title: Discovery of novel microRNAs in rat kidney using microarray analyses

city: Jefferson

first: Fanxue

last: Meng

state: AR

address: 3900 NCTR Road, HFT-130

institute: National Center for Toxicological Research

summary: MicroRNAs are small non-coding RNAs that regulate a variety of biological processes. In the last version of the miRBase database (Release 17), 720 mouse microRNAs are accompanied by only 408 rat microRNAs.  Given the importance of rat as a model organism, we used next generation sequencing and microarray technologies to discover novel microRNAs in rat kidneys.

platform_organism:
Petromyzon marinus
Danio rerio
Oryzias latipes
Xenopus laevis
Xenopus tropicalis
Gallus gallus
Ornithorhynchus anatinus
Ateles geoffroyi
Macaca mulatta
Macaca nemestrina
Symphalangus syndactylus
Pan paniscus
Pan troglodytes
Pongo pygmaeus
Homo sapiens
Canis lupus familiaris
Equus caballus
Sus scrofa
Bos taurus
Ovis aries
Mus musculus
Rattus norvegicus
Takifugu rubripes
Taeniopygia guttata
Rhinopithecus bieti
Saguinus labiatus
Tetraodon nigroviridis

overall_design: Four male, 6-week-old Big Blue rats were treated with 10.0 mg/kg aristolochic acid(AA) 5 times a week for 12 weeks, four untreated rats as control. The animals were sacrificed 1 day after the last treatment and total RNA were isolated.  All eight rat samples were used to deep sequencing analyses (University of Texas Southwestern Medical Center Microarray Core Facility), while 6 samples (3 AA-treated and 3 control) were used to custom vertebrate microRNA microarray analysis (LC Sciences).  We used the miRanalyzer standalone version for the prediction of novel microRNAs and microRNA microarray to confirm novel microRNAs.

first: Michael

last: Hackenberg

first: Zhiguang

last: Li

first: Jian

first: Tao

last: Chen


title: Transcriptional profile in macrolide susceptible and resistant Campylobacter jejuni

status: Public on Nov 02 2011

city: Ames

first: Qijing

last: Zhang

state: Iowa

address: 1600 Christensen Drive

department: Veterinary Microbiology and Preventive Medicine

country: USA

institute: Iowa State University

summary: Campylobacter jejuni is a major zoonotic pathogen transmitted to humans via the food chain. C. jejuni is prevalent in chickens, a natural reservoir for this pathogenic organism. Due to the importance of macrolide antibiotics in clinical therapy of human campylobacteriosis, development of macrolide resistance in Campylobacter has become a concern for public health.To facilitate understanding the molecular basis associated with the fitness difference between Erys and Eryr Campylobacter, we compared the transcriptomes between ATCC 700819 and its isogenic Eryr transformant T.L.101 using DNA microarray.

overall_design: The design utilized an available two color microarray slide for the entire transcriptome of Campylobacter jejuni. Four hybridizations were performed each with independently extracted samples of either macrolide susceptible ATCC 700819 cDNA samples or its isogenic Eryr transformant T.L.101 cDNA samples. A dye swap was utilized to help minimize dye dependent bias. Thus, there were four biological replicates of each sample.

first: Taradon

last: Luangtongkum

first: Zhangqi

last: Shen


title: Genome-wide binding map of the HIV Tat protein to the human genome (gene expression)

status: Public on Nov 06 2011

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E. Young Dr. South, 337

department: Biological Chemistry

institute: University of California Los Angeles

summary:
The HIV-1 Trans-Activator of Transcription (Tat) protein binds to multiple host cellular factors and greatly enhances the level of transcription of the HIV genome.  Here, we report the genome-wide binding map of Tat to the human genome in Jurkat T cells (Jurkat-Tat cells) using chromatin immunoprecipitation combined with next-generation sequencing.  cDNA microarray was used to monitor gene expression changes between Jurkat and Jurkat-Tat cells.  Additionally, we compared distribution of H3K9ac near gene promoters between Jurkat and Jurkat-Tat cells using ChIP-chip method and hybridized onto Agilent promoter array.  Our data reveal that Tat’s interaction with the host genome is more extensive than previously thought, with potentially important implications for the viral life cycle.
Agilent gene expression microarray was used to compare gene expression changes between Jurkat T cells and Jurkat T cells expressing HIV-Tat protein (Jurkat-Tat T cells)

overall_design: Expression profiles on Jurkat-Tat cells versus Jurkat cells.   ChIP on chip for H3K9ac in Jurkat-Tat versus Jurkat cells.  ChIP-seq for HIV-1 Tat protein in Jurkat-Tat cells.

first: Celine

last: Marrban

first: Trent

last: Su


title: Expression data from 6 day-old Atxn1L-/- and Atxn1-/- lung tissues

city: Houston

first: Hyojin

last: Kang

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary:
Although expansion of a polyglutamine tract in ATAXIN1 (ATXN1) causes Spinocerebellar ataxia type 1, the functions of wild-type ATXN1 and ATAXIN1-Like (ATXN1L) remain poorly understood. To gain insight into the function of these proteins, we generated and characterized Atxn1L-/- and Atxn1-/- ; Atxn1L-/- double mutant animals. We found that Atxn1L -/- mice have several developmental problems including hydrocephalus, omphalocoele and lung alveolarization defects. These phenotypes are more penetrant and severe in Atxn1-/- ; Atxn1L-/- mice, suggesting that Atxn1 and Atxn1L are functionally redundant.
To unravel the molecular mechanism underlying the alveolarization defect in Atxn1-/- mice, we carried out microarray analyses using total lung RNA from WT, Atxn1-/- and Atxn1L-/- mice

overall_design:
Lung tissues were dissected from 6 day old mice from either Atxn1 heterozyous intercrosses or Atxn1L heterozygous intercrosses. We collected lung tissue samples from 4 pairs of WT and Atxn1-/- amd 3 pairs of WT and Atxn1-/- mice. Total RNA extracted from the samples was subjected to microarray analysis using Affymetrix mouse gene ST 1.0 array.
GSM731591-GSM731598 (Atxn1L KO and controls) and GSM731599-GSM731604 (Atxn1 KO and controls) were RMA-processed separately.

first: Yoontae

last: Lee

first: Aaron

middle: B

last: Bowman

first: Huda

middle: Y

last: Zoghbi


title: MiRNA array based, miRNA expression profiles of oral leukoplakia (OLK) and malignant transformed oral leukoplakia (mtOLK)

city: Shanghai

first: Weiwen

last: Jiang

address: Room305,building1,No.639 Zhizaoju Road

country: China

institute: Shanghai Ninth People’s Hospital

summary: The unsupervised hierarchical clustering analysis of the 122 miRNAs revealed a marked separation of mtOLK from OLK, suggesting that this differential expression profile might be used as a possible phenotypic discriminator between OLK and mtOLK.Comparing with OLK, 72 up-regulated and 50 down-regulated miRNAs were found in the mtOLK (p < 0.01)

overall_design: In the study presented here,20 OLK（OLK), 5 mtOLK（Ca） tissues and 5 normal mucousal tissues（N） were examined by miRNA array

first: Wen

last: Xiao

first: Zhexuan

last: Bao


title: Gene Expression analysis of PA 3880 mutant

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary: Comparitive gene expression analysis of wild type and PA 3880 mutant when grown anaerobically and aerobically.

overall_design: Samples were hybridized on aminosilane coated slides with 70-mer oligos.

first: Marcus

last: Jones

first: Xin

last: Deng

first: Kenneth

last: shatzkes


title: Drought stressed corn grown on summit/shoulder vs. well hydrated corn grown on backslope

status: Public on Nov 05 2011

city: Fargo

first: David

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary:
This study was designed to identify changes in gene expression that occur when corn was grown on different landscape features. Specifically on the backslope or summit/shoulder of a hill.
In rolling landscapes, plant available water varies drastically by location and soil type.  Almost simultaneously, plants may be flooded out in footslope locations whereas plants in summit locations may be suffering from severe drought.  The objective of this study was to determine the influence of landscape position on corn (Zea mays) productivity and gene regulation.  Corn was sampled at V12 for plant growth characteristics and transcriptome analysis at summit/shoulder and lower backslope positions.  Plants at the summit had 16% less leaf area and biomass compared with plants at the toeslope.  Gene expression analysis using microarray chips, transcriptome analysis, and qPCR indicated that plants at the summit had 708 genes down-regulated and 399 genes up-regulated compared to control plants at the lower back slope.  GSEA (Gene Set Enrichment Analysis) indicated tolerance to cold, salt, and drying were increased in summit/should plants compared to control toeslope plants. However, nutrient uptake, recovery from wounding, pest and fungal disease resistance, along with photosynthetic capacity were all down-regulated in moderate water stresses plants.  These responses suggest that corn preferentially responses to water stress as the expense of its ability to respond to other stresses.

overall_design: Three biological replicates for the control (backslope) and six biological replicate of summit/shoulder-grown plants were collected. The resulting labeled cDNA was hybridized to the 46,000-element maize microarray chip developed by the University of Arizona using their protocol (International Microarray Workshop Handbook, 2009Gardiner et al. 2005). The hybridization scheme was a dual hybridization using a rolling circle balanced dye swap design. Thus we had three to six biological replicates for each growth condition and two technical replicates for each biological sample.

first: Stephanie

last: Hansen

first: Youssef

last: Jarachi

first: Gregg

last: Carlson

last: Clay


title: Transcriptional profile of Candida parapsilosis CLIB214 culture in low iron conditions

status: Public on Nov 04 2011

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

summary: Whole genome microarrays were used to generate the transcriptional profile of Candida parapsilosis in low iron conditions

overall_design: RNA was isolated from CLIB214 grown in SD medium and in SD medium supplemented with 200 μM BPS and labeled with Cy3 or Cy5. Seven independent biological replicates were compared. Three dye swaps were perfomed so that four out of seven samples grown in SD culture were labeled with Cy3, and 3 were labeled with Cy5.

middle: M

last: Synnott

first: Alessandro

last: Guida

first: Sarah

middle: L

last: Maguire


title: Hepatic miRNA expression in experimental biliary atresia

city: Philadelphia

first: Joshua

last: Friedman

state: PA

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

summary: Hepatic microRNA was measured by Exiqon array in the mouse RRV model of biliary atresia miRNA expression profiling. For the miRNA microarray experiment, RRV and saline injected animals were euthanized at 3, 8, and 14 days post infection (n=5 per treatment, per time point), and total RNA was purified from liver using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer's instructions. A pooled common control was assembled from an equal RNA mass from each of the samples, and samples and control were separately dye-labeled, and hybridized to a miRcury v11.0 miRNA microarray (Exiqon) at the University of Pennsylvania School of Medicine Microarray core facility. Sample hybridization intensities were scored relative to the common control, and raw intensity data were normalized and analyzed using the SAM add-in for Microsoft Excel. MiRNAs exhibiting a fold-change of greater than 10% up or down, at a false discovery rate of 5% were chosen for further study.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Three time points (3, 8, 14 days) x 2 conditions x 6 replicates - 1 failed sample = 35 samples

middle: R


title: Comparison of Thermoanaerobacter sp. X514 grown on different xylose concentrations

city: Norman

first: Christopher

last: Hemme

state: OK

address: 101 David L. Boren Blvd.

department: Botany and Microbiology

institute: University of Oklahoma

summary: Thermoanaerobacter sp. X514 was grown on 1, 10, 50 and 200 mM xylose in order to identify pathways and transporters responsible for xylose transport and conversion to ethanol.

overall_design: In this study, X514 cells were grown in difeined medium supplemented with 1, 10, 50 or 200 mM xylose as the sole carbon substrate. Each sample was harvested at mid-log phase.  Each sample was run in triplicate using genomic DNA as the control.


title: argR1-ahrC mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + 10 mM arginine

city: Groningen

first: Tomas

last: Kloosterman

address: Nijenborgh 7

department: Natural Sciences

country: Netherlands

institute: University of Groningen

summary:
Comparison of Streptococcus pneumoniae D39 argR1-ahrC mutant compared to D39 wild type in CDM with 10 mM arginine to define the regulons of the ArgR1 and AhrC regulators under this condition.

