title: Gene expression patterns of biopsies from a colonoscopy taken in 2007 of an ulcerative colitis patient infected with Trichuris trichiura

summary: Helminth infection may have the potential to suppress intestinal inflammation in inflammatory bowel diseases. Ulcerative colitis is more common in developed countries than in developing countries endemic for helminth infections. There are animal models, as well as clinical trials, suggesting therapeutic effects of experimental helminth infection. Here, we provide a comprehensive molecular portrait of dynamic changes in the intestinal mucosa of an individual who infected himself with Trichuris trichiura to treat his symptoms of ulcerative colitis. Genes involved in carbohydrate and lipid metabolism were upregulated in helminth-colonized tissue, while tissues with active colitis showed upregulation of proinflammatory genes such as IL-17, IL13RA2, and CHI3L1. T. trichiura colonization of the intestine may reduce symptomatic colitis by promoting goblet cell hyperplasia and mucus production through TH2 cytokines and IL-22. By better understanding the physiological effects of helminth infection, new therapies for ulcerative colitis could be identified. This is the first (out of three) series of arrays from this patient from a colonoscopy in 2007 when the patient had mild proctitis in the rectum and worms in the ascending and transverse colon.

overall_design: We analyzed 14 HEEBO arrays on which were hybridized RNA amplified from pinch biopsies collected from different regions of the colon. 3 samples were from the ascending colon, which was colonized by worms at the time. 2 samples were from the transverse colon, which was also colonized by worms at the time. 4 samples were from the sigmoid colon, which appeared normal at the time. 3 samples were from the rectum, which showed signs of proctitis and was inflamed at the time. 2 samples were from the terminal ileum, which was unaffected by worms or colitis.


title: Constitutively active Stat3 in mouse embryonic fibroblasts (MEFs)

status: Public on Nov 17 2010

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

summary: Signal Transducer and Activator of Transcription 3 (STAT3) is considered as an oncogene being constitutively activated in a wide variety of primary human tumours, which often become addicted to its activity. Using primary fibroblasts derived from a knock-in mouse expressing only the constitutively active form STAT3-C as well as STAT3-dependent tumor cell lines MDA-MB468, DU145 and SKBR3, we provide evidence that STAT3 can act as a central regulator of cell metabolism. STAT3C/C  MEFs are resistant to apoptosis and senescence and they show reduced mitochondrial activity but activate aerobic glycolysis, as shown by enhanced expression of master regulators of glycolysis such as PDK-1 and HIF-1α, and by increased lactate production, glucose avidity and sensitivity to glycolysis inhibitors. HIF-1α is up-regulated in the STAT3C/C  MEFs and is responsible for the glycolytic phenotype. Moreover, inhibition of STAT3 activity in STAT3-addicted tumour cell lines restores mitochondrial activity and down-regulates glycolytic metabolism, preceding the induction of massive apoptosis. Thus, the essential role observed for STAT3 in so many different cancer cell types may be partly explained by its ability to act as a molecular switch of cellular metabolism triggering abnormal cell survival/proliferation.

overall_design: Three biological replicates of MEFs from mice with constitutively active Stat3 are compared to three biological replicates of wild-type MEFs.

first: Marco

last: Demaria

first: Carlotta

last: Giorgi

first: Magdalena

last: Lebiedzinska

first: Daniel

middle: J

last: Gough

first: James

last: Turkson

first: David

middle: E

last: Levy

first: Christine

last: Watson

first: Mariusz

middle: R

last: Wieckowski

last: Pinton

first: Valeria

last: Poli


title: Comparative analysis of Tsaiya duck (Anas platyrhynchos) transcriptional profiling between high and low hatchability

status: Public on Nov 16 2010

city: Taichung

first: Mu-Chiou

last: Huang

address: 250 Kuo-Kuang Rd

country: Taiwan

institute: National Chung-Hsing University

summary:
Hatchability is one of the important reproductive traits of poulty, however, molecular biological study related to hatchability of poultry is very limited. The magnum is where the egg white components are produced. During embryo development, egg white secreted by the magnum is gradually transferred into the amniotic fluid, and albumen finally migrates to the embryo. Egg white proteins are composed of ovalbumin, conalbumin,  lysozyme, ovomucoid, riboflavin binding protein (RfBP), and other less abundant proteins. Mutation of ovalbumin and RfBP genes increases the mortality of embryos; therefore, egg white might be closely related to poultry hatchability. Tsaiya duck (Anas platyrhynchos) is the major egg-laying duck in Taiwan. In this study, gene expression profiling by cDNA microarray chip technology was performed using mRNA prepared from the magnum epithelium of Tsaiya ducks, and a number of differentially expressed transcripts were found.
Keywords = Tsaiya duck (Anas platyrhynchos),  magnum,  hachability,  cDNA microarray, transcriptional profiling.

overall_design: Analysis used low hachability RNA as control samples for comparison to the experimental samples taken from high hachability group. Total RNA was isolated by the RareRNA reagent (GenePure). The MicroMax direct labeling kit (PerkinElmer) was used to prepare the labeled cDNA and further process the hybridization on the arrays. Dye swap was design with four arrays. Arrays were scanned using a GenePix 4000B microarray scanner (Axon Instruments). GenePix Pro 4.1 software was then used to acquire the raw data. The data was analyzed by Avadis software (Strand Life Science).

first: Hsiu

middle: L

first: Yu

middle: S

last: Cheng

first: Chang

middle: W

first: Mu

middle: C

first: Wen

middle: H

last: Hsu


title: Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiura

status: Public on Nov 20 2010

city: San Francisco

first: Sajeev

last: Batra

state: CA

country: USA

institute: UCSF

summary: Helminth infection may have the potential to suppress intestinal inflammation in inflammatory bowel diseases. Ulcerative colitis is more common in developed countries than in developing countries endemic for helminth infections. There are animal models, as well as clinical trials, suggesting therapeutic effects of experimental helminth infection. Here, we provide a comprehensive molecular portrait of dynamic changes in the intestinal mucosa of an individual who infected himself with Trichuris trichiura to treat his symptoms of ulcerative colitis. Genes involved in carbohydrate and lipid metabolism were upregulated in helminth-colonized tissue, while tissues with active colitis showed upregulation of proinflammatory genes such as IL-17, IL13RA2, and CHI3L1. T. trichiura colonization of the intestine may reduce symptomatic colitis by promoting goblet cell hyperplasia and mucus production through TH2 cytokines and IL-22. By better understanding the physiological effects of helminth infection, new therapies for ulcerative colitis could be identified. This is the third (out of three) series of arrays from this patient from a colonoscopy in 2009 when the patient was in remission.

overall_design: We analyzed 12 HEEBO arrays on which were hybridized RNA amplified from pinch biopsies collected from different regions of the colon. 4 samples were from the ascending colon, which was colonized by worms at the time. 3 samples were from the transverse colon, which appeared normal at the time. 3 samples were from the recto-sigmoid colon, which had recovered from colitis at the time. 2 samples were from the terminal ileum, which was unaffected by worms or colitis.

first: Mara

last: Broadhurst

first: Jacqueline

middle: M

last: Leung

first: Vikram

last: Kashyap

first: Joseph

last: McCune

first: Uma

last: Mahadevan

last: McKerrow

first: P'ng

last: Loke


title: PPARg and IL-4-induced gene expression data from PPARg +/- LysCre and PPARg fl/- LysCre mouse bone marrow-derived alternatively activated macrophages and immature dendritic cells (iDCs)

status: Public on Nov 18 2010

city: Boston

first: Attila

last: Szanto

state: MA

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Conditional macrophage-specific PPARg knockout mice were generated on C57Bl/6 background by breeding PPARg fl/- (one allele is floxed, the other is null) and lysozyme Cre transgenic mice. PPARg and IL-4 signaling was analyzed on bone marrow-derived macrophages. Bone marrow of 4 mice per group was isolated and differentiated to alternatively activated macrophages with 20 ng/ml M-CSF and 20 ng/ml IL-4 or to iDCs with 20 ng/ml GM-CSF+20 ng/ml IL-4. 1 uM Rosiglitazone (RSG) was used to activate PPARg. From each mouse 4 samples were generated: 1. M-CSF+IL-4, 2. M-CSF+IL-4+RSG, 3. GM-CSF+IL-4 and 4. GM-CSF+IL-4+RSG. All compounds were added throughout the whole differentiation process, and fresh media was added every other day. Control cells were treated with vehicle (DMSO:ethanol). After 9 days, RNA was isolated and gene expression profiles were analyzed using ABI Mouse Genome Survey Arrays.

overall_design: 4 PPARg +/- LysCre and 4 PPARg fl/- LysCre mice were used to isolate bone marrow and from each alternatively activated macrophages were differentiated with IL-4 and simultaneously treated with vehicle or RSG, iDCs were differentiated with GM-CSF+IL-4 and simultaneously treated with vehicle or RSG. Altogether we analyzed 32 samples with 4 biological replicates as below.

first: Laszlo

last: Nagy


title: Transcriptome of Mycoplasma genitalium under osmotic stress

status: Public on Nov 15 2010

city: San Antonio

first: Wenbo

last: Zhang

state: TX

address: 7703 Floyd Curl Drive

department: Microbiology and Immunology

institute: The University of Texas Health Science Center at San Antonio

summary: Mycoplasma genitalium is the causative agent of non-gonococcal, chlamydia-negative urethritis in men and has been linked to reproductive tract disease syndromes in women. As with other mycoplasmas, M. genitalium lacks many regulatory genes because of its streamlined genome and total dependence on a parasitic existence.  Therefore, it is important to understand how gene regulation occurs in M. genitalium, particularly in response to environmental signals likely to be encountered in vivo. In this study, we developed an oligonucleotide-based microarray to investigate transcriptional changes in M. genitalium following osmotic shock. Using a physiologically relevant osmolarity condition (0.3 M sodium chloride), we identified 39 up-regulated and 72 down-regulated genes. Of the up-regulated genes, 21 were of unknown function and 15 encoded membrane-associated proteins. The majority of down-regulated genes encoded enzymes involved in energy metabolism and components of the protein translation process. These data provide insight into the in vivo response of M. genitalium to hyperosmolarity conditions and identify candidate genes that may contribute to mycoplasma survival in the urogenital tract.

overall_design: To examine the effects of hyperosmolarity on M. genitalium transcription, four 50 ml cultures of strain G37 in 75 cm2 tissue culture flasks (Corning) were grown to exponential phase, as determined by medium colour change and colony density. Then, NaCl was added to three flasks to achieve final concentrations of 0.1, 0.2 and 0.3 M. Parallel cultures of M. genitalium in the absence of NaCl served as controls. All cultures were incubated for 1 h at 37℃ prior to RNA extraction. Experiments were repeated six times, which produced six independent RNA sample pairs from NaCl-treated cultures and control cultures for each NaCl condition. Dye swap was performed on three of six RNA pairs to minimize effects caused by biased labelling efficiencies.

first: Joel

middle: B

last: Baseman


title: Analysis of gene expression in Arabidopsis thaliana after priming with BABA and infection with Pseudomonas syringae pv tomato DC3000

status: Public on Nov 19 2010

city: Lausanne

first: Johann

last: Weber

state: VD

address: Genopode Building

department: Center for integrative Genomics

country: Switzerland

institute: University of Lausanne

summary:
Arabidopsis thaliana (Col-0) plants were treated with BABA and gene expression differences to control plants were monitored after dip-inoculation with Pseudomonas syringae pv tomato DC3000.

