title: Comparative gene expression analysis upon stimulation of the human BCR or an inducible LMP2A in EBV immortalized lymphoblastoid cell lines

city: Munich

first: Wolfgang

last: Hammerschmidt

address: Marchioninistr. 25

department: Gene Vectors

institute: Helmholtz Zentrum München

summary:
Survival of all B cells depends on signals from the B-cell receptor (BCR). In BCRnegative B cells the latent membrane protein 2A (LMP2A) of Epstein-Barr virus (EBV) replaces this survival signal and might play a role in the development of EBV-positive Hodgkin lymphomas and posttransplantation lymphoproliferative disease. In these BCR-negative cells LMP2A provides a ‘tonic’ signal similar to BCR’s constitutive expression in the absence of antigen in order to maintain activating signaling pathways common to both receptor molecules. In most latently EBV-infected B cells LMP2A and BCR are co-expressed but it is largely unclear what LMP2A contributes with respect to B-cell activation, proliferation and viral latency in these BCR-positive cells. A common model suggests that LMP2A maintains herpesviral latency by blocking BCR-mediated signals but how LMP2A could serve both antithetical ends in BCRnegative and BCR-positive cells is elusive.

Our comparative analysis of BCR and LMP2A now indicates that LMP2A is a true BCR mimic that dominates BCR-operated signaling pathways in EBV-infected, BCR-positive cells to provide activation signals, support stable infections in vivo and allow exit from latency. These findings suggest that LMP2A co-opts the situation in anergic B cells, where continuous BCR signaling results in maintenance of the anergic state accompanied by unresponsiveness to acute BCR stimulation. The microarray experiment was used to compare effects of BCR and LMP2A on gene expression regulation. EBV's LMP2A and the human BCR activate similar cellular target genes; some genes are regulated solely by BCR or LMP2A, no gene is counter regulated

overall_design: A 12 chip study using cDNA from three separate 2525 LMP2A knockout LCL cultures and three separate 3696.10 LMP2A:mCD69 LCL cultures; each culture tested before and after 90 min stimulation of the BCR and LMP2A:mCD69, respectively.

first: Stephanie

last: Medele

first: Christoph

last: Mancao

first: Liudmila

last: Matskova

first: Chris

last: Bauer


title: Validation of a subset of copy number variants from GSE24424 by aCGH

status: Public on Dec 31 2010

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

type: Genome variation profiling by genome tiling array

summary: This dataset was used to validate CNV predictions from GSE24424. We designed a custom CGH array to interrogate a total of 4,420 individual CNVs and their flanks predicted in 17 individuals. On the basis of a test that compares signals of probes located within to those mapping outside of CNVs (two-tailed P<0.05, Mann-Whitney U test), we could confirm about 77% of the tested predictions and thus establish a set of 3,383 validated CNVs. The vast majority of confirmed CNVs (3,299 of 3,383 or 97.5%) show a consistent direction of change between the initial array (GSE24424) and the custom array, suggesting a false-confirmation rate of approximately 5%.

sample_organism:
Mus musculus
Mus spretus

overall_design: We interrogated a total of 4,420 individual CNVs and their flanks predicted in 17 individuals from the GSE24424 dataset by rehybridizing their DNAs on a high-resolution custom CGH array (median probe spacing 350 bp).

middle: N

first: Nicolas

last: Vinckenbosch

first: Evelyne

last: Chaignat

first: Alexandre

last: Reymond


title: Defense mechanisms against herbivory: expression regulation of spruce gene family members representative of the phenylpropanoid pathway

status: Public on Jan 01 2011

city: Vancouver

first: Ilga

last: Porth

address: 2424 Main Mall

country: Canada

institute: University of British Columbia

summary: A 21.8k spruce EST-spotted microarray was utilized to examine the genetic basis of constitutive defenses against herbivory. From twelve-year-old trees originating from partial diallel pedigree that segregates for resistance against Pissodes strobi, bark tissue of apical leaders was harvested at the onset of seasonal growth and natural weevil activity in the field. Our experimental design is based on a priori known genotype. We identified cross 26 from ♀PG87*♂PG165, cross 27 from ♀PG87*♂PG117, cross 29 from ♀PG21*♂PG165 and cross 32 from ♀PG21*♂PG117, respectively, forming a factorial diallel which showed widest segregation, based on a higher number of segregating SNP loci with genotypes significantly different between the most extreme resistance categories. The distant pair design introduced by ({Fu, 2006}) was modified for outbreds and maximized direct comparisons between different alleles at each locus. Our design resulted in 94 hybridisations profiling 48 individuals in cross 26, 36 in cross 27, and 50 in cross 29 as well as 54 individuals in cross 32. One criterion for identifying positional candidate genes involved that any association between trait variation and genotype variation had to be detected within 10 cM map distances; positional candidate genes for the studied phenotypic trait were then identified by strong collocations of transcript abundance variation and overlap of at least 40% of their expression quantitative trait loci (eQTLs) with phenotypic trait QTLs. 10,000 randomizations were run (p < 0.05).

overall_design: The experimental design optimized genetic distances between probe pairs on 94 two-color microarrays to profile 188 interior spruce F1-hybrids, independently grown and harvested.

first: Bjoern

last: Hamberger

first: Claire

last: Cullis

first: Susan

last: Findlay

first: Gillian

last: Leung

first: Michelle

last: Tang

first: Carol

last: Ritland

first: Richard

last: White

first: Kermit


title: High Frequency of CNV Mutations in Combined Schizophrenia and Epilepsy

city: Houston

first: April

middle: Burant

last: Hall

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

summary: Agilent custom designed array comparative genomic hybridization (CGH) was performed on 235 samples with a dual diagnosis of schizophrenia and epilepsy and 80 samples with a dual diagnosis of bipolar and epilpsy. ArrayCGH on 191 psychiatric screened controls was also performed. A common male reference was used for all samples and controls. Samples and controls were obtained from the NIMH cell line repositories.

overall_design: 235 samples with a dual diagnosis of schizophrenia and epilepsy,  80 samples with a dual diagnosis of bipolar and epilepsy, and 191 psychiatric screened controls

first: Arthur

last: Beaudet

last: Burant-Hall

first: Larissa

last: Stewart


title: Gene Expression Profiling of Three Tissues in Chicken with Heat Stress by Affymetrix Microarray

city: Guang- zhou

first: song

middle: xiao

last: yan

state: Guang -dong

address: wu shan

country: China

institute: South China Agricultural University

summary:
Heat stress is a very complex physiological process. At present, there are some reports about physiological function and pathological changed on chicken heat stress.
We use DNA microarrays to detail the global programme of gene expression underlying heat stress and identified distinct classes of differentially expressed (DE) genes during this process.

overall_design: Chicken were randomly divided into two groups to study the effects of heat stress on gene expression of brain, liver and leg muscle. Twenty-four birds (12 male and 12 female) were allocated to heat stress or post-heat stress group（40±1°C,3h） and control or pre-heat stress group（28±1°C）.

first: Xiao

middle: Y

last: Song

first: Qing

middle: B

last: Luo

first: Xi

middle: Q

last: Zhang


title: Differential expression of miRNA in control and CD3/CD28mAb-treated Jurkat cells

city: Xi'an

first: An-Gang

last: Yang

address: No.17,Changle West Road

institute: Fourth Military Medical University

summary: The cultured cell line Jurkat is frequently employed in studies of T cell function. Here we identified the microRNAs expressed in Jurkat cells in the presence and absence of CD3/CD28mAb treatment.

overall_design: Analyzed the expression of microRNAs extracted from untreated Jurkat cells as a control and Jurkat cells treated with CD3/CD28mAb.

first: Qian

last: Xue

first: Tao

last: Wang

first: Wei-Hong

last: Wen


title: Genome wide BZR1 binding site analysis in Arabidopsis

city: Stanford

first: Yu

last: Sun

state: CA

address: 260 panama street

department: plant biology

institute: Carnegie Institution of Washington

type: Genome binding/occupancy profiling by genome tiling array

summary: BR induces rapid dephosphorylation and nuclear localization of BZR1 through a cascade of signaling events thus regulates BR-responsive gene expression and plant development.  We use chromatin-immunoprecipitation microarray (ChIP-chip) experiments identified about 2200 high confidence BZR1 binding sites, which includes all previous known binding regions.  The binding sites are distributed throughout the genome but are rare in the centromere regions, which is similar to the distribution of expressed genes. The binding sites were substantially enriched in the 5’ and 3’ intergenic regions compared to the transcribed regions of genes. Combining with transcription profilling of BR regulated genes generated 953 BR regulated BZR1 targets.

overall_design: BZR1 promoter directed BZR1-CFP transgenic tissue precipitated with YFP antibody vs. wildtype tissue precipitated with GFP antibody.

first: Kun

last: He

first: Zhiyong


title: Gene expression of lipid metabolism-related genes correlated with milk fatty acids in dairy cows

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

country: France

institute: INRA

summary:
The aim of the present study was to correlate lipid metabolism genes in the mammary gland tissue affected by stage of lactation and nutrition to the resulting milk fatty acids composition in grazing dairy cows, and to classify milk fatty acid (FA) groups based on variations in lipid metabolism gene expression patterns.
Identifying the relationship between lipid metabolism genes in the mammary gland tissue and the resulting milk fatty acid composition is expected to greatly contribute to our understanding of milk fatty acid metabolism and to enhance opportunities to improve milk fat composition through nutrition. In fact, SNCA, SCD5, and PNPLA2 lipid metabolism-related genes affected by unsaturated fatty acids supplementation, were found to strongly correlated to different milk FA groups, but also contributed most to the classification of these FA groups, suggesting a significant role in mediating the lipid metabolism in the mammary gland tissue and determining the milk fatty acids composition.

overall_design: A total of 28 Holstein-Friesian dairy cows in mid-lactation were blocked according to parity (2.4 ± 0.63 years), days in milk (DIM; 153 ± 32.8 days), milk yield (25.7 ± 3.08 kg/d) and fat content (4.3 ± 0.12%). Cows were then randomly assigned to four UFA-sources based on rapeseed, soybean, linseed or a mixture of the three oils for 23 days (Period I) after which, all 28 cows were switched to a control diet for an additional 28 days (Period II). On the last day of both periods, mammary gland biopsies were taken to study genome-wide differences in lipid metabolism gene expression.

first: Jurgen

last: van Baal

first: Leo

last: Kruijt

first: Mari

last: Smits


title: AFP1 kO: Expression profiling analysis of embryonic and adult liver

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

summary:
The alpha-fetoprotein (AFP) gene is a member of the albumin gene family and encodes a serum glycoprotein with an onco-fetal pattern of expression. AFP is produced in high concentrations during embryonic life by the hepatocytes and the visceral endoderm of the yolk sac and to a lesser extent by the developing gastrointestinal tract and kidney. Alpha-fetoprotein is the major serum fetal protein in mammals, with a concentration that reaches the order of several mg/ml.  Its synthesis decreases dramatically shortly after birth to reach only trace amounts a few weeks later but can be restored during life when liver pathologies or some types of tumors develop (hepatitis, cirrhosis, hepatoma, teratocarcinoma, and some pancreatic and renal tumors). AFP is then mainly expressed by the adult liver.