Details described in Kloosterman TG and Kuipers OP. ArgR1 and AhrC Mediate Arginine-Dependent Regulation of Arginine Acquisition- and Virulence Genes in the Human Pathogen Streptococcus pneumoniae. JBC 2011

overall_design: One condition design comparison of two strains including a dye swap

middle: G

first: Oscar

middle: P

last: Kuipers


title: Transcriptomic and nuclear architecture of immune cells after LPS-activation

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

summary: Changes in the nuclear positioning of specific genes, depending on their expression status, have been observed in a large diversity of physiological processes. However, gene position is poorly documented in immune cells subjected to activation upon bacterial infection. Using the pig as a model organism, we focused our study on monocytes-derived macrophages and neutrophils, the first lines of defense against pathogens.  We examine whether changes in gene expression due to LPS-activation imply genes repositioning in the nuclear space. A transcriptomic analysis was first performed to identify the genes differentially expressed and analyse the networks implicated during LPS-IFNγ activation in monocytes-derived macrophages. This allowed us to select 4 up-regulated (IL1β, IL8, CXCL10 and TNFα) and 4 down-regulated (VIM, LGALS3, TUBA3, and IGF2) genes to be further studied by 3D-FISH for their behavior in the nuclear space, particularly towards their chromosome territories (CT) during macrophages activation. Among the 4 up-regulated genes, 3 changed their position during the activation process while the 4 down-regulated ones did not. The analysis of gene behaviors towards their CT was extended to neutrophils for 3 up- and 2 down-regulated genes and similar results were obtained. Our data suggest that relocation in the nuclear space of genes differentially expressed in activated immune cells is gene specific and concern mostly up-regulated ones.

overall_design: Porcine monocyte-derived macrophages: Control vs. LPS-IFNγ activated vs. T-2 toxin/LPS-IFNγ activated. A common reference hybridization scheme was used to compare the three-condition experiment, CM vs. AM vs. TAM. The reference consisted of a pool of RNA from all samples. Biological replicates: 5 control, 5 LPS-IFNγ activated, 5 T-2 toxin/LPS-IFNγ activated independently. One replicate per array.

first: Romain

last: Solinhac

first: Philippe

last: Pinton

first: Isabelle

last: Oswald


title: Comparison of Thermoanaerobacter pseudethanolicus 39E grown on different xylose concentrations

summary: Thermoanaerobacter pseudethanolicus 39E was grown on 10, 50 and 200 mM xylose in order to identify pathways and transporters responsible for xylose transport and conversion to ethanol.

sample_organism: Thermoanaerobacter pseudethanolicus ATCC 33223

overall_design: In this study, 39E cells were grown in difeined medium supplemented with 10, 50 or 200 mM xylose as the sole carbon substrate. Each sample was harvested at mid-log phase.  Each sample was run in triplicate using genomic DNA as the control.


title: Mouse heart tissue: wild-type vs. aMHC-Calcineurin transgenic (CnTg)

city: Maastricht

first: Paula

last: da Costa Martins

address: P.Debyelaan 25

institute: Maastricht University

summary: Cardiac profiling of miR expression levels in a transgenic mouse model of heart failure (MHC-CnA) to identify miRs that are co-regulated with the development of calcineurin-induced heart failure.

overall_design: Two-condition experiment: WT vs CnTg. Biological replicates: one array was performed on 3 pooled samples of each genotype (2 arrays in total).

first: Marti

middle: F

last: Bierhuizen

first: Leon

middle: J

last: de Windt


title: ahrC mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + 10 mM arginine

summary:
Comparison of Streptococcus pneumoniae D39 ahrC mutant compared to D39 wild type in CDM with 10 mM arginine to define the regulon of the AhrC regulator under this condition.

Details described in Kloosterman TG and Kuipers OP. ArgR1 and AhrC Mediate Arginine-Dependent Regulation of Arginine Acquisition- and Virulence Genes in the Human Pathogen Streptococcus pneumoniae. JBC 2011

overall_design: One condition design comparision of two strains including a dye swap


title: Transcriptomic and functional analysis of the Anopheles gambiae salivary gland in relation to blood feeding

status: Public on Nov 01 2011

city: Baltimore

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary:
Background: The Anopheles gambiae salivary glands play a major role in malaria transmission and express a variety of bioactive components that facilitate blood-feeding by preventing platelet aggregation, blood clotting, vasodilatation, and inflammatory and other reactions at the probing site on the vertebrate host.

Results: We have performed a global transcriptome analysis of the A. gambiae salivary gland response to blood-feeding, to identify candidate genes that are involved in hematophagy. A total of 4,978 genes were found to be transcribed in this tissue. A comparison of salivary gland transcriptomes prior to and after blood-feeding identified 52 and 41 transcripts that were significantly up-regulated and down-regulated, respectively. Ten genes were further selected to assess their role in the blood-feeding process using RNAi-mediated gene silencing methodology. Depletion of the salivary gland genes encoding D7L2, anophelin, peroxidase, the SG2 precursor, and a 5'nucleotidase gene significantly increased probing time of A. gambiae mosquitoes and thereby their capacity to blood-feed.

Conclusions: The salivary gland transcriptome comprises approximately 38% of the total mosquito transcriptome and a small proportion of it is dynamically changing already at two hours in response to blood feeding. A better understanding of the salivary gland transcriptome and its function can contribute to the development of pathogen transmission control strategies and the identification of medically relevant bioactive compounds.

overall_design: Salivary glands from blood-fed vs. unfed A. gambiae. 3 replicates.


title: Escherichia coli O157:H7 Isolates Related to the 2006 Spinach-associated Outbreak Exhibit Distinct Transcriptional Profiles

city: Albany

first: Craig

middle: T

last: Parker

address: 800 Buchanan St

department: PSM

institute: USDA ARS

summary: We compared the transcriptional profiles of 12 E. coli O157:H7 isolates grown to stationary phase in LB broth. These isolates possess the same two enzyme PFGE profile and are related temporally or geographically to the above outbreak. These E. coli O157:H7 isolates included three clinical isolates, five isolates from separate bags of spinach, and single isolates from pasture soil, river water, cow feces, and a feral pig.

overall_design: Twelve condition experiment, 12 E. coli O157:H7 isolates. Two biological replicates for isolates RM6067, RM6069, RM6101, RM6102, RM6103, RM6149, RM6655, RM6658, RM9992, RM9997, RM9998 and RM10002 independently grown to stationary phase in LB at 37°C and harvested. One replicate per array. A type 2 gene expression experimental design was used, with fluorescently labeled genomic DNA as a reference channel in each experiment as described by Lucchini, S., et al. 2005. Infect Immun 73:88-102.

first: Jennifer

last: Kyle

first: Steven

last: Huynh

first: Michelle

middle: Q

last: Carter

first: Maria

last: Brandl

first: Robert

middle: E

last: Mandrell


title: Sequentially acting Sox transcription factors in neural lineage development [microarray]

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary:
We report sequential binding but unique functions of different Sox transcription factors during distinct stages of neural differentiation
We used microarray to examine the molecular function of Sox3 in neural progenitor cells.

overall_design: Over-expression of Sox3 under Nestin-promoter in neural progenitor cells. Cells are transgenic for GFP in Sox1 locus and were FACS sorted to obtain pure populations.

last: Bergsland

first: Daniel

last: Ramsköld

first: Jonas

last: Muhr


title: Molecular markers to characterize the hermaphroditic reproductive system of the planarian Schmidtea mediterranea

city: Urbana

first: Phillip

middle: A

last: Newmark

state: IL

address: C609 CLSL, 601 S. Goodwin Ave.

department: Cell and Developmental Biology

institute: University of Illinois, Urbana-Champaign

summary:
Investigation of differences in gene expression between two strains of the planarian Schmidtea mediterranea.
The sexual strain are cross-fertilizing hermaphrodites with reproductive organs that develop post-embryonically and the asexual strain reproduces exclusively by transverse fission and fail to develop reproductive organs.

overall_design: A two chip study using total RNA recovered from asexual and sexual animals. Each chip measures the expression level of 16,797 ESTs from S. mediterranea with 10 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy.

first: T

last: Chong

first: J

last: Stary

first: Y

last: Wang

first: P


title: DMD vs. AGING

city: Nantes

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

institute: Institut national de la santé et de la recherche médicale-INSERM

summary:
Comparative effects of Duchenne Muscular Dystrophy (DMD) and Aging in skeletal muscle
Expression profiling established by microarray technology provides a powerful tool by which complex pathways can be assembled. The pathophysiology of Duchenne Muscular Dystrophy (DMD) is a complex process involving many pathways downstream of the primary genetic insult (lack of dystrophin). Similarly, the mechanisms implicated in muscle aging are only partially understood. The objective of the present study was to compare the muscle transcriptional response downstream of lack of dystrophin with the molecular events associated with aging using a muscle-dedicated microarray. Defining a common transcriptional profile in a range of wasting diseases should increase our understanding of the critical adaptations associated with muscle atrophy independent of the cause of the muscle wasting.

overall_design: RNA samples from 4 DMD and 4 AGE skeletal muscle tissues were analyzed by hybridization against control samples. This hybridization was done on microarrays containing quadruplicate 50-mer oligonucleotides corresponding to 3,588 muscle relevant genes. Two hybridizations were per-formed for each subject. Thus, eight values per gene were obtained for each subject. These stringent conditions conferred powerful significance to our results.

