title: Development of gene expression signatures in methylotrophic grown Bacillus methanolicus

status: Public on May 23 2012

city: Trondheim

first: Tonje

middle: Marita Bjerkan

last: Heggeset

address: Postboks 4760 Torgarden

department: Industry

country: Norway

institute: SINTEF

summary: A total gene expression approach was applied to study the methylotrophic nature of B. methanolicus by comparing the gene expression in bacteria grown methylotropic compared to non-methylotrophic. Genes of interest with different gene expression were quantified in the same RNA samples by real-time PCR, confirming the results found in the microarray experiment. Genes of special interest that are expressed higher when grown methylotrophic, were the RuMP pathway genes located on the pBM19.

overall_design: Bacillus methanolicus was grown in minimal media with either methanol or mannitol as carbon source. The experiment was preformed in triplicate, with bacterial cultures grown on 3 different days.

first: Anne

last: Krog

first: Trygve

last: Brautaset


title: Global profiling of gene expression in the ΔdigR and ΔsgmT mutant of Myxococcus xanthus

status: Public on May 18 2012

city: Marburg

first: Anke

middle: U

last: Treuner-Lange

state: Hessen

address: Karl von Frisch-Str. 10

department: Ecophysiology

country: Germany

institute: Max-Planck Institute for terrestrial Microbiology

summary: In Myxococcus xanthus 55% of the more than 250 two-component signal transduction systems (TCS) genes are orphan. We hypothesized that the histidine kinase SgmT and the response regulator DigR, which comprises a DNA binding domain of the HTH_Xer type, function together to regulate gene expression. We performed genome-wide expression profiling experiments to determine wether the same set of genes are differentially expressed in the  ΔdigR and ΔsgmT mutants.

overall_design: 3 biological replicates each; normalized ratios to vegetative cells of DK1622 (wt) Cy5

first: Tobias

last: Petters

first: Lotte

last: Sogaard-Andersen


title: BID is critical for IFN-alpha-induced cell death

status: Public on May 22 2012

city: Bethesda

first: Joseph

last: Bekisz

state: MD

address: 50 South Drive

department: NIAID

country: USA

institute: NIH

summary: Clinical applications of human interferon (IFN)-alpha have met with varying degrees of success. Nevertheless, key molecules in IFN-alpha-induced cell death have not been clearly identified. Our previous study indicated that IFN (alpha, beta and omega) receptor (IFNAR) 1/2- and IFN regulatory factor (IRF) 9-RNA interference (RNAi) completely inhibited the antiproliferative (AP) activity of IFN-alpha in human ovarian adenocarcinoma OVCAR3 cells sensitive to IFN-alpha., followed by transcription of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). Here, IFNAR1/2- and IRF9-RNAi inhibited the gene expression of TRAIL, but not of Fas ligand (FasL), following IFN-alpha treatment. In fact, TRAIL but not FasL inhibited the proliferation of OVCAR3 cells. IFN-alpha notably up-regulated the levels of TRAIL protein in the supernatant and on the membrane of OVCAR3 cells. Following TRAIL signaling, Caspase 8 inhibitor and BH3 interacting domain death agonist (BID)-RNAi significantly abrogated both AP activities of IFN-alpha and TRAIL. Furthermore, BID-RNAi prevented both IFN-alpha and TRAIL from collapsing the mitochondrial membrane potential (Delta Psi m). Finally, we provide important new evidence that BID overexpression led to a major enhancement of both AP activities of IFN-alpha and TRAIL in human lung carcinoma A549 cells resistant to IFN-alpha. Thus, this study suggests that BID is crucial in IFN-alpha-induced cell death, indicating a notable potential to be a targeted therapy for IFN-alpha resistant tumors.

overall_design: Biological replicate samples were created by treating OVCAR3 cells with IFN-alpha2c (n=8); IFNAR1-RNAi and IFN-alpha2c (n=4); IFNAR2-RNAi and IFN-alpha2c (n=5); ISGF3gamma-RNAi and IFN-alpha2c (n=3); and Negative RNAi and IFN-alpha2c (n=3). For analysis, the eight IFN-alpha2c treated OVCAR3 samples were paired with an untreated OVCAR3 control sample. The 15 RNAi treated OVCAR3 samples were paired with a Negative RNAi control sample.


title: microRNA expression analysis of circulating monocytes in obese patients

city: Leuven

first: Paul

last: Holvoet

address: Herestraat 49, PB 705

department: Department of Cardiovascular Diseases

country: Belgium

summary: Low-grade chronic inflammation plays an important role in the development of obesity and obesity-associated disorders such as insulin resistance, type 2 diabetes, the metabolic syndrome and atherosclerosis. One possible link between obesity and inflammation is the enhanced activation of circulating monocytes making them more prone to infiltration into the adipose and vascular tissues of obese persons. microRNAs are a class of small endogenous non-coding RNAs, which function as important regulators of inflammation by modulating gene expression. Therefore, microRNA analysis of circulating monocytes from control and obese patients will potentially provide insights into the pathophysiology of obesity and associated disorders and supply biomarkers for diagnostic purpose. The cohort comprised 6 lean age-matched controls (BMI: 20±0.8 kg/m2, mean±SEM) and 9 obese individuals without clinical symptoms of cardiovascular disease (BMI: 46±1.5 kg/m2, P<0.001 compared with lean controls). CD14+ monocytes were collected, total RNA was extracted and subjected to microRNA expression analysis.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Mus musculus cytomegalovirus 2
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Samples consisted of CD14+ monocytes from 6 lean controls and 9 morbidly obese patients.

first: M

last: Hulsmans

first: P


title: Human lung adenocarcinoma mRNA expression and gene mutations.

status: Public on May 17 2012

city: Chapel Hill

first: Matthew

middle: D

last: Wilkerson

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Lung adenocarcinoma expression subtypes have unknown origins.  This study associated distinct mutations with the subtypes.

overall_design: RNA from tumors and a common reference were hybridized to Agilent two color microarrays.

first: D

middle: N

last: Hayes


title: Transcriptome profie of rice in response to temperature and oxidative stress

status: Public on May 31 2012

city: New Delhi

first: Anil

last: Grover

state: Delhi

address: Benito Juarez Road

department: Plant Molecular Biology

country: India

institute: University of Delhi South Campus

summary: Here we describe stress regimes (treatment methods) that can be used in future studies. We describe global analysis of heat, cold and oxidative stress responsive transcriptome in rice.

overall_design: 10-day old rice seedlings were used for experiments. Cold stress was implied for 1 and 5h at 5°C, heat stress was given at 42°C for 10’ and 30 ‘ while oxidative stress was given by implying 10mM H202 for 1h and 4h at 28°C. Unstressed seedlings were used as control. For each condition, three biological replicates were processed in a similar manner for the microarray analysis.

first: Dheeraj

last: Mittal


title: Comparative Genomics Reveals New Molecular targets for Accelerated Improvement of Erythromycin-producing Strains

status: Public on May 24 2012

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

summary:
Information about molecular mechanisms underlying improvement of antibiotic-producing microorganisms with traditional mutation and screening approach is largely missing. This information is essential to develop rational approaches to strain improvement. In this study by using comparative genomic analysis we have identified all genetic changes that have occurred during development of an erythromycin overproducer, which was obtained by the traditional mutate-and-screen method. Compared with parental Saccharopolyspora erythraea NRRL 2338, a total of 117 deletion, 78 insertion and 12 transposition sites were found across the genome of the overproducer. Among them, 71 insertion/deletion sites mapped within coding sequences (CDSs) generating frame-shift mutations. Moreover, single nucleotide variations affecting a total of 144 CDSs were identified between the two genomes. Overall, variations affect a total of 227 proteins in the genome of the overproducer. The analysis of metabolic pathways demonstrated that a considerable number of mutations affect genes coding for key enzymes involved in central carbon and nitrogen metabolism, and biosynthesis of secondary metabolites, redirecting common precursors toward erythromycin biosynthesis. Interestingly, several mutations inactivate genes coding for proteins that play fundamental roles in basic transcription and translation machineries including the transcription anti-termination factor NusB and the transcription elongation factor Efp. These mutations, along with those affecting genes coding for pleiotropic or pathway-specific regulators, may affect global expression profile. Consistent transcriptomic data were obtained from a comparative analysis between NRRL 2338 and the erythromycin overproducer gene expression profiling performed with DNA microarray. Genomic data also indicated that the mutate-and-screen process might have been accelerated by mutations in DNA repair genes. Our findings, largely unanticipated, reveal new targets suitable for rationale improvement of antibiotic-producing strains.
According to a rough estimate, actinomycetes, which are among the most abundant bacteria in soil, produce over 70% of naturally occurring antibiotics and other biologically active substances including anti-tumour agents and immunosuppressants. However, these microorganisms must often be genetically improved for higher production before they can be used in the industry. Strain improvement has traditionally relied on multiple rounds of random mutagenesis and screening. This method is essentially empirical, and notably time-consuming and expansive. Currently, the availability of molecular genetics tools and useful information about the biosynthetic pathways and genetic control for most of biologically active substances has opened the way for improving strains by rational engineering. These rational strain improvement strategies benefit of the support of genomic and post-genomic technologies. In this study by using comparative genomic analysis we have identified all genetic changes that have occurred during development of an erythromycin overproducer, which was obtained by the traditional mutate-and-screen method. Our findings, largely unanticipated, reveal new molecular targets suitable for rationale improvement of antibiotic-producing strains by recombinant technologies, and support the evidence that combining classical and recombinant strain improvement with a solid fermentation development program is the best way to improve production of biologically active substances.

overall_design: Erythromycin over-producing Strain at various time points

first: Adelfia

last: Talà

first: Giorgio

last: Corti

first: Daniela

last: Pasanisi

first: Silvio

last: Bicciato

first: Gianluca

last: De Bellis

first: Pietro

last: Alifano


title: Lunatic fringe deficiency cooperates with the Met/Caveolin amplicon to induce basal-like breast cancer

status: Public on May 30 2012

city: Toronto

first: Sean

middle: Eoin

last: Egan

state: Ontario

address: 101 College Street, rm 14-309

department: Program in Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

type: Genome variation profiling by genome tiling array

summary: Mammary specific deletion of Lfng induces basal-like and claudin-low tumors with accumulation of Notch intracellular domain fragments, increased expression of proliferation-associated Notch targets, amplification of the Met/Caveolin locus, and elevated Met and Igf-1R signaling.

overall_design: Tumor DNAs from Lfngflox/flox; MMTV-Cre conditional mutant mice are being compared to control DNAs from the same animals in order to identify common alterations associated with tumor progression

first: Keli

last: Xu


title: A cDNA Microarray, UniShrimpChip, for Identification of Genes Relevant to Testicular Development in the Black Tiger Shrimp (Penaeus monodon)

status: Public on May 12 2012

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

summary: Comparisons of gene expression profiles from testis of wild and domesticated male brooders were made through a cDNA microarray in the black tiger shrimp (Penaeus monodon). Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR. Selected genes were further characterized.

