title: microRNA changes during Dex-induced pDC apoptosis

status: Public on Apr 20 2016

city: He Fei

first: Yongfeng

last: Hong

address: Furong Road 678

country: China

institute: The Second Affiliated Hospital to Anhui Medical University

summary: To identify microRNA changed during Dex-induced pDC apoptosis and CpG hampered Dex-induced pDC apoptosis

overall_design:
Fresh peripheral blood mononuclear cells (PBMCs) were obtained from 20 healthy individuals. PDCs were isolated by magnetic-activated cell sorting using the Human Diamond Plasmacytoid Dendritic Cell Isolation Kit (Miltenyi Biotec). The purity of the isolated PDCs was > 95%, as determined by flow cytometry (FCM).
Purified human pDCs were divided into three parts: 1) Medium alone, 2)Dex stimulation,3)Dex and CpG stimulation.
Total RNA was harvested using TRIzol (Invitrogen) and an miRNeasy mini kit (QIAGEN) according to the manufacturers’s instructions. After confirming an adequate RNA concentration using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.16.0). Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner. Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.
The Dex induction of each miRNA was calculated by the value in pDC Dex stimulation-sample divides the value in ' pDC no stimulation-sample'. The CpG induction of each miRNA during Dex stimulation was calculated by the value in pDC Dex+CpG stimulation-sample divides the value in ' pDC Dex stimulation-sample'.


title: Extruded linseed alone or in combination with fish oil modifies mammary gene expression profiles in lactating goats

status: Public on Apr 29 2016

city: Saint Genès Champanelle

first: Faulconnier

last: Yannick

address: Centre Inra Theix

department: Phase

country: France

institute: INRA

summary: Animal nutrition considerably affects milk composition that influences its nutritional quality. Milk component synthesis and secretion by the mammary gland involve the expression of a large number of genes whose nutritional regulation remains poorly defined. In this study, 14 lactating goats received 3 experimental diets: 1- the basal diet with hay prepared from regrowth of natural grassland pasture offered ad libitum and a concentrate mixture (CTRL, n = 5)), the basal diet with 530 g/d extruded linseed (EL, n = 4) or with a combination of 340 g/d extruded linseed and 39 g/d of fish oil (ELFO, n = 5). To investigate the pathways regulated by nutrition, we examined the effect of EL and ELFO diets compared with CRTL diet and the effect of EL diet compared to ELFO diet on the expression of approximately 8400 genes in caprine mammary gland using a bovine oligonucleotide microarray.

overall_design: The hybridization was performed with 40 pmol of incorporated Cy3 from the mammary mRNA from each goat fed one diet and 40 pmol of incorporated Cy5 from the mammary mRNA from goat fed another diet.  Each hybridization was repeated in a dye-swap manner for a total of 26 slides (4 slides for the comparison of EL vs. CRTL diets, 5 slides for the comparison of ELFO vs. CRTL diets, 4 slides for the comparison of EL vs. ELFO diets). One sample of mammary gland from goat fed EL diet was suppressed because after mRNA extraction the RNA integrity number was lesser than 7.

first: Y

last: Faulconnier

first: C

last: Boby

first: J

last: Domagalski

last: Leroux


title: Genome-wide binding site analysis of MaASR reveals its crucial roles in multiple drought stress response pathways

city: Haikou

first: lili

last: zhang

address: longhua County，Xueyuan Road 4

institute: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences

summary: Abscisic acid (ABA)-, stress-, and ripening-induced (ASR) proteins are involved in abiotic stress responses. However, the exact molecular mechanism underlying their function remains unclear. Notably, the direct targets of ASRs that confer drought stress tolerance have not yet been identified.In this study, we report that MaASR expression was induced by drought stress and MaASR overexpression in Arabidopsis strongly enhanced drought stress tolerance. Physiological analyses indicated that transgenic lines had higher survival rates, germination rates and proline content, and lower water loss rates (WLR) and malondialdehyde (MDA) content. MaASR-overexpressing lines also showed smaller leaves and reduced sensitivity to ABA. Further, microarray and chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis revealed that MaASR participates in regulating photosynthesis, respiration, carbohydrate and phytohormone metabolism and signal transduction to confer plants with enhanced drought stress tolerance. Direct interactions of MaASR with promoters for the hexose transporter and Rho GTPase-activating protein (RhoGAP) genes were confirmed by electrophoresis mobility shift array (EMSA) analysis.  Our results indicate that MaASR acts as a crucial regulator of photosynthesis, respiration, carbohydrate and phytohormone metabolism and signal transduction to mediate drought stress tolerance.

overall_design: Total RNA of arabidopsis was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each pooling RNA sample separately on the GeneChip_ Porcine Genome Array (Affymetrix) at CapitalBio Corporation (Beijing, China) in which GeneChip microarray service was certificated by Affymetrix.

first: Lili

last: Zhang

first: Biyu

last: Xu

first: Zhiqiang

last: Jin


title: A landscape of cellular aggregation of Rhizobium etli CFN42 by a transcriptomic approach

status: Public on Apr 15 2016

city: CUERNAVACA

first: AGUSTIN

middle: REYES

last: PEREZ

state: MORELOS

address: UNIVERSITY AV.

department: FUNCTIONAL GENOMICS

country: Mexico

institute: UNAM

summary:
Dna microarray technology was used to survey changes in gene expression in R. etli CFN42 in biofilm formation
In these organisms, two main phases, biofilm and planktonic, have been identified. In this work, using microarray assays, we evaluated global gene expression in biofilm and planktonic growth phases in rich medium, in the bacterium Rhizobium etli CFN42.

overall_design: Three independent biological materials with one dyeswap were performed.

first: Agustin

last: Reyes-Pérez

first: Magdalena

last: Hernández

first: Ernesto

last: Pérez-Rueda

first: Eneas

last: Aguirre-von-Wobeser

first: Sergio

last: Encarnacion


title: Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [Microarray]

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: The rapidly expanding information on the structural and functional characteristics of the human genome allows the development of genome-wide approaches to investigate the molecular circuitry wiring the genetic and epigenetic programs of clinically relevant stem/progenitor cells. Here, we define the transcriptional and epigenetic profile of human hematopoietic stem/progenitor cells (HSPC) and their committed, early myeloid and erythroid progeny. Cap Analysis of Gene Expression showed that the transcriptional state is largely maintained in the transition from early hematopoietic stem/progenitors to committed progenitor/precursors. A large fraction of differentially expressed active promoters in each cell type were classified as novel, possibly driving the expression of transcripts involved in HSPC commitment. Unannotated promoters harbored an enhancer chromatin signature, were enriched in cell-specific transcription factor binding sites, and were close to protein-coding cell-specific genes. To obtain a genome-wide description of regulatory regions, we performed ChIP-seq for histone modifications typical of promoters, enhancers and super-enhancers. ChIP-defined promoters were shared by HSPC and committed cells, whereas enhancer usage consistently changed upon commitment, thus indicating that the fine regulation of commitment is carried out by enhancer elements. The expression level of genes targeted by enhancers and super-enhancers was moderately higher in cells actively using these regulatory elements. However, functional annotation of targeted genes showed a low enrichment for cell-specific gene ontology categories. Finally, we used Moloney leukemia virus (MLV) to map functional regions of chromatin. Genomic regions targeted by MLV co-mapped with a fraction of epigenetically defined active regulatory elements, with two-third of MLV integrations falling in enhancers, and one-third in promoters. Most of MLV-targeted regulatory regions were differentially used between HSPC and their committed progeny. Analysis of the expression levels of promoters close to cell-specific MLV-targeted enhancers and functional assays indicated that MLV-defined regulatory regions are bona fide cell-specific enhancers. Finally, gene ontology analyses showed that MLV-targeted genes related to the peculiar cell identity. Overall, this study provided an overview of the differential transcriptional and epigenetic programs of HSPC and committed progenitors and represents a unique source of regulatory regions involved in HSPC commitment.

overall_design: Gene expression profiling of HSPC and their committed progeny.

first: Oriana

last: Romano

first: Clelia

last: Peano

first: Guidantonio

middle: M

last: Tagliazucchi

first: Luca

last: Petiti

first: Valentina

last: Poletti

first: Fabienne

last: Cocchiarella

first: Ermanno

last: Rizzi

first: Marco

last: Severgnini

first: Alessia

last: Cavazza

first: Claudia

last: Rossi

first: Pasqualepaolo

last: Pagliaro

first: Alessandro

last: Ambrosi

first: Giuliana

last: Ferrari

first: Gianluca

last: De Bellis

first: Fulvio

last: Mavilio

first: Annarita

last: Miccio


title: Trade-off between growth and carbohydrate accumulation in nutrient-limited Arthrospira sp. PCC 8005 studied by integrating transcriptomic and proteomic approaches

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary: Cyanobacteria have a strong potential for biofuel production due to their ability to accumulate large amounts of carbohydrates. Nitrogen (N) stress can be used to increase the content of carbohydrates in the biomass, but it is expected to reduce biomass productivity. To study this trade-off between carbohydrate accumulation and biomass productivity, we characterized the biomass productivity, biomass composition as well as the transcriptome and proteome of the cyanobacterium Arthrospira sp. PCC 8005 cultured under N-limiting and N-replete conditions. N limitation resulted in a large increase in the carbohydrate content of the biomass (from 14 to 74%) and a decrease in the protein content (from 37 to 10%). Nevertheless, it did not affect the biomass productivity of the culture up to five days after N was depleted from the culture medium. Transcriptomic and proteomic analysis indicated that de novo protein synthesis was down-regulated in the N-limited culture. Proteins were degraded and partly converted into carbohydrates through gluconeogenesis. Cellular N derived from protein degradation was recycled through the TCA and GS-GOGAT cycles. In addition, photosynthetic energy production and carbon fixation were both down-regulated, while glycogen synthesis was up-regulated. Our results suggested that N limitation resulted in a redirection of photosynthetic energy from protein synthesis to glycogen synthesis. The fact that glycogen synthesis has a lower energy demand than protein synthesis might explain why Arthrospira is able to achieve a similar biomass productivity under N-limited as under N-replete conditions despite the fact that photosynthetic energy production was impaired by N limitation.

overall_design: Arthrospira cultures were compared in normal growth conditions versus nitrogen-limited growth conditions

first: Orily

last: Depraetere

first: Frédéric

last: Deschoenmaeker

first: Hanene

last: Badri

first: Pieter

last: Monsieurs

first: Imogen

last: Foubert

first: Natalie

last: Leys

first: Ruddy

last: Wattiez

first: Koenraad

last: Muylaert


title: Downregulation of miR-19a as a Biomarker for Early Detection of Silicosis

status: Public on Apr 22 2016

city: tianjin

first: hongsheng

last: gao

address: dongli

institute: university

summary: To explore the early diagnostic value for silicosis we have employed the Human microRNA OneArray® v5 as a discovery platform to identify microRNAs as biomarkers of silicosis use.To be followed,a microRNA-gene network in silicosis wasestablished by the differential expression profiles so that candidate markers of silicosis could be spotted and validated. Then, the relative expression levels of potential biomarkers were measured by Quantitative Real-time PCR (qPCR) and the sensitivity and specificity were assessed by ROC curves.