Keywords: transcript profiling, response to BABA-induced priming and infection

overall_design: 3 independant replicates were analyzed by two color co-hybridizations.  Leaf RNA from Pseudomonas infected control plants (Cy3 labeled cDNA) was cohybridized with leaf RNA from Pseudomonas infected BABA pretreated plants (Cy5 labeled cDNA). Samples were collected 22 hours after bacterial inoculation. BABA pretreatment was performed two days before bacterial inoculation. To assess the effect of BABA alone on gene expression, leaf RNA from BABA treated plants (Cy5 labeled cDNA) was cohybridized with leaf RNA (Cy3 labeled cDNA) from water treated plants.

first: Chia-Hong

last: Tsai

first: Prashant

last: Singh

first: Ching-Wei

last: Chen

first: Jerome

last: Thomas

first: Brigitte

last: Mauch-Mani

first: Laurent

last: Zimmerli


title: The cell envelope stress response mediated by the LiaFSRLm three-component system of Listeria monocytogenes is controlled via the phosphatase activity of the bifunctional  histidine kinase LiaSLm

city: Würzburg

first: Frederike

last: Fritsch

address: Am Hubland

country: Germany

institute: Uni Würzburg

summary:
Most members of the phylum Firmicutes harbor a two-component system, LiaSR, which is involved in the response to cell envelope stress elicited most notably by inhibitors of the lipid II cycle. In all LiaSR systems studied in detail LiaSR-mediated signal transduction was shown to be negatively controlled by a membrane protein, LiaF, encoded upstream of liaSR.  In this
study we have analysed the LiaSR homolog of Listeria monocytogenes (LiaSRLm). Whole genome transcriptional profiling indicated that activation of LiaSRLm results in a remodeling of the cell envelope via the massive upregulation of membrane or cell-wall associated proteins in the presence of inducing stimuli. As shown for other LiaSR two-component systems LiaSRLm is activated by cell wall-active antibiotics. We demonstrate that the level of
phosphorylated LiaRLm, which is required for the induction of the LiaSRLm regulon, is controlled by the interplay between histidine kinase and phosphatase activity of the bifunctional sensor protein LiaSLm. Our data suggest that the phosphatase activity of LiaSLm is stimulated by LiaF in the absence of cell envelope stress

overall_design: A total of three independently isolated RNA samples from each strain were used for the analysis.

first: Norman

last: Mauder

first: Tatjana

last: Williams

first: Julia

last: Weiser

first: Markus

last: Oberle

first: Dagmar

last: Beier


title: Gene expression profiling after stimulation of THP-1 cells with a2NTD

city: North Chicago

first: Kenneth

last: Beaman

state: IL

address: 3333 Green Bay Rd

institute: Rosalind Franklin University of Medicine and Science

summary:
Background:  Identifying the immune components that are regulated by a2NTD, a peptide cleaved from the N-terminus of the a2 vacuolar ATPase.
Methods:  In this study, we used pathway-focused PCR arrays to determine the genes that are regulated in human monocytic cell line, THP-1 after a2NTD stimulation over time.
Results:  a2NTD up-regulated several cytokines including IL-1 alpha, IL-1 beta, and IL-10.  Several chemokines were also upregulated including the MCP and MIP families.
Conclusion:  We believe a2NTD to be an immune modulator made by tumor cells that aid in preventing immune surveillance by up-regulating proteins in monocytes that are both pro-and anti-inflammatory in nature.

overall_design: The Human Inflammatory Response and Autoimmunity RT² Profiler™ PCR Array profiles the expression of 84 key genes involved in autoimmune and inflammatory immune responses. It represents the expression of inflammatory cytokines and chemokines as well as their receptors. It also contains genes related to the metabolism of cytokines and involved in cytokine-cytokine receptor interactions. Thoroughly researched panels of genes involved in the acute-phase response, inflammatory response, and humoral immune responses are represented as well. Using real-time PCR, you can easily and reliably analyze expression of a focused panel of genes related to inflammatory and autoimmune responses with this array.

first: Christina

last: Kwong


title: Microbial community composition in sediments resists perturbation by nutrient enrichment

status: Public on Nov 13 2010

first: Jennifer

last: Bowen

address: 100 Morrissey Blvd

department: Biology Department

institute: University of Massachusetts Boston

summary: Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities.  Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance.  We present evidence for a third response: resistance.  We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene.  Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology.  The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.

sample_organism: Bacteria unidentified

overall_design: nirS gene diversity from two salt marsh experiments, GSM (4 treatments, 8 samples, duplicate arrays, four replicate blocks per array, 8 arrays per slide) and PIE (2 treatments, 16 samples, duplicate arrays four replicate blocks per array, 8 arrays per slide)

first: Bess

last: Ward

first: Hilary

middle: G

last: Morrison

first: John

last: Hobbie

first: Ivan

last: Valiela

first: Linda

middle: A

last: Deegan

first: Mitchell

last: Sogin


title: Expression Profiling of the Response to Short-Term Exposure to Fluconazole in Cryptococcus neoformans Serotype A

city: Roma

first: ada

last: florio

state: Roma

address: Largo A. Gemelli 8

department: Microbiology

institute: Catholic University of Sacred Heart

summary: Fluconazole (FLC), a triazole antifungal drug, is widely used for the maintenance therapy of cryptococcal meningoencephalitis, the most common opportunistic infection in AIDS patients, but this usage predisposes to the appearance of FLC resistance, especially in patients with no or limited access to highly active antiretroviral therapy. We used microarray analysis to examine changes in the gene expression profile of C. neoformans reference strain H99 (serotype A) following exposure to FLC in order to study the adaptive cellular responses to drug stress. Simultaneous analysis of over 6,823 C. neoformans gene transcript levels revealed that 476 genes were responsive to FLC. Up-regulated expression was observed, as expected, for genes involved in the ergosterol biosynthesis, including ERG13, ERG1, ERG7, ERG25, ERG2, ERG3, ERG5, and that encoding the azole target, ERG11, but also for the gene SRE1, that encodes a well-known regulator of sterol homeostasis in C. neoformans. In addition, several genes such as those involved in a wide variety of important cellular processes (i.e., lipid and fatty acid metabolism, cell wall maintenance, stress, virulence, etc.), were found to be up-regulated in response to fluconazole treatment. Some of these genes may represent potential therapeutic targets to be exploited in anticryptococcal therapy. Conversely, expression of AFR1, the major transporter of azoles in C. neoformans, was shown to be not affected by exposure to FLC, thus suggesting a minor involvement in the C. neoformans short-term adaptation to the azole drug.

overall_design: We studied the transient response of C. neoformans to fluconazole by analyzing differences in gene expression prior to and after exposure of strain H99. Three biological replicates were performed for each condition (FLC-exposed and -not exposed (controls)). The cells were exposed to 10 µg of FLC/ml (1/2 x MIC) or distilled water (controls) for one doubling time (90 min).

first: Ada

last: Florio

first: Selene

last: Ferrari

first: Elena

last: De Carolis

first: Giovanni

last: Fadda

first: Maurizio

last: Sanguinetti

first: Dominique

last: Sanglard

first: Brunella

last: Posteraro


title: Mouse skin: neutron irradiation

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: The objective of this investigation was to characterize, at individual level, the transcriptional response and the onset of regenerative processes in mouse skin irradiated with different doses of fast neutrons. We performed a high-throughput gene expression analysis, by DNA oligonucleotide microarray on 24 three months old C57Bl/6 mice irradiated with 0, 0,2 and 1 Gy of mono-energetic 14 MeV neutron. The results, partially validated by quantitative real time RT-PCR, showed  an up-regulation of  a sub-class of keratin and keratin associated proteins, and of components of the S100 family of Ca2+-binding proteins which was limited to the lower dose. We conclude that the dose-dependent differential gene expression, reminiscent of the onset of re-epithelialization and wound healing, depends upon the proportion of cells carrying multiple lesions at chromosomal level post-irradiation, and it represents an in vivo evidence of a skin regenerative program exerted independently from DNA repair-associated pathways.

overall_design: Four condition experiment: 6h and 24h from 0.2 Gy neutron irradiation; 6h and 24 from 1 Gy neutron irradiation. One replicate for each condition

first: Emiliano

last: Fratini

first: Mara

last: Artibani

first: Katarzyna

last: Kobos

first: Paolo

last: Colautti

first: Rodolfo

last: Negri

first: Roberto

last: Amendola


title: Gene expression regulation by C. elegans SAM-10

status: Public on Nov 12 2010

city: Saint Louis

first: Michael

last: Nonet

state: MO

address: 660 South Euclid Avenue

department: Anatomy and Neurobiology

institute: Washington University Medical School

summary: Little is known about transcriptional control of neurite branching or presynaptic differentiation, events that occur relatively late in neuronal development.   Using the C. elegans mechanosensory circuit as an in vivo model, we show that SAM-10, an ortholog of mammalian Single-Stranded DNA binding Protein (SSDP), functions cell-autonomously in the nucleus to regulate synaptic differentiation as well as positioning of a single neurite branch.  PLM mechanosensory neurons in sam-10 mutants exhibit abnormal placement of the neurite branch point, and defective synaptogenesis, characterized by an overextended synaptic varicosity, underdeveloped synaptic morphology and disrupted co-localization of active zone and synaptic vesicles.  SAM-10 functions coordinately with LDB-1 (Lim Domain Binding protein-1), demonstrated by our observations that 1) mutations in either gene show similar defects in PLM neurons; and 2) LDB-1 is required for SAM-10 nuclear localization.  SAM-10 regulates PLM synaptic differentiation by suppressing transcription of prk-2, which encodes an ortholog of the mammalian Pim kinase family.  PRK-2-mediated activities of SAM-10 are specifically involved in PLM synaptic differentiation, but not other sam-10 phenotypes such as neurite branching.   Thus, these data reveal a novel transcriptional signaling pathway that regulates neuronal specification of neurite branching and presynaptic differentiation.