overall_design: A cDNA microarray was constructed from the EST libraries of P. monodon, consisting of 5,568 features. RNA samples were extracted from testes of pooled juveniles (4 month-old, pooled from n=114), broodstocks from West and East sides of Thailand, and domesticated broodstocks of 10-, 14-, and 18-month old. The RNA from testis of pooled juveniles was labeled with Cy3 dye as a reference and those of the broodstocks were labeled with Cy5 dye.

first: Rungnapa

last: Leelatanawit

first: Umaporn

last: Uawisetwathana

first: Sirawut

last: Klinbunga

first: Nitsara

last: Karoonuthaisiri


title: Aspergillus nidulans WT, ΔcrzA and ΔcrzA/scrA-: Control vs. calcium pulse

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

summary: The main objective was to identifiy genes related to scrA- extragenic suppression of crzA. Thus, through transcriptional profiling, we characterised the transcriptional basis of calcium tolerance in our mutant strain, ΔcrzA/scrA-. To evaluate the effect of calcium on global A. nidulans gene expression, we performed competitive microarray hybridizations using RNA obtained from the wild-type, ΔcrzA and ΔcrzA/scrA- strains before and after short pulses (10 and 30 minutes) of 200 mM calcium chloride. The experiment was further validated by real-time PCR.

overall_design: Two-condition experiment : A. nidulans wild-type, ΔcrzA and ΔcrzA/scrA- strains with 200 mM CaCl2 for 10 and 30 min at 30°C and 150 rpm in 25 mL YAG medium. Firstly, the strains were grown overnight at 30°C and 150 rpm in YAG medium (preculture). Afterwards, the medium was switched by a new media (25 mL) plus calcium and incubated as described above. Control condition refers to the preculture in YAG medium without further incubation.

first: Ricardo

middle: S

last: Almeida

first: Marcela

last: Savoldi

middle: R

first: Gustavo

middle: H

last: Goldman


title: Transcriptome Profiling of Zymomonas mobilis under furfural stress

status: Public on May 09 2012

city: Chengdu

first: Mingxiong

last: He

state: Sichuan

address: Section 4-13, Renming Nanlu

department: Biomass Energy Technology Research Centre

country: China

institute: Biogas Institute of Ministry of Agriculture

summary: Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to furfural stress.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: A six chip study using total RNA recovered from three separate wild-type cultures of Zymomonas mobilis ATCC31821 and three separate cultures of a triple treated with 1.0 g/l furfural. Each chip measures the expression level of 1800 genes from Zymomonas mobilis ATCC31821 and the associated plasmids, with three-fold technical redundancy.


title: Synergistic activation by p38MAPK and glucocorticoid signaling mediates induction of M2-like tumor-associated macrophages expressing the novel CD20 homolog MS4A8A.

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Tumor-associated macrophages (TAMs) represent alternatively activated (M2) macrophages that support tumor growth. Previously, we have described a special LYVE-1(+) M2 TAM subset in vitro and in vivo; gene profiling of this TAM subset identified MS4A8A as a novel TAM molecule expressed in vivo by TAM in mammary carcinoma and malignant melanoma. In vitro, Ms4a8a mRNA and MS4A8A protein expression was strongly induced in bone marrow-derived macrophages (BMDMs) by combining M2 mediators (IL-4, glucocorticoids) and tumor-conditioned media (TCM). Admixture of MS4A8A(+) TCM/IL-4/GC-treated BMDM significantly enhanced the tumor growth rate of subcutaneously transplanted TS/A mammary carcinomas. Upon forced overexpression of MS4A8A, Raw 264.7 macrophage-like cells displayed a special gene signature. Admixture of these MS4A8A(+) Raw 264.7 cells also significantly enhanced the tumor growth rate of subcutaneously transplanted mammary carcinomas. To identify the signaling pathways involved in synergistic induction of MS4A8A, the major signaling cascades with known functions in TAM were analyzed. Although inhibitors of NF-κB activation and of the MAPK JNK and ERK did not show relevant effects, the p38α/β MAPK inhibitor SB203580 strongly and highly significantly (p > 0.001) inhibited MS4A8A expression on mRNA and protein level. In addition, MS4A8A expression was restricted in M2 BMDM from mice with defective GC receptor (GR) dimerization indicating that classical GR gene regulation is mandatory for MS4A8A induction. In conclusion, expression of MS4A8A within the complex signal integration during macrophage immune responses may act to fine tune gene regulation. Furthermore, MS4A8A(+) TAM may serve as a novel cellular target for selective cancer therapy.

overall_design: A recombinant Ms4a8a cDNA was amplified by PCR (primer: Ms4a8a-SpeI-fw 5’ATCGAATTCACTAGTAGCAAAGAGTTGGGAACCGGAGCAAGA3’ and Ms4a8a-NotI-rv: 5’ATATGCGGCCGCTAGAGCATCTTTAT3’) from Ms4a8a cDNA RZPDp981B0530D (IMAGE ID 905005), purified on agarose gel and subcloned after digestion with SpeI and NotI restriction enzymes into the expression vector pEF6/V5-His Topo (Invitrogen) according to standard molecular biology protocols. After confirming sequence identity, we transfected RAW264.7 cells with Ms4a8a vector DNA using Lipofectamine 2000 (Invitrogen) transfection reagent. Transfectants were selected by resistance to blasticidin (Invitrogen). Raw264.7Ms4a8a clone K8 with recombinant Ms4a4a expression were propagated. As a negative control, a vector-transfected RAW264.7mock (clone K3) was selected under parallel culture conditions.

first: Astrid

last: Schmieder

first: Kai

last: Schledzewski


title: Real-time quantitative PCR analysis of Human Umbilical Vein Endothelial Cells (HUVEC)

status: Public on May 16 2012

city: Ancona

first: Fabiola

last: Olivieri

state: Ancona

address: Via Tronto

department: Dept of clinical and molecular sciences

institute: Università Politecnica delle Marche

summary: In order to identify new markers of vascular cell senescence with potential in vivo implications, primary cultured  Human Umbilical Vein Endothelial Cells (HUVECs),  were analysed for microRNA (miR) expression.

overall_design: QRT-PCR microRNA expression profiling in 3 senescent (XIII passage) vs. 3 young HUVECs (II passage).

first: Rina

last: Recchioni

first: Raffaella

last: Lazzarini


title: Alterations in skeletal muscle mRNA profile by angiopoietin-1 and angiopoietin-2

city: Montreal

first: Sabah

last: Hussain

state: Quebec

address: Roo L305, 687 Pine ave west

department: Medicine

institute: McGill University

summary: Analysis of changes in skeletal muscle myoblasts in response to over-expression of angiopoietin-1 (Ang-1) and angiopoietin-2 (Ang-2). The hypothesis tested in the present study was that over-expression of Ang-1 or Ang-2 will induce the expression of pro-survival and pro-differentiation genes in skeletal myoblasts while inhibiting the expression of pro-apoptotic genes.  Results provide important information of how mRNA profile of skeletal myoblasts is altered by Ang-1 and ang-2 and provide first evidence that secondary mediators such as leptin may mediate the enhancement of skeletal myoblasts differentiation by Ang-1 and Ang-2.

overall_design: Total RNA obtained from isolated human skeletal myoblasts after 48hrs of infection with adenoviruses expressing GFP (control), Ang-1 or Ang-2.

first: Marhoo

last: Mofarrahi


title: MicroRNA expression profiling of NGF-treated PC12 cells revealed a critical role for miR-221 in neuronal differentiation

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

summary: MicroRNAs (miRNAs) are small non-coding RNAs that control protein expression through translational inhibition or mRNA degradation. MiRNAs have been implicated in diverse biological processes such as development, proliferation, apoptosis and differentiation. Upon treatment with nerve growth factor (NGF), rat pheochromocytoma PC12 cells elicit neurite outgrowth and differentiae into neuron-like cells. NGF plays a critical role not only in neuronal differentiation but also in protection against apoptosis. In an attempt to identify NGF-regulated miRNAs in PC12 cells, we performed miRNA　microarray analysis using total RNAs harvested from cells treated with NGF. In response to NGF treatment, expression of 8 and 12 miRNAs were up- and down-regulated, respectively. Quantitative RT-PCR analysis confirmed increased expression of miR-221, miR-181a* and miR-326, and decreased expression of miR-143, miR-210 and miR-532-3p after NGF treatment, among which miR-221 was drastically up-regulated. Overexpression of miR-221 induced neurite outgrowth of PC12 cells in the absence of NGF treatment, and also enhanced neurite outgrowth caused by low-dose NGF. More importantly, knockdown of miR-221 by antagomir attenuated NGF-mediated neurite outgrowth. Finally, miR-221 decreased expression of Foxo3a and Apaf-1, both of which are involved in apoptosis in PC12 cells. Our results indicate that miR-221 plays a critical role for neuronal differentiation as well as protection against apoptosis in PC12 cells.

overall_design: NGF induced miRNAs expression in rat pheochromocytoma PC12 cells was measured in cells treated with 100 ng/ml NGF for 0, 12, 24 and 48 hr.

first: Aya

last: Kitamoto

first: Nanako

last: Hamada

first: Yasunori

last: Fujita

first: Yukihiro

last: Akao

first: Yoshinori

last: Nozawa

first: Masafumi

last: Ito


title: Metabolism of a plant derived galactose-containing polysaccharide by Bifidobacterium breve UCC2003

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: In this study, we describe the functional characterisation of the B. breve UCC2003 gal locus, which is dedicated to the utilisation of galactan, a plant-derived polysaccharide. Using a combination of molecular approaches we conclude that the galA gene of B. breve UCC2003 encodes a beta-1,4-endogalactanase producing galacto-oligosaccharides, which are specifically internalised by an ABC transport system, encoded by galBCDE, and which are then hydrolysed to galactose moieties by a dedicated intracellular beta-galactosidase, specified by galG. The generated galactose molecules are presumed to be fed into the fructose-6-phosphate phosphoketolase pathway via the Leloir pathway, thereby allowing B. breve UCC2003 to use galactan as its sole carbon and energy source. In addition to these findings we demonstrate that GalR is a LacI-type DNA-binding protein, which not only appears to control transcription of the galCDEGR operon, but also that of the galA gene.

