title: MYC-negative BL frequent in posttransplant patients (cytogenetic)

status: Public on Dec 12 2014

city: Leuven

first: Julio

last: Finalet

address: Herestraat 49

country: Belgium

institute: KULeuven

summary: We performed genomic and transcriptomic analysis of seven cases of molecular Burkitt lymphoma (mBL) developed in immunosuppressed patients who underwent solid organ transplantation. Interestingly, three cases (43%) were MYC-translocation-negative and revealed the 11q-gain/loss aberration recently identified in 3% of mBL developed in immunocompetent hosts.1 Based on array CGH data, minimal gain and loss regions of 11q (MGR/~4Mb and MLR/~13.5Mb, respectively) were defined and integrative genomic and transcriptomic analysis identified 35 differentially expressed genes, when compared with classic BL. All 16 MGR-dysregulated genes were upregulated, including cancer related USP2, CBL and PAFAH1B2. As expected, all 19 MGL-dysregulated genes were downregulated and two of them, TBRG1 and EI24, are potential tumor suppressor genes. Interestingly, the vast majority of dysregulated 11q23-q25 genes are involved in the MYC and TP53 networks. We hypothesize that the 11q-gain/loss aberration represents a “molecular variant” of t(8q24/MYC) and affects the same pathological pathways as the MYC oncogene.

overall_design: Seven cases of PTLD with BL features were selected from a cohort of 174 posttransplant patients diagnosed with PTLD between 1989 and 2012 at the University Hospitals of KU Leuven (Leuven, Belgium). In addition, five classic BL cases were selected as immunocompetent controls (IC-BL). Morphologic, immunophenotypic, clinical and cytogenetic characteristics of the selected cases were reviewed.

last: Finalet Ferreiro

first: Julie

last: Morscio

first: Daan

last: Dierickx

first: Lukas

last: Marcelis

first: Gregor

last: Verhoef

first: Peter

last: Vandenberghe

first: Thomas

last: Tousseyn

first: Iwona

last: Wlodarska


title: ChIp-on-chip with Rbp3 in C-ternimal domain (CTD) of Rbp1 mutants upon Nacl Stress in yeast

status: Public on Dec 03 2014

city: madison

first: Audrey

last: Gasch

state: wi

address: 425G Henry mall

department: genetics

country: USA

institute: university of wisconsin, madison

type: Genome binding/occupancy profiling by genome tiling array

summary:
The modification of Ser 5 is important for the relocalization of RNAP II upon NaCl stress.
The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. The 5A strain carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with alanine followed by 7 wild-type-sequenced repeats.

overall_design: Two-color fluorescence arrays reporting on Rpb3 localization abundance in strains (input vs. IP) before and at 20 min after a shock with 0.7M NaCl

first: Yi-Hsuan

last: Ho

last: Gash

first: Corey

last: Nemec

first: Aseem

last: Ansari


title: Modification of C-terminal Domain (CTD) of RPB1 plays a role in transcriptome change upon salt stress

summary:
Transctriptome profiling of CTD-14 repeats, 2A, 5A mutants responding to 0.7N NaCl for 30mins. The study shows that phosphorylation at Ser5 sites plays a role in normal induction and repression of genes upon NaCl stress.
The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. 5A strains carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with Ala followed by 7 wild-type-sequenced repeats. The 2A strains carrys  8 repeats of CTD-serine 2 substituted with alanine followed by 7 wild-type-sequenced repeats.

overall_design: Two-color fluorescence arrays reporting on mRNA abunance in strains before and after 30 min with 0.7M NaCl treatment


title: Genome-wide analysis of alternative splicing points to novel leukemia-relevant genes in acute myeloid leukemia.

status: Public on Dec 15 2014

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

country: Germany

institute: Charité Universitätsmedizin Berlin

summary: Alternative mRNA splicing represents an effective mechanism of regulating gene function and is a key element to increase the coding capacity of the human genome. Today, an increasing number of reports illustrates that aberrant splicing events are common and functionally important for cancer development. However, more comprehensive analyses are warranted to get novel insights into the biology underlying malignancies like e.g. acute myeloid leukemia (AML). Here, we performed a genome-wide screening of splicing events in AML using an exon microarray platform. We analyzed complex karyotype and core binding factor (CBF) AML cases (n=64) in order to evaluate the ability to detect alternative splicing events distinguishing distinct leukemia subgroups. Testing different commercial and open source software tools to compare the respective AML subgroups, we could identify a large number of potentially alternatively spliced transcripts with a certain overlap of the different approaches. Selected candidates were further investigated by PCR and sequence analysis: out of 24 candidate genes studied, we could confirm alternative splice forms in 8 genes of potential pathogenic relevance, such as PRMT1 regulating transcription through histone methylation and participating in DNA damage response, and PTPN6, which encodes for a negative regulator of cell cycle control and apoptosis. In summary, this first large Exon microarray based study demonstrates that transcriptome splicing analysis in AML is feasible but challenging, in particular with regard to the currently available software solutions. Nevertheless, our results show that alternatively spliced candidate genes can be detected, and we provide a guide how to approach such analyses.

overall_design: Exon expression analysis was performed using GeneChip Human Exon 1.0 ST microarrays in 64 AML patients.

first: A

first: L

last: Bullinger

first: K

last: Doehner

first: H


title: Expression data from one year old leaves of Populus simonii by NaCl treatments

status: Public on Nov 27 2014

city: Beijing

first: Jin

middle: Hui

last: Chen

state: Beijing

address: No. 35, Qinghua East Road

department: College of Biological Sciences and Biotechnology, Beijing Forestry University

country: China

institute: Beijing Forestry University

summary:
We take the one year old plant for 100 mMol/L NaCl treatments 24 hours and controls. Use the Affymetrix poplar gene chip to decrypt the gene functions and mechanisms in Populus simonii leaves.
We used microarrays to detail the global programme of gene expression during NaCl treatments.

overall_design: Populus simonii leaves were taken from 100 mMol/L NaCl treatments 24 hours and controls for RNA extraction and hybridization on Affymetrix microarrays.S1, S2 and S3 from NaCl treatments, CK1, CK2 and CK3 controls.

first: Deqiang

last: Zhang

first: Jinhui

first: He


title: Microarray analysis of developing fruits from transgenic lines with increased or reduced SlARF9 mRNA levels in tomato.

