsten

last: Sticht

summary:
Deficiency of the human short stature homeobox-containing gene (SHOX) has been identified in several disorders characterized by reduced height and skeletal anomalies such as Turner, Leri-Weill and Langer syndrome as well as idiopathic short stature. Although highly conserved in vertebrates, rodents lack a SHOX orthologue.
Here, we compared gene expression profiles of wildtype and SHOX transgenic mouse limbs using microarray experiments to identify SHOX target genes in the developing limb.

overall_design: Limbs of E12.5 mouse embryos were dissected, fore- and hindlimbs were pooled and genotyped for RNA extraction. RNA from 2 to 4 littermates was pooled per genotype (Wildtype and SHOX transgene) and compared. In total, 2 microarray hybridization experiments were performed using RNA from 2 biological replicate samples for each genotype.

first: Katja

middle: U

last: Beiser

first: Norbert

last: Gretz


title: Gene expression profiling of processing glycosidase inhibitors: defining a common gene set produced by processing glycosidase inhibition in human cervical carcinoma HeLa cells

city: Kamakura

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The objective of the present study is to investigate the role of processing glycosidase inhibition induced by processing glycosidase inhibitors, namely castanospermin as the processing glucosidases inhibitor, deoxymannojirimycin as the processing mannosidases inhibitor, and deoxyfuconojirimycin as the fucosidase inhibitor. Comparative gene expression analysis was performed in human cervical carcinoma HeLa cells, with non-inhibitor-treated cells as the negative control. Gene expression was analyzed using 3D-Gene® Human 25k oligonucleotide microarrays and computational gene expression analysis tools.

overall_design: Inhibition of processing glycosidases (glucosidases, mannosidases, and fucosidase) in human cervical carcinoma HeLa cells was performed by treating with a small molecule inhibitor and then culturing at 37°C. Total RNA samples were prepared from the cells. Gene expression was analyzed using 3D-Gene® Human 25k oligonucleotide microarrays. Sample preparation for array hybridization was carried out as described in the manufacturer's instructions.

first: Wataru

last: Hakamata

first: Takumi

last: Tsukagoshi

first: Atsuko

last: Suzuki

first: Saori

last: Tamura

first: Hakako

last: Hirano

first: Toshiyuki

last: Nishio


title: NRSF mediated epigenetic mechanisms of ion channel dysfunction in experimental temporal lobe epilepsy [Control vs. Kainate, NRSE ODNs]

status: Public on Aug 12 2014

city: Irvine

first: Shawn

last: McClelland

state: CA

address: 19182 Jamboree

department: Anatomy & Neurobiology

country: USA

institute: UC Irvine

summary: Oligodeoxynucleotides used to prevent NRSF binding to NRSE containing genes were utilized to prevent many kainate induced status epilepticus changes in gene expression.

overall_design: Total RNA recovered from CA1 of hippocampus of rats receiving scrambled or NRSE oligodeoxynucleotides, and saline(controls) or kainate injections (induced status epilepticus)

first: Tallie

middle: Z

last: Baram


title: NRSF mediated epigenetic mechanisms of ion channel dysfunction in experimental temporal lobe epilepsy [Kainate, NRSE ODNs vs. Kainate, scrambled ODNs]

summary: Oligodeoxynucleotides used to prevent NRSF binding to NRSE containing genes were used to prevent many kainate induced status epilepticus changes in gene expression.

overall_design: Total RNA recovered from CA1 of hippocampus of rats receiving scrambled or NRSE oligodeoxynucleotides, and kainate injections (induced status epilepticus)


title: Global gene expression profiling of guinea pig whole-lung and hindlimb muscles following long-term exposure to cigarette smoke and/or hypoxia

status: Public on Aug 11 2014

city: Liverpool

first: Peter

last: Davidsen

state: Merseyside

address: Crown Street

institute: University of Liverpool

summary: Despite intense efforts the molecular understanding of this clinically important extra pulmonary manifestation is still limited. Cigarette smoking is the main risk factor for developing COPD and therefore animal chronic smoking models have been proposed for mechanistic studies and biomarker discovery. The overarching aim of our study was to assess whether GP hindlimb muscles (both oxidative and glycolytic) show a transcriptional response to these exposures, and whether such gene signatures can be correlated to the expression of lung secreted proteins.

overall_design: A cross-sectional microarray study was designed. Hartley guinea pigs were divided into four groups: one group was exposed to cigarette smoking for 3 months (n=3-4); a second group was kept in normoxia for 10 weeks and subsequently placed in an hypoxic environment (12% O2) for two weeks (n=3-4); a third group (n=4) was smoke-exposed for 3 months and to chronic hypoxia the last two smoking weeks; finally a forth group (n=3-4) served as controls remaining in normoxia for the whole study period.

middle: K

first: Francesco

last: Falciani


title: Characterisation of Modular Reponse of non-pathogenic E.coli K12 MG1655 and O157 Sakai Response to acid adaptation

last: Turan

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

overall_design: Refer to individual Series


title: Characterisation of Modular Reponse of non-pathogenic E.coli O157 Sakai Response to acid adaptation

first: Ayesha

last: Rahman


title: NRSF mediated epigenetic mechanisms of ion channel dysfunction in experimental temporal lobe epilepsy


title: SRp20 regulates Genome-wide Alternative RNA splicing events in MEF3T3 cells

status: Public on Aug 08 2014

city: Frederick

first: Masahiko

last: Ajiro

state: MD

address: 1050 Boyles St Bldg 539 Rm 153

institute: National Cancer Institute

summary: To examine the effects of SRp20 on genome-wide RNA splicing in mouse cells, we utilized Exonhit SpliceArrayTM to compare genome-wide changes of RNA splicing and transcription in MEF3T3 mouse fibroblasts with or without ectopic expression of SRp20.

overall_design: MEF3T3 tet-off cells were transfected with pRevTRE/T7-SRSF3 expression vector (pJR17) or pFLAG-CMV5.1 empty vector, each performed in triplicate. A mouse genome-wide splice-array assay was performed by using a service provider ExonHit Therapeutics, Inc (Gaithersburg, MD). Fifty ng of total RNA isolated from MEF3T3 cells with or without SRp20 overexpression was quality controlled and analyzed by using Affymetrix GeneChip platform.

first: Rong

last: Jia

first: Zhi-Ming

last: Zheng


title: 12plex_vitis_2011_02_48h

first: Stéphanie

last: Pateyron

summary:
12plex_vitis_2011_02_48h - Biological question (15 lines max):
Identification of grape genes regulated in response to resistance inducer treatments.

This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.
The experiment took place in the greenhouse. Six week-herbaceous grape cutting (cv Marselan) were spray-treated with 5 resistance inducers, an adjuvant (used along with some inducers) and water as control. Plants were inoculated by Plasmopara viticola (downy midew) 24h post-treatment. We used 5 plants per treatment. Leaf samples were harvested 24h post-treatment and 48h post-inoculation. Three biological repetitions were done. Each hybridization experiment was performed in comparison with water.

overall_design: 18 dye-swap - normal vs disease comparison

first: Stephanie

last: Huguet

first: Xavier

last: Daire

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: The Genetic Prehistory of the New World Arctic

status: Public on Aug 28 2014

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

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

summary: To carry out population genetics analyses of the Arctic gregion we carried out Illumina Bead-Array-based enotyping on 18 samples from Greenland.

overall_design: 19 samples were analysed with the Illumina platform Human660W-Quad v1.0 Genotyping BeadChip and are described herein.

first: Richard

last: Villems

first: Eske

last: Willerslev

first: Maanasa

last: Raghavan


title: Expression profiles of Actinobacillus pleuropneumoniae 4074 and the qseB/qseC gene-deleted mutant

status: Public on Aug 01 2014

city: Wuhan

first: Jinlin

last: Liu

address: 152# Luoyu Street

department: College of Life Science

country: China

institute: Central China Normal University

summary: To determine the role of Actinobacillus pleuropneumoniae two-component system QseBQseC, we constructed a qseBqseC gene-deleted mutant ΔqseBΔqseC based on the wild type A. pleuropneumoniae 4074. The transcriptional profiles were compared between the A. pleuropneumoniae ΔqseBΔqseC and its parental strain under the normal growth condition using microarray. A total of 44 genes were found differentially expressed (DE) compared to the wild type strain. These functional genes are primarily related to metabolism, cell wall biogenesis, energy, replication and recombination. Further investigations indicated that the type IV pili (Tfp) assembly protein PilM is regulated directly by QseB, and PilM is essential for adherence and virulence. Characterization of the QseBQseC regulon genes will provides new insight into understanding of the relevant signal transduction pathways and prevention of the infection.