overall_design: Animals were grown on fresh 8P plates (Wormbook.org) until gravid.  Eggs were collected by bleaching and hatched in M9 buffer overnight.  L1 animals were fed on fresh food for 2 hours at room temperature, harvested and separated from worm debris using a 25μm mesh.  RNA was isolated using a standard Trizol protocol.  RNA preps were stored at -80C.  Quality of RNA preps was first estimated using Agilent 2100 Bioanalyzer.  RNA was then reverse-transcribed using the Genisphere Array 350 kit, which generate tagged cDNA.  Resulted products are hybridized to the microarrays.  Four independent high quality RNA preps (RIN>=7) were chosen for microarray assay using long oligomer-based spotted microarray (Washington University, St. Louis, MO).  For dye-swap controls, we ran a technical replicate hybridization for each pair of samples in which the dyes are reversed.  Gene spots with “found/good” signals (defined by ScanArray, channel flag 3) in all scans were chosen for gene expression analysis.

first: Qun

last: Zheng


title: Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription.

city: Tsukuba

first: Koji

last: Numata

address: 3-1-1 Koyadai

country: Japan

institute: RIKEN

summary: We investigated the allele- and strand-specific transcriptional landscape of a megabase-wide genomic region of mouse Ube3a (ubiquitin protein ligase E3A) by means of a highly parallel SNP genotyping platform. We have successfully identified maternal-specific expression of Ube3a and its antisense counterpart (Ube3a-ATS) in brain, but not in liver. Because of the use of inter-subspecies hybrid mice, this megabase-wide analysis provided high-resolution picture of the transcriptional patterns of this region. First, we showed that brain-specific maternal expression of Ube3a is restricted to the second half part of the locus, but is absent from the first half part. Balance of allelic expression is altered in the middle of the locus. Second, we showed that expression of the brain-specific Ube3a-ATS appeared to be terminated in the region upstream to the Ube3a transcription start site. The present study highlights the importance of locus-wide competition between sense and antisense transcripts.

overall_design: We have listed up SNP sites within Ube3a-Snurf/Snrpn region between C57BL/6J and MSM/Ms. SNP sites were loaded onto Illumina GoldenGate Assay platform, and were assayed by targeting total RNA came from brain and liver of F1 hybrid mice.

first: Chihiro

last: Kohama

first: Kuniya

last: Abe

first: Hidenori

last: Kiyosawa


title: A first comparative map of copy number variations in the sheep genome

city: Bologna

first: Pier Luigi

last: Martelli

address: via Irnerio 42

institute: University of Bologna

type: Genome variation profiling by genome tiling array

summary:
We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome.
We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in the cattle and goat genomes indicated that overlaps between sheep and goat and sheep and cattle CNVRs are highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs.

overall_design: In this study we made use of the high conservation and homology between the cattle and sheep genomes determined by their phylogenetic closeness to identify CNVs in sheep applying the same approach we carried out to identify CNVs in the goat genome. We used a custom tiling array including ~385,000 oligonucleotide probes designed on the Btau_4.0 version of the Bos taurus genome assembly and analysed genomic DNA samples of 11 sheep belonging to 6 different Italian dairy sheep breeds (2 Sarda, 2 Bagnolese, 2 Comisana, 2 Massese, 2 Laticauda and 1 Valle del Belice) compared to the reference DNA of another Sarda sheep.

first: Luca

last: Fontanesi

first: Francesca

last: Beretti

first: PierLuigi

first: Michela

last: Colombo

first: Stefania

last: Dall'Olio

first: Mariaconsiglia

last: Occidente

first: Baldassare

last: Portolano

first: Rita

last: Casadio

first: Donato

last: Matassino

first: Vincenzo

last: Russo


title: Escherichia coli global gene expression in urine from women with urinary tract infection

city: Ann Arbor

first: Harry

last: Mobley

state: MI

address: 5641 Medical Sciences II  1150 W. Medical Center Dr.

institute: University of Michigan

summary: Examination of E. coli transcripts present in bacteria in urine samples from 8 patients attending a urology clinic with symptoms of cystitis, as compared to transcripts present in the same E. coli strains during mid-exponential growth in filter-sterilized human urine in vitro.

overall_design: A 48 array study using total RNA recovered from eight clinical E. coli isolates immediately following collection from women and following culture in pooled human urine ex vivo.  Each array measures the expression of the 5,379 ORFs in the CFT073 genome, using an average of 14 60-mer probes per ORF.  Arrays were performed in triplicate: biological replicates of the in vitro-cultured samples and technical replicates of the in vivo samples.

first: Erin

last: Hagan

first: Amanda

last: Lloyd

first: David

last: Rasko

first: Gary

last: Faerber


title: MicroRNA Expression in Human RPE Cells in Culture: Control vs Treated with IFN-γ + TNF-α + IL-1β

status: Public on Nov 11 2010

city: Bethesda

first: R

middle: Krishnan

last: Kutty

state: MD

address: 6 Center Dr., Room 112

department: National Eye Institute

institute: National Institutes of Health

summary: Human retinal pigment epithelial (HRPE) cells in culture respond to inflammatory cytokines (IFN-γ + TNF-α + IL-1β ) by increasing the expression of many cytokines and chemokines. The goal of this study was to delineate the role of miRNA in this process. We employed microarray analysis to study the effect of inflammatory cytokines on the miRNA expression in HRPE cells.

overall_design: HRPE cells were treated with a mixture of IFN-γ (100 u), TNF-α (10 ng/ml) and IL-1β (10 ng/ml) for 16 hours, and the miRNA expression was analyzed using RNA preparations isolated from control and treated cells. The experiment was repeated. Control samples were labeled with Cy3 while the treated samples with Cy5.

middle: K

first: Chandrasekharam

middle: N

last: Nagineni


title: Renormalized GSE3889 by using the parametric method

city: Akita

first: Tomokazu

last: Konishi

state: Akita

address: Shimoshinjyo Nishi

department: Bioresource Sciences

institute: Akita Prefectural University

type:
Third-party reanalysis
Expression profiling by array

summary: The GeneChip data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). http://www.super-norm.com/eng/index.html

overall_design: PM data of samples in GSE3889, GSM88872-GSM88891, were parametrically normalized in chip-wise manner according to the three-parameter lognormal distribution method (Konishi et. al., 2009 PLoS ONE 3: e3555. http://dx.plos.org/10.1371/journal.pone.0003555). Expression level of a gene was estimated by summarizing the corresponding PM data. A pseudo data was then derived in a form of antilog of the z-scores; the center of the pseudo data was 256. The pseudo data, ABS_CALL, and the normalized data (z-scores) are presented in the summary matrix file. The normalized PM data of a chip were presented in separate ascii text files.  In each of the text files, the PM data is presented in matrix form where each row of the matrix corresponds a gene and the order of PM probe data in the row is identical to that of the chip's CDF file. The parameters found in each chip data were presented in the "parameters" text file. For details for the parameters, see Konishi et al. 2009.


title: Renormalized GSE6089 by using the parametric method

summary:
Each of the channel data was normalized and summarized by using SuperNORM data service (Skylight Biotech Inc.). http://www.super-norm.com/eng/index.html
ABS_CALL: A, affected severely by noise; M, marginal; P, plausible.

overall_design: Both R and G signal data of samples in GSE6089, GSM140954-GSM140967, were parametrically normalized in channel-wise manner according to the three-parameter lognormal distribution method (Konishi, 2004 BMC Bioinformatics, 5, 5 http://www.biomedcentral.com/1471-2105/5/5).  A pseudo data was then derived in a form of antilog of the z-scores; the center of the pseudo data was 256. The pseudo data, ABS_CALL, and the normalized data (z-scores) are presented in the matrix form.


title: Escherichia coli K-12: luxS mutant LW12  vs. wild type W3110

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

summary: Transcripitonal profiling of Escherichia coli K-12 comparing luxS mutant LW12 with wild type W3110

overall_design: One-condition experiment, luxS mutant LW12 vs. wild type W3110

first: A

last: Kang

first: Matthew

last: Wook


title: Genome Sequences of Lactococcus lactis MG1363 (Revised) and NZ9000 and Comparative Physiological Studies

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Lactococcus lactis NZ9000 and its parent MG1363 are the most commonly used lactic acid bacteria for expression and physiological studies. We noted unexpected but significant differences in the growth behaviors of both strains. We sequenced the entire genomes of the original NZ9000 and MG1363 strains using an ultradeep sequencing strategy. The analysis of the L. lactis NZ9000 genome yielded 79 differences, mostly point mutations, with the annotated genome sequence of L. lactis MG1363. Resequencing of the MG1363 strain revealed that 73 out of the 79 differences were due to errors in the published sequence. Comparative transcriptomic studies revealed several differences in the regulation of genes involved in sugar fermentation, which can be explained by two specific mutations in a region of the ptcC promoter with a key role in the regulation of cellobiose and glucose uptake.

sample_organism: Lactococcus cremoris subsp. cremoris MG1363

sample_organism: Lactococcus cremoris subsp. cremoris NZ9000

overall_design: MG1363 versus NZ9000 in 2 different culture media


title: Progranulin A mediated MET signalling is essential for liver morphogenesis in zebrafish

status: Public on Nov 10 2010

city: Taipei

first: Yen-Hsing

last: Li

address: ICOB, Academia Sinica, Nankang

institute: Academia Sinica

summary: Regulation of embryonic liver growth remains largely elusive.  Progranulin has been discussed in pathological liver growth; however, the functional role of Pgrn in embryonic liver growth has never been addressed.  Knockdown of GrnA, the orthologue of mammalian pgrn in zebrafish, displayed a deficient hepatic outgrowth during hepatogenesis.  Expression profiles manifested that pgrn-deficiency impaired hepatogenesis associated with dysregulation of Met signaling.  Pgrn regulates hepatic expression of Met was further verified in vitro and in vivo.  These results indicate that Pgrn is a novel factor required for embryonic hepatic outgrowth and reveal a novel link between Pgrn and Met signaling.

overall_design: To explore the GrnA induced genomic responses during hepatic outgrowth, mRNA expression profiles were compared from grnA morphants and control embryos using zebrafish 14K oligonucleotide microarray at 72 hpf, when hepatocytes were rapid proliferating.