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


title: Regeneration of comparative genomic hybridization oligonucleotide microarrays with dimethylurea

city: Gdansk

first: Arkadiusz

last: Piotrowski

address: Hallera 107

department: Biology and Pharmaceutical Botany

country: Poland

institute: Medical University of Gdansk

summary:
Reuse of materials in DNA hybridization based methods has been known since the advent of Southern membranes. Array based comparative genomic hybridization is essentially Southern hybridization with multiple probes immobilized on a solid surface. We have shown that comparative genomic hybridization microarrays fabricated with maskless array synthesizer technology can be used up to four times with application of 1,3-dimethylurea as array-stripping agent.
We reproducibly detected chromosomal aberrations, 0.6 to 22.4 Mb in size, in four hybridization rounds using regenerated microarray slides. We have also demonstrated that regenerated arrays can detect smaller alterations, 16 – 200 kbp, such as common copy number variants, as well as complex aberration profiles in tumor.

overall_design: Peripheral blood leukocyte DNA samples from 7 individuals with subchromosomal aberrations vs a pool of female DNA (Promega). The experiments were performed in quadruplicate on succesively regenerated microarrays. One dye swap was performed..

first: Piotr

last: Madanecki


title: Suppression of the chromatin remodeling protein CHD3 and platinum resistance in ovarian cancer

status: Public on May 15 2012

city: Cold Spring Harbor

first: Kazimierz

middle: O.

last: Wrzeszczynski

state: NY

address: One Bungtown Rd.

institute: Cold Spring Harbor Laboratory

type: Methylation profiling by genome tiling array

summary: Epithelial ovarian cancer is the leading cause of death from gynecological malignancies. Currently platinum-based chemotherapy, coupled with a taxane based drug is the primary treatment for ovarian cancer. Approximately 25% of patients either present with or rapidly develop resistance to platinum based chemotherapy and all recurrent tumors ultimately become resistant. Epigenetic modifications have been associated with tumor formation and progression and may contribute to therapy response. We performed a methylation screen on a set of tumors and have found a number of genes and family members differentially methylated between resistant patients and sensitive patients. Here we show that loss of expression of CHD3, a member of the Mi-2/NuRD complex, causes increased resistance to platinum chemotherapy drugs. Additionally, ovarian cell lines transcriptionally silenced for CHD3 are more invasive, have migratory ability, and display a transformed epithelial to mesenchymal (EMT) phenotype. Taken together, we provide the first evidence of a role for CHD3 as an important epigenetic regulator of chemoresistance in ovarian cancer and hypothesize EMT as one of the underlying mechanisms.  Furthermore, CHD3 expression might represent a therapy response predictor  and could be a future therapeutic target for ovarian cancer.

overall_design: We have developed a method to profile genome wide methylation. 71 ovarian tumor samples and 9 normal tissue samples from individuals were analyzed for CpG methylation. Some of these regions were validated for their methylation as a proof of principle for the method. Kamalakaran S., et. al. Mol Oncol. 2011;5:77-92 (PMID: 21169070).

first: Robert

last: Lucito

first: Douglas

middle: A

last: Levine

middle: O

first: Nevenka

last: Dimitrova

first: James

last: Byrnes

first: Sohail

last: Kahn

first: Elena

last: Lum


title: HoxA13 gain-of-function in chicken embryo PSM progenitors.

city: ILLKIRCH

first: philippe

last: moncuquet

address: 1 rue laurent fries

country: France

institute: IGBMC

summary: Within a given vertebrate species, the total number of vertebrae in each anatomical domain is precisely defined and shows little variation among individuals. In contrast, this number can vary tremendously between different species, ranging from as few as six vertebrae in frogs to as many as several hundred in some snakes and fish. Segmental precursors of the vertebrae, called somites are produced sequentially in the embryo from the presomitic mesoderm (PSM), until a final number characteristic of the species, is reached. Here, we show in the chicken embryo that, by controlling the rate of axis elongation, Hox genes control the total number of somites generated by the embryo. We observed that activation of the most posterior Hox genes in somite precursors of the tail bud correlates with an abrupt slowing-down of the speed of axis elongation. We show that progressively more posterior Hox genes, which are collinearly activated in somitic precursors of the epiblast, repress Wnt activity with increasing strength. This leads to a graded repression of the Brachyury/T transcription factor, reducing mesoderm ingression and slowing down the elongation process. Due to the continuation of somite formation, the PSM, which is not fed with sufficient supply of new cells posteriorly, becomes progressively exhausted, ultimately leading to an arrest of segment formation. Our data provide a conceptual framework to explain how the cross-talk between the segmentation clock and the Hox clock accounts for the diversity of vertebral formulae across animal species.

overall_design: Primitive streak aera corresponding to PSM precursors were dissected in Stage 9 somites chicken embryo overexpressing HoxA13 or a control H2B-Venus. The experiment was designed to have biological duplicate in each conditions. The gain-of-function was obtained by electroporating the embryo at Stage 5HH with a vector containing HoxA13 under the CAGGS promoter with an H2B venus reporter. In order to have enough material for the microarray, 7 embryos were pooled in each sample before the hybridization.

first: Nicolas

last: Denans

first: Philippe

last: Moncuquet


title: Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

summary:
Background: Developments in DNA resequencing microarrays include mitochondrial DNA (mtDNA) sequencing and mutation detection. During automated analysis to sequence mtDNA, bases can be identified as wildtype, variant, or there may be a failure to assign a base (N-call) when compared to the mtDNA reference sequence (rCRS). The purpose of our study was to re-examine the N-call distribution of mtDNA samples, based on the hypothesis that N-calls may represent insertions or deletions in mtDNA.
Findings: We analysed mtDNA from 16 patient samples (8 blood/bone marrow origin and 8 from cultured fibroblasts) using the Affymetrix MitoChip v.2.0 which has 2 probe areas, one for sequencing compared to the rCRS and one for 500 common haplotypes. N-calls by the proprietary GSEQ software were significantly reduced when the freeware on-line algorithm ‘sPROFILER’ was utilized. Interestingly, this decrease in N-calls, in both sections of the MitoChip, had no effect on the homoplasmic or heteroplasmic mutation levels compared to GSEQ software. We then used conventional DNA sequencing to analyse continuous N-call stretches identified by sPROFILER, ranging from 2 to 22 bases, to identify changes resulting in base calling failures.
Conclusions: Our study is the first to analyse N-calls produced from GSEQ software for the MitoChip v2.0. We found that by narrowing the focus to stretches of N-calls revealed by sPROFILER, conventional sequencing was able to identify unique deletions and insertions. This study also appeared to support the contention that the GSEQ is more capable of assigning bases when used in conjunction with sPROFILER.

overall_design: mtDNA from 16 patient samples were analysed using Mitochip v2.0. Eight samples were DNA extractions directly from blood/bone marrow. The other eight samples were DNA extractions from primary cultured fibroblasts. Results were generated in GSEQ and reanalysed in sPROFILER for comparison.

first: Mazin

last: Zamzami

middle: W

last: Taylor

first: Emma

middle: L

last: Blakely

first: Iulia

last: Oancea

first: Francis

last: Bowling

first: John

last: Duley


title: Evaluation of a novel clinical platform for cardiovascular drug development

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

summary:
Objectives –To determine whether inflammation biomarkers can be used as indicators of therapeutic response, an exploratory study was performed to ascertain whether short term improvements in risk parameters will have measureable effects on a pre-defined panel of plaque inflammation biomarkers.
Methods and Results – Patients (n=121) with peripheral arterial disease were enrolled into one of three sub-studies based upon the presence of hypercholesterolemia, hypertension, or diabetes.  Patients were randomized to 6 weeks of drug treatment vs. placebo and underwent catheter excision of atherosclerotic tissue from one extremity at baseline and the contralateral extremity after treatment.  Simvastatin 40mg once daily reduced LDL-C by 43% (p<0.01), losartan 50mg once daily reduced diastolic blood pressure by 4 mm Hg (p=0.099), and pioglitazone 30mg once daily reduced serum glucose by 66mg/dL (p=0.008).  Despite these effects, there were no consistent treatment effects on a large panel of plaque protein, RNA and lipid biomarkers.
Conclusions – Short term treatment with drugs that improve cardiovascular risk parameters did not result in a measureable reduction in the levels of peripheral arterial plaque inflammation biomarkers.  Further studies are required to identify biomarkers that are sufficiently predictive to be used to identify drug candidates for testing in large cardiovascular outcome studies. (ClinicalTrials.gov: NCT00720577)

overall_design: Human peripheral atherosclerosis plaque was extracted from lower extremities, and RNA, lipids and proteins extracted. RNA was analyzed in an Agilent two-color platform.

first: Hayes

last: Dansky

first: Edward

last: O'Neill


title: Global microRNA profiling of the mouse ventricles during development of severe hypertrophic cardiomyopathy and heart failure

status: Public on May 11 2012

city: Sydney

first: Richard

last: Bagnall

address: Missenden Road

department: Molecular Cardiology

institute: Centenary Institute

type:
Expression profiling by RT-PCR
Non-coding RNA profiling by array

summary: The  study sought to determine the global miRNA profile of ventricles during early and end-stage hypertrophic cardiomyopathy in a severe double mutant mouse model of the disease. MicroRNA expression profiles of ventricles of transgenic mice with a mutation in both the myosin heavy chain gene (MYH7 Arg403Gln) and cardiac troponin I gene (TNNI3 Ser203Gln) and of non-transgenic mice were determined using Rodent TaqMan Low Density miRNA Arrays A v2.0 (TLDA, Life Technologies). MicroRNA profiles were measured at 10 days of age and 16 days of age, in 3 biological replicates.

overall_design: qRT-PCR analysis of microRNAs of ventricles of three transgenic mice and three non-transgenic mice age 10 days, and three transgenic mice and three non-transgenic mice age 16 days. 450 ng RNA was reverse transcribed, without pre-amplification, using TaqMan MicroRNA Reverse Transcription Kit and Megaplex RT Primers rodent pool A (Life Technologies). Complementary DNA (cDNA) was amplified using a TaqMan rodent microRNA A Array v2.0 (Life Technologies) with TaqMan Universal PCR Master Mix on an ABI 7900HT Sequence Detection System.

first: Chris

last: Semsarian


title: Global hepatic gene expression in rainbow trout exposed to sewage effluents

status: Public on May 10 2012

city: Gothenburg

first: Marija

last: Cvijovic

address: Chalmers Tvärgata 3

country: Sweden

institute: Chalmers Univeristy of Technology

summary: Effluents from sewage treatment plants contain a mixture of micropollutants with the potential of harming aquatic organisms. Thus, addition of advanced treatment techniques to complement existing conventional methods has been proposed. Some of the advanced techniques could, however, potentially produce additional compounds affecting exposed organisms by unknown modes of action. In the present study the aim was to improve our understanding of how exposure to different sewage effluents affects fish. This was achieved by explorative microarray and quantitative PCR analyses of hepatic gene expression, as well as relative organ sizes of rainbow trout exposed to different sewage effluents (conventionally treated, granular activated carbon, ozonation (5 or 15 mg/L), 5 mg/L ozone plus a moving bed biofilm reactor, or UV-light treatment in combination with hydrogen peroxide). Exposure to the conventionally treated effluent caused a significant increase in liver and heart somatic indexes, an effect removed by all other treatments. Genes connected to xenobiotic metabolism, including cytochrome p450 1A, were differentially expressed in the fish exposed to the conventionally treated effluents, though only effluent treatment with granular activated carbon or ozone at 15 mg/L completely removed this response. The mRNA expression of heat shock protein 70 kDa was induced in all three groups exposed to ozone-treated effluents, suggesting some form of added stress in these fish. The induction of estrogen-responsive genes in the fish exposed to the conventionally treated effluent was effectively reduced by all investigated advanced treatment technologies, although the moving bed biofilm reactor was least efficient. Taken together, granular activated carbon showed the highest potential of reducing responses in fish induced by exposure to sewage effluents.

