title: A new structural paradigm in copper resistance in a human pathogen

status: Public on May 24 2013

city: Bloomington

first: Krystyna

middle: M

last: Kazmierczak

state: IN

address: 1001 E. Third St.

department: Biology

country: USA

institute: Indiana University

summary: Copper is essential for both innate and adaptive immune function and copper resistance has emerged as an important determinant of virulence of microbial pathogens. In the human pathogen Streptococcus pneumoniae (Spn), cytoplasmic copper resistance is mediated by an operon encoding the copper-responsive repressor CopY, CupA, of unknown function, and CopA, a copper effluxing P1B-type ATPase. We show that CupA is a novel cell membrane-anchored Cu(I) chaperone for CopA, and that a Cu(I)-binding competent, membrane-localized CupA, like CopA, is obligatory for copper resistance.

overall_design:
Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) at 37C in an atmosphere of 5% CO2 to a culture density of OD620~0.2 and were processed as described in the related Sample record. Strain IU1781 (D39 rpsL1) served as the reference for the strain comparison. The experiment was repeated one time, and results are consistent with those observed by Shafeeq et al (Mol Microbiol. 2011).

Data normalization was performed using the BioArray Software Environment (BASE 1.2; Saal et al, Genome Biol. 2002) using the Lowess (subgrid) method.  Median spot intensities were normalized without background subtraction and used to calculate expression ratios. The cut-off for statistical significance of differential expression was set at an average up or down fold change of at least 1.8 fold.

first: Yue

last: Fu

first: Tiffany

last: Tsui

first: Kevin

middle: E

last: Bruce

first: Lot-To

last: Sham

first: Khadine

middle: A

last: Higgins

first: John

middle: P

last: Lisher

first: Michael

middle: J

last: Maroney

first: Charles

last: Dann

first: Malcolm

last: Winkler

first: David

last: Giedroc


title: Mechanisms of response to silver nanoparticles Enchytraeus albidus (Oligochaeta): survival, reproduction and gene expression profile

status: Public on May 22 2013

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

country: Portugal

institute: CESAM & University of Aveiro

summary: Due to its antimicrobial activity, silver nanoparticles (Ag-NPs) are among the most used NPs worldwide, yet little information is available regarding their effects, particularly in soil dwelling organisms. Enchytraeids (Oligochaeta) are important members of the soil fauna which actively contribute to the acceleration of organic matter decomposition and nutrient recycling processes. Hence, for hazard and risk assessment it is important to provide toxicity data for these organisms and to understand more in regard to the mode of action of Ag-NPs within organism. To study this we conducted toxicity experiments using the OECD standard guideline, testing Ag-NPs and AgNO3, having assessed survival, reproduction and differential gene expression. Population toxicity responses were assessed showing higher toxicity for the AgNO3. In an attempt to understand the mode of action we performed transcription profiling using the microarray.

overall_design: Gene expression profile of Enchytraeus albidus was analysed after 2 days of exposure to 100 and 200 mg/kg of two silver forms (nanoparticles and salt_silver nitrate) in OECD soil. Three biological replicates per test treatment and control (clean OECD soil) were used.

first: Amadeu

last: Soares

first: Janeck

last: Scott-Fordsmand

first: Mónica

last: Amorim


title: TH-MYCN Mice with Caspase-8 Deficiency Develop Advanced Neuroblastoma with Bone Marrow Metastasis

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Neuroblastoma, the most common extracranial pediatric solid tumor, is responsible for 15% of all childhood cancer deaths.  Patients frequently present at diagnosis with metastatic disease, particularly to the bone marrow.  Advances in therapy and understanding of the metastatic process have been limited due in part, to the lack of animal models harboring bone marrow disease.  The widely employed transgenic model, the TH-MYCN mouse, exhibits limited metastasis to this site.  Here we establish the first genetic immunocompetent mouse model for metastatic neuroblastoma with enhanced secondary tumors in the bone marrow.  This model recapitulates two frequent alterations in metastatic neuroblasoma, over-expression of MYCN and loss of caspase-8 expression.  In this model, the mouse caspase-8 gene was deleted in neural crest lineage cells by crossing a TH-Cre transgenic mouse with a caspase-8 conditional knockout mouse. This mouse was then crossed with the neuroblastoma prone TH-MYCN mouse.  While over-expression of MYCN by itself rarely caused bone marrow metastasis (5% average incidence), combining MYCN overexpression and caspase-8 deletion significantly increased bone marrow metastasis (37% average incidence).  Loss of caspase-8 expression did not alter the site, incidence, or latency of the primary tumors.  However, secondary tumors were detected in the bone marrow of these mice as early as week 9-10. The mouse model described in this work is a valuable tool to enhance our understanding of metastatic neuroblastoma and treatment options and underscores the role of caspase-8 in neuroblastoma progression.

overall_design: Survey of spontateous 13 NB tumors in wt and transgenic mice

first: Tal

last: Teitz

first: Madoka

last: Inoue

first: Marcus

middle: B

last: Valentine

first: Kejin

last: Zhu

first: Jerold

last: Rehg

first: Wei

last: Zhao

last: Finkelstein

first: Melisa

middle: D

last: Johnson

first: Chrisopher

last: Calabrese

first: Marcelo

last: Rubinstein

first: Razqallah

last: Hakem

first: William

last: Weiss

first: Jill

last: Lahti


title: Effect of temperature and irradiation intensity on grapevine berry ripening in Muscat Hamburg fruiting cuttings

status: Public on May 16 2013

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

institute: Iowa State University

summary: At the onset of ripening (veraison), Vitis vinifera L. cv Muscat Hamburg fruiting cuttings were exposed to four different environmental regimes in two growth chambers set up: 20/15ºC (day/night) and 30/25ºC (day/night) and with two different photosynthetic photon flux density (PPFD) conditions (200 and 400 μmol•m−2•s−1 PPFD) at grape bunch level during a 14 h photoperiod. Fruiting cuttings were selected to have similar grape bunch size avoiding changes in berry quality. At least 9 plants were transferred to each treatment. Global pericarp gene expression was compared among the four growth conditions using the GrapeGen GeneChip®. The transcriptomic analysis was carried out in 14 DAT berries in order to identify stable responses to differential temperature and PPFD conditions not masked by quick transient responses to the environmental change. Moreover, grapes of the same density range (100-110 g NaCl·L-1)) from all four treatments were compared to ensure that treatment effects other than ripening rate shifts  originated by the treatments, at least in terms of saccharimetric ripening, were being studied.   ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor,  Pablo Carbonell-Bejerano.  The equivalent experiment is VV46 at PLEXdb.]

overall_design: temperature: 30/25 C - light: 400 μmol·m−2·s−1(3-replications);  temperature: 30/25 C - light: 200 μmol·m−2·s−1(3-replications);  temperature: 20/15 C - light: 400 μmol·m−2·s−1(3-replications);  temperature: 20/15 C - light: 200 μmol·m−2·s−1(3-replications)

first: Pablo

last: Carbonell-Bejerano

first: José

last: Martínez-Zapater


title: ChIP-DSL H20K promoter array from human gastric cancer cells MKN28 with Sox2 overexpression

city: Xi'an

first: Wang

last: Simeng

address: Changle Road

department: Xijing Hospital of Digestive Diseases

country: China

institute: Fourth Military Medical University

type: Genome binding/occupancy profiling by array

summary:
The transcription factor Sox2 inhibits human gastric cancer growth and activates Sox2-related tumor surpressive genes in human gastric cancer cells. Conditional Sox2-overexpression in cells with a low Sox2 level demonstrated that the Sox2-regulated tumor surpressive genes demand on an enhanced Sox2 activity for better expression to work in human gastric cancer.
Chromatin immunoprecipitation (ChIP) of Sox2 together with chromatin profiling by ChIP-on-chip analysis demonstrated that Sox2 directly activates the chromatin at promoters or putative enhancers of Sox2 target genes.

overall_design: Transcription factor Sox2 promoter array in MKN28 cells with Sox2 overexpression.

first: Simeng

first: Jun

last: Tie


title: Expression analyses of red5-2 mutant cells

status: Public on May 15 2013

city: Tsukuba

first: Tomoyasu

last: Sugiyama

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary:
Investigation of whole genome gene expression level changes in red5-2, compared to the wild-type strain.
The mutants analyzed in this study will be described in Sugiyama and Sugiyama.

overall_design: A mRNA profiling study using total RNA recovered from wild-type culture of fission yeast and red5-2 mutant cultures of fission yeast.  Each chip measures the expression level of 4.997 genes from S.pombe with fourteen 60-mer probe pairs (PM/MM) per gene, with seven-fold technical redundancy.


title: Absence of host innate immune responses in SARS-CoV-infected ferrets upon subsequent challenge

status: Public on May 28 2013

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

summary:
To further investigate the underlying mechanisms of severe acute respiratory syndrome (SARS) pathogenesis and evaluate the therapeutic efficacy of potential drugs and vaccines it is necessary to use an animal model that is highly representative of the human condition in terms of respiratory anatomy, physiology and clinical sequelae.  The ferret, Mustela putorius furo, supports SARS-CoV replication and displays many of the symptoms and pathological features seen in SARS-CoV-infected humans.  We have recently established a SARS-CoV infection-challenge ferret platform for use in evaluating potential therapeutics to treat SARS.  The main objective of the current study was to extend our previous results and identify early host immune responses upon infection and determine immune correlates of protection upon challenge with SARS-CoV in ferrets.

Keywords: time course

overall_design: This study is a simple time course (58 day) examination of host responses in 35 SARS-CoV (TOR2) infected ferrets with the addition of a challenge inoculation of SARS CoV (TOR2) at day 29 post infection.  Three mock-infected ferrets are included as negative controls.    Due to the unavailability of ferret microarrays, Affymetrix Canine 2.0 oligonucleotide arrays were chosen following sequence analysis of our ferret cDNA library (~5000 clones) and demonstration of high levels of homology (>80%) between dog and ferret.

first: David

last: Kelvin


title: Distribution of total RNA polymerase II along the 5'/3' regions in xrn1 mutants

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

summary:
Determination of 3' or 5' intragenic RNA pol II occupancy.

Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. Moreover, these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation. In the nucleus, they associate with chromatin - preferentially ~30bp upstream of transcription start-sites - and directly stimulate transcription initiation and elongation. Hence, the decaysome has a dual role in maintaining mRNA levels. Significantly, proper import of some decaysome components seems to play a key role in coupling the two functions. The gene expression process is therefore circular, whereby the hitherto first and last stages are interconnected.

overall_design: This study focuses on the distribution of RNA pol II in the 3' or 5' region of 377 S. cerevisiae ORFs. S. cerevisiae cells grown in YPD to exponential phase were subjected to chromatin immunoprecipitation (ChIP) with anti-Rpb3 antibody. Data were normalized using whole cell extract hybridized on the same array. Home-made macroarrays containing 300 bp from both the 5' or 3' ends of each ORF were used.

last: Pérez-Ortín

first: Daniel

last: Medina

first: Sebastían

last: Chávez


title: Response of methicillin-resistant Staphylococcus aureus USA300 to a subinhibitory concentration of thioridazine - alone and in combination with dicloxacillin

status: Public on May 20 2013

city: Odense M

first: Mette

last: Thorsing

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Subinhibitory concentrations of the neuroleptic drug thioridazine (TDZ) are well-known to enhance the killing of methicillin-resistant S. aureus (MRSA) by β-lactam antibiotics, however, the mechanism underlying the synergy between TDZ and β-lactams is not fully understood. In the present study we have examined the effect of a subinhibitory concentration of TDZ on antimicrobial resistance, the global transcriptome, and the cell wall composition of MRSA USA300.  We show that TDZ is able to sensitize the bacteria to several classes of antimicrobials targeting the late stages of peptidoglycan synthesis. Furthermore, our microarray analysis demonstrates that TDZ modulates the expression of genes encoding membrane and surface proteins, transporters, and enzymes involved in amino acid biosynthesis. Interestingly, resemblance between the transcriptional profile of TDZ treatment and the transcriptomic response of S. aureus to known inhibitors of cell wall synthesis suggests that TDZ disturbs peptidoglycan biosynthesis at a stage that precedes transpeptidation. In support of this notion, dramatic changes in the muropeptide profile of USA300 were observed following growth in the presence of TDZ, indicating that TDZ can interfere with the formation of the pentaglycine branches. Strikingly, the addition of glycine to the growth medium relieved the effect of TDZ on the muropeptide profile. Furthermore, exogenous glycine offered a modest protective effect against TDZ-induced β-lactam sensitivity. We propose that TDZ exposure leads to a shortage of intracellular amino acids, including glycine, which is required for the production of normal peptidoglycan precursors with pentaglycine branches, the correct substrate of S. aureus penicillin-binding proteins. Collectively, this work demonstrates that TDZ has a major impact on the cell wall biosynthesis pathway in S. aureus and provides new insights into how MRSA may be sensitized towards β-lactam antibiotics.

sample_organism: Staphylococcus aureus subsp. aureus USA300_FPR3757

overall_design: Staphylococcus aureus USA300 was grown to early exponential phase and treated with TDZ (16 µg/ml) alone or in combination with DCX (0.125 µg/ml) for 30 min. Changes in global gene expression were analyzed using the untreated culture as control. Hybridizations were performed in triplicate using RNA isolated from independent cultures.

first: Janne

middle: K

last: Klitgaard

first: Marianne

middle: H

last: Skov

first: Hans

last: Kolmos

first: Birgitte

last: Kallipolitis


title: NaMYC2 transcription factor regulates a subset of plant defense responses in Nicotiana attenuata

status: Public on May 17 2013

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

summary: Identification of significantly altered transcripts in Nicotiana attenuata plants with reduced MYC2 expression after induction with oral secretions of Manduca sexta larvae.

overall_design: Gene expression in leaves of Nicotiana attenuata EV and MYC2_VIGS plants was measured at 1 hour after induction with oral secretions of Manduca sexta larvae. Three independent experiments were performed with EV plants and three independent experiments were performed with MYC2_VIGS plants. A total of 47 genes were identified as differentially regulated in MYC2_VIGS plants compared to EV plants.

first: Melkamu

middle: G

last: Woldemariam

first: Ivan

last: Galis

first: Ian

middle: T

last: Baldwin


title: The gene expression characteristics involved in amino acids formation of Lactobacillus delbrueckii subsp. bulgaricus 2038

status: Public on May 21 2013

city: Shanghai

first: Zhidong

last: zhu

state: Shanghai

address: 151# Libing road

institute: shanghai biochip Co.

summary: Transcriptional profiling of Lactobacillus delbrueckii subsp. bulgaricus 2038 during the growth in casein proteins conditioned medium compared with the start control (cells treated in whey conditioned medium). Identifying the genes that are differentially expressed during the growth of Lb. bulgaricus 2038 in casein proteins condition provides a starting point for the investigation of metabolic mechanisms.

overall_design: Twelve Samples at different growth time points. Three replicates each.

first: Huasheng

last: Xiao

first: Zai-Si

last: Ji


title: The Toxoplasma unfolded protein response

city: Indianapolis

first: Ron

last: Wek

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

summary: To characterize the nature of the unfolded protein response in this Toxoplasma, we carried out microarray analyses to measure the changes in the transcriptome and in translational control during ER stress.

overall_design: Total RNA or RNA fractionated into monosomes or polysomes were purified from parasites treated with DMSO or tunicamycin for 1 hour.  RNA was processed for microarray analysis using a ToxoGeneChip.

first: Bradley

middle: R

last: Joyce

first: William

last: Sullivan

first: Ronald


title: A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription [nucleosome profiling]

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

type: Genome binding/occupancy profiling by genome tiling array

summary: Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors including the CAF-1 complex, Spt10 and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning and these data provide a valuable resource for future studies.

overall_design: We examined 50 single-gene loss-of-function strains, comprised of gene deletions (del) and temperature-sensitive (ts) or tetracycline promoter-shutoff (tet) alleles. These genes were selected based on their known or potential role in nucleosome biology and include remodeler ATPases and chaperones, histones and histone modifiers, transcription and elongation factors, and components of RNA polymerase I and II. The compendium also includes 4 compounds targeting transcription and histone deacetylases, as well as a histone depletion time course performed with a strain in which H4 gene expression is exclusively under the control of a GAL1 promoter. Genome-wide nucleosome occupancy profiles were generated using Affymetrix Tiling arrays with probes spaced every 4 bp [PMID:16569694], or next-generation sequencing. Identically prepared samples for each strain and treatment were analyzed on the same tiling arrays for strand-specific expression differences. Each compendium condition was compared to a matched wild-type (WT) reference grown in parallel.

last: van Bakel

first: Kyle

last: Tsui

first: Marinella

last: Gebbia

first: Sanie

last: Mnaimneh

first: Timothy

last: Hughes

first: Corey

last: Nislow


title: Whole-genome expression analysis reveals a role for death-related genes in stress acclimation of the diatom Thalasiossira pseudonana

city: New Brunswick

first: Kim

last: Thamatrakoln

state: New Jersey

address: 71 Dudley Road

institute: Rutgers University

summary:
To identify genes involved in the iron-limited stress response and the induction of programmed cell death, gene expression analaysis using whole-genome microarrays was performed on cultures of T. pseudonana growing in replete or iron-limiting conditions
Samples were collected at day 3 and day 5 from duplicate cultures; RNA was extracted and microarray analysis was performed

overall_design: Duplicate biological replicates were analyzed from replete growing or iron-limited cultures; Analysis was performed on cultures harvested in late exponential phase (day 3) and stationary phase (day 5)

first: Kimberlee

first: Kay

last: Bidle


title: Gene expression changes associated with the airway wall response to injury

status: Public on May 27 2013

city: Roslin

first: David

last: Collie

address: Easter Bush Veterinary Centre

country: United Kingdom

institute: The Roslin Institute & R(D)SVS

summary:
Understanding the way in which the airway heals in response to injury is fundamental to dissecting the mechanisms underlying airway disease pathology. Only limited data is available in relation to in vivo characterisation of the molecular features of repair in the airway. This study sought to characterise the dynamic changes in gene expression that are associated with airway repair in response to physical injury. Gene expression changes in the airway wall following bronchial brush biopsy were profiled in anaesthetised sheep. The experimental design featured sequential studies in the same animals (n=8) over the course of a week and yielded data relating to the repair process at 6 hours, and 1, 3 and 7 days after injury.  Notable features of the transcriptional response included the early and sustained preponderance of down-regulated genes associated with angiogenesis and immune cell activation, selection and differentiation. Later features of the repair response included the up-regulation of cell cycle genes at d1 and d3, and the later pronounced up-regulation of extracellular matrix-related genes at d3 and d7. It is possible to follow the process of airway wall repair in response to physical injury in the same animal over the course of time. Transcriptional changes featured coordinate expression of functionally related genes in a reproducible manner both within and between animals. This characterisation will provide a foundation against which to assess the perturbations that accompany airway disease pathologies of comparative relevance.
Keywords: response to airway injury

overall_design: Each sheep was subjected to a protocol which involved the procedure of endobronchial brush biopsy (BBr) being performed, under anaesthesia, on three occasions, with two separate airway sites being subjected to brushing on each occasion. Two sheep were subjected to BBr seven days, three days and six hours prior to euthanasia, two sheep at seven days, three days and one day prior to euthanasia, two sheep at seven days, one day and six hours prior to euthanasia and two sheep at three days, one day and six hours prior to euthanasia. At post mortem examination (PME) each time point was therefore represented by material derived from six sheep. Airway tissue from a naïve site (from a segment not subjected to BBr) was also collected from each sheep at necropsy.

first: Badrul

last: Yahaya

first: Gerry

last: McLachlan

first: Caroline

last: McCorquodale


title: A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription [transcript profiling]

type: Expression profiling by genome tiling array


title: Wild type vs. Ptbp2 KO mouse embryonic cortex RNA

status: Public on May 31 2013

city: Cleveland

first: Donny

last: Licatalosi

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve University

summary: To assess the requirement of Ptbp2 for alternative processing of RNA in mouse brain

overall_design:
RNA from the cortex of 3 wild type and 3 Ptbp2 KO E18.5 mice.  One array per biological replicate.
Comparative analysis

first: Robert

last: Darnell


title: affy_mildew_sunflower-PAM2010

status: Public on May 29 2013

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary: affy_mildew_sunflower - A quantitative resistance of sunflower to downy mildew (Plasmopara halstedii) has been mapped on LG10 (Vear et al., 2008). Is this quantitative resistance involving novel biological mechanisms? Compare the pattern of expression of specific resistances harboured by the Pl5/Pl2 alleles and the quantitative resistance harboured by the favourable allele at the mapped QTL, during compatible and incompatible interactions in the pathosystem Helianthus annuus / Plasmopara halstedii

overall_design: 60 arrays - SUNFLOWER; normal vs disease comparison

first: Sandrine

last: Arribat

last: Balzergue

first: Patrick

last: Vincourt

first: Marie-Laure

last: Martin-Magniette


title: Distribution of elongating and total RNA polymerase II in xrn1 mutants using GRO and RPCC

first: Jose

last: Perez-Ortin

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Distribution of elongating RNA polymerase II along the 5'/3' regions in xrn1 mutants

summary:
Determination of the 3' or 5' intragenic nascent transcriptional rate.

Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. Moreover, these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation. In the nucleus, they associate with chromatin - preferentially ~30bp upstream of transcription start-sites - and directly stimulate transcription initiation and elongation. Hence, the decaysome has a dual role in maintaining mRNA levels. Significantly, proper import of some decaysome components seems to play a key role in coupling the two functions. The gene expression process is therefore circular, whereby the hitherto first and last stages are interconnected.

overall_design: This study focuses on the transcriptional activity of RNA pol II in the 3' or 5' region of 377 S. cerevisiae ORFs. S. cerevisiae cells grown in YPD to exponential phase were subjected to Genomic Run-On. Data were normalized using gDNA hybridized on the same array. Home-made macroarrays containing 300 bp from both the 5' or 3' ends of each ORF were used.

first: José

last: Pérez-Ortín

first: Daniel

last: Medina

first: Sebastían

last: Chávez


title: Vibrio cholerae Expression Study

status: Public on May 23 2013

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

summary: Question Addressed: What is the level of expression of genes in Vibrio cholerae recovered from various conditions.  These conditions include samples recovered directly from patients (O139 from stool samples from ICDDR,B and N16961 from stool samples from a vaccine trial held in Cincinnati) as well as standard logarithmic and stationary phase grown bacteria.   Labeling reactions were performed in duplicate for each stool derived and in quadruplicate for each in vitro grown strain.   A common reference was used for each slide, it was composed of RNA from the exponentially growing 92A1552 V. cholerae strain

overall_design: transcription profiling by array

first: Douglas

middle: S


title: Real-time quantitative PCR analysis of microRNA in keratinocytes and reconstituted epidermis

city: Liverpoo

first: Kehinde

last: Ross

address: Byrom Street

department: Pharmacy and Biomolecular Sciences

institute: Liverpool John Moores University

type:
Expression profiling by RT-PCR
Non-coding RNA profiling by array

summary: Analysis of microRNA expression in keratinocytes by relative quantification (RQ) using the comparative Ct method. Real-time quantitative PCR analysis of microRNA in keratinocytes or reconstituted epidermis exposed to IL-22, LPS or UV radiation or a small molecule drug.

overall_design: Keratinocytes or reconstituted human epidermis were exposed to indicated treatments. A qPCR analysis of 365 microRNAs in keratinocytes. RNA (20 ng per reaction) reverse transcribed using 8 x Multiplex RT pools. Each resulting cDNA pool was mixed with TaqMan Universal PCR Master Mix and loaded in corresponding port on the TaqMan Array.


title: Induction of pluripotency in mouse somatic cells with novel factors (expression)

city: Beijing

first: Hongkui

last: Deng

address: 5th Yiheyuan Road

institute: Peking University

summary:
For years, reprogramming factors that induce pluripotency have been identified primarily from ESC-enriched factors, pluripotency-associated factors such as Oct4, Sox2, Klf4, c-Myc, Nanog, Esrrb, Sall4, Utf1, Lin28, PRDM14, and Tet2. Through genome-wide screen we identified novel regulators of reprogramming.
Our study is the first proof-of-principle report to suggest a putative general mathematical model. This model provides novel mechanistic insight into the fundamental understanding of the establishment of cellular identity during programming and reprogramming.
Through genome-wide screen to identify novel factors of reprogramming in addition to Oct4, Sox2, Klf4, cMyc

overall_design: Through genome-wide screen to identify novel factors of reprogramming in addition to Oct4, Sox2, Klf4, cMyc. Induced pluripotent stem cells versus mouse embryonic fibroblast.


title: Expression data from tobacco expressing 35S-AtHMA4 compared to the wild-type plants grown in the presence of Cd

city: Warsaw

first: Danuta

middle: Maria

last: Antosiewicz

address: Miecznikowa 1

department: Plant Anatomy and Cytology

country: Poland

institute: University of Warsaw

summary:
Cd levels in the shoots, as well as in the roots were unexpectedly reduced in 35S:AtHMA4-expressing tobacco. Obtained results indicate that in the generation of the Cd-related phenotypes of transgenic plants substantial modifications of the host plant transcriptome was involved.
Microarray based analysis was performed to compare expression profiles of the roots from tobacco expressing 35S-AtHMA4 with the wild-type (WT) plants, which were grown in the presence of 0.25 µM Cd. An effort was undertaken to understand which processes were modified in tobacco as a result of the expression of 35S:AtHMA4, which lead to decreased Cd uptake and lower accumulation in the shoots. Knowing underlying mechanisms is important for developing strategies to grow low cadmium tobacco.

overall_design: 4-week old tobacco plants (35S:AtHMA4 expressing and WT) were subjected to 0.25 µM Cd (added as CdCl2) for four days. Three independent experiments were performed. At the end of each experiment roots from six transgenic plants and six wild-type plants (excluding 1/3 of the distance from their base) were pooled, frozen in liquid nitrogen and stored until RNA isolation. Total RNA isolated from three batches of roots from each studied plant line, was used for three independent microarray analysis.

middle: M

first: Oskar

last: Siemianowski


title: Global transcriptional profile of Streptomyces avermitilis wild-type strain ATCC31267 and avermectin overproducing strain 76-02-e at different time points

first: Ying

last: Wen

address: NO.2 Yuanmingyuanxi Road

department: college of biological sciences

institute: China Agricultural University

summary: To discover novel regulators that influence avermectin biosynthesis, comparative transcriptome analysis between wild-type strain ATCC31267 and avermectin overproducing strain 76-02-e were performed to reveal some differentially expressed genes.

platform_organism: Streptomyces avermitilis MA-4680 = NBRC 14893

overall_design: Global gene expression in ATCC31267 and 76-02-e was measured  at day 2 (early exponential phase) or day 6 (stationary phase), respectively. Three independent experiments for 76-02-e and one for ATCC31267 were performed at each condition.

first: Jia

last: Guo


title: ExpressionData - A public resource of high quality datasets representing gene expression across tissues, conditions, diseases and genotypes.

city: Neuchatel

first: Sam

last: Ansari

state: Neuchatel

address: Quai Jeanrenaud 5

department: Research & Development

country: Switzerland

institute: Philip Morris Products SA

summary: Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, a dozen reference datasets have been published. Typically, they consist of individual baseline or spike-in experiments carried out in a single laboratory and representing a particular set of conditions. For most organisms, however, few or no such reference datasets are publicly available. Here, we describe a new type of datasets highly representative for the spatial, temporal and response dimensions of gene expression. They result from integrating expression data from a large number of globally normalized and quality controlled public experiments and aggregating results by anatomical parts, stages of development, perturbations, drugs, diseases, neoplasms, and genotypes. The proposed datasets were created for human and several model organisms and are publicly available at www.expressiondata.org.

overall_design: PMI: 18 Samples were used with 2 different experimental factors: 1. 2 harvesting times (morning/afternoon) 2. 3 pos-harvesting times. 3 biological replicates were used.

first: Campanoni

last: Prisca

first: Oishi

last: Karen

first: Florian

last: Martin

first: Nikolai

middle: V

last: Ivanov


title: MeDIP of adult whole brain tissue from fetal alcohol exposed mice

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

type: Methylation profiling by genome tiling array

summary:
In this report we assessed alterations to adult mouse brain tissue by assaying DNA cytosine methylation and small noncoding RNA (ncRNA) expression, specifically the microRNA (miRNA) and small nucleolar RNA (snoRNA) subtypes. We found long lasting alterations in DNA methylation as a result of fetal alcohol exposure, specifically in the imprinted regions of the genome harboring ncRNAs and sequences interacting with regulatory proteins.
~20% of the altered ncRNAs mapped to three imprinted regions: Snrpn-Ube3a, Dlk1-Dio3, and Sfmbt2, which showed differential methylation and have been previously implicated in neurodevelopmental disorders. The findings of this report help to expand on the mechanisms behind the long lasting changes in the brain transcriptome of FASD individuals.

overall_design: Comparison of fetal alcohol exposed and matched control adult C57/BL6J mice brains with olfactory bulbs removed

first: B

first: S

last: Singh


title: Production of cis, cis-muconate from benzoate at high rate and yield by a mutant of P. putida KT2440

city: Munich

first: Jacek

last: Puchałka

address: Lindwurmstrasse 2a

department: University Children's Hospital

institute: Munich University Hospital

summary: P. putida KT2440-JD1 was derived from P. putida KT2440 after NTG-mutagenesis and exposure to 3-fluorobenzoate. The strain was no longer able to grow with benzoate as a single source of carbon and energy. Instead, benzoate was co-metabolized to cis, cis-muconate, which accumulated in the culture medium while grown on glucose. During continuous cultivations with glucose as a growth substrate, benzoate was co-metabolized to cis, cis-muconate with a molar product yield (Y(P/S)) of 0.88 ±0.01 mol cis, cis-muconate/ mol benzoate and a specific production rate (qpm) of 0.18 ±0.03 g cis, cis-muconate/ (gDCW* h). During wash-out cultivation a maximum growth rate of 0.6 h-1 and a maximum qpm of 1.4 g cis, cis-muconate/ (gDCW* h) were obtained. Analysis of the transcriptome revealed that the cat operon was no longer induced in P. putida KT2440-JD1 in the presence of 5 mM benzoate. This was also confirmed on the proteomic level for CatA and CatB. A point mutation in catR in P. putida KT2440-JD1 changed the highly conserved Arg50 in the DNA binding domain to Cys50, resulting in the inactivation of the transcriptional regulator of the cat operon. A catechol 1,2-dioxygenase that is encoded by gene PP_3166 (catA2) on the ben operon is likely to convert catechol to cis, cis-muconate in P. putida KT2440-JD1.

