title: The PerA regulon in Enterococcus faecalis

city: Norman

first: Scott

last: Maddox

state: OK

address: 101 David L. Boren Blvd.

department: Botany and Microbiology

institute: University of Oklahoma

summary:
Transcriptional profiling of E. faecalis E99 WT and an isogenic ΔperA strain grown in THB + 1% glucose.
Pathogenic E. faecalis are enriched for a pathogenicity island (PAI).  This 150-kb island harbors a number of well characterized virulence genes plus a number of determinants of unknown function including one encoding a transcriptional regulator, designated PerA.  In this work, we show that PerA coordinately regulates both metabolic and virulence genes, and influences the platelet binding ability of E. faecalis.  Finally, we show that PerA responds to bicarbonate, an intestinal ion frequently used by pathogens to determine the site of infection.  Together, these results indicate that PerA is a global transcriptional regulator that coordinately regulates genes responsible for enterococcal pathogenicity.  These findings highlight a novel feature of PAI-mediated virulence regulation, namely the coordinate regulation of metabolic and virulence factors in the core genome by a horizontally acquired PAI-encoded transcriptional regulator.

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

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

overall_design: RNA was obtained from E. faecalis E99 ΔperA from mid-log (OD600 0.05), late log (OD600 0.5) and stationary phase (OD600 1.0) and compared to E. faecalis E99 WT RNA extracted from the same growth phases.  Cultures were grown in THB + 1% glucose.

first: Tyrrell

last: Conway

first: Joe

last: Grissom


title: A two-component regulatory system controls serpin expression in Bifidobacterium breve UCC2003.

status: Public on Aug 28 2012

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

summary: This work reports on the identification and molecular characterization of a two-component regulatory system (2CRS), encoded by serRK, which is believed to control the expression of the ser2003 locus in Bifidobacterium breve UCC2003. The ser2003 locus consists of two genes, Bbr_1319 (sagA) and Bbr_1320 (serU), which are predicted to encode a hypothetical membrane-associated protein and a serpin-like protein, respectively. The response regulator SerR was shown to bind to the promoter region of ser2003 and the probable recognition sequence of SerR was determined by a combinatorial approach of in vitro site-directed mutagenesis, coupled to transcriptional fusion and EMSA assays. The importance of the serRK 2CRS in the response of B. breve to protease-mediated induction was confirmed by generating B. breve-s-serR and B. breve-::serU insertion mutants, which exhibited altered ser2003 transcriptional induction patterns as compared to their parent strain UCC2003.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003  (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

first: Pablo

middle: A

last: Martin


title: microRNA profiling in renal cell carcinoma subtypes

status: Public on Aug 14 2012

city: Toronto

first: George

middle: M

last: Yousef

state: ON

address: 30 Bond Street

department: Pathology

country: Canada

institute: St.Michael's Hospital

summary: Renal cell carcinoma is the most common neoplasm of the adult kidney. A few subtypes of RCC include papillary RCC (pRCC), chromophobe RCC (chRCC) and the benign oncocytoma tumor. In some cases, distinguishing between the RCC subyptes is difficult. We performed a mircroRNA (miRNA) microarray to determine differential miRNA expression between pRCC, chRCC, and oncocytoma.

overall_design: We performed a miRNA microarray on 10 tumor samples of each papillary renal cell carcinoma (pRCC), chromophobe renal cell carcinoma (chRCC), and oncocytoma.

first: Youssef

last: Youssef

first: Nicole

last: White

first: Joerg

last: Grigull


title: Genome-wide array comparative genomic hybridization (aCGH) profiling of copy number variations (CNVs) in various dog breeds in comparison to a reference sample

status: Public on Aug 21 2012

city: Uppsala

first: Matthew

last: Webster

address: Box 582

department: IMBIM

country: Sweden

institute: Uppsala University

type: Genome variation profiling by genome tiling array

summary: This study used the NimbleGen dog whole genome CGH 2.1M tiling array to assay copy number variants in the dog genome in multiple breeds and wolf.

sample_organism:
Canis lupus
Canis lupus familiaris

overall_design: 53 samples of genomic DNA were hybridized to a reference sample. The dataset comprises 2 samples from each of 15 dog breeds, 10 samples from each of 2 dog breeds and 3 samples from gray wolf.

first: Jonas

last: Berglund

first: Elisa

last: Nevalainen

first: Anna-Maja

last: Molin

first: Michele

last: Perloski

first: Catherine

last: André

first: Michael

middle: C

last: Zody

first: Ted

last: Sharpe

first: Christophe

last: Hitte

first: Kerstin

last: Lindblad-Toh

first: Hannes

last: Lohi

middle: T


title: Identification of differentially expressed genes upon shRNA knockdown of TAL1 and its regulatory partners in T-ALL cells (Jurkat)

status: Public on Aug 16 2012

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

summary: The oncogenic transcription factor TAL1/SCL is aberrantly overexpressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing the importance of the TAL1-regulated transcriptional program in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, GATA3, ETS1 and RUNX1 in T-ALL cells. We find that TAL1 forms an interconnected auto-regulatory loop with its partners, which contributes to the sustained upregulation of its direct target genes. Importantly, we also find the MYB oncogenic transcription factor is directly activated by the TAL1 complex and positively regulates many of the same target genes, thus forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program.

overall_design:
Two experiments were performed:
1. Duplicate hairpins for each transcription factor (TAL1, TCF12/HEB, TCF3/E2A, GATA3, MYB) and control hairpins (GFP and Luciferase) were used to idenfity the expression change in the T-ALL cell line (Jurkat)
2. Duplicate hairpins for RUNX1 and control hairpins (GFP and Luciferase) were used to idenfity the expression change in the T-ALL cell line (Jurkat)

first: Lee

middle: N

last: Lawton


title: High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis

city: Groningen

first: Bogumila

last: Marciniak

address: Nijenborgh 7

department: Department of Genetics

country: Netherlands

institute: Rijksuniversiteit Groningen

summary:
In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA (carbon catabolite protein A). CcpA in a complex with HPr-Ser-P (seryl-phosphorylated form of histidine-containing protein, HPr) binds to operator sites called catabolite responsive elements, cre. Depending on the cre box position relative to the promoter, the CcpA/HPr-Ser-P complex can either act as a positive or a negative regulator. The cre boxes are highly degenerate semi-palindromes with a lowly conserved consensus sequence. So far, studies aimed at revealing how CcpA can bind such diverse sites were focused on the analysis of single cre boxes. In this study, a genome-wide analysis of cre sites was performed in order to identify differences in cre sequence and position, which determine their binding affinity.
The transcriptomes of B. subtilis cultures with three different CcpA expression levels were compared. The higher the amount of CcpA in the cells, the more operons possessing cre sites were differentially regulated. The cre boxes that mediated regulation at low CcpA levels were designated as strong (high affinity) and those which responded only to high amounts of CcpA, as weak (low affinity). Differences in the sequence and position in relation to the transcription start site between strong and weak cre boxes were revealed.
Certain residues at specific positions in the cre box as well as, to a certain extent, a more palindromic nature of cre sequences and the location of cre in close vicinity to the transcription start site contribute to the strength of CcpA-dependent regulation. The main factors contributing to cre regulatory efficiencies, enabling subtle differential control of various subregulons of the CcpA regulon, are identified.

overall_design: Bacillus subtilis strain MP902 [strain MP901 (Ptet-ccpA, KmR) carrying pWH119 (Pxyl-tetR, EmR)] was grown in presence of three different concentrations of Ptet inducer, anhydrotetracycline (ATc), leading to three levels of ccpA expression induction. The control culture was grown in absence of ATc. The total RNA for transcriptome analyses was isolated at OD600 = 0.8 from 16 ml culture. Three independent cultures of each strain (target strains and controls) were used, and cells were sampled for microarray experiment.

first: Bogumiła

first: Monika

last: Pabijaniak

first: Anne

last: de Jong

first: Robert

last: Duehring

first: Gerald

last: Seidel

first: Wolfgang

last: Hillen

first: Oscar

middle: P

last: Kuipers


title: microRNA Profiling in Metastatic Renal Cell Carcinoma

first: George

last: Yousef

summary: We performed a microRNA (miRNA) microarray on 10 metastatic RCC tumors and compared differential miRNA expresison to 19 primary clear cell renal cell carcinomas (ccRCC). We found there were 65 significantly dysregulated miRNAs; 9 miRNAs were significantly upregulated and 56 miRNAs were significantly downregulated in metastatic RCC when compared to primary clear cell renal cell carcinoma.

overall_design: miRNA microarray was performed on 10 metastatic RCC tumors

first: Nicole

last: White

first: Joerg

last: Grigull


title: ChIP-on-chip from murine myeloid cell line M1 and virus-induced myeloid leukemia cell lines for H3K4me3, H3K9/14ac, H3K4me1, H3K27me3, H3K9me3 and CTCF

status: Public on Sep 01 2012

city: Bethesda

first: Junfang

last: Zhang

state: MD

address: 37 Convent Dr.

department: NCI-CCR

institute: NIH

type: Genome binding/occupancy profiling by array

summary: Histone modifcations and CTCF binding at the c-myb locus were compared in cell lines with c-myb expressing, which are myeloblatic M1 cells and leukemia cells with virus integration, VS. M1 cells without c-myb expression induced by IL-6. Distribution of active histone marks at the c-myb gene and the upstream regions are associated with active c-myb transcription. The enrichment of all of these active histone marks decreased with differentiation-induced down-regulation of c-myb, but increased and spread in tumor cells.

