title: Gene expression profiling of lymphoblastoid cell lines from autistic and nonaffected sib pairs

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

institute: The George Washington University School of Medicine and Health Sciences

summary: Despite the identification of numerous autism susceptibility genes, the pathobiology of autism remains unknown.  The present “case-control” study takes a global approach to understanding the molecular basis of autism spectrum disorders based upon large-scale gene expression profiling.  DNA microarray analyses were conducted on lymphoblastoid cell lines from over 20 sib pairs in which one sibling had a diagnosis of autism and the other was not affected in order to identify biochemical and signaling pathways which are differentially regulated in cells from autistic and nonautistic siblings.  Bioinformatics and gene ontological analyses of the data implicate genes which are involved in nervous system development, inflammation, and cytoskeletal organization, in addition to genes which may be relevant to gastrointestinal or other physiological symptoms often associated with autism. Moreover, the data further suggests that these processes may be modulated by cholesterol/steroid metabolism, especially at the level of androgenic hormones.  Elevation of male hormones, in turn, has been suggested as a possible factor influencing susceptibility to autism, which affects ~4 times as many males as females.  Metabolic profiling of steroid hormones in lymphoblastoid cell lines from several pairs of siblings reveals higher levels of testosterone in the autistic sibling, which is consistent with the increased expression of two genes involved in the steroidogenesis pathway.  Global gene expression profiling of cultured cells from ASD probands thus serves as a window to underlying metabolic and signaling deficits that may be relevant to the pathobiology of autism.

overall_design: Gene expression profiling of LCL from autistic (21) and nonautistic (17) siblings (4 sets of autistic twins included) were obtained using a custom-printed DNA microarray containing 39,936 elements (TIGR 40K Human array, GPL3427) and a reference design in which each sample was compared to the Stratagene Universal Human RNA standard.  Following data normalization, the ratios of expression values for the autistic proband relative to his normal unaffected sibling were determined.  Related siblings are identified by their common family ID# (AU****) as provided by the Autism Resource Genetic Exchange (AGRE) repository (and listed in Sample title).  Differentially expressed genes were determined across all ratioed expression values for sib pairs (autistic vs. control) using one-class SAM (Statistical Analysis of Microarrays) analysis.

first: AnhThu

last: Nguyen

first: Kyung

last: Kim

first: Mara

middle: E

last: Steinberg

first: Tewarit

last: Sarachana

first: Michele

last: Scully

first: Steven

last: Soldin

first: Truong

last: Luu

first: Norman

middle: H

last: Lee


title: Growth temperature response in Arabidopsis

status: Public on Jul 27 2009

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

summary:
Moderate increases in the ambient temperature promote hypocotyl growth in Arabidopsis, and this response is totally dependent on the proper activity of the auxin, gibberellin, and brassinosteroid pathways. We have analyzed global the changes in gene expression that occur in Arabidopsis seedlings after a moderate increase in the growth temperature (20ºC to 29ºC for 2 hours). In order to understand how the different hormone pathways affect this growth response, the same transcription profiling analysis was conducted in seedlings deficient in each hormone.

Keywords: Growth condition

overall_design: We performed three replicas of each sample category: wild type mock-treated, wild type PAC-treated, wild type NPA-treated, and det2-1 mutants. Samples transferred from 20ºC to 29ºC of replicas #2 and #3 were labelled with Cy3, whereas those kept at 20ºC were Cy5-labelled. Samples of replica #1 were reversed-labelled.

first: J

last: Stavang

last: García-Martínez

first: M

last: Blázquez

last: Alabadí


title: Illumina HapMap CEU (HumanCytoSNP-12v1)

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

country: USA

institute: Illumina Inc.

summary: HapMap samples

overall_design: 89 samples from HumanCytoSNP-12_89CEU_FinalReport.txt


title: An optimized RNA amplification method for prokaryotic expression profiling analysis

status: Public on Jul 25 2009

city: Beijing

first: liu

last: hanhua

address: 18 Life Science Parkway

country: China

institute: CBC

summary: Conventional prokaryotic RNA labeling method usually requires large amounts of starting materials and tends to generate high background signals. Recently, two novel methods based on amplification systems were introduced. Here, we compared three alternative strategies: direct labeling method, ployadenylation-involved oligo-dT priming amplification method and random priming amplification method (hereafter referred to as DL, PAOD and RPA method in this article) for prokaryotic RNA labeling employing the expression profiling investigation in Escherichia coli (E. coli) heat shock model.

overall_design: To identify an optimal RNA labeling method for prokaryotic microarray analysis, experiments were performed with starting RNA obtained from E.coli growing at control (37°C) or heat shock (43°C) condition. We employed 0.5 μg of total RNA for a single round of amplification using PAOD and RPA methods coupling to IVT to generate cDNA targets. In addition, an approach using DL method was also performed. Three types of cDNA mixtures containing Cy5-labeled (or Cy3-labeled) control DNA and Cy3-labeled (or Cy5-labeled) DNA targets were hybridized with E.coli microarrays in a dye-swap strategy. Replicate experiments were conducted from the same batch of total RNA to assess technique reproducibility of each approach.

first: Cao

last: Fenglin

first: Liu

last: Hanhua

first: Wang

last: Yahui

last: Yu

first: Zhang

last: Xiaoyu

first: Zhou

last: Jin

last: Liang


title: Response of barley roots during the host interaction with the plasmodiophorid virus vector Polymyxa graminis

status: Public on Jul 24 2009

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

summary:
Transcriptional changes were monitored in roots of the barley cultivar Regina following inoculation with zoospores of the adapted plasmodiophorid virus vector Polymyxa graminis using the Affymetrix Barley1 GeneChip®.  Barley cv. Regina seeds were imbibed in distilled water over night and then transferred on to moist heat treated (90°C over night) sand in plastic trays that were sealed.  Trays were incubated at room temperature for 4 days to allow the seeds to germinate to Zadocks stage 07 of the decimal code for the growth stages of cereals (Tottman et al., 1979 Annals of Applied Biology, 93: 221-234; Zadocks et al., 1974 Weed Research, 14: 415-421).  110 barley (cv. Regina) seedling (Zadocks stage 07) were placed into a 90 mm diameter plastic Petri dish (3 Petri dishes per treatment) and 60 mL of P. graminis zoospore suspension added (1 x 10 6 spores mL-1).  Control plants were treated exactly the same way except zoospore-free buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen) was added.  Zoospore challenge (and control) occurred at an ambient temperature of 22°C.  Roots were excised from ten plants per treatment at ten time points (15’, 30’, 45’ 1h, 2h, 3h, 4h, 5h, 6h, 7h) and frozen in liquid nitrogen.  Three independent biological replicate experiments were done.  Total RNA was isolated from each sample using TRI-reagent following the manufacturer’s instructions (Invitrogen) and then treated with DNase I (Ambion, Texas, USA) according to the manufacturer’s protocol.  RNA samples for microarray hybridisation were further purified using RNeasy Mini Spin column purification (Qiagen, Hilden, Germany).  The integrity of the RNA samples was confirmed using the BioAnalyzer 2100 (Agilent Technologies).  Affymetrix GeneChip processing, including RNA quality control, microarray hybridisation and data acquisition was performed through contract research services by Geneservice Ltd (www.geneservice.co.uk).  A total of six hybridisations were performed.
Publication: European Journal of Plant Pathology 123(1):5-15

****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Graham RD McGrann.  The equivalent experiment is BB74 at PLEXdb.]

overall_design: pathogen isolates: Mock(3-replications);  pathogen isolates: Polymyxa graminis(3-replications)

first: Graham

middle: R

last: McGrann


title: Response of barley roots during the non-host interaction with the plasmodiophorid virus vector Polymyxa betae

summary:
Transcriptional changes were monitored in roots of the barley cultivar Regina following inoculation with zoospores of the nonadapted plasmodiophorid virus vector Polymyxa betae using the Affymetrix Barley1 GeneChip®.  Barley cv. Regina seeds were imbibed in distilled water over night and then transferred on to moist heat treated (90°C over night) sand in plastic trays that were sealed.  Trays were incubated at room temperature for 4 days to allow the seeds to germinate to Zadocks stage 07 of the decimal code for the growth stages of cereals (Tottman et al., 1979 Annals of Applied Biology, 93: 221-234; Zadocks et al., 1974 Weed Research, 14: 415-421).  110 barley (cv. Regina) seedling (Zadocks stage 07) were placed into a 90 mm diameter plastic Petri dish (3 Petri dishes per treatment) and 60 mL of P. betae zoospore suspension added (1 x 10 6 spores mL-1).  Control plants were treated exactly the same way except zoospore-free buffer (0.1 g L-1 Phostrogen, 0.5% Bovine serum albumen) was added.  Zoospore challenge (and control) occurred at an ambient temperature of 22°C.  Roots were excised from ten plants per treatment at ten time points (15’, 30’, 45’ 1h, 2h, 3h, 4h, 5h, 6h, 7h) and frozen in liquid nitrogen.  Three independent biological replicate experiments were done.  Total RNA was isolated from each sample using TRI-reagent following the manufacturer’s instructions (Invitrogen) and then treated with DNase I (Ambion, Texas, USA) according to the manufacturer’s protocol.  RNA samples for microarray hybridisation were further purified using RNeasy Mini Spin column purification (Qiagen, Hilden, Germany).  The integrity of the RNA samples was confirmed using the BioAnalyzer 2100 (Agilent Technologies).  Affymetrix GeneChip processing, including RNA quality control, microarray hybridisation and data acquisition was performed through contract research services by Geneservice Ltd (www.geneservice.co.uk).  A total of six hybridisations were performed.
Publication: European Journal of Plant Pathology 123(1):5-15.<br>

