title: Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms [SNP array]

status: Public on Jul 08 2014

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: Human pluripotent stem cells hold great potential for regenerative medicine, but available cell types have important limitations. While embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the "gold standard" of pluripotency, they are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) are prone to epigenetic and transcriptional aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming or secondary to the reprogramming method, we generated a genetically matched collection of human IVF-ESCs, iPSCs, and ESCs derived by somatic cell nuclear transfer (SCNT; NT-ESCs), and subjected them to genome-wide genetic, epigenetic and transcriptional analyses. SCNT-based reprogramming is mediated by the full complement of oocyte cytoplasmic factors, thus closely recapitulating early embryogenesis. NT-ESCs and iPSCs derived from the same somatic donor cells contained comparable numbers of de novo copy number variations (CNVs), suggesting that the two reprogramming methods may not differ significantly in mutagenic or selective pressure. On the other hand, the DNA methylation and transcriptome profiles of NT-ESCs corresponded very closely to those of IVF-ESCs, while iPSCs differed markedly from IVF-ESCs and harbored residual DNA methylation patterns typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal candidates for cell replacement therapies.

overall_design: 16 matched samples, two IVF-ESCs, five sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, the parental fibroblast line, and the sperm and oocyte donor were genotyped using the Illumina Omni5, which interrogates 4.3 million SNPs across the human genome. Additionally, matched samples from a patient with Leigh syndrome, a NT-ESC line, three iPSC lines, and the parental fibroblast line were genotyped using the Illumina Omni5.


title: Stromal and epithelial changes in breast cancer following endocrine treatment

status: Public on Jul 07 2014

city: Manchester

first: Narges

last: Azadbakht

address: Wilmslow Road

department: The University of Manchester

country: United Kingdom

institute: Cancer Research UK Manchester Institute

summary:
Patients diagnosed with breast cancer were recruited to an important trial, the Tamoxifen Window Trial, in two series, series A during 1988-1989 and series B during 1989-1990. Some patients received tamoxifen for short windows. Clinical samples (biopsies) for this trial were collected before and after treatment. These biopsies were available as formalin-fixed paraffin-embedded (FFPE) tissue blocks.
Responding patients and non-responding patients were determined by the change in the Ki67 scores. Responding patients were identified as those that had demonstrated a reduction in their Ki67 scores, and non-responding patients were identified as those in which Ki67 had not changed or had increased. The change in the percentage of Ki67 positive tumour cells was obtained by comparing the pre-treatment and post-treatment scores and calculating the difference in the scores.
Laser capture microdissection (LCM) was utilised to microdissect the epithelial and stromal cells from the post-treatment breast cancer FFPE tissue sections of responding and non-responding patients.
Samples obtained following LCM underwent RNA extraction and were subsequently used for gene expression profiling.

overall_design:
Post-treatment samples from three responding patients (A29, B42, B61) and three non-responding patients (A15, A19, B59) were identified as suitable for this study and underwent LCM.
Samples were analysed using Affymetrix GeneChip® Human Exon 1.0 ST array. No technical replicates were performed.
The stromal compartments collected from post-treatment samples of patients B59 and B61 failed to generate the appropriate yield of cDNA following two rounds of amplification and consequently were excluded from further analysis.
Array hybridisation of samples were performed in 3 separate batches.

first: Göran

last: Landberg

last: Clarke

first: Jean-Marc

last: Schwartz


title: miRNA expression profile of cells and exosomes

status: Public on Jul 03 2014

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: We hypothesized that miRNAs in the bone maroow mesenchymal stem cells (BM-MSC)-derived exosomes contributed to the phenotype change of breast cancer cells through exosome transfer. We analyzed the miRNA expression signature in BM-MSC-derived exosomes. We compared the miRNA expression levels in exosomes between BM-MSCs and adult fibroblasts (as a control).

overall_design: In this study, miRNA expression including in bone-marrow mesenchymal cell (BM-MSC)-derived exosomes was examined, and compared with that of exosomes derived from adult fibroblast cells or the BM-MSC cells. In addition, miRNA expression of BM-MSC exosomes was also compared with that of breast cancer cells with or without cancer stem cell marker.

first: Makiko

last: Ono

first: Nobuyoshi

last: Kosaka


title: Defining the mobilome in clinically important lineages of Enterococcus faecium and Enterococcus faecalis

city: Tromso

first: Christopher

last: Fenton

state: Norge

address: MH bygget

department: GSCT

country: Norway

institute: Universiry of Tromso

summary: The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including mobile genetic elements (MGE) encoding antimicrobial resistance. Here, we define the mobilome in representative successful  hospital associated genetic lineages, E. faecium ST17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) using DNA microarray analyses.  The hybridization patterns of 272 targets representing plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29), and CRISPR-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. Although plasmids belonging to the RCR-, Rep_3-, RepA_N- and Inc18-families were well represented with no significant differences in prevalence, the presence of specific replicon classes differed highly between the species; E. faecium was dominated by rep17/pRUM, rep2/pRE25, rep14/EFNP1 and rep20/pLG1 and E. faecalis by rep9/pCF10, rep2/pRE25 and rep7. Tn916-elements conferring tetracycline resistance (tetM) were found in all E. faecalis strains, but only in two E. faecium strains. A significant higher prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982-, and IS4-transposases were detected in E. faecium, and of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 which have only been reported in few enterococcal isolates, were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented.   Gene targets defined as the enterococcal mobilome, including plasmids, IS elements and transposons, resistance determinants, prophage sequences and CRISPR-Cas systems were highly prevalent, underlining their potential importance in the evolution of hospital associated STs. An association between axe-txe to the RepA_N-family and ω-ε-ζ to the Inc18-family, implicates the contribution of TA-systems in stable plasmid maintenance carrying virulence and resistance determinants in enterococci. The concurrent presence of defined MGE and their associated resistance markers was generally confirmed and illustrates the importance of horizontal gene transfer in the development of multidrug resistant enterococci.

sample_organism:
Enterococcus faecalis
Enterococcus faecium

overall_design: All together 272 DNA targets representing mobile genetic elements and antimicrobial resistance determinants associated with enterococci were spotted on a CustomArray 4x2K microarray from CustomArray Inc. Each fourplex microarray slide contain four identical sectors  that were stripped and re-hybridized up to six times.  Each target was represented by 1-5 probes each. The total of 1250 probes were Tm balanced by altering their lenght between 35 and 40 nucleotides. Total DNA of 41 samples were hybridized and a control strain, the fully sequenced E. faecalis V585, was included  in one of the four sectors on each slide in each set of hybridization to monitor the overall array and hybridization quality.

first: Theresa

last: Mikalsen

first: Torunn

last: Pedersen

first: Rob

last: Willems

first: Teresa

last: Coque

first: Guido

last: Werner

first: Ewa

last: Sadowy

first: Willem

last: van Schaik

first: Lars

last: Bogø Jensen

first: Arnfinn

last: Sundsfjord

first: Kristin

last: Hegstad


title: Cdk11-Cyclin L controls the assembly of the RNA polymerase II Mediator

status: Public on Jul 11 2014

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

country: USA

institute: Mount Sinai School of Medicine

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series

first: Julie

last: Drogat

first: Valérie

last: Migeot

first: Elise

last: Mommaert

first: Caroline

last: Mullier

first: Marc

last: Dieu

last: van Bakel

first: Damien

last: Hermand


title: Cdk11-Cyclin L controls the assembly of the RNA polymerase II Mediator [ChIP-chip]

summary: The L-Mediator is a general co-activator of RNA Polymerase II transcription and is formed by the reversible association of the S-Mediator and the kinase module harbouring Cdk8. We describe the Cdk11-Lcp1 complex and show that its inactivation alter the global expression profiles in a very similar way than mutations of the kinase module. Cdk11 is broadly distributed onto chromatin and phosphorylate the Med27 and Med4 Mediator subunits on conserved residues. The inactivation of either Cdk11 or the mutation of its target residues on the Mediator leads to a strongly decreased association of the kinase module and the S-Mediator. The results show that Cdk11-Lcp1 regulates that assembly of the L-Mediator complex.

overall_design: Two independent immunoprecipitations were done for HA-tagged Cdk11 and each biological replicate was hybridized in duplicate on Agilent arrays using input DNA as the reference channel.


title: Environmentally Induced Epigenetic Transgenerational Inheritance of Altered Sertoli Cell Transcriptome and Epigenome: Molecular Etiology of Male Infertility [NimbleGen]

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by genome tiling array

summary: Environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of adult onset disease, including testis disease and male infertility. The current study was designed to determine the impact of an altered sperm epigenome on the subsequent development of an adult somatic cell (Sertoli cell) that influences the onset of a specific disease (male infertility). A gestating female rat (F0 generation) was exposed to the agriculture fungicide vinclozolin during gonadal sex determination and then the subsequent F3 generation progeny used for the isolation of Sertoli cells and assessment of testis disease. As previously observed, enhanced spermatogenic cell apoptosis was observed. The Sertoli cells provide the physical and nutritional support for the spermatogenic cells. Over 400 genes were differentially expressed in the F3 generation control versus vinclozolin lineage Sertoli cells. A number of specific cellular pathways were identified to be transgenerationally altered. One of the key metabolic processes affected was pyruvate/lactate production that is directly linked to spermatogenic cell viability. The Sertoli cell epigenome was also altered with over 100 promoter differential DNA methylation regions (DMR) modified. The genomic features and overlap with the sperm DMR were investigated. Observations demonstrate that the transgenerational sperm epigenetic alterations subsequently alters the development of a specific somatic cell (Sertoli cell) epigenome and transcriptome that correlates with adult onset disease (male infertility). The environmentally induced epigenetic transgenerational inheritance of testis disease appears to be a component of the molecular etiology of male infertility.

overall_design: The isolated Sertoli cell populations from three different groups of animals that were ancestrally exposed to vinclozolin during days 8-14 (E8-14) of fetal development and cell isolates were used to obtain Sertoli cell RNA and DNA from F3 generation control and vinclozolin lineages. The control and vinclozolin lineage Sertoli cell DNA was used in a methylated DNA immunoprecipitation (MeDIP) and genome wide promoter tiling array (Chip) analysis (MeDIP-Chip). Three different comparative (amplified MeDIP vs. amplified MeDIP) hybridizations experiments included in three sub-arrays were performed by Nimblegen. Each comparative hybridization experiment contained one biological replicate of Sertoli cell Whole Genome Amplified-MeDIP-DNA sample from each lineage-treatment.

first: Carlos

last: Guerrero-Bosagna

first: Marina

last: Savenkova

first: Md

middle: M

last: Haque

first: Eric

last: Nilsson


title: Deinococcus radiodurans R1 Cells: Control vs. bphPR deletion mutant

city: Jeongeup

first: Im

last: Seong Hun

address: Jeongeup 580-185, Republic of KoreaInstitute

country: South Korea

institute: Korea Atomic Energy Research Institute

summary: Transcriptional profiling of Deinococcus radiodurans comparing control wild type cells with bphPR deletion mutant

sample_organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

overall_design: Two-condition experiment, R1 vs. bphPR deletion cell. Biological replicates: 3 control replicates, 3 bphPR deletion mutant replicates.