first: Linda

last: Wolff


title: Identification and Characterization of the Human Leiomyoma Side Population as Putative Tumor Initiator Stem Cells

status: Public on Aug 15 2012

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

summary:
Uterine leiomyoma is the most common benign tumor of the female genital tract, and is the main cause of hysterectomy in 25-30% of affected women. Nevertheless, knowledge about stem cells initiating these common uterine tumors remains scarce.
The side population method has been used to identify different somatic stem cells in the human body. In this context, our study explores the hypothesis that human leiomyoma side population cells could be the putative somatic stem cells responsible for leiomyoma's initiation and formation.
We isolated, identified and characterized the side population cells from human leiomyomas which implies no commitment to the myometrial lineage at the molecular level, differential cloning efficiency under hypoxic conditions and provides a leiomyoma stem cells gene profile.
Based on their cloning efficiency ability, we also established two cell lines (MyoSP1-2) with a normal karyotype under hypoxic conditions. The phenotype analysis supported their mesodermal commitment as assessed by the positive expression of typical mesenchymal markers, such as CD90, CD105, and CD73, and by the absence of hematopoietic stem cell markers like CD34 and CD45. At the mRNA level, we also confirmed their undifferentiated status (OCT-4+, NANOG+, DNMT3B+, GDF3+) and mesenchymal lineage commitment as demonstrated by their ability to differentiate in vitro into adipogenic and osteogenic lineages. Finally, we demonstrated the functional capability of Myo cell lines (MyoSP1-2) to form human leiomyoma-like tissue after injecting this subset of cells either under the kidney capsule or in the subcutaneous tissue in the NOD-SCID mice model.

overall_design: 4 replicates each of leiomyoma side population (SP) cells and leiomyoma total fraction (FT) cells were analyzed.

first: Aymara

last: Mas

first: Irene

last: Cervello

first: Claudia

last: Gil-Sanchis

first: Amparo

last: Faus

first: Jaime

last: Ferro

first: Antonio

last: Pellicer

first: Carlos

last: Simon


title: Genomic diversity of Escherichia isolates from diverse habitats

status: Public on Aug 30 2012

city: Boston

first: Deborah

middle: R.

last: Yoder-Himes

address: 77 Louis Pasteur Ave, 1038 NRB

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

summary: Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates

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

overall_design: Two color experiment, Escherichia coli Sakai (reference), clinical and environmental Escherichia coli strains (testers): At least two replicates including a single dye swap for each reference-tester comparison

first: Seung-Dae

last: Oh

middle: R

first: James

last: Tiedje

first: Konstantinos

last: Konstantinidis


title: Real-time quantitative PCR analysis of DZNep treated B cell Lymphoma cell line Jeko-1

status: Public on Aug 11 2012

city: Tampa

first: jianguo

last: tao

state: FL

address: 12902 Magnolia Dr

institute: H Lee Moffitt Cancer Center

summary: Jeko-1 cells were culture with or without PRC2 inhibitor 3-deazaneplanocin A (DZNep)(1uM) for 72hrs. We used TaqMan® Human MicroRNA Array to quantitate miRNA expression profile regulated by PRC2.

overall_design: qPCR miRNA expression profiling.

first: Xiaohong

last: Zhao

first: Jianguo

last: Tao


title: Expression data from the adult hippocampus of Sox1-GFP mice

status: Public on Aug 09 2012

city: San Francisco

first: Robert

middle: Joseph Allen

last: Bell

state: CA

address: 1253 5th Ave

department: Institute of Human Genetics

institute: UCSF

summary:
The dentate gyrus of the hippocampus continues generating new neurons throughout life.  These nerve cells originate from radial astrocytes within the subgranular zone (SGZ). We find that Sox1, a member of the SoxB1 family of transcription factors, is expressed in a subset of radial astrocytes. Lineage tracing using Sox1 driven reporter mice shows that the Sox1-expressing cells represent an activated neural stem/progenitor population.
We used microarrays to evaluate the molecular constitution of neural stem cells with aging.

overall_design: Hippocampi were isolated from Sox1-GFP mice at 5-7 months (n=3) or 1 year 9 months (n=4) using a Leica dissecting scope.  Cells were immediately dissociated using papain (Worthington Biochemical Corporation. Lakewood, NJ, USA) and sorted for the GFP high or GFP negative population using a FACSAria Flow Cytometer (BD Biosciences, San Diego, CA, USA). RNA was harvested using the Arcturus PicoPure RNA isolation kit (Life Technologies Corp, Carlsbad, CA, USA) and the quality and quantity of each sample was checked using Agilent BioAnalyzer (Santa Clara, CA, USA) and Nanodrop spectrophotometer (Wilmington, DE, USA).  Samples were amplified using the NuGEN FFPE kit (San Carlos, CA, USA) and cDNA was prepared using an oligo(dT)-T7 RNA polymerase primer before biotinylation by in vitro transcription, partial hydrolysis and final hybridization to the Affymetrix (Santa Clara, CA, USA) GeneChip Mouse Gene 1.0 ST Array (Gladstone Genomics Core). Arrays were normalized using Robust Multichip Average (RMA) and the latest probe map to MM9 RefSeq genes (Irizarry et al., 2003; Dai et al., 2005).  To detect potential outlier arrays, the distributions of fold changes between all possible pairs within each group were analyzed.  One sample from a young mouse was found to have a skewed distribution when compared to other biological replicate samples and was removed from further analysis.  The statistical package R was used to perform average linkage hierarchical clustering of the remaining samples.  Significance Analysis of Microarrays (SAM) was performed to determine significant differentially expressed genes between the old and young mice with a False Discovery Rate cutoff of 5% (Tusher et al., 2001).

last: Blelloch

first: Monica

last: Venere

first: Jun

middle: S

last: Song

middle: J


title: Ni Deprivation in Synechococcus WH8102

city: San Diego

first: Chris

last: Dupont

address: 10355 Science Center Drive

institute: J. Craig Venter Institute

summary: Two sets of microarray experiments examining the transcriptional response to Ni deprivation.  One set was for growth on ammonium and the other for growth on urea

overall_design: Pairwise replicated comparisons (Ni deprivation in urea and ammonia)

first: C


title: Profiling of microRNA expression in lung cancer cells with up-regulation of Zeb1

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: The Zeb1 transcriptional repressor plays a key role in metastasis through the down-regulation of genes that are strong inducers of epithelial differentiation and inhibitors of stem-ness. Here we report that Zeb1 controls the expression of numerous oncogenic and tumor suppressive microRNAs (miRs). Zeb1 stimulated pro-migratory cytoskeletal processes by down-regulating miR-34a and activated Rho GTPases through Arhgap1, a Cdc42 GTPase activating protein and novel miR-34a target gene. Poor-prognosis human lung adenocarcinomas were highly enriched in a cytoskeletal gene signature activated by miR-34a down-regulation. These findings suggest that Zeb1 regulates a miR network and drives pro-migratory cytoskeletal processes through miR-34a.

overall_design:
Microarray-based interrogation of global miR expression changes in a non-metastatic KP cell line (393P) that undergoes EMT and gains invasive and metastatic capabilities following forced Zeb1 expression (393P_Zeb1).
two group comparison

first: Jon

last: Kurie

first: Young-Ho

last: Ahn

first: Don

last: Gibbons


title: Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [35MM]

status: Public on Aug 08 2012

city: Vienna

first: Harald

last: Scheuch

state: Vienna

address: Dr. Bohrgasse 7

department: Core Facilities

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary:
Liver carcinogenesis induced by DEN closely mimics the pathologies observed during human liver tumor initiation and progression. DEN treatment triggered c-Jun expression lasting up to at least 1 week in mouse livers as measured by Western blots and immunohistochemical staining. DEN-induced liver tumorigenesis was also dramatically reduced in Alfp-cre+/c-jun f/f mice, in which c-Jun is constitutively deleted in hepatocytes around birth. These data unambiguously demonstrate that c-Jun is specifically required during liver cancer initiation. We searched for cell death effectors downstream of c-Jun operating in cancer initiation. Expression profiling revealed that several cell death-associated genes were deregulated by comparing Alfp-cre+/c-junf/f and Alfp-cre-/c-jun f/f livers.
Mouse livers were collected before and 48hours after diethylnitrosamine treament (100mg/kg body weight). Whole genome expression profiles were analyzed using total RNAs extracted from the whole liver samples.

overall_design: By comparison of the gene expression profiles of these samples, genes with significantly altered expression levels will be selected and further characterized for their roles in DEN-induce liver cell death in tumor initiation.

first: Lijian

last: Hui

first: Erwin

middle: F

last: Wagner


title: Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [40MM]


title: Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [43MM]


title: Murine livers post DEN treatment: c-Jun f/f vs. c-Jun Dli [41MM]


title: RpoHI and RpoHII regulons in Rhodobacter sphaeroides 2.4.1 from chromatin immuno-precipitation

status: Public on Aug 03 2012

city: Madison

first: Yann

last: Dufour

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

type: Genome binding/occupancy profiling by genome tiling array

summary: In this study, we performed a ChIP-chip experiment to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and immuno-precipitated the regions of the genomic DNA interacting with the sigma factors.

overall_design: DNA immunoprecipitated with antibodies against RpoHI or RpoHII was labelled with Cy5 and hybridized on two-color tilling arrays (triplicates for each) with genomic DNA as an input control labelled with Cy3.

first: Timothy

last: Donohue


title: MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos [agilent and exiqon array data]

status: Public on Aug 02 2012

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Although many drugs and environmental chemicals are teratogenic, the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs (miRNAs),  single-stranded RNA molecules of ~22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation, are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well-known teratogen, we exposed zebrafish embryos to DMSO (0.1%) or TCDD (5 nM) for 1 hr at 30 hours post fertilization (hpf) and measured microRNA expression using several methods at 36 and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf (62-fold) and 60 hpf (135-fold) as determined by qPCR, verifying the effectiveness of the exposure.  microRNA expression profiles were determined using microarrays (Agilent and Exiqon), next-generation sequencing (SOLiD) and real time RT-PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR-451, 23a, 23b, 24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However, miR-27e was the only miRNA to be identified as differentially expressed by all three methods (both microarrays, SOLiD sequencing, and qPCR).  These results suggest that TCDD exposure causes modest changes in expression of microRNAs, including some (miR-451, 23a, 23b, 24 and 27e) that are critical for hematopoiesis and cardiovascular development.