title: Transcriptome profiling of cultivar-specific apple fruit ripening and texture attributes

status: Public on Nov 05 2010

city: Wenatchee

first: Yanmin

last: Zhu

state: WA

address: 1104 N. Western Ave

institute: USDA ARS

summary: Molecular events regulating apple fruit ripening and sensory quality are largely unknown.  Such knowledge is essential for genomic-assisted apple breeding and postharvest quality management. In this study, a parallel transcriptome profile analysis, scanning electron microscopic (SEM) examination and systematic physiological characterization were performed on two apple cultivars, Honeycrisp (HC) and Cripps Pink (CP), which have distinct ripening features and texture attributes. Systematic physiological characterization of fruit ripening based on weekly maturity data indicated substantial differences in fruit crispness and firmness at comparable ripening stages. SEM images of fruit cortex tissues prepared from fruits with equivalent maturity suggested that the cell wall thickness may contribute to the observed phenotypes of fruit firmness and crispness. A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50-70-mer isothermal probes, and representing 23,997 UniGene clusters, was manufactured on a Nimblegen array platform. Transcriptome profiling identified a total of 1793 and 1209 UniGene clusters differentially expressed during ripening from cortex tissues of HC and CP, respectively. UniGenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the prominent functional groups. Between the two cultivars, most of the identified UniGenes were similarly regulated during fruit ripening; however, a short list of gene families or specific family members exhibited distinct expression patterns between the two cultivars, which may represent candidate genes regulating cultivar-specific apple fruit ripening patterns and quality attributes.

overall_design: Using a single color labeling system, a total of 24 microarray slides were utilized, one for each cortex tissue sample, for transcriptome profiling analysis. 2 cultivars x 3 developmental stages x 4 biological replicates.

first: Ping

last: Zheng

first: Vijaya

last: Varanasi

first: Dorrie

last: Main

first: Eric

last: Curry

first: James

last: Mattheis


title: Focused transcription profiling of peripheral blood mononuclear cells from vasculitis patients

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Peripheral blood mononuclear cells (PBMCs) from 13 vasculitis patients expressed varying gene profiles.

overall_design: A total of 14 sets of one color arrays were performed.  Four technical replicates were performed for each sample.

first: Tatsunobu

last: Fukushima

first: Takahiro

last: Tougan

first: Tomonori

last: Ishii

first: Shigeto

last: Kobayashi

first: Takashi

last: Akita

first: Hiroshi

last: Nojima


title: Expression data from Streptomyces clavuligerus

city: Delft

first: Wilbert

last: Heijne

address: A.Fleminglaan 1

institute: DSM Biotechnology Center

summary:
To increase production of the important pharmaceutical compounds, both mutagenesis approaches and rational engineering have been extensively applied. Mutagenesis approaches are most popular in industry, but their effects have not yet been studied very well.
Here, we used microarrays to compare the transcriptomes of the S. clavuligerus wild type (ATCC 27064) strain and the DS48802 clavulanic acid high-producer strain, which has been obtained by classical strain improvement (mutagenesis).

overall_design: Streptomyces clavuligerus strains were grown in shake flasks. RNA was extracted after 70h and hybridized to microarrays.

first: Ulrike

last: Müller

first: Marnix

last: Medema

first: Tauqeer

last: Alam

first: Marco

last: van den Berg

first: Axel

last: Trefzer

first: Roel

last: Bovenberg

first: Rainer

last: Breitling

first: Eriko

last: Takano


title: Transcriptome of an intestine-adapted Escherichia coli K-12 mutant selected by animal passage for superior colonization

status: Public on Nov 04 2010

city: Norman

first: Tyrrell

last: Conway

state: OK

address: 101 David L. Boren Blvd.

department: Advanced Center for Genome Technology

institute: University of Oklahoma

summary:
Transcription profiling of wild type E. coli MG1655, intestine-adapted E. coli MG1655star, and E. coli MG1655 flhD mutant grown on glucose, mannose, and mucus.
We previously isolated a spontaneous mutant of E. coli K-12, strain MG1655, following passage through the streptomycin-treated mouse intestine, which has colonization traits superior to the wild-type parent strain (Leatham, et. al., 2005, Infect Immun 73:8039-49) The intestine-adapted strain (E. coli MG1655star) grew faster on several different carbon sources compared to the wild-type and was non-motile due to deletion of the flhD gene. To further characterize E. coli MG1655star, we used several high-throughput genomic approaches. Whole-genome pyrosequencing did not reveal any changes on its genome, aside from the deletion at the flhDC locus, that could explain the colonization advantage of E. coli MG1655star. Microarray analysis revealed modest, yet significant induction of catabolic gene systems across the genome in both E. coli MG1655star and the isogenic flhD mutant. Catabolome analysis with Biolog GN2 Microplates revealed an enhanced ability of both E. coli MG1655star and the isogenic flhD mutant to oxidize a wide variety of carbon sources. The results show that intestine-adapted E. coli MG1655star is more fit than the wild-type for intestinal colonization because loss of FlhD results in elevated expression of genes involved in carbon and energy metabolism, leading to more efficient carbon source utilization, which results in a higher population size in the intestine. Hence mutations that enhance metabolic efficiency confer a colonization advantage.

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

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

overall_design: Three strains were profiled: E. coli MG1655 wildtype, E. coli flhD, and an intestine adapted strain, MG1655star, derived from the wildtype and isolated from feces after 15 days in the streptomycin treated mouse intestine, which proved to be a better colonizer than the wildtype, were grown on MOPS minimal medium containing 0.2% glucose or mannose, or mucus (10 mg/ml) and RNA was extracted from logarithmic phase cultures, and also from mucus grown cells in late log phase.

first: Fabich

last: Andrew

first: Joe

last: Grissom


title: Calcium is a global regulator in Vibrio parahaemolyticus

city: Iowa City

first: Linda

last: McCarter

state: Iowa

address: 3-401 BSB  51 Newton Rd

institute: University of Iowa

summary: Here we probe the global response to calcium in the marine bacterium and pathogen Vibrio parahaemolyticus by using transcriptome, reporter and phenotypic analyses.  Swarming gene expression and motility were enhanced by calcium.  Calcium also stimulated expression and function of one of the organism’s two type three secretion systems (T3SS1 but not the T3SS2). Although low calcium is an inducing signal for the T3SS of many organisms, calcium stimulation of T3SS has not been reported before. EGTA was also a stimulus for T3SS1 expression and activity; however this appeared to be the consequence of iron rather than calcium chelation. LafK, a key regulator of swarming genes, was found necessary for calcium induction of T3SS1 gene transcription and cytotoxicity. Regulation of swarming and T3SS1 were additionally linked by a negative feedback loop propagated by ExsA. Overexpression of exsA was used to probe the extent of the T3SS1 regulon and verify its coincident induction by calcium and EGTA. The calcium transcriptome analysis revealed a calcium-repressed LysR-type transcriptional regulator; CalR was shown to repress swarming and T3SS1 gene expression. Thus in V. parahaemolyticus, calcium influences gene expression and behavior and seems a signal pertinent for surface colonization and virulence.

overall_design: The gene expression profiles of  Vibrio parahaemolyticus cells grown on rich medium or medium supplemented with CaCl2 or EGTA were compared using Affymetrix custom microarrays.

first: Cindy

last: Gode-Potratz

first: Daniel

last: Chodur


title: Identification of testis-relevant genes from testes ESTs and cDNA microarray in the black tiger shrimp

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

summary:
Identification of testis-relevant genes using in silico analysis from testes ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon)
A total of 4,803 ESTs from the testis library were unidirectionally sequenced and analyzed in silico using a customizable data analysis package, ESTplus. A total of 2,702 unique sequences from 424 contigs and 2,278 singletons were identified.  Approximately, 1,134 sequences from the total of 2,702 unique sequences (contigs and singletons) are homologous to genes with known functions. Some of which (mago nashi, insulin-degrading enzyme, actin-depolymerizing factor) are related to testicular development in studies of other organisms.  Moreover, the sequences were further characterized according to the gene ontology categories (41% biological process, 24% molecular function, 35% cellular component).  By comparing with the EST libraries of other tissues, a total of 1,579 possible testis-specific ESTs were identified.  Some of these testis-specific ESTs, such as Phospholipase A2 and Matrix Metalloproteinases, have functions relevant to testicular development. In addition, novel ESTs (621 ESTs) that have never been identified in any ESTs from the Penaeidae family were found in this study.  Through cDNA microarray analysis, some of testis-specific ESTs were preferentially expressed in testes to ovary; one of which was a saposin homolog.   Therefore, saposin was further characterized by real-time PCR and its full-length sequence was obtained by RACE-PCR.

overall_design: A cDNA microarray was constructed from the EST libraries of P. monodon, consisting of 5,376 features (1,125 features were amplified from testis EST libraries). RNA samples were extracted from testes and ovaries of juveniles (4 month-old, pooled from n=112 and n=98 for testes and ovaries, respectively) and broodstocks from Andaman Sea. The RNA from ovary was labeled with Cy3 dye as a reference and that from testes was labeled with Cy5 dye.

first: Thidathip

last: Wongsurawat

first: Rungnapa

last: Leelatanawit

first: Natechanok

last: Thamniemdee

first: Umaporn

last: Uawisetwathana

first: Nitsara

last: Karoonuthaisiri

first: Sirawut

last: Klinbunga


title: Comparative genomics of clinical Candida albicans strains

city: Shanghai

first: Feng

last: Yang

address: Guohe Road

country: China

institute: Second Military Medical University

summary: Candida albicans is the most common fungal pathogen in humans. C.albicans tolerates aneuploidy of all of its chromosomes. Genome plasticity is a hallmark of C.albicans. It is an adaptation strategy of this species. But questions like the extent of such genomic variability, which genes contribute to the divergence, and what mechanisms drive the adaptive genetic change, are not well answered yet.

overall_design: We used array-based comparative genomic hybridization (array CGH; aCGH) to investigate the diversity of gene contents of 8 clinical C.albicans strains of various anatomical origins and genotypes.  One self to self hybridization was included as a control.