last: Baron

first: Audrey

last: Bihouée

first: Raluca

last: Teusan


title: Transcriptional response of Listeria monocytogenes h7858 and f6854 to lactate and acetate

status: Public on Nov 03 2011

city: Ithaca

first: Matthew

last: Stasiewicz

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

summary: The organic acids lactate and diacetate are commonly used in combination in ready-to-eat foods because they show synergistic, i.e. greater than additive, ability to inhibit the growth of Listeria monocytogenes.  Full genome microarrays were used to investigate the synergistic transcriptomic response of two L. monocytogenes strains, h7858 (serotype 4b) and f6854 (serotype 1/2a), to organic acid, under conditions controlling for osmotic and cold stress.   Strains were exposed to BHI broth at 7°C with 4.65% water phase (w.p.) NaCl at pH 6.1 treated with 2% w.p. potassium lactate, 0.14% w.p. sodium diacetate, the combination of both at the same levels, or no inhibitors as control. RNA was extracted 8h after exposure, during lag phase, to capture gene expression changes during adaptation to the organic acid stress.  Treatment with organic acids induced massive global transcriptional changes, with 1041 and 640 genes differentially expressed in h7858 and f6854.  Major effects of treatment with lactate and diacetate are (i) a total of 474 and 209 genes, for h7858 and f6854, that showed synergistic expression differences, (ii) differential expression of membrane ion transport genes including those encoding ABC transporters of metals and decreased multi-drug transporter expression many ABC, PTS, and drug transporter systems, including increased PTS sugar transport and decreased  multi-drug transporter expression, and (iii) altered metabolism including induction of a nutrient limiting stress response, reduction of menaquinone biosynthesis, and a shift from fermentative production of lactate and acetate and lactate to energetically less favorable, neutral acetoin.  These data suggest that additional synergies in L. monocytogenes growth inhibition could be achieved by treatments that interfere with cellular energy generation processes.

overall_design: The dye-swapped, single loop design hybridizes a single biological replicate of both 2% water phase lactate (PL)  and 0.14% water phase acetate (SDA) treatments to both the control (CTRL) and combination (PLSDA) treatments (4 hybridizations), using opposite dye labels for each sample, and a second biological replicate is hybridized with dye assignments swapped (4 more hybridizations) to balance labeling effects.  The design was repeated twice comprising 16 hybridizations over 4 biological replicates for each strain, and 32 total hybridizations over both h7858 and f6854.

first: Martin

last: Wiedmann

first: Teresa

last: Bergholz


title: Salmonella Typhimurium: Immobilized growth vs. Planktonic growth

city: Kgs. Lyngby

first: Gitte

middle: M.

last: Knudsen

address: Søltofts Plads, Building 221

department: National Food Institute

country: Denmark

institute: Technical University of Denmark

summary: Transcriptional profiling of four growth phases S. Typhimurium comparing immobilised growth with planktonic growth.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. DT104

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

platform_organism: Salmonella enterica subsp. enterica serovar Enteritidis

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91

overall_design: Each array used labelled cDNA against a common genomic DNA reference. Triplicate or quadruple arrays were carried out for each of the 8 conditions as well as the inoculum culture: inoculum, planktonic MEP, planktonic LEP, planktonic ESP, planktonic LSP, immobilised MEP, immobilised LEP, immobilised ESP and immobilised LSP

first: Jay

last: Hinton


first: Tomas

last: Kloosterman

summary:
Comparison of Streptococcus pneumoniae D39 wild-type grown in CDM+10 mM arginine compared to D39 wild type grown in CDM + 0.05 mM arginine to define the genome-wide transcriptional response to arginine.

Details described in Kloosterman TG and Kuipers OP. ArgR1 and AhrC Mediate Arginine-Dependent Regulation of Arginine Acquisition- and Virulence Genes in the Human Pathogen Streptococcus pneumoniae. JBC 2011

overall_design: Two condition design comparison of wild type strain

first: Oscar

last: Kuipers


title: Inter-species array between human, rat and mouse

city: Koto

first: Jun

last: Sese

state: Tokyo

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: We propose a new microarray method, called an inter-species array, that can measure gene expression levels of multiple species at once. As the array operates simply by changing the probes on an Agilent commercial customized array, and conventional facilities and protocols can be used, the method is cost-efficient. We generated an array for humans, rats and mice that covers 6683 genes. The number of genes is larger than that of previous arrays. We measured the expression of genes in astrocyte cells for humans and rats, and in cortex cells for rats and mice.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Single array with multiple species samples.


title: Activation of Arabidopsis seed hair development by cotton fiber-related genes

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: This experiment was designed to investigate the molecular basis of cotton fiber cell initiation. 32,000 ESTs were sequenced from Gossypium hirsutum L. TM-1 immature ovules (GH_TMO) and developed cotton oligonucleotide microarrays containing ~23,000 unigenes. Transcriptome analyses were performed to compare gene expression changes in laser capture microdissected fiber cell initials (or epidermis) and inner ovules. The gene expression profiles of the fiber cell initials were compared with those of the inner ovules in each developmental stage prior to, right at, and shortly after the initiation of fiber cells. Many genes in various molecular function or biological processes were over- or under-represented between fibers and non-fiber tissues in each developmental stage, suggesting temporal regulation of gene expression during early stages of fiber development.

overall_design: For gene expression studies using a large set cotton oligo-microarray, 4 developmental stages were chosen. To study differential expression during fiber initiation, ovules at -2 DPA, 0 DPA, and 2 DPA were used. One of the fiber elongation stage tissues (7 DPA) was included. In each developmental stage, epidermis was separated from inner ovules and subjected to the hybridization. In addition, epidermis and ovule comparisons were performed individually with 0 DPA as a control point for comparison.

first: Jinsuk

last: Lee

first: Z

first: Joshua

last: Udall

first: Jonathan

last: Wendel

first: Foo

last: Cheung

first: Christopher

middle: D

last: Town


title: Coculture of Desulfovibrio vulgaris Hildenborough and Methanococcus maripaludis

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

summary: Using data from microarray experiments we investigated a coculture of D. vulgaris Hildenborough and Methanococcus maripaludis.


title: Gene expression levels with various artificial mutations -- exact match

summary: We checked the effects of mutations on expression levels by using systematically mutated probes. We used Agilent custom microarray whose probe length is 60bp. To check artificial mutation effect, we designed 56 patterns of mutations, 24 patterns of insertions and deletions. On the microarray, we used 7,987 probes from Agilent human gene probes. In these experiments, we checked the difference of expression levels about at least 73 probes for each mutation type. We performed microarray experiments with an Agilent custom microarray. We measured gene expressions using a qPCR Human reference total RNA sample provided by CloneTech. Gene expression profiles were normalized with quintile normalization according to the Agilent protocol except that only non-mutated 219 probes were used.

overall_design: 6 replicate samples


title: Gene expression levels with various artificial mutations -- with mismatch

summary: We checked the effects of mutations on expression levels by using systematically mutated probes. We used Agilent custom microarray whose probe length is 60bp. To check artificial mutation effect, we designed 56 patterns of mutations, 24 patterns of insertions and deletions. On the microarray, we used 7,987 probes from Agilent human gene probes. In these experiments, we checked the difference of expression levels about at least 73 probes for each mutation type. We performed microarray experiments with an Agilent 4x44k custom microarray. We measured gene expressions using a qPCR Human reference total RNA sample provided by CloneTech. Gene expression profiles were normalized with quintile normalization according to the Agilent protocol except that only non-mutated 219 probes were used.


title: Strigolactone biosynthesis requires the symbiotic GRAS-type transcription factors NSP1 and NSP2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Legume GRAS-type transcription factors NSP1 and NSP2 are essential for Rhizobium Nod factor-induced nodulation. Both proteins are considered to be Nod factor response factors regulating gene expression upon symbiotic signalling. However, legume NSP1 and NSP2 can be functionally replaced by non-legume orthologs; including rice (Oryza sativa) OsNSP1 and OsNSP2. This shows that both proteins are functionally conserved in higher plants, suggesting an ancient function that was conserved during evolution. Here we show that NSP1 and NSP2 are indispensable for strigolactone biosynthesis in the legume Medicago truncatula as well as rice. Mutant nsp1-nsp2 plants hardly produce strigolactones. The lack of strigolactone biosynthesis coincides with strongly reduced DWARF27 expression in both species. Rice and Medicago represent distinct phylogenetic lineages that split ~150 million years ago. Therefore we conclude that regulation of strigolactone biosynthesis by NSP1 and NSP2 is an ancestral function conserved in higher plants. Since strigolactone biosynthesis is highly regulated by environmental conditions like phosphate starvation, NSP1 and NSP2 will be important tools in future studies on the molecular mechanisms by which environmental sensing is translated into regulation of strigolactone biosynthesis. As NSP1 and NSP2 are single copy genes in legumes, it implies that a single protein complex fulfills a dual regulatory function of different downstream targets; symbiotic and non-symbiotic, respectively.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Three biological replications are used for roots of wild type A17, nsp1 and nsp2 mutant plants

first: Wei

last: Liu

first: Wouter

last: Kohlen

first: Alessandra

last: Lillo

first: Rik

last: Op den Camp

first: Sergey

last: Ivanov

first: Marijke

last: Hartog

first: Erik

last: Limpens

first: Muhammad

last: Jamil

first: Wei-Cai

last: Yang

first: Tatsiana

last: Charnikhova

first: Harro

last: Bouwmeester

first: Ton

last: Bisseling

first: René

last: Geurts


title: Effect of CovR polymorphisms on GAS gene expression

city: Houston

first: Samuel

last: Shelburne

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

summary: In this study we sought to determine the effects of single amino acid replacements in the control of virulence regulatory (CovR) regulatory protein on group A streptococcal global gene expression.

overall_design: We compared the transcriptomes of the serotype M3 strain MGAS10870 with four derivative strains: 1) a strain in which CovR had been completely inactivated (CovR knockout); 2) a strain in which the Arg 144 amino acid was changed to a cysteine (CovR-R144C); 3) a strain in which the Arg 158 amino acid was changed to a cysteine (CovR-R158C); and 4) a strain in which the the Asn 193 amino acid was changed to an isoleucine (CovR-N193I). Duplicate samples of each strain were grown to mid-exponential phase and the relative transcriptomes were compared using an Affymetrix GeneChipl.

first: Nicola

last: Horstmann

first: Pranoti

last: Sahasrobhojane

first: Bryce

last: Suber

first: Muthiah

last: Kumaraswami

first: Randall

last: Olsen

first: Anthony

last: Flores

first: James

last: Musser

first: Richard

last: Brennan


title: argR1 mutant compared to D39 wild-type in Streptococcus pneumoniae in CDM + 10 mM arginine

first: Tomas

last: Kloosterman

summary:
Comparison of Streptococcus pneumoniae D39 argR1 mutant compared to D39 wild type in CDM with 10 mM arginine to define the regulon of the ArgR1 regulator under this condition.

