title: A metagenomic study revealing unexpectedly  diverse functional groups in microbial communities of deep-ground oil

city: Beijing

first: Man

last: Cai

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: Samples of oil and production water were collected from five wells of the Qinghai Oilfield, China, and subjected to GeoChip hybridization experiments for microbial functional diversity profiling. Unexpectedly, a remarkable microbial diversity in oil samples, which was higher than that in the corresponding water samples, was observed, thus challenging previously believed assumptions about the microbial diversity in this ecosystem. Hierarchical clustering separated oil and water samples, thereby indicating distinct functional structures in the samples. Genes involved in the degradation of hydrocarbons, organic remediation, stress response, and carbon cycling were significantly abundant in crude oil, which is consistent with their important roles in residing in oil. Association analysis with environmental variables suggested that oil components comprising aromatic hydrocarbons, aliphatic hydrocarbons, and a polar fraction with nitrogen-, sulfur-, and oxygen-containing compounds were mainly influential on the structure of the microbial community. Furthermore, a comparison of microbial communities in oil samples indicated that the structures were depth/temperature-dependent. To our knowledge, this is the first thorough study to profile microbial functional diversity in crude oil samples.

overall_design: From the Qinghai Oilfield located in the Tibetan Plateau, northwest China, oil production mixtures were taken from four oil production wells (No. 813, 516, 48 and 27) and one injection well (No. 517) in the Yue-II block. The floating oil and water phases of the production mixtures were separated overnight by gravitational separation. Subsequently, the microbial community and the characteristics of the water solution (W813, W516, W48, and W27) and floating crude oil (O813, O516, O48, and O27) samples were analyzed. A similar analysis was performed with the injection water solution (W517).

first: Chang-Qiao

last: Chi

first: Yue-Qin

last: Tang

first: Yan

last: Li

first: Xing-Biao

last: Wang

first: Yong

last: Nie

first: Ze-Shen

last: Liu

first: Yunfeng

last: Yang

first: Jizhong

last: Zhou

first: Xiao-Lei

last: Wu


title: Genome-Wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis

status: Public on Mar 31 2016

city: Jena

first: Andreas

last: Dix

address: Beutenbergstraße 11a

country: Germany

institute: Hans-Knöll-Institut

summary: Invasive aspergillosis (IA) is a devastating opportunistic infection and its treatment constitutes a considerable burden for the health care system. Immunocompromised patients are at an increased risk for IA, which is mainly caused by the species Aspergillus fumigatus. An early and reliable diagnosis is required to initiate the appropriate antifungal therapy. However, diagnostic sensitivity and accuracy still needs to be improved, which can be achieved at least partly by the definition of new biomarkers. Besides the direct detection of the pathogen by the current diagnostic methods, the analysis of the host response is a promising strategy towards this aim. Following this approach, we sought to identify new biomarkers for IA. For this purpose, we analyzed gene expression profiles of haematological patients and compared profiles of patients suffering from IA with non-IA patients. Based on microarray data, we applied a comprehensive feature selection using a random forest classifier. We identified the transcript coding for the S100 calcium-binding protein B (S100B) as a potential new biomarker for the diagnosis of IA. Considering the expression of this gene, we were able to classify samples from patients with IA with 82.3% sensitivity and 74.6% specificity. Moreover, we validated the expression of S100B in a real-time RT-PCR assay and we also found a down-regulation of S100B in A. fumigatus stimulated DCs. An influence on the IL1B and CXCL1 downstream levels was demonstrated by this S100B knockdown. In conclusion, this study covers an effective feature selection revealing a key regulator of the human immune response during IA. S100B may represent an additional diagnostic marker that in combination with the established techniques may improve the accuracy of IA diagnosis.

overall_design: The gene expression data of patients with invasive aspergillosis (IA) was compared to patients without IA. 23 samples of 8 IA patients, 13 samples from 7 unclassified patients and 1 patient with  possible invasive fungal disease (IFD), and 9 control samples from 8 healthy donors were generated. Patients were classified according to the current EORTC/MSG criteria.

first: Kristin

last: Czakai

first: Jan

last: Springer

first: Mirjam

last: Fliesser

first: Michael

last: Bonin

first: Reinhard

last: Guthke

first: Anna

middle: L

last: Schmitt

first: Hermann

last: Einsele

first: Jörg

last: Linde

first: Jürgen

last: Löffler


title: Temporal Expression of Peripheral Blood Leukocyte Biomarkers in a Macaca fascicularis Primary Infection Model of Tuberculosis

city: Salisbury

first: Karen

middle: Elizabeth

last: Kempsell

state: Wiltshire

address: Porton Down

department: Science Group

country: United Kingdom

institute: UK Health Security Agency

summary: A temporal study of gene expression in peripheral blood leukocytes (PBLs) from a Mycobacterium tuberculosis primary, temporal pulmonary challenge model Macaca fascicularis has been conducted. PBL samples were taken prior to challenge and at one, two, four an six weeks post-challenge and labelled, purified RNAs hybridised to Operon Human Genome AROS V4.0 slides. Data analyses revealed a large number of differentially regulated gene entities, which exhibited temporal profiles of expression across the time course study. Further data refinements identified key groups of markers showing specific group-specific expression patterns, with a substantial reprogramming event evident at the four to six week interval. Select statistically-significant gene entities from this study and other immune and apoptotic markers were validated using qPCR. These confirmed many of the observations elucidated using microarray hybridisation. The results showed evidence of a step-change from an ‘early’ perhaps FOS-driven response, to a predominantly type I interferon-driven response, with coincident reduction of expression of other markers i.e. loss of T-cell-associate marker expression in responsive animals and elevation of markers which may be associated with a myeloid suppressor cell phenotype e.g. CD163.   The animals in the study were of different lineages, Chinese and Mauritian, which showed clear evidence of differing susceptibilities to Tuberculosis challenge. Further analyses determined a number of key differences in response profiles between the groups, particularly in expression of T-cell and apoptotic makers, among others. These have provided interesting insights into innate susceptibility phenotypes. Using a combination of parametric and non-parametric artificial neural network analyses we have identified key genes and regulatory pathways which may be important in earl and adaptive responses to TB.

overall_design: Six animals infected with Mycobacterium tuberculosis subsequent to prebleed timepoint; blood samples taken at defined weekly timepoints post-infection

middle: E


title: The maleless gene mitigates global aneuploid effect and evolutionary shift from X to autosomes

city: Hyderabad

first: Utpal

last: Bhadra

state: TG

address: Uppal Road

department: UB group

country: India

institute: CCMB

summary:
During sexual dimorphism, the loss of one entire X chromosome in Drosophila males is achieved largely via a broad genome-wide aneuploid effect. Exploring how MSL proteins and two large non coding RNAs (roX1 and roX2) modulate trans-acting aneuploid effect for equality to females, we employ a system biology approach (microarray) to investigate the global aneuploid effect of maleless(mle) mutation by disrupting MSL binding. A large number of the genes (144) that encode a broad spectrum of cellular transport proteins and transcription factors are located in the autosomes of Drosophila melanogaster.
We find these autosomal targets are sensitive to the aneuploid effect and are poorly conserved in primitive Drosophila species and Anopheles gambiae autosomes. It is expected that during evolutionary process, they shifted gradually from their X chromosomal position in primitive Drosophila to autosomes in melanogaster, suggesting that MSL favors inverse counteraction of these autosomal targets along with X-linked genes. These findings suggest a remarkable and previously unsuspected level of complexity among aneuploid-sensitive genes, that creates a functional shift of the aneuploid effect from X to autosomes during evolution, which is resolved by the binding of MSL complex on the X chromosome..

overall_design:
Drosophila  larvae were selected based on genotypes particularly with Tb phenotypes. Total cellular RNA were extracted from each genotypes and hebridized with affymetrix Drosophila Microarray chip.
Gene Expression profiling of fly base to understand the role of maleless mutation in aneuploid targets.

first: Sumit

middle: G

last: Gandhi

first: Palaparthi

last: Ramesh

first: Manoj

middle: K

last: Balyan

first: Manika

last: Pal-Bhadra


title: mTORC1 and CK2 coordinate ternary and eIF4F complex assembly

status: Public on Apr 01 2016

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: mRNA translation plays a major role in homeostasis, whereas its dysregulation underpins a variety of pathological states including cancer, metabolic syndrome and neurological disorders.  Ternary complex (TC) and eIF4F complex assembly are two major rate-limiting steps in translation initiation that are thought to be regulated by eIF2α phosphorylation, and the mTOR/4E-BP pathway, respectively2. However, how TC and eIF4F assembly are coordinated remains largely unknown. Using polysome-profiling, we show that on a genome-wide scale mTOR suppresses translation of mRNAs, which are translationally activated under short-term ER stress when TC recycling is attenuated by eIF2α phosphorylation. During acute nutrient or growth factor stimulation, mTORC1 induces eIF2β phosphorylation, which increases recruitment of NCK1 to eIF2, decreases eIF2α phosphorylation and bolsters TC recycling. Accordingly, eIF2β appears to act as a previously unidentified mediator of mTORC1 on protein synthesis and proliferation. In addition, we demonstrate a formerly undocumented role for CK2 in regulation of translation initiation, whereby CK2 stimulates phosphorylation of eIF2β and simultaneously bolsters eIF4F complex assembly via the mTORC1/4E-BP pathway. These findings imply a previously unrecognized mode of translation regulation whereby mTORC1 and CK2 coordinate TC and eIF4F complex assembly to stimulate cell proliferation.

overall_design: Comparisons of polysome-associated and cytoplasmic mRNA from starved cells or cells stimulated with insulin in the presence or absence of Torin-1.


title: ATFS-1 regulates a broad protective transcriptional program

status: Public on Mar 21 2016

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

country: USA

institute: Memorial Sloan Kettering Cancer Center

summary:
We previously identified a number of genes which were differentially expressed during mitochondrial stress in an ATFS-1-dependent manner using an atfs-1 loss-of-function mutant allele . To complement the findings from our previous microarray, we compared the transcript profiles from wild-type and atfs-1(et18) gain-of-function worms (which have constitutively active ATFS-1) in the absence of mitochondrial stress.
We used microarrays to identify genes regulated by ATFS-1 using a gain-of-function allele of atfs-1.

overall_design: RNA samples were prepared from wild-type (N2) and atfs-1(et18) (et18) worms fed E. coli OP50. Worms were synchronized by bleaching, raised on solid culture and harvested at the L4 stage. Each experiment was performed in triplicate indicated as 1,2 and 3.