status: Public on Nov 26 2014

city: Wageningen

first: Yury

last: Tikunov

address: Droevendaalsesteeg 1

department: Plant Breeding

country: Netherlands

institute: Wageningen UR

summary: The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early tomato fruit development is Solanum lycopersicum ARF9 (SlARF9).    To explore the physiological role of SlARF9 in tomato fruit set and development, we generated transgenic tomato lines in which the gene was overexpressed or silenced, and used microarray analysis to identify possible transcriptomic changes associated with the fruit developmental phenotypes observed in the transgenic lines.

overall_design: The transcript profiling analysis was done using pericarp tissue from fruits, 3-4mm in diameter, with each sample containing the pericarp of two fruits. For each seperate transgenic line, tissues were pooled from 2-3 plants (T2), resulting in a total of 6 samples for SlARF9-OE, 7 samples for SlARF9-RNAi, and 2 samples for wild type. The transcript profiling analysis was carried out using affymetrix EUTOM3 tomato exon array.

first: Maaike

last: de Jong

first: Mieke

last: Wolters-Arts

first: Bernardus

middle: C

last: Schimmel

first: Catharina

middle: L

last: Stultiens

middle: F

last: de Groot

first: Stephen

middle: J

last: Powers

middle: M

first: Arnoud

middle: G

last: Bovy

first: Celestina

last: Mariani

first: Wim

middle: H

last: Vriezen

first: Ivo

last: Rieu


title: Transcriptional and epigenetic program changes of induced beta cells over time [expression array]

status: Public on Nov 15 2014

city: Cambridge

first: Kendell

last: Clement

state: MA

address: 7 Divinity Ave.

institute: Harvard University

summary: Direct lineage conversion is a promising approach to generate therapeutically important cell types for disease modeling and tissue repair.  However, it is often unclear whether lineage-reprogrammed cells remain stable long-term and whether the properties of the reprogrammed cells evolve over time.  Here, using an improved method of converting pancreatic acinar cells to beta-cells, we show that induced beta-cells persist in the adult pancreas for up to 14 months and form islet-like structures.  Detailed analyses of induced cells over 7 months reveal that global DNA methylation changes occur rapidly whereas transcription network remodeling evolves over two months to resemble that of endogenous beta-cells and then stabilizes thereafter.  Progressive gain of beta-cell function by converted cells during the 7 month period coincides with both transcriptional changes and the formation of islet-like structures. These studies demonstrate the ability of lineage-reprogrammed cells to achieve a stable state and identify key cellular and molecular milestones during their long-term evolution.

overall_design: Acinar cells and beta cells were collected as control, as well as induced beta cell samples at day 10, day 30, day 60, and 7 months

first: Weida

last: Li

first: Jiang

last: Zhu

first: Yingying

first: Qiao

last: Zhou


title: Replication timing of control and overexpressed PolQ fibroblast cells

status: Public on Oct 28 2014

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

summary: The human A-family DNA polymerase θ (Pol q) is a large, multidomain enzyme whose physiological function is still unclear despite its in vitro translesion synthesis capacity in front of DNA damage and its involvement in some features of DNA repair after external stress. Here we present evidence that Pol q holds a novel role in the absence of external stress as a critical determinant of the replication timing program in human cells. Pol q binds to chromatin at early G1 and is required for proper formation of pre-replicative complexe and replication origin activation. Pol q-depleted cells show modified spatial organization of chromatin-loop structures at replication factories. Genome-wide analysis of replication timing shows delayed replication of a part of early replicating domains and advanced replication of a part of late replicating domains following Pol q depletion. Our results identify Pol q as one of the first critical human factors discovered in the replication timing programme.

overall_design: Two-condition experiment, control vs. over expressed polQ cells. Biological replicates: 2 control replicates, 2 transfected replicates.

first: A

last: Fernandez-Vidal

first: L

last: Guitton-Sert

first: J

first: G

last: Baldacci

first: C

last: Cazaux

last: Hoffmann


title: Real-time quantitative PCR analysis of human radioresistant breast cancer cells

status: Public on Oct 21 2014

city: Houston

first: Peijing

last: zhang

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: We wanted to use an unbiased approach to identify miRNAs that regulate radiosensitivity. To this end, we performed a Human Apoptosis miRNA PCR Array analysis to identify miRNAs deregulated in radioresistant (SUM159-P2) compared to parental (SUM159-P0) cells.

overall_design: qPCR gene expression profiling.  Parental and radioresistant breast cancer cell lines were used as indicated in the summary. Equal amount total RNA from each cell line was collected and reversely transcripted prior to gene expression analysis.

last: Zhang

first: Li

last: Wang

first: Cristian

last: Rodriguez-Aguayo

first: Yuan

last: Yuan

first: Bisrat

last: Debeb

first: Dahu

last: Chen

first: Yutong

last: Sun

first: M

last: You

first: Yongqing

last: Liu

first: Douglas

last: Dean

first: Wendy

middle: A

last: Woodward

first: Han

last: Liang

first: Xianbin

last: Yang

first: Gabriel

last: Lopez-Berestein

first: Anil

middle: K

last: Sood

first: Ye

last: Hu

first: K

last: Ang

first: Junjie

last: Ma


title: Legionella ITS oligonucleotide microarray

status: Public on Oct 04 2014

city: Tianjin

first: Boyang

last: Cao

address: #23 HongDa Street

institute: Nankai Univ

summary:
In this report, we have developed a rapid oligonucleotide microarray detection technique to identify the most common ten Legionella spp..
The sensitivity of the detection was at 1.0 ng with genomic DNA or 13 CFU/100 mL with Legionella cultures. The microarray detected seven air conditioner-condensed water samples with 100% accuracy, validating the technique as a promising method for applications in basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance. The phylogenetic study based on the ITS has also revealed interestingly that the non-pathogenic L. fairfieldensis is the closest to L. pneumophila than the nine other pathogenic Legionella spp..

sample_organism:
Legionella pneumophila
Legionella bozemanae
Legionella longbeachae
Legionella micdadei
Legionella jordanis
Fluoribacter dumoffii
Fluoribacter gormanii
Legionella maceachernii
Legionella anisa
Legionella fairfieldensis

overall_design: We have sequenced and analyzed the 16S-23S rRNA gene internal transcribed spacer (ITS) of the ten Legionella spp. Based on the ITS regions, twenty-nine probes that reproducibly detected multiple Legionella species with high specificity were included in the array. A total of 52 strains, including 30 target pathogens and 22 non-target bacteria were used to verify the oligonucleotide microarray assay.