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

overall_design: MicroRNA profiling was performed (N=3 biological replicates per group) using custom designed Agilent miRNA microarrays (8x15K) and exiqon miRCURY LNA microarrays. Custom-made Agilent oligonucleotide miRNA microarrays were designed based on zebrafish mature miRNA sequences from miRbase v.16. Each individual array contained a total of 548 unique probes representing 259 mature miRNAs from zebrafish (245), Fugu rubripes (11) and Tetraodon nigriviridis (3).  Exiqon miRNA probes were based on zebrafish miRNA sequences from miRbase v. 12.

first: Matthew

last: Jenny

first: Mark

middle: E

last: Hahn


title: Mutational analysis of the pentose phosphate pathway and the Entner-Doudoroff pathway in Gluconobacter oxydans reveals improved growth of an edd-eda deletion mutant on mannitol

status: Public on Aug 01 2012

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

summary: The obligatory aerobic acetic acid bacterium Gluconobacter oxydans 621H oxidizes sugars and sugar alcohols primarily in the periplasm and only a small fraction is metabolized in the cytoplasm. The latter can occur either via the Entner-Doudoroff pathway (EDP) or via the pentose phosphate pathway (PPP). The Embden-Meyerhof pathway is non-functional and a cyclic operation of the tricarboxylic acid cycle is prevented by the absence of succinate dehydrogenase. In this work, the cytoplasmic catabolism of fructose formed by oxidation of mannitol was analyzed with a Δgnd mutant lacking the oxidative PPP and a Δedd-eda mutant devoid of the EDP. The growth characteristics of the two mutants under controlled conditions with mannitol as carbon source and enzyme activities showed that the PPP is the main route for cytoplasmic fructose catabolism, whereas the EDP is dispensable and even unfavorable. The Δedd-eda mutant (lacking 6-phosphogluconate dehydratase and 2-keto-3-deoxy-6-phosphogluconate aldolase) formed 24% more cell mass than the reference strain. In contrast, deletion of gnd (6-phosphogluconate dehydrogenase) severely inhibited growth and caused a strong selection pressure for secondary mutations inactivating glucose-6-phosphate dehydrogenase, thus preventing fructose catabolism via the EDP, too. These Δgnd zwf* mutants were almost totally disabled in fructose catabolism, but still produced about 14% of the carbon dioxide of the reference strain, possibly by catabolizing substrates from the yeast extract. Overexpression of gnd in the reference strain improved biomass formation in a similar manner as deletion of edd-eda, further confirming the importance of the PPP for cytoplasmic fructose catabolism.

overall_design: The three transcriptome comparisons of Δupp Δgnd zwf* vs. Δupp and of Δupp Δedd-eda vs. Δupp, and of Δupp Δgnd versus Δupp, were repeated independently three times in biological replicates resulting in 3 x 3 hybridizations as termed by sample 1 to 9.

first: Janine

last: Richhardt

first: Stephanie

last: Bringer

first: Michael

last: Bott


title: Transcriptome comparison of S. pyogenes strains MGAS2221 and 2221ΔFasX following exposure to human plasma

city: Reno

first: Paul

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

summary: The fasX gene encodes a small regulatory RNA in the group A Streptococcus (GAS).  To determine the FasX regulon during GAS exposure to human plasma we compared parental strain MGAS2221 with isogenic fasX mutant strain 2221ΔFasX.  Gene expression was analyzed 0, 15, and 60 minutes post-plasma exposure.

overall_design: GAS strains were grown in THY broth to mid-exponential phase, corresponding to an O.D.600 of 0.5.  Two 16ml aliquots of each GAS culture were pelleted by centrifugation and the supernatant removed.  Each GAS cell pellet was resuspended in 16ml of pre-warmed human plasma.  Thus, four GAS-plasma suspensions were created, two each for each of the GAS strains, with one of the two using plasma from person A, and the other two using plasma from person B.  Aliquots were recovered from each of the four GAS-plasma suspensions at T = 0, 15, and 60 mins.  For the first two time-points 4.5ml of GAS-plasma suspension were added to 9ml of RNAprotect (Qiagen Inc.).  For the final time-point, 4ml was added to 8ml of RNAprotect.  Following addition of RNAprotect, samples were incubated at room temperature for 5 mins before centrifuging.  Supernatant was removed and the pellets quick frozen in liquid nitrogen and stored at -80 °C until ready to use.  RNA isolation, cDNA synthesis, and use of our custom Affymetrix microarray was as previously described (Perez et al., 2009)


title: Evolution of S. cerevisiae - S. bayanus Interspecific Hybrids

city: Stanford

first: Barbara

last: Dunn

department: Genetics

institute: Stanford University

summary: Hybrid progeny can enjoy increased fitness and stress tolerance relative to their ancestral species, a phenomenon known as hybrid vigor. Though this phenomenon has been documented throughout the Eukarya, evolution of hybrid populations has yet to be explored experimentally in the lab. To fill this knowledge gap we created a pool of Saccharomyces cerevisiae and S. bayanus homoploid and aneuploid hybrids, and then investigated how selection in the form of incrementally increased temperature or ethanol impacted hybrid genome structure and adaptation. During 500 generations of continuous ammonia-limited, glucose-sufficient culture, temperature was raised from 25C to 46??C. This selection invariably resulted in nearly-complete loss of the S. bayanus genome, although the dynamics of genome loss differed among independent replicates. Temperature-evolved isolates were significantly more thermal tolerant and exhibited greater phenotypic plasticity than parental  species and founding hybrids. By contrast, when the same hybrid pool was subjected to increases in exogenous ethanol from 0% to 14%, selection favored euploid S. cerevisiae x S. bayanus hybrids. Ethanol-evolved isolates exhibited significantly greater ethanol tolerance relative only to S. bayanus and one of the founding hybrids tested. Adaptation to thermal and ethanol stress manifested as heritable changes in cell wall structure demonstrated by resistance to zymolyase or micafungin treatment. This is the first study to show experimentally that the fate of interspecific hybrids critically depends on the type of selection they encounter during the course of evolution.

sample_organism: Saccharomyces bayanus x Saccharomyces cerevisiae

platform_organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

overall_design: Array-CGH was performed on the S. cerevisiae parent strain CEN.PK (GSY2160), the S. bayanus parent strain CBS7001 (GSY2161) and on the F1 interspecific hybrid resulting from mating the 2 parents (GSY2168). Additionally, three rare viable spores obtained after sporulation of the F1 were assayed by array-CGH (F2a, F2b, F2c). A large pool of F2 spores (and probably some number of F1 hybrid cells) were subjected to gradually increasing temperatures, in three independent vessels, with populations sampled at various generation times.  Likewise, the same pool was used to found populations in an additional three independent vessels, which were then subjected to gradually increasing ethanol concentrations (at constant temperature). Array-CGH was performed on three different clones from each of the three temperature vessels at the final 500 generation time point (T500 clones). Biological replicates of the T500 clones were performed (T500-new). Two self-self array-CGH hybridization controls were also performed (self-control).  Array-CGH was performed on one clone from each of the three ethanol vessels taken at the 400 generation timepoint (EtOH400gen clones).


title: Genome-wide transcriptional response of the archaeon Thermococcus gammatolerans to cadmium

city: Orsay

first: Arnaud

last: Lagorce

address: Université Paris-Sud 11

department: Institut de Génétique et de Microbiologie

country: France

institute: University Paris Sud

summary: Thermococcus gammatolerans, the most radioresistant archaeon known to date, is an anaerobic and hyperthermophilic sulfur-reducing organism living in deep-sea hydrothermal vents. Knowledge of mechanisms underlying archaeal metal tolerance in such metal-rich ecosystem is still poorly documented. We showed that T. gammatolerans exhibits high resistance to cadmium (Cd), cobalt (Co) and zinc (Zn), a weaker tolerance to nickel (Ni), copper (Cu) and arsenate (AsO4) and that cells exposed to 1mM Cd exhibit a cellular Cd concentration of 67µM. A time-dependent transcriptomic analysis using microarrays was performed at a non-toxic (100μM) and a toxic (1mM) Cd dose. The reliability of microarray data was strengthened by real time RT-PCR validations. Altogether, 114 Cd responsive genes were revealed and a substantial subset of genes is related to metal homeostasis, drug detoxification, re-oxidization of cofactors and ATP production. This first genome-wide expression profiling study of archaeal cells challenged with Cd showed that T. gammatolerans withstands induced stress through pathways observed in both prokaryotes and eukaryotes but also through new and original strategies. T. gammatolerans cells challenged with 1mM Cd basically promote: 1) the induction of several transporter/permease encoding genes, probably to detoxify the cell; 2) the upregulation of Fe transporters encoding genes to likely compensate Cd damages in iron-containing proteins; 3) the induction of membrane-bound hydrogenase (Mbh) and membrane-bound hydrogenlyase (Mhy2) subunits encoding genes involved in recycling reduced cofactors and/or in proton translocation for energy production. By contrast to other organisms, redox homeostasis genes appear constitutively expressed and only a few genes encoding DNA repair proteins are regulated. We compared the expression of 27 Cd responsive genes in other stress conditions (Zn, Ni, heat shock, γ-rays), and showed that the Cd transcriptional pattern is comparable to other metal stress transcriptional responses (Cd, Zn, Ni) but not to a general stress response.