overall_design: The gene expressions of 3 silicosis and 3 controls were measured.

first: Zhen

last: Yang

first: Qian

last: Li

first: Sanqiao

last: Yao

first: Ge

last: Zhang

first: Rong

last: Xue

first: Guoliang

first: Yizheng

last: Wang

first: Shixin

first: Ruichang

last: Wu

first: Hongsheng

last: Gao


title: circRNA expression in basal cell carcinoma

status: Public on Apr 21 2016

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

country: Germany

institute: Ruhr-University Bochum

summary:
Punch biopsies from patients with BCC (n=3) and non-lesional skin (n=3) were included in the study. Microarray based circRNA expression profiles were acquired using Arraystar circRNA Arrays V. 2.0 screening for 13,617 distinct human circRNA candidates.
We identified circRNAs differentially expressed in BCC compared to non-lesional skin (control).

overall_design: The circRNA expression in BCC was compared to circRNA expression in non-lesional skin (control).


title: Comparative Genomic Hybridization in traditional fermentative Saccharomyces cerevisiae yeasts

city: Valencia

first: Clara

last: Ibáñez

address: Avenue Agustín Escardino, 7

country: Spain

institute: Institute of Agrochemistry and Food Technology

summary: We study the genetics, including microarray karyotyping using comparative genomic hybridization to explore global changes in the genomic DNA, of four S. bayanus var uvarum strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNV) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media.

sample_organism:
Saccharomyces uvarum
Saccharomyces cerevisiae S288C

overall_design: Four S. bayanus var. uvarum strains were obtained from natural environments and different fermentation processes. The S. cerevisiae strain S288C was used as control for microarray hybridizations. All experiments were performed using duplicate arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.

first: Roberto

last: Pérez-Torrado

first: Jose

last: Guillamón

first: Amparo

last: Querol

first: Eladio

last: Barrio


title: Effect of artificial saliva on inflammatory response of oral fibroblasts in an in vitro study

status: Public on Apr 23 2016

city: Piracicaba

first: Bruna

last: Benso

department: Physiological Sciences

country: Brazil

institute: UNICAMP

summary:
Real-time quantitative PCR analysis of oral fibroblasts
Fibroblasts (HGF-1) was exposed for 120 seconds to human saliva (HS) and two commercially available AS (AS I and AS II). One microgram of RNA was converted in cDNA using RT2 First Strand Kit. 84 genes were analyzed using inflammatory response & Autoimmunity Array RT2 profiler (Qiagen Sabiosciences, Valencia, CA, USA) with buffers supplied by the manufacturer

overall_design: qPCR gene expression profiling. Fibroblasts (HGF-1) was exposed for 120 seconds to human saliva (HS) and two commercially available AS (AS I and AS II).The expression of cytokines was assessed by PCR array analysis, Real-Time PCR

first: Maria

middle: S

last: Marquezin

first: Silvana

last: Pasetto

first: Paula

last: Castelo

first: Ramiro

last: Murata


title: Complete Genetic Reconstitution of VISA Phenotype of Mu50 in Vancomycin-Susceptible Staphylococcus aureus.

status: Public on Apr 19 2016

city: Bunkyo-Ku

first: tomomi

last: hishinuma

state: Tokyo

country: Japan

institute: juntendo university

summary: Complete reconstitution of the vancomycin-intermediate Staphylococcus aureus (VISA) phenotype of Mu50 was achieved by sequentially introducing mutations into five genes of a vancomycin-susceptible S. aureus (VSSA) strain ∆IP.  Introduction of mutation Ser329Leu into vraS encoding the sensor histidine kinase of vraSR two-component regulatory (TCR) system and another mutation Glu146Lys into msrR, encoding putative methionine sulfoxide reductase regulator, raised vancomycin resistance to the level of heterogeneously vancomycin-intermediate S. aureus (hVISA) strain Mu3. Introduction of two more mutations, graR (Asn197Ser) of graSR TCR system and rpoB(His481Tyr) encoding ß subunit of RNA polymerase, converted the hVISA strain into a VISA strain having the level of vancomycin resistance of Mu50. Surprisingly, however, the constructed quadruple mutant strain did not have thickened cell wall, a cardinal feature of VISA phenotype. Subsequent study showed that cell-wall thickening was an inducible phenotype with the mutant strain as opposed to that of Mu50, which is a constitutive one. Finally, introduction of mutation Ala297Val into the orf SAV2309 of the mutant strain converted the inducible cell-wall thickening into a constitutive one. SAV2309 encodes a putative formate dehydrogenase (designated Fdh2). Though not a transcription regulator, the mutation of the fdh2 caused a significant change in transcriptome. Thus, all of the five mutated genes required for VISA phenotype acquisition were directly or indirectly involved in the regulation of cell physiology. VISA seemed to be achieved through multiple genetic events accompanying drastic changes in cell physiology.

overall_design: We investigated the expression of genes involved in vancomycin resistance in Staphylococcus aureus, using a 60mer oligo array.

first: Yuki

last: katayama

first: Miwa

last: Sekine

first: Tomomi

last: Hishinuma

first: Yoshifumi

last: Aiba

first: Keiichi

last: Hiramstsu


title: Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans

status: Public on Apr 18 2016

city: Lisboa

first: Cristina

middle: Silva

last: Pereira

address: Rua da Quinta Grande nº6

country: Portugal

institute: Instituto de Tecnologia Química e Biológica (ITQB)

summary: The study aims essentially in the analysis of the transcriptomic and metabolomic profiles induced by the presence of the tested ionic liquids  in the metabolism of Aspergillus nidulans. Focusing specially on the secondary metabolism, which genes are clustered.

platform_organism:
Aspergillus nidulans FGSC A4
Neurospora crassa OR74A

overall_design: Aspergillus nidulans cultures were grown for fifteen days in mineral media alone (control) or supplemented with 1-ethyl-3-methylimidazolium chloride or cholinium chloride at a concentration of half the MIC previously determined for 1-ethyl-3-methylimidazolium chloride, namely 0.7 M for A. nidulans. To investigate the impact of the tested ionic liquids in the metabolism of A. nidulans, the fungal transcriptome (three biological replicates) was analysed using Affymetrix microarrays. Pair-wise comparisons were used to identify the set of genes with altered expression levels between the control  and the media supplemented with either 1-ethyl-3-methylimidazolium chloride or cholinium chloride after fifteen days.

first: Jörg

middle: D

last: Becker

middle: C

last: Alves

first: Diego

middle: O

last: Hartmann

first: Isabel

last: Martins

first: Helga

last: Garcia


title: Comparison of two A. nidulans strains: control CV125 and transgenic NA1363 harboring E. coli LacZ transgene.

status: Public on Apr 12 2016

city: CHATENAY-MALABRY

first: Claudine

last: DELOMENIE

address: 5, rue Jean-Baptiste Clément

department: Transcriptomique

institute: University Paris Sud 11

summary:
Transcriptional profiling of two A. nidulans strains, aiming to compare the control strain CV125 (pabaA1) with the transgenic strain NA1363 (pabaA1) harbouring a gpdAp-lacZ-trpCt.riboB construct integrated in chromosome VIII.
This construct, carried out in a derivative of the pBR322 vector, contained the E. coli lacZ sequence (encoding ß-galactosidase) fused to the A. nidulans trpC terminator and placed under the control of the strong and constitutive promoter of the A. nidulans gpdA gene, and the riboB gene as a selection marker.

overall_design:
Two-condition experiment, NA1363 vs CV125 strains. Biological and technical replicates: 8 control and 8 transgenic cultures, independently grown and harvested in two culture batches (4 cultures of each strain per batch).
One sample from each indivudual culture hybridized per array, no hybridization replicates.  Each indivudual sample was labeled with Cy3 and hybridized in competition with a sample labeled with Cy5 prepared from a pool of RNA (reference).

last: Deloménie

first: Guido

last: Grentzmann

first: Nathalie

last: Oestreicher

first: Robin

last: Mesnage

first: Christian

last: Vélot


title: Transcriptional profiling of Drosophila during Listeria infection as they die and as they recover upon ampicillin treatment

city: Stanford

first: Alexander

last: Louie

state: CA

address: 299 Campus Dr

department: Microbiology and Immunology

country: USA

institute: Stanford University

overall_design: Twenty treatment groups were analyzed, with three replicates for each treatment group

first: David

last: Schneider


title: Expression data from mouse lung epithelial cells and non-epithelial cells during Pneumococcal pneumonia

city: Boston

first: Hirofumi

last: Kamata

state: Massachusetts

address: 72 East Concord Street

department: The Pulmonary Center

institute: Boston University, School of Medicine

summary:
A growing body of evidence suggests that epithelial cells have special roles during pneumonia. The purpose of this study was to elucidate epithelial-specific responses during lung infection.
Mice received intratracheal instillations of Streptococcus pneumoniae (10^6 CFU) into the left lung. 15 hours after the challenge, left lungs were collected. Single cell supensions were generated and sorted into 2 separate populations, epithelial cells (CD45-EpCAM+) and others (all non-epithelial cells). Epithelial cells from uninfected mice were also collected.

overall_design: RNA from 3 separate groups of mice (3 mice per group) was analyzed: 1) Epithelial cells from pneumonic mice; 2) Epithelial cells from uninfected mice; and 3) Non-epithelial cells from pneumonic mice.


title: Gene-expression profiling between segmental vitiligo, generalized vitiligo and healthy individual

status: Public on Apr 08 2016

city: Hangzhou

first: Ping

last: Wang

address: 38 West Lake Avenue

institute: Affiliated 3rd Hospital of Hangzhou

summary: Investigate the gene expression change in the blood of segmental vitiligo, generalized vitiligo and healthy individual.

overall_design: In the study, a consecutively operated, well-defined cohort of 60 samples in total, followed by pooling every 5 samples, was used to acquire expression profiles of a total of 31,741 probes.