first: Sangyong

last: Lim

first: Seonghun

last: Im


title: Environmentally Induced Epigenetic Transgenerational Inheritance of Altered Sertoli Cell Transcriptome and Epigenome: Molecular Etiology of Male Infertility


title: Mutation of bphP/bphR Decreases the Resistance of D. radiodurans to DNA-damaging Agents

platform_organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539


title: Fibronectin regulates Wnt7a signaling and satellite cell expansion

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

type:
Expression profiling by array
Third-party reanalysis

summary: The influence of the extracellular matrix (ECM) within the stem cell niche remains poorly understood. We found that Syndecan-4 (Sdc4) and Frizzled-7 (Fzd7) form a coreceptor complex in satellite cells and that binding of the ECM glycoprotein Fibronectin (FN) to Sdc4 stimulates the ability of Wnt7a to induce the symmetric expansion of satellite stem cells. Newly activated satellite cells dynamically remodel their niche via transient high-level expression of FN. Knockdown of FN in prospectively isolated satellite cells severely impaired their ability to repopulate the satellite cell niche. Conversely, in vivo overexpression of FN with Wnt7a dramatically stimulated the expansion of satellite stem cells in regenerating muscle. Therefore, activating satellite cells remodel their niche through autologous expression of FN that provides feedback to stimulate Wnt7a signaling through the Fzd7/Sdc4 coreceptor complex. Thus, FN and Wnt7a together regulate the homeostatic levels of satellite stem cells and satellite myogenic cells during regenerative myogenesis.

overall_design: The data set contains one microarray of pooled quiescent skeletal muscle satellite cells

middle: A

last: Rudnicki

first: Florian

last: Bentzinger


title: Assessment of the response of aerobic and anaerobic muscle tissues of gilthead sea bream (Sparus aurata L.) to caloric restriction

status: Public on Jul 09 2014

city: Castellón

first: Josep

last: Calduch-Giner

address: Ribera de Cabanes

country: Spain

institute: Institute of Aquaculture Torre de la Sal (CSIC)

summary: Fish were fed from May to August (11 weeks) with a commercial diet (D-2 Excel 1P, Skretting, Stavanger, Norway) twice per day at two different feeding levels: full ration until visual satiety (MAX group), and maintenance ration (30% of the satiation level) (MANT group). The effect of ration size on aerobic (red skeletal muscle, heart) and anaerobic (white skeletal muscle) muscle tissue transcriptome was addressed by means of microarray analysis.

overall_design: The following tissues of animal from the MAX and MANT groups were analyzed: white skeletal muscle, red skeletal muscle and heart.

first: Jaume

last: Pérez-Sánchez


title: Murine liver tissues: WT and Wip1 KO mice  after Partial Hepatectomy at 24h and 36 h.

city: hangzhou

first: Hu

last: Wang

address: wenyixi road 1378

country: China

institute: hangzhou normal university

summary: Transcriptional profiling of mouse liver tissues comparing Wild type liver tissues with Wip1 KO mice liver tissues after Partial Hepatectomy at 24h and 36 h.

overall_design: WT vs. Wip1 KO tissues after Partial Hepatectomy at 24h and 36 h .

first: Zhenyu

last: Ju

first: Lingling

last: Zhang


title: Affymetrix expression profile array data of miR-206 affected genes in left superior fat pads in canines

city: Jinan

first: Yujiao

state: Shandong province

address: Jingshi Road

department: Department of cardiology

institute: Qianfoshan Hospital affiliated to Shandong University

summary:
Mongrel dogs of either sex were randomly divided into 2 groups: 1) infection with control lentiviruses group (lenti-control, n = 6), in which control lentiviruses were injected into left superior fat pads;2) only infection with miR-206 overexpressed lentiviruses group (lenti-miR-206, n = 6), in which miR-206 lentiviruses were injected into left superior fat pads.
We used microarrays to detail the global programme of mRNA expression underlying miR-206 overexpression and identified distinct classes of up-regulated and down-regulated genes during this process.

overall_design: Microarray-based mRNA expression profiling was performed of miR-206 overexpressed group and control group using the Affymetrix Array (CA, USA). Equal quantities of RNAs from 3 dogs were mixed to generate one sample for each experimental group.

first: Yinglong

last: Hou


title: Genome-wide expression data of breast cancer samples

city: Berlin

first: Jan

last: Budczies

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite - Universitaetsmedizin Berlin

summary: DASL gene expression data of fresh-frozen breast cancer tissue samples

overall_design: Retrospective cohort

first: Carsten

last: Denkert


title: Expression data from leaves of rice plants overexpressing the OsCPK4 gene and control plants(empty vector) in normal conditions

city: Bellaterra (Cerdanyola del Vallés)

first: Sonia

last: Campo

state: Barcelona

address: Parc de Recerca UAB Edifici CRAG, Campus UAB

institute: Center for Research in Agricultural Genomics (CRAG)

summary: The OsCPK4 gene is a member of the complex gene family of the Calcium-dependent protein kinases (CPKs) in rice. Expression of OsCPK4 is induced by high salinity, drought and the phytohormone abscisic acid. The OsCPK4 protein localizes to the plasma membrane. Transgenic rice overexpressing OsCPK4 enhances tolerance to salt and drought stress, the transgenic plants having stronger water-holding capability than control plants. Microarray analysis of OsCPK4 rice plants revealed up-regulation of genes involved in metabolism, particularly lipid metabolism, as well as genes involved in oxidative stress and redox control. Meanwhile, OsCPK4 overexpression has no impact on the expression of the well-characterized abiotic stress-associated transcription factors (i.e. DREB and NAC), or the typical salt and drought-inducible genes (i.e. LEA genes, including Dehydrin genes). Under salt stress conditions, the OsCPK4 transgenic lines showed lesser membrane lipid peroxidation as compared to control plants, indicating that OsCPK4 rice plants have a better capacity to prevent oxidative damage in cellular membrane lipids. Collectively, our data suggest that OsCPK4-mediated processes protect the plant cell from uncontrolled redox reactions affecting membrane functions, which, in turn, results in salt and drought tolerance. OsCPK4 shows great promise for genetic improvement of tolerance to abiotic stress in rice.

platform_organism:
Oryza sativa
Oryza sativa Japonica Group

overall_design: Leaves of OsCPK4 and vector control plants that had been grown hydroponically for 15 days were harvested and used for total RNA extraction and hybrizations in two color customized Agilent microarrays.

first: Patricia

last: Baldrich

first: Joaquima

last: Messeguer

last: Lalanne

first: María

last: Coca

first: Blanca

last: San Segundo


title: Deinococcus radiodurans R1 Cells was treated with MMC (5 μg/ml) : Control treated with MMC (5 μg/ml) vs. bphPR deletion mutant treated with MMC (5 μg/ml)

first: Im

last: Seong Hun

summary: Transcriptional profiling of Deinococcus radiodurans comparing control wild type cells with bphPR deletion mutant were treated with MMC (5 μg/ml)

overall_design: Two-condition experiment, R1 MMC (5 μg/ml) vs. bphPR deletion cell MMC (5 μg/ml). Biological replicates: 3 control replicates, 3 bphPR deletion mutant replicates.

first: Sangyong

last: Lim

first: Seonghun

last: Im


title: Genome-wide analysis of Staufen1-bound mRNAs in prometaphase

city: Montréal

first: Luc

last: DesGroseillers

state: Québec

address: 2900 Edouard Montpetit

department: Biochimie

institute: Université de Montréal

summary:
The goal of this experiment was to identify Staufen1-bound mRNAs in prometaphase cells.
Stau1 abundance fluctuates through the cell cycle: it is high in the G2 phase of the cell cycle and rapidly decreases as cells transit through mitosis. The importance of controlling Stau1 levels was underscored by the observation that its overexpression impairs mitosis as well as proliferation of transformed cell lines. As a major post-transcriptional regulator, Stau1 may exert its role(s) through the spatial and/or temporal regulation of its bound mRNAs. Therefore, to gather clues to support this possibility, we identified Stau1-bound mRNAs in prometaphase as a means to identify mRNAs that could be subjected to post-transcriptional modulation when Stau1 is partly degraded in mitosis.

overall_design: HEK293T cells were transfected with plasmids coding for Stau155-FLAG or the empty vector as control. Cells were synchronized in prometaphase with nocodazole. Stau1-bound mRNAs were isolated after immunoprecipitation using anti-FLAG antibody.

first: Veronique

last: Trepanier


title: Genome-wide analysis of mRNAs expression in prometaphase

summary:
The goal of this experiment was to compare the transcriptome of cells that overexpressed the RNA-binding protein Staufen1 to that of cells that expressed the empty vector as control.
Stau1 abundance fluctuates through the cell cycle: it is high in the G2 phase of the cell cycle and rapidly decreases as cells transit through mitosis. The importance of controlling Stau1 levels was underscored by the observation that its overexpression impairs mitosis as well as proliferation of transformed cell lines. As a major post-transcriptional regulator, Stau1 may exert its role(s) through the spatial and/or temporal regulation of its bound mRNAs. Therefore, to gather clues to support this possibility, we determined if Stau1 overexpression significantly modified the transcriptome of transformed cells in prometaphase explaining the observed impairment in mitosis transit and/or cell proliferation.

overall_design: HEK293T cells were transfected with plasmids coding for Stau155-FLAG or the empty vector as control. Cells were synchronized in prometaphase with nocodazole.


title: Gene expression profile of human cardiac fibroblasts (HCFs), induced cardiomyocytes (iCMs), and heart

first: Satoshi

last: Kondo

summary:
Global gene expression profile of total 24460 probes in the iCMs. The gene expression shifts from a fibroblast state toward a cardiac-like phenotype by Gata4/Mef2c/Tbx5/Mesp1/Myocd (GMTMM) or GMTMM/miR-133 transduction at 7 days after transduction.
MiR-133 silenced fibroblast signatures in parallel with cardiac gene activation, and Snai1 overexpression inhibited the effects of miR-133-mediated cardiac reprogramming.

overall_design: HCFs were used for negative control, human heart tissue for positive control. Gene expression profiles were compared among HCFs, iCMs and heart. 24460 probes were analyzed in each experiment.

first: Naoto

last: Muraoka

first: Masaki

last: Ieda


title: Gene expression levels in Rhizosphere Originating Biocontrol Strain Pseudomonas aeruginosa M18 producing different amounts of phenazine-1-carboxylate acid (PCA)

status: Public on Jul 02 2014

city: Shanghai

first: yaqian

last: Li

address: Dongchuan Road

institute: Shanghai Jiaotong University

summary: To further understand the gene expression characteristics of originating biocontrol strain Pseudomonas aeruginosa M18, we have applied whole genome microarray expression profiling as a discovery platform to to specify the PCA-dependent expression of M18 genome. We constructed a series of PCA-producing mutant strains (high PCA: M18MSU1; low PCA: M18MS; and no PCA: M18MSP1P2). The comparison analysis of the M18 mutants genome expressional profiles indicated that the expression of PCA in both M18MSU1 and M18MS alters the expression of a total of 545 different genes; however, the higher level of PCA in M18MSU1 altered more genes (489) as compared to M18MS (129).