sample_organism:
Pseudomonas putida
Pseudomonas putida KT2440

overall_design: wt, JD1 both twice on 10 mM glucose and 10 mM glucose + 5 mM benzoate in total 8 chips

first: Joost

last: vanDuuren


title: Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [CGH]

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

type: Genome variation profiling by genome tiling array

summary: From a clinical and molecular perspective, colon cancer (CC) is a heterogeneous disease but to date no classification based on high-density transcriptome data has been established. The aim of this study was to build up a robust molecular classification of mRNA expression profiles (Affymetrix U133Plus2) of a large series of 443 CC and to validate it on an independent serie of 123 CC and 906 public dataset. We identified and validated six molecular subtypes in this large cohort as a combination of multiple molecular processes that complement current disease stratification based on clinicopathological variables and molecular markers. The biological relevance of these subtypes was consolidated by significant differences in survival. These insights open new perspectives for improving prognostic models and targeted therapies.

overall_design: Among a large series of colon cancers collected for the Cartes d'Identité des Tumeurs (CIT) program from the French Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net), 566 were analyzed for mRNA expression profiles using Affymetrix U133plus2 chip and, among theses, 463 could also be analyzed for DNA alteration profiles using the CGH Array ( CIT-CGHarray V6). The 566 tumors was divided into a discovery dataset of 443 CC and a validation dataset of 123 CC.

first: Laetitia

last: Marisa

first: Aurélien

last: de Reyniès

first: Alex

last: Duval

first: Janick

last: Selves

first: Marie-Pierre

last: Gaub

first: Laure

last: Vescovo

first: Marie-Christine

last: Etienne-Grimaldi

first: Renaud

last: Schiappa

first: Dominique

last: Guenot

first: Mira

last: Ayadi

first: Sylvain

last: Kirzin

first: Maurice

last: Chazal

first: Jean-François

last: Fléjou

first: Daniel

last: Benchimol

first: Erwan

last: Pencreach

first: Arnaud

last: Lagarde

first: Françoise

last: Piard

last: Elias

first: Sylviane

last: Olschwang

first: Gérard

last: Milano

first: Pierre

last: Laurent-Puig

first: Valérie

last: Boige


title: Genome wide profiling of FOXE1 binding sites in PCCL3 rat cells

status: Public on May 14 2013

city: Madrid

first: Pilar

last: Santisteban

address: Arturo Duperier 4

department: Physiopathology of Endocrine and Nervous System

institute: Instituto Investigaciones Biomédicas Alberto Sols

summary: FoxE1 transcriptional profiling of rat PCCL3 cells comparing wild type cells with FoxE1 silenced cells and scramble treated with FoxE1 silenced cells.

overall_design: Three-condition experiment, FoxE1 silenced vs. Wild type cells. Biological replicates: 4 replicates, 1pooled sample dye-swap. and FoxE1 silenced vs scramble treated cells. Biological replicates: 4 replicates, 1 pooled sample dye-swap.

first: Lara

middle: P

last: Fernández

first: Arístides

last: López-Márquez

first: Angel

last: Martínez

first: Gonzalo

last: Gómez-López


title: microRNA profiling of human monocytes and monocyte-derived macrophages

status: Public on May 10 2013

city: Baltimore

first: Kenneth

middle: W

last: Witwer

address: 733 N Broadway, BRB Rm 820

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

summary: microRNA profiling data includes biological replicates of primary monocytes and macrophages from three human donors

overall_design: Dye swap hybridization arrays were performed for total RNA isolated from fresh monocytes and 7-day monocyte-derived macrophages from each of three human donors

first: Jeanne

last: Sisk

first: Janice

middle: E

last: Clements


title: miRNA profiling in the plasma of patients with acute myocardial infarction (AMI)

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary: Studies of miRNA profiling in the plasma of AMI patients with Left ventricular end diastolic volume (LVEDV) increase or LVEDV decrease between discharge and follow-up

overall_design: Venous blood was collected in citrated tubes prior discharge. Plasma was harvested by centrifugation and stored at -80°C until assayed. Identical volumes of plasma from the 30 patients of a group (LVEDV increase or LVEDV decrease) were pooled to reach a final volume of 400µL for each group. The two pools were processed conjointly. Total RNA was extracted using miRVana isolation kit (Applied Biosystems), dephosphorylated and labeled using miRNA Complete Labeling and hybridization kit (Agilent). Hybridization was performed on miRNA Human Microarray Release 12.0 slides (Agilent). 4 arrays per pool were hybridized. Scanning was achieved with the Genepix 4000B Scanner (Molecular Devices, Sunnyvale, USA). Raw data were acquired with the Genepix Pro software (Molecular Devices).


city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

summary: An European eel-specific microarray platform was developed to identify genes involved in response to pollutants

overall_design: A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from high (Tiber river, Italy) and low pollution (Bolsena lake, Italy) environments. Gene expression profiling was performed using an European eel-specific oligo-DNA microarray of 14,913 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.

first: M

last: Pujolar

first: L

last: Zane


title: An improved method of generating total amplified tumor RNA for DC based autologous immunotherapy enhances antigen presentation and leads to more potent immune responses.

city: Durham

first: Irina

middle: Yurievna

last: Tcherepanova

state: NC

address: 4233 Technology Drive

department: REsearch and Development

institute: Argos Therapeutics Inc.

summary: To evaluate improvements introduced in the RNA amplificatio protocol the RNAs extracted from renal cell carcinoma (RCC) were amplified using old protocol and the new protocol. Microarray analysis was conducted to evaluate capture of transcripts in the RNA amplified using the new protocol and old protocol by comparing those to starting total RCC RNA.

overall_design: Expression of RCC genes was detected in the RNAs amplified using two experimental protocols (Arm2, Arm5) and compared to that of total RNA. The RNA was amplified from three independent donors and technical replicates were conducted on two of the samples.

middle: Y


title: A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [aCGH]

city: Daejeon

first: Sanghyuk

last: Lee

address: 125 Gwahak-ro

department: KOBIC

country: South Korea

institute: KRIBB

summary: One of the most fertile applications of next generation sequencing will be in the field of cancer genomics. Here, we report a high-throughput multi-dimensional sequencing study of primary non-small cell lung adenocarcinoma tumors and adjacent normal tissues of 6 never-smoker Korean female patients. Our data encompass results from exome-seq, RNA-seq, small RNA-seq, and MeDIP-seq. We identified and validated novel genetic aberrations including 47 somatic mutations and 20 fusion transcripts. We also characterized gene expression profiles which we sought to integrate with genomic aberrations and epigenetic regulations into functional networks. Importantly, among others the gene network module governing G2/M cell check point emerged as the primary source of disturbance in these patients. In addition, our study strongly suggests that microRNAs make key regulatory inputs into this gene network module. Our study offers a paradigm for integrative genomics analysis and proposes potential target pathways for the control of non-small cell lung adenocarcinoma.

overall_design: Study of primary non-small cell lung adenocarcinoma tumors and normal tissues of 6 patients.

first: Jhingook

last: Kim

first: Jaesang

first: Jong-Eun


title: Gene expression profiles of CD8+ T Lymphocytes isolated from HTLV-1 infected individuals

status: Public on May 08 2013

city: Ribeirão Preto

first: Daniel

middle: Guariz

last: Pinheiro

state: São Paulo

address: Rua Tenente Catão Roxo, 2501

department: Departamento de Genética

country: Brazil

institute: Faculdade de Medicina de Ribeirão Preto (Universidade de São Paulo)

summary: HTLV-1 is the etiologic agent of HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP). CD8+ T cells may contribute to the protection or development of HAM/TSP. In this study we used SAGE to assess gene expression profiles of CD8+ T cells isolated from HTLV-1 asymptomatic carriers (HAC) and from HAM/TSP patients, in order to identify genes involved in the HAM/TSP development. Analysis of SAGE was conducted by pooling samples according to clinical status. The comparison of gene expression profiles between controls and HAC or HAM/TSP identified around 900 genes. HAC versus HAM/TSP libraries showed 285 differentially expressed genes. We found that CXCR4 had a lower expression level in the HTLV-1 infected group than in controls. CCL5 had higher expression in HAM/TSP group, as compared to HAC. Our results provide a large-scale perspective of gene expression that may be further tested with functional assays to increase our understanding on the HTLV1-related diseases pathology.

overall_design: Comparative analysis of gene expression profiles of CD8+ T Lymphocytes isolated from HTLV-1 infected individuals.


title: Streptococcus suis 05ZY: control vs. treated by licochalcone A

status: Public on May 07 2013

first: Huaijie

last: Hao

state: Beijing

address: NO. 20, Dongda Street, Fengtai District

institute: Institute of Microbiology and Epidemiology, Academy of Millitary Medicine Sciences

summary: Streptococcus suis is an important emerging worldwide pig pathogen and zoonotic agent with rapid evolution of virulence and drug resistance. Licochalcone A, used in traditional Chinese medicine, exhibits antimicrobial, antioxidant and anti-inflammatory activities. Herein, a whole-genome DNA microarray was used to investigate the global transcriptional regulation of Streptococcus suis 05ZYH33 treated by subinhibitory concentration of licochalcone A. 132 genes were differentially regulated upon liochalcone A treatment, including 78 genes up-regulated and 54 genes down-regulated which included many central biological functions such as metabolism, transcription and translation. We tried to investigate the antimicrobial mechanism of licochalcone A in the aspect of bacterial cell cycle control. Our analysis indicated that licochalcone A might inhibit the growth of S. suis by controlling the replication initiation and cell division through amino acid metabolism.