first: Yong

last: Li


title: ChIP-Chip of TAP-tagged Ppr1 Candida albicans strains

city: Montreal

first: Walters

middle: Aji

last: Tebung

state: Quebec

address: 7141 Rue Sherbrooke Ouest

department: Chemistry and Biochemistry

country: Canada

institute: Concordia University

type: Genome binding/occupancy profiling by array

summary:
Metabolic pathways are largely conserved in eukaryotes, but the transcriptional regulation of these pathways can sometimes vary between species; this has been termed rewiring. Recently it has been established that in the Saccharomyces lineage starting from Saccharomyces castelli, genes involved in allantoin breakdown have been genomically relocated to form the DAL cluster. The formation of the DAL cluster occurred along with the loss of urate permease (UAP) and urate oxidase (UOX), reducing the requirement for oxygen and bypassing the candidate Ppr1 inducer, uric acid. In Saccharomyces cerevisiae this allantoin catabolism cluster is regulated by the transcription factor Dal82, which is not present in many of the pre-rearrangement fungal species. We have used ChIP-Chip analysis, transcriptional profiling of an activated Ppr1 protein, bioinformatics, and nitrogen utilization studies, to establish that in Candida albicans the zinc cluster transcription factor Ppr1 controls this allantoin catabolism regulon. Intriguingly, in S. cerevisiae the Ppr1 ortholog binds the same DNA motif (CGG(N6)CCG) as in C. albicans, but serves as a regulator of pyrimidine biosynthesis. This transcription factor rewiring appears to have taken place at the same phylogenetic step as the formation of the rearranged DAL cluster. This transfer of the control of allantoin degradation from Ppr1 to Dal82, together with the repositioning of Ppr1 to the regulation of pyrimidine biosynthesis, may have resulted from a switch to a metabolism that could exploit hypoxic conditions in the lineage leading to S. castellii and S. cerevisiae.
Metabolic pathways are largely conserved in eukaryotes, but the transcriptional regulation of these pathways can sometimes vary between species; this has been termed rewiring. Recently it has been established that in the Saccharomyces lineage starting from Saccharomyces castelli, genes involved in allantoin breakdown have been genomically relocated to form the DAL cluster. The formation of the DAL cluster occurred along with the loss of urate permease (UAP) and urate oxidase (UOX), reducing the requirement for oxygen and bypassing the candidate Ppr1 inducer, uric acid. In Saccharomyces cerevisiae this allantoin catabolism cluster is regulated by the transcription factor Dal82, which is not present in many of the pre-rearrangement fungal species. We have used ChIP-Chip analysis, transcriptional profiling of an activated Ppr1 protein, bioinformatics, and nitrogen utilization studies, to establish that in Candida albicans the zinc cluster transcription factor Ppr1 controls this allantoin catabolism regulon. Intriguingly, in S. cerevisiae the Ppr1 ortholog binds the same DNA motif (CGG(N6)CCG) as in C. albicans, but serves as a regulator of pyrimidine biosynthesis. This transcription factor rewiring appears to have taken place at the same phylogenetic step as the formation of the rearranged DAL cluster. This transfer of the control of allantoin degradation from Ppr1 to Dal82, together with the repositioning of Ppr1 to the regulation of pyrimidine biosynthesis, may have resulted from a switch to a metabolism that could exploit hypoxic conditions in the lineage leading to S. castellii and S. cerevisiae.

overall_design: 2 samples were analyzed. Cells were grown in YPD media at 30 degrees celcius to OD 0.6. TAP-tagged Ppr1 strain vs wild type (SN148) were hybridized. One replica per array.

first: Tebung

last: Walters Aji

first: Tebbji

last: Faiza

first: Whiteway

last: Malcolm


title: Mincle-mediated signaling leads to characteristic gene expressions in rat mast cells

city: Eiheiji

first: Chisato

last: Honjoh

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

institute: University of Fukui

summary:
Rat mast cell line RBL-2H3 was analyzed to investigate the molecular mechanism of Mincle-mediated activation and responses of mast cells.
Mincle-mediated signaling stimulated characteristic gene expression, such as IL-3, IL-4, IL-9, IL-13, IL-31 and TNFα.

overall_design: RBL-2H3 cell line stably expressing Mincle was established. Non-stimulated cells (Control) compared to Mincle-stimulated cells (Myc) in order to comfirm Mincle-mediated signaling-inducible genes. Mincle-stimulated cells compared to Syk inhibitor R406-pretreated cells (R406) in order to examine the importance of Syk for Mincle-mediated gene up-regulations.

first: Kazuyasu

last: Chihara

first: Hatsumi

last: Yoshiki

first: Shota

last: Yamauchi

first: Kenji

last: Takeuchi

first: Yuji

last: Kato

first: Yukio

last: Hida

first: Masayuki

last: Iwano

first: Tamotsu

last: Ishizuka

first: Kiyonao

last: Sada


title: Transcriptomic responses of early developmental larval stages exposed to a hypoosmotic environment in the flatfish Senegalese solea

status: Public on Apr 24 2016

city: Campanillas

first: Rocio

last: Bautista

state: Malaga

address: C/ Severo Ochoa, 34. Parque Tecnologico

department: Edificio de Bioinnovacion

institute: Universidad de Malaga

summary: Salinity is a major factor that can affect greatly the viability of the fish larvae during their developing stages. Natural populations are exposed to high fluctuation in the environmental conditions. Also, salinity management is of high relevance in hatcheries. The objective of this study was to determine the biological effects of environmental salinities on larval development in sole. Larvae were exposed to two salinities, 10 and 36 ppt, from eggs until the 3 days after hatching. Expression profiles were determined using RNA-seq, microarray and validated using qPCR. Important malformations were identified. The identification of key molecular pathways affected by salinity can help to understand the effects of salinity during early developmental stages with a profound impact to evaluate the effects of climate change and improve hatchery practices.

overall_design: Fertilized eggs of Senegalese sole were collected from spontaneous spawn at “El Toruño” facilities (El Puerto de Santa María, Cadiz). Temperature in the broodstock during the spawning was approximately 18.5ºC and salinity 34 ppt. Eggs were transferred to a 1,000-mL measuring cylinder to separate buoyant (viable) from non-buoyant (non-viable) eggs and the number in each fraction was estimated using volumetric methods (1,100 eggs mL-1). After estimating the number of fertilized eggs, we incubated embryos (at the gastrula stage) in 15-L cylinder tanks at an initial density of 2,000 embryos L-1. After seeding, two salinities (10 and 36 ppt) were established using a recirculation system that kept constant temperature (20ºC±0.5) and target salinity. Water turnover was maintained at one total renewal per hour during the experiment. Trial was done in duplicate tanks for each salinity. After hatching, larvae were sampled at day 3 using a 350 µm-mesh net. Three pools of larvae were collected from each tube (~100 larvae/pool), washed with DEPC water, frozen directly in liquid nitrogen and stored at -80 °C until analysis.

first: P

last: Armesto

first: D

last: Crespo

first: J

last: Planas

first: X

last: Cousin

first: M

last: Manchado


title: Real-time quantitative PCR analysis of miRNA in mouse peritoneal macrophages upon miR-33 or miR-33* modulation

city: New York

first: Kathryn

last: Moore

state: New York

address: 522 First Ave, Smilow 707

department: Medicine

institute: NYU Medical Center

summary:
Mouse peritoneal macrophages were transfected with 80-120 nM miRIDIAN miRNA mimics (miR-mimic-33/miR-mimic-33*) or with 80-120 nM miRIDIAN miRNA inhibitors (anti-miR-33 ASO/anti-miR-33*ASO)
Control samples were treated with an equal concentration of a non-targeting control mimics sequence (control mimic) or inhibitor negative control sequence (control aso), to control for non-specific effects in miRNA experiments.

overall_design: qPCR gene expression profiling.  Peritoneal macrophages from 2-4 donors were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was pooled prior to gene expression analysis.

last: Ouimet

first: K

middle: J


title: Cyenopyrafen resistance in the two-spotted spider mite Tetranychus urticae

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

institute: University of Ghent

summary:
Cyenopyrafen is a novel acaricide with a currently unknown mode of action.
We selected for high levels of cyenopyrafen resistance in a susceptible spider mite strain and previously published patterns of cross-resistance to other well-described acaricides (Khalighi et al., 2014). In addition, we also included an independent cyenopyrafen-susceptible mite strain (referred to as Akita) in this study.
We performed transcriptomic analysis to identify on the molecular level how T. urticae develops resistance to this novel acaricide.
Using this dataset, we show that the selection for cyenopyrafen resistance resulted in massive transcriptomic responses in T. urticae.
The multi-gene family of cytochrome P450 monooxygenases (CYPs) exhibited a drastic differential expression with a significant transcriptional induction in the acaricide resistant strain.
This transcriptomic study highlights the potential importance of CYPs in mite resistance to the cyenopyrafen acaricide.

overall_design: 8 replicates for two comparisons using an Agilent dual color GE microarray design; per replicate 150 mites were pooled. Mites of the cyenopyrafen resistant spider mite (cy5) were directly compared to mites of a susceptible strain (cy3). In a second set of samples, mites of the cyenopyrafen susceptible Akita strain (cy5) and of a reference strain (cy3) were included.

first: Mousaalreza

last: Khalighi

first: Wannes

last: Dermauw

first: Thomas

last: Van Leewen


title: Candida albicans Ppr1 ChIP chip and transcriptional profiling data

first: Walters

last: Tebung

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

overall_design: Refer to individual Series


title: A transcriptomic analysis of the response of S. cerevisiae EC1118 to nitrogen supplementation during the stationary phase of four-stages continuous fermentation (FSCF)

city: Montpellier

first: Carole

last: Camarasa

address: 2, place Pierre Viala

institute: INRA

summary:
The first aim was to investigate the suitability of FSCF to analyze yeast physiology during the stationary phase of wine making. In this way, a comparative transcriptomic analysis was performed on mRNA samples collected from the third stage of FSCF and from batch culture, at the same fermentation progress (164 g/L residual glucose).
In a second part, FSCF device was used to study the impact at the transcriptomic level of nitrogen addition performed at the beginning of the stationary phase. Gene expression profiles were compared at steady state between cells from the third stage of FSCF operating in presence or absence of continuous valine or ammonium perfusion.

overall_design: 4 conditions with 3 or 4 replicates compared: B (stationary phase of batch fermentation), WA (third stage of four-stage continuous fermentation without nitrogen addition), AA (ammonium supplementation in third stage of four-stages continuous fermentation) and VA (valine supplementation in third  stage of four-stages continuous fermentation)

first: Tiphaine

last: Clement


title: Co-regulation of Cxcl1 and Versican in inflammatory response in UVB induced reactive oxygen species in the skin.

status: Public on Apr 25 2016

city: Kobe

first: Makoto

last: Kunisada

address: 7-5-2 Kusunoki-cho

department: Dermatology

institute: Kobe university of medicine

summary: Reactive oxygen species (ROS) induced by ultraviolet B (UVB) cause DNA damage such as 8-oxoguanine (8-oxoG) in mouse skin, with long-term exposure leading skin tumor development. We previously reported that Ogg1 knockout mice, with defective repair enzyme for 8-oxoG oxidatively damaged DNA, showed greater up-regulation of inflammatory response genes and Versican, which encodes a large extracellular matrix proteoglycan, than their wild-type counterparts. Here, we focused on inflammatory response genes associated with Versican up-regulation after UVB exposure, using Ogg1 knockout mouse embryonic fibroblasts (MEFs). Gene profiling among inflammatory response-associated genes in MEFs treated with UVB showed that Cxcl1, a CXC chemokine, was most significantly up-regulated in Ogg1(-/-) MEFs, concomitant with the up-regulation of Versican. We found that Versican targeted siRNA directly regulated Cxcl1, and vice versa, in which the system of up-regulation for these two key genes were controlled by PI3kinase-NFkB activation signaling rather than conventional UV-induced p38 mitogen-activated protein kinase. Furthermore, for the initial process of differentiating inflammatory response between Ogg1(-/-) and Ogg1(+/+), we found that down-regulation of p53 along with anti-apoptotic signal was a key event in Ogg1(-/-).The results of the present study suggest suppression of skin tumor development involving UVB/ROS-induced 8-oxoG formation by targeting genes and signaling pathways.