title: Livestock-associated MRSA lack accessory virulence determinants of human-associated MRSA

city: Brussels

first: Ricardo

middle: Luis

last: De Mendonca

address: Route de Lennik 808

country: Belgium

institute: ULB - Hôpital Erasme

summary: Previous studies have documented the diversity of genetic background of methicillin-resistant S. aureus (MRSA) strains associated with healthcare (HA-MRSA), community (CA-MRSA) and livestock (LA-MRSA). The accessory and core-variable genome content of those strains remain largely unknown. To compare the composition of accessory and core-variable genome of Belgian MRSA strains according to host, population setting and genetic background, representative strains of HA- (n=21), CA- (n = 13) and ST398 LA-MRSA (n = 18) were characterized by a DNA-microarray (StaphVar Array) composed of oligonucleotide probes targeting ~400 resistance, adhesion and virulence associated genes.ST398 strains displayed very homogenous hybridization profiles (>94% gene content homology) irrespective of their host origin. This “ST398-specific” genomic profile was not distantly demarked from those of certain human-associated lineages but lacked several virulence- and colonization-associated genes harbored by strains of human origin, such as genes encoding proteases, haemolysins or adhesins. No enterotoxin gene was found among ST398 strains. In conclusion, our findings are consistent with a non-human origin of this ST398 lineage but suggest that it might have the potential to adapt further to the human host.

overall_design: CGH microarray was performed on epidemiologically distinct human and animal isolates of methicillin resistant S.aureus. S. aureus labeled genomic DNA were hybridized to StaphVar arrays containing 1326 60mer oligonucleotide probes (Eurogentec, Belgium).

first: Marie

last: Hallin

last: De Mendonça

first: Anne

last: Lefort


title: An initial comparative map of copy number variations in the goat (Capra hircus) genome

status: Public on Nov 09 2010

first: Pier Luigi

last: Martelli

summary:
Background
The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome.
Results
We identified a total of 161 CNVs (an average of 17.9 CNVs per goat), with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs): on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome). These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Genes with environmental functions were over-represented in goat CNVRs as reported in other mammals.
Conclusions
We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs and their effects on behavior, production, and disease resistance traits in goats.

overall_design:
We analysed CNVs in the goat genome by means of a cross-species aCGH experiment using the Roche NimbleGen platform (Roche NimbleGen Inc., Madison, WI; http://www.nimblegen.com) based on custom tiling arrays designed on the bovine (Bos taurus) genome, Btau_4.0 version, including a fraction of BTA13 of the University of Maryland (UMD) Bos taurus v. 2.0 assembly (ftp://ftp.cbcb.umd.edu/pub/data/Bos_taurus/Bos_taurus_UMD_2.0/). Arrays contained ~385,000 probes on a single slide to provide an evenly distributed coverage with an average interval of ~6 kb for the Btau_4.0 genome. The BTA13 of the UMD v. 2.0 assembly was included from nucleotide position 48 M bp to nucleotide position 78 M bp (4,673 oligonucleotides and average spacing of ~6 kb). This chromosome region was analysed as internal control because it contains the ASIP gene, not assembled in the BTA13 of the Btau_4.0 version
Goat genomic DNA was extracted from blood of 2 Camosciata delle Alpi, 3 Girgentana, 3 Saanen, 1 black and 1 brown Murciano-Granadina goats using the Wizard® Genomic DNA Purification kit (Promega Corporation, Madison, WI). All analysed animals were females. Reference DNA sample of one (C1) Camosciata delle Alpi goat was labeled with Cy5 and co-hybridised with the other test DNA samples labelled with Cy3 on 9 different arrays. A self hybridisation (reference labelled by both Cy5 and Cy3) was carried out in another array. Hybridization and array scanning were performed by Roche NimbleGen as previously described. Data normalization was conducted using the normalize.qsline method from the Bioconductor package in R. Then data were analysed for each hybridization using normalized log2 ratios using the CGHweb server (http://compbio.med.harvard.edu/CGHweb/) that includes multiple algorithms.

first: Luca

last: Fontanesi

first: Pier

first: Francesca

last: Beretti

first: Valentina

last: Riggio

first: Stefania

last: Dall'Olio

first: Michela

last: Colombo

first: Rita

last: Casadio

first: Vincenzo

last: Russo

first: Baldassarre

last: Portolano


title: Mapping the binding regions of the cubitus interruptus (Ci) repressor form

status: Public on Nov 03 2010

city: San Francisco

first: Brian

last: Biehs

address: 505 Parnassus Ave

institute: UCSF

type: Genome binding/occupancy profiling by genome tiling array

summary:
Paracrine Hedgehog (Hh) signaling regulates growth and patterning in many Drosophila organs.  We mapped chromatin binding sites for Cubitus interruptus (Ci), the transcription factor that mediates outputs of Hh signal transduction, and we analyzed transcription profiles of control and mutant embryos to identify genes that are regulated by Hh.  Putative targets we identified include several Hh pathway components, most previously identified targets, and many targets that are novel.  Analysis of expression patterns of pathway components and target genes gave evidence of autocrine Hh signaling in the optic primordium of the embryo.  And, every Hh target we analyzed that is not a pathway component appeared to be regulated by Hh in a tissue-specific manner.  We present evidence that Hh-dependent tissue specificity is dependent upon transcription factors that are Hh-independent, suggesting that “pre-patterns” of transcription factors partner with Ci to make Hh-dependent gene expression position-specific.
We utilized the DamID method to identify regions of CiRep methylated genomic DNA in stage 10-11 Drosophila embryos.

overall_design: Comparison of DamCiRep directed methylation vs. Dam Alone background methylation using 3 replicate experiments.

first: Katerina

last: Kechris

first: Song-Mei

last: Liu

first: Thomas

last: Kornberg


title: Identification of novel genes associated with molecular sex differentiation in the embryonic gonads of rainbow trout (Oncorhynchus mykiss)

status: Public on Nov 02 2010

city: Moscow

first: Tim

last: Cavileer

state: ID

address: BioSci LSS 252

department: Biological Sciences

institute: Tim Cavileer

summary: Abstract. The molecular pathways in embryonic vertebrates leading to gonad formation in each sex are incompletely understood. The purpose of this study was to identify novel genes that could be associated with sex-specific gonadal differentiation in a fish, the rainbow trout (Oncorhynchus mykiss). This study was facilitated by a custom microarray based on 7,681 genes derived from embryonic rainbow trout gonad cDNA libraries and public databases. Gonad samples for total RNA isolation were obtained from pvasa-green fluorescent protein (pvasa-GFP) transgenic rainbow between 300 and 700 degree days of development post-fertilization. The transgenic fish permitted the collection of gonads from embryonic rainbow trout during the period of molecular sex differentiation in advance of any morphologically distinguishable characteristics of sex. A bioinformatic method was used with the microarray data that looked for strong associations in gene expression patterns between known sex differentiation genes (the target genes) and novel genes (the target-associated genes) previously not allied with sex differentiation in fishes. The expression patterns of representative targets genes from both sexes and their target-associated genes were independently confirmed by real-time reverse transcription-polymerase chain reaction to support the validity of the bioinformatics method employed. Numerous, novel genes were identified in the gonads of embryonic female and male rainbow trout  that could be involved in sex-specific differentiation pathways in this fish.

overall_design: Embryonic gonads were removed by dissection from known genetic female (XX) and male (XY) rainbow trout (Oncorhynchus mykiss) from a transgenic population where expression of GFP is controlled by vasa-gene regulatory elements (Yoshizaki et al. 2000; Takeuchi et al. 2002). These fish were maintained in incubators containing flowing freshwater (10°C) at the Ooizumi Research Station, Yamanashi, Japan. Ten female or male transgenic rainbow trout were randomly selected every 5 days, beginning at 30 days (i.e., 300 degree days = incubation temperature in °C x number of days) post fertilization through until 70 days (i.e., 700 degree days) post fertilization. The gonads from each sex, at each sampling time, were pooled and immediately frozen for subsequent total RNA isolation.

first: Sam

last: Hunter

first: Tomoyuki

last: Okutsu

first: Goro

last: Yoshizaki

first: James

middle: J

last: Nagler


title: Identification of genetic targets of Hh signaling in Drosophila

summary: Paracrine Hedgehog (Hh) signaling regulates growth and patterning in many Drosophila organs.  We mapped chromatin binding sites for Cubitus interruptus (Ci), the transcription factor that mediates outputs of Hh signal transduction, and we analyzed transcription profiles of control and mutant embryos to identify genes that are regulated by Hh.  Putative targets we identified include several Hh pathway components, most previously identified targets, and many targets that are novel.  Analysis of expression patterns of pathway components and target genes gave evidence of autocrine Hh signaling in the optic primordium of the embryo.  And, every Hh target we analyzed that is not a pathway component appeared to be regulated by Hh in a tissue-specific manner.  We present evidence that Hh-dependent tissue specificity is dependent upon transcription factors that are Hh-independent, suggesting that “pre-patterns” of transcription factors partner with Ci to make Hh-dependent gene expression position-specific.

overall_design: Analysis of the expression profiles of loss of function mutantations in core components of the Hh signaling pathway. A total of 14 samples were analysed consisting of comparisons of hh-, ci-, smo-, ptc-, and Cim1-m4 (Activator) mis-expression embryos compared to wt sibling embryos.


title: Mapping the binding regions of the cubitus interruptus (Ci) activator form

summary:
Paracrine Hedgehog (Hh) signaling regulates growth and patterning in many Drosophila organs.  We mapped chromatin binding sites for Cubitus interruptus (Ci), the transcription factor that mediates outputs of Hh signal transduction, and we analyzed transcription profiles of control and mutant embryos to identify genes that are regulated by Hh.  Putative targets we identified include several Hh pathway components, most previously identified targets, and many targets that are novel.  Analysis of expression patterns of pathway components and target genes gave evidence of autocrine Hh signaling in the optic primordium of the embryo.  And, every Hh target we analyzed that is not a pathway component appeared to be regulated by Hh in a tissue-specific manner.  We present evidence that Hh-dependent tissue specificity is dependent upon transcription factors that are Hh-independent, suggesting that “pre-patterns” of transcription factors partner with Ci to make Hh-dependent gene expression position-specific.
We utilized the DamID method to identify regions of CiAct methylated genomic DNA in stage 10-11 Drosophila embryos.

overall_design: Comparison of DamCiAct directed methylation vs. Dam Alone background methylation using 3 replicate experiments.


title: mirna_nitrogen-To discover miRNA implied following a Nitrogen starvation and after re-supply.