first: Mark

last: Pellegrino

first: Cole

last: Haynes


title: Gene expression of soybean roots inoculated with wild-type and type III secretion mutant strains of Bradyrhizobium elkanii

status: Public on Mar 09 2016

city: Fuchu

first: Michiko

last: YASUDA

state: Tokyo

address: 3-5-8 Saiwaicho

department: International Environmental and Agricultural Science

country: Japan

institute: Tokyo University of Agriculture and Technology

summary: To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. BARC-2 (Rj4/Rj4)) were surface-sterilized and germinated at 25 °C for 2 days and were transferred to the seed pack (Seed Pack; Daiki rika Kogyo Co., Ltd., Shiga, Japan)  watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61 or its type III secretion mutant BErhcJ. Plants were cultivated in a growth chamber at 25°C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 2 and 4 days after inoculation.

overall_design: Gene expression in soybean roots inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BErhcJ was measured 2 and 4 days after inoculation. Three independent experiments were performed at each inoculation.

first: M

last: Yasuda


title: The ferric uptake regulator Fur is a potential regulator of Campylobacter jejuni acid survival and cross-protection against other stresses

status: Public on Mar 17 2016

city: ottawa

first: ALAIN

last: STINTZI

state: ONTARIO

address: 451 SMYTH ROAD

department: BIOCHEMSISTRY, MICROBIOLOGY AND IMMUNOLOGY

country: Canada

institute: UOTTAWA

summary:
Campylobacter jejuni is a prevalent cause of bacterial gastroenteritis in humans worldwide. The mechanism by which C. jejuni survives stomach acidity remains unknown. Herein, we have demonstrated that C. jejuni with a fur deletion was more sensitive to acid than the wild-type strain. Profiling the acid stimulon of the C. jejuni ∆fur mutant allowed us to uncover Fur-regulated genes under acidic conditions. The up-regulation of heat shock genes and the down-regulation of genes involved in flagellar and cell envelope biogenesis in the fur mutant highlight the importance of Fur in Campylobacter acid survival. Interestingly, prior acid exposure of C. jejuni cross-protected the bacterium against oxidative stress. Western-blot analysis and real-time qRT-PCR revealed an increased expression of the catalase KatA in acid-stressed C. jejuni relative to unstressed bacteria. The enhanced survival of C. jejuni to oxidative stress was shown to be Fur-dependent through the regulation of katA expression. Electrophoretic mobility shift assay (EMSA) demonstrated that the binding affinity between Fur and katA is reduced under low pH allowing for higher expression of katA and the defense against oxidative stress. Strikingly, the ∆fur mutant exhibited a reduced virulence capacity in both human epithelial cells and G. mellonella infection model as compared to C. jejuni wild-type. Altogether, this is the first study showing that in addition to its role in iron metabolism, Fur is an important regulator of C. jejuni acid response and cross-protection against other stresses. Moreover, our results clearly demonstrate that Fur plays a substantial role in C. jejuni host pathogenesis.
Campylobacter jejuni is a prevalent cause of bacterial gastroenteritis in humans worldwide. The mechanism by which C. jejuni survives stomach acidity remains unknown. Herein, we have demonstrated that C. jejuni with a fur deletion was more sensitive to acid than the wild-type strain. Profiling the acid stimulon of the C. jejuni ∆fur mutant allowed us to uncover Fur-regulated genes under acidic conditions. The up-regulation of heat shock genes and the down-regulation of genes involved in flagellar and cell envelope biogenesis in the fur mutant highlight the importance of Fur in Campylobacter acid survival. Interestingly, prior acid exposure of C. jejuni cross-protected the bacterium against oxidative stress. Western-blot analysis and real-time qRT-PCR revealed an increased expression of the catalase KatA in acid-stressed C. jejuni relative to unstressed bacteria. The enhanced survival of C. jejuni to oxidative stress was shown to be Fur-dependent through the regulation of katA expression. Electrophoretic mobility shift assay (EMSA) demonstrated that the binding affinity between Fur and katA is reduced under low pH allowing for higher expression of katA and the defense against oxidative stress. Strikingly, the ∆fur mutant exhibited a reduced virulence capacity in both human epithelial cells and G. mellonella infection model as compared to C. jejuni wild-type. Altogether, this is the first study showing that in addition to its role in iron metabolism, Fur is an important regulator of C. jejuni acid response and cross-protection against other stresses. Moreover, our results clearly demonstrate that Fur plays a substantial role in C. jejuni host pathogenesis.

overall_design: Three biological with three technical replicates for both test and control samples at every pH condition

first: Momen

last: Askoura

first: Alain

last: Stintzi


title: Expression profiling in extracellular miRNAs (plasma miRNAs) of CML patients after imatinib discontinuation (STOP-IM)

city: Shinjyuku

first: Tomohiro

last: Umezu

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

summary: An approximately 40% of chronic myeloid leukemia (CML) patients who discontinued imatinib (IM) therapy maintained undetectable minimal residual disease (UMRD) for more than one year (STOP-IM). We set out to examine plasma miRNAs expression in CML patients who could discontinue IM, to seek the possible distinguishable biomarker in STOP-IM CML patients. We compared CML patients who sustained UMRD for more than one year after discontinuation of imatinib (STOP-IM group) with healthy volunteers (controls).

overall_design: In 7 patients who had discontinued IM with sustained UMRD for more than 6 months (STOP-IM group), samples were collected when IM was stopped. Seven healthy volunteers served as control. Plasma samples were harvested form 2ml of whole blood. Isolation of total RNA was performed using the mirVana PARIS kit (Ambion, Austin, TX, USA). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). Synthetic ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. With the use of SDS2.2 software and Data Assist (Thermo Fisher Sciences), the expression of plasma miRNAs was calculated based on cycle threshold (Ct) values normalized by those of ath-miR-159, which was spiked in each plasma sample. Data analysis was done using GeneSiferⓇ software (Perkin Elmer, Waltham, MA, USA). The Benjamini-Hochberg algorithm was used for estimation of false discovery rates.


title: Gene expression data from Pseudomonas aeruginosa PAO1 and mutator (Δ mutS) evolved for 940 generations in LB with and without sub-inhibitory concentrations of ciprofloxacin (0.05µg/ml)

status: Public on Feb 25 2016

city: Copenhagen

first: Oana

last: Ciofu

address: Blegdamsvej 3

department: Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

summary:
Gene expression of P. aerruginosa changes after short-term exposure to ciprofloxacin at sub-inhibitory concentrations but the effect of long-term exposure which select for the most fitted subpopulations is not known.
We used microarrays to investigate the changes in gene expression of P.aeruginosa PAO1 and mutator (Δ mutS) after long-term evolution (94 daily passages) in LB in the presence and absence of ciprofloxacin

overall_design: Three different colonies from the ancestral populations of PAO1 and mutator (Δ mutS) as well as from the evolved populations (day 94) of each of the three lineages (A;B;C) in the presence or absence of ciprofloxacin at a concentration of 0.05 µg/ml were used for overnight cultures in LB and total RNA was extracted at OD600nm=1 and hybridized on P. aeruginosa Affymetrix chip.


title: Expression profiling in extracellular miRNAs of CML patients after imatinib discontinuation (STOP-IM)

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

overall_design: Refer to individual Series


title: Elucidating the effects of the macrophage environment on the efficacy of anti-mycobacterial drugs

status: Public on Feb 21 2016

city: Ithaca

first: Yancheng

last: Liu

institute: Cornell University

summary: We examined the transcriptional responses of intracellular M. tuberculosis exposed to different front-line drugs during macrophage infection. Our data reveal that Mtb experiences amplification of multiple host-derived pressures following drug exposure. The stresses from the host environment have a dominant impact on Mtb gene expression to the extent that the transcriptional profiles cluster according to environment, ie. broth vs host cell, rather than drug.

overall_design: Transcriptional responses of M. tuberculosis to front-line drugs were studied under two environmental conditions: J774 macrophages vs. 7H9 broth, and 4 drugs were examined: INH, RIF, EMB, and PZA.

first: Kyle

middle: H

last: Rohde

first: Robert

middle: B

last: Abramovitch

first: Brian

middle: C

last: VanderVen

first: David

last: Russell


title: Transcriptome profiling of tdc cluster delection mutant of Enterococcus faecalis V583

status: Public on Feb 15 2016

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

country: Spain

institute: IPLA-CSIC

summary: The aim was to study the transcriptional profiling of the tdc cluster delection mutant E. faecalis V583 Δtdc (non-tyramine producer) compared to the wild type strain E. faecalis V583 (tyramine producer). We compared the expression profile of the strains grown in M17 medium with glucose as carbon source and suplemented with tyrosine.

overall_design: E. faecalis V583 Δtdc cells (test) compared with E. faecalis V583 cells (reference). Both strains grown in GM17 medium suplemented 15 mM tyrosine.

first: Marta

last: Perez

first: Beatriz

last: del Rio

first: Begoña

last: Redruello

first: Anne

last: de Jong

first: Oscar

middle: P

last: Kuipers

first: Jan

last: Kok

last: Martin

first: Maria

last: Fernandez

first: Miguel

middle: A

last: Alvarez


title: ANAC046, a NAC family transcription factor, is involved in leaf senescence by controlling the chlorophyll catabolic gene expression in Arabidopsis

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

summary: Chlorophyll (Chl) degradation is an important process during leaf senescence, bud breaking and fruit ripening. Chlorophyll catabolic pathway has been intensively studied and nearly all the enzymes involved in the pathway are characterized. However, regulatory mechanism of the pathway is largely unknown at the molecular level. In this study, we performed a yeast one-hybrid screening using a library composed only of transcription factor cDNAs to search for factors controlling expression of the chlorophyll catabolic genes. We identified a common regulator, ANAC046, that directly binds to the promoter regions of NON-YELLOW COLORING 1, STAY-GREEN 1 (SGR1), SGR2, and pheophorbide a oxygenase. Transgenic plants overexpressing ANAC046 exhibited an early senescence phenotype with lower chlorophyll content as compared with the wild-type plants, while loss-of-function mutants exhibited a delayed senescence phenotype with higher chlorophyll content. Microarray analysis of ANAC046 showed that not only chlorophyll catabolic genes but also senescence-associated genes were positively regulated by ANAC046. Here, we demonstrate that ANAC046 is a novel positive regulator of Arabidopsis leaf senescence and exerts its effect through controlling the expressions of Chl catabolic genes and senescence-associated genes.

overall_design: Transcriptomes of leaf of ANAC046-overexpression plant (50 days after seed sawing), seedling of ANAC046-SRDX-overexpression plant (5 days after dark treatment), and seedling of ANAC046-knockout plant (5 days after dark treatment) were measured together with their respective wild-type controls.

first: Oda

middle: Y

last: Chihiro

first: Mitsuda

last: Nobutaka

first: Sakamoto

last: Shingo

first: Ogawa

last: Daisuke

first: Ohme

middle: T

last: Masaru

first: Ohmiya

last: Akemi


title: Expression profiling in extracellular miRNAs (exosomal miRNAs) of CML patients after imatinib discontinuation (STOP-IM)

first: Tomohiro

last: Umezu

summary: An approximately 40% of chronic myeloid leukemia (CML) patients who discontinued imatinib (IM) therapy maintained undetectable minimal residual disease (UMRD) for more than one year (STOP-IM). We therefore set out to examine exosomal miRNAs expression in CML patients who could discontinue IM, to seek the possible distinguishable biomarker in STOP-IM CML patients. We compared CML patients who sustained UMRD for more than one year after discontinuation of imatinib (STOP-IM group) with healthy volunteers (controls).