AFP produced by the embryo is secreted in the amniotic fluid and is able to cross the placental barrier to reach the maternal blood circulation, where its titer is used as a diagnostic marker to reveal developmental anomalies of the fetus. Abnormally high levels of AFP in the maternal serum indicates elevated risk for neural tube defects of the fetus such as spina bifida or anencephaly, whereas abnormally low levels indicates elevated risk for a Down’s syndrome. Measurements of the AFP levels in the maternal serum are undertaken at 14-22 weeks of each pregnancy and are part, along with unconjugated estradiol, human chorionic gonadotropin and inhibin A, of the quadruple test for antenatal Down’s syndrome screening. Abnormal AFP levels can also be indicative of other fetal pathologies. The reason why these pathologies induce abnormal levels of AFP is still not known.
Homozygous Afp knock-out females (AFP KO) are sterile, due to anovulation. Ovaries contain mature follicles and are functional, but lack a proper signal from the hypothalamic-pituitarian axis (HPG) in order to ovulate.
The expression profile of several genes in the HPG is impaired.
Furthermore, AFP KO females are masculinized and defeminized. They exhibit a loss of female sexual behaviour (no lordosis) and a male pattern of tyrosine hydroxylase expressing neurons distribution in some sexual dimorphic areas of the brain.
The phenotype of those mice is a consequence of an estrogen overexposure of their brains during the perinatal period. This phenotype can be reversed if these mice develop in an embryonic environment strongly reduced in estrogens. Homozygous AFP KO mice that developed in those conditions are fertile in adulthood (no further treatment needed), and exhibit proper sexual behaviour.

overall_design: cDNA microarray analysis of embryonic and adult liver tissue of AFP1 kO mice. Single mutant mice were analysed versus a pool of wt RNA in two technical replicates (only for adult tissue) including a dye swap experiment. In total 6 adult mutant male mice and 6 embryos (3 male and 3 female) were analysed

first: Johannes

last: Beckers

first: Marion

last: Horsch

first: Christelle

last: de Mees


title: Expression profiling analysis of NOX4 mutant mouse model

summary: NADPH oxidases are the only know enzyme family that has reactive oxygen species (ROS, e.g. superoxide and hydrogen peroxide) as their main metabolic product. They are therefore a prima candidate gene family to define a molecular source for ROS in physiology and pathophysiology. The type 4 NADPH oxidase (NOX4) is the most abundant isoform with the highest basal expression levels.The Nox4 knockout mouse was designed using a cre/lox recombination technique which allows to create either constitutive (type III recombination) and conditional (type I recombination) knockout alleles.

overall_design: cDNA microarray experiments of brain, kidney, muscle and pancreas of four male mutant mice versus a RNA pool of four male wild type mice. For each animal two technical replicates were performed including a dye swap experiment. All animals with the same age of 17 weeks on a C57BL/6 background.


title: Gene expression profile of peripheral blood mononuclear cells in the X-linked alpha thalassemia mental retardation (ATRX) syndrome

city: Catania

first: Vincenza

last: Barresi

address: V.le A Doria, 6

country: Italy

institute: University of Catania

summary: ATRX is a severe X-linked disorder characterized by mental retardation, facial dysmorphism, urogenital abnormalities and alpha-thalassemia. The disease is caused by mutations in ATRX gene, which encodes a protein belonging to the SWI/SNF DNA helicase family, a group of proteins involved in the regulation of gene transcription at the chromatin level. In order to identify specific genes involved in the pathogenesis of the disease, we compared, by cDNA microarray, the expression levels of approximately 8500 transcripts between ATRX and normal males of comparable age.

overall_design: The analysis has been performed on pooled RNA extracted by Peripheral blood mononuclear cell  pellet of three male ATRX patients in comparison to that obtained from a pool of 42 normal males (age 7.6+ 2.4).

first: Daniele

middle: F

last: Condorelli


title: Gene expression profiling in Salmonella Typhimurium encountered with heterophils

city: College Station

first: Huaijun

last: Zhou

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

summary: To study the pathogenicity of Salmonella Typhimurium (ST) in heterophils, a whole Salmonella genome array was used to analyze RNA isolated from Salmonella in vitro encountered with heterophils (30 min, 1 h, 2 h, and 3 h) or medium control (NS). Dual-color, direct comparisons were carried out between heterophils-encountered ST and non-encountered controls (30 min vs. NS (30M/NS), 1 h vs. NS (1HR/NS), 2 h vs. NS (2HR/NS) and 3 h vs. NS (3HR/NS)). Each comparison includes four biological replicates. Out of 4588 genes on an array, there were 605, 758, 944 and 945 genes differentially expressed in the comparisons of 30M/NS, 1HR/NS, 2HR/NS and 3HR/NS, respectively (P < 0.001, fold-change > 2). Most of the Salmonella genes associated with invasion function were found differentially expressed at 2HR/NS and 3HR/NS comparisons. These candidate genes include TypeIII-secreted protein effector sopE2, Invasion proteins (e.g. invA, invE, invG, invH), and Invasion genes tranction activator hilA. The results of continuous transcriptional changes provide important information to elucidate the pathogenicity of ST in heterophils.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Dual-color, common reference comparisons were carried out between heterophils-encountered ST and non-encountered controls (30 min vs. NS (30M/NS), 1 h vs. NS (1HR/NS), 2 h vs. NS (2HR/NS) and 3 h vs. NS (3HR/NS)). Four biological replicates, with dye swap labeling, were included in each of comparisons. Background subtracted signal intensity were collected from 16 arrays and normalized before data analysis.

first: Hsin-I

last: Chiang

first: Christina

middle: L

last: Swaggerty

first: Michael

middle: H

last: Kogut

first: Scot

middle: E

last: Dowd


title: Responsiveness of a premetamorphic Xenopus tadpole brain to hydroxylated PCBs

city: Shizuoka

first: Akinori

last: Ishihara

country: Japan

institute: Shizuoka University

summary: Hydroxylated polychlorinated biphenyls are the metabolites produced from polychlorinated biphenyls (PCBs) by drug-metabolizing enzyme cytochrome P450 1A1. These compounds are bound to transthyretin, a major plasma thyroid hormone-binding protein in amphibian tadpoles. The compounds-transthyretin complexes are transferred into the brain across the blood brain barrier in mammals. Thus these compounds are suspected to disrupt neural development in brain. We studied about the effects of hydroxylated PCBs on the thyroid system in brain using metamorphosing tadpoles of African clawed toad, Xenopus laevis. The metamorphosis assay revealed that these compounds had inhibitory effects on the thyroid hormone-induced metamorphosis. This in vivo assay was a powerful tool to detect thyroid-disrupting activities, because we were not able to detect the inhibitory effects of these compounds using thyroid hormone-responsive reporter gene assay in a cultured Xenopus cell line. A genome-wide gene expression analysis in brain following short-term exposure to these compounds demonstrated that the delay of metamorphosis and the morphological thyroid-disrupting changes could be caused partially by disruption of the thyroid hormone-induced gene expression by hydroxylated PCBs. Furthermore, we associated functional ontology terms with the transcripts whose expression were altered by thyroid hormone alone, or thyroid hormone and hydroxylated PCBs. We suggested that these approachs using a technique of bioinformatics revealed molecular mechanism of thyroid-disrupting activities in vivo.

overall_design:
Thyroid hormones induce amphibian metamorphosis and alter a lot of thyroid hormone-responsive gene expression. We studied about the effects of hydroxylated PCBs on TH-induced gene expression.
Premetamorphic tadpoles were treated with 500 nM hydroxylated PCBs in the presence of 1 nM thyroid hormone for 4 days. After exposure period total RNA was extracted from brain. Study included at least three replicate of each treatment.

first: Kiyoshi

last: Yamauchi


title: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: CGH

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

summary: This study was undertaken to identify novel tumour suppressor genes in lung adenocarcinoma.  EYA4, located at 6q23.2 was identified as a frequently lost and hypermethylated gene in the analyzed samples.

overall_design: 7 Breast cancer cell lines profiled on the SMRTr array in conjunction with matched DNA methylation data, allelic status and gene expression data for integrative analysis.

first: R

first: B

middle: P

last: Coe

first: E

middle: A

last: Vucic

first: W

middle: W

last: Lockwood

last: Lam


title: Heterologous expression analysis of wild type Fusarium fujikuroi and Ffvel1deletion strains grown under nitrogen-limiting conditions in liquid media over time.

city: Peoria

first: Daren

middle: W.

last: Brown

state: IL

address: 1815 N. University St.

department: Bacterial Foodborn Pathogens and Mycology Research

institute: USDA-ARS

summary:
Investigation of whole genome gene expression level differences of Fusarium fujikuroi between wild-type and a Ffvel1 (velvet) deletion mutant in liquid medium with minimal nitrogen between 24 hr, 72 hr and 120 hr of growth using an array based on a F. verticillioides gene call set.
Fusarium fujikuroi produces a number of secondary metabolites including gibberellins, bikaverin, fumonisin and fusarin C that are influenced by nitrogen availability and the velvet global regulatory complex.

overall_design: A twelve chip study using total RNA recovered from six cultures of wild-type Fusarium fujikuroi and six cultures of Ffvel1  F. fujikuroi deletion mutant.  Each chip measures the expression level of over 13,000 putative genes with twelve 60-mer probes per sequence.

first: D


title: Convergence of KSHV Reactivation with EBV latency and cellular growth mediated by the Notch signaling pathway in co-infected cells.

city: Newark

first: David

middle: M.