overall_design: Cells were grown to OD600=5.0 (exponential phase) in PPM medium at 28℃. Three independent experiments were performed at each time.

first: Yuquan

last: Xu

first: Xilin

last: Du


title: MicroRNA expression pattern in lung cancer and COPD

city: Seville

last: Molina-Pinelo

address: Avda. MAnuel Siurot s/n

institute: IBIS

summary: The objective is to establish robust transcriptional regulation differences between lung cancer (LC) and chronic obstructive pulmonary disease (COPD) by studying miRNA and concurrent transcriptional profiles

overall_design: To define miRNA signature of bronchoalveolar cell fraction, samples were obtained from 87 patients from Virgen del Rocío Hospital who had required flexible bronchoscopy for diagnostic reasons. PAtients were divided into COPD group, COPD-LC group, LC group and un control group neither COPD nor LC according to the pathological results. Mature human miRNA expression was detected and quantified using the TaqMan® Low Density Arrays (TLDA). The TaqMAn Human MicroRNA A Array v2.0 containing a total of 384 TaqMan® MicroRNA Assaysto enable accurate quantity of 381 human microRNAs, all catalogued in the miRBase database.Expression of target miRNAs was normalized in relation to the expression of MammU6.  Cycle threshold (Ct) values were calculated using the SDS software v.2.3 using automatic baseline settings and a threshold of 0.2. Relative quantification of miRNA expression was calculated by the 2−ΔCt method (Applied Biosystems user bulletin no. 2 (P/N 4303859)).

first: Rocio

last: Suarez

first: M

middle: D

last: Pastor

first: Ricardo

last: Meléndez

first: Beatriz

last: Romero-Romero

first: Ana

last: Salinas

first: Rocío

middle: G

last: Carbonero

first: Amancio

last: Carnero

first: Luis

last: Paz-Ares


title: Phenotype and expression profile analysis of Staphylococcus aureus biofilms and planktonic cells in response to Licochalcone A

status: Public on Jul 01 2014

city: Changchun

first: lu

last: yu

state: Jilin

address: Xi’an Road 5333#

department: Institute of Zoonosis

institute: Jilin University

summary:
Staphylococcus aureus (S. aureus) is one of the most important pathogens in humans and animals. The formation of S. aureus biofilm is considered an important mechanism of antimicrobial resistance. Therefore, finding effective drugs against the biofilm produced by S. aureus has been a high priority. Licochalcone A, a natural plant product, was reported to have antibacterial activities and showed good activity against all 21 tested strains of S. aureus biofilm and planktonic cells.
To detect the possible molecular mechanism of Licochalcone A against S. aureus biofillm or planktonic cells, Affymetrix GeneChips were used to determine the global comparative transcription of S. aureus biofilm and planktonic cells triggered by treatment with sub-bactericidal and sub-inhibitory concentrations of Licochalcone A, respectively.

overall_design: Staphylococcus aureus  planktonic cells and biofilm were exposed for 60 minutes to Licochalcone A at concentration of 2 μg/ml (1/2× MIC) and 64 μg/ml (4× MIBC), respectively. 4 samples including 4 control samples are analyzed.

first: Fengge

last: Shen

first: Xudong

last: Tang

first: Yang

last: Wang

first: Zhiqiang

last: Yang

first: Xiaochen

last: Shi

first: Chao

first: Qiaoli

last: Zhang

first: Yanan

last: An

first: Wei

last: Cheng

first: Kunqi

last: Jin

first: Mingyuan

last: Liu

last: Guo

first: Lu

last: Yu


title: Gene expression data from myelomonocytes and whole kidney marrows in zebrafish adult kidney after deletion of miR-142-3p

first: Hongbo

last: Fan

address: 320 Yueyang Road, Shanghai, China

department: Institute of Health Sciences

institute: Chinese Academy of Sciences

summary:
hematopoiesis and myelopoiesis was tightly controled by microRNAs. In the zebrafish adult kidney, specific sets of genes were dysregulated in myelomonocytes or whole kidney marrow after deletion of miR-142-3p.
microarrays were used to clarified the miR-142-3p regulatory network in myelopoiesis in miR-142-3p knockout zebrafish kidney and we identified distinct classes of up-regulated genes in zebrafish myelopoiesis or hematopoiesis after deletion of miR-142-3p.

overall_design: The myelomonocytes and whole kidney marrow (without erythrocytes) were sorted from wild-type or miR-142-3p double knockout zebrafish kidney at 60 dpf (four zebrafish kidneys and two independent repeats for each sample). Total RNA was extracted and hybridization on Affymetrix microarrays.


title: Genomic responses in blood during acute human anaphylaxis

city: Subiaco

first: Anthony

last: Bosco

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

summary:
Gene expression was profiled in peripheral blood samples collected over three time points from patients during acute anaphylaxis and from healthy controls.
Patients presented to the Emergency Department (ED) at Royal Perth Hospital with acute, moderately severe anaphylaxis. Samples were collected at ED arrival (T0), 1 hour later (T1), and 3 hours post arrival (T2).

overall_design: The study design consisted of 12 subjects, 3 time points, and 2 clinical states (acute anaphylaxis, healthy controls).

first: Shelley

last: Stone

first: Pauline

last: van Eeden

first: Simon

last: Brown


title: Comparison between GT and ntcA-overexpressing strains of cyanobacteria

city: Kawasaki

first: Takashi

last: Osanai

address: 1-1-1, Higashimita, Tamaku

department: School of Agriculture

institute: Meiji University

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

overall_design: Refer to individual Series


title: Comparison between GT and ntcA-overexpressing strains of cyanobacteria [nitrogen-replete conditions]

summary: NtcA regulates primary in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed an ntcA-overexpressing strain, named NOX10, by introducing the ntcA genes fusing psbAII promoter by homologous recombination. The transcript profiles of parental wild-type strain GT and NOX10 were compared by microarray CyanoChip (Takrara bio.). Experiments were performed three times with biologically independent RNA.

overall_design: Total RNAs from three independent wild-type (GT) and three independent ntcA-overexpressing strains were differently labeled by Cy3 or Cy5, followed by hybridization on CyanoChip.


title: Transcriptional analysis between Streptomyces clavuligerus ATCC 27064 and mutants altered in the antibiotics production

city: León

first: Paloma

last: Liras

state: León, Spain

address: Facultad de Biología. Campus de Vegazana

department: Molecular Biology

institute: Universidad de León

summary: The objective is to analyze the differential expression between the wild strain and a ccaR-deleted and oppA2::aph mutants

overall_design: 6 biological conditions were used, three strains in two times (exponential and stationary growth phase; Streptomyces clavuligerus ATCC 27064, S. clavuligerus ∆ccaR and S. clavuligerus oppA2::aph). Four biological replicates were made for each condition

first: Rubén

last: Álvarez-Álvarez

first: Antonio

last: Rodríguez-Gracía

first: Irene

last: Santamarta

first: Rosario

last: Pérez-Redondo


title: Impact of MLL5 expression on decitabine efficacy and DNA methylation in acute myeloid leukemia

city: Hannover

first: Michael

last: Heuser

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

summary:
We found previously that the effect of decitabine (DAC) on hematopoietic stem cell viability differed between Mll5 wildtype and null cells. We therefore investigated the role of MLL5 expression levels on outcome of AML patients who were treated with decitabine. High MLL5 expressing AML patients have improved overall survival when treated with decitabine. In transformed murine cells, loss of Mll5 was associated with resistance to low-dose decitabine, less frequent promoter methylation, and reduced demethylation upon decitabine treatment. These data suggest a biological link between MLL5 expression and decitabine response involving regulation of DNA methylation.
Leukemia cell model was generated by co-transfer of HOXA9 and MEIS1 into Mll5 wildtype or knockout mouse bone marrow cells. MeDIP was performed in Mll5+/+ HOXA9/MEIS1 and Mll5-/- HOXA9/MEIS1 leukemic cells, untreated or treated with 3-day exposure of 20 nM decitabine, triplicate for each condition. MeDIP-enriched DNA was amplified with the GenomePlex Complete Whole Genome Amplification (WGA) Kit (Sigma-Aldrich). DNA from three MeDIP and WGA of each cell type and treatment was pooled for subsequent microarray analysis.  The enriched DNA and corresponding input genomic DNA was labeled, hybridized and scanned on Agilent custom mouse promoter microarrays (Agilent-025976 AP_1M_Custom_CH3, assembly build mm9). The methylation value of individual probes was defined by the signal intensity ratio of MeDIP DNA (Cy3) compared to input DNA (Cy5) .

overall_design: Methylated DNA immunoprecipitation coupled with Agilent mouse promoter CpG arrays (MeDIP-chip)

first: M

first: H

last: Yun

first: R

last: Geffers


title: Comparison between GT and ntcA-overexpressing strains of cyanobacteria [nitrogen-depleted conditions]

summary: NtcA regulates primary in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed an ntcA-overexpressing strain, named NOX10, by introducing the ntcA genes fusing psbAII promoter by homologous recombination. The transcript profiles of parental wild-type strain GT and NOX10 were compared by microarray CyanoChip (Takrara bio.). Experiments were performed two times with biologically independent RNA.

overall_design: Total RNAs from two independent wild-type (GT) and two independent ntcA-overexpressing strains were differently labeled by Cy3 or Cy5, followed by hybridization on CyanoChip.


title: microRNA profiling of HepG2 cells: control vs treatment with cacao, grape seed proanthocyanidin extract or epigallocatechin gallate

city: Tarragona

first: Anna

last: Arola-Arnal

state: Tarragona

address: Campus Sescelades. C/Marcel.lí Domingo s/n

institute: Universitat Rovira i Virgili

summary: Mi(cro)RNAs are small non-coding RNAs of 18-25 nucleotides in length that modulate gene expression at the post-transcriptional level. These RNAs have been shown to be involved in a several biological processes, human diseases and metabolic disorders. Proanthocyanidins, which are the most abundant polyphenol class in the human diet, have positive heath effects on a variety of metabolic disorders such as inflammation, obesity, diabetes and insulin resistance. The present study aimed to evaluate whether proanthocyanidin-rich natural extracts modulate miRNA expression. Using microarray analysis and Q-PCR, we investigated miRNA expression in HepG2 cells treated with proanthocyanidins. Our results showed that when HepG2 cells were treated with grape seed proanthocyanidin extract (GSPE), cocoa proanthocyanidin extract (CPE) or pure epigallocatechin gallate isolated from green tea (EGCG), fifteen, six and five differentially expressed miRNAs, respectively, were identified out of 904 mRNAs. Specifically, miR-30b* was downregulated by the three treatments, and treatment with GSPE or CPE upregulated miR-1224-3p, miR-197 and miR-532-3p. Therefore, these results provide evidence of the capacity of dietary proanthocyanidins to influence microRNA expression, revealing a new mechanism of action of proanthocyanidins.