overall_design: A. pleuropneumoniae strains were cultured in TSB medium supplemented with 10 μg/ml of nicotinamide adenine dinucleotide (NAD) and 10% (v/v)filtered cattle serum at 37℃. The samples were collected at the mid-exponential phase and the total RNA were extracted using RNA-Solv Reagent (Omega) according to the manufacturer’s instructions. Expression profiles of two different Actinobacillus pleuropneumoniae (4074 and ΔqseBΔqseC) were determined. The fold changes >=1.5 or <=-1.5 were selected as differentially expressed genes.

first: J

first: W

last: Bei


title: Hepatic transcriptional profiling of mRNA and microRNA in pigs infected with Actinobacillus pleuropneumoniae

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

summary: Actinobacillus pleuropneumoniae is a gram-negative bacterium that causes porcine pleuropneumonia, which is a widespread, highly contagious, and often fatal respiratory disease in swine. In this experiment pigs were inoculated with A. pleuropneumoniae serotype 5b. Liver samples from three non-inoculated pigs and three experimental inoculated pigs were used to characterize the expression profiles of mRNA and microRNA genes using DNA microarrays and Illumina GA deep sequencing, respectively. The microarray analysis identified a large number of genes, which significantly differed in expression in infected versus non-infected animals. MicroRNAs are short single stranded RNA molecules that regulate gene expression by sequence specific binding to the 3´ untranslated region (3´UTR) of target mRNAs. The deep sequencing analysis determined the identity and abundance of nearly 400 microRNAs, of which a portion was found to significantly differ in expression between the infected and non-infected animals. Target genes for differentially expressed microRNAs were predicted using microCosm Targets, which is based on the miRanda algorithm. Comparison on the two gene lists showed many common genes, which may suggest a causative relationship between changes in microRNA expression and target gene expression.

overall_design: The expression profiles of mRNA and smallRNA in liver from three experimentally infected pigs were compared with the profiles three non-infected contol pigs.

first: Matilde

last: Nielsen

first: Rasmus

middle: O

first: Kerstin

last: Skovgaard

first: Peter

last: Heegaard

first: Christian

last: Bendixen

first: Bo

last: Thomsen


title: Integrative analysis demonstrates widespread NOTCH pathway activation in patients with renal cancer and reveals aberrant DNA methylation that targets the regulatory regions of the kidney genome

status: Public on Jul 31 2014

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Even though mutations in epigenetic regulators have been seen in renal neoplasms, their effects on the epigenome have not been elucidated. High resolution analysis of DNA methylation was performed in clear cell RCCs and matched microdissected renal tubular controls and revealed widespread hypermethylation that preferentially affected gene bodies and CpG shores. Aberrant methylation was particularly enriched in kidney specific enhancer regions associated with H3K4Me1 marks. MOTIF analysis of aberrantly methylated loci revealed enrichment for AHR, HAIRY and HIF-1 transcription factors, reflecting dysregulated hypoxia and NOTCH pathways in RCC. Parallel copy number analysis demonstrated that both genetic and epigenetic alterations led to NOTCH pathway activation in RCC. NOTCH ligands,JAGGED1 and JAGGED2, were overexpressed and associated with hypomethylation and amplification respectively in RCC samples. Examination of TCGA RNA-seq dataset revealed widespread activation of NOTCH pathway in 405 RCC samples. Samples with NOTCH pathway activation were also clinically distinct and were associated with better overall survival.  Finally, transgenic expression of NOTCH1 led to dysplastic hyperproliferation of tubular epithelial cells in vivo confirming the procarcinogenic role of NOTCH.  In summary, our study is the first global methylome analysis of RCC and reveals that mechanistic basis of NOTCH pathway activation in RCC.

overall_design: We analyzed the methylome of clear cell renal cell cancer (CCRCC) by the HELP assay. 13 cases of histologically verified CCRCC tumor samples were compared to 13 control microdissected proximal tubules from non-tumor part of nephrectomy samples

first: Caroline

last: Hu

first: A

last: Verma


title: Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

summary: Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade.

sample_organism:
Embryophyta
Digitalis purpurea
Sambucus nigra
Cornus
Camellia sinensis
Achillea millefolium
Coffea arabica
Codonopsis
Valeriana officinalis
Impatiens
Angelica archangelica
Tetrapanax papyrifer
Taraxacum officinale
Vitex agnus-castus
Trachelospermum jasminoides
asterids
Scrophularia nodosa
Platycodon grandiflorus
Rehmannia glutinosa
Lonicera japonica
Lycium barbarum
Gardenia jasminoides
Forsythia suspensa
Withania somnifera
Ilex paraguariensis
Symphytum
Leonurus cardiaca

overall_design: DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. 25 Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. 37 polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants.

first: Edwin

last: Pang


title: Cyanide response in Escherichia coli

city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

summary: The goal was to ascertain the impact of cyanide treatment on E. coli's transcriptome.

overall_design: There were 4 biological samples.  For each sample there were two replicate DNA microarray performed.  Data was analyzed with Imagene and lcDNA Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.

first: Laura

last: Jarboe


title: Elevated MAOA Expression Enhances Tumor Growth In-vivo and Alters Transcriptional Profiles

status: Public on Jul 03 2014

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Subcutaneous xenografts were derived utilizing either PC3 cells engineered to stably overexpress MAOA or empty vector controls in mice receiving docetaxel treatment.  Tumor gene expression was profiled using Agilent gene expression microarrays.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile subcutaneous xenograft tumors derived utilizing either PC3 cells engineered to stably overexpress MAOA or empty vector controls in mice receiving docetaxel treatment. Total RNA was isolated and amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Ryan

last: Gordon

first: Mengchu

last: Wu

first: Chung-Ying

last: Huang

first: William

middle: P

last: Harris

first: Hong-Gee

last: Sim

first: Jared

last: Lucas

first: Celestia

middle: S

last: Higano

first: Roman

last: Gulati

first: Lawrence

middle: D

last: True

first: Robert

last: Vessella

first: Paul

last: Lange

first: Mark

last: Garzotto

first: Tomasz

last: Beer

last: Nelson


title: Cynomolgus macaque model of H7N9 influenza infection

status: Public on Jul 22 2014

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: The objective of this study is to characterize the response to newly emerged, highly pathogenic H7N9 influenza virus isolated from human patients in 2013 in China. This study examines the pathogenesis of H7N9 influenza in cynomolgus macaques. The study compares lung lesions to adjacent right lower lobe lung tissue in animals necropsied at days 3 and 6 post-infection (n=4 animals/timepoint).  3-4 lesions from each animal were collected and equal amounts of pooled RNA from lesions from individual animals at each time point were used for microarray.

overall_design: 8 cynomolgus macaques were infected via oral, intraocular, intranasal, and intratracheal administration of a combined total of 7x10^6 TCID50. Lungs, lung lesions, and trachea samples were collected from serial sacrifices of 4 animals each at day 3 and day 6. Infection produced a moderate-severe, self-limiting respiratory infection, and was not lethal. We performed microarray analysis (using Agilent Rhesus arrays) on all lungs, lung lesions, and trachea collected for the study.

first: Angela

last: Rasmussen

first: Atsushi

last: Okumura

first: Emmie

last: de Wit

first: Heinz

last: Feldmann

first: Vincent

last: Munster


title: Gene expression profiles of human prefrontal cortex brain tissues

city: New York

first: Jun

last: Zhu

address: One Gustave L Levy, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn Medical School at Mount Sinai

summary: Dissecting the shared etiology of different diseases could benefit from a systematic search for associated molecules and their interactions. We investigated genome-wide disruptions in the co-regulation of genes in two neurodegenerative diseases, Alzheimer's or Huntington's disease (AD or HD), using expression profiles from postmortem prefrontal cortex samples of 624 demented patients and non-demented control individuals with matched genotype and clinical data. A meta-analysis based screen for changes in coordinate expression patterns revealed differentially co-expressed (DC) gene pairs that either gained or lost correlation in disease cases relative to the control group, with the former being dominant for both AD and HD. Integration of disruptions common to AD and HD with large-scale data on protein-protein and protein-DNA interactions yielded a 242-gene sub-network that was enriched for proteins involved in neuronal differentiation and genetic associations to brain structural changes and dementia in subjects aged over 70 years. Replication of the AD DC network in independent human and mouse cohorts lends confidence to the comprehensive view we offer on dysregulated brain molecular pathways in AD and HD.