overall_design: In 7 patients who had discontinued IM with sustained UMRD for more than 6 months (STOP-IM group), samples were collected when IM was stopped. Seven healthy volunteers served as control. Plasma samples were harvested form 2ml of whole blood. Exosoms were isolated from plasma using a Total exosome isolation kit for plasma (Life Technologies). Isolation of total RNA was performed using the mirVana PARIS kit (Ambion, Austin, TX, USA). The expression profile of miRNAs was determined using the Human Taqman miRNA Arrays A (Applied Biosystems). Synthetic ath-miR-159 (Hokkaido System Science, Hokkaido, Japan) were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program. With the use of SDS2.2 software and Data Assist (Thermo Fisher Sciences), the expression of plasma miRNAs was calculated based on cycle threshold (Ct) values normalized by those of ath-miR-159, which was spiked in each plasma sample. Data analysis was done using GeneSiferⓇ software (Perkin Elmer, Waltham, MA, USA). The Benjamini-Hochberg algorithm was used for estimation of false discovery rates.


title: Dosage Compensation of an Aneuploid Genome in Mouse Spermatogenic Cells

status: Public on Mar 30 2016

city: Prague

first: David

last: Homolka

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics AS CR

summary: Autosomal trisomies and monosomies bring serious threats to embryonic development through transcriptional disarray primarily caused by the dosage effect of the aneuploid part of the genome. The present study compared the effect of a mouse viable 30 Mb segmental trisomy on the genome-wide transcriptional profile of somatic (liver) cells and male germ cells. While the 1.6-fold change in expression of triplicated genes reflected the gene dosage in liver cells, the extra copy was almost fully compensated in early pachytene spermatocytes, showing 1.18-fold increase. Allele-specific semi-quantitative evaluation of steady-state mRNA levels of the triplicated Amdhd2 gene revealed silencing evenly distributed among all three copies in these meiotic cells. Although more pronounced, the dosage compensation of trisomic genes was concordant with the incidence of HORMAD2 and γH2AX markers of unsynapsed chromatin. The possible explanations include insufficient sensitivity to detect both MSUC markers in the 30 Mb region of the chromosome, or an early silencing effect of another epigenetic factor. Taken together, our results indicate that the meiotic silencing of unsynapsed chromatin is the major but not the only factor driving the dosage compensation of triplicated genes in primary spermatocytes.

overall_design: We compared the global expression profiles in isolated popoulations of meiotic cells and liver cells of Ts43H trisomic males and their t121/D17 euploid siblings.

first: Petr

last: Jansa


title: Spatial Differences in Gene Expression in the Bovine Oviduct

status: Public on Mar 01 2016

city: Dublin

first: Peadar

last: O'Gaora

address: Belfield

country: Ireland

institute: UCD

type:
Expression profiling by array
Third-party reanalysis

summary: The aim of this study was to compare the transcriptome of the different regions of the oviduct between pregnant and cyclic heifers. After synchronizing crossbred beef heifers, those in standing oestrus (=Day 0) were randomly assigned to cyclic (non bred, n=6), or pregnant (artificially inseminated, n=11) groups. They were slaughtered on Day 3 and both oviducts from each animal were isolated and cut in half to separate ampulla and isthmus. Each portion was flushed to confirm the presence of an oocyte/embryo and was then opened longitudinally and scraped to obtain epithelial cells which were snap-frozen. Oocytes and embryos were located in the isthmus of the oviduct ipsilateral to the corpus luteum. Microarray analysis of oviductal cells revealed that proximity to the corpus luteum did not affect the transcriptome of the isthmus, irrespective of pregnancy status. However, 2287 genes were differentially expressed (P<0.01) between the ampulla and isthmus of the oviduct ipsilateral to the corpus luteum. Gene ontology revealed that the main biological processes overrepresented in the isthmus were synthesis of nitrogen, lipids, nucleotides, steroids and cholesterol as well as vesicle-mediated transport, cell cycle, apoptosis, endocytosis and exocytosis, whereas cell motion, motility and migration, DNA repair, calcium ion homeostasis, carbohydrate biosynthesis and regulation of cilium movement and beat frequency were overrepresented in the ampulla. In conclusion, large differences in gene expression were observed between the isthmus and ampulla that reflect morphological and functional characteristics of each segment.

overall_design: Fifteen samples including 5 pregnant contralateral isthmus heifers, 5 cyclic contralateral isthmus heifers, and 5 pregnant ipsilateral ampulla heifers. Also, ten samples from GSE74593 were reanalyzed with these samples. The full set of processed data are linked at the bottom of the Series record.

first: Veronica

last: Maillo

first: Celia

last: de Frutos

last: Ó Gaora

first: Niamh

last: Forde

first: Gregory

middle: W

last: Burns

first: Thomas

last: Spencer

first: Alfonso

last: Gutierrez-Adan

first: Patrick

last: Lonergan

first: Dimitrios

last: Rizos


title: DNA damage Signaling Pathway PCR Array to profile the expression of human genes regulating in the DNA damage response (DDR) network

status: Public on Feb 05 2016

city: Richmond

first: Steven

last: Grant

address: 401 College Street

institute: VCU

summary: Human DNA Damage Signaling Pathway RT2 Profiler Array Kit (Qiagen, Valencia, CA) was used to profile the expression of key genes involved in the DDR network as per the manufacturer’s instructions.

overall_design: U937 cells were incubated with PXD-101 +/- MLN4924 for 16 h, after which the RT2 ProfilerTM DNA damage Signaling Pathway PCR Array was performed to profile the expression of 84 human genes involved in the DDR network.

first: Yun

last: Dai

first: Liang

last: Zhou

first: Shuang

last: Chen

first: Yu

last: Zhang


title: Psl polysaccharide deficient mutant

status: Public on Jan 26 2016

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

summary:
Analysis of Pseudomonas aeruginosa PA01 (ATCC 15692) Psl polysaccharide deficient mutant. Psl polysaccharide deficient mutant is evaluated with microarray to understand the genes affected by this polysaccharide. Our results provide new vision on the roles played by Psl polysaccharide in P. aeruginosa.
Exopolysaccharide Psl is a critical biofilm matrix component in Pseudomonas aeruginosa, which forms a fiber-like matrix to enmesh bacteria communities. Iron has been shown to serve as a signal in P. aeruginosa biofilm development, yet how iron controls biofilm formation is not clear. Here we perform a transcriptomic analysis to compare Psl negative strain versus its isogenic wild-type strain PAO1. The results indicate that the expression of genes involved in iron homeostasis and oxidative stress response increased drastically at transcriptional level in Psl negative strain, suggesting Psl deficiency induces iron limitation. Subsequent studies confirm that Psl can efficiently bind iron in vitro and Psl fibers functions as an iron storage channel in P. aeruginosa biofilms.

overall_design: We used two wild type (WT) replicates and two mutant (MT) replicates to compare the differential gene expression.

first: Luyan

middle: Z

last: Ma


title: Analysis of gene expression between monomethyl branched-chain fatty acid deficient (elo-5) and wild type N2 C. elegans L1 larvae hatched on food-free NGM plates

status: Public on Jan 14 2016

city: Boulder

first: Marina

last: Kniazeva

address: Porter Biosciences Bldg

institute: HHMI/UC Boulder

summary:
Gene expresssion is not globally shut down in elo-5 as compared to N2
Many changes in metabolic and regulatory gene expression were detected between elo-5 and N2 L1 larvae.

overall_design: RNA samples for hybridization with the C. elegans Affymetrix Gene Chips were prepared as follows. elo-5(gk208) and N2 control animals were grown from eggs for one generation on NGM plates spotted with 300µl OP50 overnight liquid culture supplemented with 1mM C17ISO in DMSO at 20°C. Gravid adults were washed off the plates with M9 and bleached. Eggs were plated on OP50/NGM plates supplemented with 1mM of either C13ISO or C17ISO and maintained at 20°C to obtain gravid adults. Adults were washed off the plates and bleached, and eggs were then plated on food-free NGM or OP50/NGM plates at 20°C. Twenty-four hours later, L1s from food-free plates were collected for RNA isolation with Trizol and Qiagen’s RNAse Easy Kit, according to the manufacturers’ protocols. On the following days, animals on OP50/NGM were checked for phenotypes to confirm C17ISO-deficiency in elo-5(gk208) grown with C13ISO supplement. Two biological replicates were prepared for each condition; elo-5(gk208) with C13ISO and C17ISO supplements and a control N2 with C13ISO supplement. Data analysis was performed with dChip analytical software (Li and Wong, 2001).

first: Min

last: Han


title: Interleukin-6 is a Potential Therapeutic Target in Interleukin-6 Dependent Estrogen Receptor-alpha Positive Breast Cancer

status: Public on Feb 04 2016

city: Beerse

first: Tine

last: Casneuf

address: Turnhoutseweg 30

department: Oncology Translational Research

country: Belgium

institute: Janssen R&D

first: Tineke

first: Amy

last: Axel

first: Peter

last: King

first: J

middle: D

last: Alvarez

first: Jillian

last: Werbeck

first: Tinne

last: Verhulst

first: Karin

last: Verstraeten

first: Brett

middle: M

last: Hall

first: A

last: Sasser


title: Translation State Array Assay for C elegans IFE-1-dependent mRNAs

status: Public on Jan 07 2016

city: Greenville

last: Keiper

state: NC

address: 600 Moye Blvd

department: Biochem and Mol Biol

institute: Brody School of Med at ECU

summary:
Relative polysomal loading changes for wild type (N2) versus ife-1(bn127) C. elegans strains
Strain ife-1(bn127) is null for the gene encoding one of five eIF4E isoforms in the worm, IFE-1.  Only this isoform associates with P granules.

overall_design:
Resolution of translating and non-translating mRNAs from WT and mutant worms on 10-45% sucrose gradients. Comparision was by ratios of polysomal content.