last: Lukac

state: NJ

address: 225 Warren St.; ICPH E350C; PO Box 1709

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers Univ./NJ Medical School

summary: Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiologic agent of primary effusion lymphoma (PEL).  All PEL cell lines are infected with KSHV, and 70% are co-infected with Epstein-Barr Virus (EBV). KSHV reactivation from latency requires promoter-specific transactivation by the KSHV Rta protein through interactions with RBP-Jk (CSL), the cellular DNA binding component of the Notch signal transduction pathway.  EBV transformation of primary B cells requires EBV nuclear antigen (EBNA)-2 to interact with RBP-Jk to direct the latent viral and cellular gene expression program.  Although KSHV Rta and EBV EBNA-2 both require RBP-Jk for transactivation, previous studies have suggested that RBP-Jk-dependent transactivators do not function identically.  We have found that the EBV latent protein LMP-1 is expressed in less than 5% of KSHV+/EBV+ PEL cells, but is induced in an Rta-dependent fashion when KSHV reactivates.   KSHV Rta transactivates the EBV latency promoters in an RBP-Jk-dependent fashion and forms a ternary complex with RBP-Jk on the promoters. In B cells that are conditionally transformed by EBV alone, we show that KSHV Rta complements a short-term EBNA2 growth deficiency in an autocrine/paracrine manner.  Complementaton of EBNA2-deficiency by Rta depends on RBP-Jk and LMP-1, and Rta transactivation is required for optimal growth of KSHV+/EBV+ PEL lines.  Our data suggest that Rta can contribute to EBV-driven cellular growth by transactivating RBP-Jk-dependent EBV latency genes.  However, our data also suggest that EBNA2 and Rta induce distinct alterations in the cellular proteomes that contribute to growth of infected cells.

overall_design: EREB2-5 cells were transfected and grown in the presence or absence of β-estradiol, as described. Seven days post-transfection, protein extracts were prepared, and 200 ugs. of each were analyzed using the RayBio Human Apoptosis Antibody Array Kit (RayBiotech) as per manufacturers suggestions.  The membranes were exposed to autoradiography film for different times to detect the chemiluminescent signals.  Images with signals in linear range were quantitated using the program ImageJ [59].  For each membrane, signals from the negative control spots were averaged, and then subtracted from each of the other spots.  A signal was considered valid if its value exceeded both its average local background, and the average of all valid negative control values.  Valid signals were normalized using the positive control spots (for cellular BID protein).  Fold change in signals for each spot were quantitated by dividing by the valid signals for each corresponding spot on the minus β-estradiol membrane.  Average fold change, and standard deviation, were calculated for each protein.

first: Sophia

last: Spadavecchia

first: Kyla

last: Driscoll Carroll

first: Diana

last: Palmeri

middle: M


title: Gene expression profile of HLRCC associated renal cell cancer

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

summary: Gene expression profiles of normal kidney (3 technical replicates) and a renal tumor (3 technical replicates) from a hereditary leiomyomatosis and renal cell cancer (HLRCC) patient carrying a germline mutation in the fumarate hydratase (FH) gene.

overall_design: Tumor and normal tissue from one patient, both in 3 techincal replicates.

first: Lauri

last: Aaltonen

first: Heli

middle: J

last: Lehtonen

first: Virpi

last: Launonen


title: Pacific salmon gill samples: fate tracking at spawning grounds

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

summary: The long-term viability of Pacific salmon stocks and the fisheries they support are threatened if large numbers die prematurely en-route to spawning grounds. Physiological profiles that were correlated with the fate of wild sockeye salmon during river migration were discovered using functional genomics studies on biopsied tissues.  Three independent biotelemetry studies tracked the biopsied fish after tagging in the marine environment over 200 km from the Fraser River, in the lower river 69 km from the river mouth and at the spawning grounds. Salmon carrying the poor performance (unhealthy) profile in the ocean exhibited a 4-times lower probability of arriving to spawning grounds than those with a healthy genomic signature, although generally migrated into the river and to the spawning grounds faster.  A related unhealthy signature observed in the river was associated with a 30% reduction in survival to spawning grounds in one of the three stocks tested.  At spawning grounds, the same poor performance signature was associated with twice the pre-spawning mortality compared with healthy fish.  Functional analysis revealed that the unhealthy signature, which intensified during migration to spawning grounds, was consistent with an intracellular pathogenic infection, likely a virus.  These results are the first to suggest a pathogen present in salmon in the marine environment could be a major source of mortality during migration and spawning in the river. This series are gill expression profiles from the study of fish at the Weaver creek spawning grounds, and were observed for pre-spawning mortality or successful spawning.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Weaver creek sockeye salmon (a late-run stock) spawn in an artificial spawning channel which has a controlled entrance and no exit, situated 100 km from the ocan. Females were dip-netted out of the entrance of the spawning channel, and placed into a sampling trough with flowing ambient water for the gill biopsy procedure and tagged with Petersen discs and returned to the spawning channel. Moribund fish were recovered daily and their gonads examined to assess whether they had spawned or not. Gene expression was assayed on the GRASP salmonid 32K cDNA microarray.

first: Pau

last: l Pavlidis

first: Louise

last: Donnison

first: Kristi

last: Miller-Saunders


title: RUNX1 mutated cases in acute myeloid leukemia share a distinct biological subgroup and are associated with inferior outcome. Results of the AML Study Group (AMLSG).

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

summary:
PURPOSE: To evaluate frequency, biological features and clinical relevance of RUNX1 mutations in acute myeloid leukemia (AML).
PATIENTS AND METHODS: Diagnostic samples from 945 patients (18 to 60 years) were analyzed for RUNX1 mutations. In a subset of cases (n=269) microarray gene expression analysis was performed.
RESULTS: Fifty-nine RUNX1 mutations were identified in 53 of 945 (5.6%) cases, predominantly in exons 3 (n=11), 4 (n=10) and 8 (n=23). RUNX1 mutations clustered in the intermediate-risk cytogenetic group (46/640, 7.2%; cytogenetically normal, 34/538, 6.3%), they were less frequent in adverse-risk cytogenetics (5/109, 4.6%), and absent in core-binding-factor AML (0/77) and acute promyelocytic leukemia (0/61); RUNX1 mutations were associated with MLL-partial tandem duplications (p=0.0007) and IDH1/IDH2 mutations (p=0.03), inversely correlated with NPM1 (p<0.0001) and in trend with CEBPA (p=0.10) mutations. RUNX1 mutations were characterized by a distinct gene expression pattern; this RUNX1 mutation-derived signature was not exclusive for the mutation, but also included mostly adverse-risk AML [eg, 7q-, -7, inv(3) or t(3;3)]. RUNX1 mutations predicted for resistance to chemotherapy (rates of refractory disease 30% and 19%, p=0.047, for RUNX1-mutated and wildtype patients, respectively), as well as inferior event-free survival (EFS; p<0.0001), relapse-free survival (RFS, p=0.022), and overall survival (p=0.051). In multivariable analysis, RUNX1 mutations were an independent prognostic marker for shorter EFS (p=0.007). Explorative subgroup analysis revealed that allogeneic hematopoietic stem cell transplantation had a favorable impact on RFS in RUNX1-mutated patients (p<0.0001).
CONCLUSION: AML with RUNX1 mutations exhibit distinct biological properties and are associated with resistance to therapy and inferior outcome.

overall_design:
A total of 269 RNA samples derived from adult AML patients were provided by the German Austrian AML Study Group (AMLSG) [AMLSG trial AML HD98A (ClinicalTrials.gov Identifier: NCT00146120)].
Conventional cytogenetic banding, and FLT3, CEBPA and NPM1 mutational analysis were performed as previously described (Schlenk et al., N Engl J Med 2008). Detailed clinical, cytogenetic and molecular cytogenetic information are also provided in the supplementary information.
Following enrichment, all samples contained at least 80% leukemic cells. Gene expression profiling (GEP) was performed as previously described (Bullinger et al., N Engl J Med 2004).


title: Effect of expression of M.HpyAVIB, a C5 cytosine methyltransferase on the E. coli BL21 (DE3) transcriptome

status: Public on Dec 29 2010

city: BANGALORE

first: RITESH

last: KUMAR

address: DEPARTMENT OF BIOCHEMISTRY, INDIAN INSTITUTE OF SCIENCE

country: India

institute: INDIAN INSTITUTE OF SCIENCE

summary:
Helicobacter pylori genome is rich in restriction - modification (R-M) systems. Around 4 % of the genome codes for components of R-M systems.
hpyAVIBM, which codes for a putative phase-variable C5 - cytosine methyltransferase (MTase) from H. pylori lacks a cognate restriction enzyme.

overall_design: To analysis the effect of expression of hpyAVIBM on the E. coli transcriptome, microarray analysis was done with the cells expressing  wild type MTase with the cells expressing catalytic inactive mutant of the MTase.

first: Ritesh

last: Kumar

middle: N

last: Rao


title: Characterization of a Medicago truncatula P450 monooxygenase mutant

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

summary: The aim of the experiment was to characterise a P450 monooxygenase mutant involved in the biosynthetic pathway of haemolytic saponins. Saponins are a group of glycosidic compounds with an antimicrobial function. The gene CYP716A12 is responsible for an early step in saponin biosythesis. Transcriptome analysis of a CYP716A12 mutant was performed to investigate its function.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 6 samples were used in the experiment: 3 biological replicates of CYP716A12 mutant plants and 3 biological replicates of wild-type plants.

first: Ornella

last: Calderini

first: Sergio

last: Arcioni


title: Molecular analysis of heterosis in alfalfa

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary: The aim of the experiment was to investigate the transcriptome changes in a double hybrid of alfala. The transcriptomes of a double hybrid (B2xB5) was compared to the two parental lines.

overall_design: 9 samples were used in the experiment, 3 biologcal replicates of the double hybrid and two parental lines.


title: Profiling of gender based transcripts of Brugia malayi

status: Public on Dec 30 2010

city: Bethesda

first: Sasisekhar

last: Bennuru

state: MD

address: 10 Center Dr, Bldg 10, Rm 11N208

department: LPD

institute: NIH/NIAID

summary:
Transcriptional profiling of adult males and females of the lymphatic dwelling filarial parasite Brugia malayi

Keywords: Gender based transcripts, filaria

overall_design: Three biological replicates of male and female RNA used for hybridization to examine the gender-specifc transcripts

first: Julius

middle: S

last: Ndi

first: Thomas

last: Nutman


title: Copy number variation in inbred and wild mice

city: Lausanne

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

institute: University of Lausanne

summary: Copy number variants were determined in 3-5 males from 13 inbred laboratory mouse strains and 21 Mus musculus individuals caught in various geographic locations, using Nimblegen 385k arrays. CopyMap was used to predict CNVs.

sample_organism:
Mus musculus
Mus musculus domesticus
Mus spretus

overall_design: 3-5 males from 13 inbred strains and 21 Mus musculus caught in various geographic locations were compared to a single C57BL/6J individual by array comparative genome hybridisation.