overall_design: microRNA profiling of Human hepatocellular liver carcinoma cell line (HepG2) comparing control untreated HepG2 cells with cells treated with grape seed proanthocyanidin extract (100 mg/L, 5h), cacao  proanthocyanidin extract (100 mg/L, 5h) or epigallocatechin gallate (50 mg/L, 5h). Two biologival replicates were used for control and  treated cells with one replicate per array.


title: Profiling circulating microRNA expression in a mouse model of nerve allotransplantation

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital


title: Real-time quantitative PCR analysis of fatty acid metabolism genes of liver tissue from wild-type and PPARa (-/-) mice exposed to 2,4-dinitrotoluene (PPARa)

status: Public on Jun 30 2014

city: Vicksburg

first: Mitchell

last: Wilbanks

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army Engineer Research and Development Center

summary: 2,4-dinitrotoluene (2,4-DNT), a nitroaromatic used in industrial and explosive manufacturing processes, is known to contaminate artillery ranges, demilitarization areas and munitions manufacturing facilities.  Previous transcriptomic and lipidomic studies identified energy metabolism as a principle biochemical process affected by 2,4-DNT where up-stream effects on PPARα signaling were hypothesized as themolecular initiating event for these effects. Here, the validity of this hypothetical adverse outcome pathway (AOP) was assessed by testing the hypothesis that 2,4-DNT-induced perturbations in PPARα signaling and resultant downstream deficits in energy metabolism, especially from lipids, would result in organism-level impacts on exercise endurance.  PPARα knock-out (-/-) and wild-type (WT) mice were exposed for 14 days to vehicle or 2,4-DNT at a dose (134 mg/kg/day) that did not exhibit overt systemic toxicity. Mice performed an exercise challenge (forced swim) 1 day after the last dose.  2,4-DNT decreased swim times in WT and PPARα (-/-) mice, but the effect was significantly less in PPARα  (-/-) mice indicating the critical of PPARα in mediating 2,4-DNT-induced energy metabolism deficits.  2,4-DNT caused down-regulation of transcripts involved in fatty acid metabolism, gluconeogenesis, triacylglycerol catabolism, and the pentose phosphate pathway, and 2,4-DNT treated wild-type mice had decreased serum trigylcerides and increased serum glucose versus 2,4-DNT treated PPARα (-/-) mice.   Our results support the hypothesis that 2,4-DNT perturbs PPARα signaling as a molecular initiating event therefore impacting  energy metabolism, especially lipid metabolism, producing reduced exercise endurance in mice.

overall_design: RNA was isolated from liver tissue of vehicle or 2,4-DNT treated wild-type or PPARα (-/-) mice (n=6) and RT-PCR performed to analyze genes involved in fatty acid metabolism

first: Kurt

last: Gust

first: Sahar

last: Atwa

first: Imran

last: Sunesara

first: Sharon

last: Meyer

first: Edward

last: Perkins


title: The pattern of genomic instability during bladder cancer progression (part 1)

city: Aarhus N

first: Philippe

last: Lamy

address: Brendstrupgårdsvej 100

department: Department of molecular medecine

country: Denmark

institute: MOMA

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

summary: The Illumina SNP bead arrays were done for two metachronous tumors and the blood from a given patient. It was used to define copy number abnormalities in order to support subclonal population analysis in this patient.

overall_design: Three samples were analysed concerning two metachronous tumor samples and a blood sample from the same patient.

first: Iver

last: Nordentoft


title: Analysis of whole-genome copy-number variation in Crohn's disease fistula tissue

city: Burwood

first: phillip

middle: david

last: parker

state: Victoria

address: 221 Burwood Highway

department: Health

institute: Deakin University

type: Genome variation profiling by high throughput sequencing

summary:
Background: Crohn’s disease is presently an incurable inflammatory bowel disease. Fistulae are extensions of the intestinal tract that may form connections with other organs. These are a common complication of Crohn’s disease affecting up to 50% of patients with the most common including perianal and rectovaginal fistulae. The dysregulated growth observed in fistulae shares several major characteristics seen in the development of tumours. These similarities include epithelial-to-mesenchymal transition (EMT), invasive cell growth, increased extracellular matrix production and remodelling, up-regulated local expression of growth factors such as IGF-1 and the down-regulation of apoptosis pathways. Although several susceptibility loci have been described within Crohn’s disease there is no individual gene or mutation that identifies susceptibility or the subsequent formation of fistulae within all people. Copy-number variation (CNV) is one mechanism that may explain much of this genetic complexity. CNV may be caused by a variety of mechanisms such as cycles of chromosomal breakage/fusion/bridging that are typical within chronically inflamed tissue. Interestingly CNV shows locus-specific mutation rates between individuals higher than that of SNPs and has been associated with complex Mendelian traits including disease susceptibility. In this current study we performed array comparative genomic hybridisation (aCGH) analysis of active fistulae resected from patients as part of a previous surgical intervention. As the control for comparison we employed tissue taken from the same patient within the same surgery at an uninvolved site of the gastrointestinal tract. This matched control was employed to better investigate CNV specific to the fistula tissue of each individual avoiding complications associated with the large number of CNV present within the healthy population.
Major question addressed by the work: What are the differences in genetic copy-number within localised intestinal fistula tissue of individuals with Crohn’s disease compared to healthy intestinal tissue from the same individual?

overall_design: Samples were selected from patients presenting with Crohn’s Disease fistulae at Eastern Health Department of Gastroenterology and Hepatology (Arnold Street, Box Hill, Victoria, Australia). The 8 samples used in this study were formalin-fixed paraffin-embedded (FFPE) specimens following a surgical intervention to remove fistula tissue. To focus on changes within the individual patient we used tissue taken from the same surgery at an uninvolved region of the intestine as the matched control for CNV analysis.

first: Phillip

last: Parker

first: Daniel

last: van Langenberg

first: Patrick

last: Hosking

first: Aaron

last: Russell


title: Validation of a genomics-based hypothetical adverse outcome pathway:  2,4-dinitrotoluene perturbs PPAR signaling impairing energy metabolism and decreasing exercise endurance


title: Early and advanced gastric cancer genomes

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

institute: Catholic University of Korea

summary:
Early gastric cancers (EGC) precede advanced gastric cancers (AGC) with a favorable clinical outcome compared to advanced gastric cancers (AGC). To understand the progression mechanisms of EGC to AGC, it is required to disclose the EGC and AGC genomes in terms of the the mutational and evolutionary perspectives.
In this study, we performed whole-exome sequencing and copy number profiling of nine microsatellite (MS)-unstable (MSI-H) (5 EGC and 4 AGC) and eight MS-stable (MSS) gastric cancers (4 EGC and 4 AGC). Unexpectedly, we observed no substantial differences in the number, sequence composition and functional consequences (potential driver mutations and affected pathways) of the mutations and CNAs between EGC and AGC genomes in both MSI-H and MSS cases.

overall_design: Gastrectomy tissues from 17 GC patients were used for this study. The hospital pathology department confirmed pathologic features of the GC (e.g., EGC vs. AGC, differentiation, lymph node metastasis and TNM stage). All of the picked areas from tumor and normal areas were frozen, cut, and stained with hematoxylin & eosin (H&E). Two pathologists selected cases with rich tumor cell population (at least 60%), which were subsequently used in the study. Copy number profiling was performed using Agilent 180K platform according to the manufacturer's protocol.

first: Seung-Hyun

first: Yeun-Jun

last: Chung


title: Comparative analysis of transcriptome profiles of G. hirsutum L. acc. TM-1 and its immature fber mutant during fiber secondary cell wall development stages

city: Nanjing

first: Cheng

last: Wang

address: Weigang No.1

institute: Nanjing Agricultural University

summary: To gain novel insights into the molecular mechanisms of fiber secondary cell wall development, fiber transcriptomes of the immature fiber mutant (im) with defective secondary cell wall development and its near-isogenic line, TM-1 (wild-type) were compared using cDNA microarray technology. The expression profiling was performed at 5 developmental time points: 13, 16, 19, 22, and 25dpa. Secondary cell wall development related genes were identified by differentially expressed gene analysis. And these genes could be used as potential candidate genes for manipulation to improve fiber quality.

overall_design: Cotton plants were grown under field condition. Flowers were tagged and cotton bolls were collected during Fiber development stages. Total RNA was isolated from fiber bearing ovules of wild-type, TM-1 and immature fiber mutant (im) collected at various (13, 16, 19, 22 and 25 dpa) fiber development stages. A total of 15 hybridizations with three biological replicates including a swap-dye experiment for each fiber developmental stage were employed.

first: Wangzhen

last: Guo


title: Profiling circulating microRNA expression in a mouse model of nerve allotransplantation (part 1)

first: Ching-Hua

last: Hsieh

summary: Background. The lack of noninvasive biomarkers of rejection remains a challenge in the accurate monitoring of deeply buried nerve allografts and precludes optimization of therapeutic intervention. This study aimed to establish the expression profile of circulating microRNAs (miRNAs) during nerve allotransplantation with or without immunosuppression.  Methods. Balb/c mice were randomized into 3 experimental groups, that is, (1) untreated isograft (Balb/c → Balb/c), (2) untreated allograft (C57BL/6 → Balb/c), and (3) allograft (C57BL/6 → Balb/c) with FK506 immunosuppression. A 1-cm Balb/c or C57BL/6 donor sciatic nerve graft was transplanted into sciatic nerve gaps created in recipient mice. At 1, 3, 7, 10, and 14 d after nerve transplantation, nerve grafts, whole blood, and sera were obtained for miRNA expression analysis with an miRNA array and subsequent validation with quantitative PCR.

overall_design: Male Balb/c and C57BL/6 mice (age, 10–12 weeks; weight, 30–35 g) were purchased from BioLasco (Yi-Lan, Taiwan). The Balb/c mice were randomized into 3 experimental groups: (1) untreated isograft, (2) untreated allograft, and (3) allograft with FK506 treatment. Additional Balb/c and C57BL/6 mice served as sciatic nerve isograft and allograft donors, respectively. These species of mice were selected on the basis of disparity at the MHC locus and prior experience with reciprocal rejection of grafts between these murine strains. FK506 was administered subcutaneously at 1 mg/(kg•d) throughout the experimental course, unless indicated otherwise. At 1, 3, 7, 10, and 14 d after initial surgery (n = 6 animals per group at each time point), sciatic nerve grafts were harvested, and whole blood samples were obtained. Additional sham-operated mice were subjected to the same procedure, including opening of the skin and muscle layers and exposing the sciatic nerve, but without nerve transection or nerve grafting, to measure the effect of FK506 injection on the expression of circulating miRNA. To test the effect of the discontinuation of FK506 treatment on the expression of circulating miRNA, whole blood was drawn at 0, 2, 4, and 6 d after discontinuation of FK506 injection in an additional group of mice with allografts and immunosuppression for 7 d. The whole blood samples (1 mL per mouse) were collected at the indicated times in tubes containing anticoagulant. After the whole blood samples were incubated at room temperature for 15 min, they were centrifuged at 3000 rpm for 10 min, white blood cells were slowly removed from the corresponding layers, and the serum was extracted and stored at –80°C before processing for RNA analyses. All the housing conditions and the surgical procedures, analgesia, and assessments were in accordance with national and institutional guidelines, and an Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC)–accredited SPF facility was used. The animal protocols were approved by the Institutional Animal Care and Use Committee (IACUC) of Kaohsiung Chang Gung Memorial Hospital.