Please note that each sample data table contains raw signal directly imported from the Affymetrix files and  the ratio of signals, P/(NP+P), and fold-changes were further calculated. The TSAA_overview.xls contains more datails about the TSAA procedure and 'complete_data.xlsx' contains complete TSAA data output.

first: Andrew

middle: J

last: Friday

first: Melissa

last: Henderson

last: Morrison

first: Jenna

last: Hoffman


title: Transcriptome analysis of Pseudomonas aeruginosa PAO1 Response to L-Glutamate or D-Arginine

status: Public on Jan 05 2016

city: ATLANTA

first: GUOQING

last: LI

state: GEORGIA

address: 161 Jessie Hill Jr. Drive

department: BIOLOGY

institute: GEORGIA STATE UNIVERSITY

summary: Arginine utilization in Pseudomonas aeruginosa with multiple catabolic pathways represents one of the best examples of metabolic versatility of this organism. To identify genes of this complex arginine network, we employed DNA microarray to analyze the transcriptional profiles of this organism in response to L-arginine. While most genes in arginine uptake, regulation and metabolism have been identified as members of the ArgR regulon in our previous study, eighteen putative transcriptional units of 38 genes including the two known genes of the arginine dehydrogenase (ADH) pathway, kauB and gbuA, were found inducible by exogenous L-arginine but independent of ArgR.

overall_design: We conducted three independent microarray experiments in the presence (experimental) of L-Glutamate or D-Arginine. P. aeruginosa PAO1 was grown aerobically in minimal medium P with 300 rpm shaking at 37°C, in the presence of L-Glu with or without the addition of D-Arg at 20 mM.

first: Zhe

last: Yang

first: Chung-Dar

last: Lu


title: Expression data from C. elegans wild type, hlh-25 mutant and hlh-29 mutant strains

status: Public on Jan 01 2016

city: Atlanta

first: Han Ting

last: Chou

state: GA

address: 1 University Park Drive

department: Biology

institute: Georgia State University

summary: In Caenorhabditis elegans, the six proteins that make up the REF-1 family are HES homologs that act in both Notch dependent and Notch-independent pathways to regulate embryonic events.  To further our understanding of how the REF-1 family works to coordinate post-embryonic cellular events, we performed transcriptome analysis of HLH-25 and HLH-29 mutant strains.

overall_design: Gene expression microarray, including probe preparation, hybridization, fluidics run and chip scan, was performed by Georgia State University DNA/Protein Core Facility. Global gene expression in synchronized young adult populations of VC1220 (hlh-25 mutant) and tm284 (hlh-29 mutant) animals were compared to expression in N2 (wild-type) animals using GeneChip C. elegans Genome Array (Affymetrix). Data collection was carried out using GCOS 1.4 software (Affymetrix).  Probe intensity values were normalized to a target value of 500 with normalization factor equal to 1. Data analysis was performed using GeneSpring GX 11 Software (Aglient, Palo Alto,CA).

first: Casonya

last: Johnson

first: Han-Ting

first: Kun

last: Wang

first: Sonja

last: Young


title: Growth-rate dependency of de novo resveratrol production in chemostat cultures of an engineered Saccharomyces cerevisiae strain

status: Public on Dec 22 2015

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary:
Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints in oxygen transfer and cooling capacities, have to be operated at low specific growth rates. Because intracellular levels of key metabolites and cellular energy status are growth-rate dependent, slow growth can significantly affect biomass-specific productivity. Using an engineered Saccharomyces cerevisiae strain expressing a heterologous pathway for resveratrol production as a model energy-requiring product, the impact of specific growth rate on yeast physiology and productivity was investigated in aerobic, glucose-limited chemostat cultures.
Stoichiometric analysis revealed that de novo resveratrol production from glucose requires a net input of 2 moles of ATP per mole of produced resveratrol. The biomass-specific production rate of resveratrol showed a strong positive correlation with the specific growth rate. At low growth rates, a substantial fraction of the carbon source was invested in cellular maintenance-energy requirements (e.g., 27% at 0.03 h-1). This distribution of resources was unaffected by resveratrol production. Formation of the by-products coumaric, phloretic and cinnamic acid had no detectable effect on maintenance energy requirement and yeast physiology in the chemostats. Expression of the heterologous pathway led to marked differences in transcript levels in the resveratrol-producing strain, including increased expression levels of genes involved in pathways for precursor supply (e.g., ARO7 and ARO9 involved in phenylalanine biosynthesis). The observed strong differential expression of many glucose-responsive genes in the resveratrol producer as compared to a congenic reference strain could be explained from higher residual glucose concentrations and higher relative growth rates in cultures of the resveratrol producer.
De novo resveratrol production by engineered S. cerevisiae is an energy demanding process. Resveratrol production by an engineered strain exhibited a strong correlation with specific growth rate. Since industrial production in fed-batch reactors typically involves low specific growth rates, this study emphasizes the need for uncoupling growth and product formation via energy-requiring pathways.

overall_design: The goal of the present study is to investigate the impact of specific growth rate on biomass-specific productivity, product yield, by-product formation and host strain physiology of an S. cerevisiae strain that was previously engineered for de novo production of resveratrol from glucose. To this end, (by)product formation, physiology and transcriptome were analysed in steady-state, glucose-limited chemostat cultures grown at different dilution rates.

first: Tim

last: Vos

first: Pilar

last: de le Torre

first: Pascale

last: Daran-Lapujade

first: Jack

last: Pronk

first: Jean


title: Expression data from Pseudomonas aeruginosa ∆sbrR and ∆sbrIR mutants versus wild type

status: Public on Dec 23 2015

city: Boston

first: Bryan

last: McGuffie

state: MA

address: 300 Longwood Ave

department: Infectious Diseases

institute: Boston Children's Hospital

summary: SbrI and SbrR are an extracytoplasmic function sigma factor and its cognate anti-sigma factor, respectively. To identify the SbrIR regulon, we measured gene expression in wild type PAO1 , PAO1 ∆sbrR, and PAO1 ∆sbrIR mutants using microarrays.

overall_design: WT PAO1 pPSV38 (empty vector), PAO1 ∆sbrR pPSV38, PAO1 ∆sbrR pSbrR, and PAO1 ∆sbrIR pPSV38 were grown to mid-log. RNA was extracted and reverse transcribed into cDNA. The cDNA was biotinylated and hybridized to Pseudomonas aeruginosa Affymetrix microarrays.

first: Simon

middle: L

last: Dove


title: Integrating high-dimensional transcriptomics and image analysis tools into early safety screening (V)

status: Public on Dec 31 2015

first: Steven

last: Osselaer

institute: Janssen Pharmaceutica NV

summary:
In this paper we demonstrated the potential to flag toxicity issues by utilizing data from exploratory experiments which are typically generated for target evaluation purposes during early drug discovery
During drug discovery and development, the early identification of adverse effects is expected to reduce costly late stage failures of candidate drugs.
As risk/safety assessment takes place rather late during the development process and due to the limited predictivity of animal models to the human situation, modern unbiased high-dimensional biology read-outs are sought, such as molecular signatures of in vivo response using high-throughput cell-based assays.
In this theoretical proof-of-concept we provide findings of an in-depth exploration of a single chemical core structure.
Via transcriptional profiling we identified a subset of close analogs which commonly down-regulate tubulin genes across cellular contexts, suggesting possible spindle poison effects.
Confirmation via a qualified toxicity assay (in vitro micronucleus test) and the identification of a characteristic aggregate-formation phenotype via exploratory high content imaging validated the inititial findings.
SAR analysis triggered the synthesis of a new set of compounds and allowed us to extend the series showing the genotoxic effect.
We demonstrate the potential to flag toxicity issues by utilizing data from exploratory experiments which are typically generated for target evaluation purposes during early drug discovery.
We  share our thoughts on how this approach may be incorporated into drug development strategies.

overall_design: Cells were cultured using standard protocols, seeded in 96 well plate, cultured for 8 hours before treatment with a number of inhouse synthesized compounds. The treatments represent different chemical structures/small molecules that have been synthesized in the context of developing a new drug targeting PDE10A.

first: Bie

last: Verbist

first: Geert

middle: R

last: Verheyen

first: Liesbet

last: Vervoort

first: Marjolein

last: Crabbe

first: Dominiek

last: Beerens

first: Cindy

last: Bosmans

first: Steffen

last: Jaensch

first: Willem

last: Talloen

first: Ilse

last: Van den Wyngaert

last: Van Hecke

first: Dirk

last: Wuyts

first: Freddy

last: Van Goethem

first: Hinrich

last: Göhlmann


title: RIP-Chip analysis of the C. elegans FOG-1 and FOG-3 proteins

status: Public on Dec 14 2015

city: Madison

first: Daniel

last: Noble

state: wi

address: 433 Babcock Dr

institute: University of Wisconsin-Madison

summary: FOG-1/CPEB and FOG-3/Tob are the terminal regulators of the sex determination in C. elegans germ cells.  CPEB and Tob proteins are both translational regulators.  To investigate how FOG-1 and FOG-3 regulate germ cell sex determination we sought to identify the target mRNAs.  We used transgenic epitope tagged animals (3xMyc::FOG-1 and FOG-3::3xFLAG).  To identify the mRNA targets of FOG-1/CPEB and FOG-3/Tob on a genome wide scale we used RNA immunoprecipitation followed by microarray analysis.  We found 81 putative mRNA targets of FOG-1 and 722 putative targets of FOG-3.  76 target mRNAs were common to both FOG-1 and FOG-3.

overall_design: FOG-1 RNA-coimmunoprecipitation (RIP) samples were prepared as follows.  Parallel RIPs were performed with wild type animals as the control IP.  Worm extracts were made from wildtype and 3xMyc::FOG-1  late L3/early L4 animals.  Myc affinity gel was used to immunoprecipitate 3xMyc::FOG-1 from the extracts.  RNA was extracted from the pellets and analyzed on Affymetrix microarrays.  7 biological replicates of both 3xMyc::FOG-1 and wildtype were used.  FOG-3 RNA-coimmunoprecipitation (RIP) samples were prepared as follows.  Parallel RIPs were performed with wild type animals as the control IP.  Worm extracts were made from wildtype and FOG-3::3xFLAG  late L3/early L4 animals.  Myc affinity gel was used to immunoprecipitate FOG-3::3xFLAG from the extracts.  RNA was extracted from the pellets and analyzed on Affymetrix microarrays.  7 biological replicates of both FOG-3::3xFLAG and wildtype were used.

first: Marco

last: Ortiz

first: Judith

middle: E

last: Kimble


title: Microsensor and transcriptome signatures of oxygen depletion in biofilms associated with chronic wounds [biofilm inoculum]

status: Public on Nov 24 2015

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

institute: Montana State University

summary: Biofilms have been implicated in delayed wound healing, although the mechanisms by which biofilms impair wound healing are poorly understood. Many species of bacteria produce exotoxins and exoenzymes that may inhibit healing. In addition, oxygen consumption by biofilms, as well as responding leukocytes, may impede wound healing. In this study, we used oxygen microsensors to measure oxygen transects through in vitro-cultured biofilms, biofilms formed in vivo within scabs from a diabetic (db/db) mouse model, and ex vivo human chronic wound specimens. The results show that oxygen levels within mouse scabs had steep gradients that reached minima ranging from 17-72 mmHg on live mice and 6.4-1.1 mmHg on euthanized mice. The oxygen gradients in the mouse scabs were similar to those observed for clinical isolates cultured in vitro and for human ex vivo specimens. No oxygen gradients were observed for heat-killed mouse scabs, suggesting that active metabolism by the viable bacteria and host cells contributed to the reduced oxygen partial pressure of the scabs. To characterize the metabolic activities of the bacteria in the mouse scabs, we performed transcriptomics analyses of Pseudomonas aeruginosa biofilms associated with the db/db mice wounds using Affymetrix microarrays. The results demonstrated that the bacteria expressed genes for metabolic activities associated with cell growth. Interestingly, the transcriptome results indicated that the bacteria within the wounds also experienced oxygen-limitation stress. Among the bacterial genes that were expressed in vivo were genes associated with the Anr-mediated hypoxia-stress response. Other bacterial stress response genes highly expressed in vivo were genes associated with stationary-phase growth, osmotic stress, and RpoH-mediated heat shock stress. Overall, the results support the hypothesis that bacterial biofilms in chronic wounds promote chronicity by contributing to the maintenance of localized low oxygen tensions.