first: Xiangqian


title: Transcriptomics Analysis and Hormonal Changes of Male and Female Rats Treated Chronically with a Low Dose of Acrylamide in their Drinking Water

status: Public on Oct 06 2014

city: Gainesville

first: Reyna

middle: Cristina

last: Colli-Dula

state: Florida

address: Mowry Drive 471

department: CEHT

institute: University of Florida

summary: Acrylamide is known to produce follicular cell tumors of the thyroid in rats. RccHan Wistar rats were exposed in utero to a carcinogenic dose of acrylamide (3 mg/Kg bw/day) from gestation day 6 to delivery and then through their drinking water to postnatal day 35. In order to identify potential mechanisms of carcinogenesis in the thyroid glands, we used a transcriptomics approach. Thyroid glands were collected from male pups at 10 PM and female pups at 10 AM or 10 PM in order to establish whether active exposure to acrylamide influenced gene expression patterns or pathways that could be related to carcinogenesis. While all animals exposed to acrylamide showed changes in expected target pathways related to carcinogenesis, such as DNA repair, DNA replication, chromosome segregation, among others, animals that were sacrificed while actively drinking acrylamide-laced water during their active period at night showed increased changes in pathways related to oxidative stress, detoxification pathways, metabolism, and activation of checkpoint pathways, among others. In addition, thyroid hormones, T3 and T4, were increased in acrylamide-treated rats sampled at night, but not in quiescent animals, compared to controls. The data clearly indicate that time of day for sample collection is critical to identifying molecular pathways that are altered by the exposures. These results suggest that carcinogenesis in the thyroids of acrylamide treated rats may ensue from several different mechanisms such as hormonal changes and oxidative stress and not only from direct genotoxicity, as has been assumed to date.

overall_design: A transcriptomics approach (microarrays and bioinformatics) was used to investigate changes in gene expression and the association with physiological responses (changes in plasma hormone levels) in rats treated with acrylamide (AA) from gestational day 6 to post natal day 35. We hypothesized that 3 mg AA/Kg bw/day exposure would produce changes in plasma hormone levels associated with key genes and pathways involved with molecular actions of AA.

first: Marvin

last: Friedman

first: Nancy

last: Denslow


title: Cytochromes Associated with Fe(III) Oxide Reduction in the Hyperthermophilic Archaeon Ferroglobus placidus

status: Public on Oct 01 2014

city: Amherst

first: Dawn

middle: E

last: Holmes

state: Massachusetts

address: 639 N Pleasant St Morrill IVN 422C

department: Microbiology

institute: University of Massachusetts Amherst

summary: Differential expression of electron transfer genes during growth with insoluble iron provided as an electron acceptor compared to soluble iron.

overall_design: A four chip study using total RNA recovered from two separate cultures of Ferroglobus placidus DSM 10642 grown with 10 mM acetate provided as electron donor and insoluble iron hydroxide provided as electron acceptor (experimental condition) and two separate cultures of Ferroglobus placidus DSM 10642 grown on 10 mM acetate with soluble iron citrate provided as electron acceptor (control condition).  Each chip measures the expression level of 2613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

first: Carla

last: Risso

first: Jessica

last: Smith

first: Derek

last: Lovley


title: Response of M. tuberculosis to 8 hour exposure to vitamin C

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: Transcriptional profiling of M.tuberculosis to 10 mM vitamin C at 8 h. This was compared to gene expression profile of untreated M. tuberculosis culture.

overall_design: Organism: Mycobacterium tuberculosis H37Rv, Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE Microarray (AMADID-020181)

first: Kriti

last: Sikri

first: Sakshi

last: Dhingra

first: Malobi

last: Nandi

first: Neetu

last: Taneja

first: Jaya

middle: S

last: Tyagi


title: Identification of genes that are differentially expressed in alt1 and WT

status: Public on Sep 27 2014

city: Beijing,

first: Xiaoqiang

last: Liu

address: No.1 West Beichen Road,Chaoyang District

department: Chinese academy of sciences

institute: the institute of genetics and developmental biology

summary: we characterized the rice alkaline tolerant mutant, alt1. Map-based cloning revealed that alt1 harbors a mutation in a putative chromatin remodeling ATPase gene. ALT1-RNAi transgenic plants mimicked the alt1 phenotype, exhibiting tolerance to alkali stress in a transcript dosage-dependent manner. We found that the predicted ALT1 protein belonged to the Ris1 subgroup of the Snf2 family and was localized in the nucleus. qRT-PCR analysis showed that ALT1 was predominantly expressed in leaf blades and sheaths, and that ALT1 transcription was rapidly suppressed after alkaline treatment. These results support the notion that ALT1 is a negative regulator of alkaline tolerance. Roots of two-leaf stage alt1 and WT seedlings grown under normal conditions were sampled for microarray analysis. The transcriptomic profiles were investigated using an Agilent-015241 Rice Gene Expression 4×44 K Microarray (Agilent Technology) containing 32,325 probes corresponding to cDNA, 6,934 probes corresponding to expressed sequence tags (ESTs), and 2,612 probes corresponding to gene predicted loci, respectively, with three independent biological replicates.

first: Mingxin

last: Guo

first: Shanguo

last: Yao


title: DNA methylation analysis of the U937 cell line

status: Public on Sep 26 2014

city: Lund

first: Carl

last: Sanden

address: BMC B13, Klinikgatan 26

department: Department of Hematology

country: Sweden

institute: Lund University

summary: DNA methylation profiling of gene promoters in the human myeloid cell line U937.

overall_design: Bisulphite converted DNA from wildtype U937 cells was hybridised to the Illumina Infinium HumanMethylation27 BeadChip to determine the methylation pattern of the U937 cell line.