overall_design: DLPFC (BA9) brain tissues of AD patients, HD patients and non-demented controls samples were obtained from Harvard Brain tissue resource center (HBTRC). The HBTRC samples were primarily of Caucasian ancestry, as only eight non-Caucasian outliers were identified, and therefore excluded for further analysis. Post-mortem interval (PMI) was 17.8+8.3 hours (mean ± standard deviation), sample pH was 6.4±0.3 and RNA integrity number (RIN) was 6.8±0.8 for the average sample in the overall cohort. Tissues were profiled on a custom-made Agilent 44K array (GPL4372). 624 individual DLPFC samples were profiled against a common DLPFC pool constructed from the same set of samples.

first: Manikandan

last: Narayanan

first: Kai

last: Wang

first: Xia

last: Yang

first: Joshua

last: McElwee

first: Bin

last: Zhang

first: Chunsheng

first: John

last: Lamb

first: Tao

last: Xie

first: Christine

last: Suver

first: Cliona

last: Molony

first: Stacey

last: Melquist

first: David

last: Stone

first: Eric

middle: E

last: Schadt

first: Valur

last: Emilsson


title: Maternal Bisphenol A effect on fetal heart and skeletal muscle gene expression

status: Public on Jul 01 2014

city: Davis

first: Matt

middle: L

last: Settles

address: 451 Health Sciences Sr

department: Genome Center

institute: University of California, Davis

summary:
Compairsion of transcriptional profiles of heart and skeletal muscle tissue of fetal rhesus monkey exposed to maternal Bisphenol A or vehicle during early or late gestaion.
Maternal exposure to the endocrine disrupting chemical, bisphenol A (BPA) affects the development of multiple organ systems in rodents and monkeys. However, effects of BPA exposure on cardiac and skeletal muscle development have not been assessed. Given that maternal BPA crosses placenta and reaches developing fetus, examining the physiological consequences of gestational exposure during development is of research significance. Therefore, we evaluate the effects of daily, oral BPA exposure of pregnant rhesus monkeys (Macaca mulatta) on the fetal heart and skeletal muscle transcriptome. Pregnant monkeys were administered daily oral doses (400 µg/kg body weight) of BPA during early (50 –100 ± 2 days post conception, dpc) or late (100 ± 2 dpc - term), gestation. At the end of treatment, fetal heart tissues; left ventricle (LV), right ventricle (RV), left atrium (LA), right atrium (RA) and skeletal muscle; biceps femoris (BFM), were collected.  Transcriptome expression was assessed using genome-wide microarray in each of the tissues and compared paired-wise between the BPA and matched control fetuses. Our results show that maternal BPA exposure alters transcriptional profile of several coding and non-coding genes in fetal heart and skeletal muscle.

overall_design: Pregnant rhesus monkey were administered a daily oral dose of 400 μg/kg. body weight of Bisphenol A (BPA) or vehicle (CON) either during early (50–100 ± 2 days) or late (100 ± 2 days–term) gestation. Gene expression profiles of each of  the  heart chambers (left ventricle, LV;  right ventricle, RV;  left atrium, LA; and right atrium, RA) and skeletal muscle (biceps femoris, BFM) were analyzed using microarrays and compared between the BPA exposed and matched control fetuses. A total of 12 samples were analyzed for each tissue; LV, RV, LA, RA and BFM. This includes 6 samples at each time period (early vs. late gestation) and 3 biological replicates for each treatment (BPA, n=3; control, n=3).

first: Matthew

first: Kalyan

middle: C

last: Chapalamadugu

first: Catherine

last: VandeVoort

first: Barrie

last: Robison

first: Gordon

last: Murdoch


title: Dose-dependent hepatic transcriptional responses in Atlantic salmon (Salmo salar) exposed to sublethal doses of gamma radiation

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

summary: To study the short term (48 h) hepatic transcriptional changes and identify potential modes of action, Atlantic salmon (Salmo salar) were exposed to 15 mGy, 70 mGy and 280 mGy external gamma radiation. A combination of high density (60 k) custom oligonucleotide salmonid microarray and quantitative real-time reverse transcription polymerase chain reaction (qPCR) was employed to perform gene expression analyses. Differentially expressed genes (DEGs) were determined using one-way analysis of variance (ANOVA) and Tukey posthoc tests. Functional enrichment analysis based on Gene Ontology (GO) was performed to link DEGs to their biological functions. The Salmo salar DEGs were further mapped to mammlian orthologs. By using ortholog DEGs, gene networks were built based on well-curated mammlian protein-protein interactions and pathways analyses were performed to link DEGs to specific toxicological/biological functions. The results obtained from microarray analysis were further verified using qPCR.

overall_design: Juvenile Atlantic salmon were exposed to external gamma radiation emitted from a cobalt-60 source for 48 h. Liver were sampled and used for gene expression analysis.

first: Brit

last: Salbu

first: Hans-Christian

last: Teien

first: Lene

last: Heier

first: Bjørn

last: Rosseland

first: Knut

last: Tollefsen


title: Identification of Angiotensin II-senstive microRNAs in mouse abdominal aortic endothelium

city: Atlanta

first: Sandeep

last: Kumar

state: GA

address: 1760 Haygood Dr.

department: Biomedical Engineering

institute: Emory University

summary: Endothelial-enriched total RNAs were obtained from the suprarenal region of the abdominal aorta which is the murine AAA prone area in AngII-infused C57BL/6 mice.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: At 12 or 36h post-AngII pump implantation, endothelial-enriched RNAs from four abdominal aortas were pooled to obtain ~30 ng total RNA as one array sample, performed in triplicates. All RNA samples used for miRNA microarray study passed the initial quality control test and each sample was linearly amplified.

first: Chanwoo

last: Kim

first: Dong

last: Son

first: In-Hwan

last: Jang

first: Hanjoong

last: Jo


title: The histone acetyl transferase GcnE (GCN5) is essential to activate asexual development in Aspergillus nidulans

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

country: Spain

institute: University of Seville

summary: It was reported that deletion of gcnE in the filamentous fungus Aspergillus nidulans results in minor defects in primary metabolism and major defects in development and secondary metabolism. Here we unveil the role of GcnE in development.

overall_design: The A. nidulans strains used in this study were the wild type FGSC26 (biA1 veA1) and the ∆gcnE mutant. Strains were grown in complete liquid medium for 18 h at 37 ºC and then conidiation was induced by transferring the vegetative cultures to complete solid media.

first: David

last: Cánovas

last: Gutiérrez


title: Early life stress in fathers impairs synaptic plasticity in the offspring

city: Basel

first: Guido

last: Steiner

address: Grenzacher Str.

country: Switzerland

institute: F. Hoffmann-La Roche


title: Early life stress in fathers impairs synaptic plasticity in the offspring -  brain collected after acute swim stress

summary: We show that traumatic stress experienced by males in early postnatal life impairs memory in their offspring, blocks long-term potentiation (LTP) and favors long-term depression (LTD). These effects are accompanied by suppression of key molecular pathways involved in neuronal plasticity both at rest and after acute stress.

overall_design: Male mice were exposed to chronic traumatic stress in early postnatal life and were later bred to naïve females to produce second-generation offspring. Memory performance was evaluated in the offspring, and synaptic plasticity was examined in the hippocampus and the amygdala, brain areas important for memory formation. The two groups tested were 1: offspring of fathers which were stressed (MSUS - maternal separation unpredictable stress)  and 2: offspring of non-stressed fathers (control). Genome-wide gene expression in hippocampus of these two groups was assessed at rest and after acute stress (this study).