overall_design: Kinetics of gene expression changes induced by Cd were performed at two different concentrations (0.1mM and 1mM) and at 3 time points (30, 120 and 270 min). A 0.1mM Cd concentration did not affect the growth rate, whereas 1mM Cd induced a transitory growth arrest for 270min. Late exponentially growing cells (7x107 cells/mL) were exposed to Cd and were collected after 30min, 120 min and after 270 min. For each time point, four slides containing the 2157 oligonucleotide gene probes printed in duplicate were hybridized. The experiment was repeated twice leading to eight data sets per time point (four per biological replicate). Microarray analyses monitored 161 transcriptional changes (⎟Fold Change (FC)⎜≥2 and p-Value ≤ 0.01) in response to Cd exposure corresponding to 114 unique genes i.e. 5,3% of T. gammatolerans gene content, most of them being upregulated. While about 25% of the upregulated genes exhibited a FC>3 with a maximum of almost 10 for one encoding a conserved hypothetical protein (tg0885, 1mM Cd at 120min), the large majority of the up- and down-regulated genes exhibited a 2 to 3-fold transcriptional change as already described in many archaeal transcriptomic studies.

first: Aude

last: Fourçans

first: Murielle

last: Dutertre

first: Brice

last: Bouyssiere

first: Yvan

last: Zivanovic

first: Fabrice

last: Confalonieri


title: Conserved epigenetic sensitivity to early life experience in the rat and human hippocampus

status: Public on May 31 2012

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

type: Methylation profiling by genome tiling array

summary: Early life experience is associated with long-term effects on behavior and epigenetic programming of the NR3C1 (glucocorticoid receptor) gene in the hippocampus of both rats and humans. However, it is unlikely that such effects completely capture the evolutionarily conserved epigenetic mechanisms of early adaptation to environment. Here we present DNA methylation profiles spanning 6.5 million base pairs centered at the NR3C1 gene in the hippocampus of humans who experienced abuse as children and nonabused controls.

overall_design: Hippocampal samples were obtained from the Quebec Suicide Brain Bank and included 10 suicide subjects with histories of severe childhood abuse and 9 controls with validated negative histories of childhood abuse who did not differ in postmortem interval, sex, age at death, or brain pH (all P > 0.05). Using custom-designed microarrays with probes tiling the 6.5 million base pair region of human chromosome 5 centered at the NR3C1 gene at 100 bp spacing, we obtained DNA methylation profiles by MeDIP-chip. Replicates were performed.

first: Patrick

last: McGowan

first: Aya

last: Sasaki

last: Suderman

first: Gustavo

last: Turecki

last: Hallett

last: Meaney


title: Type I Interferon Dependent Anti-viral Activity

status: Public on Jul 01 2012

city: Hilden

first: Folkert

last: Steinhagen

address: Breddert 37

institute: National Cancer Institute

summary: Synthetic oligonucleotides (ODN) expressing CpG motifs trigger an innate immune response via TLR9. Multiple microarray analyses were performed to identify the global effects on gene expression of stimulating the CAL-1 human pDC line with different types of CpG ODN. Results show that a subset of genes characterized by shared anti-viral activity was consistently up-regulated by ODNs that otherwise mediate discrete functions. This group of genes was largely dependant on autocrine type I interferon (IFN) signaling, as their induction was blocked by neutralizing antibody targeting the type I IFN receptor. Coupling these experiments with a meta-analysis of other published works led to the identification of a set of 32 functionally conserved genes that was reproducibly activated by different types of CpG DNA in different species and cell types. Functionally, these 'core' genes support a type I IFN response to viral infection, and differ from genes up-regulated by only a single type of CpG ODN. These findings help define the conserved and sequence-specific patterns of gene activation triggered via TLR9 and improve our understanding of the immunomodulatory effects elicited by CpG ODN.

overall_design: pDC cells were stimulated with either 3uM 'K' ODN for 1-27 hours (1 hr n=3, 3 hr n=3, 9 hr n=5, 27 hr n=3) or with 3uM 'D' ODN for 1-48 hours (1 hr n=3, 3 hr n=3, 9 hr n=3, 27 hr n=5, 48 hr n=3) or with 3uM respective control ODNs: ODN1612 for 9 hours (n=2) and D122 for 27 hours (n=2). Blocking experiments using neutralizing mAb against anti-type I IFNalpha/beta receptor chain2 (MMHAR-2, PBL) (anti-IFNR) were performed: 'K' ODN + anti-IFNR for 9 hours (n=2) and 'D' ODN + anti-IFNR for 27 hours (n=2).


title: Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA (mRNA)

status: Public on Jun 01 2012

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

department: Institute of Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

summary: Characterization of the activities of the transcription factors that AP3 and PI encode throughout flower development using perturbation assays in combination with a floral induction system (FIS) that allows a stage-specific analysis of flower development. The series contains two types of perturbation experiments, static permutations (null alleles pi-1 and ap3-3, respectively) and dynamic perturbations (temperature-sensitive ap3-1 allele).

overall_design: Two conditions (i.e. genotypes: ap3-3 or pi-1 homozygous in the FIS vs ap3-3 or pi-1 heterozygous in the FIS, respectively / ap3-1 plants vs AP3 plants shifted from 16degrees to 27 degrees ) at three developmental stages each

first: Diarmuid

last: O'Maoileidigh

first: Frank

last: Wellmer


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e14]

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

institute: University of Illinois

summary: Songbirds provide rich natural models for studying the relationships of brain anatomy, behavioral function, environmental signals and gene expression.  Under the Songbird Neurogenomics Initiative, investigators from more than a dozen laboratories collected brain samples from six species of songbird under a range of experimental conditions, and 488 of these samples were analyzed systematically for gene expression by microarray.  ANOVA was used to test 32 planned contrasts in the data, revealing the relative impact of different factors.  The brain region from which tissue was taken had the greatest influence on gene expression profile, affecting the majority of signals measured by the 18,848 non-redundant cDNAs spotted on the microarray. Social and environmental manipulations had highly variable impact, ranging from nil in some cases to robust in others.  Several specific genes were identified as points of interest in the evolution of mechanisms by which environmental signals influence behavior. The data were also analyzed using Weighted Gene Co-expression Network Analysis (WGCNA) followed by Gene Ontology (GO) analysis. This revealed modules of co-regulated genes that are also enriched for specific functional annotations such as  “ribosome” (expressed more highly in juvenile brain) and “dopamine metabolic process” (expressed more highly in striatal song control nucleus Area X).  These results underscore the complexity of influences on neural gene expression and provide a resource for studying how these influences are integrated during natural experience.

sample_organism:
Melospiza melodia
Taeniopygia guttata

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e14: Hypothalamus from adult male Song sparrows 30 minutes after Simulated Territorial Intrusion (STI) or control, in spring and fall, 8 biological replicates per group (only 7 biological replicates in Spring Control group). All samples were hybridized against the SoNG universal RNA reference pool.

first: Jenny

last: Drnevich

first: Arthur

last: Arnold

first: Gregory

last: Ball

first: Eliot

last: Brenowitz

first: Thomas

last: Hahn

last: Johnson

first: Sarah

last: London

first: Peter

last: Lovell

middle: G

last: Mast

first: Claudio

last: Mello

first: Motoko

last: Mukai

first: Christy

last: Strand

first: Juli

last: Wade

first: John

last: Wingfield

first: David

last: Clayton


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e12]

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e12: AL (auditory lobule) from post-hatch day 20 male zebra finches after 30 minutes of novel song playback or silence control, 6 biological replicates per group. All samples were hybridized against the SoNG universal RNA pool.


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e13]

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e13: Comparison of LMAN between p25 and p45 male zebra finches, 6 biological replicates per group. All samples were hybridized against the SoNG universal RNA reference pool.


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e07]

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e07: HVC of p55 and adult male zebra finches were collected after 20 days of food ad libitum or Timed Access to Food (TAF) to assess singing-driven differences in gene expression.