first: Cheng-Shyuan

last: Rau

first: Johnson

middle: C

last: Yang

first: Shao-Chun

last: Wu

first: Yi-Chun

last: Chen

first: Tsu-Hsiang

last: Lu

first: Yi-Chan

first: Siou-Ling

last: Tzeng

first: Chia-Jung


title: Comparative analysis of genes regulated by Dzip1/iguana and Hedgehog in zebrafish

city: Calgary

first: Sarah

middle: J

last: Childs

state: AB

address: 3330 Hospital Drive NW

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary:
The morphogen Sonic H edgehog governs a wide range of developmental processes. The zebrafish genetic mutant iguana has vascular stability defects due to decreased Shh signaling. Using iguana mutant embryos and embryos treated with the Hedgehog pathway inhibitor cyclopamine, we conducted a microarray to determine genes that are specifically regulated by Shh signaling, and that might mediate vascular stability. We populate a list of 40 genes to have significantly altered expression in both conditions.
Using in situ hybridization and quantitative real-time PCR, we verify the expression changes seen in a subset of genes from the list and determine their localization during embryonic development. We then assay the functional relevance of one of the array hits, the cell-cycle regulator pim1, which was upregulated on the microarray. By overexpressing pim1, we observe a loss of vascular stability, similar to that of iguana mutants. Furthermore, chemical inhibition of pim1 in iguana mutant embryos or cyclopamine treated embryos rescues vascular stability. We conclude that the microarray identified a set of genes that are differentially expressed in two distinct modes of Shh signaling interference.  Furthermore, this set of genes contains a high proportion of factors potentially involved in vascular stabilization. The identification of these genes is the first step in defining the molecular mechanism by which Shh promotes vascular stability.

overall_design: 3 biological cyclopamine treated samples plus 3 biological DMSO treated controls, plus 3 biological replicates of iguana mutants plus 3 wild type sibling controls, all collected at 30 hpf

first: Corey

middle: R

last: Arnold

first: John

middle: T

last: Walker

first: Ryan

last: Lamont

first: Jing

last: Liu

first: Kin

last: Chan

first: Chi-Yip

last: Ho


title: A. borkumensis cells: pyruvate vs. cells grown on hexadecane, canola and diesel

city: Frankfurt

first: Daniela

middle: Jasmin

last: Näther

address: Max-von-Laue-Str. 9

department: Molecular Biosciences

institute: Goethe University Frankfurt

summary: Transcriptional profiling of Alcanivorax borkumensis cells, grown on either pyruvate or hexadecane, canola and diesel as carbon source.

overall_design: Two-condition experiment, cells grown on pyruvate vs. cells grown on hexadecane, canola or diesel. For each condition 4 replicates were used, as for the control condition also 4 replicates were used for analysis.

first: Hermann

last: Heipieper

first: Martin

last: Olzog


title: Profiling circulating microRNA expression in a mouse model of nerve allotransplantation (part 2)

first: Ching-Hua

last: Hsieh

first: Johnson


title: Real-time quantitative PCR analysis of fatty acid metabolism genes of liver tissue from wild-type and PPARα (-/-) mice exposed to 2,4-dinitrotoluene (fatty acid)

first: Mitchell

last: Wilbanks

first: Kurt

last: Gust

first: Sahar

last: Atwa

first: Imran

last: Sunesara

first: Sharon

last: Meyer

first: Edward

last: Perkins


title: CD99 suppresses osteosarcoma cell migration by favouring the oncosuppressor N-cadherin/ B-catenin signalling pathway in contrast to ezrin: the central role of ROCK2

status: Public on Jun 29 2014

city: Bologna

first: Katia

last: Scotlandi

address: Via di Barbiano 1/10

country: Italy

institute: Istituto Ortopedico Rizzoli

summary: To determine the molecular basis for CD99 function in osteosarcoma, gene expression profile of U-2/CD99 wild-type(wt) expressing cell lines were compared with U-2 OS parental cells.

overall_design: Two-conditions experiment, U-2/CD99 vs U-2OS cell lines. Biological replicates:3 control replicates, 3 transfected replicates.

first: Cinzia

last: Zucchini

first: Maria

last: Manara

first: Rosa

middle: S

last: Pinca

first: Paola

last: De Sanctis

first: Clara

last: Guerzoni

first: Marika

last: Sciandra

first: Giovanna

last: Cenacchi

first: Piero

last: Picci

first: Luisa

last: Valvassori


title: Genome-wide transcriptome analysis of the oxygen response of L. johnsonii reveals that NADH oxidase is a secondary H2O2 source.

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

summary: Oxidative stress due to endogenous hydrogen peroxide production by Lactobacillus species is a well-known issue in the food industry. In this study, the transcriptional response to oxygen of Lactobacillus johnsonii, one of the H2O2-producing strains used in the food industry, was analyzed. It was found that aerobic growth conditions led to a more than two-fold downregulation of 45 genes as compared to anaerobic growth, whereas 6 genes were more than twofold upregulated. Among the upregulated genes were two genes that displayed significant homology to NADH-dependent oxidoreductase (NOX). The postulated transcriptional regulation of the nox promoter by oxygen was studied using a GUS-reporter construct, confirming a 2.1-fold upregulated GUS-expression upon aerobic growth. Exposure to sublethal levels of hydrogen peroxide did not result in significant regulation of the nox promoter. In a previous study of hydrogen peroxide production by L. johnsonii, a NADH flavin reductase (NFR) was identified to be involved in hydrogen peroxide production. An NFR-deficient derivative was strongly impaired in H2O2 production, but regained a partial H2O2 producing capacity upon prolonged oxygen exposure. The nox-promoter appeared to be 3.6-fold upregulated under aerobic conditions in the NFR-deficient background, which may imply a role of this gene in the regained H2O2 production. Indeed, deletion of the nox-gene in the NFR-deletion background, resulted in a strain that no longer produced H2O2, also during prolonged exposure to oxygen. The double-mutant (nfr, nox)  displayed strongly impaired aerobic growth and oxygenation induced rapid growth stagnation that is not caused by H2O2. We conclude that H2O2 production in L. johnsonii is primarily dependent on NFR but can also involve an oxygen-inducible NADH oxidase under aerobic conditions. Moreover, our results imply that H2O2 production plays a prominent role in oxygen tolerance of L. johnsonii.

overall_design: loop design of the samples including two shortcuts

first: Rosanne

last: Hertzberger

first: Marjo

last: Starrenburg

first: Iris

last: van Swam

first: R

last: Pridmore

first: Christof

last: Gysler

first: M

last: de Mattos

last: Kleerebezem


title: Vectorial secretion of interleukin-8 (IL-8 or CXCL8) mediates homeostatic effects on the intestinal epithelium via apically located CXCR1

status: Public on Jun 28 2014

city: Wageningen

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

institute: Wageningen University

summary: CXCL8 is produced by many cell types including epithelial, endothelial, fibroblasts and macrophages in response to TLR recognition of microbe-associated molecular patterns (MAMPs) or inflammatory cytokines and recruits phagocytes from the vasculature to sites of infection via interaction with its cognate receptors CXCR1 and CXCR2. In the intestine, CXCL8 has been demonstrated to participate in the migration of neutrophils across the epithelium during acute inflammation. Given the well-recognized role of CXCL8 as an initiator of inflammation and the constant presence of commensal bacteria in the intestinal tract, we hypothesized that in the intestinal epithelium, CXCL8 might be secreted in a vectorial fashion depending on the location and type of stimulus as a mechanism to maintain homeostasis. In addition, we hypothesized that the CXCR1 receptor might control specific functions in polarized IECs depending on its location. We tested these hypotheses using microarray gene expression profiling of IL-8 treated and mock-treated Caco-2 cell lines

overall_design: This study was set up according to a one-treatment, one-control design. It contains individual transcriptional profiles from 3 IL-8-treated and 3 buffer control-treated samples. In total, this study includes data from 3 Caco-2 samples x 2 treatments=6 arrays.

first: Oriana

last: Rossi

first: Jerry

last: Wells


title: Identifying target genes involved in subclinical respiratory disease that develop in athletes: an insight from the horse athlete and the use of microarrays

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
The aim of the present study, using microarrays, was to find hitherto unknown target genes involved in the subclinical respiratory inflammation that are responsible for drop in exercise performance. It is hoped that this may improve understanding of the physiopathological pathways that are responsible for airway inflammation depending of the discipline involved and will likely have a clinical impact on sports medicine, and on the current approach to exercise-based rehabilitation in respiratory disease.