overall_design: Irradiate UVB with 10mJ/cm2 and collected each genotype (WT and Ogg1KO) MEFs following isolation of mRNA

first: Chihiro

last: Takemori

first: Chikako

last: Nishigori


title: Transcript changes in tlpD mutant of Helicobacter pylori

city: Hannover

first: Christine

last: Josenhans

address: Carl-Neuberg-Strasse 1

department: Institute for Medical Microbiology

institute: Hannover Medical School

summary: Differential gene transcript amounts between Helicobacter pylori N6 (wild type strain) bacteria and isogenic tlpD mutant grown in liquid culture to similar O.D.600 (1.0; mid log)

overall_design: Comparative analyses of transcript levels in N6 (wild type strain) and isogenic tlpD mutant comprising four arrays of three biological experiments (one including a dye swap); each array comprising two technical replicates for each gene

first: Tobias

last: Schweinitzer

first: Sarah

last: Kuehne

first: Wiebke

last: Behrens


title: Gene expression in Zfp36l3 wildtype and knockout trophoblast stem cells and placenta

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The ZFP36L3 protein is a rodent-specific, placenta- and yolk sac-specific member of the tristetraprolin (TTP) family of CCCH tandem zinc finger proteins.  These proteins bind to AU-rich elements in target mRNAs, and promote their deadenylation and decay.  We addressed the hypotheses that the absence of ZFP36L3 would result in the accumulation of target transcripts in placenta and/or yolk sac, and that some of these would be important for female reproductive physiology and overall fecundity.   Mice deficient in ZFP36L3 exhibited decreased neonatal survival rates, but no apparent morphological changes in the placenta or surviving offspring.  We found Zfp36l3 to be paternally imprinted, with profound parent-of-origin effects on gene expression.  The protein was highly expressed in the syncytiotrophoblast cells of the labyrinth layer of the placenta, and the epithelial cells of the yolk sac.  RNA-Seq of placental mRNA from Zfp36l3 KO mice revealed many significantly up-regulated transcripts, whereas there were few changes in KO yolk sacs.  Many of the up-regulated placental transcripts exhibited decreased decay rates in differentiated trophoblast stem cells derived from KO blastocysts.   Several dozen transcripts were deemed high probability targets of ZFP36L3; these include proteins known to be involved in trophoblast and placenta physiology.  The type 1 transferrin receptor mRNA was unexpectedly decreased in KO placentas, despite an increase in its stability in KO stem cells.  This receptor is critical for placental iron uptake, and its decrease was accompanied by decreased iron stores in the KO fetus, suggesting that this intrauterine deficiency might have deleterious consequences in later life.

overall_design: Four biological replicates were analyzed for each trophoblast stem cell condition.  There are 8 different conditons: wild type and knockout undifferentiated, differentiated 0h ActD, differentiated 2h ActD, differentiated 4h ActD.  Five biological replicates were analyzed for wild type and knockout placenta.  Three replicates were analyzed for heterozygous placenta.  There are two types of heterozygous placentas: maternal or paternal transmission of the mutant allele.

first: Deborah

last: Stumpo

first: Carol

last: Trempus

first: Charles

last: Tucker

first: Weichen

last: Huang

first: Leping

last: Li

first: Kimberly

last: Kluckman

first: Donna

last: Bortner

first: Perry

last: Blackshear


title: Effect of a cardiomyocyte-specific Hira conditional knockout on gene expression in the heart

status: Public on Apr 06 2016

city: Houston

first: M. David

last: Stewart

state: TX

address: 4800 Calhoun Rd

institute: University of Houston

summary: We performed gene expression profiling by microarray using RNA extracted from healthy free wall left ventricle tissues from control and Hira cardiomyocyte-specific conditional knockout mice at 6 weeks of age.  Hira is a histone chaperone responsible for replication-independent incorporation of histone variant H3.3 at actively transcribed regions.  Conditional knockout of Hira in cardiomyocytes resulted in impaired cardiac function, cardiomyocyte degeneration and focal replacement fibrosis.  These results illustrate the role of Hira in controlling the cardiac gene program.

overall_design: 4 animals per group (control and Hira conditional knockout) hybridized in triplicate. RNA was extracted from healthy free wall left ventricle.

first: M


title: Transcriptomics Responses to Hypoxia and Ketamine in Ovine Fetal Cerebral Cortex

city: GAINESVILLE

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

summary: Transient hypoxia in pregnancy stimulates a physiological reflex response that redistributes blood flow and defends oxygen delivery to the fetal brain.  The chemoreceptor reflex that is responsible for this physiological response is dependent on glutamatergic neurotransmission which, in times of vigorous activity, could produce cell death secondary to calcium uptake.  We designed the present experiment to test the hypotheses that transient hypoxia produces damage of the cerebral cortex and that ketamine, an antagonist of NMDA receptors, reduces the damage.  Late-gestation, chronically catheterized fetal sheep were subjected to a 30 min period of ventilatory hypoxia that decreased fetal PaO2 from 17±1 to 10±1 mm Hg, or normoxia (PaO2 17±1 mm Hg), with or without pretreatment (10 min before hypoxia/normoxia) with ketamine (3 mg/kg, iv).  One day (24 h) after hypoxia/normoxia, fetal cerebral cortex was removed and mRNA extracted for transcriptomics and systems biology analysis.  Hypoxia stimulated a transcriptomics response consistent with a reduction in cellular metabolism and an increase in inflammation.  Ketamine pretreatment reduced both of these responses. The inflammation response modeled with transcriptomic system biology was validated by immunohistochemistry and showed increased abundance of microglia/macrophages after hypoxia in the cerebral cortical tissue that ketamine significantly reduced.  We conclude that transient hypoxia produces inflammation of the fetal cerebral cortex and that ketamine, in a standard clinical dose, reduces the inflammation response.

overall_design: 4 groups: hypoxia, hypoxia plus ketamine, normoxia, normoxia plus ketamine.  Hypoxia produced by low PO2 in maternal inspired gas for 30 min, followed by normoxia recovery for 23.5 hours. Control fetuses maintained at normoxia for 30 min, followed by another 23.5 h of normoxia.  Fetal frontal cerebral cortex collected for mRNA at end of 23.5 h recovery period.

first: Eileen

middle: I

last: Chang

first: Miguel

last: Zarate

first: Maria

middle: B

last: Rabaglino

first: Elaine

last: Richards

first: Thomas

last: Arndt

first: Maureen

last: Keller-Wood

middle: E


title: Microarray analysis of a hybrid weakness in the cross between rice cultivars

city: Mishima

first: Nori

last: Kurata

state: Shizuoka

address: 1111 Yata

institute: National Institute of Genetics

summary: To study a hybrid weakness of rice, we have employed microarray expression profiling as a discovery platform to identify genes increased or decreased their expression specifically in the hybrid. Expression profiles of ‘Nipponbare’, ‘Jamaica’, and F1 hybrid were analyzed with ‘Rice oligo microarray kit’ of Agilent Technologies.

overall_design: ‘Nipponbare’, ‘Jamaica’, and F1 hybrid were used for analysis. Plants were aseptically germinated and cultivated on MS medium at 25˚C. After two weeks cultivation, roots were frozen and used for measurement. Three or four independent experiments were performed at each cultivar using different plant individuals.

first: Masahiro

last: Fujita

first: Yuuya

last: Okiyama

first: Katsuyuki

last: Ichitani

first: Tsutomu

last: Kuboyama


title: SpdR regulon

city: Sao Paulo

first: Rogerio

last: Lourenco

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748

department: Bioquimica

institute: Universidade de Sao Paulo

summary: As bacterial cells enter stationary phase, they adjust their growth rate to comply with nutrient restriction and acquire increased resistance to several stresses. These events are regulated by controlling gene expression at this phase, changing the mode of exponential growth into that of growth arrest, and increasing the expression of proteins involved in stress resistance. The two-component system SpdR/SpdS is required for the activation of transcription of the Caulobacter crescentus cspD gene at the onset of stationary phase. A Global transcriptional analysis at early stationary phase of a spdR null mutant strain compared to the wild type strain was carried out by DNA microarray. Twenty-three genes showed at least twofold decreased expression in the spdR deletion mutant strain relative to its parental strain, including cspD, while five genes showed increased expression in the mutant. The expression of a set of ten genes was evaluated by quantitative real time PCR, validating the microarray data. Several of the differentially expressed genes can be involved in modulating gene expression, including four transcriptional regulators, and the RNA regulatory protein Hfq. The ribosomal proteins NusE and NusG, which also that have additional regulatory functions in transcription and translation, were also downregulated in the spdR mutant, as well as the ParE1 toxin. The results indicate that SpdR regulates several genes encoding proteins of regulatory function, which in turn may be required for the expression of other genes important for the transition to stationary phase.

overall_design: Four replicates perfomed with independent biological samples

first: C

middle: A

last: da Silva

first: R

middle: F

middle: R

last: Mazzon

last: Ribeiro

middle: V

last: Marques


title: Regular physical activity followed by detraining increases the sensitivity of global gene expression to acute exercise stress

status: Public on Apr 05 2016

city: Washington

first: Jon-Philippe

middle: K.

last: Hyatt

state: DC

address: 3700 Reservoir Rd.

institute: Georgetown University

summary: To determine the influence of a previous physcial activity period (e.g., exercise) on global gene expression, we compared differential expression in sedentary (SED) and detrained (DETR) rats relative to trained (TR) rats with regular access to physcial activity.

overall_design:
TR and DETR rats had voluntary access to caged running wheels for 8 and 4 weeks, respectively. DETR rats were moved to sedentary conditions (normal cage activity) for another 4 weeks. SED rats experienced 8 weeks of normal caged activity; n=8 per group.
At the end of each group's respective 8 weeks, all rats underwent 1 hr of moderate of acute exercise stress (e.g., forced wheel running at a speed of 20 m/min). Soleus muscles were harvested 24h post-running.

middle: K

first: Emily

last: Brown

first: Elisa

last: Bienenstock

first: Gary

last: McCall


title: Expression data from cold stress in Sanhe cattle

status: Public on Apr 02 2016

city: Beijing

first: Qing

last: Xu

address: Institute of Life Science and Biotechnology, Beijing Jiaotong University

institute: Beijing Jiaotong University

summary:
While cold stress has been shown to seriously impact cattle industry, there are only a few reports investigating the effect of cold stress on cattle. Whether severe cold stress results in alterations in gene expression and affects molecular genetic mechanisms remains unknown.
We used microarrays to analyze the alterations in gene expression in peripheral blood samples in response to cold exposure and identified differentially regulated genes.