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e08]

sample_organism:
Sturnus vulgaris
Taeniopygia guttata

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e08: Comparing Area X, HVC, POA and RA from adult male European starlings (Sturnus vulgaris) that were gonadally-intact and photostimulated (7 and 21 days on long days, 16:8 light: dark), castrated and photostimulated (7 days on long days), and photorefractory (56 days on long days), with short-day control (56 days on short days, 11:13 light:dark), 6 biological replicates per group. All samples were hybridized against the SoNG universal RNA reference pool.


title: Ares Swanson MBNL mutant study

status: Public on Jul 31 2012

city: Santa Cruz

first: Manny

last: Ares

address: 1125 High St

department: Molecular and Cellular Biology

institute: UCSC

summary:
MBNL1 is a known splicing factor and is related to Myotonic Dystrophy (DM).
This study examines the tissue specific splicing patterns of MBNL1 using a
mutant and wild type mouse across three tissues (heart,brain,quadricep)

related publications:

Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy.
Du H, etal
Nat Struct Mol Biol. 2010 Feb;17(2):187-93.

and

Muscleblind-like 1 knockout mice reveal novel splicing defects in the myotonic dystrophy brain.
Suenaga K, Lee KY, Nakamori M, Tatsumi Y, Takahashi MP, Fujimura H, Jinnai K, Yoshikawa H, Du H, Ares M Jr, Swanson MS, Kimura T.
PLoS One. 2012;7(3):e33218. Epub 2012 Mar 13.
PMID:     22427994

and

Hum Mol Genet. 2006 Jul 1;15(13):2087-97.
Failure of MBNL1-dependent post-natal splicing transitions in myotonic
dystrophy.
Lin X, Miller JW, Mankodi A, Kanadia RN, Yuan Y, Moxley RT, Swanson MS, Thornton CA.

overall_design:
We examined quadricep,heart and brain of a mouse MBNL1 mutant
to test whether MBNL mutants creates a tissue specific splicing defect.
These samples were compared to the tissues of a wild type mouse.

first: Hong

last: Du

first: Maurice

last: Swanson


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e06]

first: Kirstin

last: Replogle

sample_organism:
Haemorhous mexicanus
Taeniopygia guttata

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e06: HVC of adult male house finches on short days (8:16 light:dark) collected at time zero, 24, and 48 hours after implantation with testosterone-containing silastic capsules, 8 biological replicates per group. All samples were hybridized against the SoNG universal RNA reference pool.

last: Drnevich

last: Arnold

first: Frank


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e11]

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e11: Auditory lobules (AL) were collected from adult male zebra finches (Taeniopygia guttata) after 30 minutes of novel or familiar song playback, or silence control.

first: Jenny

first: Arthur

last: Ball

last: Brenowitz

last: Hahn


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e10]

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e10: NCM and L2a from adult female zebra finches, 30 or 90 minutes after onset of novel song playback, or silence control, 6 biological replicates per group. All samples were hybridized against the SoNG universal RNA reference pool.

first: Gregory

first: Eliot

last: Johnson

last: London

last: Lovell


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e05]

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e05: Whole telencephalon of p1 and p7 female zebra finches, implanted on hatch day with estrogen-containing silastic capsules or blank controls, 6 biological replicates per group. All samples hybridized against the universal SoNG reference RNA pool.

first: Thomas

first: Sarah

last: Mast

last: Mello

last: Mukai


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e09]

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e09: Comparison of HVC and shelf regions from adult male zebra finches, 6 biological replicates per group. Each sample was hybridized against the SoNG universal reference RNA pool.

first: Peter

first: Claudio

last: Strand

last: Wade

last: Wingfield


title: Expression data from human with lupus nephritis (LN)

status: Public on Jun 28 2012

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary:
Nephritis (LN) is a serious manifestation of SLE. Therapeutic studies in mouse LN models do not always predict outcomes of human therapeutic trials, raising concerns about the human relevance of these models. In this study we used an unbiased transcriptional network approach to define similarities and differences between three lupus models and human LN. Affymetrix-based expression profiles were analyzed using Genomatix Bibliosphere software and transcriptional networks were compared using the Tool for Approximate LargE graph matching (TALE).  The 20 network hubs (nodes) shared between all three models and human LN reflect key pathologic processes, namely immune cell infiltration/activation, macrophage/dendritic cell activation, endothelial cell activation/injury and tissue remodeling/fibrosis. Each model also shares unique features with human LN. Pathway analysis of the TALE nodes highlighted macrophage/DC activation as a cross-species shared feature. To distinguish which genes and activation pathways might derive from mononuclear phagocytes in the human kidneys the gene expression profile of isolated NZB/W renal mononuclear cells was compared with human LN kidney profiles. Network analysis of the shared signature highlighted NFkappaB1 and PPARgamma as major hubs in the tubulointerstitial and glomerular networks respectively. Key nodes in the renal macrophage inflammatory response form the basis for further mechanistic and therapeutic studies.
We used microarrays to analyze the transcriptome of microdissected renal biopsies from patients with lupus nephritis (LN)

overall_design: RNA from glomeruli and tubulointerstitial compartments was extracted and processed for hybridization on Affymetrix microarrays.

first: Ramalingam

last: Bethunaickan

first: Tania

last: Gonzalez-Rivera

first: Viji

last: Nair

first: Meera

last: Ramanujam

first: Weija

last: Zhang

first: Erwin

last: Bottinger

first: Stephan

last: Segerer

first: Maja

last: Lindenmeyer

first: Clemens

middle: D

last: Cohen

first: Anne

last: Davidson

first: Matthias

last: Kretzler


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e15]

first: Kirstin

last: Replogle

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e15: AL (auditory lobule) from adult male European starlings after 30 minutes of novel song playback or silence contro, 6 biological replicates per group. All samples were hybridized against the SoNG universal RNA reference pool.

first: Jenny

last: Drnevich

first: Arthur

last: Arnold

first: Gregory

last: Ball

first: Eliot

last: Brenowitz

last: Hahn

first: Frank

last: Johnson

last: London

last: Lovell

last: Mast

last: Mello

first: Motoko

first: Christy

first: Juli

first: John

first: David

last: Clayton


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e02]

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e02: Area X of p35 zebra finch males who had been individually acoustically isolated at p30, then at p35 placed next to a stimulus female and exposed to no tutor, father tutor, or unfamiliar tutor for 2 hours then sacrificed, 5 biological replicates in the familiar tutor and no tutor treatment groups, 6 biological replicates in the unfamiliar tutor group. All samples were hybridized against the SoNG universal RNA reference pool.

first: Thomas

first: Sarah

first: Peter

first: Claudio

last: Mukai

last: Strand

last: Wade

last: Wingfield


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e04]

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e04: Whole telencephalon of p1, p25, p45 and adult zebra finches, both males and females, 6 biological replicates per group. All samples were hybridized against the SoNG universal reference RNA pool.


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e03]

sample_organism:
Haemorhous mexicanus
Taeniopygia guttata
Loxia curvirostra

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e03: Diencephalons were collected under short days (8:16 light:dark) from birds on either standard or enriched diets, in 2 species that differ in effects of diet on reproductive behavior (responsive Red crossbills, non-responsive House finches). Red crossbills on a standard diet and long days (20:4 light:dark) were also compared to the short day group to assess effects of photostimulation in this species. All samples were hybridized against the SoNG universal RNA reference pool.


title: The impact of experience-dependent and independent factors on gene expression in songbird brain [e01]

sample_organism:
Taeniopygia guttata
Zonotrichia leucophrys gambelii

overall_design:
RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different “treatments”, i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA).
e01: Brain regions HVC and RA were collected from Gambel's White crowned sparrows (Zonotrichia leucophrys gambelii) from the following  experimental groups: long-term Short Day (SD); Long Day (LD) with Testosterone (T) for 3, 7, and 21 days (3LD+T, 7LD+T, 21LD+T respectively); SD and removal of T at 1 and 2 days (1SD-T, 2SD-T). Six biological replicates per group, five biological replicates in 3LD+T.HVC group. All samples were hybridized against the SoNG universal reference RNA pool.


title: Chicken embryonic cerebral cortex exposed to two doses of PFHxS.

status: Public on Apr 18 2012

city: Ottawa

first: Cristina

last: Cassone

address: 620 Kochar Drive

institute: University of Ottawa

summary: In a recent egg injection study, we showed that in ovo exposure to perfluorohexane sulfonate (PFHxS) affects the pipping success of developing chicken (Gallus gallus domesticus) embryos. We also found evidence of thyroid hormone (TH) pathway interference at multiple levels of biological organization (i.e. somatic growth, mRNA expression and circulating free thyroxine levels). Based on these findings, we hypothesize that PFHxS exposure interferes with TH-dependent neurodevelopmental pathways. The present study investigates global transcriptional profiles of cerebral cortex tissue from chicken embryos following exposure to a solvent control, 890 or 38,000 ng PFHxS/g egg (n=4-5 per group); doses which lead to the adverse effects above. PFHxS significantly alters the expression (≥1.5-fold, p≤0.001) of 11 transcripts at the low dose (LD; 890 ng/g) and 101 transcripts at the high dose (HD; 38,000 ng/g). Functional enrichment analysis shows that PFHxS affects genes involved in tissue development and morphology, cellular assembly and organization, and cell-to-cell signalling. Pathway and interactome analyses suggest that genes may be affected through several potential regulatory molecules, including integrin receptors, myelocytomatosis viral oncogene and CCAAT/enhancer binding protein. This study identifies key functional and regulatory modes of PFHxS action involving TH-dependent and -independent neurodevelopmental pathways. Some of these TH-dependent mechanisms that occur during embryonic development include tight junction formation, signal transduction and integrin signaling, while TH-independent mechanisms include gap junction intercellular communication.

overall_design: Reference Design. Reference = pool of equal parts of all control and treated samples. Control groups and 2 treatment groups. Control samples were chicken embryonic cerebral cortex exposed DMSO only (solvent). Treatments were: chicken embryonic cerebral cortex exposed to 890 ng/g PFHxS (LD) and 38,000 ng/g PFHxS (HD).

first: Jessica

last: Taylor

first: Jason

last: O'Brien

first: Andrew

last: Williams

first: Carole

middle: L

last: Yauk

first: Doug

last: Crump

first: Sean

middle: W

last: Kennedy


title: Response of Atf3-/- and WT BMDMs to treatment with LPS for 4 h

status: Public on Mar 23 2012

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

summary:
Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of lipid-loaded macrophages in the arterial wall. Intimal macrophages internalize modified lipoproteins such as oxidized LDL (oxLDL) through scavenger receptors, leading to storage of excess cholesteryl esters in lipid bodies and a "foam cell" phenotype. In addition, stimulation of macrophage Toll-like receptors (TLRs) has been shown to promote lipid body proliferation. We investigated the possibility that there are transcriptional regulators that are common to both pathways for stimulating foam cell formation (modified lipoproteins and TLR stimulation), and identified the transcription factor ATF3 as a candidate regulator.