overall_design:
The fish exposure was carried out in March 3-17, 2008 at Henriksdal STP (Stockholm, Sweden) using a large scale pilot plant with parallel treatment lines under ethic permits approved by the local animal committee in Gothenburg (permission no. 36-2007). A thorough description of the different treatment steps (both conventional and advanced) and the experimental setup during the exposure (Fig. 1) has been previously described elsewhere (Samuelsson et al., 2011). In brief, the raw influent underwent conventional activated sludge treatment to generate a reference effluent (Conventional Activated Sludge; CAS). This includes mechanical treatment (removal of large objects using grids with 3 mm column width); primary sedimentation; biological treatment (activated sludge aged 20 days); secondary sedimentation; sand filter. The additional advanced treatment processes were granular activated carbon (GAC), ozonation at 5 mg/L (OZ5) or 15 mg/L (OZ15), ozonation 5 mg/L followed by a moving bed biofilm reactor (MBBR) and irradiation by ultraviolet radiation (0.75 Wh/L) plus hydrogen peroxide (10 mg/L; UH). Two aquaria were used for positive controls. As the tap water available is not as well accepted by the fish, and to better reflect the organic content and overall chemistry of surface water, the control aquaria (TW1 and TW2, together TW) contained carbon-filtered tap water supplemented by 2% of conventionally treated reference effluent. We consider evaluation of implementation and running costs to be outside the scope of this paper.
Juvenile rainbow trout (Oncorhynchus mykiss; 113±23 g; mean bodyweight ± standard deviation) of both sexes were obtained from Antens Laxodling AB (Alingsås, Sweden). Rainbow trout is a commonly used species for this type of studies and our lab have ample experience using this species. Furthermore, rainbow trout of sufficient size for metabolomic studies (Samuelsson et al., 2011) can easily be obtained. Finally, the use of trout provides the opportunity for comparisons with other studies (e.g. Gunnarsson et al., 2009 and Albertsson et al., 2010). During an acclimatization period of four days on site, the fish were kept in tanks containing carbon-filtered tap water + 2% reference effluent. On the onset of the experiment, the fish were randomly distributed among eight 100 L aquaria (n=25/aquarium), supplied with treated effluent  from the different parallel treatment lines. Aquaria duplicates were used for the controls. During both the acclimatization period as well as the 14 day exposure, the aquaria were aerated and the fish were not fed to reduce variability due to differences in food intake. It should be stressed that trout easily cope with food deprivations for several weeks (Kullgren et al., 2010).  Measurements of temperature (13.5±0.5°C), oxygen saturation (97±3%), pH (7.4±0.3), conductivity and flow rate were monitored 5 d per week throughout the exposure. In addition, to evaluate differences in removal efficiency between the treatments, total organic carbon (TOC), 7-day biochemical oxygen demand (BOD7), suspended solids (SS), total nitrogen (Tot-N) and total phosphorus (Tot-P) were measured in all effluents (Samuelsson et al., 2011).
The sampling took place during two consecutive days (day 14 and 15) due to the large number of fish. For each day, an equal number of fish from each treatment was sampled in random order and killed by a blow to the head. The fish were weighed, their fork length was measured and their sex was determined by macroscopical observation of their gonads.
Liver samples were collected for several different studies (hence sample size limitations), frozen on dry ice and stored at -70°C until analysis.  Homogenization of the frozen liver tissue was carried out using Tissuelyser (Qiagen, Hilden, Germany) and hepatic total RNA was extracted and purified using QIAcube and RNeasy® Plus Mini Kit (Qiagen). The RNA quantity and quality were assessed by spectrophotometric measurements with the Nanodrop 1000 (NanoDrop Technologies, Wilmington, DE). To ensure that no degradation had occurred, the isolated RNA was analyzed using Experion automated electrophoresis (Bio-Rad, Hercules, CA).
A 15k rainbow trout gene expression microarray was designed for the RT analyzer platform (febit, Heidelberg, Germany) by using The Institute for Genomic Research (TIGR) Rainbow Trout Gene Index (RTGI) database version 7.0 (http://compbio.dfci.harvard.edu/tgi/). Details on the probe design strategy, but for eelpout (Zoarces viviparus), and transcript selection strategy are described elsewhere (Kristiansson et al., 2009; Cuklev et al., 2011). However, in the present study, singletons and non-annotated expressed sequence tags (ESTs) were replaced by newly well-annotated ESTs in rainbow trout. When available, transcripts at GenBank (http://www.ncbi.nlm.nih.gov/nucleotide) were used. In our lab, results from similar microarrays using the same platform have shown good correlation with quantitative polymerase chain reaction (qPCR) data (Gunnarsson et al., 2009b; Kristiansson et al., 2009; Cuklev et al., 2011; Lennquist et al., 2011).
To reduce variation in estrogen-responsive genes, only males were used for the subsequent gene expression analyses. Biotinylated antisense RNA (aRNA) was synthesized using MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion®). The aRNA samples (20 µg) were vacuum dried in a vacuum centrifuge, dissolved in 10 µl water and fragmented according to the manufacturer’s protocol. The following steps described in this subchapter were all performed by febit.  Oligonucleotide arrays were synthesized by photo-controlled in situ synthesis using the Geniom One system (febit). Each biochip consists of eight individually accessible micro channels, each of which is referred to as a microarray in this manuscript. Eight individual samples from each aquarium were included in the analysis. In total, 64 microarrays were analyzed. A customized protocol, described in detail elsewhere (Cuklev et al., 2011), was used for prehybridization and hybridization. All samples were randomly placed on the biochips, with one sample from each exposure on each biochip. Signals were detected using the internal CCD-camera system of the RT analyzer instrument (febit) and quantified using the Geniom Wizard software. Integration times were between 156 and 570 ms, determined automatically by the instrument software.
All microarray data processing and statistical calculations were performed in R-2.12.2 (www.r-project.org; R Development Core Team, 2010). The quality of pre- and post normalized arrays was verified with box- and MA plots.  The data analysis was performed in the R-package LIMMA (Smyth, 2005). Data were normalized using the ‘quantile’ method. Moderated t-statistics and adjusted p-values of differential expression were calculated using the empirical Bayes model.

first: Filip

last: Cuklev

first: Lina

last: Gunnarsson

first: Erik

last: Kristiansson

first: Carolin

last: Rutgersson

first: Berndt

last: Björlenius

last: Larsson


title: The transcriptional profiles of bluestem and Indian grass - Konza 2006 [Zea mays; Andropogon gerardii; Sorghastrum nutans]

city: New Haven

first: shenghua

last: yuan

state: CT

address: 165 Prospect St.

department: Ecology and Evolutionary Biology

institute: Yale University

summary: We measured transcriptional profiles of individuals of Andropogon gerardii and Sorghastrum nutans, two C4 grass species native to North American grasslands, in a field experiment in which both temperature and precipitation have been manipulated to simulate key aspects of forecasted climate change.

sample_organism:
Andropogon gerardi
Sorghastrum nutans

overall_design: 99 samples were analyzed.

first: Shenghua

last: Yuan

first: Jianfa

last: Bai

first: Karen

last: Garrett

first: Scot

last: Hulbert

first: Jan

middle: E

last: Leach

first: Amgad

last: Saleh

first: Patrick

last: Schnable

first: Steven

last: Travers

first: Melinda

last: Smith


title: Losses of chromosome 5q and 14q mark a subset of gastric cancers with good clinical outcome

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

summary: Purpose: To improve clinical outcome of gastric cancer patients, most emphasis is on improving therapeutic regimens, including more extensive surgery as well as (neo)adjuvant chemotherapy. The present study set out to identify, based on DNA copy number profiling, subgroups of patients with different clinical outcomes who thus would qualify for different therapy intensities.  Experimental Design: DNA of 206 gastric cancer patients was isolated and analyzed by genome wide array comparative genomic hybridization. DNA copy number profiles were evaluated and correlated to lymph node status and survival. In addition, HSP90 protein expression was analyzed and correlated to survival in 290 gastric cancer patients.  Results: Frequent (>20%) DNA copy number gains were observed on chromosomes 1p, 6p, 7p, 7q, 8q, 11q, 12q, 13q, 16p, 16q, 17q, 19p, 19q, 20p, 20q, 21q and 22q, and losses on chromosomes 4p, 4q, 6p, 6q, 9p, 13q and 21q. Lymph node negative gastric cancers showed significantly more losses on chromosomes 5q11.2-q35.1, 10q11.23-21.3 and 14q32.11-q32.33. In addition, losses on 5q11.2-q31.3 and 14q32.11-q32.33 were highly correlated to good clinical outcome, in both lymph node negative and positive gastric cancer patients. Loss of expression of HSP90, located on chromosome 14q32.2, correlated to good survival time.   Conclusion: Genome wide DNA copy number profiling allows to identify a subgroup of gastric cancers, marked by losses on chromosomes 5q11.2-q31.3 and 14q32.11-q32.33 that have an excellent clinical outcome after surgery alone, and patients with these tumors are unlikely to benefit from additional intensified therapies. Possible biological mechanisms could involve loss of heat shock proteins, of which the coding genes are located at these chromosomal regions.

overall_design: 183 gastric adenocarcinomas

first: Tineke

last: Buffart

first: Beatriz

last: Carvalho

first: Nicole

middle: C

last: van Grieken

first: Wessel

last: van Wieringen

first: Marianne

last: Tijssen

first: Elma

last: Klein Kranenbarg

first: Heike

middle: I

last: Grabsch

first: Bauke

last: Ylstra

first: Cornelis

middle: J

last: van de Velde

first: Gerrit

last: Meijer


title: Genetic characterization of large parathyroid adenomas

city: Stockholm

first: Jamileh

last: Hashemi

address: Karolinska University Hospital

department: Molecular Medicine & Surgery

institute: Karolinska Institutet

summary: We genetically characterized parathyroid adenomas with large glandular weights, for which independent observations suggest pronounced clinical manifestations. Large parathyroid adenomas (LPTAs) were defined as the 5% largest sporadic parathyroid adenomas identified among the 590 cases operated on in our institution during 2005-2009. The LPTA group showed a higher relative number of male cases and significantly higher levels of total plasma and ionized serum calcium (P <0.001). Further analysis of 21 LPTAs revealed low MIB-1 proliferation index (0.1-1.5%), MEN1 mutations in 5 cases and one HRPT2 mutation. Total or partial loss of parafibromin expression was observed in 10 tumors, two of which also showed loss of APC expression. Using array-CGH, we demonstrated recurrent copy number alterations most frequently involving loss in 1p (29%), gain in 5 (38%) and loss in 11q (33%). Totally 21 minimal overlapping regions were defined for losses in 1p, 7q, 9p, 11 and 15q, and gains in 3q, 5, 7p, 8p, 16q, 17p and 19q. In addition, 12 tumors showed gross alterations of entire or almost entire chromosomes, most frequently gain of 5 and loss of 11. While gain of 5 was the most frequent alteration observed in LPTAs, it was only detected in a small proportion (4/58 cases, 7%) of parathyroid adenomas. A significant positive correlation was observed between parathyroid hormone level and total copy number gain (r = 0.48, P = 0.031). These results support that LPTAs represent a group of patients with pronounced parathyroid hyperfunction and associated with specific genomic features.