last: Sandén

first: Andreas

last: Lennartsson

first: Urban

last: Gullberg


title: BRMS1L suppresses breast cancer metastasis by inducing epigenetic silence of FZD10

status: Public on Sep 12 2014

city: Guangzhou

first: shaohua

last: Qu

address: 107 Yanjiang West Road

institute: Sun Yat-Sen university

summary:
BRMS1L (breast cancer metastasis suppressor 1 like，BRMS1-like) is a component of the SIN3A-HDAC corepressor complex that suppresses target gene transcription. Here, we show that reduced BRMS1L in breast cancer tissues is associated with tumor metastasis and poor patient survival. Functionally, BRMS1L inhibits migration and invasion of breast cancer cells by inhibiting epithelial-mesenchymal transition (EMT). These effects are mediated by epigenetic silencing of FZD10, a receptor for Wnt signaling, by facilitating the recruitment of HDAC1 to its promoter and enhancing histone H3K9 deacetylation. Consequently, BRMS1L-induced FZD10 silencing inhibits aberrant activation of WNT3-FZD10--catenin signaling. Furthermore, BRMS1L is a target of miR-106b and miR-106b upregulation leads to BRMS1L reduction in breast cancer cells. RNAi-mediated silencing of BRMS1L expression promotes metastasis of breast cancer xenografts in immunocompromised mice, while ectopic BRMS1L expression inhibits metastasis. Therefore, BRMS1L provides an epigenetic regulation of Wnt signaling in breast cancer cells and acts as a breast cancer metastasis suppressor.
Ther transfection analysis used here were further desxribed in Chang Gong, eta al.2013. miR-106b expression determines the proliferation paradox of TGF-β in breast cancer cells. Oncogene. 2013

overall_design: A two chip study using total RNA recovered from MDA-MB-231 breast cancer cells transfected with negative control vector or vector overexpressing BRMS1L for 24 hours. Each chip measures the expression 45033 genes were collected from the authoritative data source including NCBI.

first: Shaohua

first: Chang

last: Gong


title: ChIP-chip and MeDIP-chip from glioblastoma BTSCs (brain tumor stem cells) with H3K4me3, H3K27me3, H3K9me3, methylated DNA

status: Public on Aug 30 2014

city: Calgary

first: Mark

last: Bieda

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

type: Methylation profiling by genome tiling array

summary:
Aberrational epigenetic marks are believed to play a major role in establishing the abnormal features of cancer cells. Rational use and development of drugs aimed at epigenetic processes requires an understanding of the range, extent, and roles of epigenetic reprogramming in cancer cells. Using ChIP-chip and MeDIP-chip approaches, we localized well-established and prevalent epigenetic marks (H3K27me3, H3K4me3, H3K9me3, DNA methylation) on a genome scale in several lines of putative glioma stem cells (brain tumor stem cells, BTSCs) and, for comparison, normal human fetal neural stem cells (fNSCs). We determined a substantial “core” set of promoters possessing each mark in every surveyed BTSC cell type, which largely overlapped the corresponding fNSC sets. However, there was substantial diversity among cell types in mark localization. We observed large differences among cell types in total number of H3K9me3+ positive promoters and peaks and in broad modification areas for H3K27me3 and, to a lesser extent, H3K9me3. We verified that a change in a broad modification (defined as >50 kb peak length) affected gene expression of CACNG7. We detected large numbers of bivalent promoters, but most bivalent promoters did not display direct overlap of contrasting epigenetic marks, but rather occupied nearby regions of the proximal promoter. There were significant differences in the sets of promoters bearing bivalent marks in the different cell types and few consistent differences between fNSCs and BTSCs. Overall, our “core set” data establishes sets of potential therapeutic targets, but the diversity in sets of sites and broad modifications among cell types underscores the need to carefully consider BTSC subtype variation in epigenetic therapy. Our results point toward substantial differences among cell types in the activity of the production/maintenance systems for H3K9me3 and for broad regions of modification (H3K27me3 or H3K9me3). Finally, the unexpected diversity in bivalent promoter sets among these multipotent cells indicates that bivalent promoters may play complex roles in the overall biology of these cells. These results provide key information for forming the basis for future rational drug therapy aimed at epigenetic processes in these cells.
ChIP-chip and MeDIP-chip localization of histone modifications and DNA methylation in glioma stem cells and fetal neural stem cells

overall_design: comparison of 4 lines of brain tumor stem cells to each other and to normal fetal neural stem cells

first: Sally

last: Yoo


title: Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms

status: Public on Sep 01 2014

city: South San Francisco

first: Brigit

middle: Erin

last: Riley

state: CA

address: 180 Oyster Point Blvd.

institute: Elan Pharmaceuticals

summary:
Detailed analysis of disease-affected tissue provides insight into molecular mechanisms contributing to pathogenesis. Substantia nigra, striatum and cortex are functionally connected with increasing degrees
of alpha-synuclein pathology in Parkinson's disease. Functional and causal pathway analysis of gene expression and proteomic alterations in these three regions revealed pathways that correlated with deposition
of alpha-synuclein. Microarray and RNAseq experiments revealed previously unidentified causal changes related to oligodendrocyte function and synaptic vesicle release and other changes were reflected across
all brain regions. Importantly a subset of these changes were replicated in Parkinson's disease blood. Proteomic assessment revealed alterations in mitochondria and vesicular transport proteins that preceded gene
gene expression changes indicating defects in translation and/or protein turnover. Our combined approach of proteomics, RNAseq and microarray analyses provides a comprehensive view of the molecular changes
that accompany alpha-synculein pathology in Parkinson's disease, and may be instrumental in understanding and diagnosing Parkinson's disease progression.

overall_design:
Substantia Nigra (3 normal, 3 PD), Striatum (6 normal, 6 PD), Cortex (5 normal, 5 PD), Cortex non-PD neurodegeneration (2 normal, 3 DLB).
Note Sample X201264 was used both for Cortex normal and for Cortex nonPD normal

first: Shyra

last: Gardai

first: Dorothea

last: Emig-Agius

first: Marina

last: Bessarabova

first: Alexander

last: Ivliev

first: Birgit

last: Schule

first: Jeff

last: Alexander

first: William

last: Wallace

first: Glenda

last: Halliday

first: J

middle: W

last: Langston

first: Scott

last: Braxton

first: Ted

last: Yednock

first: Thomas

last: Shaler

first: Jennifer

last: Johnston


title: Extrinsic and Intrinsic Regulation of DOR/TRP53INP2 Expression in Mice

status: Public on Sep 30 2014

city: Göttingen

first: Silvia

last: von der Heyde

address: Humboldtalle 32

department: Medical Statistics

institute: University Medical Center Göttingen

summary:
The objective is to relate changes in expression of DOR/TRP53INP2, a factor involved in thyroid hormone action and autophagy, to body composition in mice fed a fat (FD) or high fat diet (HFD) for 8 days and in a genetically obese mouse model.
We conclude that DOR expression depends on sex, fat content of diet, age, tissue type and tissue weight.