overall_design:
Transcriptional profiling of two independent biological replicates of Pseudomonas aeruginosa biofilms, as grown to 72 hours and used as inocula applied to the murine wounds, was performed. A principle components analysis (PCA) was used to provide an overview of the transcriptome data from the 28-day mouse wound scab, comparing the data to the biofilm inoculum, and to published reports of P. aeruginosa biofilm and planktonic samples. The analysis shows that the transcriptome of the mouse wound scab was distinct from the biofilm inoculum that was applied to the wound, demonstrating a shift in biofilm gene expression following 28 days of infection.
We sought to characterize P. aeruginosa activity within biofilms in the mouse wound model by isolating and identifying mRNA from the biofilms used as inocula and from the wound scabs 28 days post infection.

first: Garth

last: James

first: Alice

middle: G

last: Zhao

first: Marcia

last: Usui

first: Robert

last: Underwood

first: Hung

last: Nguyen

first: Haluk

last: Beyenal

first: Elinor

middle: d

last: Pulcini

first: Alessandra

last: Agostinho

first: Hans

last: Bernstein

first: Philip

last: Fleckman

first: John

last: Olerud

first: Michael

last: Franklin

last: Stewart


title: Expression data of worms under different caloric restriction mimetic treatments

city: Liverpool

first: João Pedro

last: de Magalhães

address: Crown Street,

department: Institute of Integrative Biology

institute: The University of Liverpool

summary: We used microarray analysis to further our understanding of the mode of action of the well know caloric restriction mimetic rapamycin and the compound Allantoin first studied in the context of aging in this study. His work helps build on our understanding of potential caloric restriction mimetics predicted from our bioinformatic aproach of quering the Connectivity Map, a database of drug-induced gene expression profiles, using the transcriptional profile of CR to identify drugs that induce a similar or opposite gene expression profile.

overall_design: Wild type worms of eat-2 mutants (a model of caloric restriction) were treated with the compounds of study with 2% DMSO or DMSO alone to serve as controls. All samples were peformed in triplicate.

first: Shaun

last: Calvert

first: Robi

last: Tacutu

first: Joao

last: De Magalhaes


title: LncRNA expression profile in minor salivary gland of Sjögren’s syndrome (SjS)

status: Public on Dec 16 2015

city: Shanghai

first: Huan

last: Shi

address: No.639, ZhiZaoJu Road

department: Oral and maxillafacial surgery

institute: Shanghai JiaoTong University school of medicine, affiliated 9th people's hospital

summary: The present study was aimed to identify aberrantly expressed lncRNAs involved in the progression of SjS and explore their potential functions. Labial salivary gland of 4 SjS patients and 4 healthy controls was collected. LncRNA expression profile in labial salivary gland was analyzed by LncRNA microarray.

overall_design: LncRNA expression profile in labial salivary gland of 4 SjS patients and 4 healthy controls was analysised. Patients with SjS were fulfilled the American-European consensus group criteria for SjS. No immunosuppressive treatment was conducted in these patients before the sample conllection. All healthy donors were confirmed to be free of acute infection or systemic diseases.

first: Chuangqi

last: Yu

first: Lingyan

last: Zheng


title: Microsensor and transcriptome signatures of oxygen depletion in biofilms associated with chronic wounds

first: Kerry

last: Williamson

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

overall_design: Refer to individual Series


title: Integrating high-dimensional transcriptomics and image analysis tools into early safety screening (IV)

first: Steven

last: Osselaer

first: Bie

last: Verbist

first: Geert

last: Verheyen

first: Liesbet

last: Vervoort

first: Marjolein

last: Crabbe

first: Dominiek

last: Beerens

first: Cindy

last: Bosmans

first: Steffen

last: Jaensch

first: Willem

last: Talloen

first: Ilse

last: Van den Wyngaert

last: Van Hecke

first: Dirk

last: Wuyts

first: Freddy

last: Van Goethem

first: Hinrich

last: Göhlmann


title: Lysine catabolic pathways in P. aeruginosa

status: Public on Dec 09 2015

first: Han Ting

last: Chou

summary: Among multiple interconnected pathways for L-Lysine (L-Lys) catabolism in pseudomonads, Pseudomonas aeruginosa PAO1 employed the decarboxylase and the transaminase pathways. However, up till now several genes involved in the operation and regulation of these pathways were still missing. Transcriptome analyses coupled with promoter activity measurements and mutant growth phenotype analysis lead us to identify several new members of the L-Lys and D-Lys catabolic pathways and their regulatory elements, including argR to trigger lysine decarboxylation into cadaverine, PauR for the γ-glutamylation pathway of polyamine catabolism into 5-aminovalerate, gcdR-gcdHG for glutarate utilization, dpkA, amaR-amaAB and PA2035 for D-Lys catabolism, lysR-lysXE for L-Lys efflux, and lysP for L-Lys uptake.

overall_design:
Gene expression microarray, including probe preparation, hybridization, fluidics run and chip scan, was performed by Georgia State University DNA/Protein Core Facility. P. aeruginosa PAO1 was grown aerobically in minimal medium P with 350 rpm shaking at 37C, in the presence of 10mM L-glutamate supplemented with 10 mM L-lysine, cadaverine, 5-amino valerate, glutaric acid, D-lysine or 5mM L-pipecolate. Cells were harvested when the optical density at 600 nm reached 0.5~0.6 by centrifugation for 5 minutes at 4C. Total RNA samples were isolated by RNeasy purification kit following instructions of the manufacturer (Qiagen). Reverse transcription for cDNA synthesis, fragmentation by DNase I treatment, cDNA probe labeling and hybridization were performed according to the instructions of GeneChip manufacturer (Affymetrix). Data were processed by Microarray Suite 5.0 software normalizing the absolute expression signal values of all chips to a target intensity of 500. GeneSpring software (Silicon Genetics) was used for expression pattern analysis and comparison. Data collection was carried out using GCOS 1.4 software (Affymetrix).  Probe intensity values were normalized to a target value of 500 with normalization factor equal to 1. Data analysis was performed using GeneSpring GX 11 Software (Aglient, Palo Alto,CA).
Related Research Papers:                                                                                1. Indurthi SM, Chou HT, Lu CD. Molecular Characterization of lysR-lysXE, gcdR-gcdHG, and amaR-amaAB Operons for Lysine Export and Catabolism: A Comprehensive Lysine Catabolic Network in Pseudomonas aeruginosa PAO1. Microbiology. 2015 Submitted [EMID:04803de65c782]  2. Chou HT, Li J, and Lu CD. Functional Characterization of the agtABCD and agtSR Operons for γ-Aminobutyrate and δ-Aminovalerate Uptake and Regulation in Pseudomonas aeruginosa PAO1. Curr. Microbiology. 2014 Jan;68(1):59-63.  3. Chou HT, Li JY, Peng YC, Lu CD. Molecular characterization of PauR and its role in control of putrescine and cadaverine catabolism through the γ-glutamylation pathway in Pseudomonas aeruginosa PAO1. J Bacteriol. 2013 Sep; 195(17):3906-13.   4. Chou HT, Hegazy M, Lu CD. L-lysine Catabolism is Controlled by Arginine/ArgR in Pseudomonas aeruginosa PAO1. J Bacteriol. 2010 Nov;192(22):5874-80

first: Chung-Dar

last: Lu

first: Han

first: Sai

last: Indurthi


title: Expression data from Caenorhabditis elegans fed with the bacterial strain Bifidobacterium animalis sbsp. lactis CECT 8145

status: Public on Nov 22 2015

city: Paterna

first: Patricia

last: Martorell

state: Valencia

address: Catedrático Agustín Escardino Benlloch, 9, Building 2

department: Agrifood Biotechnology

institute: Biópolis SL

summary:
Modulation of gut microbiota through probiotic supplementation  is an interesting strategy to prevent obesity
We use microarrays to study the global genome expression of C. elegans fed with the probiotic strain Bifidobacterium animalis sbsp. lactis CECT 8145

overall_design: Wild type strain N2 of C. elegans was cutured in  Nematode Growth medium (NGM, control fed) or NGM with a bacterial lawn fed of the strain B. animalis subsp. lactis CECT 8145,  until reach young adult stage. Worm population were age-synchronized. RNA was isolated from each populations (control and treated) using RNAasy Kit (Qiagen) and hybridizated on Affymetrix microarrays.

first: Salvador

last: Genovés

first: Daniel

last: Ramón


title: OsMYC2-responsive genes in OsMYC2-overexpressing transgenic rice

status: Public on Dec 01 2015

city: miki

first: kenji

last: gomi

state: kagawa

institute: Kagawa University

summary: A rice transcription factor OsMYC2 plays important role in the regulation of defense responses in rice. To clarify the OsMYC2-responsive genes, we performed a microarray analysis using the Agilent Rice Oligo Microarray (44k, Agilent Technologies, Redwood City, CA, USA). As a result, many defense-related genes including pathogenesis-related (PR) genes were upregulated in the OsMYC2-overexpressing transgenic rice.

overall_design: An Agilent Rice Oligo Microarray (44k; Agilent Technologies, Redwood City, CA, USA) was used for the microarray analysis. Total RNA was extracted from leaf blades of four-leaf stage rice plants. Line 14 was used as the OsMYC2-overexpressing transgenic rice plant. For each biological replicate, material from at least three rice plants was pooled to provide a single sample for RNA extraction. We performed 3 biological replicates for each treatment. All microarray procedures and data analyses were performed according to the manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (100 ng) was labeled with Cy-3 using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, following wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2565CA; Agilent Technologies). Feature extraction software (Agilent Feature Extraction; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.