****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Graham McGrann.  The equivalent experiment is BB75 at PLEXdb.]

overall_design: pathogen isolates: Mock inoculated control(3-replications);  pathogen isolates: Polymyxa betae(3-replications)


title: Transcriptional profiling of an evolved polymorphism in E. coli

city: Missoula

first: Frank

last: Rosenzweig

state: MT

address: 32 Campus Drive, HS 104

department: Division of Biological Sciences

institute: University of Montana

summary: Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic. We sought to understand how stable polymorphism arose in an Escherichia coli population that evolved for 765 generations under continuous glucose limitation. Apart from a 29 kb deletion in the dominant clone, no large-scale genomic changes distinguish evolved clones from their common ancestor. However, when co-evolved clones are cultured separately their transcriptional profiles differ markedly from that ancestor, and do so in ways that are consistent with our understanding of how E. coli adapts to glucose limitation. All adaptive clones exhibit reduced activity of the stationary-phase sigma factor σS and increased expression of glucose transport genes, including the glycoporin LamB and the galactose transporter MglABC. Other expression differences, such as up-regulation of acetyl-CoA synthetase, are clone-specific and confirm previous reports of acetate cross-feeding in this system. When co-evolved clones are cultured together, transcription profiling reveals another class of genes whose expression in the dominant clone differs from that observed when the clone is cultured by itself. Many of these genes are part of the CpxR-mediated stress response. CpxR activation in monoculture likely results from extracellular accumulation of acetate that is removed by acetate-scavenging strains in co-culture. Targeted gene sequencing reveals that global regulatory mutations in σS as well as small-scale regulatory mutations in the maltose and acetyl CoA synthetase operons contribute to the evolution of cross-feeding. Finally, we identified two mutations in the founder that likely pre-disposed the experimental population to develop specialists that thrive on overflow metabolites. Subsequent mutations that lead to specialization emphasize the importance of compensatory rather than gain-of-function mutations in this system. Observations that polymorphism readily evolves in an asexual population, that adaptive mutants arise without large-scale change in genome architecture, and that morphs have both common and unique patterns of gene expression influenced by whether they are cultured separately or together, underscore the importance of regulatory change, founder genotype, and the biotic environment in the adaptive evolution of microbes.

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

overall_design: Four isolates of E. coli evolved under long-term glucose limitation were grown in glucose-limited chemostat culture to steady state.  Each isolate was grown separately (i.e in monoculture) in triplicate and three of the four (CV101, CV103, CV115 and CV116) were grown as a consortium in duplicate.  Each experiment, or biological replicate, was sampled twice for monoculture experiments and once for consortium experiments.  Total RNA from each sample was competitvely hybridized against total RNA from the common ancestor of the isolates grown at the same time in a separate chemostat using the same feed medium.  For monoculture experiments,  three hybridizations were done for each experiment: two hybridizations comparison for the first sample and a single hybridization for the second (with the exception of sample Jv116-1A which was only hybridized twice due to lack of sufficient RNA).  For consortium experiments, two hybridizations were done for each biological replicate.

first: Margie

middle: A

last: Kinnersley

first: William

last: Holben


title: Zoarces viviparus evaluation data

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

summary: A 50-mer oligonucleotide microarray was designed for large-scale gene expression analysis in Z. viviparus. To measure the expression of the probes and the corresponding assembled transcripts, the pool of mRNA used for the sequencing was hybridized.

overall_design: 1 Sample hybridized to microarray used to evaluate the transcript assembly described in Kristiansson et al 2009.

first: Noomi

last: Asker

first: Lars

last: Förlin

first: Joakim

last: Larsson


title: Array comparative genome hybridization of an evolved polymorphism in E. coli

overall_design: Four isolates of E. coli evolved under long-term glucose limitation and their common ancestor were grown in Luria broth to stationary phase.   Genomic DNA from each of the evolved isolates was competitively hybridized against genomic DNA from the ancestral strain.


title: Parallel expression evolution of oxidative stress-related genes in fiber of wild/domesticated & diploid/polyploid cotton

city: Athens

first: Alan

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

summary: Reactive oxygen species (ROS) play a prominent role in signal transduction and cellular homeostasis in plants. However, imbalances between generation and elimination of ROS can give rise to oxidative stress in growing cells. Because ROS are important to cell growth, ROS modulation could be responsive to natural or human-mediated selection pressure in plants. To study the evolution of oxidative stress related genes in a single plant cell, we conducted comparative expression profiling analyses of the elongated seed trichomes (‘‘fibers’’) of cotton (Gossypium), using a phylogenetic approach.  We measured expression changes during diploid progenitor species divergence, allopolyploid formation and parallel domestication of diploid and allopolyploid species, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes in progenitor diploid species revealed significant up-regulation of ROS scavenging and potential signaling processes in domesticated G. arboreum. Similarly, in two independently domesticated allopolyploid species (G. barbadense and G. hirsutum) antioxidant genes were substantially up-regulated in comparison to antecedent wild forms. In contrast, analyses of three wild allopolyploid species indicate that genomic merger and ancient allopolyploid formation had no significant influences on regulation of ROS related genes. Remarkably, many of the ROS-related processes diagnosed as possible targets of selection were shared among diploid and allopolyploid cultigens, but involved different sets of antioxidant genes.  Our data suggests that parallel human selection for enhanced fiber growth in several geographically widely dispersed species of domesticated cotton resulted in similar and overlapping metabolic transformations of the manner in which cellular redox levels have become modulated.

sample_organism:
Gossypium hirsutum
Gossypium arboreum
Gossypium raimondii
Gossypium tomentosum

overall_design: We measured expression changes during diploid progenitor species divergence, allopolyploid formation and parallel domestication of diploid and allopolyploid species, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes was studied for domesticated G. arboreum and two independently domesticated allopolyploid species (G. barbadense and G. hirsutum). These were compared to three wild allopolyploid species.  Three biological replicates were performed.

first: Bhupendra

last: Chaudhary

first: Ran

last: Hovav

first: Lex

last: Flagel

first: Ron

last: Mittler

first: Jonathan

middle: F

last: Wendel


city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

department: Biology

country: Portugal

institute: University of Aveiro

summary: miRNA expression profiling of human monocyte-derived dendritic cells (moDCs) during maturation. Immature, 4h and 16h LPS-activated moDCs were used.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study were analysed 2 biological samples of RNA extracted from 4h-post LPS stimulation moDCs and 2 bfrom 16h-post LPS stimulation. The RNA from 0h-post LPS stimulation were used as reference sample. Were also performed dye-swaps of each biological sample as technical replicates.

first: Maurizio

last: Ceppi

first: Patricia

middle: M

first: Isabelle

last: Dunand-Sauthier

first: Walter

last: Reith W

first: Manuel

last: Santos

first: Philippe

last: Pierre


title: A host type I interferon response is induced by cytosolic sensing of the bacterial second messenger cyclic-di-GMP

status: Public on Jul 22 2009

city: Berkeley

first: Russell

last: Vance

address: 415 Life Science Addition

institute: UC Berkeley

summary: The innate immune system responds to unique molecular signatures that are widely conserved among microbes but that are not normally present in host cells.  Compounds that stimulate innate immune pathways may be valuable in the design of novel adjuvants, vaccines, and other immunotherapeutics.The cyclic dinucleotide cyclic-di-guanosine  monophosphate (c-di-GMP) is a recently appreciated second messenger that plays critical  regulatory roles in many species of bacteria but is not produced by eukaryotic cells. In  vivo and in vitro studies have previously suggested that c-di-GMP is a potent  immunostimulatory compound recognized by mouse and human cells. Here we provide  evidence that c-di-GMP is sensed in the cytosol of mammalian cells via a novel  immunosurveillance pathway. The potency of cytosolic signaling induced by cyclic-di-  GMP is comparable to that induced by cytosolic delivery of DNA, and both nucleic acids  induce a similar transcriptional profile, including triggering of type I interferons and coregulated  genes via induction of TBK1, IRF3, NF-!B and MAP kinases. However, the  cytosolic pathway that senses c-di-GMP appears to be distinct from all known nucleic  acid-sensing pathways.Our results suggest a novel mechanism by which host cells can  induce an inflammatory response to a widely produced bacterial ligand.

overall_design: Three-condition experiment: macrophages transfected with mono-GMP (negative control), double-stranded DNA (positive control), or cyclic-di-GMP (experimental condition).  Biological replicates: two, independently treated, harvested, and hybridized to arrays.  One replicate per array, except two technical replicates were performed for one of the positive control samples.

first: Sarah

last: McWhirter

first: Roman

last: Barbalat

first: Kathryn

last: Monroe

first: Mary

last: Fontana

first: Mamoru

last: Hyodo

first: Nathalie

middle: T

last: Joncker

first: Ken

middle: J

last: Ishii

first: Shizuo

last: Akira

first: Marco

last: Colonna

first: Zhijian

last: Chen

first: Katherine

last: Fitzgerald

first: Yoshihiro

last: Hayakawa


title: Transcriptional profile comparison of M. tuberculosis PDIM spontaneous mutants

city: Montreal

first: Pilar

last: Domenech

state: Quebec

address: 1001 Décarie Boulevard

department: IDIGH Program

country: Canada

institute: Research Institute of McGill University Health Centre

summary: Transcriptional profile comparison among PDIM positive and negative isolates. Standard in vitro exponential phase cultures of M. tuberculosis H37Rv ATCC27294 were plated on 7H11 plates. Individual colonies were sub-cultured in 7H9 broth and metabolically labeled with [14C] propionic acid. The apolar lipid fraction was then extracted from those cultures and assayed for PDIM (phthiocerol dimycocerosate) content via TLC. Individual isolates producing and deficient in PDIM were selected for performing transcriptional profile comparisons.

overall_design: Four M. tuberculosis clones derived from the same parental strain were compared. Two of them were PDIM producers while the other two were PDIM deficient. Two or four replicates were performed for each comparison using two different biological samples.