first: Bohacek

last: Johannes

first: Farinelli

last: Melissa

first: Mirante

last: Osvaldo

first: Coiret

last: Guyllaume

first: Steiner

last: Guido

first: Ebeling

last: Martin

first: Duran

last: Gonzalo

first: Iniguez

last: A Leonardo

first: Kashuk

last: Carl

first: Manuella

last: Francesca

first: Gapp

last: Katharina

first: Moreau

last: Jean-Luc

first: Mansuy

last: Isabelle M


title: Early life stress in fathers impairs synaptic plasticity in the offspring - brain collected at rest

overall_design: Male mice were exposed to chronic traumatic stress in early postnatal life and were later bred to naïve females to produce second-generation offspring. Memory performance was evaluated in the offspring, and synaptic plasticity was examined in the hippocampus and the amygdala, brain areas important for memory formation. The two groups tested were 1: offspring of fathers which were stressed (MSUS - maternal separation unpredictable stress)  and 2: offspring of non-stressed fathers (control). Genome-wide gene expression in hippocampus of these two groups was assessed at rest (this study) and after acute stress.


title: Expression data of Actinobacillus pleuropneumoniae 4074 under aerobic and anaerobic environment

status: Public on Jun 30 2014

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

summary: Actinobacillus pleuropneumoniae is an important porcine respiratory pathogen causing great economic losses in the pig industry worldwide. Oxygen deprivation is a stress that A. pleuropneumoniae will encounter during both early infection and the later, persistent stage. To understand modulation of A. pleuropneumoniae gene expression in response to the stress caused by anaerobic conditions, gene expression profiles under anaerobic and aerobic conditions were compared in this study. The microarray results showed that 631 genes (27.7% of the total ORFs) were differentially expressed in anaerobic conditions. Many genes encoding proteins involved in glycolysis, carbon source uptake systems, pyruvate metabolism, fermentation and the electron respiration transport chain were up-regulated. These changes led to an increased amount of pyruvate, lactate, ethanol and acetate in the bacterial cells as confirmed by metabolite detection. Genes encoding proteins involved in cell surface structures, especially biofilm formation, peptidoglycan biosynthesis and lipopolysaccharide biosynthesis were up-regulated as well. Biofilm formation was significantly enhanced under anaerobic conditions. These results indicate that induction of central metabolism is important for basic survival of A. pleuropneumoniae after a shift to an anaerobic environment. Enhanced biofilm formation may contribute to the persistence of this pathogen in the damaged anaerobic host tissue and also in the early colonization stage. These discoveries give new insights into adaptation mechanisms of A. pleuropneumoniae in response to environmental stress.

sample_organism: Actinobacillus pleuropneumoniae serovar 1 str. 4074

overall_design: Transcriptional profiles were analyzed using microarray to compare the gene expressions of A. pleuropneumoniae cultured under aerobic and anaerobic condition. The bacteria was cultured under aerobic condition to mid-log phase (3 hours) and then divided into two separate groups, one group was continually cultured under aerobic condition for 1 hour (OD600nm = 0.417 ± 0.008) and the other group was cultured under anaerobic condition for 1 hour (OD600nm = 0.333 ± 0.015). Three independent biological replicates were performed. The total RNA were extracted and hybridized with the whole genome microarray of A. pleuropneumoniae. The signal intensities were normalized and transformed into log2 values. The genes with P-value < 0.05 were selected as differentially expressed genes.

first: Zhuofei

last: Xu

first: Rui

last: Zhou

first: Jiawen

last: Zhu


title: Gene expression profile analysis of Manila clam (Ruditapes philippinarum) hemocytes after a Vibrio alginolyticus challenge using an immune-enriched oligo-microarray

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: The Manila clam (Ruditapes philippinarum) is a cultured bivalve species with high worldwide commercial importance. Nevertheless, diseases can cause high economical losses. For this reason, the study of immune genes in bivalve mollusks has increased in the last years. The present work describes the construction of the first R. philippinarum microarray containing immune-related hemocyte sequences and its application for the study of the gene transcription profiles of hemocytes from clams challenged with Vibrio alginolyticus through a time course.

overall_design: A comparative analysis of gene expression was conducted between R. philippinarum infected and non-infected by V. alginolyticus clam hemocytes. Clams (n=100) were notched in the shell next to the adductor muscles and injected with 100 µl of Vibrio alginolyticus, strain TA15, (10^8 UFC/ml in PBS) to mimic an intramuscular infection. Controls (n=100) were injected with 100 µl of PBS. After stimulation, clams were returned to the tanks and maintained at 15ºC until sampling at 3, 8, 24, and 72 hours after challenge Hemolymph (1 ml) was withdrawn from the adductor muscle of the clams with a 0.5mm diameter (25G) disposable needle. Hemolymph from four individuals was pooled and biological replicates were taken at each sampling point. Hemolymph was centrifuged at 4°C at 3000 g for 10 minutes. The pellet was resuspended in 250 µl of Trizol (Invitrogen). Total RNA isolation was conducted following the manufacturer's specifications in combination with the RNeasy mini kit (Qiagen) for RNA purification after DNase I treatment. Gene expression profiling was performed using an R. philippinarum oligo-DNA microarray of 13,671 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Luca

last: Bargelloni

first: Rebeca

last: Moreira

first: Pablo

last: Balseiro

first: Antonio

last: Figueras

first: Beatriz

last: Novoa


title: Naturally occurring tumours in the basal metazoan Hydra.

status: Public on Jun 24 2014

city: Zagreb

first: Tomislav

last: Domazet-Loso

address: Bijenicka cesta 54

department: Division of Molecluar Biology

country: Croatia

institute: Ruder Boskovic Institute

summary: The molecular nature of malignant tumors is well studied in vertebrates, while their evolutionary origin remains unknown. In particular, there is no evidence for naturally occurring malignant tumors in pre-bilaterian animals, such as sponges and cnidarians. This is somewhat surprising given that recent computational studies have predicted that all metazoans are prone to develop tumors. Here we provide first evidence for naturally occurring tumors in Hydra oligactis. Histological, cellular and molecular data reveal that these tumors are transplantable and caused by differentiation arrest of female gametes. Growth of tumor cells is independent from the cellular environment. Tumor bearing polyps have significantly reduced fitness. In addition, Hydra tumors show a greatly altered transcriptome that mimics expression shifts in vertebrate cancers. Therefore, this study shows, that invasive tumors have deep roots in animal phylogeny, and that early branching animals may be informative in revealing the fundamental mechanisms of tumorigenesis.

overall_design: We compared four samples of Hydra oligactis tumor-bearing animals to three samples of female polyps undergoing oogenesis and six samples of female asexual control polyps

last: Domazet-Lošo

first: Alexander

last: Klimovich

first: Thomas

last: Bosch


title: Transcriptomic analysis of Sorghum bicolor responding to combined heat and drought stress

status: Public on Jun 20 2014

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

institute: Unilever

summary: Sorghum is an important crop often subjected to simultaneous high temperatures and drought in the field. We examined the gene expression response to heat and drought stress both individually, and in combination, with the aim of identifying important stress tolerance mechanisms.

overall_design: Plants were subjected to 4 different conditions (control, heat shock, drought stress and combined heat and drought stress). 3 replicates were carried out for each treatment type giving a total of 12 samples

first: Stephanie

last: Johnson

first: Fei

first: Marc

last: Knight


title: Array CGH data of A. oryzae strains bearing targeted tandem chromosomal duplications

city: Noda City

first: Masahiro

last: Ogawa

state: Chiba Prefecture

address: 399 Noda

department: Research and Developmental Division

institute: Kikkoman Corporation

summary: We here describe the first successful construction of a targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had 5’ΔpyrG upstream of the region targeted for tandem chromosomal duplication and 3’ΔpyrG downstream of the target region. Consequently, strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks (DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under non-selective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method.

overall_design: A. oryzae strain bearing a 210-kb targeted tandem chromosomal duplication, A. oryzae strain bearing a 700-kb targeted tandem chromosomal duplication, and A. oryzae RIB40 (wild type strain), were cultivated in Polypeptone-dextrin medium. After 3 days cultivation, genomic DNAs from the samples were extracted, and array CGH analysis was carried out to confirm the chromosomal duplications in the strains.

first: Tadashi

last: Takahashi

first: Atsushi

last: Sato

first: Yoshiki

last: Hanya

first: Tetsuya

last: Oguma


title: Detect genomic aberrations between PB1 and its counterpart, spindle-chromosome complex in human MII oocyte, PB2 and female pronucleus in human zygote at a single-cell level.