In this specific microarray study, we re-analyzed a subset of the data from a 2006 microarray experiment (Gilchrist et al., Nature, 441:173-178, 2006) in which wild-type and Atf3-/- murine macrophages were stimulated with LPS. The goal of this analysis was to identify genes whose LPS responses are significantly affected by loss of ATF3 in macrophages, using up-to-date genome annotations.

overall_design:
The raw microarray data files included in this submission were originally released to the public as a part of a larger microarray dataset that accompanied the Gilchrist et al. study (ArrayExpress accession # E-TABM-102). These data were re-analyzed using the CustomCDF v13 ENSG probesets as a part of a transcriptomic study of the response of macrophages to stimuli, including LPS,  that induce foam cell formation (see GSE32358 and GSE32359).

In the Gilchrist study, the experiment design was as follows:  Female mice of the indicated strains were sacrificed at 8-12 weeks of age, and macrophages were derived from the femoral bone marrow using rhM-CSF. On day six, macrophages were plated and LPS introduced into the medium as indicated.  After four hours, RNA was isolated using Trizol. Labeled cRNA derived from the RNA samples was hybridized to Affymetrix Mouse Genome 430 2.0 GeneChips.

For the current study, probe-level instensity data were re-processed using gene-level probesets from the CustomCDF project (ENSG, v13), and are in log2 scale.

first: Mark

last: Gilchrist

first: Kathleen

middle: A

first: Carrie

last: Johnson

first: Elizabeth

last: Gold

first: Alan

last: Aderem


title: Comparison of gene expression during meiosis between wild-type and rad50-deficient strains of Coprinopsis cinerea

status: Public on May 15 2012

city: Bloomington

first: Claire

last: Burns

state: IN

address: 1001 E 3rd St

institute: Indiana University

summary:
Meiosis was compared in rad50-1 and wild type strains of C. cinerea at 6 time points spanning the meiotic timecourse.
Abstract: The basidiomycete Coprinopsis cinerea is well-suited to studies of meiosis because meiosis progresses synchronously in ten million cells within each mushroom cap. Approximately 20% of C. cinerea genes exhibit changing expression during meiosis, but meiosis and mushroom development happen concurrently so differentially expressed genes might not be directly involved in meiotic processes. Using microarrays, we examined global gene expression across a meiotic time course in two mutants in which meiosis arrests but mushrooms develop normally. Genes differentially expressed in the mutants compared to wild type are likely to be involved in meiosis and sporulation as opposed to mushroom development. In rad50-1, which arrests in late prophase, RNA abundance for a group of early meiotic genes remains high, while the expression of a group of late meiotic genes is never induced. In contrast, in msh5-22 (which fails to undergo pre-meiotic DNA replication), both early and late meiotic genes are underexpressed relative to wild type at late meiotic time points as the cells die. Genes that are differentially expressed in both mutants are particularly strong candidates for playing roles in meiosis and sporulation.

overall_design: Five time points were analyzed, with four biological replicate rad50-1 samples used for each timepoint.  Reference wild-type samples consisted of pooled RNA from ten samples at the appropriate timepoint.

first: Erika

last: Anderson

first: Miriam

last: Zolan


title: Taking microarrays to the field: Differential hepatic gene expression of caged fathead minnow from Nebraska watersheds

status: Public on Mar 01 2012

city: Alachua

first: Barbara

middle: Joan

last: Carter

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

summary: This study aimed to evaluate the utility of microarrays as a biomonitoring tool in field studies.  A 15,000-oligonucleotide microarray was used to measure the hepatic gene expression of fathead minnows (Pimephales promelas) caged in four Nebraska, USA watersheds - the Niobrara and Dismal Rivers (low-impact agricultural sites) and the Platte and Elkhorn Rivers (high-impact agricultural sites).  Gene expression profiles were site specific and fish from the low- and high-impact sites aggregated into distinct groups.  Over 1500 genes were differentially regulated between fish from the low- and high-impact sites.  Many gene expression differences (1218) were also noted when the Platte and Elkhorn minnows were compared to one another and Platte fish experienced a higher degree of transcript alterations than Elkhorn fish.  These findings indicate that there are differences between the low-impact and high-impact sites, as well as between the high-impact sites.  Historical water quality data supports these results as only trace levels of agrichemicals have been detected at the low-impact sites, while substantial levels of agrichemicals have been reported at the high-impact sites with agrichemical loads at the Platte generally exceeding those at the Elkhorn.  Overall, this study demonstrates that microarrays can be utilized to discriminate sites with different contaminant loads from one another.

first: Marlo

middle: K

last: Sellin Jeffries

first: Alvina

middle: C

last: Mehinto

first: Nancy

last: Denslow

last: Kolok


title: ssDNA in S phase compared to G1 phase at different timepoints

status: Public on May 10 2012

city: Houston

first: Sara

middle: Chloe

last: Di Rienzi

address: 1 Baylor Plaza Room 743E

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

summary: To identify origins of replication in Lachancea waltii by mapping regions of ssDNA that are enriched in S phase.

overall_design: L. waltii cells are grown in the presence of hydroxyurea, which slows replication forks and causes the accumulation of ssDNA at the replication fork.

first: Kimberly

last: Lindstrom

first: Tobias

last: Mann

first: William

last: Noble

first: MK

last: Raghuraman

first: Bonita

last: Brewer


title: Density Transfer Data for Lachancea waltii DNA Replication Profile

summary: Array data detailing the progression of DNA replication in the yeast Lachancea waltii.

overall_design: L. waltii cells were pregrown in heavy isotope medium and synchronized at early S phase. They were then released into normal medium, wherein DNA replication proceeds. Replicated DNA molecules are thus of heavy-light (HL) composition as compared to unreplicated molecules, which are heavy-heavy (HH). 4 time points were taken and the percent of heavy-light DNA was determined at each time point. The heavy-heavy and heavy-light DNA molecules were separated by ultracentrifugation, differentially labeled, and hybridized to a genomic array for L. waltii.  The array thus shows the progression of DNA replication.


title: Gene expression analysis of bovine blastocyst produced under alternative in vivo and in vitro culture conditions during EGA time

status: Public on Feb 29 2012

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

institute: Colorado State University

summary: There is an inevitable need for combining in vitro and in vivo culture systems during specific developmental time points to facilitate a comprehensive understanding of early embryo development which would yield insights into the molecular pathways controlling early development and to improve our knowledge in regulation of embryonic development. In current study, we aimed to understand the influences of alternative culture conditions (in vivo or in vitro) during EGA event on embryonic developmental rate, gene expression pattern and subsequent influences on pathways and biological functions controlling bovine embryo development.

overall_design: Six different blastocyst groups were produced under alternative in vivo and in vitro culture conditions. The first two groups (Vitro_4-cell and Vitro_16-cell) were matured, fertilized and cultured in vitro until 4- and 16-cell stage, respectively then transferred to synchronized recipients and continued culture in vivo until day 7 blastocyst stage. The second two groups (Vivo_4-cell and Vivo_16-cell) were matured, fertilized and cultured in vivo until 4- and 16-cell stage, respectively then flushed out and cultured in vitro until day 7 blastocyst stage. Complete in vitro (IVP) and in vivo (control group) blastocysts were also produced. Samples from the three pools (biological replicates) of each blastocyst group and in vivo control blastocyst were hybridized on EmbryoGENE’s bovine microarray using a dye-swap design (technical replicates) for a total of six arrays.


title: Comparison of gene expression during meiosis between wild-type and msh5-deficient strains of Coprinopsis cinerea

summary:
Meiosis was compared in msh5-22 and wild type strains of C. cinerea at 6 time points spanning the meiotic timecourse.
Abstract: The basidiomycete Coprinopsis cinerea is well-suited to studies of meiosis because meiosis progresses synchronously in ten million cells within each mushroom cap. Approximately 20% of C. cinerea genes exhibit changing expression during meiosis, but meiosis and mushroom development happen concurrently so differentially expressed genes might not be directly involved in meiotic processes. Using microarrays, we examined global gene expression across a meiotic time course in two mutants in which meiosis arrests but mushrooms develop normally. Genes differentially expressed in the mutants compared to wild type are likely to be involved in meiosis and sporulation as opposed to mushroom development. In rad50-1, which arrests in late prophase, RNA abundance for a group of early meiotic genes remains high, while the expression of a group of late meiotic genes is never induced. In contrast, in msh5-22 (which fails to undergo pre-meiotic DNA replication), both early and late meiotic genes are underexpressed relative to wild type at late meiotic time points as the cells die. Genes that are differentially expressed in both mutants are particularly strong candidates for playing roles in meiosis and sporulation.