first: Michael

last: Reed


title: Genomic comparison of M. tuberculosis PDIM spontaneous mutants

summary:
Genomic comparisons among PDIM positive and negative isolates.
Standard in vitro exponential phase cultures of M. tuberculosis H37Rv ATCC27294 were plated on 7H11 plates. Individual colonies were sub-cultured in 7H9 broth and metabolically labeled with [14C] propionic acid. The apolar lipid fraction was then extracted from those cultures and assayed for PDIM (phthiocerol dimycocerosate) content via TLC. Individual isolates producing and deficient in PDIM were selected for performing genomic comparisons.

overall_design: Four M. tuberculosis clones derived from the same parental strain were compared. Two of them were PDIM producers while the other two were PDIM deficient. Two replicates were performed for each comparison.


title: Global survey of miRNA microarray of MCF-7 cells with or without estrogen (E2) treatment

city: bukyo-ku

first: kaoru

last: yamagata

state: Tokyo

address: yayoi 1-1-1

country: Japan

institute: university of tokyo

summary: To examine the effect of E2 treatment for the miRNA expression in human MCF-7 cells, MCF-7 cells were treated with or without E2 (100 nM) for 4 hr or 24 hr.

overall_design:
Four group experiments;
E2 (100 nM) treatment for 4 hr (MCF-7 E2 4h_1, MCF-7 E2 4h_2),
vehicle (ethanol) treatment for 4 hr as Mock control (MCF-7 Mock1, MCF-7 Mock2),
E2 (100 nM) treatment for 24 hr (MCF-7 E2 24h_1, MCF-7 E2 24h_2, MCF-7 E2 24h_3),
vehicle treatment for 24 hr as Mock control (MCF-7 Mock_3, MCF-7 Mock_4, MCF-7 Mock_5).

first: Kaoru

last: Yamagata

first: Ken-ichi

last: Takeyama

first: Shigeaki

last: Kato


title: Involvement of the brain renin-angiotensin system in the effects of maternal separation

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute for Developmental Genetics

country: Germany

institute: German Research Center for Environmental Health

summary:
The postnatal development of the mouse is characterized by a stress hyporesponsive period (SHRP), where basal corticosterone levels are low and responsiveness to mild stressors is reduced. Maternal separation is able to disrupt the SHRP and is widely used to model early trauma. In this study we aimed at identifying of brain systems involved in acute and possible long-term effects of maternal separation. We conducted a microarray-based gene expression analysis in the hypothalamic paraventricular nucleus after maternal separation, which revealed 52 differently regulated genes compared to undisturbed controls, among them are 37 up-regulated and 15 down-regulated genes. One of the prominently unregulated genes,  angiotensinogen, was validated using a in-situ hybridization. Angiotensinogen is the precursor of angiotensin II the main effector of the brain renin-angiotensin system (RAS), which is known to be involved in stress system modulation in adult animals. Using the selective angiotensin type I receptor (AT(1)) antagonist candesartan we found strong effects on CRH and GR mRNA expression in the brain and ACTH release following maternal separation. AT(1) receptor blockade appears to enhance central effects of maternal separation in the neonate, suggesting a suppressing function of brain RAS during the SHRP. Taken together, our results illustrate the molecular adaptations that occur in the paraventricular nucleus following maternal separation and identify signaling cascades, that control stress system activity in the neonate.

Keywords: phenotype

overall_design: Litters were randomly assigned to either a maternally non-separated or 24 hour maternally separated condition. At the time of testing, all pups from a litter were sacrificed immediately by decapitation.

first: Claudia

last: Liebl

first: Marcus

last: Panhuysen

first: Benno

last: Pütz

first: Jan

last: Deussing

first: Wolfgang

last: Wurst

first: Marianne

middle: B

last: Müller

first: Mathias

middle: V

last: Schmidt


title: Gene expression based identification of potential genes involved in Fanconi anemia

status: Public on Jul 21 2009

city: chennai

first: pavithra

last: shyamsunder

address: iitm

country: India

institute: iit madras

summary: Fanconi anemia is a rare inherited hematological disorder which commonly presents with bone marrow failure, developmental abnormalities and susceptibility to cancer with high rates of prevalence in ethnic populations.  The objective of this study was to identify potential genes that aid in the progression of the disease or produce its principal symptoms and to hypothesize enabling roles for certain genes that are not part of the central molecular machinery causing the disease.

overall_design: A total of 2 Fanconi anemia samples were collected from patients who displayed characteristic FA features. All of them gave positive results for the DNA breakage test after mitomycin C treatment. Samples were referred by Dr. Sheila Mohan of REFAIN (Registry for Fanconi anemia in India). Whole genome microarray analysis of peripheral blood from 2 patient samples and one normal individual. Sequential analysis of microarray data was carried out using gene ontology and pathway analysis to identify candidate genes.

first: Rama

middle: S

last: Verma

first: Pavithra

last: Shyamsunder

first: Prasanna

last: Vidyasekar

first: Sheila

last: Mohan


title: Global survey of miRNA microarray of whole embryo, wild type vs estrogen receptor alpha knockout mice

first: kaoru

last: yamagata

summary: To examine the effect of estrogen receptor alpha for the miRNA expression, total RNA extracted from whole embryos at E18.5 of wild type and Estrogen Receptor alpha knock-out mice

overall_design: Two group experiment (wild type and ER alpha KO)


title: Phaseolotoxin synthesis is regulated by the GacS/GacA two-component system

status: Public on Jul 20 2009

city: Irapuato

first: Jose Luis

last: Hernandez-Flores

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

summary: Pseudomonas syringae pv. phaseolicola is the causal agent of halo blight disease of beans (Phaseolus vulgaris L.), which is characterized by water-soaked lesions surrounded by a chlorotic halo resulting from the action of a non-host-specific toxin known as phaseolotoxin, that inhibits the enzyme ornithine carbamoyltransferase involved in the arginine biosynthesis pathway. It was previously reported that genes within the Pht cluster were involved in the regulation and synthesis of phaseolotoxin. The GacS/GacA two component signal transduction system controls important pathogenicity and virulence mechanisms in several Gram-negative bacteria. In the present study we hybridized a genomic microarray of P. syringae pv. phaseolicola NPS3121 to compare transcriptional profiles from wild type strain and a gacA- null mutant with a Tox- 11 phenotype. Results show that GacA controls expression of genes within the Pht cluster as well as another group of clustered genes located in a 13 different region in the bacterial chromosome that contains at least one gene unambiguously shown to be directly involved in phaseolotoxin biosynthesis. Results suggest that this cluster is a new pathogenicity island containing genes whose regulation is also under GacA regulatory cascade and it will require further investigation to determine gene functions and their relationship to virulence mechanisms

overall_design: Transcriptional profiles of a P. syringae pv. phaseolicola NPS3121 null gacA mutant were compared to those of the wild-type strain. Cultures were grown in minimal medium at 18°C (which is the temperature at which phaseolotoxin is produced and the bacteria achieves full virulence) and harvested during the late log phase of the exponential growth. RNA from three biological replicates and each with two technical replicates were hybridize to control variation that might affect data interpretation.

first: Susana

last: De La Torre- Zavala

first: Alejandro

last: Hernández-Morales

first: Selene

last: Aguilera-Aguirre

first: Enrique

last: Ibarra-Laclette

first: José-Luis

last: Hernández-Flores

first: Ariel

last: Álvarez-Morales


title: Global survey of miRNA Taqman RT-PCR of whole embryo: wild-type vs. estrogen receptor alpha knockout mice

first: Kaoru

last: Yamagata

first: Ken-ichi

last: Takeyama

first: Shigeaki

last: Kato


title: PSY3642_to_PSY3639_SC_aerobic

city: Boston

first: Caleb

middle: John

last: Kennedy

state: MA

address: 200 Longwood Avenue, WAB 536

department: Systems Biology

institute: Harvard Medical School

summary: We designed and experimentally validated an in silico gene deletion strategy for engineering endogenous one-carbon (C1) metabolism in yeast.  Specifically, a Flux Balance Analysis (FBA) model predicted that five genes ALT2, FDH1, FDH2, FUM1, and ZWF1, when deleted in combination, would cause Saccharomyces cerevisiae to overproduce and secrete formic acid under aerobic growth conditions. Once constructed, the quintuple mutant strain showed the predicted increase in formic acid secretion relative to a formate dehydrogenase mutant (fdh1 fdh2 ), while formic acid secretion in wild-type yeast was undetectable. Gene expression and physiological data generated post hoc identified a mitochondrial deficiency phenotype in the engineered strain and regulatory events that suggest a role for multisite modulation—the coordinated expression of multiple pathway enzymes—in controlling yeast C1 metabolism. Together, these results demonstrate that FBA-based modeling strategies can be useful tools for non-fermentative pathway design and discovery in eukaryotic microbes. In addition, the results indicate that seemingly unrelated mutations can be combined to modulate flux through biochemical reactions that interact at a systems level across subcellular compartments.

overall_design: Samples were processed in biological triplicate with one sample processed with dye orientations reversed to minimize the effects of incorporation bias.

first: Pamela

last: Silver

first: Patrick

last: Boyle


title: Global survey of miRNA microarray of uterus, ovariectomized female mice with or without estrogen (E2) treatment

summary: To examine the effect of E2 treatment for the miRNA expression, at 15 week old, female wiled type mice were ovariectomized, and after one week, estradiol (E2) was delivered at a concentration of 0.050 mg/kg body weight/day. 24 hours after chemical treatment, uteruses from mice treated with or without E2 were dissected.

overall_design: Two group experiment (WT-OVX and WT-OVX-E2) three replicates per condition


title: miRNA expression in cytokine-stimulated airway smooth muscle cells

city: Reno

first: Cherie

last: Singer

state: NV

address: 1664 N. Virginia St

department: Pharmacology MS318

institute: University of Nevada School of Medicine

summary: We used microarrays to determine if miRNA expression in human airway smooth muscle cells is altered by a pro-inflammatory stimulus.   A majority of the miRNAs on the array exhibited very low signal intensity. In ASM cells exposed to IL-1β, TNFα, and IFNγ, none of the miRNA expressed were significantly up-regulated with cytokine treatment.  We did observe 11 miRNA down-regulated > 2-fold in both cultures with cytokine treatment. These miRNA include described human miRNA miR-23a, -23b, -25, -188, -320, -363, -489, as well as mouse and rat miRNA homologous to miR-140*, mouse miR-329 and a novel miRNA, abi-13268.