Details described in Kloosterman TG and Kuipers OP. ArgR1 and AhrC Mediate Arginine-Dependent Regulation of Arginine Acquisition- and Virulence Genes in the Human Pathogen Streptococcus pneumoniae. JBC 2011

overall_design: One condition design comparison of two strains including a dye swap

first: Oscar

last: Kuipers


title: A Novel Copper Responsive Regulon in Mycobacterium tuberculosis strains mpA and pafA

city: Rockville

first: Chun-Hua

last: Wan

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

summary: In this study, we report the identification of a five-locus copper-inducible regulon in Mycobacterium tuberculosis. The identification of a copper responsive regulon unique to pathogenic Mycobacteria suggests copper homeostasis must be maintained during an infection.

overall_design: WT and mutant Mtb cells were grown in Sauton’s minimal media to early stationary phase (OD580 = 1.5) and treated with 500 mM copper sulfate (CuSO4) for four hours or the absence.

last: Festa

first: Marcus

last: Jones

first: Susan

last: Butler-Wu

first: Daniel

last: Sinsimer

first: Russell

last: Gerads

first: William

last: Bishai

first: Scott

middle: N

last: Peterson

first: K.

middle: H

last: Darwin


title: Analysis of Culex quinquefasciatus responses to WNV infection

first: George

last: Dimopoulos

summary: Analysis of Culex quinquefasciatus responses to West Nile virus (WNV) infection at 7 and 14 days after ingestion of infected blood in the gut and carcass tissues.

overall_design: Comparison of WNV-infected to non-infected carcass and gut samples.


title: The 'PUCE CAFÉ' project: A genome-wide  15K coffee microarray, a new tool to discover candidate genes correlated to quality traits

city: Notre Dame d’OE - BP 49716-3709 Tours

first: Isabelle

last: Privat

address: 101 Av. Gustave Eiffel

department: Centre de Recherche Nestlé

institute: NESTLE

summary:
Background: Understanding the genetic elements that contribute to key aspects of coffee biology will impact future agronomical improvements for this economically important tree. The past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics.
Results: The project PUCE CAFE, set up by the scientific consortium NESTLE/IRD/CIRAD has developed of long oligonucleotide coffee array using public coffee EST sequences mainly obtained from different stages during fruit development and leaves in Coffea canephora (Robusta). We have performed a validation experiment in order to check the array usability and the reproducibility of hybridizations.
Conclusion: We have generated the first 15K Coffee array during this three years project PUCE CAFE, granted by The French National Research Agency (ANR, Programme Génoplante) . This new tool was dedicated to large scale transcriptomic analysis during grain development of Coffea canephora grown in different countries . Furthermore, other analysis have been also initiated by the different partners like analysis of polyploidy or drought resistance. In any case, at the end of the project, the generated arrays will be available to the international scientific community.

overall_design: three biological replicates were made for each tissue analyzed (i.e. leaves, flowers and mature beans). The following comparisons were made:  Bean-Flower, Leaf-Flower and Leaf-Bean. In all, we performed microarray analyses on 18 slides [3 (replicates) x 2 (dyes) x 3 (organs)]

first: Benoit

last: Bertrand

first: Amélie

last: Bardil

first: Dany

last: Severac

first: Christelle

last: Dantec

first: Ivanna

last: Fuentes

first: Lukas

last: Mueller

first: Thierry

last: Joët

first: David

last: Pot

first: Séverine

last: Foucrier

first: Stéphane

last: Dussert

last: Leroy

first: Laurent

last: Journot

first: Alexandre

last: de Kochko

first: Claudine

last: Campa

first: Marie-Christine

last: Combes

first: Philippe

last: Lashermes


title: Different Mutants in Desulfovibrio vulgaris Hildenborough

first: Adam

last: Arkin

summary: Using gene expression changes at mid-log phase data from microarray experiments, we investigated the roles of global transcription regulators in D. vulgaris.

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Comparison of cells treated with DVU2097, DVU3111, DVU0379, DVU2547 Mutant to untreated Wildtype cells at times of 0 min


title: CCL17-expressing dendritic cells are crucial  for the development of atherosclerosis

city: Aachen

first: Alma

last: Dr. Zernecke

address: Pauwelsstr. 30

country: Germany

institute: IMCAR

summary: Dendritic cells (DCs) are essential for priming of immune responses. Although immune mechanisms are known to control the pathogenesis of atherosclerosis, the role of DCs remains elusive. Here we show that Ccl17 expressing mature, myeloid DCs accumulate within atherosclerotic lesions. Deletion of Ccl17 in apolipoprotein E-deficient (Apoe-/-) mice reduces the development and progression of atherosclerosis in several disease models. While Ccl17 expression by DCs dampened antigen-specific T cell proliferation, it is required for efficient polarization of T helper type 1 (Th1) and Th17 as reflected by a preponderance of Th2 cytokines in Ccl17-/- Apoe-/- mice. In line with these findings, only transfer of T cells from Apoe-/-, but not from Ccl17-/- Apoe-/- precipitated atherosclerosis in T cell depleted Apoe-/- recipients. These findings identify Ccl17+ DCs as central immune regulators in atherosclerosis and Ccl17 as a potential target in the treatment of this disease.

overall_design: There were two samples analyzed with no replicates included. The two samples should be compared with each other.

last: Zernecke

first: Christian

last: Weber


title: Genome-wide transcriptomic profiling of Anopheles gambiae hemocytes reveals pathogen-specific signatures upon bacterial challenge and Plasmodium berghei infection

status: Public on Oct 31 2011

first: George

last: Dimopoulos

summary:
Background: The mosquito Anopheles gambiae is a major vector of human malaria. Increasing evidence indicates that blood cells (hemocytes) comprise an essential arm of the mosquito innate immune response against both bacteria and malaria parasites. To further characterize the role of hemocytes in mosquito immunity, we undertook the first genome-wide transcriptomic analyses of adult female An. gambiae hemocytes following infection by two species of bacteria and a malaria parasite.

Results: We identified 4047 genes expressed in hemocytes, using An. gambiae genome-wide microarrays. While 279 transcripts were significantly enriched in hemocytes relative to whole adult female mosquitoes, 959 transcripts exhibited immune challenge-related regulation. The global transcriptomic responses of hemocytes to challenge with different species of bacteria and/or different stages of malaria parasite infection revealed discrete, minimally overlapping, pathogen-specific signatures of infection-responsive gene expression; 105 of these represented putative immunity-related genes including anti-Plasmodium factors. Of particular interest was the specific co-regulation of various members of the Imd and JNK immune signaling pathways during malaria parasite invasion of the mosquito midgut epithelium.

Conclusion: Our genome-wide transcriptomic analysis of adult mosquito hemocytes reveals pathogen-specific signatures of gene regulation and identifies several novel candidate genes for future functional studies.

overall_design:
In order to identify hemocyte-specific and immune-responsive transcripts, we first compared transcripts expressed in hemocytes from one day old sugar-fed mosquitoes to transcripts detected in whole mosquitoes of the same age and feeding status. This resulted in identification of the hemocyte-enriched transcriptome. We then compared hemocytes from 1 day old mosquitoes, 1 hour after immune challenge with heat-killed Escherichia coli or Micrococcus luteus, to control female mosquitoes injected with sterile PBS to determine the bacteria challenge responsive transcriptomes. We used heat-killed bacteria in these assays, because our primary interest was in identifying the bacterial responsive transcriptome and to avoid the potentially confounding effects of altered gene expression due to the lethal effects of a systemic infection associated with injection of living bacteria. Lastly, we compared hemocytes from mosquitoes at 24 hours and 19 days after ingestion of a blood meal infected with Plasmodium berghei to mosquitoes of the same age fed a non-infected blood meal to determine the ookinete and sporozoite infection responsive transcriptomes, respectively. This design resulted in a total of five experimental treatments.

The following samples are not included in this submission:
Hemo E coli vs. hemo unchallenged A
Hemo E coli vs. hemo unchallenged B
Hemo m luteus vs. hemo unchallenged A
Hemo m luteus vs. hemo unchallenged B


title: Imaging of Plasmodium liver stages to drive next-generation antimalarial drug discovery

city: La Jolla

first: Elizabeth

middle: Ann

last: Winzeler

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

type: Genome variation profiling by genome tiling array

summary: Most malaria drug development focuses on parasite stages detected in red-blood cells even though to achieve eradication next-generation drugs active against both erythrocytic and exo-erythrocytic forms would be preferable. We applied a multifactorial approach to a set of >4,000 commercially available compounds with previously demonstrated blood stage activity (IC50 < 1 µM), and identified chemical scaffolds with potent activity against both forms. From this screen, we identified an imidazolopiperazine scaffold series that was highly enriched among compounds active against Plasmodium liver stages. Our orally bioavailable lead imidazolopiperazine confers complete causal prophylactic protection (15 mg/kg) in rodent models of malaria and shows potent in vivo blood-stage therapeutic activity. The open source chemical tools resulting from our effort provide starting points for future drug discovery programs, as well as opportunities for researchers to investigate the biology of exo-erythrocytic forms.

overall_design: Genome DNA from IP resistant strains vs. Reference 3D7 or Dd2

first: S

last: Meister

first: E


title: Widespread Generation of Alternative UTRs Contributes to Sex-specific RNA Binding by UNR

city: Barcelona

first: Francesco

middle: Mattia

last: Mancuso

address: C/ Dr. Aiguader, 88

country: Spain

institute: CRG (Centre for Genomic Regulation)

summary: Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, sex-specific binding of UNR to various RNAs plays key roles in the control of X chromosome dosage compensation in both sexes. In order to investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of non-coding RNAs in a sex-specific fashion. The analyses also reveal a strong correlation between sex-specific binding of UNR and sex-specific differential expression of UTRs in target genes. Validation experiments indicate that UNR indeed recognizes sex-specifically processed transcripts. These results suggest that UNR exploits the transcript diversity generated by alternative processing and alternative promoter usage to bind and regulate target genes in a sex-specific manner.

overall_design: Of the total 6 chips, three are independent immunoprecipitations, while the other three microarrays are their dye-swaps (same IPs).

first: Marija

last: Mihailovich

first: Laurence

last: Würth

first: Federico

last: Zambelli

first: Irina

last: Abaza

first: Cristina

last: Militti

middle: M

first: Guglielmo

last: Roma

first: Giulio

last: Pavesi

first: Fátima

last: Gebauer


title: Comparison of Aspergillus fumigatus transcriptome grown on selected nitrogen sources

status: Public on Oct 30 2011

city: Wuerzburg

first: Patrick

last: Olbermann

address: Josef-Schneider-Strasse 2

department: Research Center for Infectious diseases research

institute: University of Wuerzburg

summary:
Transcriptome of A. fumigatus shifted from ammoniumtartrate to different nitrogen sources and incubated for a defined time was compared.
After 16h preculture, the fungus was transferred into fresh medium containing ammonium tartrate, sodium nitrate, proline or bsa as nitrogen source.
After 1h, fungus was reisolated, RNA was prepared from fungus, transcriptome was assessed and used for further analysis.

overall_design:
Ammoniumtartrate, sodiumnitrate, BSA and proline as nitrogen sources, 2 biological replicates for each source.