overall_design: This study was performed on 30 healthy Sanhe heifers with similar genetic backgrounds, weight, and age. In order to induce cold stress, the cattle were transferred outdoor and were exposed to a temperature of -32°C for 3 hours followed by housing in cowshed at 5°C for 15 hours. Blood samples with EDTA were collected from each animal before and after the cold exposure. After total RNA was isolated from blood cells, six RNA samples (three derived before and three after the cold exposure), were collected from three animals randomly selected from the 30 healthy heifers for gene expression profiling in response to severe cold stress.

first: Yachun

last: Wang


title: GRH-inducible genes in rice plants

city: Tsukuba

first: Takayuki

last: ASANO

state: Ibaraki

address: 2-1-2 Kannondai

department: Plant Genome Research Unit

institute: National Institute of Agrobiological Sciences

summary: The green rice leafhopper (GRH), Nephotettix cincticeps Uhler, is a major insect pest of cultivated rice in temperate Asia. GRH2-near-isogenic line (NIL) TGRH11, GRH4-NIL (TGRH16) and GRH2/GRH4-pyramided line (PYL) TGRH29 were developed by introducing the GRH2 and GRH4 from indica rice (DV85). We identified GRH-inducible genes in respective rice lines. Furthermore, we compared the gene expression levels between NILs/PYL and control plants (T65).

overall_design: The gene expression changes in respective rice lines were detected by comparison between GRH-infested and pre-infested plants. Seedlings at the second-leaf stage were infested with 10 to 15 first- or second-instar nymphs in test tubes and shoots were collected at 30 h after GRH infestation. Detached-leaf blades at heading stage were infested with 10 to 15 first- or second-instar nymphs in test tubes and samples were collected at 30 h after GRH infestation. For each treatment, two biological replicates were performed.

last: Asano

first: Yasumori

last: Tamura

first: Hiroe

last: Yasui

first: Kouji

last: Satoh

first: Makoto

last: Hattori

first: Hideshi

first: Shoshi

last: Kikuchi


title: Tonicity induced changes in Gene expression in IMCD cells

status: Public on Apr 01 2016

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

summary:
Tonicity induced massive changes in gene expression. Already the acute challange for 3 h affected significantly the expression of thousands of genes.
The overall differences in gene expression were hightes between cells cultivated at 300 compared to cells cultivated at 900 mosmol/kg

overall_design: 30 Samples were analyzed


title: Microarray analysis of the hyperthermophilic archaeon Thermococcus kodakarensis grown at lowest growth temperature

city: Sanda

first: Ryota

last: Hidese

state: Hyogo

address: Gakuen 2-1

department: School of Science and Technology

institute: Kwansei-Gakuin University

summary: A hyperthermophilic archaeon Thermococcus kodakarensis can grow in a wide range of temperatures from 60°C to 93°C, optimally at 85°C. To screen the genes that being specifically expressed at lowest growth temperature, 60°C, we investigated the transcriptional profilings of T. kodakarensis grown at 60˚C by comparing with those grown at 85°C.

overall_design: One-condition experiment, KU216 grown at optimal growth temperature, 85°C vs. KU216 grown at lowest growth temperature, 60°C. Technical replicates: 2 KU216 grown at 60°C, independently measured. One replicate per array.

first: Wakao

last: Fukuda

first: Shinsuke

last: Fujiwara

first: Tamotsu

last: Kanai

first: Haruyuki

last: Atomi

first: Tadayuki

last: Imanaka


title: Aberrant calcium influx causes fiber type shift and mitochondrial loss in skeletal muscle

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

summary: Skeletal muscle excitation-contraction (EC) coupling is independent of calcium influx. In fact alternative splicing of the voltage-gated calcium channel CaV1.1 actively suppresses calcium currents in mature muscle. Why this might be necessary is not known. However, splicing defects causing aberrant expression of the calcium-conducting embryonic CaV1.1e splice variant correlate with muscle weakness in myotonic dystrophy. Here we deleted CaV1.1 exon 29 in mice. The continued expression of CaV1.1e resulted in increased calcium influx during EC coupling and spontaneous calcium sparks. While overall motor performance was normal, muscle force was reduced, endurance enhanced, and the fiber type composition shifted toward slower fibers. In contrast, oxidative enzyme activity and the mitochondrial content declined. Together with the dysregulation of key regulators of the slow program these findings indicate that limiting calcium influx during skeletal muscle EC coupling is important for the calcium signal’s secondary function in the activity-dependent regulation of fiber type composition.

overall_design: Differential gene expression between soleus and EDL muscle fibres from wildtype and Cav1.1 delta E29 mice.

first: Nasreen

last: Sultana

first: Peter

last: Szentesi

first: Ariane

last: Benedetti

first: Petronel

last: Tuluc

first: Beatrix

last: Dienes

first: Monika

last: Sztretye

first: Micheal

last: Hess

first: Christoph

last: Schwarzer

first: Gerald

last: Obermair

first: Laszlo

last: Csernoch

first: Bernhard

last: Flucher


title: The effect of HTLV-1 bZIP factor (HBZ) RNA and protein in mouse CD4 T cells

city: Kyoto

first: Yuichi

last: Mitobe

address: Shogoin Kawaharatyo

institute: Kyoto University

summary: Human T-cell leukemia virus type 1 (HTLV-1) bZIP factor (HBZ) which is encoded in the minus strand of HTLV-1 provirus, possesses dual function as protein, and also as RNA. To know the effect of HBZ RNA and protein in primary T-cells, we introduced HBZ, or its mutant TTG (exclude protein activity), or SM (exclude RNA activity) with retrovirus vector into CD4 positive murine T cells, and analysed the transcriptome profiling. We found that HBZ RNA altered cell cycle progression, cell survival related genes, while HBZ protein altered immunology related genes. This microarray results demonstrated that HBZ RNA and protein possess distinct functions in primary cells.

overall_design: CD4 positive cells were enriched from murine splenocyte, and cultured with irradiated antigen presenting cells (APC). HBZ, or its mutant were introduced with retroviral vector. Forty eight hours after introduction, cells were washed and cultured with recombinant human IL-2. Further  48 hours after culture, virus infected cells were sorted and analysed by agilent microarray.

first: Mitobe

last: Yuichi


title: Gene expression profile of carbon starvation gene knockouts, ΔcstA and ΔyjiY, in Salmonella typhimurium

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

summary: Two carbon starvation (cst) genes, cstA and yjiY, in Salmonella are predicted to mediate peptide utilization under nutrient stress. However, the mechanistic details of their function and their importance in the context of Salmonella pathogenesis is not addressed. In this study, the transcriptomes of cst gene knockouts were compared to that of wild type to check the global impact of cst genes on Salmonella metabolism as well as pathogenesis. Microarray was done for duplicate samples for each strain in late log phase of growth in LB, which is also marked by the expression of many virulence associated genes.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Organism : Salmonella typhimurium , Agilent Custom Salmonella Typhimurium Gene Expression  8x15k Array (AMADID: 046639) designed  by Genotypic Technology Private Limited.

first: Dipshikha

last: Chakravortty

first: Preeti

last: Garai


title: Differentially expressed genes in xenografts and organoids derived from human cholangiocarcinoma [mRNA]

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
We established xenografts and organoids derived from human cholangiocarcinoma.
To investigate the signature of cancer stem cells, gene expression profiles were analyzed in cholangiocarcinoma xenografts and organoids (passage 7 and 32).

overall_design: Microarray analyses were conducted in cholangiocarcioma xenografts and organoids (passage 7 and 32).

first: Yoshimasa

last: Saito


title: DNA methylation in Hippocampus across Alzheimer Braak Stages

status: Public on Apr 03 2016

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

summary: Genome wide DNA methylation profiling of normal and different Alzheimer Braak stages samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs. Samples included 5 controls, 5 Braak stage I-II, 5 Braak stage III-IV and 5 Braak stage V-VI.

overall_design: Bisulphite converted DNA from the 20 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

first: Jose

last: Sanchez-Mut

first: M


title: Rice bHLH transcription factor RERJ1 dependent wound inducible genes in rice leaves

city: Tokyo

first: Kazunori

last: Okada

address: 1-1-1, Yayoi, Bunkyo-ku

department: Biotechnology Research Center

institute: The University of Tokyo

summary: The plant hormone jasmonic acid (JA) has been known as a signal molecule that is induced by various stresses and mediates plant defense responses. Rice O. sativa inductively produces variety of defensive compounds upon abiotic and biotic stress conditions, such as wounding and insect attack. The bHLH transcription factor RERJ1 has previously been identified as JA-inducible factor whose expression is also rapidly induced by wounding. We identified RERJ1-dependent and wound-inducible genes by comparison with transcriptomes of wound treated wild-type and a Tos17-rerj1 defective mutant rice.

overall_design: Expression profiling between rice leaves of wild-type and tos17-rerj1 mutant treated by wounding for 0, 0.5, 1 and 2 h was compared using two-color method with two biological replicates.

first: Koji

last: Miyamoto


title: Wound inducible gene in rice leaves

summary: The plant hormone jasmonic acid (JA) has been known as a signal molecule that is induced by various stresses and mediates plant defense responses. Rice O. sativa inductively produces variety of defensive compounds upon abiotic and biotic stress conditions, such as wounding and insect attack. We identified wound-inducible genes by comparison with transcriptomes between wounded and untreated wild-type rice leaves.

overall_design: Expression profiling in wild-type rice leaves treated by wounding  for 0.5, 1, 2 and 4 h was compared with that in untreated control using two-color method with two biological replicates.


title: Identification of circadian-related gene expression profiles in entrained MCF7

city: Monterrey

first: Sean-Patrick

last: Scott

state: Neuvo Leon

address: Morones Prieto 3000 Pte

department: Cellular Therapy

institute: Tecnológico de Monterrey

summary: Cancer cells have broken circadian clocks as compared to their normal tissue counterparts. Moreover, it has been shown in breast cancer that disruption of common circadian oscillations are associated to worse prognosis. Numerous studies focused at conical circadian genes in breast cancer cell lines have suggested that there are no mRNA circadian-like oscillations. Nevertheless, cancer cell lines have not been extensively characterized and it is unknown to what extent the circadian oscillations are disrupted. We have chosen representative breast cancer cell lines (MCF-10A, MCF-7, ZR-75-30, MDA-MB-231, and HCC-1954) in order to determine the degree which the circadian clock is damaged. We used serum shock to synchronize the circadian clocks in culture. Our aim was to observe the time course of gene expression using cDNA microarrays in the noncancerous MCF-10A and the cancerous MCF-7 cells and characterize specific genes in other cell lines. We used a cosine function to select highly correlated profiles. Some of the identified genes were validated by qPCR and further evaluated in the other breast cancer cell lines. Interestingly, we observed that breast cancer and noncancerous cultured cells are able to generate specific circadian expression profiles in response to the serum shock. The rhythmic genes suggested via microarray and measured in each particular subtype suggest that each breast cancer cell type respond differently to the circadian synchronization. Future results could identify circadian-like genes that are altered in breast cancer and noncancerous cells which can be used to propose novel treatments. Breast cell lines are potential models for in vitro studies of circadian clocks and clock-controlled pathways.

overall_design: There are 8 total samples representing 0 to 28 hours in 4 hour intervals in MFC-7 breast cancer epitheleal cell line.