first: Kenji

last: Gomi

first: Yuya

last: Uji

first: Daisuke

last: Tamaoki

first: Kazuya

last: Akimitsu


title: Real-time quantitative PCR analysis of UPR genes in human normal and osteoarthritic chondrocytes

status: Public on Oct 06 2015

city: Montreal

first: Johanne

last: Martel-Pelletier

state: Quebec

address: 900 rue St-Denis

institute: CRCHUM

summary: Human  chondrocytes were obtained from the cartilage of femoral condyles and tibial plateaus from individuals within 12 hours of death (normal) and from patients undergoing total knee arthroplasty (osteoarthritic, OA). The chondrocytes were released from the cartilage, seeded at high density, and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum and an antibiotic mixture (100 units/ml penicillin base and 100 μg/ml streptomycin base) at 37°C in a humidified atmosphere of 5% CO2/95% air. Total RNA was extracted from the primary chondrocytes and processed for qPCR according to the manufacturer's  instructions (SA Biosciences  RT2 Profiler PCR Array PAHS-089Z).

overall_design: qPCR gene expression profiling: chondrocytes from three normal and three OA human donors were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was used for gene expression analysis.  The average of the values obtained from the three OA samples were compared to  the average of the values from the three normal samples

first: Ying-Hua

last: Li


title: Real-time quantitative PCR analysis of UPR genes in  human osteoarthritic chondrocytes specimens treated with tunicamycin compared to the untreated (control) chondrocytes

summary: Human osteoarthritic (OA)  chondrocytes were obtained from the cartilage of femoral condyles and tibial plateaus from  three patients undergoing total knee arthroplasty. The chondrocytes were released from the cartilage, seeded at high density, and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum and an antibiotic mixture (100 units/ml penicillin base and 100 μg/ml streptomycin base) at 37°C in a humidified atmosphere of 5% CO2/95% air. The chondrocytes from each of the three donors were left untreated (control) and treated  with tunicamycin (500ng/ml for 20 hours).Total RNA was extracted from the  chondrocytes and processed for qPCR according to the manufacturer's  instructions (SA Biosciences  RT2 Profiler PCR Array PAHS-089Z).

overall_design: qPCR gene expression profiling: chondrocytes from three OA donors were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was used for gene expression analysis. The average of the values obtained from the three treated cells were compared to the average of the three untreated control chondrocytes.


title: Real-time quantitative PCR analysis of UPR genes in  human osteoarthritic chondrocytes specimens treated with thapsigargin compared to the untreated (control) chondrocytes

summary: Human osteoarthritic (OA)  chondrocytes were obtained from the cartilage of femoral condyles and tibial plateaus from  three patients undergoing total knee arthroplasty. The chondrocytes were released from the cartilage, seeded at high density, and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% heat-inactivated fetal bovine serum and an antibiotic mixture (100 units/ml penicillin base and 100 μg/ml streptomycin base) at 37°C in a humidified atmosphere of 5% CO2/95% air. The chondrocytes from each of the three donors were left untreated (control) and treated  with thapsigargin (50nM for 20hours).Total RNA was extracted from the  chondrocytes and processed for qPCR according to the manufacturer's  instructions (SA Biosciences  RT2 Profiler PCR Array PAHS-089Z).

overall_design: qPCR gene expression profiling: chondrocytes from three OA donors were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was used for gene expression analysis.  The average of the values obtained from the three treated cells were compared to the average of the three untreated control chondrocytes.


title: Integrating high-dimensional transcriptomics and image analysis tools into early safety screening

first: Steven

last: Osselaer


title: Characterization of the SouR regulon in Pseudomonas aeruginosa

status: Public on Nov 16 2015

city: Burlington

first: Matthew

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

summary:
The sarcosine oxidase locus is controlled by GbdR and SouR independently induced by glycine betaine and sarcosine, respectively. The goal of this study was to identify the members of the SouR regulon. Therefore, the comparison strains were a gbdR mutant and a gbdRsouR double mutant.
The conditions for inclusion in the souR regulon were: (i) called present in the array, (ii) changed more than 2.5-fold in signal in a statistically significant manner, (iii) altered in the presence of sarcosine and dependent on souR.

overall_design: gbdR mutants and gbdR souR double mutants  were pre-grown in MOPS minimal media and then split and resuspended in MOPS pyruvate or MOPS pyruvate + sarcosine.

first: Graham

last: Willsey


title: Response of Pseudomonas aeruginosa strain PAO1 to 10 mM added calcium in planktonic culture

status: Public on Dec 02 2015

first: Kerry

last: Williamson

summary:
PAO1  was cultured planktonically to stationary phase with 10 mM calcium and no added calcium. The transcriptional response to calcium addition was determined.
Pseudomonas aeruginosa is an opportunistic human pathogen that causes severe, life threatening infections in patients with cystic fibrosis (CF), endocarditis, wounds, or with artificial implants. During CF pulmonary infections, P. aeruginosa often encounters environments where the levels of calcium (Ca2+) are elevated.  Previously, we showed that P. aeruginosa responds to externally added Ca2+ through enhanced biofilm formation, increased production of several secreted virulence factors, and by developing a transient increase in the intracellular Ca2+ followed by its removal to the basal sub-micromolar level.  However, the molecular mechanisms responsible for regulating Ca2+-induced virulence factor production and Ca2+ homeostasis are not known.  Here, we characterized the genome-wide transcriptional response of P. aeruginosa strains PAO1 and FRD1 to elevated [Ca2+] in both planktonic cultures and in biofilms.  Among the genes induced by CaCl2 in PAO1 was an operon containing the two-component regulator PA2656-PA2657 (here called carS and carR), while the closely related two-component regulators, phoPQ and pmrAB were repressed by CaCl2 addition.  To identify the regulatory targets of CarSR, we constructed a deletion mutant of carR, and performed transcriptome analysis of the mutant strain at low and high [Ca2+].  Among the genes regulated by CarSR in response to CaCl2 are the predicted periplasmic OB-fold protein, PA0320 and the inner membrane-anchored five-bladed -propeller protein, PA0327. Mutations in both PA0320 and PA0327 affected Ca2+ homeostasis, reducing the ability of P. aeruginosa to export excess Ca2+.  In addition, a mutation in PA0327 had a pleotrophic effect in a Ca2+-dependent manner, altering swarming motility, pyocyanin production, and tobramycin sensitivity. Overall, the results indicate that the two-component system CarSR is responsible for sensing high levels of external Ca2+, and responding through its regulatory targets that modulate Ca2+ homeostasis, surface-associated motility, and production of the virulence factor, pyocyanin.

overall_design: Two biological replicates of PAO1 grown with 10 mM calcium, and two biological replicates of PAO1 grown with no added calcium. This data was used to validate the two-color JCVI array data used in this publication.

first: Manita

last: Guragain

first: Michelle

last: King

first: Ailyn

last: Pérez-Osorio

first: Tatsuya

last: Akiyama

first: Sharmily

last: Khanama

first: Michael

last: Franklin

first: Marianna

last: Patrauchan


title: C. elegans gene expression in healthy and PA14-infected wild-type and fshr-1 mutant worms

status: Public on Sep 30 2015

city: Gettysburg

first: Jennifer

last: Powell

state: PA

address: 300 N. Washington Street

institute: Gettysburg College

summary: Analysis of gene expression in worms exposed to PA14 for 4 hours.  Worms used were wild-type or fshr-1(ok778) mutants.  Comparisons allowed determination of fshr-1-dependent gene expression.

overall_design: Three independent biological replicates were analyzed for each of the four conditions.  For any given replicate, all four conditions were prepared in parallel.  Conditions were N2 worms on OP50, N2 worms on PA14, fshr-1(ok778) worms on OP50, and fshr-1(ok778) worms on PA14


title: The response of Pseudomonas aeruginosa strains PAO1 and FRD1 to 10 mM calcium under planktonic and biofilm conditions


title: Microsensor and transcriptome signatures of oxygen depletion in biofilms associated with chronic wounds [wound]

summary: Biofilms have been implicated in delayed wound healing, although the mechanisms by which biofilms impair wound healing are poorly understood. Many species of bacteria produce exotoxins and exoenzymes that may inhibit healing. In addition, oxygen consumption by biofilms, as well as responding leukocytes, may impede wound healing. In this study, we used oxygen microsensors to measure oxygen transects through in vitro-cultured biofilms, biofilms formed in vivo within scabs from a diabetic (db/db) mouse model, and ex vivo human chronic wound specimens.  The results show that oxygen levels within mouse scabs had steep gradients that reached minima ranging from 17-72 mmHg on live mice and 6.4-1.1 mmHg on euthanized mice. The oxygen gradients in the mouse scabs were similar to those observed for clinical isolates cultured in vitro and for human ex vivo specimens. No oxygen gradients were observed for heat-killed mouse scabs, suggesting that active metabolism by the viable bacteria and host cells contributed to the reduced oxygen partial pressure of the scabs. To characterize the metabolic activities of the bacteria in the mouse scabs, we performed transcriptomics analyses of Pseudomonas aeruginosa biofilms associated with the db/db mice wounds using Affymetrix microarrays. The results demonstrated that the bacteria expressed genes for metabolic activities associated with cell growth. Interestingly, the transcriptome results indicated that the bacteria within the wounds also experienced oxygen-limitation stress. Among the bacterial genes that were expressed in vivo were genes associated with the Anr-mediated hypoxia-stress response. Other bacterial stress response genes highly expressed in vivo were genes associated with stationary-phase growth, osmotic stress, and RpoH-mediated heat shock stress. Overall, the results support the hypothesis that bacterial biofilms in chronic wounds promote chronicity by contributing to the maintenance of localized low oxygen tensions.

overall_design:
The following procedure was performed on two mice, resulting in two biological replicates. A punch biopsy wound was created on the dorsal surface of a diabetic mouse, subsequently infected with a P. aeruginosa biofilm two days post-wounding, and covered with semi-occlusive dressings for two weeks. At 28 days post wounding, the wound crust was surgically excised and RNA was extracted for analysis on Affymetrix P. aeruginosa microarrays. To conservatively identify the most abundant transcripts in the mouse wound scabs, the transcripts with the highest signal intensities (the top 5% of the transcripts represented on the arrays) were selected for further analysis.
We sought to characterize the persistence of P. aeruginosa activity within biofilms in the mouse wound model by isolating and identifying mRNA from the wounds 28 days post infection.