overall_design: We applied high-resolution array-CGH to assess copy number alterations (CNAs) in 21 tumors representing the 5% largest sporadic parathyroid adenomas in our institution.

first: L

last: Sulaiman

first: I

last: Nilsson

first: C

last: Juhlin

first: F

last: Haglund

first: A

last: Höög

last: Larsson

first: J


title: Expression analysis of Fusarium verticillioides wild-type cultured in liquid media

status: Public on May 21 2012

city: Peoria

first: Robert

last: Butchko

state: IL

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

summary:
Investigation of whole genome gene expression level changes over time of Fusarium verticillioides wild-type in liquid fumonisin inducing media (GYAM)
Fusarium verticillioides produces a polyketide derived mycotoxin, fumonsin, over time in liquid media, Proctor et al, Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis, Fungal Genetics and Biology, 38:237-249

overall_design: Wild type F. verticillioides strain 7600 cultured for two and five days in liquid GYAM.


title: Global profiling of gene expression in A signal mutants of Myxococcus xanthus

city: Marburg

first: Lotte

last: Sogaard-Andersen

address: Karl-von-Frisch-Str.

department: Ecophysiology

institute: Max Planck Institute for Terrestrial Microbiology

summary:
In response to starvation Myxococcus xanthus initiates a developmental program that culminates in the formation of fruiting bodies inside which the rod-shaped cells differentiate to spores. Fruiting body formation depends on intercellular communication and two intercellular signals are known, the A-signal and the C-signal. Five genes have been identified which are required for A-signal synthesis. To begin to understand the function of the genes required for A-signal synthesis, we have analysed gene expression in the asgA and the asgB mutant.

Keywords: Vegetative cells of WT (DK1622) and AsgA mutant (DK5057) and AsgB mutant (DK4398)

overall_design: 3 biological replicates each; normalized ratios to vegetative cells of  DK1622 (wt) Cy5

first: Arne

last: Weinhold

first: Sigrun

last: Wegener-Feldbrügge


title: Aspergillus niger : Control (fructose) vs. xylose + arabinose (XA)

status: Public on May 07 2012

city: Ribeirao Preto

first: Wagner

last: de Souza

address: Av do Cafe

institute: University of Sao Paulo

summary: Transcriptional profiling of A. niger comparing different strains (WT, ΔXlnR, ΔaraR and ΔaraRΔXlnR) treated with 25mM xylose + 25mM arabinose for 2 and 8h. The main objective was to identifiy genes related to primary metabolism and carbohydrate metabolism in general, for instance, cellulases and hemicellulases. The study will compare the differences between WT strain and the strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant,after treatment with xylose+arabinose (XA treatment). The experiment was further validated by real-time PCR and enzymatic assays.

overall_design: Two-condition experiment : A. niger mutant strains on XA for 2 and 8 h at 30 oC in batch culture. Firstly, the strains were pre-grown in minimal medium with fructose as carbon source (control), and then transferred to xylose+arabinose (25 mM each) as carbon source.


title: MicroRNA Signatures Correlate with Diagnosis, Distant Metastasis and Prognosis in nasopharyngeal carcinoma

city: Guangzhou

first: Rongrong

last: wei

address: 651 Dongfeng East Road

department: cancer center

institute: Sun-Yat Sen university

summary: microRNA signatures with diagnosis, distant metastasis and prognosis for nasopharyngeal carcinoma

overall_design: 62 nasopharyngeal carcinoma and 6 non-cancer nasopharyngitis fresh tissues were detected by microRNA microarray

last: Wei

first: Huiyun

last: Wang


title: Aspergillus niger : Control (fructose) vs. steam-exploded sugarcane induction (SEB)

summary: Transcriptional profiling of A. niger comparing mutant strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant (ΔXlnR, ΔaraR and ΔaraRΔXlnR, repsectively) treated with steam-exploded sugarcane bagasse (SEB) for 12 and 24 h. The main objective was to identify genes related to cellulases and hemicellulases in mutant strains grown on SEB, with indirect comparisons with the WT strain grown on SEB [the (WT/SEB) data deposited in GSE24798]. The experiment was further validated by real-time PCR and enzymatic assay.

overall_design: Two-condition experiment : A. niger mutant strains on SEB for 12 and 24 h at 30 oC in batch culture. Firstly, the strains were pre-grown in minimal medium with fructose as carbon source (control), and then transferred to SEB as carbon source.


title: Mutant p53 cooperates with ETS2 to promote etoposide resistance [ChIP-chip]

status: Public on May 03 2012

city: Jackson

first: Luis

last: Martinez

state: MS

address: 1500 North State St

department: Biochemistry

institute: University of Mississippi Medical Center

type: Genome binding/occupancy profiling by genome tiling array

summary: Mutant p53 (mtp53) promotes chemotherapy resistance through multiple mechanisms including disabling pro-apoptotic proteins and by regulating gene expression. Analysis of promoter regions identified through CHIP-on-CHIP and CHIP-SEQ platforms reveal that the ETS motif (EBS) is prevalent within predicted mtp53 binding sites. We demonstrate that mtp53 regulates gene expression through EBS in promoters, and that ETS2 mediates the interaction with this motif. Importantly, we identified TDP2, a 5’-tyrosyl DNA phosphodiesterase involved in the repair of DNA damage caused by etoposide, as a transcriptional target of mtp53. We demonstrate that suppression of TDP2 sensitizes mtp53 expressing cells to etoposide, and that mtp53 and TDP2 are frequently overexpressed in human lung cancer; thus, our analysis identifies a potentially “druggable” component of mtp53’s gain-of-function activity.

overall_design: Comparison of two different transcriptional binding analysis (ChIP-on-ChIP and ChIP-Seq) for the identification of novel mutant p53 (R248W) binding.

first: Phi

middle: M

last: Do

first: Lakshman

last: Varanasi

first: Song

last: Fan

first: Chunyang

last: Li

first: Lwona

last: Kubacka

first: Virginia

last: Newman

first: Krishna

last: Chauhan

first: Silvano

last: Daniels

first: Maurizio

last: Boccetta

first: Michael

last: Garrett

first: Runzhao


title: Expression data from chick embryos overexpressing NEUROG2 or NEUROG2AQ in the neural tube

status: Public on May 05 2012

city: Toulouse

first: Sophie

middle: Bel

last: Vialar

address: 118 rte de narbonne

institute: CNRS

summary: The proneural NEUROG2 is essential for neuronal commitment, cell cycle exit and neuronal differentiation. Characterizing genes networks regulated downstream of NEUROG2 is therefore of prime importance. To identify NEUROG2 early response genes, we combined gain of function in the neural tube with a global detection of modified transcripts using microarrays. We included in our study a mutant form of NEUROG2 (NEUROG2AQ) that cannot bind DNA and cannot trigger neurogenesis. Using this approach, we identified 942 genes modified at the onset of NEUROG2 activation. The global analysis of functions regulated by NEUROG2 allowed unmasking its rapid impact on cell cycle control. We found that NEUROG2 specifically represses a subset of cyclins acting at the G1 and S phases of the cell cycle, thereby impeding S phase re-entry. This repression occurs before modification of p27kip1, indicating that the decision to leave the cell cycle precedes the activation of this Cyclin-dependant Kinase Inhibitor. Moreover, NEUROG2 down-regulates only one of the D-type cyclins, cyclinD1, and maintaining cyclinD1 blocks the ability of the proneural to trigger cell cycle exit, without altering its capacity to trigger neuronal differentiation. The fact that NEUROG2 represses a subset but not all cell cycle regulators indicates that cell cycle exit is not an indirect consequence of neuronal differentiation but is precisely controlled by NEUROG2. Altogether our findings indicate that NEUROG2, by specifically repressing G1 and S cyclins, allows committed neuronal precursors to perform their last mitosis but blocks their re-entry in the cell cycle, thus favouring cell cycle exit.

overall_design: Stage HH10-11 embryos (11 to 15 somites) were electroporated with a control vector (pGIG-GFP), a NEUROG2-expressing vector (pCIGNEUROG2-GFP), or a NEUROG2AQ-expressing vector (pCIGNEUROG2AQ-GFP). For each biological replicate, neural tubes from 20 embryos were pooled for GFP+ cells collection. GFP+ cells were collected 6h later using FACS sorting (Epics Altra HSS cell sorter, Toulouse Rio platform) and processed for RNA probe preparation and hybridization on Affymetrix microarrays. For each experimental condition, four biological replicates were processed.

first: Marine

last: Lacomme

first: Laurence

last: Liaubet

first: Fabienne

last: Pituello

last: Bel-Vialar


title: Functional characterization of genes/proteins differentially expressed in phototrophic and heterotrophic tissues in Arabidopsis thaliana mutants lacking chloroplastic and cytosolic fructose-1,6-bisphosphatase genes

status: Public on May 04 2012

city: Granada

first: Mariam

middle: Sahrawy

last: Barragán

state: Granada

address: Profesor Albareda,

department: Department of biochemistry, cellular and molecular biology of plants

country: Spain

institute: Estación Experimental del Zaidín (EEZ)

summary: Photosynthesis is arguably the most important biological process on earth. In plants, energy harvested in photosynthesis is converted into sugar and starch, which are important products from species with agronomic interest. During the photosynthesis in the chloroplast, the intermediate carbon metabolites (triose phosphates) produced by the Calvin cycle can either be exported to the cytosol for sucrose synthesis or stay in the chloroplast for starch synthesis (formation). Two fructose-1,6-bisphosphatase (FBPase) enzymes, the chloroplastidial (cpFBPaseI) and the cytosolic (cyFBPase) isoforms, catalyse the first irreversible step during the conversion of triose phosphate to starch or sucrose, respectively. Recently, another cpFBPase isoform (cpFBPaseII) with unknown function  was identified. It has been reported that the reduction of cyFBPase or cpFBPaseI activity leads to an alteration in starch and sucrose content. In our laboratory, Arabidopsis thaliana knock-out mutants for the cyFBPase and cpFBPaseI are now available. The objective this research project is to identify and functionally characterize genes differentially expressed in Arabidopsis thaliana knock-out mutants lacking FBPase genes. We make use of high throughput methodologies, such as the transcriptomic and proteomic analyses which represent invaluable tools to identify new loci responsible for agronomically important traits.