A. fumigatus liquid media shifts were performed according to ref. (Narendja et al.,2002) with minor modifications: 200 ml minimal medium base with 5 mM ammonium tartrate was inoculated with 10^8 conidia freshly harvested. A. fumigatus ATCC 46645 conidia were grown at 37°C and 150 rpm for 16 hours. This pre-culture was then harvested, washed liberally with sterile saline and divided into mycelial masses of equal size on a sterile surface. The portions were then added to 100 ml of minimal medium base without nitrogen source. When a defined carbon source was needed, 1% glucose was added. Flasks were incubated for 20 min at 37°C. Thereafter, one of the following sterile nitrogen sources was added: ammonium tartrate to a final concentration of 5 mM, Sodiumnitrate to a final concentration of 10 mM, 1 g proline suspended in 2 ml minimal medium base, or 0.5 g BSA (Albumin Fraktion V, Roth), suspended in 15 ml minimal medium base. The cultures were incubated for another 60 minutes, harvested by filtering through Miracloth, snap frozen in liquid nitrogen, and ground using a cooled mortar to obtain a fine powder.

first: Thomas

last: Hartmann

first: Sven

last: Krappmann


title: Induction of the neuronal major histocompatibility complex class I and paired immunoglobulin-like receptor B pathway in the hippocampus with aging and cognitive decline

city: Hershey

first: Penn State

last: COM

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

summary: The aim of this study was to identify alterations in hippocampal synaptic mRNA expression with aging and cognitive decline.  Transcriptional profiling and subsequent bioinformatic analysis was performed to identify the most highly regulated pathways of genes.  Interestingly, the antigen processing and presentation pathway was identified as the most highly regulated pathway with aging.

overall_design: Adult (12 month) and aged (28 month) Fischer 344 x Brown Norway (F1) hybrid rats were assessed for cognitive performance using the Morris water maze task and were divided into Adult (n=5), Aged Cognitively Intact (n=8), and Aged Cognitively Impaired (n=7) groups.  One week following testing, all animals were sacrificed, the hippocampi were dissected, and synaptosomes were isolated for subsequent transcriptomic profiling. Only 5 cognitively intact animals were processed on the arrays.

first: Colleen

last: Van Kirk

first: Heather

last: VanGuilder

first: Georgina

middle: V

last: Bixler

first: Caesar

middle: G

last: Imperio

first: Vijay

middle: P

last: Kale

first: Jacob

last: Serfass

first: Julie

last: Farley

first: Han

last: Yan

first: Song

last: Han

first: Junie

last: Warrington

first: Matthew

last: Mitschelen

first: William

last: Sonntag

first: Willard

last: Freeman


title: Growing pains: natural stress response during growth of B. subtilis (high density time-resolved transcriptome analysis)

city: Haren

first: EJ

last: Blom

address: Kerklaan 30

department: Molecular Genetics

institute: University of Groningen

summary:
We have determined the time-resolved transcriptome of the model gram-positive organism B. subtilis during growth on rich medium. DNA microarrays were used to monitor gene transcription in 10-minute intervals at 40 consecutive timepoints.
From the growth curve and a PCA analysis of all gene expression levels, we identified 4 distinct growth phases: a lag phase, an exponential growth phase, and very clearly separated early and late stationary growth phases

overall_design: For each time point, labeled cDNA was hybridized to a microarray slide together with labeled cDNA from the previous timepoint. In addition, the same DNA was used in a dye swap hybridization with the labeled cDNA from the subsequent timepoint. Lastly, labeled cDNA from each timepoint was hybridized with labeled cDNA from 30 mins later (e.g., 1 vs 4, 2 vs 5 etc.). The three slides resulted in six measurements per gene, since each slide contains two duplicate spots for all genes.  Duplicate spots on the same array were analyzed separately, for a total of 118 Samples from the 56 hybridizations.  Therefore, the same raw data file is associated with the '#1' and '#2' sample of a given comparison (eg. GSM495251 and GSM495252).

first: Evert-Jan

first: Anja

last: Ridder

first: Andrzej

last: Lulko

first: Jos

middle: B

last: Roerdink

first: Oscar

last: Kuipers


title: CCL17-expressing dendritic cells are crucial  for the development of atherosclerosis: T cell priming

first: Alma

last: Dr. Zernecke

overall_design: There are three samples analyzed with no replicates included. There is one control sample included.

last: Zernecke

first: Christian

last: Weber


title: Comparing global transcriptional changes that resulted from loss of Ypk1 or Ypk2 activity

status: Public on Oct 29 2011

city: Davis

first: Ted

last: Powers

address: One Shields Ave

department: Molecular and Cellular Biology

institute: UC Davis

summary: To identify genes regulated by the AGC kinases Ypk1 and Ypk2

overall_design: Experiment is designed to identify genes regulated by the kinases Ypk1 and Ypk2.  These are functionally redundant AGC kinases such that yeast cells can grow in the presence of either one but the absence of both is lethal.  We used a chemical genetic approach to selectively inhibit engineered ATP analog sensitive alleles (AS alleles) of each kinase.  Experimental design is such that wild type (WT) Ypk1 or Ypk2 or (AS) Ypk1 or Ypk2 genes are expressed individually on plasmids in a strain background that is deleted for both Ypk1 and Ypk2 (ypk1 delta ypk2 delta).  Cultures expressing these plasmids are treated with an ATP analog that is specific for AS Ypk1 or AS Ypk2.  Thus, cells expressing wild type Ypk1 or Ypk2 are not sensitive but cells expressing their AS counterparts are sensitive.  Arrays typically compare expression patterns in WT versus AS expressing cells at the same time point following inhibitor treatment.

first: Brad

last: Niles


title: The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset (ChIP)

city: Munich

last: Feller

address: Schillerstraße 44

department: Molecular Biology

institute: Adolf-Butenandt Institute at the LMU University Munich

type: Genome binding/occupancy profiling by genome tiling array

summary: The MOF-containing NSL complex binds to many but not all promoters of active genes and potentially contributes to their proper gene expression. It is currently unknown what determines whether an active gene is bound or not. Here, we provide evidence that the NSL complex primarily targets active promoters of most housekeeping genes. There, it co-localizes with the chromatin remodeler NURF and the histone methyltransferase Trithorax. Moreover, despite binding to most housekeeping genes, the NSL complex regulates only a subset of them, which are depleted for certain insulator binding-proteins and enriched for the core promoter motif “Ohler 5”. We suggest that the combination of general chromatin factors and core promoter motifs is predictive for whether a housekeeping gene is transcriptionally regulated by the NSL complex.

overall_design: ChIP-chip profiling of NSL1 in adult male and female whole fly extracts and the embryonically derived male S2 cell line.

first: Peter

last: Becker


title: Potential Prognostic Biomarkers for Bone Metastasis from Hepatocellular Carcinoma

status: Public on Oct 28 2011

city: Shanghai

first: Zuolin

last: Xiang

address: 136 Yi Xue Yuan Road

institute: Zhongshan Hospital, Fudan University

summary: RNA was extracted from 48 pairs of intratumoral and peritumoral formalin-fixed, paraffin-embedded (FFPE) tissue from hepatocellular carcinoma (HCC) patients with and without bone metastases (BM). The Human Cancer Panel DASL Assay containing 502 cancer-related genes was used to identify novel BM-associated genes. A cDNA-mediated annealing, selection, extension, and ligation assay was performed with an array of 502 known cancer-related genes to identify differentially expressed genes in 96 RNA samples.

overall_design: Total RNA was purified from the tissue specimens using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. DASL experiments were performed to identify genes that were differentially expressed between the BM and NBM groups of matched intratumoral and peritumoral tissues by using A cDNA-mediated annealing, selection, extension, and ligation assay.

first: Zuo-lin

first: Zhao-chong

last: Zeng

first: Zhao-you

last: Tang

first: Jia

last: Fan

first: Jian

last: He

first: Hai-ying

first: Xiao-dong

last: Zhu


title: Jarid1b targets genes regulating development and is involved in neural differentiation [expression array]

status: Public on Oct 27 2011

city: Copenhagen

first: Sandra

middle: Ursula

last: Schmitz

address: Ole Maaløes Vej 5

institute: Biotech Research and Innovation Centre

summary: The H3K4me2/3 histone demethylase Jarid1b (Kdm5b/Plu1) is dispensable for embryonic stem cell (ESC) self-renewal, but essential for ESC differentiation along the neural lineage. During neural differentiation, Jarid1b depleted ESCs fail to efficiently silence lineage-inappropriate genes, specifically stem and germ cell genes. Our results delineate an essential role for Jarid1b-mediated transcriptional control during ESC differentiation.

overall_design: Control (LKOScr) or Jarid1b knockdown (LKOJarid1b) mouse ES cells were used.Each experiment was performed in triplicates.


title: R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 (blue light, semiaerobic conditions)

status: Public on Oct 26 2011

city: Giessen

first: Sebastian

middle: Harald Michael

last: Metz

address: Heinrich-Buff-Ring 26-32

department: Institut für Mikro- und Molekularbiologie

institute: Justus-Liebig-Universität Giessen

summary: Transcriptional profiling of R. sphaeroides Δlov compared to control R. sphaeroides 2.4.1 under blue light, semiaerobic conditions.

overall_design: Two-strain experiment under blue light illumination (20µmol m-2 s-1) and semiaerobic (90 µM O2) conditions

first: Andreas

last: Jäger

first: Gabriele

last: Klug


title: R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 (singlet oxygen stress, aerobic conditions)

summary: Transcriptional profiling of R. sphaeroides Δlov compared to control R. sphaeroides 2.4.1 under singlet oxygen stress, aerobic conditions

overall_design: Two-strain experiment with overnight cultures of the wild type 2.4.1 and the Δlov mutant. Both were diluted to an OD660 of 0.2 and gassed to adjust aerobic conditions (≈ 170 µM O2). 0.2 µM of methylene blue was added to the cultures to act as photosensitizer. After one doubling time of growth in the darkness cells were illuminated with 800 W m-2 of white light for 7 min.


title: ChIP-chip of Spo14 and Mvp1

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

type: Genome binding/occupancy profiling by array

summary:
Genome-wide localization of two new RNA pol II interacting proteins. We use C-LYTAG to map binding sites of Spo14 and Mvp1 along the S. cerevisiae genome. Two biological replicates of each experiment were done.