Keywords: microarray, subclinical, airway, inflammation, sport, respiratory disease

overall_design: The study included 8 French Standardbred trotters, aged 2–8 years, 8 thoroughbred, aged 2-5 years, and 8 endurance horses, aged 7-12 years, referred to the Centre of Imaging and Research on Equine Locomotor Disease (CIRALE) between October 2006 and February 2008. To be included in the study, horses had to be either in competition at the time of the study or in active race training during the preceding 3 months. In each discipline, 4 fit and performing horses with no clinical disease and defined as healthy at the end of the tests were selected as controls and 4 horses not performing as expected and diagnosed as affected by inflammatory airway disease (IAD) following the criteria previously described (Robinson and Hoffman, 2003; Couëtil et al., 2007, Richard et al., 2009), were selected as inflammatory. Hybridisation on the Horse Gene Expression Microarray (Agilent) was performed in a single horse per chip and in a monocolore mode, using cyanine-3 (Cy3) labeling.

first: Eve

last: Ramery

first: Audrey

last: Fraipont

first: Eric

last: Richard

first: Marie

last: Toussaint

first: Tatiana

last: Art

first: Dimitri

last: Pirottin

first: Fabrice

last: Bureau

first: Pierre

last: Lekeux


title: Real-time quantitative PCR analysis of fatty acid metabolism genes of liver tissue from wild-type and PPARα (-/-) mice exposed to 2,4-dinitrotoluene (glucose)

first: Mitchell

last: Wilbanks

first: Kurt

last: Gust

first: Sahar

last: Atwa

first: Imran

last: Sunesara

first: Sharon

last: Meyer

first: Edward

last: Perkins


title: Comparision of Bmi-1, Ring1B, H3K27me3, Ser2 Pol II, Ser 5 Pol II binding on Hox and non-Hox genes

status: Public on Jun 27 2014

city: London

first: Pradeepa

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

summary: Bmi-1, Ring1B, H3K27me3, Ser2 Pol II, Ser 5 Pol II binding pattern  in WT and Psip1 KO MEFs Menin occupancy is studied over Hox genes and several non-hox genes

overall_design: Bmi-1, Ring1B, H3K27me3, Ser2 Pol II, Ser 5 Pol II ChIPs from WT and Psip1 KO MEFs

last: Marulasiddappa

first: Graeme

last: Grimes

first: Wendy

last: Bickmore


title: Gene expression profiling in TPC1 cell line treated with the RTK inhibitor RPI-1

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: We treated the papillary thyroid carcinoma-derived cell line TPC1 with the RTK inhibitor RPI-1 to obtain a thyroid carcinoma cell model. The RET tyrosine kinase is a target of the inhibitor. Gene expression changes were evaluated comparing cells treated with the inhibitor for 24 hours versus cells treated with DMSO for 24 hours.

overall_design: Biological triplicates for RPI-1 and DMSO treated cells were generated by independent treatments and total RNA extractions.

first: Maria

last: Borrello

first: Emanuela

last: Minna

first: Paola

last: Romeo

first: Giuliana

last: Cassinelli

first: Cinzia

last: Lanzi

first: Debora

last: Degl'Innocenti

first: Loris

last: De Cecco


title: Psip1/p75 restrains Hox gene expression by recruiting both trithorax and polycomb group proteins

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

overall_design: Refer to individual Series


title: Ozone Exposure Alters MicroRNA Expression Profiles in Humans

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary: We set out to test the hypothesis that ozone inhalation exposure significantly alters miRNA expression profiles within the airway of humans. Adult human volunteers were exposed to 0.4 ppm ozone for two hours. Induced sputum samples were collected from each subject 48 hours pre-exposure and 6 hours post-exposure. Genome-wide miRNA expression profiles were evaluated using microarray analysis.

overall_design: Twenty healthy non-asthmatic adult subjects aged 18 – 37 years, with no history of smoking in the past 10 years, completed the study. The ozone exposures were conducted in an exposure chamber. Each subject was exposed to 0.4 ppm ozone for two hours while performing four 15-minute sessions of intermittent moderate exercise (expiratory minute ventilation, 30–40 L/min) on a treadmill, separated by 15 minutes of seated rest. Induced sputum samples were collected from each subject 48 hours pre-exposure and 6 hours post-exposure. RNA samples were homogenized in TRIzol, and extracted according to standard TRIzol protocol. RNA was labeled and hybridized to the Agilent Human miRNA Microarray (v1.0).

first: Julia

last: Rager

first: Ilona

last: Jaspers

first: Neil

last: Alexis


title: Comparision of Psip1/p75, Mll and Menin binding on the Hox and non-Hox genes

summary: Menin binding pattern  in WT and Psip1 KO MEFs Menin occupancy is studied over Hox genes

overall_design: Menin ChIP from WT and Psip1 KO MEFs ChIP-chip


title: Comparision of Psip1/p75 binding and Mll1 binding sites on Hox and non-Hox genes

summary: Psip1/p75 binds to Hox genes and colocalizes with Mll1 and in Psip1 KO MEFs Mll1 occupancy is reduced over Hox genes

overall_design: Psip1/p75 ChIP using A300-848 abtibody (recognises p75 isoform of Psip1) and Mll1 ChIP from WT and Psip1 KO MEFs ChIP-chip


title: Molecular Analysis of the Genes Involved in Aroma Synthesis in the Species S. cerevisiae, S. kudriavzevii and S. bayanus var. uvarum in Winemaking

status: Public on Jun 23 2014

city: Paterna

first: Amparo

last: Gamero

state: Valencia

address: Avda. Agustín Escardino 7

department: Food Biotechnology

institute: IATA-CSIC

summary: This research work investigates the expression of the genes involved in flavor compound production in three different Saccharomyces species (S. cerevisiae, S. bayanus var. uvarum and S. kudriavzevii) under low (12°C) and moderate fermentation temperatures (28°C).

sample_organism:
Saccharomyces cerevisiae
Saccharomyces kudriavzevii
Saccharomyces uvarum

overall_design: RNA samples taken from wine fermentations at 12ºC and 28ºC at the beginning of stationary phase. Three biological replicates. S. cerevisiae Lalvin T.73 used as reference strain.

first: Carmela

last: Belloch

first: Clara

last: Ibáñez

last: Querol


summary: This research work investigates the hybridization of the genes of Saccharomyces bayanus var. uvarum CECT 12600 and S. kudriavzevii IFO1802 employing S. cerevisiae microarrays.

overall_design: Two strains,one S. kudriavzevii and one S. bayanus var. uvarum were employed for the study. The S. cerevisiae strain S288C was used as control for microarray hybridizations. All experiments were performed using duplicate arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.

first: Gamero

last: Amparo

first: Belloch

last: Carmela

first: Ibáñez

last: Clara

first: Querol


title: BSA Vs RSV G Protein

status: Public on Jun 21 2014

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary:
Rationale: Respiratory syncytial virus (RSV) and Streptococcus pneumoniae are major respiratory pathogens. Co-infection with RSV and S. pneumoniae is associated with severe and often fatal pneumonia but the molecular basis for this remains unclear.

Objectives: To determine if interaction between RSV and pneumococci enhances pneumococcal virulence.

Methods: We used confocal microscopy and western blot to identify the receptors involved in direct binding of RSV and pneumococci, the effects of which were studied in both in vivo and in vitro models of infection. Human ciliated respiratory epithelial cell cultures were infected with RSV for 72h and then challenged with pneumococci. Pneumococci were collected after 2h exposure and changes in gene expression determined using qRT-PCR.

Results: Following incubation with RSV or purified G protein, pneumococci demonstrated a significant increase in the inflammatory response and bacterial adherence to human ciliated epithelial cultures and markedly increased virulence in a pneumonia model in mice. This was associated with extensive changes in the pneumococcal transcriptome and significant upregulation in the expression of key pneumococcal virulence genes, including the gene for the pneumococcal toxin, pneumolysin. We show that mechanistically this is due to RSV G glycoprotein binding penicillin binding protein 1a.

Conclusion: The direct interaction between a respiratory virus protein and the pneumococcus resulting in increased bacterial virulence and worsening disease outcome is a new paradigm in respiratory infection.

overall_design:
Comparison of the Streptococcus pneumoniae D39 BSA treated compared to RSV G Protein Treated in BEBM medium
One condition design comparision of two strains including a dye swap

first: Oscar

middle: P

last: Kuipers

first: Claire

last: Smith

first: Christopher

last: O’Callaghan


title: miRNA profiling of Macaca mulatta intact colon samples during acute SIV infection

status: Public on Jun 01 2014

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

summary: This study describes differential miRNA expression in intact colon tissue during acute SIV infection of rhesus macaques. Nine miRNAs were found to be significantly affected by infection, with 5 down-regulated and 4 up-regulated miRNAs. The expression of one upregulated miRNA was further characterized and found to be significantly elevated specifically in response to SIV replication and not immune activation/inflammation accompanying SIV infection.

overall_design: We performed TaqMan Low Density Array based high throughput miRNA analysis on intact colon tissue from 10 acutely SIV-infected and 5 uninfected control macaques. All SIV-infected animals were inoculated intravenously with 100TCID50 of SIV. Out of the ten, one animal each was at 7, 8 and 10DPI (days post infection), 3 each at 13 and 21DPI, and 1 at 29DPI. microRNA reverse transcription and preamplification was performed according to the manufacturer’s recommendation. Data analysis was performed using RQ Manager 1.2.2 and DataAssist v3.01 software. Data was normalized using Global normalization method and multiple comparisons correction was performed using Benjamini-Hochberg method.

first: M

first: L

last: Chandra

first: W

last: Torben

first: P

last: Aye

first: X

last: Alvarez

first: A

last: Lackner


title: mTORC1 maintains renal tubular homeostasis and is essential in response to ischemic stress

status: Public on Jun 09 2014

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: The mechanistic target of rapamycin mTORC1 is a key regulator of cell metabolism and autophagy. Despite widespread clinical use of mTOR inhibitors, the role of mTORC1 in renal tubular function and kidney homeostasis remains elusive. By utilizing constitutive and inducible deletion of conditional Raptor alleles in renal tubular epithelial cells, we discovered that mTORC1 deficiency caused a marked concentrating defect, loss of tubular cells and slowly progressive renal fibrosis. Transcriptional profiling revealed that mTORC1 maintains renal tubular homeostasis by controlling mitochondrial metabolism and biogenesis as well as transcellular transport processes involved in counter-current multiplication and urine concentration. Although mTORC2 partially compensated the loss of mTORC1, exposure to ischemia and reperfusion injury exaggerated the tubular damage in mTORC1-deficient mice, and caused pronounced apoptosis, diminished proliferation rates and delayed recovery. These findings identify mTORC1 as an essential regulator of tubular energy metabolism and as a crucial component of ischemic stress responses. Pharmacological inhibition of mTORC1 likely affects tubular homeostasis, and may be particularly deleterious if the kidney is exposed to acute injury. Furthermore, the combined inhibition of mTORC1 and mTORC2 may increase the susceptibility to renal damage.

overall_design: Raptor fl/fl*KspCre and Raptor fl/fl animals were sacrificed at P14 before the development of an overt functional phenotype. Kidneys were split in half and immediately snap frozen in liquid nitrogen.

first: Melanie

last: Boerries

first: Pierre

last: Moulin

first: Tobias

last: Huber

first: Florian

last: Grahammer


title: Changes in granulosa cells gene expression associated with growth, plateau and atretic phases in medium bovine follicles.

status: Public on Jun 02 2014

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: Granulosa cells originating from three different phases of antral follicle growth were compared: growing (G), plateau (P) and atresia (A), as categorized by flow cytometry profiles of DNA. The growing and atretic conditions were each hybridized against the plateau condition as a reference in order to understand the specific biological mechanisms modulated in this class of follicles.

overall_design: Three-condition experiment, Plateau, Growing vs Atretic granulosa cells. Biological replicates: 4 . Dye-swap experiment.

first: Gabriel

last: Douville


title: Gene expression response in avian enterocytes cells isolated from genetically resistant and susceptible chickens infected with Salmonella Enteritidis.

city: Nouzilly

first: Olivier

last: Grépinet

address: Centre de Tours

department: Tours

country: France

institute: INRA

summary:
In this study, we analyzed the global gene expression of enterocytes during carrier-state in chicken lines N and 61 which are respectively resistant and susceptible to Salmonella carrier-state. Transcriptome analysis was performed at three weeks post-inoculation, on purified enterocytes, by comparing the expression profiles of infected and control chicks in the two lines. Three weeks post-inoculation correspond to the period where bacterial load starts to decrease in the resistant line but is still high in the susceptible line; this point could conceptually corresponds to genes which are differentially regulated leading to the resistant or susceptible phenotypes. Functional annotation of differentially expressed genes allowed us to identify numerous biological processes modulated during Salmonella carriage.