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: adt06-04_mirna_nitrogen - mirna_nitrogen - Nitrogen starvation and re-supply. - To discover miRNA implied following a deficiency out of nitrogen and after reinduction.

overall_design: 6 dye-swap - time course

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: DNA methylation analysis by MeDIP-on-chip in mouse E3.5 blastocysts, E6.5 epiblasts and E9.5 whole embryos.

status: Public on Nov 01 2010

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

type: Methylation profiling by genome tiling array

summary:
DNA methylation is extensively reprogrammed during early phases of mammalian development yet individual genomic targets of this process are largely unknown.
We optimized MeDIP (Methylated DNA Immunoprecipitation) for low numbers of cells and profiled DNA methylation genome-wide during early development of the mouse embryonic lineage in vivo.

overall_design:
We mapped DNA methylation at 3 consecutive stages of early development: E3.5 blastocysts, E6.5 epiblasts and E9.5 whole embryos.
MeDIP and Input samples were hybridized to Nimblegen HD2 MM8 promoter deluxe arrays covering 12 kb of all gene promoters.
Experiments were performed in duplicates for E3.5 blastocysts and triplicates for E6.5 epibalsts and E9.5 embryos.
As a control we also hybridized pooled unamplified MeDIPs from E9.5 to Nimblegen 385K MM8 RefSeq promoter arrays.

first: Julie

last: BORGEL

first: Sylvain

last: GUIBERT

last: WEBER


title: Expression profiling of ligand-stimulated wild type and tamoxifen-resistant MCF-7

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN RCAI

summary: Quantitative phosphoproteome and transcriptome analysis of ligand-stimulated MCF-7 human breast cancer cells was performed to understand the mechanisms of tamoxifen resistance at a systems level. Phosphoproteome data revealed that wild type (WT) cells were more enriched with phospho-proteins than tamoxifen-resistant (TamR) cells after stimulation with ligands. Surprisingly, decreased phosphorylation after ligand perturbation was more common than increased phosphorylation. In particular, 17beta-estradiol (E2) induced down-regulation in WT cells at a very high rate. E2 and the ErbB ligand, heregulin (HRG) induced almost equal numbers of up-regulated phospho-proteins in WT cells. Pathway and motif activity analyses using transcriptome data additionally suggested that deregulated activation of GSK3B　(glycogen synthase kinase 3 beta) and MAPK1/3 signaling might be associated with altered activation of CREB and AP-1 transcription factors in TamR cells and this hypothesis was validated by reporter assays. An examination of clinical samples revealed that, inhibitory phosphorylation of GSK3B at serine 9 was significantly lower in tamoxifen-treated breast cancer patients that eventually had relapses, implying that activation of GSK3B may be associated with the tamoxifen resistant phenotype. Thus, the combined phosphoproteome and transcriptome dataset analyses revealed distinct signal-transcription programs in tumor cells and provided a novel molecular target to understand tamoxifen resistance.

overall_design: The MCF-7 human breast cancer cell line and tamoxifen-resistant MCF-7 cells were stimulated by the growth hormone heregulin (HRG) or 17beta-estradiol (E2) in the presence or absence of tamoxifen. Control was set as non-treated cells.

last: Okada-Hatakeyama


title: ZNF274 colocalizes with the histone methyltransferase SETDB1 at ZNF 3' ends.

city: Seattle

first: Vitalina

last: Komashko

address: 1100 Fairview Ave N

institute: Sage Bionetworks

summary: Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factors that drive different cellular lineages.  Several histone modifications have been associated with gene silencing, including H3K27me3 and H3K9me3. We have previously shown that the two largest classes of mammalian transcription factors are marked by distinct histone modifications; homeobox genes are marked by H3K27me3 and zinc finger genes are marked by H3K9me3. Several histone methyltransferases (e.g. G9a and SETDB1) may be involved in mediating the H3K9me3 silencing mark. We have used ChIP-chip and ChIP-seq (GSE24632) to demonstrate that SETDB1, but not G9a, is associated with regions of the genome enriched for H3K9me3. A current model is that SETDB1 is recruited to specific genomic locations via interaction with the corepressor TRIM28 (KAP1), which is in turn recruited to the genome via interaction with zinc finger transcription factors that contain a Kruppel-associated box (KRAB) domain. However, specific KRAB-ZNFs that recruit TRIM28 (KAP1) and SETDB1 to the genome have not been identified. We now show that ZNF274 (a KRAB-ZNF that contains 5 C2H2 zinc finger domains), can interact with KAP1 in vitro and, using ChIP-seq, we show that ZNF274 binding sites co-localize with SETDB1, KAP1, and H3K9me3 at the 3’ ends of zinc finger genes. Knockdown of ZNF274 with siRNAs reduced the levels of KAP1 and SETDB1 recruitment to the binding sites. These studies provide the first identification of a KRAB domain-containing ZNFs that is involved in recruitment of the KAP1 and SETDB1 to the human genome.

overall_design: This study includes the 4 ChIP-chip arrays only.

first: Seth

last: Frietze

first: Peggy

last: Farnham


title: Nutrient-regulated transcriptional responses in the brown tide forming alga Aureococcus anophagefferens

city: Woods Hole

first: Sonya

last: Dyhrman

address: 266 Woods Hole Road

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Relatively little is known about the presence and regulation of pathways involved in nutrient acquisition in the brown tide forming alga, Aureococcus anophagefferens.  In this study, Long-SAGE (Serial Analysis of Gene Expression) was used to profile the A. anophagefferens transcriptome under nutrient replete (control), and nitrogen (N) and phosphorus (P) deficiency with the goal of understanding how this organism responds at the transcriptional level to varying nutrient conditions.  This approach has aided A. anophagefferens genome annotation efforts and identified a suite of genes up-regulated by N and P deficiency, some of which have known roles in nutrient metabolism.  Genes up-regulated under N deficiency include an ammonium transporter, an acetamidase/formamidase, and two peptidases.  This suggests an ability to utilize reduced N compounds and dissolved organic nitrogen, supporting the hypothesized importance of these N sources in A. anophagefferens bloom formation.  There are also a broad suite of P-regulated genes, including an alkaline phosphatase, and two 5’-nucleotidases, suggesting A. anophagefferens may use dissolved organic phosphorus under low phosphate conditions.  These N- and P-regulated genes may be important targets for exploring nutrient controls on bloom formation in field populations.

overall_design: Aureococcus anophagefferens CCMP 1984 was obtained from the Provasoli-Guillard Center for the Culture of Marine Phytoplankton (CCMP).  The cultures were grown at 18C on a 14 h:10 h light:dark cycle (140 µmol quanta m-2 s-1).  Nitrogen- and phosphate-replete (883 µM NO3- and 36.3 µM PO43-) cells, –N (40 µM NO3-) cells, and –P (1 µM PO43-) cells were grown in autoclaved L1 media with no Si (Guillard and Hargraves 1993), prepared using 0.2 µm filtered Vineyard Sound seawater.  Vitamins (thiamine, biotin, and B12) were sterile filtered and added to the media after autoclaving.  Replete cells were harvested during mid log phase of growth, while –N and –P cells were harvested at the onset of stationary phase when N or P was depleted.

first: Louie

last: Wurch

first: Sheean

middle: T

last: Haley

first: Elizabeth

middle: D

last: Orchard

first: Christopher

last: Gobler


title: Group A Streptococcus Gene Expression in Humans with Pharyngitis Using a Microarray

city: San Antonio

first: Jeffrey

last: Livezey

address: 3400 Rawley E Chambers Ave

department: Clinical Investigation

institute: Brooke Army Medical Center

summary: This study represents the first in vivo genome wide analysis of gene epxression of Group A Streptococcus (GAS) in humans with pharyngitis. The micorarray used is a custom microarray that relies on an electrochemical reaction as the measured signal rather than flourescence. Distinct clusters of gene expression were discovered and analyzed.  A functional analysis examining differences and similarities between the clusters was performed.

platform_organism:
Streptococcus pyogenes M1 GAS
Streptococcus pyogenes SSI-1
Streptococcus pyogenes MGAS315
Streptococcus pyogenes MGAS5005
Streptococcus pyogenes MGAS6180
Streptococcus pyogenes MGAS9429
Streptococcus pyogenes MGAS2096
Streptococcus pyogenes MGAS10750

overall_design: Samples were taken from pediatric patients who had received a throat swab as part of their clinical care for evaluating pharyngitis.  Eleven samples that were culture postive for GAS were used along with 3 samples from subjects who were GAS culture negative. The microarray was a composite comprised of 12,000 probes, representing 2724 GAS open reading frames belonging to serotypes M1, M3, M4, M12, and M28.  There were 1671 probe sets that were homologous for the M1 serotype and represented over 95% of the total predicted coding region.   Probe sets were 30-40mers in length and were selected using a Combimatrix probe selection algorithm taking into account gene (>90% BLAST score) and serotype specificity, Tm, hairpins and GC content. In addition, 70 Combimatrix built in probes were used as negative controls for background subtraction.

middle: R

first: Luis

last: Perez

first: Dominic

last: Suciu

first: Brian

last: Robinson

first: David

last: Bush

first: Gerald

last: Merrill


title: Large intergenic non-coding RNAs as novel modulators of reprogramming: human embryonic stem cells, CD34+ cells, and CD34+ derived induced pluripotent stem cells (LincRNA expression)

city: Cambridge

first: Nataly

middle: Moran

last: Cabili

address: 7  Cambridge Center

institute: Broad Institute ;  Harvard University

type: Non-coding RNA profiling by genome tiling array

summary: LincRNA expression profiles of human embryonic stem cells, CD34+ cells, and CD34+ derived induced pluripotent stem cells

overall_design:
Total RNA was extracted from human ESCs, CD34+ cells, and CD34+ derived iPSC lines, then hybridized to Nimblegen tiling array
GPL8792; Human lincRNA 391k Tiling Array V2

first: Sabine

last: Loewer

first: George

middle: Q

last: Daley

first: John

middle: L

last: Rinn


title: Human LSD2/KDM1b/AOF1 regulates gene transcription by modulating intragenic H3K4me2 methylation (ChIP-chip)

city: Boston

first: Yujiang

last: Shi

address: 221 Longwood Ave

department: Medicine

institute: Brigham & Women's Hospital

summary: Dynamic histone H3K4 methylation is an important epigenetic component of transcriptional regulation. However, most of our current understanding of this histone mark is confined to regulation of transcriptional initiation. We now show that human LSD2/KDM1b/AOF1, the human homolog of LSD1, is a novel H3K4me1/2 demethylase that specifically regulates histone H3K4 methylation within intragenic regions of its target genes. Genome-wide mapping reveals that LSD2 associates predominantly with the gene bodies of actively transcribed genes, but is markedly absent from promoters. Depletion of endogenous LSD2 results in an increase of H3K4me2 as well as a decrease of H3K9me2 at LSD2 binding sites, and a consequent dysregulation of target gene transcription. Furthermore, characterization of LSD2 complex revealed that LSD2 forms active complexes with euchromatic histone methyltransferases EHMT1/2 and NSD3 as well as cellular factors involved in active transcription elongation. These data provide a possible molecular mechanism linking LSD2 to transcriptional regulation post initiation.