overall_design: Six time points were analyzed, with four biological replicate msh5-22 samples used for each timepoint.  Reference wild-type samples consisted of pooled RNA from ten samples at the appropriate timepoint.

first: Anderson

last: Erika

first: Burns

last: Claire

first: Zolan

last: Miriam E.


title: Expression data from human with IgA nephropathy (IgAN) [HG-U133A_ENTREZG_10]

status: Public on Feb 02 2012

first: Celine

last: Berthier

summary:
Proteinuria is the most important predictor of outcome in glomerulonephritis and experimental data suggest that the tubular cell response to proteinuria is an important determinant of progressive fibrosis in the kidney.  However, it is unclear whether proteinuria is a marker of disease severity or has a direct effect on tubular cells in the kidneys of patients with glomerulonephritis.   Accordingly we studied an in vitro model of proteinuria, and identified 231 albumin-regulated genes differentially expressed by primary human kidney tubular epithelial cells exposed to albumin. We translated these findings to human disease by studying mRNA levels of these genes in the tubulo-interstitial compartment of kidney biopsies from patients with IgA nephropathy using microarrays. Biopsies from patients with IgAN (n=25) could be distinguished from those of control subjects (n=6) based solely upon the expression of these 231 albumin-regulated genes.  The expression of an 11-transcript subset related to the degree of proteinuria, and this 11-mRNA subset was also sufficient to distinguish biopsies of subjects with IgAN from control biopsies.  We tested if these findings could be extrapolated to other proteinuric diseases beyond IgAN and found that the all forms of primary glomerulonephritis (n=33) can be distinguished from controls (n=21) based solely on the expression levels of these 11 genes derived from our in vitro proteinuria model.  Pathway analysis suggests common regulatory elements shared by these 11 transcripts.  In conclusion, we have identified an albumin-regulated 11-gene signature shared between all forms of primary glomerulonephritis.  Our findings support the hypothesis that albuminuria may directly promote injury in the tubulo-interstitial compartment of the kidney in patients with glomerulonephritis.
We used microarrays to analyze the transcriptome of microdissected renal biopsies from patients with IgA nephropathy (IgAN)

overall_design: RNA from tubulointerstitial compartments was extracted and processed for hybridization on Affymetrix HG-U133A microarrays.

first: Heather

middle: N

last: Reich

first: David

last: Tritchler

first: Daniel

last: Cattran

first: Andrew

middle: M

last: Herzenberg

first: Felix

last: Eichinger

first: Anissa

last: Boucherot

first: Anna

last: Henger

first: Viji

last: Nair

first: Clemens

last: Cohen

first: James

last: Scholey

first: Matthias

last: Kretzler


title: Impaired Chromatin Remodelling at STAT1-Regulated Promoters Leads to Global Unresponsiveness of Toxoplasma gondii-Infected Macrophages to IFN-Gamma

status: Public on Jan 25 2012

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Intracellular pathogens including the apicomplexan and opportunistic parasite Toxoplasma gondii profoundly modify their host cells in order to establish infection. We have shown previously that intracellular T. gondii inhibit up-regulation of regulatory and effector functions in murine macrophages (MΦ) stimulated with interferon (IFN)-γ, which is the cytokine crucial for controlling the parasites’ replication. Using genome-wide transcriptome analysis we show herein that infection with T. gondii leads to global unresponsiveness of murine macrophages to IFN-γ. More than 61% and 89% of the transcripts, which were induced or repressed by IFN-γ in non-infected MΦ, respectively, were not altered after stimulation of T. gondii-infected cells with IFN-γ. These genes are involved in a variety of biological processes, which are mostly but not exclusively related to immune responses. Analyses of the underlying mechanisms revealed that IFN-γ-triggered nuclear translocation of STAT1 still occurred in Toxoplasma-infected MΦ. However, STAT1 bound aberrantly to oligonucleotides containing the IFN-γ-responsive gamma-activated site (GAS) consensus sequence. Conversely, IFN-γ did not induce formation of active GAS-STAT1 complexes in nuclear extracts from infected MΦ. Mass spectrometry of protein complexes bound to GAS oligonucleotides showed that T. gondii-infected MΦ are unable to recruit non-muscle actin to IFN-γ-responsive DNA sequences, which appeared to be independent of stimulation with IFN-γ and of STAT1 binding. IFN-γ-induced recruitment of BRG-1 and acetylation of core histones at the IFN-γ-regulated CIITA promoter IV, but not β-actin was diminished by >90% in Toxoplasma-infected MΦ as compared to non-infected control cells. Remarkably, treatment with histone deacetylase inhibitors restored the ability of infected macrophages to express the IFN-γ regulated genes H2-A/E and CIITA. Taken together, these results indicate that Toxoplasma-infected MΦ are unable to respond to IFN-γ due to disturbed chromatin remodelling, but can be rescued using histone deacetylase inhibitors.

overall_design: Comparison of 4 different RNA pools with a 2-Color-Loop Design including 10 microarrays: [1] T. gondii infected and IFN-gamma treated, [2] T. gondii infected and untreated, [3] Non-infected and IFN-gamma treated, and [4] Non-infected and untreated.

first: Christine

last: Lang

first: Anke

last: Hildebrandt

first: Franziska

last: Brand

first: Lennart

last: Opitz

first: Hassan

last: Dihazi

first: Carsten

last: Lueder


title: miRNA profiles in unstimulated and TLR stimulated MDMs

status: Public on Dec 14 2011

city: Philadelphia

first: Julio

last: Martin-Garcia

state: PA

department: Microbiology and Immunology

institute: Drexel University College of Medicine

summary: Macrophages play a crucial role in HIV-1 pathogenesis. Toll-like receptors (TLRs) are fundamental for innate and adaptive immune responses, but their role in HIV-1 infection is still incompletely understood. The TLR3 and TLR4 ligands poly(I:C) and LPS are known to modulate HIV-1 infection of and replication in monocyte-derived macrophages (MDMs), but the mechanism is incompletely understood. We found that MDMs stimulation with poly(I:C) or LPS abrogated infection by CCR5-using, macrophage-tropic HIV-1, or by VSV-G-pseudotyped HIV-1 virions, while TLR7 and TLR9 agonists Imiquimod and CpG only reduced infection to varying extent. Suppression of infection, or lack thereof, did not correlate with differential effects on CD4 or CCR5 expression, type I interferon induction, or production of pro-inflammatory cytokines. Furthermore, integrated pro-viruses were readily detected in unstimulated, TLR7- and TLR9-stimulated cells, but not in TLR3- or TLR4-stimulated MDMs, suggesting the alteration of post-entry, pre-integration event(s). MicroRNA (miRNA) microarray and real time PCR demonstrated increased miR-155 levels in MDMs upon TLR3/4, but not TLR7, stimulation, and a miR-155 inhibitor partially restored infectivity in poly(I:C)-stimulated MDMs. Finally, miR-155 over-expression in MDMs and cell lines remarkably diminished HIV-1 infection, inducing an accumulation of late reverse transcription products, concurrently with a decrease in mRNA levels of several HIV-1 dependency factors involved in nuclear import of pre-integration complexes. Our results suggest that miR-155 may target mRNA(s) for host cell protein(s) that either participate in or facilitate post-entry, pre-integration events, resulting in severely diminished HIV-1 infection.

overall_design: miRNA profiles were investigated in total RNA isolated from unstimulated and TLR3-, TLR4- and TLR7-stimulated human MDMs from a single normal donor

first: Sonia

last: Navas-Martin


title: Microarray analysis of the intestinal host response in Giardia duodenalis assemblage E infected calves

status: Public on Apr 08 2012

city: Beltsville

first: Robert

last: Li

address: Barc East

department: Animal & Natural Resources Institute

institute: USDA

summary: Despite Giardia duodenalis being one of the most commonly found intestinal pathogens in humans and animals, little is known about the host-parasite interactions in its natural hosts. Therefore, the objective of this study was to investigate the intestinal response in calves following a G. duodenalis infection, using a bovine high-density oligo microarray to analyze global gene expression in the small intestine. The resulting microarray data suggested a decrease in inflammation, immune response, and immune cell migration in infected animals. These findings were examined in more detail by histological analyses combined with quantitative real-time PCR on a panel of cytokines. The transcription levels of IL-6, IL-8, IL-13, IL-17, and IFN-γ showed a trend of being downregulated in the jejunum of infected animals compared to the negative controls. No immune cell recruitment could be seen after infection, and no intestinal pathologies, such as villus shortening or increased levels of apoptosis. Possible regulators of this intestinal response are the nuclear peroxisome proliferator-activated receptors alpha (PPARα), and gamma (PPARγ) and the enzyme adenosine deaminase (ADA), all for which an upregulated expression was found in the microarray and qRT-PCR analyses.

overall_design: Eight male Holstein calves aged two to four weeks old were used for the trial. Prior to arrival, all animals were screened for the presence of Giardia cysts in their faecal samples.  After confirming their negative status for all these pathogens, four of the animals were randomly chosen and placed in a G. duodenalis contaminated environment, whereas the four remaining animals were kept as negative controls in separate G. duodenalis-free stables. All calves in the study received the same commercial milk replacer. After three weeks, the presence or absence of a G. duodenalis infection was confirmed by IFA on faecal samples after which the animals were euthanized. Changes in gene expression profiles induced by Giardia duodenalis infection were compared using a high-density 60mer bovine oligo microarray.