first: Miguel

last: Gutierrez-Monreal


title: Screening for RERJ1 dependent genes under wound stress condition in rice leaves

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

overall_design: Refer to individual Series


title: MiRNA expression pattern in different prognosis of colon cancer patients

city: Shanghai

first: Chunxian

last: Zhou

address: 138 Yi Xue Yuan Road

institute: Fudan University

summary:
We measured the expression of human microRNAs in tumor cells derived from 8 FFPE samples among non-invasive CRC patients with different prognosis. Patients lived for more than 5 years after surgery were classified as good prognosis, and patients died within 5 years from surgery were classified as poor prognosis.
Tumor tissues were macrodissected under the control HE staining slides. And there were at least 75 percent cancer cells in the samples.

overall_design: MicroRNA microarray was used to measure the expression of human miRNAs in tumor cells derived from 8 FFPE samples among early stage CRC patients with different prognosis.

first: Shuyang

last: Wang


title: Identification of circadian-related gene expression profiles in entrained MCF10A

overall_design: There are 8 total samples representing 0 to 28 hours in 4 hour intervals in MFC-10A breast noncancerous epitheleal cell line.


title: Global expression analysis of differential expression of genes working under Soil Water Stress condition in different genotypes of rice in Vegetative and Grain-filling stage [set 1]

city: Kharagpur

first: ALPGE

last: IITKGP

state: West Bengal

address: Formerly BREF Biotech

department: Advanced Technology Development Centre

institute: Indian Institute of Technology, Kharagpur

summary: One of the serious constraints to realize high level of rice crop productivity in Indian agriculture has been due to soil moisture stress (SMS) situation that growing plants often face. In order to increase or maintain the crop productivity in SMS situation our initial aim is to understand the drought response mechanism in different genotypes of rice. For thorough analysis of SMS situation in rice we have taken here two wild genotypes of rice namely Oryza nivara, Oryza rufipogan and three Indian cultivar namely Oryza Nagina-22, Oryza IR20 and Oryza Vandana, where IR20 is known to be susceptible and Vandana is known to be tolerant under SMS condition. Global analysis of transcript profiling under SMS condition reveal the actual picture of genes responsive to stress situation in different genetic background of rice. Furthermore it would help us in the selection of most desirable resource for crop breeding without compromising the yield of crop. We used the 44k rice Oligoarray from Agilent technologies to study the transcript profiling from five genotypes of rice under control, soil moisture stress and after recovery conditions during vegetative and grainfilling phase.Here in case of Nagina-22 we have taken grainfilling stage.

overall_design: Organism : Oryza sativa , Custom Gene Expression Oryza sativa 4X44K (AMADID: 015241) designed by Genotypic Technology Private Limited.

first: Soumitra

last: Sen

first: Sunita

last: Yadav

first: Avishek

last: Dey

first: Ranjeet

last: Kaur


title: Global expression analysis of differential expression of genes working under Soil Water Stress condition in different genotypes of rice in Vegetative and Grain-filling stage [set 2]

summary: One of the serious constraints to realize high level of rice crop productivity in agriculture has been due to Soil Water Stress (SWS) situation that growing plants often face. In order to increase or maintain the crop productivity in SWS situation, our initial aim is to understand the drought response mechanism in different genotypes of rice. For thorough analysis of SWS situation in rice we have taken here two wild genotypes of rice namely Oryza nivara, Oryza rufipogon and three Oryza sativa indica cultivars namely Nagina-22, IR20 and Vandana, where IR20 is known to be susceptible and Vandana is known to be tolerant under SWS condition [GSE49364 and the current study]. Global analysis of transcript profiling under SWS condition reveal the actual picture of genes responsive to stress situation in different genetic background of rice. Furthermore it would help us in the selection of most desirable resource for crop breeding without compromising the yield of crop. We used the 44k rice Oligoarray from Agilent technologies to study the expression profiles from five rice genotypes during vegetative (Veg) and grain-filling (GF) stages under varying water conditions, viz. Before Stress (BS), After Stress (AS) and After Recovery (AR).

overall_design: Oryza sativa , Custom Gene Expression Oryza sativa 4X44K (AMADID: 015241) designed by Genotypic Technology Private Limited.


title: Gene expression profiles in human ESCs and ESC-derived purified cardiomyocytes

status: Public on Mar 31 2016

summary: Differences of metabolism-related gene expression profiles in human ESCs and ESC-derived purified cardiomyocytes were analyzed and successfully identified.

overall_design: Human ESCs and ESC-derived purified cardiomyocytes were used for this experiment.

first: Shugo

last: Tohyama


title: The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: We present a functional characterisation of two members of the IDA-LIKE (IDL) peptide family in Arabidopsis thaliana, IDL6 and IDL7. They are processed both C- and N-terminally to produce active peptides. Structure analyses of synthesized IDL6 and IDL7 peptides indicate that they lack secondary structure elements. Localisation studies suggest that the peptides require a signal peptide and C-terminally processing to be correctly transported out of the cell. Treatment of plants with synthetic IDL6 and IDL7 peptides resulted in down-regulation of a broad range of stress-responsive genes, including early stress-responsive transcripts, dominated by a large group of ZINC FINGER PROTEINS (ZFPs), WRKYs and genes encoding calcium-dependent proteins. idl6 and idl7 mutants were more tolerant to salt, whereas the respective overexpression lines displayed increased sensitivity to both salt and oxidative stress. Taken together, our results suggest that the putative peptide ligands IDL6 and IDL7 act as suppressors of abiotic stress responses in Arabidopsis.

overall_design: Two weeks old seedlings were treated either with 100 nM IDL6 or IDL7 peptide (treated) or 100 nM mock peptide (control) and whole rosettes were harvested 2 hours after treatment. 4 biological replicaes per treatment. Two color microarray. Biological replicas are dye-swapped between slides.

first: Ane

last: Vie

first: Tore

last: Brembu

first: Ester

last: Cattan

first: Michael

last: Wrzaczek

first: Javad

last: Najafi

first: Jaakko

last: Kangasjärvi

first: Finn

middle: L

last: Aachmann

first: Gad

last: Miller

first: Atle

middle: M

last: Bones


title: D4Z4-located miRNA

city: Iowa City

first: Rolf

last: Turk

state: IA

address: 285 Newton Road, 4283CBRB

department: Molecular Physiology and Biophysics

institute: University of Iowa

type: Expression profiling by genome tiling array

summary: We have used a tiled microarray based on the D4Z4 sequence, and hybridized amplified transcripts from facioscapulohumeral muscular dystrophy (FSHD) and control (CTRL) samples to detect D4Z4 related expression.

overall_design: Microarrays were analyzed by GenePix Pro 6 (Axon). Local background corrected, median spot intensities were normalized using VSN in R. Due to this normalization strategy, we have treated the microarrays as single channels. The normalized values are uploaded with each sample. Hybridizations were performed in a dye-swap fashion. Samples GSM306099 and GSM306100 are on a single array, and so are GSM306101 and GSM306102, GSM306103 and GSM306104, GSM306105 and GSM306106.

first: Kevin

middle: P

last: Campbell


title: Global expression analysis of differential expression of genes working under Soil Water Stress condition in different genotypes of rice in Vegetative and Grain-filling stage

first: ALPGE

last: IITKGP


title: Identification of circadian-related gene expression profiles in entrained breast cancer cell lines

first: Sean-Patrick

last: Scott


city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada

summary: Geographical and host plant influences on transcriptional variation in Drosophila mojavensis: mapping gene expression differences in both sexes. (1. Punta Onah:PO07; 2. Organ Pipe National Monument:OPNM08; 3. Punta Prieta:PP08; & 4. San Quintin:SQ08). The experiment was designed to investigate effects of host plant (diet), mating status (mated:M or nonmated:V) and sex (male:male or Female:F) on transcriptome.

overall_design: A total of 128 hybridizations were performed in this entire experiment (127 in the final analysis). We used 135K 12-plex NimbleGen arrays. Total RNA was recovered from each sample listed below. The experimental design consisted a total of four populations (1. Punta Onah:PO; 2. Organ Pipe National Monument:OPNM; 3. Punta Prieta:PP; & 4. San Quintin:SQ), two mating status (mated:M or nonmated:V), both the sexes (male:male or Female:F) fed on two different diet regimes (Agria and Organ pipe). Each chip measures the expression level of 15528 transcripts. Four to 5 replicates were used for each type (R-1, R-2, R-3 etc.)

middle: G

first: William

last: Etges

first: Subhash

last: Rajpurohit

first: Cassia

middle: C

last: de Oliveira


title: Inhibition of canonical Wnt/β-catenin signaling is involved in leflunomide (LEF)-mediated cytotoxic effects on renal carcinoma cells

city: Hangzhou

first: yicheng

last: chen

address: 3 East Qingchun Road

department: Department of Urology

institute: Sir Run-Run Shaw Hospital, College of Medicine, Zhejiang University

overall_design: In the study presented here, 4 samples [2 control groups (Caki-2 treated with 0.1%DMSO for 48h) and 2 experimental groups (Caki-2 treated with 200μM leflunomide for 48h)], were used to acquire expression profiles of 115 up-regulated and 176 down-regulated mRNA

first: Yicheng

last: Chen

first: Tao

last: Li


title: Analysis of Colletotrichum orbiculare whi2Δ mutant infection of Cucumis sativus at 4hpi

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: Colletotrichum orbiculare Whi2, yeast stress response Whi2 homolog, is involved in switch from biotrophic to necrotrophic stage. To elucidate downstream genes regulated by Co Whi2, we have conducted DNA microarray. About 3100 genes were up or down regulated in the Co whi2Δ mutant compared with the wild-type. In particularly, 44 genes among up-regulated 58 genes in the Co whi2Δ mutant are ribosomal protein related gene. Eukaryote is widely conserved TOR (Target Of Rapamycin) which is known to regulator of ribosomal gene expression. To elucidate whether up-regulated ribosomal genes in the Co whi2Δ mutant are regulated by TOR activity, we have conducted DNA microarray in the Co whi2Δ mutant treated with rapamycin inhibiting TOR activity.  The enormous ribosomal gene expression in the Co whi2Δ mutant treated with the rapamycin is lower than that without rapamycin treatment.

overall_design: In gene expression of the Co whi2Δ mutant, the wild-type and the Co whi2Δ mutant infecting on cucumber cotyledons were assessed at 4 hours post-inoculation. In gene expression of the Co whi2Δ mutant with rapamycin treatment, Co whi2Δ mutant treated with 100nM rapamycin and Co whi2Δ mutant without rapamycin treatment infecting on cucumber cotyledons were assesed at 4 hours post-inoculation. Four replication were performed for each experiments.

first: Ken

last: Harata

first: Yasuyuki

last: Kubo


title: Gene expression profiles of the wild-type Cited4-transduced cells and the nontransduced cells.

city: Yonago

first: Junichiro

last: Miake

address: 36-1 Nishi-cho

department: Multidisciplinary Internal Medicine

institute: Tottori University Faculty of Medicine

summary: We compared the gene expression profiles of the wild-type Cited4-transduced cells and the nontransduced cells.