first: Nicolas

last: Vinckenbosch

first: Evelyne

last: Chaignat

first: Alexandre

last: Reymond


title: Myeloid Derived Suppressor Cells and Cancer

city: Chapel Hill

first: June

last: Brickey

state: NC

address: 450 West Drive

institute: UNC

summary: Transcriptional profiling of FACS-sorted and splenic control mouse cells, comparing splenic cells from FVBneuN vs Neu+ expressing FVBneuN mice with Gr1+ CD11b+ sorted tumor-infiltrating mononuclear or splenic myeloid-derived suppressor cells

overall_design:
4 groups or conditions. Biological replicates: 2 or 3 per condition. One replicate array per sample.
manuscript: van Deventer, H, J Burgents, QP Wu, R Woodford, WJ Brickey, I Allen, E McElvania-Tekippe, J Serody, and J Ting. (2010) The inflammasome component Nlrp3 impairs antitumor vaccine by enhancing the accumulation of tumor-associated myeloid-derived suppressor cells. Cancer Research.
variable: cell type: splenic cells from normal FVB-neuN mice, splenic cells from Neu+ tumor-bearing FVB-neuN mice, Gr1+ CD11b+ sorted cells from tumor, Gr1+ CD11b+ sorted cells from spleen
repear: biological replicate: #1, #2, #3

first: W

first: Jenny

last: Ting

first: Timothy

last: Moran

first: Jonathan

last: Serody

first: Hendrick

last: van Deventer


title: Gene expression profiling between chicken tissues

first: Huaijun

last: Zhou

summary: Different organs play viable function. Different gene expression profiling between tissues will help us to understand the molecular mechanism played in different tissue and provide the fundamental knowledge for research on response to pathogens in different tissues.

overall_design: Three main tissues, liver, kidney, and bone marrow, were selected in the current study. Shelf hybridization was performed within each tissue. Eight biological replicates were used for each tissue.

first: W.

last: Chou

first: X.

last: Li

first: C.

last: Bailey

first: H.


title: Ustilago maydis fox1 mediated gene expression during pathogenic development

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

summary: Ustilago maydis is a plant-pathogenic fungus that establishes a biotrophic relationship with its host Zea mays. The biotrophic interaction is initiated upon host penetration, and involves expansion of the host plasma membrane around hyphae, which is thought to facilitate the exchange of nutrients and virulence factors. Transcriptional regulators involved in the establishment of an infectious dikaryon and penetration into the host have been identified, however, regulators involved in the post-penetration stages remained to be elucidated. In the study we report the identification of an Ustilago maydis forkhead transcription factor, Fox1, which is exclusively expressed during biotrophic development. Deletion of fox1 results in reduced virulence and impaired tumour development in planta. Microarray analyses of Δfox1-infected plant tissue identified Fox1 as a transcriptional activator, involved in the expression of secreted effectors required for virulence.

overall_design: Maize plants were infected with a mixture of either FB1 and FB2 (wild-type), or FB1∆fox1 and FB2∆fox1 crossings, to measure the impact of fox1 on pathogenic development. Early Golden Bantam maize plants were grown in a phytochamber in a 15h/9h light-dark cycle; light period started/ended with 1h ramping of light intensity. Maize plants were kept at 28°C (light) and 20° (dark). Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) and infected 7 days after sowing, 1 h before end of the light period. Infected leaf tumor material from at least 10 plants was collected 5 days post infection, 1 h before the end of the light period and directly frozen in liquid nitrogen for RNA-extraction. RNA samples were extracted from infected leaf tissue 5 days after infection.

first: Alexander

last: Zahiri

first: Ramon

last: Wahl


title: TIME-COURSE GENE EXPRESSION OF Metharizium anisopliae GROWING IN PLANT ROOT EXUDATE

city: College Park

first: Monica

last: Pava-Ripoll

address: 4112 Plant Sciencies Bldg

department: Entomology

institute: University of Maryland

summary: The presence of genetic groups of the entomopathogenic fungus Metarhizium anisopliae in soil is shaped by its adaptability to specific soil and habitat types, and by soil insect populations.  Although the entomopathogenic life style of this fungus is well studied, its saprophytic life style has received little consideration. While a set of functionally related genes can be commonly expressed for the adaptability of this fungus to different environments (insect cuticle, insect blood and root exudates), a different subset of genes is also expected for each environment. In order to increase the knowledge of the potential use of M. anisopliae as a rhizosphere competent organism, in this study we evaluated the genetic expression of this fungus while growing on plant root exudates in laboratory conditions during a time course.

overall_design: One fungal strain: Metarhizium anisopliae ARSEF 2575; Five time conditions: 0h, 1h, 4h, 8h, 12h; Five-condition experiment: Time0h vs. Time1h, Time1h vs. Time4h, Time4h vs. Time8h, Time8h vs. Time12h and Time12h vs. Time0h. Two Biological replicates: independently grown and harvested. Three replicates per array. Dye-swap was performed on replicate 2.

first: Claudia

last: Angelini

first: Weiguo

last: Fang

first: Sibao

last: Wang

first: Francisco

last: Posada-Florez

first: Raymond


title: Differential Gene Expression in Daphnia magna Suggests Distinct Modes of Action and Bioavailability for ZnO nanoparticles and Zn ions

city: Boston

first: Helen

middle: C

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

summary: Zinc Oxide nanoparticles (ZnO NPs) are being rapidly developed for use in consumer products, wastewater treatment and chemotherapy providing several possible routes for ZnO NP exposure to humans and aquatic organisms.  Recent studies have shown that ZnO NPs undergo rapid dissolution to Zn+2, but the relative contribution of Zn+2 to ZnO NP bioavailability and toxicity is not clear.  Gene expression profiling of D.  magna exposed to ZnO NPs or ZnSO4 at equitoxic concentrations demonstrated that the particles cause toxicity through a distinct mechanism compared with Zn+2.  D. magna were also exposed to a SiO NPs as a particle control at equimolar concentrations.  The SiO NPs resulted in few differentially expressed genes and there was very little overlap between the genes affected by the ZnO NPs and the SiO NPs, suggesting that ZnO NPs cause a distinct pattern of differentially expressed genes. In the ZnO NP exposures, effects were observed to genes involved in cytoskeletal transport, cellular respiration and reproduction.  Three biomarker genes including a multi-cystatin, ferritin and a C1q containing gene were confirmed as differentially expressed in a specific pattern by ZnO NP and provide a suite of biomarkers for identifying environmental exposure to ZnO NP and differentiating between NP and ionic exposure.

overall_design: We exposed Daphnia magna to the 1/10 LC50 and LC25 of ZnO nanoparticles and Zn++ as ZnSO4 for 24-h.  For each exposure condition, we performed 3 exposures and 2 technical replicates (as dye swap) for each exposure (6 microarrays total).  All exposures were compared to a unexposed laboratory control

first: James

last: Lazorchak

first: Christopher

last: Impelliteri

first: Mark

last: Smith

first: Kim

last: Rogers

first: Manomita

last: Patra

first: Katherine

last: Hammer

first: H

last: Allen

first: Chris

middle: D

last: Vulpe


title: Transcriptional profile in the macrolide resistant C. jejuni strains selected from 81-176

status: Public on Dec 28 2010

city: Ames

first: Haihong

last: Hao

state: IA

address: 1600 Christensen Drive

institute: Iowa State University

summary:
Campylobacter, a major foodborne pathogen, is increasingly resistant to macrolide antibibotics. previous findings suggeted that development of macrolide resistance in campylobacter requires a multi-step process, but the molecular mechanisms involved in the process are not known. In our study, multiple seriess of macrolide-resistant C. jejuni mutants were selected in vitro by stepwise exposure of C. jejuni 81-176 to increasing concentrations of erythromycin and tylosin. A set of the selected resistance were subjected to microarray and the the global transcriptional profile was analyzed.
In this sery, DNA microarray was used to compare the gene expression profiles of  macrolide resistant strains (76E2, 76E8 and 76E64) with its parent wild-type strain C. jejuni 81-176.
This assay identified a large number of genes that showed >1.5 fold changes (q-value<0.1)  in expression in the  macrolide resistant strains. The up-regulated genes are involved in surface structure,ribosomal, heat shock and some specific Misc memerbrane , while the majority of the down-regulated genes are involved in energy metabolism, amino acid biosynthesis. The over-expression of genes involved in surface structure and Misc memerbrance  was associated with the development of intermedial-level resistance to macrolide in campylobacter 81-176.
Keywords:intermedial-level macrolide resistant C. jejuni selected from C. jejuni 81-176. step-wise selection.

overall_design: The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni. Four hybridizations were performed each with independently extracted samples of either macrolide susceptible C. jejuni 81-176 cDNA samples or macrolide resistant C. jejuni cDNA samples. A dye swap was utilized to help minimize dye dependent bias. Thus there were three to four biological replicates of each sample.

first: Zonghui

last: Yuan

first: Qijing

last: Zhang


title: Differential expression of microRNAs between eutopic and ectopic endometrium in ovarian endometriosis

city: Novara

first: Ilaria

last: Gregnanin

address: V. Solaroli 17

institute: Università del Piemonte Orientale

summary: Endometriosis is defined as the presence of endometrial tissue (eutopic tissue) outside the uterus (ectopic tissue). We assessed differentially expressed microRNAs in ectopic endometrium compared with eutopic endometrium.

overall_design: Comparison of paired eutopic/ectopic endometrium microRNAs from three patients.

first: Nicoletta

last: Filigheddu


title: Gene expression profiles of Daphnia magna exposed to Cd at the 1/10 LC50

summary: Cadmium (Cd) is a toxic metal causing sublethal and chronic effects in crustaceans.  Omic technologies offer unprecedented opportunities to better understand modes of toxicity by providing a holistic view of the molecular changes underlying physiological disruption.  We sought to use gene expression and metabolomic analyses to reveal the processes leading to chronic Cd toxicity in the indicator species, Daphnia magna, after a 24-h sublethal exposure (18 ug/L, corresponding to 1/10 LC50).  We first confirmed that metabolites can be detected and identified in small volumes (~3-6 ul) of D. magna hemolymph using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and NMR spectroscopy.  We then compared the altered metabolite levels from a mass spectrometry metabolomics study to differentially expressed genes identified by a D. magna 44k oligonucleotide microarray.  Metabolomics identified several essential amino acids, nucleotides and fatty acids as decreased in D. magna hemolymph following Cd exposure.  Transcriptional changes included decreased levels of digestive enzymes and increased expression of genes related to embryonic development.  The integration of metabolomic and transcriptomic profiles, as well as incorporation of results from previous studies, has enabled construction of a conceptual model detailing how sublethal Cd disrupts energy reserves and reproduction resulting in chronic toxicity.

overall_design:
Daphnia magna were exposed to 18 micrograms/L Cadmium sulfate for 24 hours.  RNA was extracted and hybridized to a custom Daphnia magna microarray to determine genes differentially expressed by the treatment.
Two treament experiment:Unexposed and Cd treatment, 6 replicates for each condition


title: The prior probability can derive the variety in the interpretation of p-value

status: Public on Jan 12 2011

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

type:
Expression profiling by array
Third-party reanalysis

summary:
In contrast to its common definition and calculating process, interpretations of p-value differ among statisticians. Since p-value is the basis of various methodologies, this divergence has led to distinct test methodologies as well as various opinions for evaluating test results, producing a chaotic situation. Here the origin of the divergence is found in the differences among Pr(H0 = true), which gives a prior probability in the definition of p-values. Effects of differences in the prior probability on the character of p-values are investigated by comparing microarray data and random numbers as subjects.
The summarized levels the genes are presented in the matrix files (linked below as supplementary files). Student t-test was applied between the two groups (0h and 14d): p-values presented in the matrix files.

overall_design:
Re-normalization of GSE3231 data by third party.
Re-normalization of GSE3749 data by third party.
Re-normalization of GSE2972 data by third party.
Re-normalization of GSE15859 data by third party.