overall_design: Three independent biological replicates were used for each type of sample. Three hybridizations were performed, representing the three independent biological replicates, being one of them a dye swap

last: Sahrawy

first: Mauricio

last: Soto-Suárez.

first: Antonio

last: Serrato


title: The Streptomyces coelicolor DegS-DegU-like regulon

city: Campus de Cantoblanco

first: Sonia

last: Gullón

state: Madrid

address: Darwin 3

institute: CNB-CSIC

summary: The Streptomyces coelicolor two genes operon SCO5784-SCO5785 encodes a two-component system which functions in a similar manner to that of the Bacillus subtilis DegS-DegU system. Propagation of the regulatory gene in high copy number results in the overproduction of several extracellular enzymes, among them the major extracellular protease, as well as in a higher level of synthesis of the antibiotic actinorhodin. This two-component system seems to control various processes characterised by the transition from primary to secondary metabolism in S. coelicolor, as determined by proteomic and transcriptomic analices. The presence of the regulatory gene in high copy number in S. coelicolor additionally seems to elicit a stringent response in the bacterial cell. Therefore, we propose renaming S. coelicolor genes SCO5784 and SCO5785 as degS and degU, respectively.

overall_design: All microarray analyses were performed with RNA samples obtained from three independent cultures grown under identical conditions. Hybridisation assays were carried out with cDNA obtained from RNA extracted at the late exponential phase of growth (24h).   The transcriptional profile of wild type (S. coelicolor M145) cells carrying the multicopy plasmid pIJ487 was compared with that of the same strain carrying the degU gene cloned in the same plasmid under the control of its own promoter (S. coelicolor M28). And the transcriptional profile of wild type (S, coelicolor M145) cells was compared to that of the DegU deficient strain (S. coelicolor I32).

first: Rozas

last: Daniel

first: Rafael

middle: P

last: Mellado


title: Translocase malfunction causes extracellular protein translocation stress ( EPTS) in Streptomyces lividans

summary: The genomic and proteomic analyses of Streptomyces lividans strains deficient in the major signal peptidase SipY or in the translocase complex protein SecG resulted in a set of genes being equally regulated. These genes are apparently responsible for the common deficiencies in extracellular protein production and sporulation shared by both mutant strains, constituting a cellular response to the stress caused by the potential malfunction of the translocase complex, which we have named “extracellular protein translocation stress (EPTS)”.

overall_design: All microarray analyses were performed with RNA samples obtained from three independent cultures grown under identical conditions. The cDNA obtained from each RNA preparation of the SipY-deficient strain or the SecG-deficient strain were hybridised with the cDNA obtained from the equivalent RNA preparation of the wild type strain (S. lividans TK21).

first: Carmen

last: Palomino


title: The microRNA expression profile of C2C12 cell upon 72 hours of BMP2 treatment

city: Houston

first: Yangjin

last: Bae

state: TX

address: One Baylor Plaza

department: Molecular Human Genetics

institute: Baylor College of Medicine

summary: To identify osteoblast specific miRNAs that can contribute to osteoblastogenesis by post-transcriptionally regulates their targets, BMP2 are treated to C2C12 for 72 hours and performed miRNA microarray.

overall_design: C2C12 cells were treated with vehicles or BMP2 (300 ng/mL) supplemented alpha-MEM media for 72 days and total RNA was harvested and performed exiqon miRNA microarray. Duplicates were used for each condition. Dye swaps were done.

first: Brian

last: Dawson


title: Ube3a-ATS characterization with strand-speicific microarray

first: Linyan

last: Meng

department: Molecular and Human Genetics

summary: This strand-specific array is performed to characterize expression features of Ube3a-ATS, including its imprinting status, its exon-intron structure, its transcriptional initiation and termination site as well as its polyadenylation status. The array contains reverse-complementary probes detecting transcripts from both strands and therefore we are able to pick up signal from both Ube3a sense and antisense. By comparing wild-type with various mutants, and total RNA with polyA RNA, we concluded that Ube3a-ATS is a paternally imprinted gene covering the whole gene body of Ube3a in the antisense orientation. It does not have an obvious exon-intron structure. Its transcription initiates at Snrpn major promoter and terminates ~40kb upstream of Ube3a transcriptional start site.

overall_design: Total RNA from Snrpn-Ube3a maternal deletion mutant (del s-u/+), its wild-type littermate, paternal deletion mutant and its wildtype littermate were analyzed. Mutant mice with S-U maternal deletion and Snrpn promoter paternal deleiton which leads to depletion of Ube3a-ATS (del s-u/0.9 and del s-u/4.8) were also analyzed. polyA RNA was purified from the sample 2 and sample 4. All eight samples were hybridized to the custom 8X60k Agilent CGH array.

first: Richard

last: Person


title: Epigenetic analysis of gastric cancer cell lines

city: Singapore

first: Tatiana

last: Ivanova

address: 2 Jalan Bukit Merah Singapore 169547

department: Cancer & Stem Cell Biology Program

country: Singapore

institute: Duke-NUS Graduate Medical School

summary: Genome wide DNA methylation profiling of gastric cancer cell lines. The Illumina Goldengate DNA methylation Beadchip was used to obtain DNA methylation profiles across 1,505 CpG CpGs in 20 gastric cancer cell lines.

overall_design: Bisulphite converted DNA from the 20 gastric cancer cell lines were hybridised to the Illumina Goldengate Methylation Beadchip

first: Patrick

last: Tan


title: microRNA profiling of follicular lymphoma cells

city: Bethesda

first: Weixin

last: Wang

state: MD

address: 9000 Rockville Pike

department: DLM/CC

country: USA

institute: NIH

summary: The hallmark of follicular lymphoma (FL) is the t(14;18) chromosomal translocation.  However, constitutive expression of anti-apoptotic Bcl-2 alone is insufficient for lymphomagenesis and subsequent molecular hits are required.  We explored the role of microRNA (miRNA or miR) in the biology of FL by generating miRNA profiles of enriched sorted grade 1 and 2 FL tumor cells derived from 18 patients compared with enriched germinal center B-cells derived from seven follicular hyperplasia (FH).   Expression levels of 851 human miRs were assayed and 133 miRs were significantly differentially expressed in FL tumor cells.  The expression of 44 miRs in three major groups generated a unique FL signature.   MiRs in group 1 were increased in FL (miR-193-5p, -193b*, -345, -513b, -574-3p, -584, -663, -1287, -1295, and -1471).  Group 2 was increased in the majority of FL cases but showed lower levels of expression in a subset of FL (let-7a, let-7f, miR-7-1*, -9, -9*, -20a, -20b, -30b, -96, -98, -194, -195, -221*, -374a, -451, -454, -502-3p, -532-3p, -574-3p, -664*, -1274a, -1274b, and -1260).  MiR group 3 was decreased in FL (miR-17*, -30a, 33a, 106a*, -141, 202, -205, -222, 301b, -431*, and -570).   Two patterns within FL were detected, largely due to the variable expression of group 2 miRs.  The pattern with higher expression of group 2 miRs was associated with complete response to chemotherapy.   Gene expression analysis of 199 genes related to lymphoma and tumor development performed in tandem indicated differential expression of 47 genes in FL including increased expression of AKT-1, PRKCE, IL4R, DROSHA, and MAPK1; and decreased expression of CHEK1, RAD51, CDKN1A, SOCS2, KLF4, BLIMP1 and IRF4.  Functional studies provide evidence that miR-20a and -20b target CDKN1A/p21, miR-194 targets SOCS2, and miR-301b targets MAPK1 in FL, affecting cell proliferation and potentially contributing to lymphomagenesis. These findings suggest a role for aberrant miRNA expression in the biology of FL with prognostic and mechanistic implications.

overall_design: miRNA profiling was performed using Agilent miRNA array platform with RNAs isolated from sorted follicular lymphoma B cells and follicular hyperplasia B cells.

first: Meghan

last: Corrigan-Cummins

first: Irina

last: Maric

first: Olga

last: Simakova

first: Sattva

last: Neelapu

first: Larry

last: Kwak

first: John

last: Janik

first: Barry

last: Gause

first: Elaine

last: Jaffe

first: Katherine

last: Calvo


title: Expression analysis of Arabidopsis mpk11 mutant treated with flg22

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

summary: Arabidopsis MPK11 is activated and plays a role in the flg22 sensing. Mitogen-activated protein kinases (MAPKs) mediate cellular signal transduction during stress responses, as well as diverse growth and developmental steps in eukaryotes. Pathogen infection or treatment with conserved pathogen-associated molecular patterns (PAMPs) such as the bacterial flagellin-derived flg22 peptide are known to activate three Arabidopsis thaliana MAPKs, MPK3, MPK4 and MPK6. Several stresses, including flg22 treatment, are known to increase MPK11 expression but activation of MPK11 has not been shown. Here, we show that MPK11 activity can indeed be increased through flg22 elicitation. Expression profiling using a small-scale microarray for defense-related genes revealed that cinnamyl alcohol dehyrogenase 5 (CAD5) requires MPK11 for full flg22-induced expression. An mpk11 mutant showed increased flg22-mediated growth inhibition but no altered susceptibility to Pseudomonas syringae, Botrytis cinerea or Alternaria brassicicola.

overall_design: A 24 DNA microarray study using toral RNA from an Arabidopsis mutant (mpk11 SALK049352) as well as wild type treated with water or flg22.

first: Gerit

last: Bethke

first: Fumiaki

last: Katagiri

first: Justin

last: lee


title: Upregulation of pro-apoptotic microRNA mir-125a following massive small bowel resection in rats

city: Boston

first: Jonathan

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Upregulation of mir-125a suppresses the pro-survival protein Mcl1, producing the increase in apoptosis known to accompany the proliferative changes characteristic of intestinal adaptation. Our data highlight a potential role for microRNAs as mediators of the adaptive process and may facilitate the development of new therapeutic options for short bowel syndrome.

overall_design: Two-condition experiment: resected rat jejunum vs. pooled transected control, with dye-swaps.


title: Comparative Analysis of Seed Transcriptomes of Ambient Ozone-Fumigated Two Different Rice Cultivars

status: Public on May 01 2012

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

summary: High ozone (O3) concentration causes serious damages in plant productivity.  Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses.  With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip.  Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs).  First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment.  Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar.  Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.

overall_design: Comparison between O. sativa L. indica cv. Takanari and japonica cv. Koshihikari grown under ozone for their lifetime was performed. Controls were plants grown under filtered air. Three biological replicates (4 plants in each biologicla rpelicate in each small open top chamber - seed; pooled) were used, and dye-swaped.

first: Kyoungwon

last: Cho

first: Junko

last: Shibato

first: Akihiro

last: Kubo

first: Kouji

last: Satoh

first: Shoshi

last: Kikuchi

first: Ganesh

middle: K

last: Agrawal

first: Randeep

last: Rakwal


title: Effects of eyestalk ablation on the gene expression levels in female black tiger shrimp broodstock (Penaeus monodon)

status: Public on May 02 2012

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

institute: BIOTEC

summary: Comparisons of gene expression profiles between ovaries of before (day 0) and after eyestalk ablation (days 1, 4 and 7) of domesticated 14-month-old black tiger shrimp (Penaeus monodon) were made using a cDNA microarray.  Differentially expressed genes were identified through the microarray analysis, and the microarray results were confirmed by real-time PCR.  Selected genes were further characterized.