overall_design: Native chromatin of HeLa-S stably expressing FgHA-LSD2 was prepared by micrococcal nuclease digestion as previously described (Umlauf et al., 2004), and was primarily composed of mono-, di-, and tri-nucleosomes. Native chromatin fragments were sequential immunoprecipited using anti-flag and anti-HA agarose beads (Sigma). After extensive washing, Flag or HA peptides (Sigma) were used for elution after each immunoprecipitation. DNA from the final step was purified and processed for tiling array hybridization to Human Genome tiling 2.0 Array (Affymetrix) per manufacture’s instructions. Input DNA was used as control. Regions enriched by TAP N-ChIP were identified using algorithm Model-Based Analysis of Tiling arrays (MAT) (Johnson et al., 2006), and displayed by Integrated Genome Browser (IGB). CEAS (cis-element annotation system) was used for statistic analysis of the distribution pattern of LSD2 binding sites on promoter and non-promoter regions (Ji et al., 2006). To estimate the statistical significance of colocalization between LSD2 and histone modification marks previously identified (Barski et al., 2007), we estimated the null distribution of overlap by generating 100 randomly permutated sample of the histone modification loci and the overlap is calculated for each permutated sample.

first: Shi

last: Yujiang

first: Fang

last: Rui


title: Large intergenic non-coding RNAs as novel modulators of reprogramming: human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells (LincRNA expression)

summary:
Expression profiling of non coding RNAs using tilling arrays from ES, Fibroblasts and Fibroblasts derived iPSC
LincRNA profiles of human embryonic stem cells, fibroblasts, and fibroblast-derived induced pluripotent stem cells

overall_design:
Total RNA was extracted from human ESCs, fibroblast, and fibroblast-derived iPSC lines, then hybridized to Nimblegen tiling array
GPL8791; Human lincRNA 364k Tiling Array V1


title: Analysis of germination and outgrowth of sorbic acid-stressed Bacillus cereus ATCC 14579 spores.

city: Wageningen

first: Clint

last: van Melis

address: Bomenweg 2

department: Agro- & Food Science Group

institute: Wageningen University and Research centre

summary: Sorbic acid (SA) is widely used as a preservative, but the effect of SA on spore germination and outgrowth has gained limited attention up to now. Therefore, the effect of sorbic acid on germination of spores of B. cereus strain ATCC 14579 was analyzed both at phenotype and transcriptome level. Spore germination and outgrowth was assessed at pH 5.5 without and with 0.75, 1.5 and 3.0mM (final concentrations) undissociated sorbic acid (HSA). This resulted in distinct HSA concentration-dependent phenotypes, varying from delays in germination and outgrowth to complete blockage of germination at 3.0mM HSA. The phenotypes reflecting different stages in the germination process could be confirmed using flow cytometry and could be recognized at transcriptome level by distinct expression profiles. In the absence and presence of 0.75 and 1.5mM HSA, similar cellular ATP levels were found up to the initial stage of outgrowth, suggesting that HSA-induced inhibition of outgrowth is not caused by depletion of ATP. Transcriptome analysis revealed the presence of a limited number of transcripts in dormant spores, outgrowth related expression, and genes specifically associated with sorbic acid stress, including alterations in cell envelope and multi-drug resistance. The potential role of these HSA-stress associated genes in spore outgrowth is discussed.

overall_design: Per concentration of undissociated sorbic acid (0, 0.75, and 1.5mM) four exposure times (10, 30, 60, and 120 minutes) were each compared with dormant spores (i.e., t0). The experiments were performed in duplicate and the duplicate samples were hybridized with a dye-swap

first: Masja

last: Nierop Groot

first: Marcel

last: Tempelaars

first: Roy

last: Moezelaar

first: Tjakko

last: Abee


title: Transcriptional profiling of six normal Angus tissues

city: St. Paul

last: Garbe

state: MN

address: 1988 Fitch Ave

department: Animal Science

institute: University of Minnesota

summary: Transcriptional profiling of six bovine tissues (small intestine, spleen, liver, adrenal gland, anterior pituitary, and thymus). Samples collected from each of 6 Angus steers at 14 months of age. Experiment was duplicated at two locations to measure reproducability of results.

overall_design: Six tissues, six biological replicates, and two technical replicates of each sample for a total of 72 samples. The experiment was run seperatly at two different locations, for a total of 144 samples.

first: Christine

last: Elsik

first: James

last: Reecy

first: Karl

last: Clark

first: Robert

last: Schnabel

first: C

last: Dickens

first: Russell

last: Wolfinger

first: Scott

middle: C

last: Fahrenkrug

first: Jeremy

middle: F

last: Taylor


title: Expression profiling analysis of brain from ADAR2 mutant mice

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum München GmbH

summary:
ADARs, short for adenosine deaminases acting on RNA, were first found by their characteristic activity of deaminating up to 50% of all adenosines in double-stranded RNA in vitro. C. elegans has two ADARs, only one is found in the fly, and mammals express three ADARs. Importantly, the spectrum of physiological roles of these enzymes in the different organisms remains largely unknown. ADARs are ~750-1150 amino acids in size, feature 2-3 N-terminal double-stranded RNA binding motifs, an enzymatic domain related to that of prokaryotic cytidine deaminases, and a ~190 residue extended C-terminal domain of unknown function. The mammalian ADARs are detectable in many if not all tissues, with relatively prominent expression in the central nervous system, predicting tissue- or cell type-specific tasks for the mammalian ADARs.
Studies over the last decade collectively indicated that one function of ADARs is the editing of nuclear transcripts to introduce select amino acid substitutions in proteins. Arguably the best-studied example for this type of RNA editing (‘A-to-I editing’) in the mammal is performed by ADAR2 and occurs in primary transcripts for the GluA2 subunit (also known as GluR-B or GluR2 subunit) of AMPA receptors mediating fast excitatory neurotransmission. A particular glutamine codon (CAG) in the exonic sequence for the inner lining of the glutamate-activated AMPA receptor is converted by deamination of the central adenosine into an unusual arginine codon (CIG; the resultant inosine is seen as guanosine by the protein translation machinery). This substitution of the gene-encoded glutamine codon by the edited arginine codon is found in nearly 100% of all GluA2 cDNA derived from brain mRNA. RNA editing in this instance ensures that GluA2-containing AMPA receptors become impermeable to Ca2+.
In addition to switching a key functional determinant in GluA2 to nearly 100%, ADAR2 has been implicated in generating numerous amino acid substitutions at lower levels in various mammalian neurotransmitter receptors and voltage-gated ion channels, primarily but not exclusively of nervous tissue. Most of these substitutions elicit distinct functional consequences, which led to the notion that site-selective RNA editing by ADAR2 may ensure the functional fine-tuning of the affected transmembrane proteins. Such fine-tuning should reflect the expansion of the protein sequence directed by the respective gene into sequence subpopulations, each differing in particular functional aspects, such as transmitter efficacy, desensitization, or voltage threshold. If this notion is correct, ADAR2 knockout should elicit phenotypes, which might range from subtle to severe, depending on the physiological role(s) of the ADAR2 targets in different tissues.
ADAR2 knockout mice, however, die soon after birth from severe epileptic seizures, a consequence of the changed ion conductance properties of AMPA receptors containing unedited GluA2. Fortunately, mice lacking ADAR2 are robust and have normal life span if they carry GluA2 alleles genetically altered to contain the particular arginine codon for a Ca2+ impermeable ion channel pore of AMPA receptors, thus rescinding the need for ADAR2-mediated GluA2 transcript editing. These mice are thus eminently suitable to study the phenotypic consequences of failure to edit all ADAR2 targets excepting GluA2. We therefore tested cohorts of ADAR2-/-/GluA2(R)/(R) mice in 16 well-established paradigms for central and peripheral phenotypic abnormalities. We report that we found few differences to control mice (GluA2(R)/(R)) and hence, the lack of ADAR2 appears not to affect most of the physiological functions tested.

overall_design: Brain of four mutant animals of ADAR-/-/GluR-BR/R versus a pool of four reference (wildtype) mice; two technical replicates for each mutant mouse including a dye swap experiment - in total 8 chip hybridisations

first: Johannes

last: Beckers

first: Marion

last: Horsch

first: Peter

last: Seeburg


title: ACTH-independent macronodular adrenocortical hyperplasia (AIMAH)

status: Public on Oct 30 2010

city: Bethesda

first: Madson

last: Almeida

address: 10 Center Drive, MSC 1103

department: Section on Genetics and Endocrinology / NICHD

institute: NIH

summary: ACTH-independent macronodular adrenal hyperplasia (AIMAH) is a clinically and genetically heterogeneous disorder that can be associated with aberrant hormone receptors. Whole-genome expression profiling was analyzed in samples of different nodules from a patient with AIMAH.

overall_design: Total RNA obtained from adrenal nodules were compared to those samples obtained normal adrenal pools

first: M

last: Nesterova

last: Stratakis

last: Cheadle

first: T

last: Watkins


title: Murine bone-marrow derived macrophages: Wild type Control vs. DICER1 (Dcr1) hypomorphic cells.

status: Public on Oct 31 2010

city: Singapore

last: Nissom

address: 20 Biopolis Way

institute: Bioprocessing Technology Institute

summary:
This study aims to identify miRNA molecules that are involved in inflammatory response in macrophages. A miRNA expression profiling of mouse macrophages comparing control wild type cells with DICER hypomorphic cells were conducted after these were subjected to treatment with LPS.