status: Public on Jun 19 2014

city: Shanghai

first: Tian

last: Wang

address: 138 Yi Xue Yuan Road

institute: Fudan University

type: Genome variation profiling by genome tiling array

summary: Inherited mitochondrial DNA (mtDNA) diseases transmit maternally and cause severe phenotypes. Since no effective treatment or genetic screening is available, nuclear genome transfer between patients’ and healthy eggs to replace mutant mtDNAs holds promises. Since polar body contains very few mitochondria and share same genomic material as oocyte, here we perform polar body transfer to prevent the transmission of inherited mtDNA variants. We compare the value of different germline genome transfer (spindle-chromosome, pronuclear, first and second polar body) in a mouse model. Reconstructed embryos support normal fertilization and produce live offspring. Strikingly, genetic analysis confirms F1 generation after polar body transfer possesses minimal donor mtDNA carry-over compared with spindle-chromosome (low/medium carry-over) and pronuclear (medium/high carry-over) transfer. Moreover, mtDNA genotype remains stable in F2 generation of progeny after polar body transfer. Our preclinical model demonstrates polar body transfer holds great potential in preventing the transmission of inherited mtDNA diseases.

overall_design: The objective of the present study was to detect genomic aberrations between PB1 and its counterpart, spindle-chromosome complex in human MII oocyte, PB2 and female pronucleus in human zygote at a single-cell level.

first: Hongying

last: SHA

last: WANG

first: Dongmei

last: JI

first: Helen

last: ZHANG

first: Dawei

last: CHEN

first: Yunxia

last: CAO

first: Jianhong

last: ZHU


title: Genome-wide profiling of altered gene expression in the neocortex of Alzheimer's disease (exon level)

city: Singapore

first: Michelle

middle: GK

last: Tan

address: 20 College Road

department: Clinical Translational Research

country: Singapore

institute: Singapore General Hospital

summary: We investigated genome-wide gene alterations in the temporal cortex of a well-characterized cohort of Alzheimer’s disease (AD) patients using Affymetrix exon arrays.

overall_design:
The AD patients and controls are subjects originally recruited into OPTIMA (Oxford Project to Investigate Memory and Ageing). Subjects underwent annual clinical and neuropsychological assessments, including the Cambridge Cognitive Examination (CAMCOG). Among subjects who died with autopsy consent given by next of kin, 1 cm3 blocks of grey matter from BA22 were dissected from fresh frozen brains of AD subjects. Tissues from elderly controls, followed longitudinally in life and with CAMCOG scores >80 at the last assessment before death, were collected. Affymetrix exon array was carried out in 8 control and 8 AD samples. The samples processed in each hybridization run were matched for AD vs. control, sex and postmortem interval (PMI) as far as possible.

This submission includes the exon-level analysis.

first: Mitchell

last: Lai


title: Global gene expression in rice blast pathogen Magnaporthe oryzae treated with a natural rice soil isolate

city: Newark

first: Carla

last: Spence

state: Delaware

address: 15 Innovation Way

institute: University of Delaware

summary: M. oryzae 70-15 was treated with multiple bacteria which inhibit 70-15's growth.  The bacterial treatments were EA105, a pseudomonad naturally isolated from rice soil, as well as P. fluorescens biocontrol strain CHAO and the cyanide non-producing mutant of CHAO, CHA77.

overall_design: On a standard petri dish with solid complete medium, a 5 mm plug of M. oryzae 70-15 was placed 4 cm from a 5 uL droplet of bacteria (1 X 10 ^ 6 cells per mL)

first: Vidhyavathi

last: Raman

first: Nicole

last: Donofrio

first: Harsh

last: Bais


title: Translational regulation of specific mRNAs controls feedback inhibition and survival during macrophage activation [array]

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

country: Germany

institute: Heidelberg University

summary: When macrophages encounter pathogens, they transiently induce an orchestrated cascade of pro- and anti-inflammatory genes. We systematically analyzed the contribution of translational regulation to the early phase of macrophage activation. While the expression of most cytokines is regulated by changes in mRNA levels, de-repression of translation was found to permit expression of many feedback inhibitors of the inflammatory response. This includes NF-kB inhibitors (IkBd, IkBz, Nr4a1, Ier3), a p38 MAPK antagonist (Dusp1) and post-transcriptional suppressors of cytokine expression (TTP and Zc3h12a). Ier3 is tightly co-regulated with TNF at the level of mRNA abundance and translation. Macrophages lacking Ier3 show reduced survival upon activation, indicating that induction of Ier3 is required to protect macrophages from lipopolysaccharide-induced cell death. Our analysis reveals an important role of translational regulation in the resolution of inflammation and macrophage survival.

overall_design: RNA was purified from cytoplasmic lysate or polysome fractionation before and 1 h after stimulation of RAW264.7 macrophages with LPS. Fractions were pooled into four samples per condition: Free RNA (F), 40S-associated RNA (S), light (L) and heavy polysomes (H). The experiment was performed in three biological replicates, and RNA was quantified with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix).

first: Sonja

last: Reitter

first: Janine

last: Philipp

first: Heiner

last: Schaefer

first: Georg

last: Stoecklin


title: Replication timing of siRNA control and siRNA PolQRKO cells

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

institute: CNRS/ Université de Paris

summary: The human A-family DNA polymerase θ (Pol q) is a large, multidomain enzyme whose physiological function is still unclear despite its in vitro translesion synthesis capacity in front of DNA damage and its involvement in some features of DNA repair after external stress. Here we present evidence that Pol q holds a novel role in the absence of external stress as a critical determinant of the replication timing program in human cells. Pol q binds to chromatin at early G1 and is required for proper formation of pre-replicative complexe and replication origin activation. Pol q-depleted cells show modified spatial organization of chromatin-loop structures at replication factories. Genome-wide analysis of replication timing shows delayed replication of a part of early replicating domains and advanced replication of a part of late replicating domains following Pol q depletion. Our results identify Pol q as one of the first critical human factors discovered in the replication timing programme.

overall_design: Two-condition experiment, siRNA control vs. siRNA polQ cells. Biological replicates: 2 control replicates, 2 transfected replicates.

first: Anne

last: Fernandez-Vidal

first: Laure

last: Guitton-Sert

first: Giuseppe

last: Baldacci

first: Christophe

last: Cazaux

first: Jean-Sébastien

last: Hoffmann


title: Gene expression profiling of breast fibroadenomas

status: Public on Jun 13 2014

first: Weng Khong

last: Lim

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

institute: National Cancer Centre Singapore

summary: Fibroadenomas are the most common benign breast tumors in women under 30. Unlike their malignant counterparts, relatively molecular profiling has been done on fibroadenomas. Here we performed gene expression profiling on ten fibroadenomas in order to better characterize these tumors. Through targeted amplicon sequencing, we have found that six of these tumors have MED12 mutations. We show that the MED12 mutations, among others, are associated with activated estrogen signaling, as well as increased invasiveness through upregulation of ECM remodelling genes.

overall_design: Microarray gene expression profiling was performed on 10 breast fibroadenomas and a combination of unsupervised and supervised clustering was performed to determine any differentially activated pathways between samples with mutated and non-mutated MED12.

first: Weng

first: Jing

last: Tan

first: Choon

last: Ong

first: Bin

middle: T

last: Teh


title: RNAi silencing of the SoxE gene suppresses cell proliferation in silkworm BmN4 cells

status: Public on Jun 28 2014

city: Chongqing

first: Ling

last: Wei

address: No 2, Tiansheng street, Beibei district

institute: Southwest University

summary: Transcriptional profiling of silkworm BmN4-SID1 cells comparing the test of  BmSoxE knockdown with the control of EGFP Knockdown.

overall_design: Two-condition experiment,  BmSoxE knockdown vs EGFP Knockdown. Biological replicates: 3. One replicate per array.

first: Cheng

last: Lu


title: Haploinsufficiency of an RB-E2F1-Condensin II complex causes replication stress and contributes to mesenchymal cancers [CGH]