PM data of samples in GSE3231 (and separately in GSE3749, GSE2972, and GSE15859) were parametrically normalized in chip-wise manner according to the three-parameter lognormal distribution method (using SuperNORM data service (Skylight Biotech Inc.). http://www.super-norm.com/eng/index.html).  For full details, see Konishi et. al., 2009 PLoS ONE 3: e3555. http://dx.plos.org/10.1371/journal.pone.0003555.   Expression level of a gene was estimated by summarizing the corresponding PM data. A pseudo data was then derived in a form of antilog of the z-scores; the center of the pseudo data was 256. The pseudo data, ABS_CALL, and the normalized data (z-scores) are presented in the matrix files.

The normalized PM data of a chip were presented separately in Ascii text format (linked below as supplementary files). The parameters found in each chip data were presented in this form. For details for the parameters, see Konishi et al. 2009.


title: Human NTERA2 (NT2/D1) cells lines: Genomewide distribution of ZRF1 at gene promoters during RA administration

status: Public on Dec 24 2010

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

type: Genome binding/occupancy profiling by array

summary:
Chip-on-chip experiment with NT2 wildtype cells  untreated (0 h) or treated with Retinoic Acid (1h and 3 h) at 0.01 µM.
The goal was to determine the genome-wide occupancy of ZRF1 at gene promoters in undifferentiated cells and at the onset of differentiation.

overall_design: Three-condition experiment. Biological replicates: NT2 cells were treated with or without RA on three different days from cycling NT2 cells (0h, 1h and 3h of RA). Chromatin was prepared and a triplicate of IPs was performed with specific ZRF1 antibodies for every condition. A triplicate of control IPs was performed with IgGs.

first: Holger

last: Richly

first: Nuria

last: Lopez-Bigas


first: Marta

last: Catalfamo

state: Maryland

address: 9000 Rockville Pike

department: Laboratory of Immunoregulation

institute: NIAID, NIH

summary: CD8+  and CD4+  T cells from HIV infected patients with HIV-RNA viremia of >50 copies/ml and CD8+  and CD4+  T cells from healthy controls were isolated by negative selection (Miltenyi Biotech, Auburn, CA). Cell sorting of the CD4 and CD8 T cell subsets were performed based on surface staining of CD3+CD8+ or CD3+CD4+ and na ve CD45RA+CD27+CD127highHLA-DRlow, and CD3+CD8+ or CD3+CD4+ and memory CD45RA-CD27+CD127highHLA-DRlow. Sorted cell populations were spun down and stored as dry pellets at -80°C. Samples analyzed by transcript levels of genes related to cytokine signaling were determined by the JAK/STAT Signaling Pathway microarray.

overall_design: CD8+  and CD4+  T cells from HIV infected patients with HIV-RNA viremia of >50 copies/ml and CD8+  and CD4+  T cells from healthy controls were isolated by negative selection (Miltenyi Biotech, Auburn, CA). Cell sorting of the CD4 and CD8 T cell subsets were performed based on surface staining of CD3+CD8+ or CD3+CD4+ and naïve CD45RA+CD27+CD127highHLA-DRlow, and CD3+CD8+ or CD3+CD4+ and memory CD45RA-CD27+CD127highHLA-DRlow. Sorted cell populations were spun down and stored as dry pellets at -80°C. Samples analyzed by transcript levels of genes related to cytokine signaling were determined by the JAK/STAT Signaling Pathway microarray (http://www.sabiosciences.com/rt_pcr_product/HTML/PAHS-039A.html, SABiosciences Frederick, MD). Briefly, total RNA was harvested from each individual T cell subset from each patient or healthy control and contaminating DNA was digested with DNase. Messenger RNA was converted to cDNA and loaded onto PCR array plates for quantitative real-time PCR. Quantification of transcript levels was determined by normalizing to 5 housekeeping genes from each individual sample. Relative gene expression levels for each subset were averaged and compared between cell populations from the patient group and healthy controls. Because of the multiple comparisons only p values ≤ 0.01 were considered significant.


title: Cell cycle-dependent, intercellular transmission of Toxoplasma gondii is accompanied by marked changes in parasite gene expression.

status: Public on Dec 27 2010

city: St Louis

first: Michael

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

summary: Intracellular microbes have evolved efficient strategies for transitioning from one cell to another in a process termed intercellular transmission. Here we show that host cell transmission of the obligate intracellular parasite Toxoplasma gondii is closely tied to specific cell cycle distributions, with egress and reinvasion occurring most proficiently by parasites in the G1 phase. We also reveal that Toxoplasma undergoes marked changes in mRNA expression when transitioning from the extracellular environment to its intracellular niche. These mRNA level changes reflect a modal switch from expression of proteins involved in invasion, motility and signal transduction in extracellular parasites to expression of metabolic and DNA replication proteins in intracellular parasites. Host cell binding and signalling associated with the discharge of parasite secretory proteins was not sufficient to induce this switch in gene expression, suggesting that the regulatory mechanisms responsible are tied to the establishment of the intracellular environment. The genes whose expression increased after parasite invasion belong to a progressive cascade known to underlie the parasite division cycle indicating that the unique relationship between the G1 phase and invasion effectively synchronizes short-term population growth. This work provides new insight into how this highly successful parasite competently transits from cell to cell.

overall_design: Three sample types were harvested: extracellular, intracellular 0hr, intracellular 2hr. 2 replicates each. Expression for >80% of the regulated genes exhibits a steady downregulation during invasion.

first: Raj

middle: Y

last: Gaji

first: Vern

middle: B

last: Carruthers

last: White


title: Extraction of Total RNA from Single Neurons: Mauthner-cell Cytoplasm vs. Whole Brain

status: Public on Dec 23 2010

city: Austin

first: Lin

last: Huffman

address: 2400 Speedway, PAT 141

department: Institute for Cellular and Molecular Biology

institute: The University of Texas

summary: Astatotilapia burtoni males change their startle behavior in accordance with changes in a socially-mediated phenotypic state. When dominant (DOM), males are brightly colored, isolated from the school and startle readily in response to an auditory pulse. When subordinate (SUB), males are cryptically colored, school and startle less frequently. We hypothesize that the difference in startle responsiveness is governed by serotonergic modulation on the command-like Mauthner cells (M-cells). We used the selective serotonin receptor subtype 2 (5HTR2) antagonist ketanserin to show that serotonin receptors can modulate startle frequency and that the behavioral difference correlates with differences in electrophysiological recordings of M-cells. Specifically, SUB males have a higher serotonergic tone and demonstrate, by behavior and electrophysiological properties, increased sensitivity to 5-HT manipulations compared to DOMs. Immunohistochemistry for serotonin is present around the M-cells. Furthermore, we identified serotonin receptor transcripts in A. burtoni and used single-cell transcriptomics to determine the presence or absence of specific receptor subtypes in the M-cells. Microarray analysis of M-cell samples shows that the neuron’s transcriptome is relatively stable in individuals of different social status. These results are consistent with a role for serotonin in modulating the behavioral response to sensory stimuli in an ecologically-relevant manner through inhibitory interneurons, which establish the membrane resistance of the M-cell before the auditory stimulus.

overall_design: Simple loop with dye-swap containing 6 arrays from 2 sources with 3 biological replicates per source (3 M-cell and 3 whole brain samples).

first: Hans

last: Hofmann


title: Network Analysis of Skin Tumor Progression Identifies a Rewired Genetic Architecture Affecting Inflammation and Tumor Susceptibility (aCGH)

city: San Francisco

first: David

last: Quigley

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

summary: Background: Germline polymorphisms can influence gene expression networks in normal mammalian tissues and can affect disease susceptibility. We and others have shown that analysis of this genetic architecture can identify single genes and whole pathways that influence complex traits including inflammation and cancer susceptibility. Whether germline variants affect gene expression in tumors which have undergone somatic alterations, and the extent to which these variants influence tumor progression, is unknown. Results: Using an integrated linkage and genomic analysis of a mouse model of skin cancer that produces both benign tumors and malignant carcinomas, we document major changes in germline control of gene expression during skin tumor development resulting from cell selection, somatic genetic events, and changes in the tumor microenvironment. The number of significant expression Quantitative Trait Loci (eQTLs) is progressively reduced in benign and malignant skin tumors when compared to normal skin. However, novel tumor-specific eQTLs are detected for several genes associated with tumor susceptibility, including Interleukin 18, Granzyme E, Sprouty homolog 2, and MAP kinase kinase 4.  Conclusions: We conclude that the genetic architecture is substantially altered in tumors, and that eQTL analysis of tumors can identify host factors that influence the tumor microenvironment, MAP kinase signaling, and cancer susceptibility.

overall_design: A backcross was generated using male Mus spretus and female FVB/N mice; female F1 hybrids were mated with male FVB/N mice. Backcross mice (8-12 weeks old) received a single dose of DMBA (25 µg per mouse in 200 µl acetone). Starting one week after the initiation tumors were promoted with TPA (200 µl of 10-4 M solution in acetone) twice weekly for 20 weeks. Initiation and promotion were performed on doral back skin. DNA from 62 Carcinomas and matched untreated tails (used for normal DNA comparison) was obtained from tissue that was snap frozen when animals were sacrificed.