Keywords: ChIp-chip

overall_design:
Two independent biological replicates of each IP. We used three macroarrays:
V5R2-L1-20, V5R2-L1-21 and V5R2-L1-22 that were hybridized with Whole Cell Extract (WCE) and then with two biological samples of immunoprecipitated (IP) Mvp1 (V5R2-L1-20 and V5R2-L1-21) and Spo14 (V5R2-L1-20 and V5R2-L1-22)

first: Maria

middle: C

last: García-López

first: Vicent

last: Pelechano

middle: E

last: Pérez-Ortín

first: Francisco

last: Navarro


title: Comparative gene expression profiles on contrasting mealy phenotypes in peach fruits reveal candidate genes associated with fruit quality

city: Santiago

first: Leonardo

middle: Ignacio

last: Pavez

state: Santiago

address: Av Manuel Montt #948

country: Chile

institute: Universidad de Las Américas

summary: Storage at low temperatures is one of the most used methods to prolong the life of postharvest peaches (Prunus persica (L) Batch.). However, fruit quality is adversely affected by the development of woolliness, a physiological disorder that is apparent when the fruit is ripened after prolonged periods of cold storage and is mainly manifested as loss of juice in the peaches. The aim of this study was to obtain a more detailed cohort of genes that underlie the wolliness in a segregating population with contrasting phenotypes of mealiness after being exposed to cold storage at 4 °C. For this, a transcriptomics approach was applied to fruits from a progeny of individuals accounted for 6% more juicy and woolly 6% over a 2 years. Our results suggest that not only genes related to the maintenance of cell wall architecture may contribute to the development of mealy phenotype. Based on its possible physiological process and differential pattern of expression transcriptomic profiles show that genes related to maintenance (modification I) and membrane fluidity account for the differences between fruits that exhibit contrasting phenotypes of mealiness. These genes may contribute to tolerance to cold during storage.

overall_design: We analyzed a total of 9 woolly fruits (from 3 different trees, 3 fruits from each tree) and 12 juicy fruits (from 4 different trees, 3 fruits from each tree). An RNA pool from 9 woolly fruits was used as reference and was compared to an RNA pool of 3 juicy fruits from each individual tree. Two technical replicates were done for each comparison, thus making in total 8 hybridizations.

first: Talía

last: Del pozo

first: Felipe

last: Olivares

first: Mauricio

last: González


title: Gene expression data from arbuscular mycorrhizal and phosphate-treated Medicago truncatula roots.

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

summary:
Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression in Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on whole mycorrhizal roots.
We used GeneChips to detail the global programme of gene expression in response to colonization by arbuscular mycorrhizal fungi and in response to a treatment with phosphate and identified genes differentially expressed during this process.

overall_design: Medicago truncatula roots were harvested at 28 days post inoculation with the two different arbuscular mycorrhizal fungi Glomus intraradices (Gi-Myc) and Glomus mosseae (Gm-Myc) under low phosphate conditions (20 µM phosphate) or after a 28 days treatment with 2 mM phosphate in the absence of arbuscular mycorrhizal fungi (2mM-P). As a control, uninfected roots grown under low phosphate conditions (20 µM phosphate) were used (20miM-P). Three biological replicates consisting of pools of five roots were used for RNA extraction and hybridization on Affymetrix GeneChips.

first: Natalija

last: Hohnjec

first: Claudia

last: Hogekamp

first: Jörg

middle: D

last: Becker

first: Damaris

last: Arndt


title: R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 (microarobic conditions)

last: Metz

summary: Transcriptional profiling of R. sphaeroides Δlov comparing to control R. sphaeroides 2.4.1 under microarobic conditions

overall_design: Two strain experiment under microarobic conditions. 6 Biological replicas, independetly grown and harvested at OD660=0,8 - 1-3 pooled in replicate 1 and 4-6 pooled in replicate 2


title: Substrate selectivity for semisynthetic CK2 proteins with Pin1

status: Public on Oct 25 2011

city: Baltimore

first: Mary Katherine

last: Tarrant

address: 725 N. Wolfe Street, 317 Hunterian Bldg.

department: Pharmacology and Molecular Sciences

institute: Johns Hopkins University School of Medicine

summary:
Protein Ser/Thr kinase CK2 is involved in a myriad of cellular processes including cell growth and proliferation by phosphorylating hundreds of substrates, yet the regulation process of CK2 function is poorly understood.  The CK2 catalytic subunit, CK2α, is phosphorylated at Thr344 and phosphorylation on the C-terminal tail of CK2α is required for interaction with Pin1 protein.  The substrate selectivity for protein kinase CK2α was examined by performing kinase assays on protein microarrays spotted with 17,000 human proteins.  Semisynthetic CK2α proteins were prepared to contain an unmodified C-terminal tail or phospho-Thr (pThr) at T344.  These semisynthetic proteins were used to determine if the phosphorylation-dependent interaction of CK2α with Pin1 can modulate the substrate selectivity for CK2.
The different semisynthetic CK2α proteins (unmodified and pThr344) were tested alone and in the presence of the recombinant Pin1 protein.  Pin1 has been shown to interaction with CK2α only when CK2α is phoshorylated on its C-terminal site (including Thr344).

overall_design: In the study presented here, kinase assays were performed using two different semisynthetic CK2α proteins: unmodified C-terminal tail and phospho-Thr (pThr) at 344.     The semisynthetic proteins were each tested alone and in the presence of the recombinant Pin1 protein.  There were four different kinase conditions and each condition was performed in duplicate.

first: Mary

middle: K

first: Philip

middle: A

last: Cole

first: Hee-Sool

last: Rho

first: Heng

last: Zhu

first: Zhi

last: Xie

first: Jiang

last: Qian


title: Profiling of plant miRNAs induced by drought stress in the rice plant

first: Zaochang

last: Liu

address: 2901 Beidi Rd., Minhang District

department: Lab

institute: SAAS

summary: Expression profiles were analyzed between drought stress and normal watered control at the tillering and inflorescence stages.

overall_design:
1. We applied microarray analysis to detect drought-stress-regulated miRNAs from tillering to inflorescence-forming stages in rice.
2. Three time courses at the tillering stage and two time courses at the inflorescence-forming stage. Two replicates were carried out in each time course.

first: Liu

last: Zaochang

last: Yunhua

first: Zhou

last: Liguo

first: Duan

last: Mei

first: Kong

last: Deyan

first: Wen

last: Guoli

first: Luo

last: Lijun


title: Detection of miRNAs in exosomes released by mouse immature and mature dendritic cells

city: Pittsburgh

first: Adrian

middle: Eduardo

last: Morelli

address: E1546. Biomedical Science Tower. 200 Lothrop St.

department: T.E. Starzl Transplantation Institute. Dept. of Surgery

institute: University of Pittsburgh

summary: Dendritic cells (DCs) are the most potent antigen (Ag)-presenting cells. Whereas immature DCs down-regulate T cell responses to induce/maintain immunological tolerance, mature DCs promote immunity. To amplify their functions, DCs communicate with neighboring DCs through soluble mediators, cell-to-cell contact and vesicle exchange. Transfer of nanovesicles (<100nm) derived from the endocytic pathway (termed exosomes) represents a novel mechanism of DC-to-DC communication. The facts that exosomes contain exosome-shuttle microRNAs (miRNAs), and DC functions can be regulated by exogenous miRNAs, suggest that DC-to-DC interactions could be mediated through exosome-shuttle miRNAs, an hypothesis that remains to be tested. Importantly, the mechanism of transfer of exosome-shuttle miRNAs from the exosome lumen to the cytosol of target cells is unknown. Here, we demonstrate that DCs release exosomes with different miRNAs depending on the maturation of the DCs. By visualizing spontaneous transfer of exosomes between DCs, we demonstrate that exosomes fused with the target DCs, the latter followed by release of the exosome content into the DC cytosol. Importantly, exosome-shuttle miRNAs are functional, as they repress target mRNAs of acceptor DCs. Our findings unveil a mechanism of transfer of exosome-shuttle miRNAs between DCs and its role as a means of communication and post-transcriptional regulation between DCs.

overall_design: The study has analyzed the microRNA content of 4 samples of immature exosomes, 4 samples of matures exosomes, 2 samples of immature bone-marrow-derived DCs, and 2 samples of mature bone marrow-derived DCs.

first: Angela

last: Montecalvo


title: Sexually Dimorphic Gene Expression in the Adult Mouse Hypothalamus and Bed Nucleus of the Stria Terminalis

city: San Francisco

first: Xiaohong

last: Xu

address: 1550 4th Street, Rock Hall 345 Mission Bay

department: Anatomy

institute: University of California at San Francisco

summary:
To identify genes that are downstream of gonadal hormones and that control dimorphic behaviors, we used a MEEBO array platform to profile gene expression of adult male and female hypothalamus against a whole brain reference sample. The experimental design allowed us to identify genes that are upreguated in the hypothalamus compared to the whole brain and are dimorphically expressed between the two sexes. In situ hybridization of candiate genes were carried out to validate the dimorphic expression of these genes in the hypothalamus.

Array results were used to create a list of genes to screen by in situ hybridization. For each normalization method, a list of genes that were upregulated in the male or the female was created, and a gene had to be on a set number of these individual normalization lists in order to be considered for screening. A similar method was used to create a list of hypothalamic upregulated genes. The final screening list was comprised of genes that were upregulated in the male or female as well as in the hypothalamus. If in situ hybridization proved that the gene was upregulated in the male or female brain, we concluded that that transcript was differentially expressed. No one normalization method was weighted over another, and the array results were used to create a screening list for in situ hybridizations.

overall_design:
Hypothalami from 4 adult animals of each sex were microdissected and pooled for each experimental sample and the whole brain plus pituitary from one male and one female were pooled to provide the reference sample. Each set of samples (male and female) was hybridized to two arrays to provide two technical replicates for each set of samples taken. A total of three sets of samples were taken (three biological replicates).