overall_design: miRNA arrays for cytokine-stimulated ASM cells were completed in duplicate from two different cultures to identify candidate miRNA for further study.  Cultures were growth arrested for 48 hours and treated with 10 ng/ml IL-1β, TNFα, and IFNγ for 24 hrs.  A comparison of miRNA expression under cytokine-stimulated and non-treated conditions from hybridized miRNA arrays was calculated as described.

first: Andrew

last: Kuhn

first: Karen

last: Schlauch

last: Halayko

first: William

last: Gerthoffer


title: Downregulation of cinnamoyl-coenzyme A reductase in maize (affy_ccr_maize)

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary:
affy_ccr_maize - affy_ccr_maize - Cinnamoyl-CoA reductase (CCR) catalyzes a key step in monolignol biosynthesis. We show that downregulation of CCR in maize was associated with lower lignin content and a strong decrease in H units. Concomitantly, these cell wall modifications were associated with higher digestibility. On another hand, immunocytochemistry indicated a modification of lignification pattern and cellulose content. Transcript profiling was used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers. -2 wild type and 2 CCR mutants were compared. Plants were grown in greenhouse condition and harvested at 7-8 leaf stages.

Keywords: gene knock in (transgenic)

overall_design: 4 arrays - maize

first: Sandrine

last: Balzergue

first: Deborah

last: Goffner

first: Magalie

last: Pichon

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Characterization of Two Outer Membrane Proteins, FlgO and FlgP, that Influence Vibrio cholerae Motility

status: Public on Jul 18 2009

city: Hanover

first: Ronald

middle: K

last: Taylor

state: NH

address: N. College Street HB7550

department: Microbiology

institute: Dartmouth Medical School

summary: Vibrio cholerae is highly motile by the action of a single polar flagellum. The loss of motility reduces the infectivity of V. cholerae, demonstrating that motility is an important virulence factor. FlrC is the sigma-54-dependent positive regulator of flagellar genes. Recently, the genes VC2206 (flgP) and VC2207 (flgO) were identified as being regulated by FlrC by microarray analysis of an flrC mutant. FlgP is reported to be an outer membrane lipoprotein required for motility that functions as a colonization factor. The study reported here focuses on the characterization of flgO, the first gene in the flgOP operon. We show FlgO/P are important for motility, as these mutants have reduced motility phenotypes. The flgO/P mutant populations display fewer motile cells as well as reduced numbers of flagellated cells. The flagella produced by the flgO/P mutant strains are shorter in length than the WT flagella, which can be restored by inhibiting rotation of the flagellum. FlgO is an outer membrane protein that localizes throughout the membrane and not at the flagellar pole. Although FlgO/P do not specifically localize to the flagellum, they are required for flagellar stability. Due to the nature of these motility defects, we established that the flagellum is not sufficient for adherence, rather, motility is the essential factor required for attachment and thus colonization by V. cholerae O1 of the classical biotype. This study reveals a novel mechanism for which the OMPs FlgO and FlgP function in motility to mediate flagellar stability and influence attachment and colonization.

overall_design: Vibrio cholerae O395 vs. rpoN mutant

first: Raquel

last: Martinez

first: Madushini

middle: N

last: Dharmasena

first: Thomas

last: Kirn

first: Carol

last: Ringelberg


title: miRNA expression in human tracheal smooth muscle

summary: We surveyed miRNA expression in intact airway smooth muscle tissue to evaluate candidate miRNA for further studies.  We found 60 miRNA expressed at a detectable level in all four donors and another 118 miRNA expressed in three of the four donors.  There were 18 miRNAs with expression levels > 2-fold above normalized expression values.  These consisted of 12 described human miRNA, including let-7c, miR-16, -23b, -24, -26a, -125b, -143, -145, -200c and -205; 3 mouse miRNAs including miR-99a, -140* and -370; and 3 novel miRNA termed abi-13143, -13232 and -13268.

overall_design: Total RNA was obtained commerically from tracheal smooth muscle of 4 donors ranging in age from 20 years old to 87 years old.  The donors included one female, were of varying races and care was taken to ensure that the cause of death was not due to clinical signs of asthma. Each sample was hybridized to miRNA arrays in duplicate, except for the sample from the female donor, which was hybridized to one array only due to lack of material. Normalized intensities were averaged across sample replicates, except for the female patient which was only analyzed on one array to generate this data set.


title: Implications of high level pseudogene transcription in Mycobacterium leprae

city: Baton Rouge

first: Diana

last: Williams

state: LA

address: Skip Bertman Dr.

department: Laboratory Res Branch

institute: HRSA, BPHC, NHDP

summary:
Approximately half of M. leprae’s transcriptome consists of inactive gene products. This has an impact on overall energy and resource consumption without potential benefit to this organism. However, multiple translational ‘silencing’ mechanisms are present, reducing additional energy and resource expenditure required for protein production from these transcripts.

The Mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. Preliminary evidence suggests that some pseudogenes are expressed. Therefore, defining pseudogene transcriptional and translational potentials should increase our understanding of their impact on M. leprae physiology.

To address this, M. leprae was purified from the granulomatous hind footpad tissue of four individual nu/nu nude mice six months post-infection. M. leprae whole genome DNA microarrays representing the 1,614 annotated ORFs and 1,133 identified pseudogenes, were obtained from the Leprosy Research Support and Maintenance of an Armadillo Colony Post-Genome Era, Part I: Leprosy Research Support Contract (NO1 AI-25469) at Colorado State University. To validate 20% of genes positive by microarray analysis, RT-PCR was performed.

Results of this study Gene expression analysis identified transcripts from 49% of all M. leprae genes including 57% of all ORFs and 43% of all pseudogenes in the genome. Pseudogenes were randomly distributed throughout the chromosome. Factors resulting in pseudogene transcription included: 1) co-orientation of transcribed pseudogenes with transcribed ORFs within or exclusive of operon-like structures; 2) the paucity of intrinsic stem-loop transcriptional terminators between transcribed ORFs and downstream pseudogenes; and 3) predicted pseudogene promoters. Mechanisms for translational silencing of pseudogene transcripts included the lack of both translational start codons and strong Shine-Dalgarno sequences. Transcribed pseudogenes also contained multiple in-frame stop codons and high Ka/Ks ratios, compared to that of homologs in M. tuberculosis and ORFs in M. leprae. A pseudogene transcript containing an active promoter, strong SD site, a start codon, but containing two in frame stop codons yielded a protein product when expressed in E. coli. Approximately half of M. leprae's transcriptome consists of inactive gene products consuming energy and resources without potential benefit to M. leprae. Presently it is unclear what additional detrimental affect(s) this large number of inactive mRNAs has on the functional capability of this organism. Translation of these pseudogenes may play an important role in overall energy consumption and resultant pathophysiological characteristics of M. leprae. However, this study also demonstrated that multiple translational silencing mechanisms are present, reducing additional energy and resource expenditure required for protein production from the vast majority of these transcripts.

overall_design: The overall design of this study was to identify the transcriptome of M. leprae in the granulomatous tissue of the mouse hind foot pad 6 months post infection.

first: Richard

last: Slayden

first: Alejandra

first: Tana

last: Pittman

first: Alex

last: Mira

first: Anirban

last: Mitra

first: Valakunja

last: Nagaraja

first: Norman

middle: E

last: Morrison

first: Milton

last: Moraes

middle: P

last: Gillis


title: Fish oil supplementation induces anti-atherogenic gene expression profiles in human blood mononuclear cells

status: Public on Jul 17 2009

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Fish oil supplementation is generally seen as beneficial for human health, due to the presence of n-3 polyunsaturated fatty acids (n-3 PUFAs). These fatty acids can elicit their effect through changes in gene expression. Effects of n-3 PUFAs on gene expression of inflammatory and atherogenic markers have been shown in several in vitro and animal studies. However, little evidence is available on human in vivo studies on n-3 PUFA related gene expression. In the present study we investigate the effects of EPA and DHA supplementation for 6 months on gene expression profiles of peripheral blood mononuclear cells (PBMCs). Whole genome microarray analysis was performed on PBMC RNA from subjects who received 1.8 grams of EPA and DHA in capsules (n=23) or capsules containing high oleic acid sunflower oil (HOSF)(n=25). Intake of EPA and DHA resulted in a change of 1040 genes. We found a down-regulation in inflammatory and atherogenic related pathways, such as NF-κB signaling, eicosanoid synthesis, scavenger receptors activity and cell adhesion. These results seem to point to an improvement in health status, in which lymphocytes are less prone to produce chemokines and adhesion molecules and monocytes show reduced susceptibility to differentiate into foam cells. Overall, beneficial effects of n-3 PUFAs that have been described in vitro and in animal studies, were shown in vivo in human subjects in this study. This not only confirms that EPA and DHA elicits beneficial effects on inflammatory and atherogenic processes of elderly subjects, but also shows that PBMC gene expression profiles can be used to show effects of nutrition on human health status.

overall_design: Fasting venous blood samples were collected at baseline and after 26 weeks of supplementation with either 1.8 g EPA and DHA or HOSF. 4 ml blood was collected for PBMC isolation, using BD Vacutainer Cell Preparation Tubes with sodium citrate (BD, Breda, The Netherlands). Immediately after blood collection PBMCs were isolated according to the manufacturer’s manual.  PBMC RNA was isolated from all PBMC samples using Qiagen RNeasy Micro kit (Qiagen, Venlo, the Netherlands). Total RNA from PBMCs from 48 subjects was labeled using a one-cycle cDNA labeling kit (MessageAmpTM II-Biotin Enhanced Kit, Ambion, Inc.) and hybridized to custom designed NuGO GeneChip arrays.