overall_design: A cDNA microarray consisting of 5,568 features was constructed from EST libraries of P. monodon. RNA samples were extracted from the ovaries of before (day 0) and after eyestalk ablation at days 1, 4 and 7 from shrimp from the Shrimp Genetic Improvement Center, Thailand. The RNA was converted into cDNA by indirect aminoallyl-cDNA labelling method (LabelStar Array, Qiagen). aa-cDNA from day 0 samples were coupled with Cy3 dye as a reference,  and those from days 1, 4 and 7 were coupled with Cy5 dye.

first: Umaporn

last: Uawisetwathana

first: Rungnapa

last: Leelatanawit

first: Amornpan

last: Klanchui

first: Sirawut

last: Klinbunga

first: Nitsara

last: Karoonuthaisiri


title: MiRNA expression in chronic lymphocytic leukemia

city: Heidelberg

first: Valentina

last: Kovaleva

address: INF 280

department: B060, Molecular Genetics

country: Germany

institute: DKFZ

summary: MiRNA expression is known to be deregulated in chronic lymphocytic leukemia (CLL). To get insight into miRNA expression pattern in CLL, we compaired miRNA expression profiling of peripheral blood-derived CLL cells and the healthy donor, peripheral blood-derived B-lymphocytes. A set of differentially expressed miRNAs was revealed.

overall_design: MiRNA expression profiling was performed on 18 CLL samples and one sample, which is a pool of 5 RNA samples of healthy donor peripheral blood-derived B-lymphocytes

first: Kovaleva

last: Valentina

first: Seiffert

last: Martina

first: Pscherer

last: Armin

first: Lichter

last: Peter

first: Stilgenbauer

last: Stephan

first: Döhner

last: Hartmut


title: Responses of tobacco BY-2 cells to boron deprivation

city: Kyoto

first: Masaru

last: Kobayashi

state: Kyoto

address: Kitasirakawa Oiwakecho, Sakyo

department: Graduate School of Agriculture

institute: Kyoto University

summary: Boron (B) is an essential micronutrient for vascular plants. Boron works to build the cell wall structure by forming borate ester cross-links with pectin, and the deficiency of this element brings about oxidative damage and cell death. However, the process via which B deficiency leads to such serious damage has not been well understood. We investigated the temporal changes in metabolism of B-deprived cultured tobacco (Nicotiana tabacum) BY-2 cells by analyzing their gene expression using cDNA microarray.

sample_organism:
Nicotiana tabacum
synthetic construct

overall_design: Three-day-old cells were deprived of B by washing with and transferred to B-free growth media ("-B" cells). Cells similarly treated with standard growth media were employed as a control for the effects of mechanical stress ("+B cells"). Cells were sampled at 1, 3, 6, 12 and 36 h after transfer to the B-free or standard media. Cells without washing treatment were also included in the analysis ("before-treatment cells"). Two independent sets of samples were analyzed (replicate 1 and 2).

first: Taichi

last: Koshiba

first: Ken

last: Matsuoka

first: Toru

last: Fujiwara

last: Matoh


title: Free fatty acids and TNF-alpha in HepG2 cell culture

city: East Lansing

first: Xuewei

last: Wang

address: 2527 Engineering building, Michigan State University

institute: Michigan State University

summary: The regulation of complex cellular activities in palmitate treated HepG2 cells, and the ensuing cytotoxic phenotype, involves cooperative interactions between genes. While previous approaches have largely focused on identifying individual target genes, elucidating interacting genes has thus far remained elusive. We applied the concept of information synergy to reconstruct a ?gene-cooperativity? network for palmititate-induced cytotoxicity in liver cells. Our approach integrated gene expression data with metabolic profiles to select a subset of genes for network reconstruction. Subsequent analysis of the network revealed insulin signaling as the most significantly enriched pathway, and desmoplakin (DSP) as its top neighbor. We determined that palmitate significantly reduces DSP expression, and treatment with insulin restores the lost expression of DSP. Insulin resistance is a common pathological feature of fatty liver and related ailments, whereas loss of DSP has been noted in liver carcinoma. Reduced DSP expression can lead to loss of cell-cell adhesion via desmosomes, and disrupt the keratin intermediate filament network. Our findings suggest that DSP expression may be perturbed by palmitate and, along with insulin resistance, may play a role in palmitate induced cytotoxicity, and serve as potential targets for further studies on non-alcoholic fatty liver disease (NAFLD).

overall_design:
free fatty acids(palmitate, oleate, linoleate) 0.7mM and tnf-alpha (0 20,100 ng/ml) were subjected to HepG2 cell line to study the cytotoxicity induced by these two factors.
control(Hepg2 medium and BSA medium)
treatment(combinations of TNFa+FFAs)
two biological replicates for each condition, color swap for each sample

first: Christina

last: Chan

first: Aritro

last: Nath


title: Differential gene expression analysis of MAT1-1 and MAT1-2 strains in Aspergillus oryzae

status: Public on Apr 30 2012

city: Bunkyo-ku

first: Ryuta

last: Wada

state: Tokyo

address: 1-1-1 Yayoi

department: Biotechnology

institute: University of Tokyo

summary:
The potential for sexual reproduction in Aspergillus oryzae was assessed by investigating the presence and functionality of MAT genes. Previous genome studies had identified a MAT1-1 gene in the RIB40 reference strain. We now report the existence of a complimentary MAT1-2 gene and sequencing of an idiomorph region from A. oryzae strain AO6. This allowed the development of a PCR diagnostic assay, which detected isolates of MAT1-1 and MAT1-2 genotype among 180 strains assayed including industrial tane-koji isolates. Strains used for sake and miso production showed a near 1:1 ratio of MAT1-1 and MAT1-2 mating-types, whereas strains used for soy sauce production showed a significant bias towards the MAT1-2 mating type.
MAT1-1 and MAT1-2 isogenic strains were then created by genetic manipulation of the resident idiomorph, and comparisons were made of gene expression by DNA microarray and RT-PCR methodologies under conditions when MAT genes were expressed. 33 genes were found to be up-regulated greater than 10-fold in either the MAT1-1 host or MAT1-2 gene replacement strains relative to each other, showing that both MAT1-1 and MAT1-2 genes functionally regulate gene expression in A. oryzae in a mating-type dependent manner, the first such report from a supposedly asexual fungus. MAT1-1 expression specifically up-regulated an a-pheromone precursor gene, but most genes affected were of unknown function. Results are consistent with a heterothallic breeding system in A. oryzae, and prospects for the discovery of a sexual cycle are discussed.

overall_design: On a condition that induces mating-type genes descrived in growth protocol section, each cogenic MAT1-1 and MAT1-2 mating-type strains were processed into RNA extraction and hybridization on Affymetrix microarrays. In a speculation that genes involved in putative mating process were reguated in mating-type dependent manner, we designed the cogenic strains that differs only in mating-type gene locus to analyze differential gene expression of MAT1-1 vs MAT1-2 strains.

first: Jun-ichi

last: Maruyama

first: Haruka

last: Yamaguchi

first: Nanase

last: Yamamoto

first: Yutaka

last: Wagu

first: Matthieu

last: Paoletti

first: David

middle: B

last: Archer

first: Paul

middle: S

last: Dyer

first: Katsuhiko

last: Kitamoto


title: Dermatan sulfate is involved in the tumorigenic properties of Esophagus Squamous Cell Carcinoma

city: Lund

first: Anna

middle: Isinger

last: Ekstrand

address: Barngatan 2b

department: Oncology

institute: Clinical Sciences

summary: Extracellular matrix, either produced by cancer cells or by cancer-associated fibroblasts, influences angiogenesis, invasion and metastasis. Chondroitin/dermatan sulfate (CS/DS) proteoglycans, which occur both in the matrix and at the cell surface, play important roles in these processes. The unique feature that distinguishes DS from CS is the presence of iduronic acid (IdoA) in DS.  The main IdoA-producing enzyme, DS epimerase 1 (DS-epi1) was highly up-regulated in ESCC biopsies. To further understand the roles of IdoA in tumor development, DS-epi1 expression, and consequently IdoA content, was downregulated in ESCC cells. IdoA-deficient cells exhibited decreased migration and invasion capabilities in vitro, which was associated with reduced cellular binding of hepatocyte growth factor, inhibition of pERK-1/2 signaling, and de-regulated actin cytoskeleton dynamics and focal adhesion formation. Our findings demonstrate that IdoA in DS influences tumorigenesis by affecting cancer cell behavior.

overall_design: Gene expression data including 10 Esophageal squamous carcinoma specimens and 27 gastroesophageal adenocarcinoma specimens.


title: 5-azacytidine resistance: THP-1 control vs. THP-1 resistant cell line(TAR) by CodeLinkTM Human Whole Genome Bioarray.

status: Public on Apr 28 2012

city: Shimotsuke

first: PIYANUCH

last: SRIPAYAP

state: Tochigi

address: 3311-1 Yakushiji

department: Medicine, Division of Hematology

institute: Jichi Medical University

summary: Generated AZA resistant cell line (TAR) and analysis markedly different gene expression levels between THP-1 and TAR.

overall_design: Two condition experiment, THP-1 control vs. AZA resistant cell line.

first: Piyanuch

last: Sripayap

first: Tadashi

last: Nagai

first: Mitsuyo

last: Uesawa

first: Hiroyuki

last: Kobayashi

first: Tomonori

last: Tsukahara

last: Ohmine

first: Kazuo

last: Muroi

first: Keiya

last: Ozawa


title: Identification and characterization of potent, broad-spectrum antifungal compounds using a yeast reporter bioassay.