first: Minh

last: To

first: Il-Jin

last: Kim

first: Kevin

middle: K

last: Lin

first: Donna

middle: G

last: Albertson

first: Jonas

last: Sjolund

first: Jesús

last: Pérez-Losada

first: Allan

last: Balmain


title: 2.5D tubulogenesis

first: SH

last: Kwon

address: 600 16th St./N214 Mostov lab

institute: University of California San Francisco

summary: Hepatocyte growth factor-induced three-dimensional tubulogenesis (3D) is a simple and highly controllable system for studying epithelial tubule initiation and maintenance. However, due to its limited efficiency and asynchronous development, isolating genes associated with specific morphological changes observed during tubule formation has been unfeasible. Here we report a significantly enhanced in vitro culture method called 2.5-dimensional tubulogenesis (2.5D). Detailed image analysis of 2.5D has revealed morphologically distinct stages -- monolayer, extension, and tubule -- and finds that these stages display in a highly synchronized manner. Using time-course transcriptional profiling, we collected genes whose expression changes specifically associate with extension and tubule stage.

overall_design: Time-course microarrays to identify genes whose temporal regulation is associated with extension and tubule stages. Four biological replicates for each stage (monolayer, extension, and tubule).

first: S

middle: H

first: K

middle: E

last: Mostov


title: Genomic expression profiles of blood and placenta in Chinese women with gestational diabetes

city: Beijing

first: Dapeng

last: Wang

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: Beijing Institute of Genomics

summary:
Genomic expression profiles of blood and placenta reveal significant immune-related pathways and categories in Chinese women with Gestational Diabetes
Gestational diabetes mellitus (GDM) is a complex metabolic disease which occurs in pregnancy with high prevalence, and its pathogenesis remains elusive. Thus far, there has been no comprehensive gene expression profiling in Chinese women with GDM. In this study, we attempt to define the genes and/or pathways that are involved in GDM with Chinese ethnicity, by the Illumina microarray technique. We found 5,197 and 243 genes with significantly altered expression due to GDM in blood and placenta tissues, respectively. Previously known genes (such as TNF, IL1B, LEP, IFNG, and HLA-G) with altered gene expression in GDM were also validated here. In addition, we identified undescribed genes VAV3, PTPN6, CD48 and IL15, in which expression was related to GDM by microarray and Q-RT-PCR assays. To identify GDM-associated pathways, we used analyses with integrated functional annotation (i.e. KEGG) and extracted two significant pathways, which were Natural killer cell mediated cytotoxicity (hsa04650; FDR = 7.10E-09) in blood and Cytokine-cytokine receptor interaction (hsa04060; FDR = 1.07E-03) in placenta tissues. Immune system process (GO: 0002376) was identified by GO analysis with FDR P-value = 7.01E-60 in blood and FDR P-value = 3.57E-08 in placenta tissues, indicating the importance of immunological and inflammatory categories in GDM. Furthermore, despite differences in the quantity of gene expression, we observed a similar functional distribution between expression of blood and placenta tissues in GDM under the categories of immunity. These newly identified key genes and pathways may provide valuable information for the pathogenesis of GDM and advance disease diagnosis, prevention, medication design, and clinical treatment of the disease.

overall_design: One individual GDM blood tissue sample and one pooled GDM blood tissue sample were compared to one pooled healthy blood tissue sample. One pooled GDM placenta tissue sample was compared to one pooled healthy placenta tissue sample.

first: Yanhui

last: Zhao


title: Gis2 mutant versus wild-type cells

status: Public on Dec 22 2010

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

institute: Swiss Federal Institute of Technology

summary: To measure the relative changes of gene expression upon Gis2p depletion, 50 ml of delta Gis2 cells or the respective wild-type strain BY4741 were grown in YPD at 30 degrees celsius to an OD600 of 0.5- 0.6. Cells were harvested by centrifugation and washed twice with 5ml of bidistilled water (ddH2O). RNA was isolated by hot phenol extraction for microarray analysis. 20 ug of total RNA derived from wild-type and knock-out cells were reverse transcribed in the presence of 5-(3-aminoallyl)-dUTP and natural dNTPs with a mixture of N9 and dT20V primers, and cDNAs were covalently linked to Cy3 and Cy5 NHS-monoesters (GE HealthSciences Cat# RPN5661), respectively, and competitively hybridized onto yeast oligo arrays at 42 degrees celsius for 14 hours in formamide-based hybridization buffer. Microarrays were scanned with an Axonscanner 4200 (Molecular Devices) and analyzed with GenePix Pro 5.1 (Molecular devices) before uploading into Stanford Microarray Database.

overall_design: Biological Replicate

first: Tanja

last: Scherrer


title: A Leukemic Stem Cell Expression Signature is Associated with Clinical Outcomes in Acute Myeloid Leukemia

city: Stanford

first: Ash

middle: A

last: Alizadeh

address: 269 Campus Drive, CCSR 1145c

department: Medicine, Divisions of Hematology and of Oncology

institute: Stanford University School of Medicine

summary:
Context: In many cancers, specific subpopulations of cells appear to be uniquely capable of initiating and maintaining tumors. The strongest support for this cancer stem cell model comes from transplantation assays in immune-deficient mice indicating that human acute myeloid leukemia (AML) is organized as a cellular hierarchy driven by self-renewing leukemia stem cells (LSC). This model has significant implications for the development of novel therapies, but its clinical significance remains unclear.
Objective: To measure associations between a leukemic stem cell expression signature and clinical outcomes in AML.
Design, Setting, and Patients: We defined a gene expression signature of LSC-enriched subpopulations from primary AML patient samples and xenografts, based on a functional definition in transplantation assays. Using previously published gene expression data of bulk AML from four independent cohorts totaling 1047 patients, we performed a retrospective cohort study, defining an LSC score and evaluating it for associations with known predictors of risk including cytogenetic subtype and molecular mutations, and as an independent prognostic factor.
Main Outcome Measures: Reproducible associations between a leukemic stem cell signature and overall, event-free, and relapse-free survival.
Results: The LSC score was similar across most AML subtypes, but was lower in promyelocytic leukemia, and prognostically favorable cases harboring NPM1 or CEBPA mutations. Strikingly, high scores associated with inferior overall (OS), event-free (EFS), and relapse-free survival (RFS) in these independent cohorts, whether considering patients with a normal karyotype [hazard ratio (HR) range for OS 1.13-1.18, p<0.012 in all cases], or those with cytogenetic anomalies (HR range for OS 1.07-1.15, p<0.01 in all cases). In multivariate analysis, the LSC score was associated with poor outcomes independently of age, FLT3 or NPM1 mutations, and cytogenetic risk group, and added to their prognostic value.
Conclusions: High expression of a leukemic stem cell gene expression signature is independently associated with adverse outcomes in AML

overall_design:
Cellular fractionation and expression profiling of normal and leukemic subsets:  Human samples were obtained at the Stanford University Medical Center  according to an approved protocol of the Institutional Review Board after informed consent.  Normal human bone marrow mononuclear cells were purchased from AllCells Inc. (Emeryville, CA) and human cord blood was obtained from Stanford University. For AML specimens, peripheral blood and/or bone marrow was obtained, and gene expression microarray data were generated using Affymetrix U133 Plus 2.0 microarrays from the following populations purified by fluorescence-activated cell sorting: AML LSC (Lin-CD34+CD38-CD90-, n=7), AML LPC (Lin-CD34+CD38+, n=7), AML Blasts (Lin-CD34-), normal hematopoietic stem cells (HSC, Lin-CD34+CD38-CD90+CD45RA-; bone marrow and cord blood, n=7), multipotent progenitors (Lin-CD34+CD38-CD90-CD45RA-; bone marrow and cord blood, n=7), common myeloid progenitors (Lin-CD34+CD38+CD123+CD45RA-; bone marrow, n=4), granulocyte-monocyte progenitors (Lin-CD34+CD38+CD123+CD45RA+; bone marrow, n=4), and megakaryocyte-erthythrocyte progenitors (Lin-CD34+CD38+CD123-CD45RA-; bone marrow, n=4). Raw data were deposited at the National Center for Biotechnology Information Gene Expression Omnibus (GEO, accession GSE24006). Detailed methods for purification of cellular subsets and clinical features of the corresponding AML patients have been reported previously.
Microarray analysis and definition of LSC signature:   Fourteen paired LSC and LPC samples from 7 patients described above were combined with 16 paired samples (8 LSC and 8 LPC) from an independent study to produce one dataset for analysis. Individual genes differentially expressed between paired LSC and LPC were identified using Significance Analysis of Microarrays, employing a paired metric (false discovery rate<10%). The ‘LSC signature’ in a given dataset was defined as the first principal component of these genes (the linear weighted sum of gene expression values that summarizes the maximum possible proportion of their total variance) across samples from that dataset. The LSC signature was evaluated across all purified subpopulations described above. To identify biological themes distinguishing LSC from LPC, all genes on microarrays were ranked by their geometric mean difference in expression between paired LSC/LPC samples, and evaluated using Gene Set Enrichment Analysis.
Raw microarray data were obtained as Affymetrix CEL files for four publicly available bulk AML gene expression studies from NCBI GEO (GSE12417, n=163 normal-karyotype AML only, with OS outcomes; GSE10358, n=184, OS and EFS; GSE14468, n=527, OS, EFS and RFS) and the National Cancer Institute caArray database (accession willm-00119, n=170 non-FAB M3, OS only). Matrices of re-analyzed data linked below as supplementary files.  Ingenuity Pathways Analysis was used to identify interaction networks of genes.

first: Andrew

last: Gentles

first: Ravindra

last: Majeti


title: Gis2 affinity isolations

summary:
To identify RNAs specifically associated with Gis2p, cells expressing TAP-tagged Gis2 or the wild-type strain BY4741 (mock control) were grown to mid-log phase  in rich medium and harvested by centrifugation. RNA affinity isolations were essentially performed as described (Gerber et al. 2004 PLoS Biol.; see associated protocol 526). In brief, TAP-tagged protein were captured from cell extracts with IgG coupled agarose beads (Sigma) and released by incubation with a site-specific protease (AcTEV, Sigma). from the extract (input) and from the affinity isolates was purified with the RNeasy Mini/ Micro Kit (Qiagen). RNAs were reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/dNTP mixture. cDNAs were fluorescently labeled and hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer.
Set of arrays that are part of repeated experiments
Genotype: TAP-tagged Gis2 expressing or wild-type strain BY4741 (wt/gis2)


title: Bombyx mori Posterior and Median Silk Gland SAGE transcriptome

city: Villeurbanne

first: Pierre

middle: Marie

last: Couble

address: 16 rue Dubois

department: Biology - INSB

institute: CNRS-University Lyon 1

summary: To identify functions that distinguish the posterior and median cells producing fibroin and sericin in the silk gland of Bombyx mori, serial analysis of gene expression (SAGE) profiles from both silk gland regions were analyzed and compared. The construction of a B. mori reference tag collection extracted from a set of 38000 Bombyx EST sequenced from the 3’ side, helped annotating the SAGE libraries. Most of the tags appeared at similar relative concentration in the two libraries except for those corresponding to silk proteins that were found region-specific and highly abundant. Strikingly, besides tags from silk protein mRNAs, 19 tags were found in the class of high abundance in the median cell library, which were absent in the posterior cell tag collection. Except tags from SP1 mRNA, no PSG specific tags were found in the same class of abundance. The analysis of MSG-specific different transcripts led to suggest that middle silk gland cell realizes more diversified functions as those already known, of synthesis and secretion of the silk sericins.