first: Mark

last: Bouwens

first: Mechteld

last: Grootte Bromhaar

first: Michael

last: Müller

first: Lydia

last: Afman


title: Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush

status: Public on Jul 16 2009

city: Memphis

first: William

middle: Edwin

last: Orr

state: TN

address: 930 Madison Avenue, Suite 757

department: Ophthalmology

institute: University of Tennessee Health Science Center

summary: Retinal ganglion cell (RGC) death is the final consequence of many blinding diseases, where there is considerable variation in the time course and severity of RGC loss. Indeed, this process appears to be influenced by a wide variety of genetic and environmental factors. In this study we explored the genetic basis for differences in ganglion cell death in two inbred strains of mice. We found that RGCs are more susceptible to death following optic nerve crush in C57BL/6J mice (54% survival) than in DBA2/J mice (62% survival). Using the Illumina Mouse-6 microarray, we identified 1,580 genes with significant change in expression following optic nerve crush in these two strains of mice. Our analysis of the changes occurring after optic nerve crush demonstrated that the greatest amount of change (44% of the variance) was due to the injury itself. This included changes associated with ganglion cell death, reactive gliosis, and abortive regeneration. The second pattern of gene changes (23% of the variance) was primarily related to differences in gene expressions observed between the C57BL/6J and DBA/2J mouse strains. The remaining changes in gene expression represent interactions between the effects of optic nerve crush and the genetic background of the mouse. We extracted one genetic network from this dataset that appears to be related to tissue remodeling. One of the most intriguing sets of changes included members of the crystallin family of genes, which may represent a signature of pathways modulating the susceptibility of cells to death. Differential responses to optic nerve crush between two widely used strains of mice were used to define molecular networks associated with ganglion cell death and reactive gliosis. These results form the basis for our continuing interest in the modifiers of retinal injury.

overall_design: 18 Samples: 9 per strain (C57BL/6J & DBA/2J); 3 conditions per strain

first: Justin

last: Templeton

first: Mohamed

last: Nassr

first: Felix

last: Vazquez-Chona

first: Natalie

last: Freeman-Anderson

first: Robert

middle: W

first: Eldon

last: Geisert


title: DNA methylation comparison of ntTS, TS and ES cells

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

institute: Keio University

type: Methylation profiling by genome tiling array

summary: Placental abnormalities occur frequently in cloned animals. To investigate DNA methylation profile of trophoblast cell lineage of somatic cell nuclear transferred (NT) embryos, we established TS cells from blastocysts produced by NT at the blastocyst stage.

overall_design: Three independent TS cell lines derived from NT embryos rom BDF1 background were used in this study. Two control lines, derived from native blastocysts of BDF1 background, were also used.

first: Keiji

last: Hirabayashi

first: Shintaro

last: Yagi

first: Kunio

last: Shiota


title: Within and between-species transcript profiling during cotton fibre development

city: Canberra

first: Yves

last: Al-Ghazi

state: ACT

address: Clunies Ross

department: Plant Industry

country: Australia

institute: CSIRO

summary:
A gene expression profiling study on two major cotton species that are cultivated for fibre, Gossypium hirsutum (L.) and Gossypium barbadense (L.), at different stages during fibre development using a printed cDNA microarray was undertaken to identify potential candidate genes for manipulation to improve fibre quality.
Keywords: Species comparison, development

sample_organism:
Gossypium barbadense
Gossypium hirsutum

overall_design: Three-condition experiment: 7, 11 and 21 day post anthesis. Biological replicates: 3, Two species compared at each condition: Gossypium.hirsutum and Gossypium.barbadense.  One replicate per array, dye swap, one rep per array.

first: Danny

last: Llewellyn


title: Murine fetal liver TER119-negative erythroid precursors: Hipk1 or Hipk2 knockdown versus control

city: Cambridge

first: Shilpa

middle: Manohar

last: Hattangadi

address: 9 Cambridge Center

department: Lodish Lab

institute: Whitehead Institute (WIBR)

summary: Expression profiling of fetal liver erythroid precursors after either Hipk1 or Hipk2 knockdown by shRNA versus control shRNA

overall_design: Two condition experiment, Hipk1 or Hipk2 knockdown versus control (shRNA against luciferase), two replicates each shRNA

first: Karly

last: Burke


title: Gene Expression Data from Senescent vs Non-senescent Cells in the in Vivo Human Annulus

status: Public on Jul 15 2009

city: Charlotte

first: Helen

last: Gruber

state: NC

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

summary:
The presence of senescent cells in the aging/degenerating human disc is now well-recognized. Senescent cells are viable, cannot divide, remain metabolically active and accumulate within the disc over time. Molecular analysis of senescent cells in tissue, however, offers a special challenge since there are no cell surface markers for senescence which would let one use fluorescence-activated cell sorting as a method for separating out senescent cells. Here we use a novel experimental design using laser capture microdissection to selectively separately harvest senescent and non-senescent annulus cells in paraffin-embedded tissue, and then compare their gene expression with microarray analysis.
An initial in vitro study using cultured human annulus cells was first performed to test whether there was any difference in identification of senescent cells using the accepted histochemical methodology vs. the immunofluoresent identification of cells positive for senescence-associated-ß-galactosidase in control cells and cells induced into stress-induced premature senescence via hydrogen peroxide exposure. No statistically significant difference was found between the 2 methods. Laser capture microdissection was used to separately harvest senescent and non-senescent cells from 11 human annulus specimens, and microarray analysis was used to determine gene expression levels. Genes with established relationships to senescence were found to be significantly upregulated in senescent cells vs. non-senescent cells. Additional genes related to cytokines, cell proliferation, and other cell processes were also identified.

overall_design: Disc Tissue samples were obtained from surgical disc procedures performed on patients with herniated discs and degenerative disc disease. Tissue was fixed and paraffin embedded. Standard laser capture microdissection (LCM) techniques were used to collect senescent cells. Remaining non-senescent cells were scraped from the histology slide. Total RNA was isolated and analyzed via mircoarray. Gene expression from senescent cells was compared to non-senescent cells. Eight histological samples were used to obtain both senescent and non-senescent cells. From an additional 3 samples, only senescent cells were harvested.

first: Gretchen

last: Hoelscher

first: Jane

middle: A

last: Ingram

first: Natalia

last: Zinchenko

first: Edward

last: Hanley Jr


title: Transcriptome of S.pyogenes induced by the signaling peptide SilCR

city: Jerusalem

first: Ilia

last: Belotserkovsky

address: Ein-Kerem Campus

department: Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University

summary: Transcriptional regulation of S. pyogenes strain JS95, containing streptococcal invasion locus (sil) by the pheromone quorum-sensing peptide SilCR. Transcriptional profiling was conducted by comparing untreated JS95 culture with SilCR-treated cultures, using two concentrations of SilCR (10 or 0.05 µg/ml) and two incubation times (10 or 180 minutes). As a control, we used JS95-derived mutant deficient of the two-component system SilA-SilB that is necessary for SilCR signaling (ΔsilAB).

overall_design: Two-condition experiment: with vs. without SilCR of WT JS95 strain; without vs. with SilCR of ΔsilAB mutant. Two biological repeates were performed for experiment using WT JS95 treated with 10 µg/ml SilCR for 10 minutes.

first: Miriam

last: Ravins

first: Yoav

last: Smith

first: Asaf

last: Peer

first: Emanuel

last: Hanski


title: Drosophila developmental expression data

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

summary: In this study we aimed to obtain gene expression data during development of Drosophila melanogaster. Therefore 10 critical stages from egg to adult fly were chosen. Specifically the purpose of the project was to study gene expression in the under-replicated regions of polytene chromosomes that were discovered earlier (see GSE2551).

overall_design: Biological samples from ten developmental stages were collected: 0-1 hour embryos, 5-6 hours embryos, 11-12 hours embryos, 1st instar larvae 0-1 hour after hatching, 2nd instar larvae after molt, 3rd instar larvae after molt, 0-1 hour prepupae, 13-14 hours pupae, adult males and adult females. 0-1h embryos demonstrate maternally expressed genes. 5-6h embryos represent early zygotic expression. 11-12h embryos represent organogenesis of larva. 1st instar larvae are freshly hatched completely formed larvae. 2nd instar larvae were collected after first molt. 3rd instar larvae were collected after second molt. 0-1h prepupae represent early metamorphosis. 13-14h pupae represent organogenesis of adult fly. Adult males and females collected separately represent differences between sexes. Embryos were collected as follows: flies were allowed to lay eggs for 45 min on the agar/apple juice medium with some yeast. Embryos were either collected immediately and frozen at -80°C or allowed to develop at 25°C to the stage of interest and then collected and frozen. 1st instar larvae were collected right after hatching. 2nd and 3rd larvae were collected after corresponding molts, 24 hours and 48 hours after hatching. 0-1 hour prepupae were picked each hour from the tube walls and either frozen at -80°C immediately or allowed to develop at 25°C to for 13 hours to obtain 13-14 hours pupae. Adult males and females were collected twice a day, kept for 3 days at 25°C and then separated and frozen at -80°C. The females collected in this way were mated. Total RNA isolation from the frozen samples was performed with TRIzol reagent (Invitrogen, #155-96-011). RNAs from ten stages were isolated in parallel and diluted to the same concentration (4ug/ul). The reference sample was prepared by mixing of the same amount of total RNA from each stage. 25ug of sample and reference RNAs were labeled with either Cy-3 or Cy-5 dUTPs (Amersham, #PA53022 and #PA55022) using SuperScript Direct cDNA Labeling System (Invitrogen, # L1015-02) according to provided protocol. Labeled cDNAs were purified using QIAquick PCR purification kit (QIAGEN, #28104) and combined in one tube. 20ug of sonicated salmon sperm DNA were added. DNA mixture was dried in the stream of nitrogen and dissolved in 60ul of hybridization buffer (50% deionized formamide, 6xSSC, 0.5% SDS and 5xDenhardt’s). Microarray slides were prehybridized in 6xSSC, 0.5% SDS and 1% BSA at 42°C water bath for 1 hour, rinsed with deionized water and dried in bucket rotor centrifuge in 50ml Falcon tubes (5 min, 1000xg). Labeled cDNAs were denatured at 100°C heat block for 2 min, cooled at room temperature, pipetted on the surface of microarray and covered with 25x60 mm LifterSlip (Erie Scientific Company). Assembled microarray was hybridized for 12-14 hours in the VersArray hybridization chamber (Bio-Rad) at 42°C water bath. After hybridization arrays were placed to the beaker with 1xSSC and 0.1% SDS to remove the LifterSlips. Then three washes were performed in the same solution (10 min, 5 min and 5 min) After that microarrays were rinsed with 1xSSC (30 sec), 0.1xSSC (30 sec) and dried in centrifuge as described above. Dry microarrays were scanned at 10 um resolution on ScanArray Lite instrument (Perkin Elmer). The scans were analyzed using TIGR Spotfinder program (www.tm4.org). Data were lowess normalized and filtered using MIDAS software (www.tm4.org). The final datasets were compiled in Microsoft Excel.