overall_design: 4 samples: 2 (normal diet control, fat diet) x2 replicates

first: Carolin

last: Fromm-Dornieden

first: Oleksandr

last: Lytovchenko

first: Nina

last: Behnke

first: Sebastian

last: Hogl

first: Janina

last: Berghoff

first: Frederik

last: Köpper

first: Tim

last: Beissbarth

first: Lennart

last: Opitz

first: Ulla

last: Renne

first: Andreas

last: Hoeflich

first: Bertram

last: Brenig

first: Bernhard

last: Baumgartner


title: miRNA expression data from embryonic ureteric bud (UB) cells

status: Public on Aug 28 2014

city: Charlottesville

first: Jing

last: Yu

state: VA

address: 1340 Jefferson Park Ave.

department: Cell Biology

institute: University of Virginia School of Medicine

summary: UB cells FACS sorted from E15.5 mouse kidneys were analyzed for miRNAs expression.

overall_design: E15.5 UB cells FACS sorted from Rosa26YFP; Hoxb7Cre mice, total RNAs including miRNAs were purified and used for miRNA microarray

first: N

last: Vidya


title: Expression profiling of BIK-suppressed MCF-7 cells under the action of tamoxifen

city: Estado de Mexico

first: Rubi

last: Viedma

state: Estado de Mexico

address: Av. de los Barrios 1, Los Reyes Ixtacala,  Tlalnepantla,

department: bioquimica

country: Mexico

institute: unam

summary: In the comparison between TAM-treated BIK-suppressed MCF7 cells vs. MCF.7 treated with TAM, we found some genes which have been associated with drug resistance.

overall_design: Two-condition experiment, MCF-7 cell groups: TAM (control), and siRNA BIK with TAM. Biological replicates: Tam (control), compared to siRNA BIK with TAM, independently grown and harvested. One replicate array.

first: Rubí

last: Viedma-Rodriguez

first: Diego

last: Arenas


title: Comprehensive analysis of host gene expression in Autographa californica nucleopolyhedrovirus-infected Spodoptera frugiperda cells

status: Public on Aug 26 2014

city: 6th of october

first: Tamer

middle: Zaki

last: Salem

state: Giza

address: Shiekh Zayed

department: Biomedical sciences

country: Egypt

institute: Zewail city of science and technology

summary: Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) is the best-studied baculovirus and most commonly used virus vector for baculovirus expression vector systems. The effect of AcMNPV infection on host cells is incompletely understood. A microarray based on Spodoptera frugiperda ESTs was used to investigate the impact of AcMNPV on host gene expression in cultured S. frugiperda, Sf21 cells. Most host genes were down-regulated over the time course of infection, although a small number were up-regulated. The most highly up-regulated genes encoded heat shock protein 70s and several poorly characterized proteins. Regulated genes with the highest score identified by functional annotation clustering included primarily products required for protein expression and trafficking in the ER and golgi. All were significantly down-regulated by approximately 12h post-infection. Microarray data were validated by qRT-PCR. This study provides the first comprehensive host transcriptome overview of Sf21 cells during AcMNPV infection.

overall_design: Host gene expression of the Sf21 cells was measured in AcMNPV mock-infected Sf21cells as well as AcMNPV-infected Sf21 cells at 6, 12, and 24 hours post infection (hpi). Four independent experiments were performed at each time (6, 12, and 24 hpi) using different donors for each experiment. Only two 24 hour sample data sets were used in the final analysis as two did not meet QC criteria.

middle: Z

first: Fengrui

last: Zhang

first: Yan

last: Xie

first: Suzanne

last: Thiem


title: NOTCH1 ChIP-Seq in HBPALL cell lines

status: Public on Sep 07 2014

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-Seq detected global binding of NOTCH1 oncogene in a human T-Cell Leukemia Cell line.

overall_design: ChIP-Seq of NOTCH1 in HBALL cell lines and Whole Cell Extract (WCE) as control.

first: Teresa

last: Palomero

first: Pavel

last: Sumazin

first: Adolfo

last: Ferrando


title: Cross-platform toxicogenomics for the prediction of nongenotoxic hepatocarcinogenesis in rat (miRNA)

status: Public on Aug 18 2014

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

summary: In this study we performed microarray-based molecular profiling of liver samples from Wistar rats exposed to genotoxic carcinogens (GC), nongenotoxic carcinogens (NGC) or non-hepatocarcinogens (NC) for up to 14 days. In contrast to previous toxicogenomics studies aimed at the inference of molecular signatures for assessing the potential and mode of compound carcinogenicity, we considered multi-level omics data. Besides evaluating the predictive power of signatures observed on individual biological levels, such as mRNA, miRNA and protein expression, we also introduced novel feature representations which capture putative molecular interactions or pathway alterations by integrating expression profiles across platforms interrogating different biological levels.

overall_design: Male Wistar rats were treated by oral gavage with the eight nongenotoxic hepatocarcinogens Phenobarbital sodium (PB), Piperonylbutoxide (PBO), Dehydroepiandrosterone (DHEA), Acetamide (AA), Methapyrilene HCl (MPy), Methylcarbamate (Mcarb), Diethylstilbestrol (DES) and Ethionine (ETH), the two genotoxic carcinogens C.I Direct Black (CIDB) and dimethylnitrosamine (DMN), the two non-hepatocarcinogens Cefuroxime (CFX) and Nifedipine (Nif), and the three compounds with undefined carcinogenic class Cyproterone acetate (CPA), Thioacetamid (TAA) and Wy-14643 (Wy). Depending on the administered compound, livers were taken after 3, 7, or 14 days for histopathological evaluation. From the five animals per treatment group three animals were selected based on the histopathological findings and subjected to molecular profiling using Affymetrix RG-230A arrays (mRNA expression), Agilent G4473A arrays (miRNA expression) and Zeptosens ZeptoMARK reverse arrays (protein expression).

first: Michael

last: Römer

first: Heidrun

last: Ellinger-Ziegelbauer

first: Johannes

last: Eichner


title: IF002 - Custom designed Agilent arrays result on the Cystic Fibrosis model in ferrets.

status: Public on Jul 18 2014

city: Seattle

last: Katze

state: WA

address: Rosen Building 960 Republican St.