Keywords: Expression profiling by array

overall_design: For each chicken line, twenty slides including ten biological replicates and the corresponding dye-swaps with the fluorophores reversed were carried out on control and infected animals.

last: Chausse

first: O

last: Grepinet

first: E

last: Bottreau

first: V

last: Robert

first: C

last: Hennequet-Antier

last: Velge


title: Investigation of miRNA expression patterns in Y79 cells

status: Public on May 30 2014

city: Seoul

first: Jeong Hun

last: Kim

address: 101, Daehak-ro, Jongno-gu

institute: Seoul National University

summary: We aimed to investigate the miRNA expression patterns in Y79 cells, which are from a representative retinoblastoma cell line.

overall_design: We prepared 3 independent sets of cell lysates of Y79 cells in normal culture conditions. Total RNA was prepared from each set of cell lysates using Trizol reagent.

first: Dong

middle: H

last: Jo

first: Jin

first: Chang

last: Cho

first: Hyoung

middle: O

last: Jun

first: Young

last: Yu

first: Jeong


title: Mycobacterium tuberculosis Lsr2 is a global transcriptional regulator required for adaptation to changing oxygen levels and virulence

status: Public on May 24 2014

city: Aurora

first: Martin

last: Voskuil

state: CO

address: 12800 E. 19th Ave. Mail Stop 8333 RC1-North Room P18-9115

department: Microbiology

institute: CU-AMC

summary: To survive a dynamic host environment, Mycobacterium tuberculosis must endure a series of challenges from reactive oxygen and nitrogen stress, to drastic shifts in oxygen availability. The mycobacterial Lsr2 protein has been implicated in reactive oxygen defense via direct protection of DNA. To examine the role of Lsr2 in pathogenesis and physiology of M. tuberculosis, we generated a strain deleted for lsr2. Analysis of the M. tuberculosis Δlsr2 strain demonstrated that Lsr2 is not required for DNA protection, as this strain was as equally susceptible as the wild-type to DNA-damaging agents. The lsr2 mutant did display severe growth defects under normoxic and hyperoxic conditions, but was not required for growth under low oxygen conditions. However, it was also required for adaptation to anaerobiosis. The defect in anaerobic adaptation led to a marked decrease in viability during, as well as a lag in recovery from, anaerobiosis. Gene expression profiling of Δlsr2 under aerobic and anaerobic conditions in conjunction with published DNA binding-site data indicate that Lsr2 is a global transcriptional regulator controlling adaptation to changing oxygen levels. The Δlsr2 strain was capable of establishing an early infection in the Balb/c mouse model; however, it was severely defective in persisting in the lungs and caused no discernible lung pathology. These findings demonstrate M. tuberculosis Lsr2 is a global transcriptional regulator required for control of genes involved in adaptation to extremes in oxygen availability and is required for persistent infection.

platform_organism:
Mycobacterium tuberculosis CDC1551
Mycobacterium tuberculosis H37Rv

overall_design: Wild type H37Rv or lsr2 mutant strains were grown aerobically or in a Rach dormancy model in dubos tween albumin media and analyzed. Alternately, either aerobically grown or Rach model hypoxic samples were challenged with H2O2 samples and harvested 1h later. Experiments were repeated in triplicate or quadruplicate.

first: Iona

last: Bartek


title: CRL4(CRBN) ubiquitin ligase profiling

status: Public on May 13 2014

city: Boston

first: Eric

last: Fischer

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary:
In the 1950s the drug thalidomide administered as a sedative to pregnant women led ot the birth of thousands of children with multiple defects. Despite its teratogenicity, thalidomide and ist IMiD derivatives recently emerged as effective treatments for multiple myeloma and 5q-dysplasia. IMiDs target the CUL4-RBX1-DDB1-CRBN (CRL4(CRBN)) ubiquitin ligase.
Through an unbiased screen we identify the homeobox trranscription factor MEIS2 as an endogenous substrate of CRL4(CRBN).

overall_design:
By definition, a specific target of CRL4(CRBN) is expected to have a very low intensity on negative control arrays (E1_E2), (E1_CRBN), (E1_E2_Cdt2), (E1_E2_Cdt2_revlimid), (E1_E2_Cdt2_CSN) or with CRL4(CRBN) in presence of inhibitor (E1_E2_CRBN_revlimid) and high intensity on arrays with CRL4(CRBN) (E1_E2_CRBN) or CRL4(CRBN) in presence of CSN (E1_E2_CRBN_CSN)
Accordingly 16 protein microarrays were subjected to in vitro ubiquitylation using the following enzyme combinations:
3x Uba1+UbcH5a; 2x Uba1+UbcH5a+CRL4(DDB2); 3x Uba1+UbcH5a+CRL4(CRBN); 2x Uba1+UbcH5a+CRL4(CRBN)+lenalidomide; 2x Uba1+UbcH5a+CRL4(CRBN)+CSN; 2x Uba1+UbcH5a+CRL4(Cdt2); 1x Uba1+UbcH5a+CRL4(Cdt2)+CSN; 1x Uba1+UbcH5a+CRL4(Cdt2)+lenalidomide

first: Michael

middle: B

last: Stadler

first: Nicolas

last: Thoma


title: Whole blood gene expression profile associated with spontaneous preterm birth

status: Public on May 15 2014

city: Toronto

first: Jan

last: Heng

state: ON

address: 25 Orde Street

institute: Lunenfeld-Tanenbaum Research Institute

summary: Threatened preterm labor (TPTL) is defined as persistent premature uterine contractions between 20 and 37 weeks of gestation and is the most common condition that requires hospitalization during pregnancy. Most of these TPTL women continue their pregnancies to term while only an estimated 5% will deliver a premature baby within ten days. The aim of this work was to study differential whole blood gene expression associated with spontaneous preterm birth (sPTB) within 48 hours of hospital admission. Peripheral blood was collected at point of hospital admission from 154 women with TPTL before any medical treatment. Microarrays were utilized to investigate differential whole blood gene expression between TPTL women who did (n = 48) or did not have a sPTB (n = 106) within 48 hours of admission. Total leukocyte and neutrophil counts were significantly higher (35% and 41% respectively) in women who had sPTB than women who did not deliver within 48 hours (p<0.001). Fetal fibronectin (fFN) test was performed on 62 women. There was no difference in the urine, vaginal and placental microbiology and histopathology reports between the two groups of women. There were 469 significant differentially expressed genes (FDR<0.05); 28 differentially expressed genes were chosen for microarray validation using qRT-PCR and 20 out of 28 genes were successfully validated (p<0.05). An optimal random forest classifier model to predict sPTB was achieved using the top nine differentially expressed genes coupled with peripheral clinical blood data (sensitivity 70.8%, specificity 75.5%). These differentially expressed genes may further elucidate the underlying mechanisms of sPTB and pave the way for future systems biology studies to predict sPTB.

overall_design: Total 154; 48 delivered within 48 hours of hospital admission; 106 did not deliver within 48 hours

first: Yujing

first: Craig

middle: E

last: Pennell

first: Hon

middle: N

last: Chua

first: Jonathan

last: Perkins

first: Stephen

last: Lye


title: Genome Rearrangements and Pervasive Meiotic Drive Cause Hybrid Infertility in Fission Yeast

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

summary: Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Uncovering the mechanisms of hybrid sterilitynot only provides insight into the origins of species but also potentially revealsnovel causes of intra-species infertility.Here we identify causes underlying hybrid infertilityofSchizosaccharomyces pombeand S. kambucha, two fission yeast species that are 99.5% identical at the nucleotide level.These yeasts mate to form viable diploids that efficiently complete meiosis. However,S. kambucha/S. pombe hybrids generate few viable gametes, most of which are either aneuploid or diploid.We find that chromosomal rearrangements and related recombination defectsare major causes of hybrid infertility. Surprisingly, using experiments in which we eliminate meiotic recombination, we find thatrecombination defects cannot completely explain the hybrid infertility. Instead, we find that a significant fraction of hybrid infertility is caused by the action of at least three distinct meiotic drive alleles, one on each S. kambucha chromosome,that “cheat” to be transmitted to more than half (up to 90%) of viable gametes.Two of these driving lociare linked by a chromosomal translocation and thus constitute a novel type of paired meiotic drive complex. We find that all three S. kambuchadrive loci independently contribute to hybrid infertility by causing nonrandom spore death. This study reveals how quickly multiple barriers to fertility can arise.In addition, it provides further support for models in which genetic conflicts, such as those caused by meiotic drive alleles, can drive speciation.

sample_organism: Schizosaccharomyces kambucha (nom. inval.)

overall_design: Meiotic DNA double-strand break analysis of Schizosaccharomyces kambucha by immunoprecipitating accumulated Rec12-FLAG covalently linked to DNA (without exogenous crosslinking agent used) following nitrogen starvation .

first: SaraH

last: Zanders

last: Eickbush

first: Ji-Won

last: Kang

first: Gerald

last: Smith

first: Harmit

last: Malik


title: The role of nicotinamide phosphoribosyltransferase (Nampt) in hippocampal neural stem/progenitor cells

status: Public on May 08 2014

city: St. Louis

first: Liana

middle: Roberts

last: Stein

state: MO

address: Campus Box 8103, 660 South Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

summary: Neural stem/progenitor cell (NSPC) proliferation and self-renewal, as well as insult-induced differentiation, decrease markedly with age, but the molecular mechanisms responsible for these declines remain unclear.  Here we show that levels of NAD+ and nicotinamide phosphoribosyltransferase (Nampt), the rate-limiting enzyme in mammalian NAD+ biosynthesis, decrease with age in the hippocampus.  Ablation of Nampt in adult NSPCs reduced their pool and proliferation in vivo.  The decrease in the NSPC pool during aging can be rescued by enhancing hippocampal NAD+ levels.  Nampt is the main source of NSPC NAD+ levels and required for G1/S progression of the NSPC cell cycle.  Nampt is also critical for oligodendrocytic lineage fate decisions through a mechanism mediated redundantly by Sirt1 and Sirt2.  Ablation of Nampt in the adult NSPCs in vivo reduced NSPC-mediated oligodendrogenesis upon injury.  These phenotypes recapitulate defects in NSPCs during aging, implicating Nampt-mediated NAD+ biosynthesis as a mediator of these age-associated functional declines.

overall_design: Total RNA obtained from neurospheres derived from postnatal hippocampi subjected to 48 hours in vitro of incubation with Nampt-specific inhibitor FK866 (10 nM, 4 samples) or vehicle (DMSO, 1:1000, 4 samples).