first: Stepan

last: Belyakin

first: Viktor

last: Shloma

first: Igor

middle: F

last: Zhimulev

first: Elena

last: Belyaeva

first: Evgeny

middle: Z

last: Kvon

first: Vladimir

last: Babenko


title: Trf4p in vivo crosslinking and ribonucleoprotein-immunopurification-chip analysis (X-RIP-Chip)

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

summary:
In vivo cross-linking and ribonucleoprotein-immunopurification experiments followed by microarray analysis of bound RNAs (X-RIP-chip). Cells expressing recombinant tandem-affinity purification (TAP)-tagged Trf4 protein were cross-linked with formaldehyde, and Trf4-containing ribonucleoprotein complexes were recovered by affinity selection on IgG-coupled beads (see linked protocol). As a control for non-specifically enriched RNAs, the same experiment was done with untagged WT cells and with cells expressing Fpr1-TAP, a peptidyl-prolyl-cis-trans-isomerase not expected to bind RNA.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Antigenic peptide used in IP: Protein A derivative

overall_design: Computed


title: Wild-type versus trf4, trf5, and trf4-DADA mutant cells

summary:
Measurement of the relative changes of gene expression of S. cerevisiae cells lacking either trf4 (trf4delta) or trf5 (trf5delta), and trf4delta/TRF4-DADA mutants compared to wild-type (WT) cells using yeast oligo microarrays that contain features representing all annotated yeast ORFs, ncRNAs, introns, rRNA precursors, as well as some intergenic regions (IGRs) and tiled regions downstream of a few genes.  Total RNA was isolated by hot phenol extraction from exponentially growing cells, and reverse transcribed with a mixture of random nonamers and oligo(dT) primers in the presence of amino-allyl dUTP/dNTP mixture. Cy5 fluorescently labeled cDNAs derived from total RNA isolated from either the trf4delta or the trf5delta mutants, and the trf4delta/TRF4-DADA mutants were then competitively hybridized with Cy3 labeled cDNAs from WT cells. cDNAs were hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
mutated gene: paralogous non-canonical poly(A) polymerases Trf4p and Trf5p forming TRAMP4 and TRAMP5 complexes


title: Interference of hemozoin formation in Schistosoma mansoni by quinine reduces experimental schistosomiasis

status: Public on Jul 13 2009

city: Campos dos Goytacazes

first: Thiago

middle: Motta

last: Venancio

state: RJ

address: Av Alberto Lamego 2000

country: Brazil

institute: UENF

summary:
Background:

The parasitic trematode Schistosoma mansoni is one of the major causative agents of human schistosomiasis, which afflicts 200 million people worldwide. Praziquantel is still the only drug used for schistosomiasis treatment and reduction in drug efficiency has prompting the search for new therapeutic compounds against this disease. Our group has demonstrated that heme crystallization into hemozoin (Hz) within S. mansoni gut is a major heme detoxification route involving lipid droplets in this process and acting as a potential chemotherapeutical target. In the present work, we investigated the effects of the antimalarial quinine (QN) in a murine schistosomiasis model by using a combination of biochemical, cell biology and molecular biology approaches.

Methodology/Principal Findings:

Treatment of S. mansoni-infected female Swiss mice with daily intraperitoneal injections of QN (75mg/kg/day) from 11th to 17th day after infection decreased not only total, males and females worm burden (46.2 %-51.0 %), eggs production, but also the granulomatous reaction to parasite eggs trapped in the liver. These effects correlated with a significant impairment of Hz production (40%) specifically in S. mansoni females, being parallel to remarkable ultrastructural changes in female worms, particularly in the gut epithelium. Microarray gene expression analysis indicated that QN treatment increased the expression of transcripts related to musculature, protein synthesis and repair mechanisms.

Conclusions:

The overall significant reduction in several disease burden parameters by QN treatment indicates that interference of Hz formation in S. mansoni is a valid chemotherapeutical target for development of new antischistosomal drugs.

overall_design: The perfused adult female worms were incubated with cold RNAlater solution (Ambion) and kept at 4 0C until RNA extraction. Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacture's instructions. RNA was quantified using Nanodrop ND-1000 UV/Vis spectrophotometer and its quality was assured with Agilent 2100 Bioanalyzer, a micro fluidics-based electrophoresis platform. 1 μg total RNA from each sample was amplified using the T7-RNA polymerase based SuperScript Indirect RNA amplification system (Invitrogen) and subsequently 3 μg of aminoallyl-modified amplified RNA was labeled using Cy3 or Cy5 by indirect labeling (General Electric). Amplification and labeling were done according to manufacturer specifications. The Cy3 and Cy5 labeled samples were then combined, dried and re-suspended in hybridization buffer (50 % formamide, 25 % RNase free water and 25 % Microarray Hybridization buffer 4x) (General Electric). Pools of RNA from worms treated with QN were hybridized against RNA from control worms. In order to ensure the uniformity of data, all experiments were performed using slides from the same printing batch and dyes from the same lot. The same washing protocol was used and immediately after washing we scanned the slides using the same parameters. Technical and biological replicates were performed. Dye swap was employed in order to account for dye biases. A total of eight different replicated data values were obtained for each probe on the array. The samples were hybridized overnight to cDNA microarray slides containing 4,000 elements in duplicate (GEO accession: GPL3929) using ASP hybridization chambers (GE, USA) at 42 °C. Slides were washed once for 3 minutes in low stringency wash solution at 45 °C (1 x SSC + 0.2 % SDS), followed by one wash for 5 minutes in medium stringency wash solution (0.1 x SSC + 0.2%SDS) and one wash of 1 minute in high stringency wash solution (0.1 x SSC).  Moreover, slides were air dried and scanned using a microarray dual channel laser scanner (GenePix 4000B, Molecular Devices, USA) at 5 μm resolution, 100 % laser power and PMT levels were adjusted in order to obtain similar average intensities of red and green signal. Data were extracted using Array Vision 8.0 program. To correct for systematic biases on the data originated from small differences in the labeling and/or detection efficiencies between the fluorescent dyes, expression ratios were logged (base 2) and normalized using a locally weighted linear regression (LOWESS) algorithm [60]. Normalized log2 (ratios) were further analyzed with the Significance Analysis of Microarrays tool (SAM) [61] using a 0.1 % false discovery rate (FDR) to find differentially expressed genes. The genes identified in the previous step were filtered using a 1.7 fold change cut-off in at least 4 out of the 8 data points. This step is critical in identifying more biological relevant changes. It is important to stress that the fold change filter was used after the identification of differentially expressed genes, and our results are not influenced by the potentially misleading effects caused by the use of arbitrary thresholds to trim data sets before significance testing .

first: Juliana

last: Correa-Soares

first: Diego

last: Menezes

first: Marcos

last: Vannier-Santos

first: Antonio

last: Ferreira-Pereira

first: Giulliana

middle: T

last: Almeida

middle: M

first: Sergio

last: Verjovski-Almeida

first: Vincent

last: Zishiri

first: David

last: Kuter

first: Roger

last: Hunter

first: Timothy

last: Egan

first: Marcus

last: Oliveira


title: fliA regulon of Helicobacter hepaticus

status: Public on Jul 14 2009

city: Hannover

first: Christine

last: Josenhans

address: Carl-Neuberg-Strasse 1

department: Institute for Medical Microbiology

institute: Hannover Medical School

summary: Differential gene regulation in Helicobacter hepaticus between wild type bacteria and fliA mutant

overall_design: 3 biological experiments of both wild type and fliA mutant bacteria (1-3) and 2 replicates (dye flip) of each biological experiment

first: Torsten

last: Sterzenbach

first: Wiebke

last: Behrens

first: Sebastian

last: Suerbaum


title: Pharmaceutical industry effluent diluted 1:500 affects gene expression, CYP1A activity and plasma phosphate in fish

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

institute: Chalmers University of Technology

summary: Patancheru, near Hyderabad, India, is a major production site for the global bulk drug market. About 90 manufacturers send their wastewater to a common treatment plant in Patancheru. Extraordinary high levels of a wide range of pharmaceuticals have recently been demonstrated in the treated effluent. As little as 0.2% of this effluent can strongly reduce the growth rate of tadpoles, but the underlying mechanisms of toxicity are not known. To begin addressing how the effluent affects aquatic vertebrates, rainbow trout (Oncorhynchus mykiss) were exposed to 0.2% effluent for five days. Several physiological endpoints, together with effects on global hepatic gene expression patterns, were analyzed. The exposed fish showed both an induction of hepatic cytochrome P450 1A (CYP1A) gene expression, as well as EROD activity. Clinical blood chemistry analyses revealed an increase in plasma phosphate levels, which in humans indicates impaired kidney function. Several oxidative stress-related genes were induced in the livers, however, no significant changes in antioxidant enzyme activities or in the hepatic glutathione levels were found. Furthermore, estrogen-regulated genes were slightly up-regulated following exposure, and moderate levels of estriol were detected in the effluent. This study identifies changes in gene expression triggered by exposure to a high dilution of the effluent, supporting the hypothesis that these fish are responding to chemical exposure. The pattern of regulated genes may contribute to the identification of mechanisms of sub-lethal toxicity, as well as illuminate possible causative agents.