For the "_amp" Samples, source (hypothalamus and whole brain) mRNA was amplified using T7 based method. For this set, data were not normalized, rather the raw intensities were used to calculate ratios. Candidate genes from this study was also included in final list in situ screening.

first: Jennifer

last: Coats

first: Nirao

last: Shah


title: Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in Maize

status: Public on Oct 22 2011

city: Saint Louis

first: Jim

last: Morrell

state: Missouri

address: 800 North Lindbergh Blvd

department: Biotechnology

institute: Monsanto Co.

summary: We have characterized the transcriptional response in Maize under limiting and sufficient nitrogen conditions, and have identified a set of genes whose expression profiles can quantitatively assess the response of plants to those conditions.

overall_design:
Four lines, three timepoints, multiple treatments, and three biological replicates for a total of 90 samples.
Genotypes : Four Monsanto proprietary Zea mays lines were used, designated Line1, Line2, Line3 and Line4
N02: (Limiting Nitrogen) grown for 28 days to V6 stage with 2mM ammonium nitrate
N20: (Sufficient Nitrogen) grown for 21 days to V6 stage with 20mM ammonium nitrate
N02T20: (Limiting Nitrogen Supplemented) grown for 28 days to V6 with 2mM ammonium nitrate followed by application of 20mM ammonium nitrate applied at 8AM (and sampled at 10AM, 11PM on the same day, and 10AM the following day)
Sampling Times: Day1@10AM, Day1@11PM. Another sample was taken at Day2@10AM (the following day) for Line4 and for all the Nitrogen Supplemented (N02T20) samples of all lines.
Development Stage: V6 stage (21 days for sufficient nitrogen treatment and 28 days for limiting nitrogen treatment.  Planting was staggered so all sampling was done on the same days.)
Plants were grown in green house.  Leaf tissue from 4 plants were combined to form each replicate.


title: Expression data from laboratory evolution of Escherichia coli on lactate or glycerol

city: Richmond

first: Stephen

last: Fong

state: VA

address: 601 W. Main Street

institute: VCU

summary:
Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days.  7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol.
Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. coli (day 0) to a midpoint evolved strain (day 20) and evolutionary endpoints

overall_design: Biological replicate arrays were conducted for each of the time points tested for the different evolution strains

middle: S

first: Andrew

middle: R

last: Joyce

first: Bernhard

middle: O

last: Palsson


title: Human bone marrow precursor cells

first: Corinna

middle: Cavan

last: Pedersen

address: Juliane Mariesvej 20, 9322

institute: Rigshospitalet

summary: The aim of this study was to characterize in vivo miRNA expression in normal myeloid development of the neutrophil granulocyte (granulopoiesis) to gain insight into miRNA control of these processes. Cell populations highly enriched in precursors from successive stages of granulopoiesis and mature neutrophils were isolated from bone marrow (BM) and peripheral blood (PB) samples, respectively, from 4 healthy human donors. Total RNA was extracted from each cell population and subjected to miRNA gene expression profiling using miRCURYTM LNA microRNA Arrays

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

overall_design: Total RNA from cell populations highly enriched in precursors from three succesive stages of neutrophil granulopoiesis and mature neutrophils isolated from bone marrow and peripheral blood, respectively, from four healthy donors (SKP, AJ, AO, JO). The three cell populations from bone marrow where extracted and named B3, B2, and B1, corresponding to immature (myeloblasts [MBs] and promyelocytes [PMs]);  intermediate mature (myelocytes [MCs] and metamyelocytes [MMs]); and mature neutrophil cells (band cells [BCs] and segmented neutrophil cells [SCs]), respectively, as described in Bjerregaard MD, Jurlander J, Klausen P, Borregaard N, Cowland JB: The in vivo profile of transcription factors during neutrophil differentiation in human bone marrow. Blood 2003, 101: 4322-4332. In total, 16 samples were compared (4 cell maturation stages from 4 donors)

first: Hanne

last: Jarmer

first: Christoffer

last: Hother

first: Kirsten

last: Grønbæk

first: Niels

last: Borregaard

first: Jack

last: Cowland


title: Post-transcriptional fine-tuning of COP9 signalosome subunit biosynthesis is regulated by the c-Myc/Lin28B/let-7 pathway

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: MACSmolecular Business Unit

institute: Miltenyi Biotec GmbH

summary:
The COP9 signalosome (CSN) is a conserved protein complex occurring in all eukaryotes. The mammalian CSN consists of eight subunits (CSN1 – CSN8) and possesses an intrinsic metalloprotease JAMM motif localised to CSN5. In addition, it is associated with kinases such as protein kinase CK2 and D and the ubiquitin (Ub) specific protease 15. It regulates cullin-RING Ub ligases (CRLs) that label proteins for proteolysis with poly-Ub chains in the Ub proteasome system (UPS). CRLs contain one of the scaffolding cullins 1 – 7, a RING domain protein e. g. Rbx1, and one of hundreds of substrate binding units such as F-box or BTB proteins that specifically target proteins for ubiquitination. The CSN forms functional supercomplexes with CRLs. It removes the Ub-like protein Nedd8 from cullins by its metalloprotease activity and thereby inactivates CRLs. On the other hand, it is essential for CRL function by protecting components and allowing reassembly of the complexes. As a regulator of the UPS the CSN is involved in cell cycle10, DNA repair and development. Overexpression of CSN subunits has been reported in tumour cells.   Up to date nothing is known about CSN biogenesis and its regulation. Ten years ago we have observed that overexpression of selected CSN subunits caused a coordinated increase of all CSN subunits and a de novo biosynthesis of the entire complex. Here we show that overexpression of CSN1 mediates an increase of c-Myc which coordinates CSN subunit expression via microRNAs (miRNAs). miRNAs are evolutionarily conserved, endogenous, small, noncoding RNA molecules of about 22 nucleotides that function as posttranscriptional gene regulators. We found that inhibitors of let-7 family miRNAs or upregulation of c-Myc, which represses let-7 miRNAs, resulted in a coordinated increase of CSN subunits and de novo CSN biogenesis.

Keywords: Gene expression analysis of human RNA samples using topic-defined PIQOR™ Ubiquitin-PS Microarrays. Two different platforms were used (these are two different microarray batches which are identical in terms of the spotted cDNAs, but differ in the position of some cDNAs)

overall_design:
Gene expression analysis of Hela cells overexpressing either CSN2 or CSN1 was performed to study CSN biogenesis and its regulation.

Curcumin, Nr. 8 (Curcumin analogon) and Piceatannol were used for the treatment of Hela cells since they inhibit the CSN associated kinases. The aim was to investigate the effect on the signalosome. For each treatment 50 µM Curcumin, Nr. 8 and Piceatannol were used.

first: Ulrike

last: Leppert

first: Wolfgang

last: Henke

first: Xiaohua

last: Huang

first: Joachim

middle: M

last: Müller

last: Dubiel


title: Insights into Transcriptional Regulatory Pathways on Systemic Communication under Flooding in Arabidopsis

status: Public on Oct 21 2011

city: Taipei

first: Fu-Chiun

last: Hsu

address: No. 128, Sec. 2, Academia Road, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

summary:
We analyzed global transcriptional changes in both shoots and roots of root-flooded Arabidopsis seedlings by microarrays.  We also interpreted the significance of the systemic communication between roots and shoots by functional classification of affected genes.  We performed genetic analysis with an ethylene signaling mutant, ein2-5, to correlate systemic flooding responses with ethylene signaling.
We identified a class of genes that were up- or downregulated in shoots, but not affected in roots, under hypoxic conditions.  A comprehensive managing program of carbohydrate metabolism was observed, providing an example of how systemic communications might facilitate the survival of plants under flooding.  A proportion of long-distance hypoxic regulation was altered in ein2-5.

overall_design: Time course experiments (0.5, 1, 3, 6, and 12h for Columbia; 0.5, 3, and 6h for ein2-5).  Tissues from root-flooded seedlings vs. Tissues from un-flooded seedlings.  Biological replicates: 4 replicates for each time point, independently grown, treated, and harvested. One replicate per array.  2 of 4 replicates are dye-swapped.

first: Mei-Yi

last: Chou

first: Hsiao-Ping

last: Peng

first: Shu-Jen

first: Ming-Che

last: Shih


title: Isocitrate dehydrogenase 1 (IDH1) mutant gliomas demonstrate a distinct global CpG island methylation profile compared to IDH1 wildtype gliomas using MRSE

city: Los Angeles

first: Reshmi

last: Chowdhury

address: 635 Charles E. Young Drive South

department: Neuro-Oncology

institute: UCLA

type: Methylation profiling by genome tiling array

summary: In order to identify other molecular aberrations that may cooperate with IDH1R132MUT in gliomagenesis, we performed CpG-island methylation profiling analysis using MSRE (Tran et al. Front. Neurosci. 3:57. Doi: 10.3389/neuro.15.005.2009) on a subset of IDH1R132MUT and IDH1R132WT GBMs and found a distinct pattern of CpG island hypermethylation that was detected in all GBMs and lower grade gliomas with IDH1R132MUT. While absent from nearly all IDH1R132WT glioma, the methylation pattern in IDH1R132MUT GBMs shows similarity to the recently reported CpG island methylator phenotype (CIMP) found to be tightly associated with IDH1R132MUT gliomas(Noushmehr et al. Cancer Cell, Volume 17, Issue 5, 18 May 2010, Pages 510-522, ISSN 1535-6108, DOI: 10.1016/j.ccr.2010.03.017).

overall_design: Methylation profiling performed on 40 distinct brain tumor samples: 7 Anaplastic Astrocytomas, including 3 IDH1MUT and 4 IDH1WT; 5 Lowgrade Astrocytomas, including 4 IDH1MUT and 1 IDH1WT; 28 Glioblastoma, including 8 IDH1MUT and 20 IDH1WT.

first: Albert

last: Lai


title: Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis

status: Public on Oct 24 2011

city: Beijing

first: Dongsheng

last: Zhou

address: NO.20 Dongdajie, Fengtai

institute: Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China

summary:
Background
The osmotic regulator OmpR in Escherichia coli regulates differentially the expression of major porin proteins OmpF and OmpC. In Yersinia enterocolitica and Y. pseudotuberculosis, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory roles of OmpR in Y. pestis are not yet fully understood.

Results
Y. pestis OmpR is involved in building resistance against phagocytosis and controls the adaptation to various stressful conditions met in macrophages. The ompR mutation likely did not affect the virulence of Y. pestis strain 201 that was a human-avirulent enzootic strain. The microarray-based comparative transcriptome analysis disclosed a set of 224 genes whose expressions were affected by the ompR mutation, indicating the global regulatory role of OmpR in Y. pestis. Real-time RT-PCR or lacZ fusion reporter assay further validated 16 OmpR-dependent genes, for which OmpR consensus-like sequences were found within their upstream DNA regions. ompC, F, X, and R were up-regulated dramatically with the increase of medium osmolarity, which was mediated by OmpR occupying the target promoter regions in a tandem manner.