overall_design:
EST libraries from 11 silkworm tissues were 3’-sequenced to ensure the identification of the most terminal tag. 37,920 sequences were analyzed on ABI 3700 or 3730XL sequencers. Electrophoregrams were processed with KB Basecaller (3730XL traces) or with PHRED (3700 traces) to obtain the .phd files from which were extracted text sequences and their corresponding quality files in Fasta format (Phd2Fasta, Green and Ewing, 1995; 2002). Vector sequences and bad quality regions were removed with an home made software after identification by Lucy (Chou and Holmes, 2001). Chimera were removed by an home made software and retrotransposon sequences were masked by RepeatMasker (http://repeatmasker.org). The cleaned sequences were clusterized with TGICL package (TIGR) and assembled into contigs with CAP3 (Huang and Madan, 1999). Contigs were identified with Blastn and Blastx on GenBank and SwissProt/TREMBL, respectively. Some clusters, splitted by CAP3 procedure, have been regrouped on the basis of Blastx identity. Identitag (Keime et al., 2004) was used to extract all possible tags (forward and reverse) to create a reference database. Moreover, a quality index is attached to each tag depending to the presense of poly-A, polyadenylation signal and its proximity to 3-prime extremity in the original mRNA sequence. This database was supplemented with the tags extracted from public B. mori sequences (GenBank, Silkbase) with the same software.

Tags were extracted from MSG and PSG libraries (from 2304 and 3072 sequenced inserts respectively) with the Sagenhaft software (Beissbarth et al., 2004) then identified and compared with Identitag. The assessment of significant differences among the two libraries was performed by using the Z-test used for comparison of SAGE libraries of different size (Kal et al., 1999). For graphic purpose and to avoid division by zero we used a tag value of 1 for tags that were not detected in MSG or PSG libraries. Since the two SAGE libraries showed up different TAG number, we used the Z-test for comparing the two mRNA populations.

first: CORINNE

last: ROYER

first: JEROME

last: BRIOLAY

first: ANNIE

last: GAREL

first: PATRICK

last: BROUILLY

first: SHUN-ICHI

last: SASANUMA

first: MOTOE

first: CELINE

last: KEIME

first: OLIVIER

last: GANDRILLON

first: YONGPING

last: HUANG

first: GERARD

last: CHAVANCY

first: KASUEI

last: MITA

first: PIERRE

last: COUBLE


title: Gis2 overexpression versus control cells

first: Andre

last: Gerber

summary: Measure the relative changes of gene expression upon GIS2 overexpression; 100 ml of BY4741 cells bearing plasmid pBG1805-Gis2 (GIS2 under the control of the galactose promotor) or the empty plasmid pBG1805 (=control) were grown in synthetic medium lacking uracil (SC-Ura supplemented with 2% raffinose) at 30 degrees to an OD600 of 0.45- 0.5. Expression of GIS2 was induced with 2% galactose for 1.5 h and cells were harvested by centrifugation, washed twice with 800 ul of ice-cold sterile water. 100 ul (1/8) of cells were removed and RNA was isolated by hot phenol extraction for microarray analysis. 6.7 ug of total RNA derived from cells expressing the empty vector (pBG1805) or Gis2p (pBG1805-Gis) were reverse transcribed in the presence of 5-(3-aminoallyl)-dUTP and natural dNTPs with a mixture of N9 and dT20V primers, and cDNAs were covalently linked to Cy3 and Cy5 NHS-monoesters (GE HealthSciences Cat# RPN5661), respectively, and competitively hybridized on yeast oligo arrays at 42 degrees celsius for 14 hours in formamide-based hybridization buffer. Microarrays were scanned with an Axonscanner 4200 (Molecular Devices) and analyzed with GenePix Pro 5.1 (Molecular devices).

first: Tanja


title: Expression of 50-500nt ncRNAs in silkworm Bombyx mori during two developmental transitions

city: Nanyang

first: Yunchao

last: Kan

state: Henan

address: Wolong road 1638

institute: China-UK-NYNU-RRes Joint Libratory of insect biology

summary: We have performed the first systematic identification and analysis of intermediate size ncRNAs (50-500 nt) in the silkworm genome. We identified 194 novel ncRNAs, the expression profiles of them during the transitions from the egg to the first instar larva and from the fifth instar larva to the pupa were anlyzed by dual-channel microarray. Results showed that 12 ncRNAs had significantly differential expression during the two developmental transitions.

overall_design: The first instar larva sample was used for comparison to the sample of embryo, the fifth instar larva sample was used for comparison to the sample of pupa, respectively.

first: Dandan

last: Li

first: Yinghao

last: Cao

first: Yanhong

last: Wang


title: Gene expression in developing wild and domesticated fibers of Upland cotton (Gossypium hirsutum)

first: Lex

last: Flagel

address: 251 Bessey Hall

institute: Iowa State Univ.

summary: We explored the transcriptomic alterations associated with domestication by interrogating a developmental time course of cotton fibers from the wild G. hirsutum var. yucatanense and a representative of an elite domesticated line.

overall_design: 30 chip design - including 2 species (wild and domesticated cotton), by 1 tissue (fiber), for 5 timepoints (2,7,10,20, and 25 days after anthesis), with 3 replicates per timepoint

first: Jonathan

last: Wendel


title: Identification of differentially methylated regions between placentas and maternal blood cells on chromosome 18

city: Hong Kong

first: Yuk Ming

middle: Dennis

last: Lo

address: The Prince of Wales Hospital

department: Department of Chemical Pathology

institute: The Chinese University of Hong Kong

type: Methylation profiling by genome tiling array

summary: Comparison of DNA methylation levels of chromosome 18 between placentas and blood cells of pregnant women

overall_design: Extracted DNA from 5 cases of placental tissues and 5 cases of maternal blood cell was subjected to MeDIP (methylated DNA immunoprecipitation) and hybridized to Affymetrix GeneChip® Human Tiling 2.0R Array sets. A control without immunoprecipitation (IP) was also processed in parallel with the immunoprecipitated DNA samples. The results were validated with bisulfite sequencing and mass spectrometry-based analysis

first: Dana

middle: W

last: Tsui

first: Doris

last: Lam

first: Wing

last: Lee

first: Tak

last: Leung

first: Tze

last: Lau

first: Elizabeth

middle: T

first: Mary

last: Tang

first: Ranjit

last: Akolekar

first: Kypros

last: Nicolaides

first: Rossa

last: Chiu

first: Dennis

first: Stephen

last: Chim


title: Expression of 50-500nt ncRNAs in silkworm Bombyx mori during development

first: Yunchao

last: Kan

summary: With an experimental RNomics, we identified 194 novel ncRNAs in silkworm through four developmental stages (egg, larva, pupa and adult). Oligos of 132 ncRNAs were sucessfully designed, the expression of these ncRNAs were analyzed by dual-channel microarray, results showed that 36 ncRNAs had significantly differential expression during development.

overall_design: The RNA from four samples (egg, larva, pupa and adult) were analyzed, the sample of larva was used as reference.

first: Dandan

first: Yinghao


title: Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes

city: Beltsville

first: George

last: Liu

address: 10300 Baltimore Ave

institute: United States Department of Agriculture

summary: Here we describe the initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes

overall_design: The custom aCGH chips that interrogated the whole genome CNVs were build for 3 pairs of contemporary parasite-susceptible and resistant Angus.

first: Twain

last: Brown

first: Deborah

last: Hebert

first: Maria

middle: F

last: Cardone

first: Yali

last: Hou

first: Ratan

last: Choudhary

first: Jessica

last: Shaffer

first: Chinwendu

last: Amazu

first: Erin

last: Connor

first: Mario

last: Ventura

first: Louis

last: Gasbarre


title: Differential gene expression profiling in the presence and absence of cohesin in Drosophila salivary glands (gene expression data)

city: Cambridge

first: Andrea

last: Pauli

address: 16 Divinity Street

institute: Harvard University

summary: Analysis of differential gene expression in third instar Drosophila salivary glands in the absence versus presence of cohesin. ABSTRACT: Developmental abnormalities observed in Cornelia de Lange Syndrome (CdLS) have been genetically linked to mutations in the cohesin machinery. These findings raise the possibility that cohesin, in addition to its canonical function of mediating sister chromatid cohesion, might also be involved in regulating gene expression. We report that cleavage of cohesinÕs kleisin subunit in post-mitotic Drosophila salivary glands induces major changes (both up and down) in the transcript levels of many genes. Kinetic analyses of changes in transcript levels upon cohesin cleavage reveal that a subset of genes responds to cohesin cleavage within a few hours. In addition, cohesin binds to most of these loci, suggesting that cohesin is directly regulating their expression. Amongst these genes are several that are regulated by the steroid hormone Ecdysone. Transcripts at EcR and Eip74EF, which encode an Ecdysone Receptor and an Ecdysone-regulated transcription factor, respectively, decline ten-fold within four hours of cohesin cleavage. Cytological visualization of transcription at selected Ecdysone-responsive genes reveals that puffing at Eip74EF ceases within an hour or two of cohesin cleavage, long before any decline in EcR associated with this locus. We conclude that cohesin regulates expression of a distinct set of genes, including those mediating the Ecdysone response.

overall_design: A heat-inducible transgene (hs-TEV) was used to induce TEV in terminally differentiated third instar Drosophila salivary glands expressing either wild type (+ cohesin) or TEV-cleavable myc10-tagged Rad21 protein (Rad21TEV, - cohesin). Total RNA was isolated from + and - cohesin salivary glands 10-12 hours after heat shock induction of TEV (7 independent biological samples each). RNA samples were converted to cDNA, labeled with Cy3 and Cy5 respectively (3x) and vice versa (4x; dye swaps), and hybridized to INDAC FL003 arrays. Analysis of seven arrays, each hybridized to an independently generated sample-pair revealed major differences in transcript levels between + and - cohesin samples.