overall_design: Two exposure experiments were conducted with control fish and fish exposed to 0.2% effluent. 19 pools of RNA, each containing three fish, were hybrdizied to in situ synthesized custom-made oligonucleotide microarrays. In total, four exposed and four control pools from exposure experiment I and five exposed and six control pools from exposure experiment II were analyzed.


title: MiRNA expression in adipose tissue and liver from a spontaneous rat model of Type 2 diabetes

city: Oxford

first: Cecilia

last: Lindgren

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics, University of Oxford

summary: MicroRNAs (miRNAs) are non-coding RNA molecules involved in post-transcriptional control of gene expression of a wide number of genes, including those involved in glucose homeostasis. Type 2 diabetes (T2D) is characterized by hyperglycaemia and defects in insulin secretion and action at target tissues. Using a miRNA microarray platform, we sought to establish differences in miRNA expression in two insulin-target tissues (liver and adipose tissue) from seven-month-old spontaneously diabetic (Goto-Kakizaki [GK]) and non-diabetic (Brown-Norway [BN]) rats. MiRNA data were integrated with gene expression data from the same rats to investigate how differentially expressed miRNAs affected the expression of their predicted target genes.

overall_design: Two-colour experiment comparing GK and BN rat strains for two different tissues. Biological replicates: 4 GK and 4 BN rats; adipose tissue and liver extracted from each rat. Two samples were hybridised to each array (one of each strain, same tissue)

first: Helen

last: Lockstone

first: Blanca

last: Herrera

first: Jennifer

last: Taylor

first: Quin

last: Wills

first: Amy

last: Barrett

first: Pamela

last: Kaisaki

first: Carme

last: Camps

first: Cristina

last: Fernandez

first: Jiannis

last: Ragoussis

first: Dominique

last: Gauguier

first: Mark

middle: I

last: McCarthy


title: Arterial vs venous expression of genes: differences in inflammatory genes

city: East Lansing

first: Theodora

last: Szasz

state: MI

address: B 445 Life Sciences

department: Pharmacology and Toxicology

country: USA

institute: Michigan State University

summary: Arteries and veins modulate cardiovascular homeostasis and contribute to the pathogenesis of hypertension.  Functional differences between normal arteries and veins are based upon differences in gene expression.  To better characterize these expression patterns, and to identify candidate genes that could be manipulated selectively in the venous system, we performed whole genome expression profiling of rat arteries and veins using the CodeLink platform.  We used the major artery and vein of the rat, the thoracic aorta and caudal vena cava, respectively.  Expression of mRNA for thrombospondins (TSP-1, 2, 4) was greater than 5-fold higher in veins vs arteries.  The most prominent gene expression difference between the normal aorta and vena cava was pancreatitis associated protein (PAP1), a protein with anti-inflammatory functions that was 64-fold higher in vena cava vs aorta. Higher mRNA expression of TSP-1, TSP-2, TSP-4 and PAP1 in vena cava vs aorta was confirmed with real time RT-PCR.  Importantly, immunohistochemical analysis of blood vessels sections qualitatively confirmed a higher expression of proteins in vena cava vs aorta.  These studies report a difference in inflammatory genes in arteries vs veins.  A particularly notable finding is the discovery of PAP1 mRNA and protein expression in peripheral blood vessels with a substantially higher expression in the veins.  Data from these studies may provide novel insights into the genetic basis for functional differences between arteries and veins in health and disease.

overall_design: Whole genome expression profiling of aorta and vena cava whole tissues from normal male Sprague-Dawley rats (6 biological replicates each) was performed using the CodeLink Rat Whole Genome Bioarrays.

first: Susan

last: Eddy

first: Joseph

last: Paulauskis

first: Stephanie

last: Watts


title: Gene expression and synergistic interactions induced by CpG ODN and/or poly(I:C)

city: Frederick

first: Debra

last: Tross

state: MD

institute: NCI

summary: Bioinformatic analysis of microarray data was used to identify the regulatory patterns underlying changes in gene expression induced when RAW 264.7 macrophages were stimulated via TLR9 by CpG oligonucleotides (ODN) and/or via TLR3 by poly (I:C). While the genes activated by each ligand mediated similar functions, poly (I:C) elicited a larger and more diverse change in gene expression. Co-stimulation with both ligands accelerated gene expression and synergistically activated genes primarily associated with immune function. This is the first work to compare global changes in gene regulation triggered by distinct TLR pathways and clarify their impact on gene expression.

overall_design: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 3.2 ug/ml CpG ODN and/or 32 ug/ml poly(I:C) for 4 - 12 hr. All experiments were independently repeated three times, and data from all experiments combined for analysis. Control samples included RAW 264.7 cells that were unstimulated and collected at 4 and 12 hours. All arrays used reverse transcribed mRNA from stimulted and unstimulated RAW cells as well as Universal Mouse Reference RNA purchased from Stratagene, La Holla, CA.


title: Expression of sense and antisense transcripts at the ribosomal locus

status: Public on Jul 11 2009

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

institute: EPFL

type: Non-coding RNA profiling by genome tiling array

summary:
Epigenetic methyl-CpG silencing of the ribosomal RNA (rRNA) genes is thought to down-regulate rRNA synthesis in mammals. In contrast, we now show that CpG methylation in fact positively influences rRNA synthesis and processing. Human HCT116 cells, inactivated for DNMT1 and DNMT3b or treated with aza-dC, lack CpG methylation and reactivate a large fraction of normally silent rRNA genes. Unexpectedly, these cells display reduced rRNA synthesis and processing, and accumulate unprocessed 45S rRNA. Reactivation of the rRNA genes is associated with their cryptic transcription by RNA polymerase II. Ectopic expression of cryptic rRNA gene transcripts recapitulates the defects associated with loss of CpG methylation. The data demonstrate that rRNA gene silencing prevents cryptic RNA polymerase II transcription of these genes. Lack of silencing leads to the partial disruption of rRNA synthesis and rRNA processing, providing an unexpected explanation for the cytotoxic effects of loss of CpG methylation.
Agilent custom microarray analyses of transcripts from sense and antisense strands of the human rRNA genes present in total nuclear RNA from HCT116-DNMT1-/-;DNMT3b-/- (DKO) and HCT116 (PS) cells. The DKO/PS RNA  ratio was normalized within the 5’ region of the 45S ribosomal RNA, since this sense coding region was found by quantitative Northern and S1-mapping analyses to equally present in the RNA pools from both cells (as compared to total RNA levels and 18S and 28S levels).  The distribution for sense RNAs from the coding region is strongly influenced by the predominant RPI 45S rRNA transcript and hence peaks at 0, the DKO and PS 45S rRNA signals having been normalized.

overall_design: 60-mer probes were designed to tile Human rDNA (GenBank accession U13369) on both strands using ArrayOligoSelector (Wardle et al., 2006). A total of 1,146 different non-overlapping probes (573 for each DNA strand) were designed to cover the 43 kb of human rDNA and each printed in triplicate on the array. The experiment was performed using a dye-swap duplicate analysis. The microarrays were scanned on a G2565CA DNA microarray scanner (Agilent Technologies) and the quantification performed using the Feature Extraction software (Agilent technologies). The data were analyzed using the LIMMA software package in R (Smyth and Speed, 2003).

first: Tom

last: Moss

first: Frédéric

last: Langlois


title: Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

city: Amherst

first: Derek

last: Lovley

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

institute: University of Massachusetts Amherst

summary:
In this experiment two strains were compared. The control strain was the wild type strain containing the plasmid, pCD341. pCD341 is an inducible expression vector, a plasmid which can be used to make a bacterium produce a protein of interest. It is called inducible, because the protein of interest will only be produced if an inducer, in this case, IPTG, is present. In the control strain pCD341 is "empty", meaning the gene encoding the protein of interest has not been inserted into the vector, so when you add IPTG nothing will be produced. Because producing plasmid and being exposed to IPTG can stress cells, the wild type strain harboring the "empty" plasmid was used as the control. The experimental strain DL1/pCD341RpoN contained the a "full" vector into which the gene for the sigma factor RpoN was been inserted. Thus when IPTG is added to the growth medium, this strain will overproduce RpoN.