overall_design: Embryoid body was formed as in vitro cardiogenesis. For comparison of gene expression profiles of  the wild-type Cited4-transduced cells and the nontransduced cells, total RNA was extracted from  the wild-type Cited4-transduced cells at day 6.5 and the nontransduced cells at day 6.5.


title: Transcriptional response of Arabidopsis sweet11/sweet12 double mutants upon Colletotrichum higginsianum infection

city: Erlangen

first: Lars

middle: Matthias

last: Voll

address: Staudtstrasse 5

department: Division of Biochemistry

summary: In compatible interactions, biotrophic microbial phytopathogens rely on the supply of carbon and nitrogen assimilates by the colonized host tissue. Successful biotrophs need to reprogram host metabolism, which also involves the stimulation of assimilate export from living host cells into the plant-pathogen interface at the infection site. In rice and cassava, SWEET sucrose transporters, are induced by bacterial TAL (transcriptional activator-like) effectors to establish compatibility. A pathogen-specific transcriptional induction of SWEET transporters has also been observed in Arabidopsis leaves upon microbial challenge. Here, we have assessed the question, whether the phloem localized AtSWEET11 and AtSWEET12 transporters represent susceptibility factors in the interaction of Arabidopsis with the fungal hemibiotroph Colletotrichum higginsianum (Ch). Compared to wild type, sweet11/sweet12 double mutants exhibited priming of the SA pathway in mock conditions.

overall_design: To investigate transcriptional changes in C. higgsinanum infected leaves, five-week old Arabidopsis plants were spray infected with 2 Mio. conidia/ ml 1h before lights off and fully expanded leaves of wild type Col-0 and the sweet11/sweet12 double mutant were harvested in three situations: 1) immediately before treatment, 2) from mock treated plants (sprayed with water) at 2.5 days post treatment and 3) from C. higginsianum inoculated leaves during biotrophic colonization at 2.5 days post treatment

first: P

last: Gebauer

first: L


title: Gene expression profiles of the Cited4 overexpressed and downregulated cells.

summary: We compared the gene expression profiles of the Cited4 overexpressed and downregulated cells.

overall_design: Embryoid body was formed as in vitro cardiogenesis. For comparison of gene expression profiles of the Cited4 overexpressed and downregulated cells, total RNA was extracted from the Cited4 overexpressed and downregulated cells at day 6.5.


title: Gene expression profiles in in vitro cardiogenesis.

summary: We performed time-dependent, genome-wide analysis to explore gene expression profiles during in vitro cardiogenesis from embryonic stem cells to cardiac progenitor cells. Total RNA was extracted from undifferentiated stem cells, early mesodermal cells, cardiac mesodermal cells and cardiac progenitor cells. As a result of cluster analysis, Cited gene family was considered as candidate genes in cardiogenesis. Cited4 gene expression was specific for early cardiogenesis and Cited4 functioned as a cell cycle controling factor for early cardiac progenitor cells.

overall_design: Embryoid body was formed as in vitro cardiogenesis. Total RNA was extracted from Rex1-positive undifferentiated stem cells at day 0, Bra-positive early mesodermal cells at day 4.5, Flk1-positive cardiac mesodermal cells at day 4.5 and Nkx2.5-positive cardiac progenitor cells at day 7.5.


title: Transcriptional profiling of Ppr1 gain of function mutant Candida albicans strains

city: Montreal

first: Walters

middle: Aji

last: Tebung

state: Quebec

address: 7141 Rue Sherbrooke Ouest

department: Chemistry and Biochemistry

institute: Concordia University

summary: Metabolic pathways are largely conserved in eukaryotes, but the transcriptional regulation of these pathways can sometimes vary between species; this has been termed rewiring. Recently it has been established that in the Saccharomyces lineage starting from Saccharomyces castelli, genes involved in allantoin breakdown have been genomically relocated to form the DAL cluster. The formation of the DAL cluster occurred along with the loss of urate permease (UAP) and urate oxidase (UOX), reducing the requirement for oxygen and bypassing the candidate Ppr1 inducer, uric acid. In Saccharomyces cerevisiae this allantoin catabolism cluster is regulated by the transcription factor Dal82, which is not present in many of the pre-rearrangement fungal species. We have used ChIP-Chip analysis, transcriptional profiling of an activated Ppr1 protein, bioinformatics, and nitrogen utilization studies, to establish that in Candida albicans the zinc cluster transcription factor Ppr1 controls this allantoin catabolism regulon. Intriguingly, in S. cerevisiae the Ppr1 ortholog binds the same DNA motif (CGG(N6)CCG) as in C. albicans, but serves as a regulator of pyrimidine biosynthesis. This transcription factor rewiring appears to have taken place at the same phylogenetic step as the formation of the rearranged DAL cluster. This transfer of the control of allantoin degradation from Ppr1 to Dal82, together with the repositioning of Ppr1 to the regulation of pyrimidine biosynthesis, may have resulted from a switch to a metabolism that could exploit hypoxic conditions in the lineage leading to S. castellii and S. cerevisiae.

overall_design: 2 samples were analyzed. Cells were grown in YPD media at 30 degrees celcius to OD 0.8. Ppr1 gain of function mutant strain (SCPPR1GAD1A) vs wild type (SC5314) were hybridized, dye swap was done. One replica per array.

first: Malcolm

last: Whiteway


title: Psoralen binding across the Escherichia coli chromosome

status: Public on Mar 22 2016

first: Avantika

last: Lal

address: GKVK, Bellary Road

institute: National Centre for Biological Sciences

summary: We used trimethylpsoralen intercalation to map supercoiling across the E. coli chromosome. We treated E. coli cells with trimethylpsoralen and exposed them to UV light. Psoralen enters cells, intercalates between DNA base pairs, and crosslinks the two strands of DNA at a rate proportional to the local superhelical density. We then fragmented DNA and hybridized crosslinked and non-crosslinked DNA fragments separately to tiling microarrays.

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

overall_design: In total 14 samples; 6 for wild-type in stationary phase (3 replicates x 2 samples as there are crosslinked and non-crosslinked samples for each replicate); 4 for wild-type in mid-exponential phase (2 replicates x 2 samples); 4 for the delta hupAB mutant in stationary phase (2 replicates x 2 samples)

first: Amlanjyoti

last: Dhar

first: Sankar

last: Adhya

first: Aswin

last: Sai Narain Seshasayee


title: Transgenic overexpression of Pla2g10

status: Public on Jan 29 2016

city: Setagaya

first: Kei

last: Yamamoto

state: Tokyo

address: 2-1-6 kamikitazawa

department: Lipid Metabolism Project

institute: Tokyo Metropolitan Institute of Medical Science

summary: Microarray gene profiling of thymus from PLA2G10-Tg mice in comparison with that from control mice.

overall_design: Pla2g10-Tg/+ mice and littermate controls (C57BL/6 background); 6-months old; thymus; pooled from 4 mice for each genotype.

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: DNA Damage Response Is Involved in the Developmental Toxicity of Mebendazole in Zebrafish Retina

status: Public on Mar 24 2016

city: Tsu

first: Yuhei

last: Nishimura

state: Mie

address: 2-174 Edobashi

department: Integrative Pharmacology

institute: Mie University Graduate School of Medicine

summary: Intestinal helminths cause iron-deficiency anemia in pregnant women, associated with premature delivery, low birth weight, maternal ill health, and maternal death. Although benzimidazole compounds such as mebendazole (MBZ) are highly efficacious against helminths, there are limited data on its use during pregnancy. In this study, we performed in vivo imaging of the retinas of zebrafish larvae exposed to MBZ, and found that exposure to MBZ during 2 and 3 days post-fertilization caused malformation of the retinal layers. To identify the molecular mechanism underlying the developmental toxicity of MBZ, we performed transcriptome analysis of zebrafish eyes. The analysis revealed that the DNA damage response was involved in the developmental toxicity of MBZ. We were also able to demonstrate that inhibition of ATM significantly attenuated the apoptosis induced by MBZ in the zebrafish retina. These results suggest that MBZ causes developmental toxicity in the zebrafish retina at least partly by activating the DNA damage response, including ATM signaling, providing a potential adverse outcome pathway in the developmental toxicity of MBZ in mammals.

overall_design: Gene expression regulated by mebendazole (MBZ) in zebrafish eye was measured. Four independent experiments were performed for each group.

first: Tetsuo

last: Kon

first: Toshio

last: Tanaka


title: Gene expression-based, etiology analysis for Hirschsprung's Disease

status: Public on Jan 28 2016

city: Chongqing

first: Zhenhua

last: Guo

address: No.136, 2nd Zhongshan Road, Yuzhong District

institute: Children's Hospitoal of Chongqing Medical University

summary: Several microRNAs which assosiate with Hirschsprung's disease were screened from 271 differentially expressed microRNAs between pathological changed colon segments of Hirschsprung's Disease and normal colon.These identified miRNAs could be used as diagnostic markers of HSCR segments.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Using microarray technology, we screened colon tissue to detect miRNAs whose expression profiles were altered in HSCR and 271 differentially expressed microRNAs. Several of these differetially expressed microRNAs were found assosited with the etiology of Hirschsprung's Disease which could be used as new diagnostic markers of HSCR segments.

first: Zhen-hua

first: Shuang-shuang

last: Li

first: Shi-qi

last: Wang


title: A NOVEL EPIGENETIC SILENCING PATHWAY INVOLVING the HIGHLY CONSERVED 5'-3' EXORIBONUCLEASE Dhp1/Rat1/Xrn2 in SCHIZOSACCHAROMYCES POMBE [gene expression]

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

summary:
Epigenetic gene silencing plays a critical role in regulating gene expression and contributes to organismal development and cell fate acquisition in eukaryotes.
In fission yeast, Schizosaccharomyces pombe, heterochromatin-associated gene silencing is known to be mediated by RNA processing pathways including RNA interference (RNAi) and a 3’-5’ exoribonuclease complex exosome.
Here, we report a new RNA-processing pathway that contributes to epigenetic gene silencing and assembly of heterochromatin mediated by 5’-3’ exoribonuclease Dhp1/Xrn2.
Dhp1 mutation causes defective gene silencing both at peri-centromeric regions and at the silent mating type locus.
Intriguingly, mutation of either one of two well-characterized Dhp1-interacting proteins, the Din1 pyrophosphohydrolase or the Rhn1 transcription termination factor, does not show silencing defects at the main heterochromatic regions.
Dhp1 is essential in the sequential steps of establishing silencing in a manner independent of both RNAi and the exosome.
Genomic and genetic analysis suggest that Dhp1 is involved in post-transcriptional silencing of repetitive regions through its catalytic activity. Our study is the first investigation into an unexpected role of Dhp1/Rat1/Xrn2 in chromatin-based silencing. These results elucidate how various RNA-processing pathways, acting together or independently, contribute to epigenetic regulation of the eukaryotic genome.

overall_design: Dhp1-1 was performed twice in biological replicates, din1∆ once.