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

country: Canada

institute: Western University

summary: Genome instability is a characteristic of malignant cells, however, evidence for its contribution to tumorigenesis has been enigmatic. In this study we demonstrate that a complex containing the retinoblastoma protein, E2F1, and Condensin II localizes to major satellite repeats at pericentromeres. In the absence of this complex, this genomic region fails to properly replicate and H2AX phosphorylation at pericentromeric repeats is increased. Our data indicates that these lesions contribute to defective chromosome segregation in the ensuing mitosis. Surprisingly, loss of even one copy of the retinoblastoma gene was sufficient to reduce recruitment of Condensin II to pericentromeres and cause this phenotype. Furthermore, we determined that human RB1 mutation status in cancers of mesenchymal origin correlated with copy number variation, chromosomal gains and losses, as well as chromothriptic rearrangements. Importantly, the magnitude of these chromosomal abnormalities was indistinguishable between RB1+/- and RB1-/- genotypes. Lastly, using gene-targeted mice we determined that mutation of just one copy of the murine Rb1 gene causes sarcomas and lymphomas with increased chromosome copy number variation. Our study connects replication stress with a number of common chromosomal abnormalities in cancer through a dosage sensitive complex present at pericentromeric repeats.

overall_design: Copy number data of thymic lymphomas from 12 different RB1 Δ/+; Trp53-/- mice were analyzed.  Tumor DNA was hybridized against same sex control samples (pooled DNA from 5 normal male or female mice).  NimbleGen performed a control male vs control female hybridization.  All hybridizations were done on a mouse whole genome array (design 2006-07-26-MM8-WG-CGH).  Conclusions were drawn from 10X window avereaged, CGH-segMNT analysed data files.

first: Courtney

middle: H

last: Coschi

first: Alison

last: Martens

first: Frederick

middle: A


title: L. dorsi muscle transcriptome study in pure and crossbred young Iberian pigs

status: Public on Jun 11 2014

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

institute: INIA-CSIC

summary:
We studied the influence of genetic type (pure Iberian pigs vs crossbred with Duroc) on l.dorsi transcriptome
Background: The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in young animals of both genetic types, in order to identify genes, pathways and transcription factors responsible of their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DUxIB) were generated. Piglets (14 from each genetic type) were sacrificed at weaning (28 days) and longissimus dorsi  muscle was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays.  Results: Loin muscle composition showed significant differences between genetic types in intramuscular fat content (6% vs. 4.2% in IB and DUxIB animals, respectively, P=0.009) and in saturated and monounsaturated fatty acid contents (P=0.019 and P=0.044, respectively). Statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR<0.10), 102 upregulated in IB and 154 upregulated in DUxIB. The size of the effects ranged between 1.2x and 7.8x. Transcript differences were validated for a subset of DE genes by qPCR. Some candidate genes with known effects on muscle growth were found among the DE genes upregulated in DUxIB (IGF2, collagens, integrins). Genes related to lipid metabolism and proteolysis were found among the genes upregulated in IB (ME1, ELOVL6, caspases, catepsins, ubiquitination proteins). We observed alteration in biological functions related to extracellular matrix organization, cellular adhesion, muscle growth and lipid metabolism. Transcription factors (TF) potentially involved in the expression differences found were identified by calculating the regulatory impact factors (RIF). Sixteen TF were found, some of them with known relationship with muscle development (MSTN, SIX4), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these TF and DE genes show relevant differences between genetic types.  Conclusion: The results contribute valuable information about molecular mechanisms determining the phenotypic differences of growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism.

overall_design: 28 male piglets were employed. 14 animals coming for pure Iberian parents and 14 coming from the crossing of Duroc boars with Iberian sows. Animals were sacrificed at 28 d of age. At the sacrifice, longissimus dorsi muscle tissue was sampled from each animal.


title: Oxidative Stress and Reduced Responsiveness of Challenged Circulating Leukocytes Following Pulmonary Instillation of Metal-Rich Particulate Matter in Rats

status: Public on Jun 15 2014

city: Morgantown

first: Patti

middle: Christine

last: Zeidler-Erdely

state: WV

address: 1095 Willowdale Road

department: HELD

institute: CDC/NIOSH

summary: Exposure to welding fume consists of a mixed exposure of metal-rich particulate matter with gases (ozone, carbon monoxide) and/or vapors (VOCs). Data suggests that welders are immune compromised. Given the inability of pulmonary leukocytes to properly respond to a secondary infection, the question arose concerning how far upstream the dysfunction persisted. Our aim was to evaluate circulating leukocyte functionality after welding fume exposure. The results showed that welding fume exposure has rapid effects on the circulating leukocyte population as identified by relative mRNA expression changes. Instillation of MMA-SS reduced inflammatory protein production of circulating leukocytes when challenged with the secondary stimulus LPS. The effects were not related to transcription, but were observed in conjunction with oxidative stress.

overall_design: Rats were intratracheally instilled (ITI) with phosphate buffered saline or 2 mg of welding fume collected from a manual metal arc-stainles steel weld. Rats were sacrificed 4 and 24 h post-exposure and whole blood was collected. Whole blood was used for cellular differential counts, RNA isolation with subsequent microarray and Ingenuity Pathway Analysis, and secondary stimulation with lipopolysaccharide utilizing TruCulture technology from Myriad/Rules Based Medicine. Also, mononuclear cells were isolated 24 h post-exposure to measure oxidative stress by flow cytometry and confocal microscopy. Whole blood collected 4 and 24 h post-exposure was challenged (a paired non-stimulant (null) and stimulant (LPS) tube) for 24 h using Truculture technology from Myriad/ RBM. After the challenge, cells were recovered using RNA later for subsequent RNA isolation and microarray.

first: Aaron

last: Erdely


title: Identification of direct androgen-target genes in the prostate cancer cell line LNCaP

status: Public on Jun 14 2014

city: Lyon Cedex 07

first: Nathalie

last: ALLIOLI

address: 46 Allée d'Italie

department: Institut de Génomique Fonctionnelle de Lyon (IGFL)

institute: Ecole Normale Supérieure de Lyon (ENS)

summary: Transcriptional profiling of the LNCaP cell line treated with R1881 synthetic androgen and/or cycloheximide.

overall_design: LNCaP cells were stimulated with R1881 alone, with cycloheximide alone, or with R1881 in the presence of cycloheximide for 24h and compared to control untreated cells. Two independent cell culture experiments for each treatment condition were performed for microarray analysis. Each experiment was repeated with a switch in fluorescent Cy3/Cy5 labels to account for dye effects to produce four data points per hybridization spot.

last: Allioli

first: Jacques

last: Samarut


title: Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes

status: Public on Jun 07 2014

city: Umeå

first: Yuri

middle: B

last: Schwartz

address: Byggnad 6L, NUS

country: Sweden

institute: Umeå University

type: Genome binding/occupancy profiling by genome tiling array

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

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Refer to individual Series


title: miRNA profiling of pediatric T cell lymphoblastic lymphoma

status: Public on Jun 10 2014

city: New York

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: miRNA profiling has been performed on primary tumor samples collected at diagnosis from pediatric patients affected by T-cell lymphoblastic lymphoma.

overall_design: Tumor tissue was frozen at the time of surgery. Mononucleated cells  were isolated from pleural effusions upon red blood cell lysis and frozen. The experiment does not include technical replicates.

first: Lara

last: Mussolin

first: Katia

last: Basso


title: Epigenetics and the Evolution of Darwin’s Finches

city: Pullman

first: Michael

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by genome tiling array

summary: The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts.  However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change.  A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations.  The possibility that epigenetic changes could accumulate over macroevolutionary time has been considered, but not yet seldom been tested empirically.  The current study was designed to compare epigenetic changes among several closely related species of Darwin’s finches, a well-known example of adaptive radiation.  Erythrocyte DNA was obtained from five species of sympatric Darwin's finches that vary in phylogenetic relatedness.  Genome wide alterations in genetic mutations using copy number variation (CNV) were compared to epigenetic alterations associated with differential DNA methylation regions (epimutations).  Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance.  Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance.  The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggests that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin’s finches.  The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds.  Specific epimutations were associated with genes related to the bone morphogenic protein (BMP), toll receptor, and melanogenesis signaling pathways. Species- specific epimutations were significantly over-represented in these pathways.  Since environmental factors are known to rapidly alter heritable changes in the epigenome, it is possible that epigenetic changes have played a contributing role in the molecular basis of the evolution of Darwin's finches.