RpoN is an alternative sigma factor, a subunit of the RNA polymerase which is required for binding of the polymerase to specific promoters and is therefore required for the transcription of genes with these promoter sequences. Most bacteria have multiple sigma factors, many of which have specialized functions. In many other bacteria, RpoN is required for the expression of genes involved in nitrogen fixation. However, in G.sulfurreducens and myxococcus xanthus, RpoN appears to essential for survival under all conditions tested and its function and promoter specificity are not known. This experiment was performed in order to gain insight into the physiological function of G. sulfurreducens RpoN. Since we could not knock out RpoN, we decided to try overproducing it, hoping that overproducing RpoN would increase expression of genes who's promoters are recognized by RpoN. We took the wild type strain + empty vector and and the wild type strain with the RpoN vector and transferred them both into medium containing IPTG. For this experiment, we used batch cultures, or closed culture containers (no media nutrients or cells flowing in and out). We harvested cells at mid log phase for RNA preparation. There were three biological replicates and two replicate hybridizations were carried out for each.
Keywords: cell type comparison

overall_design: RNA samples from three biological replicates were hybridized in duplicate on 12K Combimatrix sense-detecting arrays.  The experiment (DL1/pCDrpoN; rpoN overexpressor) was labeled with cy5, the control (DL1/pCD341) was labeled with cy3.

first: Ching

last: Leang

first: Toshiyuki

last: Ueki

first: Katy

last: Juarez-Lopez

first: Bradley

last: Postier

first: Raymond

last: DiDonato

first: Cinthia

last: Nunez

first: Gemma

last: Reguera


title: Variation in the Genomic islands of porcine enteropathogenic E. coli strains of serogroup O45 revealed by CGH and PCR.

city: Lethbridge

first: Chad

last: Laing

state: Alberta

address: Twp Rd 9-1

department: Laboratory for Foodborne Zoonoses

institute: Public Health Agency of Canada

summary:
Background: Members of E. coli serogroup O45 are porcine enteropathogenic E. coli (PEPEC) strains which cause post-weaning diarrhea and produce characteristic attaching and effacing (A/E) lesions. Most of O45 PEPEC strains possess the locus of enterocyte effacement (LEE), encoding the virulence factors for A/E lesions, and often possess the paa gene, which is thought to contribute to the early stages of PEPEC virulence.
Methodology: Nine O45 PEPEC strains and a rabbit enteropathogenic (REPEC) strain, known to produce A/E lesions, were characterized using an E. coli O157-E. coli K12 whole genome microarray and a virulence gene-specific microarray, and by PCR experiments.
Results: Based on their virulence genes profiles, the 10 strains were characterized as atypical EPEC. The differences in their genomes pointed to two distinct evolutionary groups of O45 PEPEC, Group I and Group II, and to the contribution these genetic differences have on virulence in pigs. Group I contained the REPEC strain and four O45 PEPEC strains known to induce severe A/E lesions in challenged pigs whereas Group II was composed of five other O45 PEPEC strains which induced less severe or no A/E lesions in challenged pigs. Significant differences between Groups I and II were found in the presence or absence of 50 O-Islands (OIs) or S-loops and 13 K-islands (KIs) or K-loops, including the virulence-associated islands OI#1 (S-loop#1), OI#47 (S-loop#71), OI#57 (S-loop#85), OI#71 (S-loop#108), OI#115, OI#122, and OI#154 (S-loop#253).

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

overall_design: 10 samples, with two microarrays per sample.  Each microarray includes duplicates of every spot.

first: Guillaume

last: Bruant

first: Yongxiang

last: Zhang

first: Philippe

last: Garneau

first: Justine

last: Wong

first: John

last: Fairbrother

first: Victor

last: Gannon

first: Josée

last: Harel


title: Dynamic mRNA Expression analysis of cells undergoing synchronous life-cycle differentiation in Trypanosoma brucei

status: Public on Jul 10 2009

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary:
mRNA expression profiles of trypanosomes from two discrete bloodstream form stages of the parasite (slender and stumpy forms), as well as during the transition of the stumpy population to the procyclic life-cycle stage were studied.
Our analysis represents the first comparison of in vivo derived pleomorphic slender cells with genetically identical stumpy forms, and a first analysis of the dynamic changes in mRNA profile that accompany the transition to procyclic forms.

overall_design: Twenty nine RNA samples were generated (5 biological replicates of Stumpy (0h), 1h, 6h, 18h and 48h, and 4 biological replicates of slender forms.  Four arrays failed QC.

first: Keith

last: Matthews


title: Sex of Blood

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

institute: Universitätsklinikum Schleswig-Holstein

summary:
Blood samples were taken at 1:00 pm +/- 1 h (Potassium-EDTA-monovettes, Sarstedt, Numbrecht, Germany) to control for circadian influences on gene expression. Blood was taken from normal male controls, normal female controls as well as different patients with disorders of sex development leading to a dissection of sex chromosomes and external genital phenotype. All samples were analyzed by a blood cell counter (Beckmann-Coulter, Krefeld, Germany) and white blood cell counts did not differ between the normal males and the normal females (by t-test). PBMCs were isolated from whole blood using PBS (pH 7.2) and Ficoll (Biochrom, Berlin, Germany) gradient centrifugation.
A reference experiement design type is where all samples are compared to a common reference.
Disease State: diagnosis
Genotype: sex genotype
Age: age at blood sample collection (yrs;mo)
Phenotype: external genitalia (Prader classification)
Keywords: reference_design


title: Analysis of alternative splicing in mouse tissues with differentiation, disease and development.

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary:
Two major goals for regenerative medicine are to reproducibly transform adult somatic cells into a pluripotent state and to control their differentiation into specific cell fates. These goals could be furthered by obtaining a complete picture of the RNA isoforms produced by these cells due to alternative splicing (AS) and alternative promoter selection (APS).
To investigate the roles of AS and APS, reciprocal exon-exon junctions were interrogated on a genome-wide scale in differentiating mouse embryonic stem cells (ESCs), mouse myometrium throughout gestation and cardiac remodeling with disease using a prototype Affymetrix microarray. Using a custom analysis package named AltAnalyze (http://www.AltAnalyze.org), we identified a large number of putative AS and APS events, the majority of which were predicted to alter protein sequence and domain composition. Over a dozen AS and APS events were validated in mouse ESCs with differentiation to embryoid bodies.

overall_design: Alternative splicing analysis of mouse tissue differentiation, disease and developmental remodeling paradigms.


title: Tumor T20 Sectors

city: Cold Spring Harbor

first: Nicholas

last: Navin

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

type: Genome variation profiling by genome tiling array

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T20) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.

overall_design: The genomic DNA from each tumor subpopulation was labeled with Cy5 and hybridized to an 390K Rubble-Rep ROMA Microarray.  A normal reference male fibroblast was labeled with Cy3 as a control.  Samples were cohybridize to the same single microarray.


title: Tumor T18 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T18) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T19 Sectors

summary: The following CGH experiments were conducted on six sectors (S1-S6) from a single primary ductal carcinoma tumor (T19) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T15 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T15) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.

overall_design: The genomic DNA from each tumor subpopulation was labeled with Cy5 and hybridized to an 390K Rubble-Rep ROMA Microarray.  A normal reference male fibroblast was labeled with Cy3 as a control.  Samples were cohybridized to the same single microarray. Samples were dye-swapped and the experiments were conducted in color-reversal.


title: Tumor T16 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T16) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T17 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T17) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T11 Sectors

summary: The following CGH experiments were conducted on six sectors (S1-S6) from a single primary ductal carcinoma tumor (T11) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.

overall_design: The genomic DNA from each tumor subpopulation was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray.  A normal reference male fibroblast was labeled with Cy3 as a control.  Samples were dye-swapped and the experiments were conducted in color-reversal.  The value data repesents a log ratio of the mean of two dye-swapped samples


title: Tumor T14 Sectors

summary: The following CGH experiments were conducted on six sectors (S1-S6) from a single primary ductal carcinoma tumor (T14) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T13 Sectors

summary: The following CGH experiments were conducted on six sectors (S1-S6) from a single primary ductal carcinoma tumor (T13) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T10 Sectors

summary: The following CGH experiments were conducted on six sectors (S1-S6) from a single primary ductal carcinoma tumor (T10) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T9 Sectors

summary: The following CGH experiments were conducted on six sectors (S1-S6) from a single primary ductal carcinoma tumor (T9) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T7 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T7) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T6 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T6) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T5 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T4) using the Sector-Ploidy-Profiling (SPP) Approach.  SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations.


title: Tumor T4 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T4).

overall_design: The genomic DNA from each tumor sector was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray.  A normal reference male fibroblast was labeled with Cy3 as a control.  Samples were dye-swapped and the experiments were conducted in color-reversal.  The value data repesents a log ratio of the mean of two dye-swapped samples


title: Tumor T3 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T3).


title: Tumor T2 Sectors

summary: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T2).


title: Factorial Microarray Analysis of Zebra Mussel Adhesion Process under the Impact of Multiple Environmental Factors

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

summary:
Factorial Microarray Analysis of Zebra Mussel (Dreissena polymorpha) Adhesion Process under the Impact of Multiple Environmental Factors

The expression profiles of the zebra mussel byssus unique genes in our cDNA microarray can be influenced by multiple factors. Three environmental factors plus adhesion status were considered as four main factors in this study.

overall_design: Two different levels in each factor were created, therefore, a 2x2x2x2 factorial experimental design was made by sixteen treatment groups with four biological replicates in each group. There were 32 dual-channel microarray slides included in this study and the effects of main factors on gene expression profiles as well as the two-way, three-way, and four-way interactions of the main factors were analyzed. Factors: temperature, water agitation, oxygen level, and adhesion status

first: Mohamed

last: Faisal


title: Discovery of swine as a host for the Reston ebolavirus

city: Greenport

first: Roger

middle: William

last: Barrette

address: PO Box 848

department: FADDL

institute: USDA-APHIS

summary: Since the discovery of filoviruses, comprised of Marburg and Ebola species, seemingly random, sporadic fatal outbreaks of disease in humans and non-human primates have evoked interest in delineation of host tropisms and potential reservoirs.  We now describe identification of Reston ebolavirus (REBOV) by microarray, in domestic swine from the Philippines experiencing unusually severe outbreaks of porcine reproductive and respiratory disease syndrome. While REBOV is the only member of Filoviridae that has not been associated with disease in humans, its emergence in the human food chain heightens concerns for public health, swine agriculture and international trade. REBOV isolates were found to be significantly more divergent from each other than from the original virus isolate from 1989, indicating polyphyletic origins in swine.  This further suggests that REBOV has been circulating since, and possibly before, the initial discovery of REBOV in monkeys.  These results identify swine as the first non-primate susceptible host for REBOV.

overall_design: A lymph node cultured in Vero cells and a tonsil cultured in SK6 cells revealed cytopathic effects indicating the presence of a virus. Different scanner conditions used for the 2 Samples.

first: Michael

last: McIntosh