first: Shin-ichiro

last: Imai


title: Somatic copy number variation profiling in matched brain and extracranial metastases of melanoma

city: Houston

first: Guo

last: Chen

state: TX

address: 7435 Fannin Street

department: Melanoma Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

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

summary: An improved understanding of the molecular pathogenesis of brain metastases, one of the most common and devastating complications of advanced melanoma, may identify and prioritize rational therapeutic approaches for this disease. In particular, the identification of molecular differences between brain and extracranial metastases would support the need for the development of organ-specific therapeutic approaches. Hotspot mutations, copy number variations (CNV), global mRNA expression patterns, and protein expression and activation, quantitatively analyzed by mass-array genotyping, molecular inversion probe arrays, microarrays and reverse phase protein array (RPPA) were evaluated in pairs of melanoma brain metastases and extracranial metastases from patients who had undergone surgical resection for both types of tumors.

overall_design: Somatic copy number variation (CNV) in 47 melanoma brain metastases (BM, except for patient 01, who had a spinal cord metastasis) and extracranial metastases (EM) were analyzed by molecular inversion probe (MIP) array (Affymetrix OncoScan FFPE Express 2.0). DNA were extracted from regions with >70% viable tumor cells from formalin-fixed and paraffin-embedded (FFPE) tissues. Of the 47 tumor samples, 22 were matched BM and EM from the same patients. In addition, 24 DNA samples from normal tissues were included as diploid controls.

first: Kimberly

last: Aardalen

first: Nitin

last: Charkravarti

first: Alexander

last: Lazar

last: Tetzlaff

first: Bradley

last: Wubberhorst

first: Sang-Bae

last: Kim

first: Scott

last: Kopetz

first: Alicia

middle: A

last: Ledoux

first: Y

middle: V

last: Gopel

first: Cristiano

last: Pereira

first: Wanleng

last: Deng

first: Ju-Seog

last: Lee

first: Katherine

middle: L

last: Nathanson

first: Kenneth

middle: D

last: Aldape

first: Victor

last: Prieto

first: Darrin

last: Stuart

last: Davies


title: Inflammation-induced acute phase response in skeletal muscle and critical illness myopathy

status: Public on May 06 2014

city: Berlin

first: Jens

last: Fielitz

address: Augustenburger Platz 1

department: Cardiology

institute: Charité Universitätsmedizin Berlin

summary:
Objectives: Systemic inflammation is a major risk factor for critical-illness myopathy (CIM) but its pathogenic role in muscle is uncertain. We observed that interleukin 6 (IL-6) and serum amyloid A1 (SAA1) expression was upregulated in muscle of critically ill patients. To test the relevance of these responses we assessed inflammation and acute-phase response at early and late time points in muscle of patients at risk for CIM.
Design: Prospective observational clinical study and prospective animal trial.
Setting: Two intensive care units (ICU) and research laboratory.
Patients/Subjects: 33 patients with Sequential Organ Failure Assessment scores ≥8 on 3 consecutive days within 5 days in ICU were investigated.  A subgroup analysis of 12 patients with, and 18 patients without CIM (non-CIM) was performed. Two consecutive biopsies from vastus lateralis were obtained at median days 5 and 15, early and late time points. Controls were 5 healthy subjects undergoing elective orthopedic surgery. A septic mouse model and cultured myoblasts were used for mechanistic analyses.
Measurements and Main Results: Early SAA1 expression was significantly higher in skeletal muscle of CIM compared to non-CIM patients. Immunohistochemistry showed SAA1 accumulations in CIM patients at the early time point, which resolved later. SAA1 expression was induced by IL-6 and tumor necrosis factor-alpha in human and mouse myocytes in vitro. Inflammation-induced muscular SAA1 accumulation could be reproduced in a sepsis mouse model.
Conclusions: Skeletal muscle contributes to general inflammation and acute-phase response in CIM patients. Muscular SAA1 could be important for CIM pathogenesis.
Trial registration: ISRCTN77569430.

overall_design:
Expression analysis of patients with and without CIM (non-CIM) was performed.
Date were quantile normalized using Partek Genomic Suite 6.5, RMA background correction, pre background adjustment for GC content and data were limited to the full dataset

first: Steffen

last: Weber-Carstens


title: Expression data from Xenopus embryos treated with TTNPB (RAR-agonist), AGN193109 (RAR-antagonist), or Control Vehicle

city: Stanford

first: Stefan

last: Heller

state: CA

address: 801 Welch Road

department: Otolaryngology

institute: Stanford University

summary: Percellome analysis of whole Xenopus embryos at developmental stage 18

overall_design: Xenopus embryos were treated with TTNPB (RAR-agonist), AGN193109 (RAR-antagonist), or Control Vehicle at Nieuwkoop and Faber Stage 7.  Embryos were collected at stage 18, followed by RNA extraction, hybridization on Affymetrix microarrays, and Percellome analysis.

first: Amanda

last: Janesick

first: Ken-ichi

last: Aisaki

first: Katsuhide

last: Igarashi

first: Satoshi

last: Kitajima

first: Jun

last: Kanno

first: Bruce

last: Blumberg


title: Effects of sustained swimming on the red and white muscle transcriptome of rainbow trout (Oncorhynchus mykiss) fed a carbohydrate-rich diet

status: Public on May 01 2014

city: Barcelona

first: Josep

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

institute: Universitat de Barcelona

summary: Training at sustainable swimming speeds can produce changes in fish skeletal muscle that are important for aquaculture due to their growth-potentiating effects. Such changes may be even more relevant when fish are fed diets containing an increasing proportion of carbohydrates as an energy source. We evaluated the effects of moderate-intensity sustained swimming on the transcriptomic response of red and white muscle in rainbow trout fed a carbohydrate-rich diet using microarray and qPCR. Analysis of the red and white muscle transcriptome revealed significant changes in the expression of a large number of genes (395 and 597, respectively), with a total of 218 differentially expressed genes (DEGs) common for both muscles. A large number of the genes involved in glucose use and energy generation, contraction, development, synthesis and catabolism of proteins were up-regulated in red and white muscle. Additionally, DEGs in both muscles were involved in processes of defense response and apoptosis. Skeletal muscle contraction activates a transcriptional program required for the successful adaptation of both muscles to the changing demands imposed by swimming conditions. Future studies should further clarify the mechanisms involved in the adaptation of both tissues to exercise and assess possible benefits of such conditions for cultured fish.

overall_design: Total RNA from pooled red and white skeletal muscle samples of individual rainbow trout from each group (resting fish, n=8; swimming fish, n=8) was labeled with Cy3-dUTP and Cy5-dUTP (GE Healthcare, Barcelona, Spain). We used a dye swap experimental design and each cDNA from a pooled RNA sample was hybridized to two microarrays. For the first slide, cDNAs from resting and swimming fish were labeled with Cy5 and Cy3, respectively, and for the second array dye assignment was reversed. Therefore, samples from individual fish within each group were pooled and expression values shown represent the means of 6 × 2 = 12 technical replicates. A total of four slides were used in this study


title: The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells

city: Martinsried/Munich

first: Tim

last: Ammon

address: Am Klopferspitz 18

department: Dept. of Molecular Cell Biology

institute: Max-Planck-Institute of Biochemistry

summary: Different from canonical ubiquitin-like proteins, Hub1 does not form covalent conjugates with substrates but binds proteins non-covalently. In Saccharomyces cerevisiae, Hub1 associates with spliceosomes and mediates alternative splicing of SRC1, without affecting pre-mRNA splicing generally. Human Hub1 is highly similar to its yeast homolog, but its cellular function remains largely unexplored. Here, we show that human Hub1 binds to the spliceosomal protein Snu66 as in yeast, however, unlike its S. cerevisiae homolog, human Hub1 is essential for viability. Prolonged in vivo depletion of human Hub1 leads to various cellular defects, including splicing speckle abnormalities, partial nuclear retention of mRNAs, mitotic catastrophe and consequently cell death by apoptosis. Early consequences of Hub1 depletion are severe splicing defects, however, only for specific splice sites leading to exon skipping and intron retention. Thus, the ubiquitin-like protein Hub1 is not a canonical spliceosomal factor needed generally for splicing, but rather a modulator of spliceosome performance and facilitator of alternative splicing.

overall_design: Human U2OS cells were transfected with siRNAs to specifically knockdown the ubiquitn-like protein Hub1. Cells treated with non-targeting oligos (GL2) served as negative control. Total RNAs of three biological replicates of each knockdown experiment were isolated and changes of splicing patterns were subsequently analyzed by Affymetrix GeneChip Human Exon 1.0 ST arrays

first: Shravan

middle: K

last: Mishra

first: Kaja

last: Kowalska

first: Grzegorz

middle: M

last: Popowicz

first: Tad

last: Holak

last: Jentsch


title: Slu7 is essential for liver differentiation, metabolism and quiescence

status: Public on May 29 2014

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

institute: FIMA

summary: The equilibrium between cellular differentiation and proliferation is fundamental for tissue homeostasis. This is particularly important for the liver, a highly differentiated organ with systemic metabolic functions still endowed with unparalleled regenerative potential. Hepatocellular de-differentiation and uncontrolled proliferation are at the basis of liver carcinogenesis. We have identified SLU7, a pre-mRNA splicing regulator inhibited in hepatocarcinoma as a pivotal gene for hepatocellular homeostasis. SLU7 knockdown in human liver cells and mouse liver resulted in profound changes in pre-mRNA splicing and gene expression, leading to impaired glucose and lipid metabolism, refractoriness to key metabolic hormones, and reversion to a fetal-like gene expression pattern. Hepatocellular proliferation and a switch to a tumor-like glycolytic phenotype were also observed. Mechanistically, SLU7 governed the splicing and/or expression of essential genes for hepatocellular differentiation like SRSF3 and HNF4a, and was identified as a critical factor in cAMP-regulated gene transcription. SLU7 is therefore central for hepatocyte identity and quiescence.

overall_design: The expression of the splicing factor SLU7 in the human hepatocellular carcinoma cell line PLC/PRF/5 was knocked down with specific siRNAs (siSlu7). An irrelevant siRNA (siGL2) was used as negative control. The RNAto perfrom the array analysis was extracted 48h after transfection.

first: Maria

last: Elizalde

first: Jesús

last: Prieto

first: Matias

last: Avila

first: Carmen

last: Berasain


title: Genome-wide effects of maternal undernutrition

status: Public on Apr 30 2014

city: London

first: Gioia

last: Altobelli

address: 5 University Street

country: United Kingdom

institute: UCL

summary: A comparison of the liver transcriptomes of 1 day old rats that are born to mothers fed with three different diets during gestation. The first animal group was fed with a normal diet (control); second group received much less protein than normal and slightly more carbs (low protein); third group diet was same as low protein but with an extra dosage of folic acid (lowp.+f). All diets were matched for energy.

overall_design: Total RNA was extracted from rat livers of 4 offsprings per animal group (4 biological replicates x group)

first: Irina

middle: G

last: Bogdarina