first: L.

last: Dreesen

first: M.

last: Rinaldi

first: K.

last: Chiers

first: T.

last: Geurden T.

first: W.

last: Van den Broeck

first: B.

last: Goddeeris

first: J.

last: Vercruysse

first: E.

last: Claerebout

first: Peter

last: Geldhof


title: A novel preclinical mouse model of spontaneous breast cancer metastasis

status: Public on Dec 23 2011

city: Amsterdam

first: Chris

last: Doornebal

address: Plesmanlaan 121

department: Molecular Biology

institute: Netherlands Cancer Institute

summary:
Metastatic disease remains one of the most urgent clinical challenges accounting for over 90% of cancer-related deaths. Yet, the identification of novel therapeutic targets to fight or prevent metastatic disease has been hampered by the limited availability of clinically relevant mouse models of metastasis formation. To address this caveat, we developed a novel preclinical mouse model of spontaneous metastatic breast cancer that recapitulates the key biological events of the metastatic cascade and mimics the clinical course of metastatic disease in humans. Exploiting the conditional K14cre;CdhF/F;Trp53F/F mouse model of de novo mammary tumor formation, we orthotopically transplanted K14cre;CdhF/F;Trp53F/F derived mouse invasive lobular carcinoma (mILC) fragments into mammary glands of wild-type syngeneic hosts. Once recipient mammary tumors were established, we mimicked the clinical setting and performed a mastectomy.  Following surgery, recipient mice eventually succumbed to wide-spread clinically overt metastatic disease in lymph nodes, lungs and gastrointestinal tract.
Using aCGH analyses, we explored the relationship between the genomic profiles of mammary donor tumors and paired recipient outgrowths and observed a strong correlation, indicating that the genomic profile of the parental K14cre;CdhF/F;Trp53F/F mILC is highly conserved in recipient mammary tumors. To investigate the genomic relationship between recipient mammary tumors and their metastases, we examined the correlation structure of genomic profiles derived from paired sets of primary tumors and metastases. Genomic profiles of clonally-related recipient mammary tumors were highly conserved in local and distant metastases, indicating that few genomic alterations occur during transition from a primary tumor to a distant site. To more thoroughly examine potential site-specific genomic alterations, we constructed so-called ‘delta-profiles’ by calculating the difference between the genomic profile of a recipient mammary tumor and its paired lymph node- and lung metastasis. Site-specific recurrent alterations were not observed in lymph node nor lung metastases. Taken together, these data show that genomic profiles of metastases are highly similar to those of parental recipient tumors and that, if changes occurred, they did not recur in different independent samples.

overall_design: We performed aCGH analyses on DNA isolated from K14cre;Cdh-/-;Trp53-/- derived donor mILCs (n=3) and their recipient mammary tumor outgrowths (n=10). Furthermore, we also analyzed genomic profiles derived from lung (n=10), tumor-draining (n=7) and distant lymph node metastases (n=5) isolated from the same recipient mice. DNA from each of these samples was hybridized against related donor splenic DNA.

first: Sjoerd

last: Klarenbeek

first: Tanya

last: Braumuller

first: Christiaan

last: Klijn

first: Metamia

last: Ciampricotti

first: Cheei-Sing

last: Hau

first: Markus

last: Hollmann

first: Jos

last: Jonkers

first: Karin

last: de Visser


title: A genome-wide analysis reveals that the Drosophila transcription factor, Lola, promotes axon growth in part by suppressing expression of the actin nucleation factor, Spire (allele lola_ORE76)

status: Public on Dec 03 2011

city: Bethesda

first: Edward

last: Giniger

department: NINDS

institute: NIH

summary: Transcriptional profiling of Drosophila embryos comparing lola mutant 10-12 hour after egg lay (AEL) embryos to age-matched control embryos. Mutants are homozygous lola nulls (allele lola_ORE76).

overall_design: Two-condition experiment: lola mutant embryos vs. age-matched control embryos. 7 biological replicates, each sample independently collected and containing RNA from approximately 300 embryos. Mutant and control embryos for each replicate were collected simultaneously. Dye-swaps were performed.

first: Michael

last: Gates


title: A genome-wide analysis reveals that the Drosophila transcription factor, Lola, promotes axon growth in part by suppressing expression of the actin nucleation factor, Spire (allele lola_ORC4)

summary: Transcriptional profiling of Drosophila embryos comparing lola mutant 10-12 hour after egg lay (AEL) embryos to age-matched control embryos. Mutants are homozygous isoform K nulls (allele lola_ORC4).


title: Tumor-microenvironment interactions studied by zonal transcriptional profiling of squamous cell lung carcinoma

status: Public on Dec 01 2011

city: Stanford

first: Daniel

last: Haag

state: Santa Clara

address: 265 Campus Drive

department: ISCBRM

institute: Stanford School of Medicine

summary: To better understand the interaction between tumor cells and their microenvironment with regard to mechanisms of invasion, total RNA was isolated from the inner-tumor, tumor invasion front, adjacent lung and distant normal lung tissue from 18 patients with squamous cell lung carcinoma using punch-aided laser capture microdissection. Comprehensive mRNA expression profiles were obtained from microarray expreiments and statistical analyses revealed extensive changes in gene expression when comparing the inner tumor and tumor front with the normal lung and lung front. However, only a few genes were differentially expressed between the tumor front and the inner tumor. The identified genes indicate prostaglandin mediated inflammatory processes at the invasion front

overall_design: Sample for microarray experiments were taken from the inner-tumor, tumor invasion front, adjacent lung and distant normal lung tissue from 18 patients with squamous cell lung carcinoma using punch-aided laser capture microdissection.  Sample RNA and Universal Reference RNA (Stratagene, La Jolla, USA) were amplified and separately labeled with both Cy3 and Cy5. All samples were subjected to two-color hybridizations (sample against reference) with color-switch experiments yielding two technical replicates, respectively.

first: Hui

last: Wu

first: Hans

last: Hoffmann

last: Lichter


title: Exposure of zebrafish embryos to organic solvents, dimethylformamide and dimethyl sulfoxide

status: Public on Oct 06 2011

city: Liverpool

first: Catherine

last: Turner

state: Merseyside

address: Crown Street

department: Institute of Integrative Biology

country: United Kingdom

institute: University of Liverpool

summary: Current aquatic chemical testing guidelines recognise that solvents can potentially interfere with the organism or environmental conditions of aquatic ecotoxicity tests and therefore recommend concentration limits for their use. These recommendations are based on evidence of adverse solvent effects in apical level tests. The growing importance of sub-apical and chronic endpoints in future test strategies, however, suggests the limits may need re-assessment. To address this concern, microarrays were used to determine the effects of organic solvents, dimethylformamide (DMF) and dimethyl sulfoxide (DMSO), upon the transcriptome of zebrafish (Danio rerio) embryos. Embryos were exposed for 48 h to 0.025 and 0.1 ml/L DMF or DMSO. Effects on survival and development after 24 and 48 h were assessed microscopically with no effects on mortality or morphology. However, analysis of 48-h embryonic RNA revealed large numbers of differentially expressed genes for both solvent at both concentrations. The enrichment of differentially expressed genes was found for metabolic, development and other key biological processes, some of which could be linked to observed morphological effects at higher solvent concentrations. These findings emphasise the need to remove or lower as far as possible, the concentrations of solvent carriers in ecotoxicology tests.

overall_design: Balanced loop design consisting of five separate conditions - two exposure concentrations for each of the two solvents and a control treatment - using four replicates for each condition all of which were dye swapped, resulting in a total of twenty independant samples on twenty arrays.

first: Ashley

last: Sawle

first: Martina

last: Fenske

first: Andrew

middle: R

last: Cossins


title: Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots

status: Public on Aug 06 2011

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

summary: Long intergenic noncoding RNAs (lincRNA) transcribed from intergenic regions of eukaryotic genomes play important roles in key biological processes; yet, plant lincRNAs remain poorly characterized. Here we profiled lincRNA expression in inflorescences, leaves and roots using ATH lincRNA v1 array. we found 92% lincRNAs could be detected in at least 2 ATH lincRNA v1 arrays and majority of the lincRNAs were expressed at levels higher than those of pri-miRNAs but lower than those of mRNAs.Using a cut-off of 2-fold change, we identified 149 lincRNAs preferentially expressed in inflorescences, 232 in leaves and 164 in roots.

overall_design: Nine arrays were hybridized with RNAs from inflorescences, leaves and roots with 3 biological replicates.

last: Xu

first: Choonkyun

last: Jung

first: Lucia

last: Bernad

first: Huan

last: Wang

first: Catalina

last: Arenas

first: Nam-Hai

last: Chua


title: Tetradecylthioacetic acid effect on heart ventricle

status: Public on Aug 01 2011

city: aas

first: Fabian

last: Grammes

address: Arboretvn. 2

department: CIGENE

country: Norway

institute: Norwegian University of Life Sciences

summary: Identifying genes that show differential cardiac expression by comparing Atlantic salmon fed with a tetradecylthioacetic acid (TTA) supplemented diet to those fed a control diet for two sampling time points.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Comparing cardiac gene expression from Atlantic salmon with 2 different diets (TTA and control) and sampled at 2 time points. 6 biological replicates (individuals), totally 24 arrays.

first: Kjell-Arne

last: R¿rvik

first: Magny

middle: S

last: Thomassen

first: Harald

last: Takle