first: James

last: Tucker

first: Corina

last: Ohle

first: Géza

last: Schermann

first: Katja

last: Bendrin

first: Wei

last: Zhang

first: Tamás

first: Ke


title: Genomic profiling of IPMN with an associated invasive carcinomas (IPMN-inv) and invasive ductal carcinomas (IDC) by array-based comparative genomic hybridization

status: Public on Jan 22 2016

city: Yufu

first: Naoki

last: Hijiya

state: Oita

address: 1-1, Idaigaoka Hasama-machi

department: Medicine

institute: Oita University

summary: In this study, we aimed to identify gene abnormalities necessary for the transformation from carcinoma in situ (CIS) of pancreas to invasive PC. We compared the genomic profiles of paired samples from invasive region and CIS region of the identical IPMN-inv. We further determined genomic profiles of IDC.

overall_design: 10 CIS region of IPMN-inv vs control (genomic DNA was extracted from normal renal cortex obtained from 12 patients with ureteral or renal pelvic carcinoma).  10 invasive region of IPMN-inv vs control (genomic DNA was extracted from normal renal cortex obtained from 12 patients with ureteral or renal pelvic carcinoma)  19 IDCs vs control (genomic DNA was extracted from normal renal cortex obtained from 12 patients with ureteral or renal pelvic carcinoma)

first: Yoshiyuki

last: Tsukamoto

first: Chisato

last: Nakada

first: Nguyen

last: Lam Tung

first: Tomoki

last: Kai

first: Keiko

last: Matsuura

first: Kohei

last: Shibata

first: Masafumi

last: Inomata

first: Tomohisa

last: Uchida

first: Akinori

last: Tokunaga

last: Amada

first: Kuniaki

last: Shirao

first: Yasunari

last: Yamada

first: Hiromu

last: Mori

first: Ichiro

last: Takeuchi

first: Masao

last: Seto

first: Masahiro

last: Aoki

first: Mutsuhiro

last: Takekawa

first: Masatsugu

last: Moriyama


title: Transcriptome analysis of the C. glutamicum deletion mutant of rnc, which encodes an RNase III homolog

status: Public on Jan 17 2016

city: Kizugawa-shi

first: Tomoya

last: Maeda

state: Kyoto

address: 9-2 Kizugawadai

department: Molecular Microbiology and Biotechnology Group

institute: Research Institute of Innovative Technology for the Earth

summary: The Corynebacterium glutamicum R cgR_1959 gene encodes an endoribonuclease of the RNase III family. Deletion mutant of cgR_1959 (Δrnc mutant) showed an elongated cell shape, and presence of several lines on the cell surface, indicating a required of RNase III for maintaining normal cell morphology in C. glutamicum. The level of mraZ mRNA was increased, whereas cgR_1596 mRNA encoding a putative cell wall hydrolase  and ftsEX mRNA were decreased in the Δrnc mutant. The half-life of mraZ mRNA was significantly prolonged in the Δrnc and the Δpnp mutant strains. This indicated that the degradation of mraZ mRNA was performed by RNase III and the 3′-to-5′ exoribonuclease, PNPase. Northern hybridization and primer extension analysis revealed that the cleavage site for mraZ mRNA by RNase III is in the coding region. Overproduction of MraZ resulted in an elongated cell shape. The expression of ftsEX decreased while that of cgR_1596 unchanged in an MraZ-overexpressing strain. An electrophoretic mobility shift assay and a transcriptional reporter assay indicate that MraZ is a transcriptional repressor of ftsEX in C. glutamicum. These results indicate that RNase III is required for efficient expression of MraZ-dependent ftsEX and MraZ-independent cgR_1596.

overall_design: Gene expression profile of the wild type at the exponential phase was compared with that of the rnc mutant. Three indepent experiments were performed.

first: Yuya

last: Tanaka

first: Norihiko

last: Takemoto

first: Nagisa

last: Hamamoto

first: Masayuki

last: Inui


title: Oyster reproduction is affected by exposure to polystyrene microplastics

status: Public on Jan 15 2016

city: Nantes

first: Rossana

last: Sussarellu

address: Rue de l'Ile d'Yeu

department: Ressources Biologiques et Environnement

institute: Ifremer

summary:
Plastics are persistent synthetic polymers that accumulate in the marine environment as waste. Microplastic (MP) particles are derived from the breakdown of larger debris or can enter the environment as microscopic fragments. Filter-feeder organisms ingest MP while feeding and are likely to be impacted by MP pollution. To assess the impact of polystyrene microspheres (PS) on the physiology of the Pacific oyster, adult oysters were experimentally exposed to virgin micro-PS (2 and 6 µm in diameter; 32 µg L-1) for two months during a reproductive cycle. Effects were investigated on transcriptomic responses, in digestive gland gonads and oocytes of exposed oysters.
Transcriptomic profiles in the tissues of the exposed oyster showed endocrine disrupting signals, notably highlighting alteration in glucocorticoid response, insulin pathway and fatty-acid metabolism in response to micro-PS exposition. In oocytes from exposed females, several transcripts coding for proteins involved in Ca2+ binding were differentially expressed suggesting a disruption of the Ca2+ signaling pathway with crucial consequences on oocyte maturation.

overall_design:
To assess the impact of polystyrene microspheres (PS) on the physiology of the Pacific oyster, adult oysters were experimentally exposed to virgin micro-PS (2 and 6 µm in diameter; 32 µg L-1) for two months during a reproductive cycle and compared to control oysters.
Adults were sampled 2 and 8 weeks after the beginning of exposure (corresponding to T1 and T3, respectively, 8-9 replicates per time of sampling and condition for a total of 56). Tissues were immediately dissected from each oyster, frozen in liquid nitrogen, then crushed to a fine powder at -196°C with an oscillating mill mixer and stored in liquid nitrogen until RNA extraction.
Oocytes were collected from 5 females per condition, filtered in a 40 µm sieve, counted and transferred into 1.5 mL of Extract-all reagent (Eurobio, Courtaboeuf, France) (20,000 oocytes).
Total RNA was isolated using 1.5 mL of Extract-all Reagent per 50 mg of gonad powder. For microarray hybridizations, 200 ng of total RNA were indirectly labeled with Cy3 using the Low Input Quick Amp Labeling kit One-Color. Hybridization was performed using the Agilent Gene expression hybridization kit (5188-5242), with 1.65 μg of labeled RNA, for 16 h at 65 °C. The employed arrays were Agilent 60-mer 4x44K custom microarrays, containing 31,918 C. gigas ESTs, designed by Dheilly et al. (2011). Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters. Features were extracted using the Agilent Feature Extraction software 6.1.

first: Marc

last: Suquet

first: Thomas

last: Yoann

first: Christophe

last: Lambert

first: Caroline

last: Fabioux

first: Marie

last: Arsenault-Pernet

first: Nelly

last: Le Goic

first: Virgile

last: Quillien

first: Christian

last: Mingant

first: Ika

last: Paul-Pont

first: Yanouk

last: Epelboin

first: Charlotte

last: Corporeau

first: Julien

last: Guyomarch

first: Johan

last: Robbens

first: Philippe

last: Soudant

first: Arnaud

last: Huvet


title: E. coli transcriptome in stationary and mid-exponential phase

city: Bangalore

first: Avantika

last: Lal

summary: E. coli RNA was hybridized to tiling arrays to study the pattern of gene expression across the chromosome.

overall_design: 1 sample for stationary phase and 1 for mid-exponential phase

first: Amlanjyoti

last: Dhar

first: Sankar

last: Adhya

first: Aswin

last: Sai Narain Seshasayee


title: A comprehensive analysis of blood host responses to Yersinia Pestis infection Temporal Progression of Pneumonic Plague in Blood of Nonhuman Primate: A Transcriptomic Analysis

status: Public on Jan 14 2016

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary:
transcriptomic analyses showed there was a very rapid proliferation of Y. pestis in assault on African green monkeys.  The bacterial loads were enumerated in the blood at delayed time points supporting earlier observations (Layton et al., 2011).  Interpretation of transcriptomic changes reveals that the host defense has been essentially shattered, and the process of multi-organ failure was initiated one day after inhalation exposure.  At 24 h post-exposure, the diseased animals were possibly at the middle of their survival curves. Hence, such molecular indicators could have critical therapeutic values, particularly when therapies fail to intervene at the earliest opportunity.
In the early phase of pathogenesis, systematic reprogramming of both adaptive and innate immunity programs is mediated, leading to sepsis.  Results suggest the possibility of early molecular perturbations in the lungs and muscle tissues, and catabolic related activities, such as biosynthesis.   Apoptosis ensued at the early stage, which potentially became rapid by recruiting an increasing number of apoptotic networks.  Beyond 24 h, rapid apoptosis could have acted in concert with hypercytokinemia and hyperchemokinemia, resulting in failures of many peripheral organs.

overall_design: Following a published report (Layton et al., 2011), the present study was designed to expose the nonhuman primates with a target dose of 100 ± 50 ED50 aerosolized Y. pestis strain CO92 under ABSL-3 conditions.  Seventy-two hours prior to aerosol exposure, all animals were moved into the ABSL-3 for acclimatization.  As described in Figure S1, initial blood draws were carried out 24 h before Y. pestis aerosol challenge.  The animals were challenged via aerosol with 1 x 106 virulent organisms while under anesthesia with 4 mg/kg Telazol (Fort Dodge Animal Health, Fort Dodge, IA).  Post-exposure clinical illness and disseminated infection were evaluated by direct clinical observations.  All animals within each group were exposed on the same day at 30 minute intervals, and subsequent blood draws were conducted at 45 m, 6 h, 9 h, 12 h, 18 h, 24 h, 32 h and 42 h.

first: Rasha

last: Hammamieh

first: Seid

last: Muhie

first: Richard

last: Borschel

first: Stacy-Ann

last: Miller

first: Nabarun

last: Chakraborty

first: Meskerem

last: Jibitu

first: Marti

last: Jett


title: Copy number variation analysis of human Barrett's esophagus stem cells (HumanOmniZhongHua-8 v1.0 Beadchip)

status: Public on Jan 13 2016

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Barrett’s esophagus confers significant risk of esophageal adenocarcinoma. We have established the cloning system of patient-matched stem cells of Barrett’s esophagus and  gastric cardia. Barrett's esophagus (BE) stem cells and gastric cardia (GC) stem cells from 12 patients were cloned.  To analyze copy number variation in BE and GC stem cells, we have performed SNP array.   It has shown that deletions such as p16 and FHIT in BE stem cells are significantly detected, while amplifications in BE stem cells are not. Also, we found some of BE stem cells did not share these deletions, suggesting emerging of BE does not require specific CNV.

overall_design: SNP array based copy number variation study was performed for BE and GC stem cells from human endoscopic biopsy (12 patients) to assess genomic stability at chromosomal level.

first: Yusuke

last: Yamamoto

first: Xia

last: Wang

first: Hoan

last: Nguyen

first: Florian

last: Kern

first: Yuanyu

last: Hu

first: Marcin

last: Duleba

first: Ting

last: Zhang

first: Wa

last: Xian