Keywords: miRNA; DICER hypomorphic macrophages, microarray

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Pairwise comparison of Control versus DICER1 (Dcr1) hypomorphic cells. Two biological replicates were performed with three technical replicates for each biological replicate: 1 Control, 1 DICER1 (Dcr1) hypomorph, 2 treatment conditions. Exposed to LPS, harvested at 2hr and 4hr post treatment.

first: Subhra

last: Biswas

middle: M


title: Gene expression based, effect of DNA minor groove binding ligand on human cells in response to ionizing radiation

city: Delhi

first: Vibha

last: Tandon

state: Delhi

address: University of Delhi

department: Department of Chemistry

country: India

institute: University of Delhi

summary: Radiation induced DNA damage initiates a complex series of overlapping responses responsible for the maintenance of genome integrity. The data reports the expression analysis in response to DNA minor groove binding ligand with an emphasis on its ability to afford better protection in cells exposed to ionizing radiation.

overall_design: Four different types if samples were employed in analysis- Control i.e. untreated cells, 50µM ligand treated cells, 8.5Gy radiation treated cells, cells treated with 50µM ligand one hour prior to irradiation.

first: Navrinder

last: Kaur


title: To study the molecular mechanism of DNA minor groove binding ligand as a radiaiton modulator

overall_design: Four different types if samples were employed in analysis- Control i.e. untreated cells, 50µM ligand treated cells, 2Gy radiation treated cells, cells treated with 50µM ligand one hour prior to 2 Gy irradiation.

first: Atul

last: Ranjan


title: miRNA profile of Neonatal Rat Cardiomyocytes treated with 0.5% or 1.5% Oxygen for 48 h versus Normoxia

status: Public on Oct 28 2010

city: Chicago

first: Raja

last: Mutharasan

address: 303 E Chicago Ave

institute: Northwestern University

summary: The Purpose of this study is to screen for microRNAs regulated by hypoxia in neonatal rat cardiomyocytes.

platform_organism:
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: 3 biological replicates were perfomed for each each group, normoxia and hypoxia.  One normoxic and one hypoxic sample was hybridized to each chip for a total of 6 2-color experiments.  A dye swap for each oxygen treatment were performed.


title: Gene expression under low O2 in Synechocystis sp. PCC 6803 wild type and hik31 mutant

city: Dunedin

first: Tina

last: Summerfield

address: 464 Great King Street

department: Botany

country: New Zealand

institute: University of Otago

summary: We have investigated the response of the cyanobacterium Synechocystis sp. PCC 6803 during growth at very low O2 concentration (bubbled with 99.9% N2/0.1% CO2).  Significant transcriptional changes upon low O2 incubation included up-regulation of a cluster of genes that contained psbA1 and an operon that includes a gene encoding the two-component regulatory histidine kinase, Hik31.  This regulatory cluster is of particular interest, since there are virtually identical copies on both the chromosome and on plasmid pSYSX.  We used a knockout mutant lacking the chromosomal copy of hik31 and studied differential transcription during the aerobic- low O2 transition in this ΔHik31 strain and the wild type.  We observed two distinct responses to this transition, one Hik31 dependent, the other Hik31 independent.  The Hik31 independent responses included the psbA1 induction and genes involved in chlorophyll biosynthesis.  In addition, there were changes in a number of genes that may be in involved in assembling or stabilizing Photosystem II (PSII), and the hox operon and the LexA-like protein (Sll1626) were up-regulated during low O2 growth.  This family of responses mostly focused on PSII and overall redox control.  There was also a large set of genes that responded differently in the absence of the chromosomal Hik31.  In the vast majority of these cases, Hik31 functioned as a repressor and transcription was enhanced when Hik31 was deleted.  Genes in this category encoded both core and peripheral proteins for Photosystem I and PS II, the main phycobilisome proteins, chaperones, the ATP synthase cluster and virtually all of the ribosomal proteins.  These findings, coupled with the fact that ΔHik31 grew better than the wild-type under low O2 conditions, suggested that Hik31 helped to regulate growth and overall cellular homeostasis.  We detected changes in the transcription of other regulatory genes that may compensate for the loss of Hik31.  We conclude that Hik31 regulates an important series of genes that relate to energy production and growth and that helps to determine how Synechocystis responds to changes in O2 conditions.

overall_design: The microarray experiment involved a loop design that compared the wild type and the ΔHik31 strain under aerobic conditions and 1 h following a transition to low oxygen by using an ANOVA model. RNA was extracted from three biological replicates of both the wild type and the ΔHik31 mutant. The three replicates of each strain were grown in a photobioreactor with air bubbling and then bubbled with a 99.9% nitrogen/0.1% carbon dioxide mix. Cells were harvested for RNA extraction at t0, prior to bubbling with nitrogen/carbon dioxide and at t1 after 1 h of nitrogen/carbon dioxide bubbling.


title: Mouse Dendritic and Antigen Presenting Cell RT² Profiler PCR

city: Doylestown

first: Saifur

last: Rahman

state: PA

address: 3805 Old Easton Rd

department: Microbiology and Immunology

institute: Drexel University

summary: Infection of mouse bone marrow Flts3L-derived dendritic cells (FL-DCs) with chimeric human T cell leukemia virus type 1 (HTLV-1) results in the upregulation as well as selective downregulation of various DC-specific genes.

overall_design: Mouse bone marrow Flt3L-derived dendritic cells were infected with chimeric HTLV-1 and analyzed for the expression of various DC-specific genes after 12 hours. The expression of various genes was compared to the control (non-infected) cells.

first: Zafar

last: Khan

first: Pooja

last: Jain


title: Mouse Interferon α, β RT² Profiler PCR

summary: Infection of mouse bone marrow Flts3L-derived dendritic cells (FL-DCs) with chimeric human T cell leukemia virus type 1 (HTLV-1) results in the upregulation as well as selective downregulation of various interferon-stimulated genes.

overall_design: Mouse bone marrow Flt3L-derived dendritic cells were infected with chimeric HTLV-1 and analyzed for the expression of type 1 interferon-stimulated genes after 4 hours. The expression of various genes was compared to the control (non-infected) cells.


title: affy-agro-bi-medicago-AGRO-BI-Toulouse

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary:
affy_agro-bi_medicago - Identification of genes from the model legume Medicago truncatula whose expression is affected by the plant nitrogen status, with or without inoculation with the symbiotic bacteria Sinorhizobium meliloti. - Comparison of the supernodulant, nitrogen-insensitive, sunn-2 mutant with the A17 wild type genotype.-The plant root systems of plants were split into two parts, each one being installed in a separate compartment. For the “S” treatment, one part was supplied with 10 mM NH4NO3 while the other part was supplied with a nitrogen-free nutrient solution. For the “L” treatment, one part was supplied 0.5mM NO3- and the other part was supplied with the nitrogen free solution. Eight biological materials (designated AL, AS, SL, SS, IL, IS, NIL, NIS), with three biological repeats for each, were collected and analyzed. The effects of the S and L conditions were investigated on wild-type A17 (AL vs. AS) and sunn-2 mutant plants (SL vs. SS); one set of A17 plants was inoculated with Sinorhizobium meliloti (IL vs. IS), harvested at four days post inoculation and compared to non-inoculated plants (NIL vs. NIS).

Keywords: growth in nitrogen-sufficient (s) vs. nitrogen-limited (l) conditions

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: 18 arrays - Medicago

first: Sandra

last: Moreau

first: Sandrine

last: Balzergue

first: Pascal

last: Gamas

first: Marie-Laure

last: Martin-Magniette


title: Reference:  MicroRNA expression profiling in adult mouse liver following BaP treatment [Agilent miRNA array]

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

summary:
We have investigated the effect of exposure to 150 mg/kg benzo(a)pyrene (BaP) for 3 days on mRNA and miRNA expression levels in adult mouse liver. We used Agilent miRNA array platforms to assess effects of BaP exposure on miRNA expression levels. Our results indicate a distinct lack of effect of BaP of miRNA expression, despite widespread changes in mRNA levels. The data in the attached array files were used a positive control for the Agilent platform, to indicate that the platform was able to detect significant differences in abundance of miRNA between two samples with great differences in miRNA content.

Keywords: Toxicology, miRNA

overall_design: Two reference pools were created from commercially available reference RNA (FirstChoice® mouse Total RNA including the small fraction (Catalogue # AM7800-AM7828, Ambion, Streetsville, ON)). Reference #1 contained equal parts of mouse testicle, ovary and 10-12 day embryo. Reference #2 contained liver, heart and lung. These references were hybridized to a single mouse Agilent 8x15K miRNA array (4 replicates each), normalized by cyclic lowess and analysed with MAANOVA to find differences in the samples.One reference #1 sample was not included in the analysis because it did not pass Agilent quality control metrics.

first: Carole

last: Yauk

first: Kelly

last: Jackson

first: Morie

last: Malowany


title: Transcriptome analysis of Ciona intestinalis to identify genes expressed in the adult organs.

status: Public on Oct 27 2010

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

institute: Okayama University

summary: Among urochordates (tunicates)—the closest living relatives of vertebrates—Ciona intestinalis is increasingly being used as a model organism in the field of developmental biology. Ciona intestinalis is the seventh animal which genome published; the ~120-Mbp euchromatin region is estimated to contain ~16,000 protein-coding genes. In addition, analyses of more than one million ESTs have provided the foundation for gene models and associated transcriptomes. The fertilized Ciona intestinalis egg develops into a tadpole larva with a simplified chordate body plan, and then it metamorphose into adult sea squirt of sessile filter feeder. One of interests in the field of developmental biology is to understand what kind of genes are expressed in the body and how spatially and/or temporally coordinated expression of genes is controlled. In this study, we investigated the entire gene expression of 11 organs of adult Ciona; the neural complex, branchial sac, esophagus, stomach, endostyle, intestine, body-wall muscle, heart, blood cells, ovary, and testis. Our data would provides basic information of transcriptome in each organ and help to understand gene expression control of organ specific genes.

overall_design: Gene expressions in 11 organs of adult Ciona intestinalis; blood cells, branchial sac, intestine, endostyle, esophagus, heart, body-wall muscle, neural complex, ovary, stomach and testis. Three independent experiments were performed at each tissue using different individuals for each experiment.

first: Manabu

last: Fujie

first: Eiich

last: Shoguchi

first: Nori

last: Satoh


title: Comparative transcriptome analysis of 16M and its vjbR mutant under a condition simulating environments of macrophage

city: Beijing

first: Zeliang

last: Chen

address: NO. 20,Dongdajie

institute: Beijing Institute of Disease Control and Prevention

summary: Quorum sensing system (QS) is a global regulator that regulates gene expression in response to cell density and other environmental factors. Two QS genes have been identified in Brucella, one of which (vjbR) is involved in Brucella intracellular survival and virulence. But the regulation mechanism of Brucella intracellular survival by the vjbR remains unknown.To characterize the regulation roles of vjbR, the in vitro vjbR induction conditions simulating intracellular environments were firstly defined, and then, transcriptome of the vjbR mutant is compared to that of the wild type strain. The vjbR gene was highly activated under acidified nutrition limitation condition. Comparative transcriptome analysis showed that a total of 126 genes were greatly differentially expressed in the vjbR mutant.

overall_design: 2 wild type samples and 2 vjbR mutant samples were analyzed.

first: Qing

last: Qu

first: Zhijun

last: Zhong

first: Xiaotao

last: Zeng

first: Dongsheng

last: Zhou