institute: University of Washington

summary: The goal of this study is to use newly designed ferret Agilent arrays to compare transcriptome profiles between wild type, CF3959(-/-) and CF3959(+/-) ferrets.  Lung and trachea tissues from newborn and 15 day-old ferrets were RNA-extracted and subsequently analyzed by microarray.

overall_design: Using the newly designed ferret Agilent arrays, we compared the transcriptome profiles between wild type, CF3959(-/-) and CF3959(+/-) ferrets.  Samples sets: RNA from a combination of trachea and lung tissue from 4 newborn wild type ferrets and 4 newborn CF3959(-/-) ferrets.  In addition, lung tissue from two 15 day-old wild type, three 15 day-old CF3959(+/-) and three 15 day-old CF3959(-/-) ferrets was RNA-extracted and subsequently analyzed by microarray.

first: John

last: Engelhardt

first: Xinxia

last: Peng

first: Jean

last: Chang


title: Copy number profiles of pheochromocytoma and paraganglioma

status: Public on Aug 17 2014

city: Seoul

first: Yoon-La

last: Choi

address: 81 Irwon-Ro, Gangnam-gu

department: Department of pathology

country: South Korea

institute: Samsung medical center

summary: Until now, it is nearly impossible to diagnose malignancy of pheochromocytoma/paraganglioma with pathological examinations. The aim of the study is to find the genes which can be applied as a biomarker in the clinic to distinguish benign and malignant forms of pheochromocytoma/paraganglioma.

overall_design: We generated aCGH profiles of 9 samples of benign tumors and 3 samples of malignant tumors

first: Yool-La

first: Seung

last: Lee

first: Ensel

last: Oh

first: Ji

middle: Y

last: Song

first: Eunseo

last: Ahn


title: Changes in global gene expression of Vibrio parahaemolyticus induced by cold- and heat-stress

status: Public on Aug 27 2014

city: Berlin

first: Stephan

last: Huehn

address: Koenigsweg 69

institute: Freie Universität Berlin

summary: Vibrio (V.) parahaemolyticus is the leading cause of seafood borne gastro-intestinal infections in humans worldwide. It is widely found in marine environments and is isolated frequently from seawater, estuarine waters, sediments and raw or insufficiently cooked seafood. Within the food chain, V. parahaemolyticus encounters different temperature conditions that might alter the metabolism and pathogenicity of the bacterium. In this study, we performed gene expression profiling of V. parahaemolyticus RIMD 2210633 after exposure to 4°C, 15°C, 20°C, 37°C and 42°C to describe the cold and heat shock response. Analysis of transcriptomics data resulted in differential expression of 19 genes at 20°C, 193 genes at 4°C, 625 genes at 42°C and 639 genes at 15°C. Thus the highest portion of significantly expressed genes was observed at 15°C and 42°C with 13.3% and 13%, respectively. Genes of many functional categories were highly regulated even at lower temperatures. Our results showed that virulence associated genes (tdh1, tdh2, toxR, toxS, vopC, T6SS1, T6SS2) remained largely unaffected by heat or cold stresses. Along with folding and temperature shock depending systems, an overall temperature depended regulation of expression could be shown. Particularly the energy metabolism was affected most by changed temperatures. Whole-genome gene expression studies of food related pathogens such as V. parahaemolyticus reveal how these pathogens react to stress impacts for prediction of its behaviour under conditions like storage and transport.

overall_design: Temperature induced gene expression was detected in total bacterial RNA of V. parahaemolyticus. Five different temperatures (4°C, 15°C, 20°C, 37°C, 42°C) were used in at least 3 biological replicates (4 replicates for 37°C). Gene expression at 37°C was used for normalization.

first: Sara

last: Urmersbach

first: Tommi

last: Aho

first: Thomas

last: Alter

first: Sveda

last: Hassan

first: Reija

last: Autio


title: IF001 - Microarray analysis from ferret infections with highly pathogenic reconstructed H1N1 1918 influenza virus.

first: Michael

summary: The objective of this study was test and compared two custom designed ferret Agilent microarrays

overall_design: We designed two versions of oligonucleotide microarray using Agilent eArray Web portal (https://earray.chem.agilent.com/earray) to profile both Ensembl annotated transcripts and intergenic transcripts derived from ferret RNA-seq data as described above. In both cases, the longest isoform of each locus was selected for probe design with the ‘Design with 3’ Bias’ checked, and probe length was set to 60nt.  For first version of microarray (design ID: 048471) 36,950 probes were selected to target Ensembl annotated genes and intergenic transcripts uncovered from mRNA-seq data, which was intended to work with conventional experimental protocols using polyA priming for cDNA synthesis. For the second version (design ID: 048472) 64,238 probes were selected to target Ensembl annotated genes, intergenic transcripts uncovered from both mRNA-seq and Total RNA-seq data, which was intended to work with experimental protocols using random priming for cDNA synthesis to capture both polyA and non-polyA transcripts.  The samples used for the array test came from an infection of 4-8-month old ferrets infected with either reconstructed H1N1 1918 influenza virus or mock infected. Infections were done with 1x10^6pfu and samples were collected at 1 d.p.i.  RNA was isolated from lung and trachea from 1 mock and 1 infected animal for a total of 4 RNA samples. One probe preparation for each samples was done for each array design. Two arrays were run for each samples type for each array design for a total of 16 arrays.

first: Yoshi

last: Kawoaka

first: Lynn

last: Law

first: Amie

last: Eisfeld


title: Expression data from different chicken tissues at 7-week of age

city: Harbin

first: Hongbao

last: Wang

address: No. 59 Mucai Street, Xiangfang District

institute: Northeast Agricultural University

summary:
A better understanding of the regulation of gene expression and lipid metabolism in the chicken will benefit producers, as well as scientists who use the chicken as a model organism for studies of developmental biology and human therapeutics.
We constructed the gene expression profiles of major chicken tissues to screened genes prominently high expressed in chicken adipose tissue and liver using the Chicken Genome arrays by comparing their expression profiles with twenty other tissue types.

overall_design: Our objectives have been to construct gene expression profiles of the major chicken tissues, identify genes prominently high expressed in chicken adipose tissue and liver than other tissues.