overall_design: A cDNA microarray imprinted with 2156 genes representing about 98% of Streptococcus suis serotype 2 genome was used for transcriptome analysis. For two-sample (reference vs. test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation. Four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias. A ratio of mRNA levels (test/reference) was calculated for each gene. Significant changes of gene expression were identified with the SAM software. After the SAM analysis, only genes with at least 2-fold changes in expression were collected for further analysis.

first: Wenjia

last: Hui

first: Peng

last: Liu

first: Qingyu

last: Lv

first: Xiaotao

last: Zeng

first: Hua

last: Jiang

first: Yanzi

last: Wang

first: Xin

last: Zheng

first: Yuling

first: Jianchun

last: Li

first: Xuyu

last: Zhou

first: Yongqiang


title: A role for programmed cell death in the microbial loop

city: Seattle

first: Monica

middle: V.

last: Orellana

state: WA

address: 401 Terry Ave North

institute: Institute for Systems Biology

summary: The microbial loop is the conventional model by which nutrients and minerals are recycled in aquatic eco-systems. Biochemical pathways in different organisms become metabolically inter-connected such that nutrients are utilized, processed, released and re-utilized by others. The result is that unrelated individuals end up impacting each others’ fitness directly through their metabolic activities. This study focused on the impact of programmed cell death (PCD) on a population’s growth as well as its role in the exchange of carbon between two naturally co-occurring halophilic organisms. Flow cytometric, biochemical, 14C radioisotope tracing assays, and global transcriptomic analyses show that organic algal photosynthate released by Dunalliela salina cells undergoing PCD complements the nutritional needs of other non-PCD D. salina cells. This occurs in vitro in a carbon limited environment and enhances the growth of the population.  In addition, a co-occurring heterotroph Halobacterium salinarum re-mineralizes the carbon providing elemental nutrients for the mixoheterotrophic chlorophyte. The significance of this is uncertain and the archaeon can also subsist entirely on the lysate of apoptotic algae.  PCD is now well established in unicellular organisms; however its ecological relevance has been difficult to decipher. In this study we found that PCD in D. salina causes the release of organic nutrients such as glycerol, which can be used by others in the population as well as a co-occurring halophilic archaeon. H. salinarum also re-mineralizes the dissolved material promoting algal growth. PCD in D. salina was the mechanism for the flow of dissolved photosynthate between unrelated organisms. Ironically, programmed death plays a central role in an organism’s own population growth and in the exchange of nutrients in the microbial loop.

overall_design: Halobacterium NRC-1 was grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2. Cells were harvested and washed in  MM1 and incubated in MM1 (control) or in Dunaliella harvested supernatant. Cells were harvested at time zero, 5, 10, 20, 40, 80, 160 minutes. RNA from two biological replicate time courses were prepared, averages of these replicates are reported in the published study. The zero time point was harvested immediately after incubation Halobacteria-NRC1 in MM1 or in Dunaliella salina's supernatant.

first: Wyming

middle: L

last: Pang

first: Pierre

last: Durand

first: Kenia

last: Whitehead

first: Nitin

last: Baliga


title: Deciphering the Bacterial Microbiome of Citrus Plants in Response to ‘Candidatus Liberibacter asiaticus’-Infection and Antibiotic Treatments

status: Public on May 09 2013

city: Fort Pierce

first: muqing

last: zhang

state: Florida

address: 2199 South Rock Road

institute: University of Florida

summary:
Huanglongbing (HLB) is a worldwide devastating disease of citrus. There are no effective control measures for this newly emerging but century-old disease. A powerful oligonucleotide microarray of high-density 16S rRNA genes, the PhyloChip microarray, has been developed and effectively used to study bacterial diversity, especially from environmental samples.
In this article, we aim to decipher the bacterial microbiome in HLB-affected citrus versus non-infected citrus as well as in citrus plants treated with ampicillin and gentamicin using PhyloChip-based metagenomics.

platform_organism: Bacteria Archaea

overall_design: The antibiotic treatments were conducted on the randomized complete block design with three replicates. For each replicate, 15 scions were treated in each antibiotic treatment (Amp and Gm) and control (CK1 and CK2). HLB-affected budsticks were sampled from severely HLB-affected field rough lemons (cv. Lemon #76) at the USDA-ARS-USHRL farm in Fort Pierce, FL and tested positive for Las by real-time qPCR. They were soaked in the antibiotic treatments; ampicillin sodium at a concentration of 1.0 g/L (Amp, Sigma-Aldrich, St. Louis, MO) or gentamicin sulfate at a concentration of 100 mg/L (Gm, Sigma-Aldrich, St. Louis, MO) and water as the diseased control (CK1), overnight in a fume hood under ventilation and lighting. Las-free budsticks, which tested negative by qPCR from healthy rough lemons, were also soaked in water as the healthy control (CK2). The budsticks were grafted onto two-year-old healthy grapefruit (Citrus paradisi 'Duncan') rootstocks and covered using plastic tape  for three weeks. To improve scion growth, new flush from the rootstocks was removed after grafting and then allowed to grow. All experimental plants were grown in an insect-proof greenhouse. The first leaf samples from scions (rough lemon) and rootstocks (grapefruit) for DNA extraction were taken four months after inoculation, and second samplings were taken at six month after inoculation. The leaves were washed in tap water and then rinsed three times with sterile water. The midribs of the leaves were excised, frozen in liquid nitrogen, and stored at -80°C. The midribs of five leaves from each sample were pooled, and DNA was isolated for qPCR analysis for Las bacterium. DNA from the leaf midribs of scions for the PhyloChipT G3 analysis, which was extracted from all samples of the same treatment, was pooled in equal amounts and quantified by the PicoGreen® method. The PhyloChipTM G3 analysis was conducted by Second Genome Inc. (San Francisco, CA).

first: Muqing

last: Zhang

first: Charles

middle: A

last: Powell

first: Lesley

last: Benyon

first: Hui

last: zhou

first: Yongping

last: Duan


title: Murine splenic macrophage Cells: Control mice vs. Schistosoma japonicum-infected mice

city: Taipei

first: Po-Ching

last: Cheng

address: 250 Wuxing St,

department: Department of Parasitology, College of Medicine

country: Taiwan

institute: Taipei Medical University

summary: Macrophages initiate, modulate, and also serve as final effector cells in immune responses during course of schistosomal infections. Presently, we discussed the roles of the gene expression profile and functional changes of macrophages in immune responses against the Schistosoma japonicum by microarray experiments. Hierarchical clustering analysis demonstrated that a significant switch in gene transformation associated with a type-1 response and linked with a type-2 cytokine phenotype occurs between 4.5 and 8 weeks post-infection. Moreover, the gene profiles at 3 later time-points following egg challenge were similar in complexity and magnitude. These data also showed that there are mostly inhibition in gene expression related TLR, IFN, MHC and TNFrsf at the switch between 4.5 and 8 weeks post-infection, It is suggested that these immunomodulatory genes may be down-regulated in resistance against S. japonicum eggs and granuloma pathology. The induction of alternatively activated macrophage was important for dampening the inflammation in hepatic granulomas and contributing to a decrease in cytotoxicity. The genes expressions involved in repair/remodeling during liver fibrosis were also observed after eggs production. Understanding these immune mechanisms related to parasite resistance, pathology, and growth with regard to the disease will be helpful in further studies on S. japonicum.

overall_design: Two-condition experiment, Control mice vs. Schistosoma japonicum-infected mice. replicates: 2 infected replicates. Different post-infection weeks

first: Kin-Mu

last: Lee


title: Plasma microRNA profiles in women with and without endometriosis at different menstrual cycle phases

city: Adelaide

first: Victoria

last: Nisenblat

address: Frome road

country: Australia

institute: University of Adelaide

summary:
The objectives of the study:
1. Does the phase of the menstrual cycle alter microRNA (miRNA) plasma profiles in healthy women of reproductive age and in women with endometriosis? 2. Does this alter prospects for development of a miRNA-based diagnostic test  for endometriosis?

overall_design: Prospectively recruited asymptomatic control women and women with surgically diagnosed endometriosis (n = 8 in each group) were included. Each patient provided blood samples in the early proliferative, late proliferative and mid luteal phases of the menstrual cycle (n = 47 total plasma samples). The cycle phase was verified by hormonal profile. RNA was extracted from each sample and expression of microRNAs was assessed using TaqMan Low Density Human miRNA arrays.

first: Cristin

middle: G

last: Print

first: Susan

middle: F

last: Evans

first: E

last: Ohlsson Teague

first: Sarah

last: Robertson

first: M

last: Hull


title: Recruitment of FOXP1 to target genes in diffuse large B-cell lymphoma (DLBCL) cells

status: Public on May 03 2013

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

institute: University of Navarra

summary: Identification of FOXP1 target genes in the OCI-Ly1 DLBCL cell line by ChIP-on-chip

overall_design: Three replicates of the FOXP1 ChIP-on-chip were performed in the OCI-Ly1 cells

first: Ainara

last: Sagardoy

first: Jose

last: Martinez-Ferrandis

first: Sergio

last: Roa

first: Karen

last: Bunting

first: Maria

last: Aznar

first: Olivier

last: Elemento

first: Rita

last: Shaknovich

first: Lorena

last: Fontán

first: Vicente

last: Fresquet

first: Ignacio

last: Perez-Roger

first: Eloy

last: Robles

first: Linde

last: De Smedt

first: Xavier

last: Sagaert

first: Ari

last: Melnick

last: Martinez-Climent


title: Affect of liver transcriptome by acute acetaminophen exposure [miRNA]

first: Ji-Hoon

last: Cho

address: 401 Terry Avenue North

country: USA

summary: To study the global changes of liver transcriptome after acetaminophen overdose.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: To study the global changes of transcriptome in the liver after acetaminophen overdose.  Eight week old female C57BL/6 mice were fasted for 24 hours prior to a single intraperitoneal injection of 350mg/kg of acetaminophen in phosphate buffer saline (PBS) (treatment group) or PBS (control group). The mice were euthanized at different time points post exposure; plasma and tissue samples were collected for pathological examination and biochemical analyses.

first: Kai

last: Wang

first: Yue

last: Yuan

first: Hong

last: Li

first: David

last: Huang

first: Li

last: Gray

first: Shizhen

last: Qin

middle: J

last: Galas


title: A Characterization of Osteoblastic and Osteolytic Proteins in Prostate Cancer Bone Metastases