Conclusion
OmpR contributes to the resistance against phagocytosis or survival within macrophages, which is conserved in the pathogenic yersiniae. Y. pestis OmpR regulates ompC, F, X, and R directly through OmpR-promoter DNA association. There is an inducible expressions of the pore-forming proteins OmpF, C, and X at high osmolarity in Y. pestis, in contrast to the reciprocal regulation of them in E. coli. The main difference is that ompF expression is not repressed at high osmolarity in Y. pestis, which is likely due to the absence of a promoter-distal OmpR-binding site for ompF.

overall_design:
Bacterial strains
The wild-type (WT) Y. pestis biovar microtus strain 201 is avirulent to humans but highly lethal to mice [1]. The 43 to 666 base pairs of ompR (720bp in total length) were replaced by the kanamycin resistance cassette using the one-step inactivation method based on the lambda Red phage recombination system, with the helper plasmid pKD46, to generate the ompR mutants of Y. pestis (designated as ΔompR) [2]. Chromosomal integration of the mutagenic cassette was confirmed by PCR and sequencing using oligonucleotides external to the integrated cassette (data not shown). The elimination of pKD46 in ΔompR was verified by PCR.

Bacterial growth and RNA isolation
Overnight cultures (an OD620 of about 1.0) of WT or ΔompR in the chemically defined TMH medium [3] were diluted 1:20 into the fresh TMH. Bacterial cells were grown at 26°C to the middle exponential growth phase (an OD620 of about 1.0). To trigger the high osmolarity conditions in OmpR-related experiments, a final concentration of 0.5 M sorbitol was added, after which the cell cultures were allowed to grow for another 20 min.
Total RNA of bacterial cells was extracted using the TRIzol Reagent (Invitrogen) without the DNA removal step (for RT-PCR and primer extension) or by using MasterPureTM RNA Purification kit (Epicenter) with the removal of contaminated DNA (for microarray). Immediately before harvesting, bacterial cultures were mixed with RNAprotect Bacteria Reagent (Qiagen) to minimize RNA degradation. RNA quality was monitored by agarose gel electrophoresis, and RNA quantity was determined using a spectrophotometer.

Microarray expression analysis
Gene expression profiles were compared between WT and ΔompR using a Y. pestis whole-genome cDNA microarray as described in a previous work [4]. RNA samples were isolated from four individual bacterial cultures as biological replicates for each strain. The dual-fluorescently (Cy3 or Cy5 dye) labeled cDNA probes, for which the incorporated dye was reversed, were synthesized from the RNA samples. These were then hybridized to 4 separated microarray slides. A ratio of mRNA levels was calculated for each gene. Significant changes of gene expression were identified using the SAM software [5]. After the SAM analysis, only genes with at least two-fold changes in expression were collected for further analysis.

References

1. Zhou D, Tong Z, Song Y, Han Y, Pei D, et al. (2004) Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus. J Bacteriol 186: 5147-5152.
2. Zhan L, Han Y, Yang L, Geng J, Li Y, et al. (2008) The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus. Infect Immun 76: 5028-5037.
3. Straley SC, Bowmer WS (1986) Virulence genes regulated at the transcriptional level by Ca2+ in Yersinia pestis include structural genes for outer membrane proteins. Infect Immun 51: 445-454.
4. Zhou D, Qin L, Han Y, Qiu J, Chen Z, et al. (2006) Global analysis of iron assimilation and fur regulation in Yersinia pestis. FEMS Microbiol Lett 258: 9-17.
5. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121.


title: Substrate selectivity for semisynthetic CK2 proteins with various posttranslational modifications

first: Mary Katherine

last: Tarrant

summary:
Protein Ser/Thr kinase CK2 is involved in a myriad of cellular processes including cell growth and proliferation by phosphorylating hundreds of substrates, yet the regulation process of CK2 function is poorly understood.  The CK2 catalytic subunit, CK2α, is modified by O-GlcNAc on Ser347 proximal to a Cdk1 phosphorylation site at Thr344 on the same protein.  The substrate selectivity for protein kinase CK2 was examined by performing kinase assays on protein microarrays spotted with 17,000 human proteins.  Semisynthetic CK2α proteins were prepared to contain an unmodified C-terminal tail, S-GlcNAc-Serine at S347, or Pfa (non-hyrdolyzeable phosphomimic) at T344.  These semisynthetic proteins were used to determine if the posttranslational modifications on CK2 alpha modulate the substrate selectivity for this pleiotropic kinase.
The different semisynthetic CK2α proteins were tested alone and in the presence of the regulatory subunit CK2β since it is known that the CK2α subunit is active both in its isolated state and in the heterotetrameric state formed in the presence of the regulatory beta subunit.  The CK2β subunit has been shown to modulate CK2 activity with some substrates and not others.

overall_design: In the study presented here, kinase assays were performed using three different semisynthetic CK2 alpha proteins: unmodified C-terminal tail; S-GlcNAc-Ser at 347; and Pfa (phosphomimic) at 344.  The semisynthetic proteins were each tested alone and in the presence of the regualatory CK2 beta subunit.  There were six different kinase conditions and each condition was performed in duplicate and one no kinase control was performed to eliminate autophorylated proteins.

first: Mary

first: Philip

last: Cole

first: Hee-Sool

last: Rho

first: Heng

last: Zhu

first: Zhi

last: Xie

first: Jiang

last: Qian


title: Comparative genomic hybridization of strains of Leishmania infantum, Leishmania major and Leishmania tarentolae

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

summary:
The genomic DNAs of strains JPCM5 and 263 of L. infantum, strains LV39 and Friedlin of L. major and strains Parrot-TarII and S125 of L. tarentolae were used in comparative genomic hybridizations to reveal the intra-species and inter-species gene content, and to validate L. tarentolae Parrot-TarII genome sequencing results.
Leishmania (Sauroleishmania) tarentolae was first isolated in the lizard Tarentola mauritanica. This species is not known to be pathogenic to humans but is often used as a model organism for molecular analyses or protein overproduction. The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved by high-throughput sequencing technologies. The L. tarentolae genome was first assembled de novo and then aligned against the reference L. major Friedlin genome to facilitate contig positioning and annotation, providing a 23-fold coverage of the genome. This is the first non-pathogenic to humans kinetoplastid protozoan genome to be described, and it provides an opportunity for comparison with the completed genomes of the pathogenic Leishmania species. A high synteny was observed in de novo assembled contigs between all sequenced Leishmania species. A number of limited chromosomal regions diverged between L. tarentolae and L. infantum, while remaining syntenic with L. major. Globally, over 90% of the L. tarentolae gene content was shared with the other Leishmania species. There were 250 L. major genes absent from L. tarentolae, and interestingly these missing genes were primarily expressed in the intracellular amastigote stage of the pathogenic parasites. This implies that L. tarentolae may have impaired ability to survive as an intracellular parasite. In contrast to other Leishmania genomes, two gene families were expanded in L. tarentolae, namely the leishmanolysin (GP63) and a gene related to the promastigote surface antigen (PSA31C). Overall, L. tarentolae appears to have a gene content more adapted to the insect stage rather than the mammalian one. This may partly explain its inability to replicate within mammalian macrophages and its suspected preferred life style as promastigote in the lizards.

sample_organism:
Leishmania major
Leishmania infantum
Leishmania tarentolae

overall_design:
Six strains of three Leishmania species were hybridizated to 12 microarrays, each with four biological replicates (independent cultures).

Supplementary file: Represents final results obtained after statistical analysis of all replicates.

first: Frédéric

first: Sébastien

last: Boisvert

first: Gaétan

last: Roy

first: Jean-François

last: Ritt

first: Danielle

last: Légaré

first: Mario

last: Stanke

first: Martin

last: Olivier

first: Michel

middle: J

last: Tremblay

first: Barbara

last: Papadopoulou

first: Marc

last: Ouellette

first: Jacques

last: Corbeil


title: Transcriptional responses underlying the hormetic and detrimental effects of gossypol on Helicoverpa armigera

status: Public on Oct 20 2011

city: Stockholm

first: Maria de la Paz

last: Celorio-Mancera

address: Svante Arrheniusväg 18 B

department: Zoology

institute: Stockholm University

summary:
Gut and rest of body tissue from fifth instar larvae which fed for three days a diet containing different doses of gossypol. Transcriptional profiling comparing gut and rest of body samples for three gossypol concentrations (0%, 0.016%-hormetic dose & 0.16%-detrimental dose).
Hormesis is a biphasic biological response characterized by the stimulatory effect at relatively low amounts of chemical compounds otherwise known to be detrimental at higher concentrations. A hormetic response in larval growth rates has been observed in cotton-feeding insects in response to increasing concentrations of gossypol, a toxic metabolite found in the pigment glands of some Malvaceae plants. We investigated the developmental effect of gossypol in the cotton bollworm, Helicoverpa armigera, an important heliothine pest species, by exposing larvae to different doses of this metabolite in their diet. In addition, we sought to determine the underlying transcriptional responses to different gossypol doses. Larval weight gain, pupal weight and larval development time were measured in feeding experiments and a hormetic response was seen for the first two characters. On the basis of net larval weight gain responses to gossypol, three treatments, that is 0%, 0.016%  and 0.16% gossypol , were selected for transcript profiling in the gut and the rest of the body in a two-color double reference design microarray experiment.

overall_design: Two-color double reference design. Reference sample was the 0% (CT) gossypol condition (either Gut or Rest of Body) or one of two experimental conditions  {0.016(T5) and 0.16%(T7)}. Biological replicates: 4 (10 individuals per replicate). 32 samples  total.

first: Heiko

last: Vogel

first: Maria

middle: d


title: Comparison of miRNA profile in body fluids (plasma and bronchoalveolar fluid cytology)

city: Seville

first: Sonia

last: Molina-Pinelo

address: Avda. MAnuel Siurot s/n

institute: IBIS

summary:
The objective is to obtain miRNA representative signatures both in plasma and bronchoalveolar cell fraction that could serve as biomarker in respiratory diseases.
The identification of new less invasive biomarkers is necessary to improve the detection and prognostic outcome of respiratory pathological processes. The measurement of miRNA expression through less invasive techniques such as plasma and serum have been suggested to analysis of several lung malignancies including lung cancer. These studies are assuming a common deregulated miRNA expression both in blood and lung tissue. The present study aimed to obtain miRNA representative signatures both in plasma and bronchoalveolar cell fraction that could serve as biomarker in respiratory diseases.

overall_design: we have compared circulating plasma miRNA with the bronchoalveolar cell fraction-derived miRNA patterns from 10 patients with several lung disease using a RT-qPCR assay.

first: Rocío

last: Suárez

first: María

last: Pastor

first: Ana

last: Nogal

first: Eduardo

last: Marquez-Martín

first: José

last: Martín-Juan

first: Amancio

last: Carnero

first: Luis

last: Paz-Ares