first: Hui

last: Li


title: Copy number of oral cell lines [CGH]

status: Public on Jul 15 2014

city: Vancouver

first: Christopher

middle: Trevor Daniel

last: Dickman

state: BC

address: 675 West 10th Ave

institute: BC Cancer Research Center

summary: Profiling of copy number mutations in commonly used non-cancerous oral cell lines

overall_design: Observational Study on 8 cell lines: 6 imortalized normal, 1 dysplasia and 1 immortalized dysplasia

first: Rebecca

last: Towle

first: Rajan

last: Saini

first: Cathie

last: Garnis


title: Microarray study of the Sex Inducer Proteins in Cryptococcus neoformans var. neoformans (JEC20/21)

status: Public on Jul 01 2014

city: Madison

first: Christina

last: Hull

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry, Medical Microbiology and Immunology

institute: University of Wisconsin- Madison

summary: To identify genes regulated by the homeodomain transcription factors Sxi1α and Sxi2a (Sex Inducer 1α and 2a) in Cryptococcus neoformans, we carried out a whole-genome expression experiment. We performed two independent whole-genome microarray experiments comparing transcript levels in cells that either possessed or were lacking the Sxi proteins. In the first experiment we compared the expression profile of a haploid sxi1αΔ strain to that of a haploid strain expressing both SXI1α and an inducible copy of SXI2a (Sxi +). In the second experiment, we compared the expression profile of a wild type cross (JEC20 x JEC21) to the expression profile of a cross whose mating partners did not possess either of the transcription factors (sxi2a∆ x sxi1α∆)(Sxi -). In both experiments RNA from each condition was harvested, labeled, and hybridized competitively to a spotted oligonucleotide microarray representing the approximately 6,500 genes in the C. neoformans genome. The resulting data was analyzed in Limma using standard methods.

overall_design: In the Sxi (+) experiment, each strain (Δsxi1α and the Sxi-Inducible strain) were grown overnight in liquid YPD, diluted back to an OD600 of 0.2, grown to log phase, and then switched to growth in liquid YPGal media for 6 hrs. The Δsxi1α strain was designated the control condition. Two biological replicates were used and in the first replicate there were two technical replicates for each dye orientation (4 replicates total). For the second Sxi (+) biological replicate, there were three total technical replicates, and one of those was a dye swap. For Sxi deletion crosses, strains (JEC20 x JEC21 or Δsxi1α x Δsxi2a) were mixed and plated onto V8 media (pH 7.0) and incubated at 22°C in the dark for approximately 16 hours. The wild type (JEC20 x JEC21) cross was designated as the control in this experiment. Eight total hybridizations were carried out that consisted of 2 biological replicates and four technical replicates for each biological replicate (2 technical replicates per dye swap).

first: Matthew

last: Mead


title: miRNA array analysis following gefinitib/luteolin administration to PC-3 cells

status: Public on Jun 29 2014

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: To determine if any altered miRNA expression is actually involved in the growth inhibition and/or cell death induction by luteolin and/or gefitinib, we performed miR-array analysis using RNA from PC-3 cells after 24h of treatment with 60μM luteolin and/or 60μM gefitinib.

overall_design: PC-3 cells were treated for 24h with DMSO, 60μM luteolin (Lut), 60μM gefitinib (Gef) or their co-administration (Lut+Gef). Each sample was run in duplicate.

first: Hiroshi

last: Nojima


title: Comparative genomics of a fluconazole-resistant Candida albicans strain CaLY350.

status: Public on Jun 24 2014

city: Shanghai

first: xingxing

last: li

address: Guohe Road

institute: Second Military Medical University

summary: To investigate the diversity of gene contents of Candida albicans strain by array-based comparative genomic hybridization (array CGH; aCGH).

overall_design: A fluconazole-resistant Candida albicans strain CaLY350 was selected to carry out the comparative genomics microarray. Two-condition experiment, CaLY350 vs.SN152. Biological replicates: 2 control, 2 transfected, independently grown and harvested. One replicate per array.

first: Xingxing

first: Dedong


title: Comparative genomics of the srd1 null mutant Candida albicans strain CaLY202.

overall_design: the srd1 null mutant Candida albicans strain CaLY202 was selected to carry out the comparative genomics microarray. Two-condition experiment, CaLY202 vs.SN152. Biological replicates: 2 control, 2 transfected, independently grown and harvested. One replicate per array.


title: Comparative genomics of a fluconazole-resistant variant Candida albicans strain CaLY188.

overall_design: A fluconazole-resistant variant Candida albicans strain CaLY188 was selected to carry out the comparative genomics microarray. Two-condition experiment, CaLY188 vs.SN152. Biological replicates: 2 control, 2 transfected, independently grown and harvested. One replicate per array.


title: Chronic Psychological Stress regulates Visceral Adipocyte-mediated Glucose Metabolism and Inflammatory Circuits in male Rats

status: Public on Jun 03 2014

city: Los Angeles

first: Iordanis

last: Karagiannidis

address: 675 Charles E. Young Dr. South

institute: UCLA, David Geffen School of Medicine

summary: In this study we employed the chronic unpredictable stress (CUS) rat model that leads to anxiety features comparable to humans and validated in several published reports as a well-characterized model of depression symptoms with high predictive validity. Cytokines and activated intracellular kinase levels were determined using high throughput multiplex assays. RNA from freshly isolated adipocytes was used to run whole genome expression microarray profiling in control and stressed rats. Adipocyte function was assessed via tritiated glucose uptake assay. The expression of four cytokines (TNFα, IL-1β, IL-6 and MCP-1) was validated via real-time PCR and the all showed increased expression levels with chronic unpredictable stress.

overall_design: Male rats were subjected to chronic unpredictable stress for 35 days and total body fat was measured. The analyses presented here represents data from experiments performed in 6 control and 6 stressed rats in parallel. All cells for RNA isolation were collected at the conclusion of the 35 day stress protocol.

first: Iordanes

last: Karagiannides

first: Sylvie

last: Bradesi

first: Charalabos

last: Pothoulakis


title: Application of array-CGH for the detection of genomic rearrangements responsible for syndromic mental retardation of unknown cause

status: Public on May 22 2014

city: Valencia

first: Francisco

last: Martinez

state: Valencia

address: Avenida Campanar 21

department: Unidad de Genetica

country: Spain

institute: Hospital Universitari i Politecnic La Fe

type: Genome variation profiling by genome tiling array

summary: Here we describe an interstitial pure duplication of 19p13.3 that was initially considered as a de novo alteration, in a patient with intellectual disability studied by array-CGH. The finding of the same chromosomal alteration in a first-degree cousin of this patient led us to investigate the presence of insertional translocations. An intrachromosomal insertional translocation was found in at least three generations. Three intellectually disabled patients with the same duplication and multiples abortions among translocation carrier family members were found. A review of other published cases has allowed us to find three other cases with a similar pure duplication and some clinical findings present in all patients as intrauterine growth retardation, microcephaly, motor and speech delay, moderate to severe intellectual disability and dysmorphic features. These findings allow us to suggest the existence of a new microduplication syndrome in chromosomal region 19p13.3.