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Our goal was to determine whether previously identified and novel proteins are associated with the osteoblastic or osteolytic response in clinical specimens of PCa bone metastases.

overall_design: Custom Agilent 44K whole human genome expression oligonucleotide microarrays were used to profile 14 PCa metastases from 11 patients with highly osteoblastic and highly osteolytic bone reactions.  Total RNA was isolated and amplified prior to hybridization against a common reference pool of prostate tumor cell lines.

first: Sandy

last: Larson

first: Xiaotun

last: Zhang

first: Ruth

last: Dumpit

first: Bryce

last: Lakely

first: Martine

last: Roudier

first: Celestia

last: Higano

first: Lawrence

middle: D

last: True

first: Paul

middle: H

last: Lange

first: Bruce

last: Montgomery

first: Peter

middle: S

last: Nelson

first: Eva

last: Corey

first: Robert

last: Vessella

first: Colm

last: Morrissey


title: Steady-state samples of Methanococcus maripaludis MM901 grown on formate under hydrogen limited conditions

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

institute: Konkuk University

summary: Hydrogenotrophic methanogenic Archaea are defined by a H2 requirement for growth. Despite this requirement, many hydrogenotrophs are also capable of growth with formate as an electron donor for methanogenesis. Hydrogenotrophs respond to H2 starvation both phenotypically and at the level of gene expression; however, the responses during growth on formate have not been characterized. Here we report that during continuous culture of Methanococcus maripaludis under defined nutrient conditions, growth yields relative to methane production decreased markedly with either H2 excess or formate excess, suggesting that energy spilling occurs. Using microarray analysis, we show that the expression of genes encoding F420-dependent steps of methanogenesis, including one of two formate dehydrogenases, increased with H2 starvation, but with formate occurred at high levels regardless of limitation or excess. One gene, encoding H2-dependent methylene-tetrahydromethanopterin dehydrogenase, decreased in expression with either H2 limitation or formate limitation. Expression of genes for the second formate dehydrogenase, molybdenum-dependent formylmethanofuran dehydrogenase, and molybdenum transport increased specifically with formate limitation. Of the two formate dehydrogenases, only the first could support growth on formate in batch culture where formate was in excess.

overall_design: The strain was grown by continuous culture in a one-liter fermenter (New Brunswick Scientific, Edison, NJ) at 37°C (FEMS Microbiol Lett 238: 85-91, 2004). Medium and gas compositions were modified from those for non-limiting conditions (BMC Microbiol 9: 149, 2009). The medium contained 380 mM sodium formate in place of NaCl.  The agitation rate was 250 revolutions per minute. The gas mixture initially supplied to the chemostat was H2/Ar/CO2/1% H2S (21/125/40/14 mLs min-1) (Proc Natl Acad Sci USA 104: 8930-8934, 2007). After the OD increased above 0.6 (24 h), the medium flow was turned on at 0.083 L/h. Medium was either non-limiting (described above), formate limiting (modified to contain 200 mM sodium formate and 180 mM NaCl), nitrogen limiting (2 mM NH4Cl), or phosphate limiting (0.08 mM K2HPO4). Also at this point, gas flow through the vessel was shut off, a 1 psi check valve was installed on the exhaust line to maintain positive pressure within the vessel while also allowing for exhaust of gaseous metabolic byproducts, and a 1% Na2S9H2O feed was started into the vessel at 0.83 mL/h. 48 hours later, samples were taken for physiological measurements or microarray analysis. Samples were collected for microarray analysis as follows: 1.5 mLs of chemostat culture (OD660 ~0.65) was centrifuged at 13,000 x g for 30 seconds and supernatant was discarded. The pellet was immediately placed in a dry ice/ethanol bath and stored at -80C until RNA extraction and microarrays could be performed.  Total RNA from each sample was compared against a reference RNA pool that was generated in bulk from a mid-log phase culture of MM901. Total RNA from samples and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. After hybridization and washing according to array manufacturer's instructions, the arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Dye-flip experiments were done for each sample.

first: Sung-Ho

first: Kyle

middle: C

last: Costa

first: Min

last: Pan

first: John

last: Leigh

first: Nitin

last: Baliga


title: Copy number aberrations of genes regulating normal thymus development in thymic epithelial tumors

city: Pisa

first: Iacopo

last: Petrini

address: Via Roma 67

institute: Pisa University

summary: Thymic epithelial tumors are a group of neoplasms with heterogeneous histological features and clinical behavior. The identification of markers useful to predict patient prognosis and molecular targets for therapies is limited by a very little understanding of the biology of these neoplasms. We evaluated the copy number (CN) aberrations of genes involved in normal thymus development in thymic epithelial tumors, following the intriguing idea that the ectopic deregulation of genes relevant for proliferation and differentiation of embryonic cells, can contribute to tumor growth. Frequent CN losses of FOXC1 were observed in more aggressive tumors and correlated with a reduced protein expression; tumors negative for FOXC1 expression were associated with a shorter time to progression. In addition, FOXC1 showed tumor suppressor activity in in-vitro models. Our data indicate that FOXC1 loss can identify a group of thymic epithelial tumors with poor prognosis, possibly because its tumor suppressor properties.

overall_design: Two color array CGH of a series of 59 thymic epithelial tumors plus evaluation of 2 thymic carcinoma cell lines and one thymoma B1 cell line.

first: Yisong

last: Wang

first: Paolo

last: Zucali

first: Hye

last: Lee

first: Pham

last: Trung

first: Donna

last: Voeller

last: Meltzer

first: Giuseppe

last: Giaccone


title: DNA methylation profiles in the uterus during early pregnancy

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

summary: Co-ordinated regulation of endometrial gene expression is essential for successful pregnancy establishment.  A non-receptive uterine environment may be a key contributor to pregnancy loss, as the majority of pregnancy losses occur prior to embryo implantation. DNA methylation has been highlighted as a potential contributor in regulating early pregnancy events in the uterus.  It was hypothesized that DNA methylation regulates expression of key genes in the uterus during pregnancy. To gain support for this hypothesis the correlation between DNA methylation and gene expression was tested. Endometrial samples from fertile and sub-fertile dairy cow strains were obtained at day 17 of pregnancy or the reproductive cycle.  Microarrays were used to characterize genome-wide DNA methylation profiles and data compared with transcription profiles which have been previously reported.  39% of DNA methylation probes assayed mapped to RefSeq genes with transcription measurements. The 1,000 most significant correlations were used for subsequent analysis. Of these, 52% percent were negatively correlated with gene expression. When this gene list was compared with previously reported gene expression studies on the same tissues, 42% were differentially expressed when comparing pregnant and cycling animals and 11% were differentially expressed comparing pregnant fertile and sub-fertile animals.   DNA methylation status was correlated with gene expression in several pathways implicated in early pregnancy events. Although these data do not provide direct evidence of a causative association between DNA methylation and gene expression, this study provides critical support for an effect of DNA methylation in early pregnancy events and highlights candidate genes for future studies.

overall_design: The estrous cycles of 24 lactating dairy cows were synchronized (at 58.8 (SEM 3.77) and 60.2 (SEM 1.51) days post calving in dairy cows of sub-fertile and fertile strains, respectively) and 14 received a single embryo transferred on day 7 of the estrous cycle.  Animals were slaughtered at day 17 of the reproductive cycle and endometrial tissues (both caruncular and intercaruncular) were sampled. Selection criteria for the study included strain and calving date, and health postcalving was an exclusion criterion (cows with severe uterine infections or mastitis were excluded before being enrolled in the embryo transfer round). Cows in each strain were matched for calving number and age. A total of 10 cycling and 12 pregnant animals enrolled in the study were utilized, due to the associated costs of slaughtering the cows. These animals represented fertile (six pregnant and five cycling Holstein-Friesian cows with New Zealand ancestry/≤30% North American genetics, n=11, NZ) and sub-fertile (six pregnant and five cycling Holstein-Friesian cows with >87% North American ancestry, n=11, NA) phenotypes of Holstein-Friesian dairy cows

first: Mathew

last: Littlejohn

first: Susanne

last: Meier

middle: R

last: Roche


title: Gene Expression in Forebrain of Male Goldfish Following Exposure to Waterborne Sex Pheromones

status: Public on May 01 2013

city: Ottawa

first: Wudu

middle: E.

last: Lado

address: 30 Marie Private

department: Biology

institute: University of Ottawa

summary: Sex pheromones rapidly affect endocrine physiology and behaviour, but little is known about their effects on gene expression in the neuroendocrine tissues that mediate olfactory processing. In this study we exposed male goldfish for 6 h to waterborne 17,20betaP (4.3 nM) and PGF2α (3 nM), the main pre-ovulatory and post-ovulatory pheromones, respectively. Both treatments elevated milt volume (P = 0.001).  Microarray hybridizations were used to male telencephalon samples following PGF2α treatment and identified 71 unique transcripts that were differentially expressed (q < 5%; 67 up, 4 down). Functional annotation of these regulated genes indicates that PGF2α pheromone exposure affects diverse biological processes including nervous system functions, energy metabolism, cholesterol/lipoprotein transport, translational regulation, transcription and chromatin remodelling, protein processing, cytoskeletal organization, and signalling. By using real-time RT-PCR, we further validated three candidate genes, ependymin-II, calmodulin-A and aldolase C, which exhibited 3 - 5 fold increase in expression following PGF2α exposure. Expression levels of some other genes that are thought to be important for reproduction were also determined using real-time RT-PCR.  Expression of sGnRH was increased by PGF2α, but not 17,20betaP, whereas cGnRH expression was increased by 17,20betaP but not PGF2α. In contrast,  both pheromones increase the expression of glutamate (GluR2a, NR2A) and gamma-aminobutyric acid (GABAA gamma2) receptor subunit mRNAs.  This gene expression data link milt release and rapid modulation of neuronal transcription as part of the response to female sex pheromones.

platform_organism:
Carassius auratus
Cyprinus carpio

overall_design: A total of four microarray slides were hybridized to study the effects of PGF2α on gene expression in the telencephalon. Control samples (N = 4) were pooled to form our reference or technical replicates while treatment samples (N = 4), which formed our biological replicates, were ran separately. In addition, two dye swaps were performed for our biological samples for the treatments.