first: Joke

last: van Bemmel

first: Raquel

last: Oliveira

first: Takehiko

last: Itoh

first: Katsuhiko

last: Shirahige

first: Bas

last: van Steensel

first: Kim

last: Nasmyth


title: Titanium dioxide nanoparticles exposure

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

summary:
This project utilized oligonucleotide microarrays to examine gene expression patterns in adult male fathead minnows (Pimephales promelas) exposed to a common nanomaterial, titanium dioxide (TiO2, stearate-coated particles, MT-100TV®).  We exposed adult male fathead minnows for 96 hr to three doses (0,   1, and 10 mg/L nominal) of TiO2 under static renewal conditions.
TiO2 is stearate coated, 15 nm particle size.

overall_design:
Three-condition experiment: high dose, controls (untreated, low dose). Three tissues: liver, gill, brain.  Biological replicates: 4 control replicates, 4 low dose, 4 high dose for gill and liver.  One array for brain control and low dose; and 2 arrays for brain high dose.
Contributor: Johnson & Johnson Worldwide Envrionmental

middle: J


city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Helicobacter pylori is a human gastric pathogen associated with gastric and duodenal ulcers as well as specific gastric cancers. It is well-evidenced that motility is essential for this pathogen to colonize human gastric tissues. We found that the H. pylori G27 HP0518 mutant showed greater motility than the parental strain, leading to increased cell adhesion and subsequent CagA translocation and NF-κB activation in AGS cells. This mutant expressed a higher molecular mass flagellin A (FlaA) than the parental wild-type strain and the complemented HP0518 mutant, which correlated with differences in motility. Deglycosylation assays indicated that the increased molecular mass of the FlaA protein expressed by the mutant was due to O-linked glycoside modifications. Electron micrographs demonstrated that expression of bundle-formed flagellin filaments in the HP0518 mutant was enhanced in comparison to the wild-type strain. Different degrees of FlaA glycosylation between H. pylori strains suggested that glycosylation could affect both virulence and persistence in vivo. In conclusion, HP0518 inactivation resulted in FlaA hyper-glycosylation leading to increased virulence and motility.

overall_design: Microarray experiments were carried out as two-color hybridizations with a color-swap dye-reversal setting to compensate Cy-dye specific effects and to ensure statistically relevant data.

first: Hiroshi

last: Asakura

first: Hans

last: Molenkopf

first: Thomas

last: Meyer


title: Gene expression analysis in polytrauma patients comparing sepsis vs. non-sepsis

city: Giessen

first: Hamid

last: Hossain

address: Frankfurter Str. 107

department: University of Giessen

institute: Institute for Medical Microbiology

summary:
BACKGROUND: Despite best supportive intensive care, the development of severe sepsis and septic shock after trauma is still associated with a high mortality rate in intensive care units (ICU). Incomplete knowledge of the pathophysiological and biochemical mechanisms that lead to perturbations of the host system is a major cause for this clinical entity. This lack of knowledge is mirrored in a delay in both diagnosis of sepsis and stratification of patients at risk. The current diagnostic and classification methods do not provide an early and reliable evidence for the development of sepsis and consequently lead to uncertainty in the classification and a delay in the initiation of an adequate therapy. Here, we present a prospective study performed with a well-defined patient cohort suffering from severe multiple trauma (n=85), in which we aimed to uncover the biological reasons why patients with multiple trauma can have dramatically different outcomes after suffering similar traumatic insults.
METHODS: We used peripheral whole blood obtained with the PaxGene system at the time of admission to the ICU, i.e., 12 hours after trauma, for transcriptome analysis and monitored clinically the sequence of events from the admission to the ICU, to the very onset of sepsis and finally to the full development of multiple organ dysfunction syndrome (MODS). Study protocols and standard operating procedures (SOPs) regarding ethics, patient recruitment, logistics in sample acquisition and storage, microarray experiments, data analysis and data management have been developed and provided for a high feasibility and reproducibility of the investigations.
FINDINGS: The transcriptome analysis from peripheral blood revealed a strong host response upon severe injury and demonstrated the suitability of whole blood in the PaxGene system as a surrogate marker in clinical gene expression studies. It was evident that patients who developed sepsis in the course of the disease (3-5 days after admission) showed an imbalance in the TH1/TH2 response towards a pronounced TH2 response, soon after trauma. The imbalanced TH1/TH2 shift along with inactivation of T cells, neutrophils, monocytes and macrophages might be critical factors for the initiation of a septic program seen in these patients 12 hours after trauma.
INTERPRETATION: First, in this study, we provide protocols for logistics and infrastructure that can be applied generally to successfully integrate gene expression analysis studies in a clinical routine and demonstrate that by following these protocols, dedicated and reproducible results can be obtained. Second, we showed that peripheral whole blood is a suitable surrogate marker for the host response as it contains lots of “information” and is easily accessible. Third, we identified mechanisms involved in the perturbations of the immune system that lead to sepsis.

Keywords: Prospective study

overall_design: 159 consecutive traumatized patients were included in the study upon admission to the intensive care unit (ICU), fulfilling all of the following inclusion criteria: severe injuries to at least two body regions or three major fractures, between 18 and 65 years of age, an estimated Injury Severity Score (ISS) of ≥15 points after thorough assessment of injuries, <12 hours between the occurrence of the accident and the time of admission to the ICU, and at least greater than 3 days of survival. None of the patients underwent neuro- or cardiac surgery. We excluded patients with severe intracranial head injuries, coagulation abnormalities known at the day of admission to the ICU, acute renal failure, liver failure, malignant disease, or hemofiltration in the patient`s history. The Patients were divided into two groups depending on their posttraumatic course: Patients not complicatd by sepsis (Group: N) and Patients complicated by sepsis (Group: S). Using the CodeLink UniSet Human 10 K Bioarrays (GE Healthcare, Freiburg, Germany), we searched for early differences in the transcriptome of these two groups. Only whole blood samples drawn upon admission to the ICU were used for this investigation. Microarray results were validated by quantification of mRNA by TaqMan® technology. Each patient sample was hybridized in duplicate or triplicate on microarrays (label-extract technical replicate). A total of 72 arrays (36 group N, 36 group S) were subjected to microarray quality analysis. Of these, 2 arrays (0 group N, 2 group S) were excluded from the data set due to quality reasons and a final set of 70 arrays (36 group N and 34 group S) were subjected to microarray analysis. Since the eliminated 2 arrays belonged to patients with three replicates, they were treated as two replicates in the further analysis. The arrays were designated N_xx_yy_z or S_xx_yy_z, with x for the patient-ID (1,2,3,4..) and z for the technical replicate number (1,2 or 3).

first: Felix

last: Thierer


title: Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

status: Public on Dec 21 2010

city: Seattle

first: Tie

last: Koide

state: WA

address: 1441 N 34th street

institute: Institute for Systems Biology

summary:
Background: Xylella fastidiosa, a Gram-negative fastidious bacterium, grows exclusively in the xylem of several plants, causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat.

Results: In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time-course experiment (2, 8 and 12 hours) revealed many differentially expressed genes under nitrogen starvation, such as genes related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding a glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter and contains a predicted NtrC binding site.

Conclusions: Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.

overall_design:
For time-course studies, cells cultivated at late-exponential phase in PWG medium were used to inoculate a culture in 100 ml XDM2 medium to an optical density at 600 nm (OD600 nm) of 0.1. Cells were grown during 12 days in the XDM2 medium (mid-log phase) and harvested by centrifugation. Then, the culture was divided into two 6 portions and cells were washed with XDM2 medium (zero time) or XDM2 medium lacking all nitrogen sources (XDM0), respectively. The cultivation was continued for 2h, 8h and 12h in XDM0 to establish nitrogen starvation conditions. For each time point, cells in a 25-ml culture were collected by centrifugation and rapidly frozen in dry ice, until RNA isolation. Three RNA samples isolated from independently grown cultures of the cells at each starvation period (2h, 8h and 12h) were examined, and each preparation was subjected to microarray analysis. As the genes were spotted at least in duplicate, we obtained six replicates for each gene from three independent data sets per gene per starvation period.

Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes induced by nitrogen starvation in a σ54-dependent manner. To determine the effect of rpoN inactivation on gene expression after nitrogen starvation, the transcriptomes of the wild type and the rpoN strains were compared using DNA microarrays, with both strains grown on XDM2 medium and submitted to nitrogen starvation (XDM0) during 2 hours. Three RNA samples isolated from independently grown cultures of the cells were examined.

Due to the platform design, each microarray slide was divided into "LEFT" and "RIGHT", allowing the probing of two technical replicates per slide.

first: José

last: da Silva Neto

first: Suely

middle: L

last: Gomes

first: Marilis

middle: V

last: Marques


title: MicroRNA 144 impairs insulin signaling by inhibiting the expression of insulin receptor substrate 1 in Type 2 Diabetes mellitus

status: Public on Dec 18 2010

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

summary: Dysregulation in expression of microRNAs (miRNAs) in various tissues has been linked to a wide spectrum of diseases, including Type 2 Diabetes mellitus (T2D). In this study, we compared the expression profiles of miRNAs in blood samples from Impaired Fasting Glucose (IFG) and T2D male patients with tissues from T2D rat models. Healthy adult males with no past history of T2D (n=158) and with desirable cholesterol and blood pressure profiles were enrolled in this study. They were then classified according to fasting glucose levels to have T2D, IFG or as healthy controls (CTL), for comparison of miRNA expression profiles. Employing miRNA microarray, we identified ‘signature miRNAs’ in peripheral blood samples that distinguished IFG and T2D. Eight selected miRNAs were further validated using stem-loop real-time RT-PCR. miR-144 expression was found to be dysregulated in Type 2 Diabetes, wherein its expression was significantly higher than in healthy controls. Insulin receptor substrate 1 (IRS1) has been predicted to be a potential target of miR-144. Consistent with this observation, IRS1 mRNA and protein levels, verified by quantitative real-time PCR and western blotting respectively, were found to be down-regulated. Using luciferase assay, we further demonstrated that miR-144 directly targets IRS1 and showed its effects on protein expression via immunocytochemistry. From this cross-sectional study in humans, we have identified signature miRNAs which could explain the pathogenesis of T2D. Whether miRNAs like miR-144 could be potential therapeutic targets for management of T2D will need to be explored by further mechanistic and functional studies.

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

overall_design: miRNA profiling of tissues from T2D rat models.  Total RNA (plus miRNAs) was isolated using a modification of the RiboPure™-Blood kit from Ambion (Austin,TX) according to the manufacturer’s protocol. The concentration of total RNA and integrity were determined by using Nano-Drop ND-1000 Spectrophotometry (NanoDrop Tech, Rockland, Del) and gel electrophoresis respectively.

first: DwiSetyowati

last: Karolina

first: Arunmozhiarasi

last: Armugam

first: Tavintharan

last: Subramaniam