first: Garth

last: James

first: Alice

last: Zhao

first: Marcia

last: Usui

first: Robert

last: Underwood

first: Hung

last: Nguyen

first: Haluk

last: Beyenal

first: Elinor

last: Pulcini

first: Alessandra

last: Agostinho

first: Hans

last: Bernstein

first: Philip

last: Fleckman

first: John

last: Olerud

last: Stewart


title: Transcriptome analysis of Pseudomonas aeruginosa PAO1 Response to Hydroxyproline

status: Public on Sep 22 2015

first: GUOQING

last: LI

summary: Hydroxy-L-proline (L-Hyp) mainly exists in animal collagens through post-translational modification on peptidyl proline. Utilization of L-Hyp as carbon and nitrogen sources in bacteria including P. aeruginosa requires conversion of L-Hyp to D-Hyp followed by the D-Hyp dehydrogenase pathway. However, the molecular mechanism in control of L-Hyp catabolism and transport at the genetic level was not clear. We performed a detailed transcriptome profile analysis of P. aeruginosa in response to L-Hyp and D-Hyp with an emphasis in catabolism and regulation, which revealed the presence of twelve genes in two adjacent loci that were induced by exogenous L-Hyp and D-Hyp. The first locus includes lhpABFE encoding a Hyp epimerase (LhpA) and D-Hyp dehydrogenase (LhpBEF), while the second locus covers genes for a putative ABC transporter (LhpPMNO), a protein of unknown function (LhpH), Hyp/Pro racemase (LhpK), and two enzymes in L-Hyp catabolism (LhpC and LhpG). In addition, proximal to these two loci, lhpR encodes a transcriptional regulator of the AraC family.

overall_design: We conducted four independent microarray experiments in the presence (experimental) of L-Hyp or D-Hyp. P. aeruginosa PAO1 was grown aerobically in minimal medium P with 300 rpm shaking at 37°C, in the presence of L-glutamate with the addition of L-Hyp or D-Hyp at 5 mM.

first: Guoqing

last: Li

first: Chung-Dar

last: Lu


title: Transcriptional response induced by Wnt signaling in Caenorhabditis elegans affects lateral and ventral hypodermal cell development

status: Public on Nov 18 2015

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: The evolutionarily conserved Wnt/?-catenin signaling pathway plays a fundamental role during metazoan development, regulating numerous processes including cell fate specification, cell migration, and stem cell renewal. Wnt ligand binding leads to stabilization of the transcriptional effector ?-catenin and upregulation of target gene expression to mediate a cellular response. During larval development of the nematode Caenorhabditis elegans, Wnt/?-catenin pathways act in fate specification of two hypodermal cell types, the ventral vulval precursor cells (VPCs) and the lateral seam cells. Because little is known about targets of the Wnt signaling pathways acting during larval VPC and seam cell differentiation, we sought to identify genes regulated by Wnt signaling in these two hypodermal cell types. We conditionally activated Wnt signaling in larval animals and performed cell type?specific "mRNA tagging" to enrich for VPC and seam cell?specific mRNAs, and then used microarray analysis to examine gene expression compared to control animals. Two hundred thirty-nine genes activated in response to Wnt signaling were identified, and we characterized 50 genes further. The majority of these genes are expressed in seam and/or vulval lineages during normal development, and reduction of function for nine genes caused defects in the proper division, fate specification, fate execution, or differentiation of seam cells and vulval cells. Therefore, the combination of these techniques was successful at identifying potential cell type?specific Wnt pathway target genes from a small number of cells and at increasing our knowledge of the specification and behavior of these C. elegans larval hypodermal cells.

overall_design: Identification of genes expressed in seam cells and VPCs at L2-L3 stage with three replications

first: Lakshmi

last: Gorrepati

first: Michael

last: Krause

first: Weiping

first: Thomas

last: Brodigan

first: Margarita

last: Correa-Mendez

first: David

last: Eisenmann


title: Phase I study of Veliparib in combination with Cisplatin and Vinorelbine for patients with advanced triple-negative breast cancer (TNBC) and/or BRCA mutation-associated breast cancer

status: Public on Sep 09 2015

city: Seattle

first: Jamie

last: Guenthoer

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: PURPOSE:  Preclinically, cisplatin is synergistic with vinorelbine and the poly(ADP-ribose) polymerase (PARP) inhibitor veliparib, and has anti-neoplastic activity in TNBC and BRCA mutation-associated breast cancer. This phase I study assessed veliparib with cisplatin and vinorelbine. PATIENTS AND METHODS:  A 3+3 dose escalation design evaluated veliparib administered BID for 14 days with cisplatin (75 mg/m2 day 1) and vinorelbine (25 mg/m2 days 1,8) every 21 days, for six to ten cycles, followed by veliparib monotherapy. Pharmacokinetics, measurement of poly(ADP-ribose) in peripheral blood mononuclear cells, and preliminary efficacy were assessed. Immunohistochemistry and gene expression profiling were performed to evaluate potential predictors of response.

overall_design: Thirty-nine samples were assessed, six samples were run as technical duplicates. Two of the samples had a high rate of missing probes and were excluded during the normalization/pre-processing. Each sample represents a pre- or post-treatment breast cancer specimen from individual patients.

first: Eve

last: Rodler

first: Brenda

middle: F

last: Kurland

first: Melissa

last: Griffin

first: Julie

last: Gralow

first: Peggy

last: Porter

first: Rosa

last: Yeh

first: Vijayakrishna

middle: K

last: Gadi

first: Jan

middle: H

last: Beumer

first: Larissa

last: Korde

first: Sandra

last: Strychor

first: Brian

last: Kiesel

first: Hannah

last: Linden

last: Thompson

first: Elizabeth

last: Swisher

first: Xiaoyu

last: Chai

first: Stacie

last: Shepherd

first: Vincent

last: Giranda

first: Jennifer

last: Specht


title: Definition of the AmrZ regulon under a twitching-promoting condition

status: Public on Sep 06 2015

city: Columbus

first: Binjie

last: Xu

state: OH

address: 460 W. 12th Ave

department: Microbiology

institute: The Ohio State University

summary:
A novel approach using cellophane sheets was designed to promote Pseudomonas aeruginosa twitching motility, as well as to provide convenience for cell harvest.
The AmrZ regulon was defined under this specific growth condition by microarray analysis.

overall_design: WT P. aeruginosa and amrZ mutants were cultivated under this novel condition, and their transcriptional profiles were defined. WT P. aeruginosa strains include PAO1 and WFPA510 (complemented strain), while amrZ mutants include WFPA205 (ΔamrZ) and WFPA513 (AmrZV20A, DNA binding deficient). Each strain has 3 biological replicates.

first: Daniel

last: Wozniak


title: Identification of Predictive Gene Markers for Multipotent Stromal Cell Proliferation

status: Public on Oct 23 2015

city: Silver Spring

first: Raj

last: Puri

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

type:
Expression profiling by array
Expression profiling by RT-PCR

overall_design:
Identification of genes that can predict the proliferation potential of multipotent stromal cells.

Gene expression study by microarray and confirmation with RT-qPCR. Gene expression by microarray includes the 54 arrays originally present in GSE56362 and 9 additional arrays added to GSE56362 on October 23, 2015. These additional microarray datasets were completed in a randomized block design in combination with the microarray data originally present in GSE56362.


title: Comparison of gene expression between sams-1(RNAi) and sams-1(RNAi) animals rescued by choline

status: Public on Aug 27 2015

city: Worcester

first: Amy

last: Walker

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: UMASS Medical School

summary: Gene expression was compared from adult C. elegans after RNAi

overall_design: Triplicate control RNAi (Empty vector), control RNAi, choline treated, sams-1(RNAi) and sams-1(RNAi) choline treated animals were grown to young adulthood and RNA was extracted


title: Toxicogenomic responses of Caenorhabditis elegans exposed to  sulfidized silver nanoparticles

status: Public on Aug 22 2015

city: Lexington

last: Starnes

state: KY

address: 1100 Nicholasville Road

department: Plant and Soil Science

institute: University of Kentucky

summary: We assessed the whole genome response of C. elegans exposed for 48 hours from L1 to the pristine silver nanomterials, artifically aged silver nanomatierls, and AgNO3.

overall_design: Single time point RNA extraction from a population of 2000-3000 nematodes exposed to the EC30 for reproduction.

first: Olga

middle: V

last: Tsyusko


title: Expression data from DD neurons isolated from early L1 stage C. elegans larvae.

status: Public on Aug 01 2015

city: Nasvhille

first: Siwei

last: He

state: TN

address: 465 21st Ave South

department: Cell and Developmental Biology

institute: Vanderbilt University

summary:
Six DD class GABAergic neurons are generated in the embryo to synapse with ventral muscles and receive input from cholinergic neurons in the dorsal nerve cord. After hatching and toward the end of the first larval (L1) stage, DD neurons reverse polarity (i.e., synapse with dorsal muscles, receive ventral cholinergic inputs). Expression profiles were generated from DD neurons in the early L1 stage before the initiation of the remodeling program.
We used microarray analysis to detect transcripts with potential roles in DD remodeling.

overall_design: We used FACS to isolate ttr-39::mCherry labeled DD GABAergic motor neurons from a synchronized population of L1 larvae and amplified and labeled total RNA to generate Affymetrix Genome Array data. The DD data sets were compared to an expression profile obtained from all cells in a matched population of synchronized L1 larvae. See Spencer et al. PLOS One 9, e112102 (2014).

first: Rebecca

last: McWhirter

first: David

last: Miller III


title: caArray_krahe-00060: Expression profiling reveals fundamental biological differences in acute myeloid leukemia

status: Public on Jun 26 2015

city: Rockville

first: Mervi

last: Heiskanen

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

summary:
Acute myeloid leukemia (AML) is a heterogeneous group of diseases. Normal cytogenetics (CN) constitutes the single largest group, while trisomy 8 (+8) as a sole abnormality is the most frequent trisomy. How trisomy contributes to tumorigenesis is unknown. We used oligonucleotide-based DNA microarrays to study global gene expression in AML+8 patients with +8 as the sole chromosomal abnormality and AML-CN patients. CD34+ cells purified from normal bone marrow (BM) were also analyzed as a representative heterogeneous population of stem and progenitor cells. Expression patterns of AML patients were clearly distinct from those of CD34+ cells of normal individuals. We show that AML+8 blasts overexpress genes on chromosome 8, estimated at 32% on average, suggesting gene-dosage effects underlying AML+8. Systematic analysis by cellular function indicated up-regulation of genes involved in cell adhesion in both groups of AML compared with CD34+ blasts from normal individuals. Perhaps most interestingly, apoptosis-regulating genes were significantly down-regulated in AML+8 compared with AML-CN. We conclude that the clinical and cytogenetic heterogeneity of AML is due to fundamental biological differences.
**NOTE: Migrated from caArray 1.x, identifier='gov.nih.nci.ncicb.caarray:Experiment:1015897559579654:1'

overall_design:
krahe-00060
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: Hu6800
Organism: Homo sapiens (ncbitax)
Tissue Sites: Bone marrow
Material Types: synthetic_DNA, synthetic_RNA, organism_part
Cell Types: Myeloid Cell
Disease States: Acute Myeloid Leukemia, Normal


title: Assessment of mTOR-Dependent Translational Regulation of Interferon Stimulated Genes

status: Public on Jul 07 2015

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

type:
Expression profiling by array
Other

summary: Type-I interferon (IFN)-induced activation of the mammalian target of rapamycin (mTOR) signaling pathway has been implicated in translational control of mRNAs encoding interferon-stimulated genes (ISGs). However, mTOR-sensitive translatomes commonly include mRNAs with a 5’ terminal oligopyrimidine tract (TOP), such as those encoding ribosomal proteins, but not ISGs. Because these translatomes were obtained under conditions when ISG expression is not induced, we examined the mTOR-sensitive translatome in human WISH cells stimulated with IFNβ. The mTOR inhibitor Torin1 resulted in a repression of global protein synthesis, including that of ISG products, and translation of all but 3 ISG mRNAs (TLR3, NT5C3A, and RNF19B) was not selectively more sensitive to mTOR inhibition. Detailed studies of NT5C3A revealed an IFN-induced change in transcription start site resulting in a switch from a non-TOP to a TOP-like transcript variant and mTOR sensitive translation. Thus, we show that, in the cell model used, translation of the vast majority of ISG mRNAs is not selectively sensitive to mTOR activity and describe an uncharacterized mechanism wherein the 5’-UTR of an mRNA is altered in response to a cytokine, resulting in a shift from mTOR-insensitive to mTOR-sensitive translation.