first: Dapeng

last: Zhang

first: Jan

last: Mennigen

first: Jacob

middle: M

last: Zamora

first: Jason

middle: T

last: Popesku

first: Vance

last: Trudeau


title: Interactions of wheat aleurine and plant omega-3 fatty acids on the rat gut microbiota

status: Public on May 02 2013

city: Clermont-Ferrand

first: william

last: tottey

address: 28 place Henry Dunant

institute: EA-CIDAM 4678

summary:
Microbiota from rats fed with wheat aleurone and plant omega fatty acids
In this study we investigated how an AX-rich WA and ALA from linseed oil (LO) modulate the gut microbiota of rats. Wistar rats were fed a standard diet and received either an iso-energetic control oil (PO), control oil + aleurone (A+PO), linseed oil (LO) or linseed oil + aleurone (A+LO) during 12 weeks. Feacal samples were recovered after the 12 week treatments. DNA extractions were performed using using the Qiagen's DNA Stool Kit (Qiagen, West Sussex, UK). 10ng of DNA template were amplified by PCR (16S gene) and purified using Qiagen's Qiaquick PCR purification kit (Qiagen, West Sussex, UK). 1ug of purified PCR product were labelled with either Cy3 or Cy5 using Genomic DNA ULS Labelling kit (Agilent Technologies, Palo Alto, CA). 250ng of labelled DNA were hybridized on the microarray for 24h at 65°C. Washings were performed as recommended by the manufacturer. Microarray scanning was performed on a Surescan Microarray scanner (Agilent Technologies, Palo Alto, CA). Data were extracted using the Feature extraction software (Agilent Technologies, Palo Alto, CA). The retained intensity value for each probe was the ratio between the spot’s median intensity signals and the median of background signals.

overall_design:
A 13 chip study was realized to analyze the feacal microbiota of rats treated with either an iso-energetic control oil (PO), control oil + aleurone (A+PO), linseed oil (LO) or linseed oil + aleurone (A+LO) during 12 weeks. Each microarray corresponding to hybridization with 250ng of labelled 16S rRNA gene amplicons from 2 rat DNA faecal samples. Microbiota structure and diversity were assessed using the HuGChip (Tottey et al., 2013). Each probe (4441) was synthetized in three replicates.
On the same array, 2 different samples were hybridized. One labelled with the Cy3 dye and one with the Cy5 dye. The results were processed as single channel (13 raw data files available on Series records for 25 samples).

first: Florence

last: Privée

first: William

last: Tottey

first: Fayçal

last: Ounnas

first: Hubert

last: Roth

first: Pierre

last: Peyret

first: Christine

last: Demeilliers

first: Patricia

last: Salen

first: Jean-François

last: Brugère

first: Michel

last: de Lorgeril


title: affy_strigolactone_sunflower-Identification of Strigolactone -regulated genes in sunflower

status: Public on May 06 2013

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary: affy_strigolactone_sunflower - affy_strigolactone_sunflower - Abiotic stress and more specifically drought is the major limiting factor for sunflower production. Sunflower response to drought includes root plasticity to adapt to water availability and reach soil water. We identified genotype-specific responses of root architecture to strigolactone application. This experiment aims at identifying strigolactone responsive pathways in 6 genotypes in order to better understand molecular control of root development in sunflower and therefore its response to drought. The ultimate goal will be to improve sunflower breeding through selection of key drought response genes.-The experiment consisted of 2 repeats of four 12-day-old-plantlets of 6 sunflower genotype SF193 (INRA code: XRQ), SF326 (INRA code: PSC8), SF056 (INRA code: FU), SF306 (INRA code: PAZ2), SF302 (INRA code: PAC2), SF268 (INRA code: RHA266), grown in growth chamber conditions and submitted to a 24-hour-treatment of 100 nM strigolactone analogue rac-GR24 (Chiralix, Nijmegen, Netherland) or not. Growth conditions were 14h light at 23°C and 10h night at 20°C under fluorescent bulbs. Plants were grown in hydroponic boxes containing 20 litres of aerated liquid culture medium (as described in Massonneau et al., 2001 Planta). The entire root systems were harvested 4 hours after light onset and frozen immediately in liquid nitrogen.

overall_design: 24 arrays - SUNFLOWER; treated vs untreated comparison

first: Sandrine

last: Arribat

last: Balzergue

first: Nicolas

last: Langlade

first: Marie-Laure

last: Martin-Magniette


title: The investigational Aurora kinase A inhibitor MLN8237 induces defects in cell viability and cell cycle progression in mouse bladder cancer cells in vitro and in vivo

city: Grand Rapids

first: Jacob

last: Zhang

state: MI

address: 333 Bostwick Ave

department: Cancer Genetics

institute: Van Andel Institute

summary:
PURPOSE: Despite over 70,000 new cases of bladder cancer in the United States annually, patients with advanced disease have a poor prognosis due to limited treatment modalities.  We evaluate the role of Aurora A, identified as an upregulated candidate molecule in bladder cancer, in regulating bladder tumor growth.
EXPERIMENTAL DESIGN: Gene expression in human bladder cancer samples was evaluated using RNA microarray and reverse-transcriptase PCR. The specific Aurora kinase A inhibitor MLN8237 (Millennium) was used to determine effects on bladder cancer cell growth using in vitro and in vivo models using malignant T24 and UM-UC-3 and papilloma-derived RT4 bladder cells.
RESULTS: Urothelial carcinoma upregulates a set of 13 mitotic spindle associated transcripts, as compared to normal urothelium, including MAD2L1 (7.6-fold), BUB1B (8.8-fold), Aurora kinases A (5.6-fold) and Aurora kinase B (6.2-fold). Application of MLN8237 (10nM-1µM) to the human bladder tumor cell lines T24 and UM-UC-3 induced dose-dependent G2 cell cycle arrest, aneuploidy, mitotic spindle abnormalities, and apoptosis. MLN8237 arrested tumor growth when administered orally over 4 weeks in a mouse bladder cancer xenograft model (p<0.05). Finally, in vitro combination of MLN8237 with either paclitaxel or gemcitabine produced schedule-dependent synergistic antiproliferative effects in T24 cells when administered sequentially.
CONCLUSIONS:  Mitotic spindle checkpoint dysfunction is a common characteristic of human urothelial carcinoma, and can be exploited with pharmacologic Aurora A inhibition. Future studies that explore the mechanisms of spindle checkpoint failure in bladder cancer and evaluate the therapeutic role of Aurora kinases for bladder cancer patients would be of value.

overall_design: Tissue samples with urothelial cell carcinoma  from  bladder  as well as normal  references  were collected and the gene expression profiles were compared. No technical replicates.

first: Bin

last: The

first: Hansel

last: Donna

first: Zhongfa


title: Cardiac miRNA expression (random section containing both ventricles) in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

summary: C57BL/6 mice were exposed to vehicle or 0.162 mg carbon black nanoparticles by intratracheal installation and were sacrificed 1, 3 and 28 days post-exposure. Gene expression was investigated in two sets of mice treated according to the identical exposure protocol. MicroRNAs were investigated in the second set of mice.

overall_design: C57BL/6 mice were exposed to 0.000 or 0.162 mg Printex 90 and were sacrificed 1, 3 and 28 days after exposure. Individual total RNA enriched with small RNA from 6 mice per treatment group (control and 0.162mg) was hybridized to 8 x 15K Agilent miRNA slides.

first: Julie

last: Bourdon

first: Anne

last: Saber

first: Nicklas

last: Jacobsen

first: Sabina

last: Halappanavar

first: Hakan

last: Wallin

first: Carole

last: Yauk

first: Ulla

last: Vogel


title: Differential gene expression profiles between myeloid-biased and lymphoid-biased hematopoietic stem cells.

city: La Jolla

first: Hans

last: Sieburg

state: CA

address: 10901 North Torrey Pines Road

department: Stem Cells and Regenerative Biology

institute: Sanford Burnham Medical Research Institute

summary: Array analysis of My-bi and Ly-bi HSC identifies candidate molecules for myeloid-bias. Collectively the data show that HSC in adults are largely epigenetically fixed in differentiation and self-renewal behavior. A direct examination of the epigenetic mechanisms that imprint HSC is difficult. However, an indirect way of assessing the effects of epigenetic imprinting is to look for the expressed gene programs of different types of HSC. Therefore, we performed an array analysis in collaboration with Dr. Michael Cooke. My-bi and Ly-bi HSC were identified in clonally repopulated hosts.  The analysis returned 218 differentially expressed genes (≥ Log2 ≥2, p< 0.05) of which 36 were found to be overexpressed in My-bi HSC and the rest was overexpressed in Ly-bi HSC (Appendix A). There was no difference in expression levels for genes known to be involved in fate decisions during differentiation.  This agrees well with our data that lineage bias is a stable function of a HSC, and does not reflect a differentiated type of cell.

overall_design: Gene expression profiles of myeloid-biased (My-bi) and lymphoid-biased (Ly-bi) stem cells were analyzed.  Clonally repopulated hosts were generated by limiting dilution of bone marrow into ablated hosts and lineage bias was determined.  Single My-bi (Tenor) and Ly-bi (Mort) repopulated hosts were sacrificed and Donor type HSC were enriched for Sca-1+, Lin- cells.  Two technical replicates of RNA extract were run from each clone.

first: Rebecca

last: Cho

first: Michael

last: Cooke

first: Christa

middle: E

last: Muller-Sieburg


title: TAK1 deficient liver parenchymal cells with Rip3 double knockout TAK1LPC

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: Genomic copy number profiling of TAK1 deficient liver parenchymal cells with Rip3 double knockout

overall_design: Sample vs. Reference (pool of 4 normal liver tissues)

first: Florian

last: Reisinger

first: Mathias

last: Heikenwalder


title: Molecular profile of parvalbumin-immunoreactive neurons in superior temporal cortex in schizophrenia

city: Belmont

first: Sarah

last: Mauney

state: MA

address: 115 Mill St.