sample_organism:
Geospiza fortis
Geospiza fuliginosa
Geospiza scandens
Platyspiza crassirostris
Camarhynchus parvulus

first: Carlos

last: Gurerrero-Bosagna

first: M

middle: M

last: Haque

first: Eric

last: Nilsson

first: Jennifer

last: Koop

first: Sarah

last: Knutie

first: Dale

last: Clayton


title: Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes (Fruit Fly)

summary: PcG proteins are critical epigenetic regulators of development. Here we have determined genomic distributions of PHO, PHOL and SFMBT proteins in cultured Drosophila cells by hybridization of ChIP products with tiling microarrays.

first: T

middle: G

last: Kahn

first: V

last: Pirrotta

first: Y


title: Metabolic and transcriptional activities of Staphylococcus aureus challenged with high-doses of daptomycin

status: Public on Jun 06 2014

city: Tuebingen

first: Alexander

last: Herbig

address: Ruemelinstr. 23

department: Archaeo- and Paleogenetics

institute: University of Tuebingen

summary: Treatment of stationary growth phase Staphylococcus aureus SA113 with 100-fold of the MIC of the lipopeptide antibiotic daptomycin leaves alive a small fraction of drug tolerant albeit genetically susceptible bacteria. This study shows that cells of this subpopulation exhibit active metabolism even hours after the onset of the drug challenge. Isotopologue profiling using fully 13C-labeled glucose revealed de novo biosynthesis of the amino acids Ala, Asp, Glu, Ser, Gly and His. The isotopologue composition in Asp and Glu suggested an increased activity of the TCA cycle under daptomycin treatment compared to unaffected stationary growth phase cells. Microarray analysis showed differential expression of specific genes 10 minutes and 3 hours after addition of the drug. Besides factors involved in drug response, a number of metabolic genes appear to shape the signature of daptomycin-tolerant S. aureus cells. These observations will be useful towards the development of new strategies against persisters and related forms of bacterial cells with downshifted physiology.

overall_design: Altogether 12 samples were analysed. Bacteria were treated with Daptomycin and samples were taken 10 minutes (3 replicates) and 3 hours later (3 replicates). For each time-point untreated cultures were sampled as controls (3 replicates for each time-point).

first: Sabrina

last: Lechner

first: Marcel

last: Prax

first: Birgit

last: Lange

first: Claudia

last: Huber

first: Wolfgang

last: Eisenreich

first: Kay

last: Nieselt

first: Ralph

last: Bertram


title: Protein interactions within PLEIOHOMEOTIC-repressive complex are critical for its recruitment to Polycomb target genes (Human)

first: Yuri

last: Schwartz

summary: PcG proteins are critical epigenetic regulators of development. Here we have determined genomic distributions of H3K27me3, BMI1, MEL18, EZH2 and YY1 proteins on chromosomes 8, 11,12 of cultured human NTERA-2 cl.D1 cells by hybridization of ChIP products with tiling microarrays.


title: The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive

status: Public on Jun 05 2014

city: Sydney

first: Sergey

last: Kurdyukov

address: Reserve Road

institute: Kolling Institute of Medical Research

summary: Background: The Medicago truncatula 2HA seed line is highly embryogenic while the parental line Jemalong rarely produces embryos. The 2HA line was developed from one of the rare Jemalong regenerates and this method for obtaining a highly regenerable genotype in M. truncatula is readily reproducible suggesting an epigenetic mechanism. Microarray transcriptomic analysis showed down regulation of an ETHYLENE INSENSITIVE 3-like gene in 2HA callus which provided an approach to investigating epigenetic regulation of genes related to ethylene signalling and the 2HA phenotype. Ethylene is involved in many developmental processes including somatic embryogenesis (SE) and is associated with stress responses.  Results: Microarray transcriptomic analysis showed a significant number of up-regulated transcripts in 2HA tissue culture, including nodule and embryo specific genes and transposon-like genes, while only a few genes were down-regulated, including an EIN3-like gene we called MtEIL1. This reduced expression was associated with ethylene insensitivity of 2HA plants that was further investigated. The weak ethylene insensitivity affected root and nodule development. Sequencing of MtEIL1 found no difference between 2HA and wild-type plants. DNA methylation analysis of MtEIL1 revealed significant difference between 2HA and wild-type plants. Tiling arrays demonstrated an elevated level of miRNA in 2HA plants that hybridised to the antisense strand of the MtEIL1 gene. AFLP-like methylation profiling revealed more differences in DNA methylation between 2HA and wild-type. Segregation analysis demonstrated the recessive nature of the eil1 phenotype and the dominant nature of the SE trait.    Conclusions: We have demonstrated that EIL1 of Medicago truncatula (MtEIL1) is epigenetically silenced in the 2HA seed line. The possible cause is an elevated level of miRNA that targets its 3’UTR leading to DNA methylation. Down regulation of MtEIL1 makes it possible to form nodules in the presence of ethylene and affects root growth under normal conditions. Segregation analysis showed no association between MtEIL1 expression and SE in culture but the role and mechanism of ethylene signalling in the process of plant regeneration through SE requires further investigation.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Comparison of transcriptome of WT and highly embryogenic 2HA spontaneous mutant of Medicago truncatula in 4 weeks tissue culture

first: Ulrike

last: Mathesius

first: Kim

last: Nolan

first: Michael

last: Sheahan

first: Nicolas

last: Goffard

first: Bernard

middle: J

last: Carroll

first: Ray

last: Rose


title: Erythropoietin suppresses the activation of pro-apoptotic genes in head and neck squamous cell carcinoma xenografts exposed to surgical trauma

status: Public on Jun 04 2014

city: Lund

first: Gustaf

last: Lindgren

address: Lasarettsgatan 21

department: Depoartment of Otolaryngology/Head and Neck surgery

institute: Lund University

summary: Abstract  Background: Several studies on the use of erythropoietin (Epo) to treat anaemia in patients undergoing cancer treatment have shown adverse effects on tumour control and survival. Experimental studies indicate that this could be linked to an interaction with wound healing processes and not an effect on tumour cells per se. We have previously shown that erythropoietin in combination with surgical trauma stimulates tumour growth. In the present study, we investigated the effect of surgery and Epo on gene expression.   Methods: Human tumours from oral squamous cell cancer were xenotransplanted to nude mice treated with Epo. The tumours were then transected in a standardised procedure to mimic surgical trauma and the change in gene expression of the tumours was investigated by microarray analysis. qRT-PCR was used to measure the levels of mRNAs of pro-apoptotic genes. The frequency of apoptosis in the tumours was assessed using immunohistochemistry for caspase-3.  Results: There was little change in the expression of genes involved in tumour growth and angiogenesis but a significant down-regulation of the expression of genes involved in apoptosis. This effect on apoptosis was confirmed by a general decrease in the expression of mRNA for selected pro-apoptotic genes. Epo-treated tumours had a significantly lower frequency of apoptosis as measured by immunohistochemistry for caspase 3.  Conclusions: Our results suggest that the increased tumour growth during erythropoietin treatment might be due to inhibition of apoptosis, an effect that becomes significant during tissue damage such as surgery.  This further suggests that the decreased tumour survival during erythropoietin treatment might be due to inhibition of apoptosis.  Key words: Erythropoietin, Head and neck cancer, surgery, apoptosis, wound healing, xenograft.

overall_design: We wanted to study the effect of wound healing mechanisms on remaining tumour tissue efter incomplete surgery or biopsy. We xenografted human Head and Neck squamous Cell Cancer (HNSCC) tumours on Balb/c nude mice. The mice were divided in six groups. Three of the groups received intrapertoneal doses of erythropoietin (Epo) and the other three groups were given NaCl as placebo. One treated and one non-treated group were harvested without surgical transection. In the other four groups, the tumours were transected mimicking subtotal surgery. One Epo-treated and one non-treated group was analysed after 24 hours after transection and the remaining two groups 48 hours after surgery. Groups C and D were not analyzed due to harvesting at an unsuitable time interval.     Group A No surgery (=FALSE) + Epo  Group B No surgery (=FALSE) +  NaCl  Group E Surgery (=TRUE) + Epo 24 hours after surgical transection  Group F Surgery (=TRUE) + NaCl 24 hours after surgical resection  Group G Surgery (=TRUE) + Epo  48 hours after surgical transection  Group H Surgery (=TRUE) + Nacl  48 hours after surgical transection

first: Lars

last: Ekblad

first: Johan

last: Vallon-Christersson

first: Elisabet

last: Kjellén

first: Maria

last: Gebre-Medhin

last: Wennerberg


title: Analysis of structural diversity in wolf-like canids reveals post-domestication variants

city: Barcelona

first: Oscar

last: Ramirez

state: APO/FPO EUROPE / ATLANTIC

address: Dr. Aiguader, 88

institute: Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra)

summary: This study uses a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 23 hybridizations were performed in a panel of diverse dogs and a single wolf.