overall_design: WISH cells were induced with interferon in the presence of vehicle, torin-1 or rapamycin. Both polysome-associated and total RNA was analyzed.


status: Public on Jul 28 2015

city: Toronto

first: Matthew

last: Gazzellone

state: ON

address: 686 Bay Street

institute: The Centre for Applied Genomics

summary:
Cerebral palsy (CP) represents a group of non-progressive clinically heterogeneous disorders that are characterized by motor impairment and early age-of-onset, frequently accompanied by co-morbidities. The cause of CP has historically been attributed to environmental stressors resulting in brain damage. While genetic risk factors are also implicated, guidelines for diagnostic assessment of CP do not recommend for routine genetic testing. Given numerous reports of etiologic copy number variations (CNVs) in other neurodevelopmental disorders, we used microarrays to genotype a population-based prospective cohort of children with CP and their parents. Here we identify de novo CNVs in 8/115 (7.0%) CP patients (~1% rate in controls). In four children, large chromosomal abnormalities deemed pathogenic were found, and they were significantly more likely to have severe neuro-motor impairments than those CP subjects without such alterations. Overall the CNV data would have impacted our diagnosis or classification of CP in 11/115 (9.6%) families.
Dr. Maryam Oskoui* , Mr. Matthew Gazzellone* , Ms. Bhooma Thiruvahindrapuram , Dr. Mehdi Zarrei , Dr. John Andersen , Dr. John Wei , Dr. Zhouzhi Wang , Dr. Richard Wintle , Dr. Christian Marshall , Dr. Ronald Cohn , Dr. Rosanna Weksberg , Dr. James Stavropoulos , Dr. Darcy Fehlings , Dr. Michael Shevell, Dr. Stephen Scherer. Clinically Relevant Copy Number Variations Detected in Cerebral Palsy. Nature Communications, 2015.

overall_design: Following our rigorous quality control procedure, we successfully genotyped 147 proband samples from individuals with cerebral palsy (81 males and 66 females) and 282 samples obtained from parents (134 males and 148 females). This facilitated the identification of de novo and rare inherited copy number variations of clinical interest.

first: Stephen

last: Scherer


title: Effect of Pseudomonas fluorescens pyoverdine on A. thaliana defence responses and iron homeostasis [INRA13-03_PYO]

status: Public on Sep 01 2015

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra13-03_pyo - effect of pseudomonas fluorescens pyoverdine on a.thaliana defence responses and iron homeostasis - Analyse de l’effet d’un traitement par la pyoverdine sur les gènes liés à l’homéostasie du fer et à l’induction des réactions de défense. - Arabidopsis thaliana plants cultivated in hydroponic conditions were treated for 3 days by pyoverdin, a bacteriosiderophore from Pseudomonas fluorescens C7R12 in a medium supplemented or deprived of iron.

overall_design: 12 dye-swap - organ comparison,treated vs untreated comparison

first: Angélique

last: Besson-Bard

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Exposure of C. elegans to AOBr-containing surface water samples and to a M. aeruginosa batch culture

status: Public on May 12 2015

city: Berlin

first: Nadine

last: Saul

address: Philippstr. 13, House 22

department: Department of Biology

institute: Humboldt-Universitaet zu Berlin

summary: Elevated levels of adsorbable organic bromine compounds (AOBr) have been detected in German lakes, and cyanobacteria like Microcystis, which are known for the synthesis of microcystins, are one of the main producers of natural organobromines. However, very little is known about how environmental realistic concentrations of organobromines impact invertebrates. Here, the nematode C. elegans was exposed to AOBr-containing surface water samples and to a Microcystis aeruginosa enriched batch culture (MC-BA) and compared to single organobromines and microcystin-LR exposures. Stimulatory effects were observed in certain life trait variables, which were particularly pronounced in nematodes exposed to MC-BA. A whole genome DNA-microarray revealed that MC-BA led to the differential expression of more than 2000 genes, many of which are known to be involved in metabolic, neurologic, and morphologic processes. Moreover, the up-regulation of cyp- and the down-regulation of abu-genes suggested the presence of chronic stress. However, the nematodes were not marked by negative phenotypic responses. The observed difference in MC-BA and microcystin-LR (which impacted lifespan, growth and reproduction) exposed nematodes was hypothesized to be likely due to other compounds within the batch culture. Most likely the exposure to low concentrations of organobromines appears to buffer the effects of toxic substances, like microcystin-LR.

overall_design: Nematodes were exposed to filtrated samples of Lake Stößensee Berlin (August and October) and compared to the control-group (exposure to water). Furthermore, nematodes were exposed to filtrated M. aeruinosa batch culture samples and compared to another control-group (exposure to Z-Medium). Three samples (biological replicates) were prepared for each group.

last: Stürzenbaum

first: Shumon

last: Chakrabarti

first: Nora

last: Baberschke

first: Thora

last: Lieke

first: Anke

last: Putschew

first: Cindy

last: Kochan

first: Ralph

last: Menzel

first: Christian

last: Steinberg


title: caArray_hanas-00078: Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis

status: Public on Jun 25 2015

last: Heiskanen

summary: Astrocytomas are heterogeneous intracranial glial neoplasms ranging from the highly aggressive malignant glioblastoma multiforme (GBM) to the indolent, low-grade pilocytic astrocytoma. We have investigated whether DNA microarrays can identify gene expression differences between high-grade and low-grade glial tumors. We compared the transcriptional profile of 45 astrocytic tumors including 21 GBMs and 19 pilocytic astrocytomas using oligonucleotide-based microarrays. Of the approximately 6800 genes that were analyzed, a set of 360 genes provided a molecular signature that distinguished between GBMs and pilocytic astrocytomas. Many transcripts that were increased in GBM were not previously associated with gliomas and were found to encode proteins with properties that suggest their involvement in cell proliferation or cell migration. Microarray-based data for a subset of genes was validated using real-time quantitative reverse transcription-PCR. Immunohistochemical analysis also localized the protein products of specific genes of interest to the neoplastic cells of high-grade astrocytomas. Our study has identified a large number of novel genes with distinct expression patterns in high-grade and low-grade gliomas.

overall_design:
hanas-00078
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: Hu6800
Organism: Homo sapiens (ncbitax)
Tissue Sites: Brain
Material Types: synthetic_DNA, synthetic_RNA, organism_part
Disease States: Primary Glioma, Normal


title: caArray_golub-00236: Multiclass cancer diagnosis using tumor gene expression signatures

status: Public on May 16 2015

summary: The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is difficult or impossible because of atypical clinical presentation or histopathology. To determine whether the diagnosis of multiple common adult malignancies could be achieved purely by molecular classification, we subjected 218 tumor samples, spanning 14 common tumor types, and 90 normal tissue samples to oligonucleotide microarray gene expression analysis. The expression levels of 16,063 genes and expressed sequence tags were used to evaluate the accuracy of a multiclass classifier based on a support vector machine algorithm. Overall classification accuracy was 78%, far exceeding the accuracy of random classification (9%). Poorly differentiated cancers resulted in low-confidence predictions and could not be accurately classified according to their tissue of origin, indicating that they are molecularly distinct entities with dramatically different gene expression patterns compared with their well differentiated counterparts. Taken together, these results demonstrate the feasibility of accurate, multiclass molecular cancer classification and suggest a strategy for future clinical implementation of molecular cancer diagnostics.

overall_design:
golub-00236
Assay Type: Gene Expression
Provider: Affymetrix
Array Designs: Hu35KsubA, Hu6800
Organism: Homo sapiens (ncbitax)
Material Types: synthetic_RNA, organism_part, whole_organism, total_RNA
Disease States: Colorectal Adenocarcinoma, Melanoma, Normal, pancreatic adenocarcinoma, Acute Myeloid Leukemia, Breast Adenocarcinoma, T-cell ALL, Lung Adenocarcinoma, bladder transitional cell carcinoma, Ovarian Adenocarcinoma, Mesothelioma, B-cell ALL, prostate adenocarcinoma, Medulloblastoma, Follicular Lymphoma, renal cell carcinoma, uterine adenocarcinoma, large B-cell lymphoma, Glioblastoma, bladder transitonal cell carcinoma


title: caArray_golub-00095: Diffuse large B-cell lymphoma outcome prediction

status: Public on May 15 2015

summary: Diffuse large B-cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is curable in less than 50% of patients. Prognostic models based on pre-treatment characteristics, such as the International Prognostic Index (IPI), are currently used to predict outcome in DLBCL. However, clinical outcome models identify neither the molecular basis of clinical heterogeneity, nor specific therapeutic targets. We analyzed the expression of 6,817 genes in diagnostic tumor specimens from DLBCL patients who received cyclophosphamide, adriamycin, vincristine and prednisone (CHOP)-based chemotherapy, and applied a supervised learning prediction method to identify cured versus fatal or refractory disease. The algorithm classified two categories of patients with very different five-year overall survival rates (70% versus 12%). The model also effectively delineated patients within specific IPI risk categories who were likely to be cured or to die of their disease. Genes implicated in DLBCL outcome included some that regulate responses to B-cell-receptor signaling, critical serine/threonine phosphorylation pathways and apoptosis. Our data indicate that supervised learning classification techniques can predict outcome in DLBCL and identify rational targets for intervention.

overall_design:
golub-00095
Assay Type:  Gene Expression
Provider: Affymetrix
Array Designs: Hu6800
Organism: Homo sapiens (ncbitax)
Tissue Sites: Lymphoid tissue
Material Types: synthetic_DNA, synthetic_RNA, organism_part
Cell Types: B-Lymphocyte
Disease States: Diffuse large B-cell Lymphoma, Follicular Lymphoma


title: Identification of genes involved with P. aeruginosa biofilms

status: Public on May 11 2015

city: Bozeman

first: Kerry

last: Williamson

address: 109 Lewis Hall

institute: Montana State University

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

overall_design: Refer to individual Series