institute: McLean Hospital

summary: Dysregulation of pyramidal cell network function by the soma- and axon-targeting inhibitory neurons that contain the calcium-binding protein parvalbumin (PV) represents a core pathophysiological feature of schizophrenia. In order to gain insight into the molecular basis of their functional impairment, we used laser capture microdissection (LCM) to isolate PV-immunolabeled neurons from layer 3 of Brodmann’s area 42 of the superior temporal gyrus (STG) from postmortem schizophrenia and normal control brains. We then extracted ribonucleic acid (RNA) from these neurons and determined their messenger RNA (mRNA) expression profile using the Affymetrix platform of microarray technology. 739 mRNA transcripts were found to be differentially expressed in PV neurons in subjects with schizophrenia, including genes associated with WNT (wingless-type), NOTCH and PGE2 (prostaglandin E2) signaling, in addition to genes that regulate cell cycle and apoptosis. Of these 739 genes, only 89 (12%) were also differentially expressed in pyramidal neurons as found in the accompanying study, suggesting that the molecular pathophysiology of schizophrenia appears to be predominantly neuronal type-specific. Taken together, findings of this study provide a neurobiological framework within which hypotheses of the molecular mechanisms that underlie the dysfunction of PV neurons in schizophrenia can be generated and experimentally explored and, as such, may ultimately inform the conceptualization of targeted molecular intervention.

overall_design: Gene expression microarray from mRNA isolated from parvalbumin cells in layer 3 of the STG from 8 normal controls  and 8 subjects with schizophrenia. There was no significant difference between diagnosis groups for age, sex, and post mortem interval (PMI).

first: Charmaine

middle: Y

last: Pietersen

first: Susie

last: Kim

first: Eleonora

last: Passeri

first: Maribel

middle: P

last: Lim

first: Jill

last: Goldstein

first: Tracey

last: Petreyshen

first: Larry

last: Seidman

first: Martha

last: Shenton

first: Robert

middle: W

last: McCarley

first: Kai-C

last: Sonntag

first: Tsung-Ung

last: Woo


title: Comparative Genomic Hybridization of Leishmania major SbIII resistant mutants and L. major WT

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

institute: Université Laval

summary:
SbIII clonal mutants and an isogenic WT clonal line. Genomic DNA from clonal WT or mutants were digested and hybridized to whole genome DNA microarrays.
Antimonials are still the mainstay of treatment against Leishmaniasis but in the past decade resistance has been a severe threat. We carried out short read next generation sequencing (NGS) and comparative genomic hybridization (CGH) of three independent Leishmania major antimony resistant mutants. Copy number variations were consistently detected in both NGS and CGH where several chromosomal aneuploidies were correlated to antimony resistance. A major attribute of antimony resistance was a novel terminal deletion of variable length (67kb-204kb) of the polyploid chromosome 31 in the three mutants and was experimentally validated. Terminal deletion in two mutants occurred at the level of inverted repeated sequences in chromosome 31. AQP1 (LmjF.31.0020), a gene encoding for an aquaglyceroporin, which facilitates uptake of trivalent metalloids, was a part of the deleted region. Transfection of AQP1 into resistant mutants rendered them hypersensitive to SbIII. CGH, NGS and Southern blot analysis also highlighted a novel stable, intrachromosomal amplification of a subtelomeric locus on chromosome 34 in one mutant. This region encoded redox enzymes like ascorbate dependent peroxidase (APX) and glucose-6-phosphate dehydrogenase (G6PDH) and overexpression of the genes coding for these enzymes in revertant backgrounds demonstrated resistance to SbIII and protection from reactive oxygen species (ROS) accumulation. Generation of G6PDH null mutant in one revertant exhibited SbIII sensitivity and protection from ROS which were rescued in the add back. Our genomic analyses and parallel functional validation highlighted novel genomic rearrangements, functionally important resistant loci and the implication of new genes in antimony resistance in Leishmania.
This submission represents the microarray component of the study

overall_design: 3 biological replicates of each sample

first: Angana

last: Mukherjee

first: Eric

last: Madore


title: The whole genome transcription analysis reveals the regulatory network for Listeria monocytogenes biofilm formation is modified in the prfA deletion mutant

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

summary: The foodborne pathogen Listeria monocytogenes has the ability to develop biofilm in food-processing environment, which becomes a major concern for the food safety. PrfA, a key transcriptional activator that regulates most of the known listerial virulence gene expression, has been shown to promote L. monocytogenes biofilm formation. In this study, the whole genome microarray was used to identify differentially expressed genes associated with the putative interaction between biofilm formation and PrfA in L. monocytogenes. Comparative transcriptome analyses indicated over 21.9% of the L. monocytogenes EGDe genes (627 out of 2857 predicted) were altered in their expression in biofilm cells relative to planktonic cell populations. These genes were classed into different functional categories which cover most of the biochemical functions encountered in bacterial cells, especially involved in ion transport, DNA repair, and cell wall biosynthesis based on significant enrichment of GO terms. Among them, 185 genes were identified to be associated with PrfA and biofilm formation by comparison of the whole gene expression profiles of L. monocytogenes EGDe and its ΔprfA mutant. The expression tendency of these PrfA-associated and biofilm-specific genes were mainly opposite in ΔprfA biofilm, and most of them are involved in phage-related function, membrane bioenergetics, and cell wall. Our results indicated that L. monocytogenes biofilm formation is probably controlled by the complex regulation network involved variable genes required for the different biological pathways. This regulatory network is modified in the prfA deletion mutant in order to maintain its stable biofilm lifestyle.

overall_design: Gene expression of planktonic cells and biofilm cells in Listeria monocytogenes EGDe and prfA isogenic deletion strain EGDeΔprfA with cultivated in MEM and BHI for 48 hours, were mesasued using Agilent Listeria monocytogenes customized whole-genome microarray 8x15 array. Three replicates.

first: Qin

last: Luo

first: Junli

last: Shang

first: Xiaoqin

last: Feng

first: Xinxin

last: Guo

first: Yuanhong

last: Zhuang

first: Qingchun

last: Zhou


title: Transcriptional profiling of a genome-reduced strain in Schizosaccharomyces pombe

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Gene number of the fission yeast Schizosaccharomyces pombe is the lowest in free-living eukaryotes. We further reduced the gene number to examine a minimal gene set required for growth. The genome-reduced strain, named ASP3894, has four chromosomal deletion regions: 168.4 kb deletion in the left arm of chromosome 1 (ALT), 155.4 kb deletion in the right arm of chromosome 1 (ART), 211.7 kb deletion in the left arm of chromosome 2 (BLT) and 121.6 kb deletion in the right arm of chromosome 2 (BRT). As a result of the 657.3 kb genome reduction, 224 genes of approximately 5100 total genes were reduced. ASP3894 transcriptional profiling was compared with a parent strain, ASP3880, that is a non-genome-reduced strain to examine the influence of genome reduction.

overall_design: Three independent experiments. 3 control ASP3880 samples and 3 genome-reduced strain ASP3894 samples were independently grown in EMM medium and harvested at the logarithmic phase.

first: Mayumi

last: Sasaki

first: Hideki

last: Tohda


title: Human SKOV-3 cells, Input DNA vs ChIP DNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Identification of  target genes of PITX2 homeodomain transcription factor in ovary using human ovarian adenocarcinoma cells, SKOV-3 to determine the transcriptional network of PITX2.

overall_design: Genotypic Technology designed Custom Human Promoter 244k ChIP-on-chip Array  (AMADID-019469)

first: Moitri

last: Basu

first: SibSankar

last: Roy


title: A roadmap of cell-type specific gene expression during late stages of the arbuscular mycorrhiza symbiosis

status: Public on Apr 28 2013

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

summary: Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel cell-type specific gene expression during late stages of Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on laser-microdissected cells. We used Medicago GeneChips to detail the cell-type specific programme of gene expression in late stages of colonization by arbuscular mycorrhizal fungi and identified genes differentially expressed during these stages.

platform_organism:
Sinorhizobium meliloti
Medicago sativa
Medicago truncatula

overall_design: Medicago truncatula Gaertn ‘Jemalong’ genotype A17 plantlets were grown in the climate chamber. Plants grown for the collection of root cortical cells containing arbuscules (ARB), root cortical cells from mycorrhizal roots (CMR), and root epidermal cells from mycorrhizal roots (EPI) were mycorrhized after 2 weeks with Glomus intraradices and mycorrhizal roots were harvested at around 21 days post inoculation (dpi).

first: Claudia

last: Hogekamp

first: Jörg

last: Becker


title: A roadmap of cell-type specific gene expression during early stages of the arbuscular mycorrhiza symbiosis

summary: Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel cell-type specific gene expression during early stages of Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on laser-microdissected cells. We used Medicago GeneChips to detail the cell-type specific programme of gene expression in early stages of colonization by arbuscular mycorrhizal fungi and identified genes differentially expressed during these stages.

overall_design: Medicago truncatula Gaertn ‘Jemalong’ genotype A17 plantlets were grown in the climate chamber. Plants grown for the collection appressorial root areas (APP) and the corresponding non-appressorial root areas (NAP) were mycorrhized after 3 weeks and roots were harvested at 5-6 dpi.


title: Differential gene expression between left and right chicken HH14 sinus horns

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

summary: Microarrays experiments were performed in order to assess which genes are differentially expressed between the embryonic chicken sinus horns at HH14.

overall_design: Three, technical, dye swapped comparisons between Left and Right sinus horns. In total six arrays were used in this study

first: Angela

last: Torlopp

first: Peter-Bram

middle: A

last: 't Hoen

first: Thomas

last: Brand


title: A roadmap of cell-type specific gene expression during sequential stages of the arbuscular mycorrhiza symbiosis

country: Germany

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression in cellular compartments of Aplysia sensory neurons

status: Public on Apr 26 2013

city: New York

first: Sergey

last: Kalachikov

state: NY

address: NWC Bld, 550 West 120th Street Rm 1002

department: Chemical Engineering

institute: Columbia University

summary:
Whole genome transcriptional profiling is used to compare ESTs found in cell bodies and processes of Aplysia sensory neurons
RNA samples derived from cell bodies or processes of Aplysia single cultured sensory neurons were hybridized to custom Aplysia EST microarrays.

overall_design: Two-condition experiment; four biological replicates for each condition were reciprocally hybridized on each two-color array

first: Sathyaramayanan

last: Puthanveetil

first: Irina

last: Morozova


title: Aplysia kinesin mRNA cargo study