sample_organism:
Canis lupus
Canis latrans
Canis lupus familiaris
Canis rufus
Canis aureus

overall_design: This study focuses on the use a custom made Nimblegen aCGH chip to genotype 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication

first: Iñigo

last: Olalde

first: Jonas

last: Berglund

first: Belen

last: Lorente-Galdos

first: Jessica

last: Hernandez-Rodriguez

first: Matthew

last: Webster

first: Robert

middle: K

last: Wayne

first: Carles

last: Lalueza-Fox

last: Vilà

first: Tomas

last: Marques-Bonet


title: A microarrays-based analysis of gametogenesis in two Portuguese populations of the European clam Ruditapes decussatus

status: Public on Jun 03 2014

city: Legnaro

first: Massimo

last: Milan

address: Viale dell'Università 16

institute: University of Padova

summary: The European clam, Ruditapes decussatus (Linnaeus, 1758) is a bivalve mollusc of the family Veneridae native to the European Atlantic and Mediterranean coastal waters. Its production is exclusively based on natural recruitment, which is subject to high annual fluctuations due to adversely affected by pollution and other environmental factors. Microarray analyses have been performed in four gonadal maturation stages of two higly productive Portuguese wild populations (Ria Formosa in South and Ria de Aveiro in North) characterized by different responses to spawning induction.

overall_design: Twenty clams (Ruditapes decussatus)were monthly sampled between July 2011 and July 2012 in two different Portuguese wild populations: Ria Formosa and Ria de Aveiro. At each sampling date the gonads of the collected clams were immediately dissected for RNA extraction and fixed for histological analysis.  Total RNA was isolated using Extract-all (Eurobio) procedure. RNA quality and integrity was controlled on the Agilent bioanalyzer using RNA nanochips and Agilent RNA 6000 nanoreagents (Agilent Technologies, Waldbronn, Germany). RNA concentrations were measured at 260 nm using a ND-1000 spectrophotometer (Nanodrop Technologies) using the conversion factor 1 OD = 40 mg/mL total RNA. Samples were stored at -80°C until further use. Gene expression profiling was performed using an R.decussatus oligo-DNA microarray of 59,951 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 2 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. FeatureExtraction v10.7.3.1 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: Luca

last: Bargelloni

first: Marianna

last: Pauletto

first: Arnaud

last: Huvet

first: Teixeira

last: de Sousa Joana


title: Beta- lactam antibiotics stimulate biofilm formation in non-typeable Haemophilus influenzae by up-regulating carbohydrate metabolism

city: Los Angeles

first: Paul

state: CA

address: 804 Bloom Walk

department: CEMMA

institute: University of Southern California

summary: Non-typeable Haemophilus influenzae (NTHi) is a common acute otitis media pathogen, with an incidence that is increased by previous antibiotic treatment. NTHi is also an emerging causative agent of other chronic infections in humans, some linked to morbidity, and all of which impose substantial treatment costs. In this study we explore the possibility that antibiotic exposure may stimulate biofilm formation by NTHi bacteria. We discovered that sub-inhibitory concentrations of beta-lactam antibiotic (i.e., amounts that partially inhibit bacterial growth) stimulated the biofilm-forming ability of NTHi strains, an effect that was strain and antibiotic dependent. When exposed to sub-inhibitory concentrations of beta-lactam antibiotics NTHi strains produced tightly packed biofilms with decreased numbers of culturable bacteria but increased biomass. The ratio of protein per unit weight of biofilm decreased as a result of antibiotic exposure. Antibiotic-stimulated biofilms had altered ultrastructure, and genes involved in glycogen production and transporter function were up regulated in response to antibiotic exposure. Down-regulated genes were linked to multiple metabolic processes but not those involved in stress response. Antibiotic-stimulated biofilm bacteria were more resistant to a lethal dose (10µg/mL) of cefuroxime. Our results suggest that beta-lactam antibiotic exposure may act as a signaling molecule that promotes transformation into the biofilm phenotype. Loss of viable bacteria, increase in biofilm biomass and decreased protein production coupled with a concomitant up-regulation of genes involved with glycogen production might result in a biofilm of sessile, metabolically inactive bacteria sustained by stored glycogen. These biofilms may protect surviving bacteria from subsequent antibiotic challenges, and act as a reservoir of viable bacteria once antibiotic exposure has ended.

overall_design: 12 samples

first: Siva

last: Wu

first: Xiaojin

last: Li

first: Charles

last: Wang


title: Expression data from Sheep kidney fat (KF) in lambs at 12 weeks of age; comparison of two genotypes, Callipyge (NCpat (CN)) and wild type (NN)

city: Brisbane

first: Ross

last: Tellam

state: QLD

address: 306 Carmody Road St.Lucia

department: Level 6 Queensland Biosciences Precinct

institute: CSIRO Animal, Food and Health Sciences

summary:
The ovine Callipyge mutation causes postnatal muscle hypertrophy localized to the pelvic limbs and torso, as well as body leanness. The mechanism underpinning enhanced muscle mass is unclear, as is the systemic impact of the mutation. Using muscle fibre typing immunohistochemistry we confirmed muscle specific effects and demonstrated that affected muscles had greater prevalence and hypertrophy of type 2X fast twitch glycolytic fibres and decreased representation of types 1, 2C, 2A and/or 2AX fibres. To investigate potential systemic effects of the mutation, proton NMR spectra of plasma taken from lambs at 8 and 12 weeks of age were measured. Multivariate statistical analysis of plasma metabolite profiles demonstrated effects of development and genotype but not gender. Plasma from Callipyge lambs at 12 weeks of age, but not 8 weeks, was characterized by a metabolic profile consistent with contributions from the affected hypertrophic fast twitch glycolytic muscle fibres. Microarray analysis of the perirenal adipose tissue depot did not reveal a transcriptional effect of the mutation in this tissue. We conclude that there is an indirect systemic effect of the Callipyge mutation in skeletal muscle in the form of changes of blood metabolites, which may contribute to secondary phenotypes such as body leanness.
Microarrays were used for transcription profiling of kidney fat samples taken from Callipyge (n=4) and wild type (n=4) lambs at 12 weeks of age.

overall_design: Sheep used in this experiment were bred from a research flock of Dorset/Suffolk/Rambouillet cross-bred sheep raised at Utah State University and cared for and euthanased for sample collection in accordance with the animal ethics guidelines of Utah State University (Utah, USA).  Kidney fat (KF) samples were taken from lambs at 12 weeks of age; four callipyge (CN) genotype animals and four normal (NN) genotype animals were compared.

first: Juan

last: Greenwood

first: Noelle

last: Cockett

first: Tracey

last: Hadfield

first: Tony

last: Vuocolo

first: Keren

last: Byrne

first: Jason

last: White

first: Horst

last: Schirra


title: Targeting the epigenetic regulation of Hedgehog transcriptional output through BET bromodomain inhibition

city: Stanford

first: Yujie

last: Tang

address: 265 Campus Dr SIM1 G3055

department: Neurology

institute: Stanford University School of Medicine

summary: Comparison of gene expression changes in Ptch-deficient mouse medulloblastoma cell line SmoWT-MB upon treatment with SMOi GDC-0449 or BETi JQ1. The hypothesis is that they can both inhibit the expressions of Hh signaling target genes in this Hh-driven tumor cell line.

overall_design: Total RNA from JQ1 or GDC-0449 treated SmoWT-MB cells in comparison with DMSO treated cells

first: Yoon-Jae

last: Cho


title: Chromosome 17/17q gain and unaltered profiles in high resolution array-CGH are prognostically informative in neuroblastoma

status: Public on Jun 01 2014

city: Cologne

first: Jessica

last: Theissen

state: NRW

address: Kerpener Straße 62

department: Department of Pediatric Oncology and Hematology

institute: University of Cologne

summary: Oligonucleotide aCGH profiles from 37 neuroblastoma tumor samples were generated using 44K or 105K microarrays.

overall_design: Two-color array-based comparative genome hybridization (aCGH)

first: Rüdiger

last: Spitz

first: Anja

last: Hombach