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

institute: National Research Council of Canada

summary: New antifungal drugs are urgently needed due to the currently limited selection, the emergence of drug resistance, and the toxicity of several commonly used drugs.  To identify drug leads, we screened small molecules using a Saccharomyces reporter bioassay in which the yeast heterologously expresses Hik1, a group III hybrid histidine kinase (HHK) from Magnaporthe grisea.  Group III HHKs are integral in fungal cell physiology, and highly conserved throughout this kingdom; they are absent in mammals, making them an attractive drug target.  Our screen identified compounds 13 and 33, which showed robust activity against numerous fungal genera including Candida, Cryptococcus and molds such as Aspergillus and Rhizopus.  Drug-resistant Candida from patients were also highly susceptible to compounds 13 and 33.  While the compounds do not act directly on HHKs, microarray analysis showed that compound 13 induced transcripts associated with oxidative stress, and compound 33, transcripts linked with heavy metal stress. Both compounds were highly active against Candida biofilm, in vitro and in vivo, and exerted synergy with fluconazole, which was inactive alone. Thus, we identified potent, broad-spectrum antifungal drug leads from a small molecule screen using a high-throughput, yeast reporter bioassay.

overall_design: Two-color experimental design testing the effects of 2 antifungal compounds (13 and 33) after 0, 20, 40 60 min. In the referred publication, the t=20, 40, 60 data was normalized against the t=0 data

first: Brad

last: Tebbets

first: Douglas

last: Stewart

first: Stephanie

last: Lawry

first: Jeniel

last: Nett

last: Andes

first: Bruce

last: Klein


title: Helicobacter pylori pathogenic mechanism

city: guangzhou

first: yang

middle: ze

last: min

address: Panyu university cener

department: Pi-Wei Institute

institute: Guangzhou University of Chinese Medicine

summary:
Helicobacter pylori infection reprograms host gene expression and influences various cellular processes, which have been investigated by cDNA microarray in vitro culture cells and in vivo patients of the chronic abdominal complaint.
In this study，the effects of H. pylori infection on host gene expression in the gastric antral mucosa of patients with chronic gastritis were examined.

overall_design: The gastric antral mucosa was obtained from a total of 6 untreated patients undergoing gastroscopic and pathologic confirmation of chronic superficial gastritis. Three patients infected by H. pylori and 3 patients uninfected were used to cDNA microarray experiment.

first: Chen

last: Wei-Wen

first: Yang

last: Ze-Min

first: Wang

last: Ying-Fang


title: Expression data from mouse lungs during E. coli pneumonia in the presence or absence of LIF neutralization

status: Public on Apr 26 2012

first: Lee

last: Quinton

address: 72 E Concord St

institute: Boston University School of Medicine

summary:
Leukemia inhibitory factor (LIF) is amongst the IL-6 family cytokines expressed in the lungs during pneumonia.  However, the function of endogenous LIF during pneumonia has never been explored.  The purpose of this study was to determine the transcriptional response to pneumonia in the lungs and whether or how this response is influenced by LIF.
Mice received intratracheal instillations of vehicle (PBS) or Escherichia coli (10^6 CFU).  Control IgG or anti-LIF specific IgG was included in the instillate.  24 hours after the challenge, lungs were collected for RNA isolation and microarray analysis.

overall_design: RNA from 3 separate groups of mice (3 mice per group) was analyzed: 1) 24h Vehicle/control IgG-treated; 2) 24h E. coli/control IgG-treated; and 3) 24h E. coli/anti-LIF-specific IgG.


title: Psip1 ChIP using A300-847 antibody (Immunoprecipitates  mainly p52 isoform of Psip1) Chip-chip from Mouse MEFs cells with H3K36me3, H3K4me3, Psip1 ChIP using A300-847 antibody

status: Public on Apr 12 2012

city: London

first: Pradeepa

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London

summary:
The p52 isoform of Psip1/Ledgf links histone H3K36 methylation and the regulation of alternative splicing.
Chromatin immunoprecipitation (ChIP) of Psip1 together with H3K36me3 and H3K4me3 and by ChIP-on-chip analysis demonstrated that, Like H3K36me3, Psip1 is enriched on exons of highly expressed genes,

overall_design: Comparision of H3K36me3 and Psip1 binding sites on the expressed and non expressed genes.

last: Marulasiddappa

first: Graeme

middle: R

last: Grimes

first: Wendy

middle: A

last: Bickmore


title: Gene array analysis of Human Umbilical Vein Endothelial Cells (HUVEC) transduced with lentivirus containing cDNA of NKX2,5 or GATA4 or GFP.

status: Public on Apr 21 2012

city: paris

first: isabelle

middle: catherine

last: vigon

address: 22 rue Méchain

institute: Institut Cochin, inserm u1016, cnrs umr8104, Université Paris-Descarte

summary: The aim of this study was to induce cardiomyogenic conversion of Human Umbilical Vein Endothelial Cells (HUVEC ) by triggering ectopic expression of the cardiac transcription factors Nkx2.5 and GATA4. Cells were cultured without cell myocardial co-culture system and transduced  with lentivirus containing coding sequence of Nkx2.5, GATA4 or GFP as control. Cells were cultured in the EBM-2/ EGM-2 medium, 12 days before microarray analysis.   We report in this study that over-expression of NKX2.5 and GATA4 in HUVECs stimulates the expression of some specific genes important in the cardiomyogenic differentiation process, leading to partial switch of these cells from the endothelial to the myocardial course.

overall_design: 12 arrays were analysed. Three competitive hybridizations to the arrays were performed in duplicate using each time, two dye-swap following this experimental design:     AWA065 : CY5 (HUVEC+NKX2,5) / CY3 (HUVEC)    AWA067 : CY5 (HUVEC) / CY3 (HUVEC+NKX2,5)    AWA075 :  CY5 (HUVEC+NKX2,5) / CY3 (HUVEC)    AWA076 : CY5 (HUVEC) / CY3 (HUVEC+NKX2,5)    AWA068 : CY5 ((HUVEC) / CY3 (HUVEC+GATA4)    AWA070 : CY5 (HUVEC+GATA4) / CY3 ((HUVEC)    AWA073 : CY5 (HUVEC+GATA4) / CY3 ((HUVEC)    AWA002 : CY5 ((HUVEC) / CY3 (HUVEC+GATA4)    AWA066 : CY5 (HUVEC) / CY3 (HUVEC+NKX2.5+GATA4)    AWA069 : CY5 (HUVEC+NKX2.5+GATA4) / CY3 (HUVEC)    AWA071 :  CY5 (HUVEC+NKX2.5+GATA4) / CY3 (HUVEC)    AWA074 ; CY5 (HUVEC) / CY3 (HUVEC+NKX2.5+GATA4)

first: C

last: Philippe

first: S

last: Tendil

first: V

last: Frouin

first: X

last: Gidrol


title: Using Shewanella baltica ecotypes as a model for transcriptional variation

city: Arlington

first: Sealy

last: Hambright

address: 701 S. Nedderman Dr.

department: Biology

institute: UT Arlington

summary: Assessment of individual whole cell transcriptional variation among closely related bacterial ecotypes

sample_organism:
Shewanella baltica OS155
Shewanella baltica OS195
Shewanella baltica OS185
Shewanella baltica OS223

overall_design: Here we used 4 replicates each containing 3 independent biological replicates as well as dye swaps per each replicate. We hybridized in a two color format but analyzed in a one color format.

first: W

first: J

last: Rodrigues


title: Mouse E15.5 cortices: Snf2l Ex6 deleted mice versus wild type controls

status: Public on Apr 10 2012

city: Ottawa

first: Alan

last: Mears

state: ON

address: 401 Smyth Rd

department: Research Institute

institute: Children's Hospital of Eastern Ontario

summary: Gene expression profiling of mouse cortices in which the experimental strain lacks Exon 6 of the Snf2l gene which encodes an ATP-binding motif that is critical for chromatin re-modeling

overall_design: Comparison of gene expression in E15.5 cortices of Snf2l-Ex6DEL mice versus wild type controls. Two samples of each strain were used, with one pair of samples utilized for two of the replicates (dye-flip), the second pair then used for the third replicate.

first: Darren

last: Yip

first: Chelsea

last: Corcoran

first: Matías

last: Alvarez-Saavedra

first: Adriana

last: DeMaria

first: Stephen

last: Rennick

first: Michael

last: Rudnicki

first: Claude

last: Messier

first: David

last: Picketts


title: Methylated DNA immunoprecipitation (MeDIP) microarray data from IL13-induced allergic airway inflammation of mouse lungs

status: Public on Apr 07 2012

city: Los Angeles

first: Aik

middle: T

last: Ooi

address: 650 Charles E Young Dr S, Factor 9-240

department: Pediatrics

institute: UCLA

summary:
Epigenetic changes have been implicated in pathogenesis of asthma. We sought to determine if IL13, a key cytokine in airway inflammation and remodeling, induced epigenetic DNA methylation changes in the airways in conjunction with its transcriptional gene regulation.
For our studies, we used a well-characterized transgenic mouse model of allergic airway inflammation induced by IL13. In this model, IL13 is conditionally overexpressed in the mouse lung when treated with doxycycline. Upon IL13 induction, these mice showed inflammatory cell infiltration, pronounced emphysema, increased pulmonary compliance, lung volume enlargement, mucus metaplasia, and increased expression of matrix metalloproteinases and cathepsins in the lung. We performed MeDIP microarray to examine the changes in DNA promoter methylation during IL13-induced allergic airway inflammation.

overall_design: The CC10-rtTA-IL13 transgenic (TG) and wildtype (WT) mice were treated with doxycycline for seven days. Mice were euthanized and the left lower lobes from all mice were removed for DNA extraction followed by MeDIP array analysis.

first: Sonal

last: Ram

last: Kuo

first: Derek

middle: W

last: Nickerson

first: Jennifer

middle: L

last: Gilbert

first: Weihong

last: Yan

first: Matteo

last: Pellegrini

first: Talal

last: Chatila

first: Brigitte

middle: N

last: Gomperts


title: Genome-wide survey of large rare copy number variations in Alzheimer’s disease   among Caribbean Hispanics

city: Toronto

first: Ekaterina

last: Rogaeva

address: 6 Queen’s Park Crescent West

institute: Tanz Centre for Neurodegenerative Diseases

summary: Recently genome-wide association studies have identified significant association between Alzheimer’s disease and variations in CLU, PICALM, BIN1, CR1, MS4A4/MS4A6E, CD2AP, CD33, EPHA1 and ABCA7. However, the pathogenic variants in these loci have not yet been found. We conducted a genome-wide scan for large copy number variations (CNVs) in a dataset of Caribbean Hispanic origin (554 controls and 559 cases with late-onset Alzheimer’s disease) that was previously investigated in a SNP-based genome-wide association study using Illumina HumanHap 650Y platform. We ran four CNV calling algorithms and analyzed rare large CNVs (>100 Kb) to obtain high-confidence calls that were detected by at least two algorithms. In total, 734 such CNVs were observed in our dataset. Global burden analyses did not reveal significant differences between cases and controls in CNV rate, distribution of deletions or duplications, total or average CNV size; and number of genes affected by CNVs. However, we observed a nominal association between Alzheimer’s disease and a ~470 Kb duplication on chromosome15q11.2 (P=0.037). This duplication, encompassing up to five genes (TUBGCP5, CYFIP1, NIPA2, NIPA1 and WHAMML1) was present in 10 cases (2.6%) and 3 controls (0.8%). The dosage increase of CYFIP1 and NIPA1 genes was further confirmed by quantitative PCR. The current study did not detect CNVs (including common CNVs) that affect novel Alzheimer’s disease loci reported by large genome-wide association studies. However, since the array technology used in our study has limitations in detecting small CNVs, future studies must carefully assess novel AD associated genes for the presence of disease related CNVs.

overall_design: Case-control analysis, screening of large copy number variation in 559 Alzheimer cases and 554 control subjects of Caribbean Hispanic ancestry

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