overall_design: Whole genome array-CGH was performed on Agilent oligo-chip 44K (human genome CGH microarray G4410B from Agilent Technologies, Palo Alto, CA) as recommended. The patients’ DNA samples were tested against a pool of 10 sex-matched normal DNA samples, all of them (patients and normal controls) from our geographical area. Scanned images were quantified using Agilent Feature Extraction Software (v9.0). The results were analyzed using Agilent Genomic Workbench software. Annotations have been obtained from UCSC (http://genome.ucsc.edu) based on human genome build GRCh37/hg19.

first: Carmen

last: Orellana

last: Martínez

first: Mónica

last: Rosello

first: Silvestre

last: Oltra

first: Sandra

last: Monfort

first: Sonia

last: Mayo


title: H3K27me3 and H3K4me2 profiles along the length of the X chromosome in trophoblast stem (TS) cells and Extra-embryonic endoderm stem cells (XEN), ChIP-chip

status: Public on Jun 01 2014

city: Paris

first: Celine

last: Morey

address: 35 rue Hélène Brion

department: University Paris 7

institute: UMR7216-Epigenetics and stem cell

summary: This analysis includes H3K27me3 and H3K4me2 profiles along the length of the X-chromosome in male (F2) and female (F3) TS cells and in male (GHP7/7) and female (GHP7/9) XEN cells.

overall_design: Analysis of H3K27me3 and H3K4me2 profiles in four different cell populations. Two independent biological replicates for each cell population are provided. The array includes approx. 162,5 Mb of the X chromosome and approx. 14,6 Mb of chromosome 17 as a control.

first: Sarra

last: Merzouk

first: Agnes

last: Dubois

first: Pablo

last: Navarro

first: Philip

middle: R

last: Avner

first: Céline


title: Functional characterization of a P. chrysogenum mutanase identified by co-cultivation with Bacillus subtilis.

status: Public on May 12 2014

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

summary: Background: Microbial gene expression is to a large extend determined by environmental growth conditions. Differential gene expression analysis between two conditions has been frequently used to reveal regulatory networks and to assign physiological function to unknown genes. In nature, microorganisms cohabit however these interactions have been rarely studied and reproduced in laboratory set-up. Thus to quantitatively explore the genome-wide responses of microbial interaction, we co-cultivated Penicillium chrysogenum and Bacillus subtilis in chemostat culture.     Results: Time course expression analysis of P. chrysogenum to co-cultivation with B. subtilis was carried out to understand the natural responses of P. chrysogenum to prokaryotes. Steady state chemostats of P. chrysogenum in non-B-lactam producing conditions was pulsed with B. subtilis and co-cultivation was followed for 72 hours. The dynamic physiological and transcriptional responses of P. chrysogenum in mixed culture were monitored. B. subtilis outcompeted growth of P. chrysogenum resulting in an increased B. subtilis biomass by more than three fold of its original size and a reduction in P. chrysogenum biomass to half of its original size after 72 h of mixed culture. Genes of the penicillin pathway, synthesis of the side-chain and precursors were overall unresponsive to the presence of B. subtilis. Moreover Penicillium polyketide synthase and nonribosomal peptide synthetase genes either remained silent or down-regulated, whereas genes responsible for protein synthesis, metabolism, energy conservation, respiration and transport were upregulated in the presence of B. subtilis. Among highly responsive genes, two putative B-1,3 endoglucanase (mutanase) genes viz Pc12g07500 and Pc12g13330 were upregulated by more than 15-fold and 8-fold respectively. Measurement of enzyme activity in the supernatant of mixed culture confirmed that the co-cultivation with B. subtilis induced mutanase production in P. chrysogenum. Mutanase activity was not observed in pure cultures of P. chrysogenum and B. subtilis or when P. chrysogenum was co-cultured with B. subtilis supernatant or heat inactivated B. subtilis cells. However, mutanase production was observed in cultures of P. chrysogenum pulsed with filter sterilized supernatants from mixed cultures P. chrysogenum and B. subtilis. Heterologous expression of Pc12g07500 and Pc12g13330 genes in Saccharomyces cerevisiae confirmed that at least Pc12g07500 encoded an B-1,3 endoglucanase.    Conclusion: Time course transcriptional profiling of P. chrysogenum revealed several differentially expressed genes during mixed culture, potentially reflecting interactions between the eukaryotic and the prokaryotic systems. -1,3 endoglucanase produced by P. chrysogenum against B. subtilis signals may have application in improving the efficacy of antibiotics by degrading exopolysacchride biofilms of pathogenic bacteria.

overall_design: The objective of the present study is to investigate the response of P. chrysogenum to co-cultivation with B. subtilis. To trigger an interaction specific behaviour, steady state chemostat of P. chrysogenum Wisconsin 54-1255 was pulsed with B. subtilis. The dynamic, transcriptional and physiological responses of P. chrysogenum in mixed culture were monitored and analyzed. Several differentially expressed genes potentially reflected interactions between the eukaryotic and the prokaryotic systems. To test whether any bacterial signaling molecules are responsible for differential expression of selected fungal genes, P. chrysogenum cultures were inoculated with supernatant of B. subtilis culture, supernatants from mixed culture and with heat-inactivated B. subtilis. The specific transcriptional responses identified using microarray was verified by analysis of fermentation broth and functional characterization by expression of selected genes in S. cerevisiae.

first: Ishwar

last: Bajaj

first: Pilar

last: de le Torre

first: Dino

last: van Dissel

first: Tania

last: Veiga

first: Jack

middle: T

last: Pronk


title: The ability of VSL#3 to restore the age-related deficit in LTP is associated with changes in brain genes expression

status: Public on Apr 02 2014

city: Perugia

first: Stefano

last: Fiorucci

address: Via E dal Pozzo

department: Dipartimento di Medicina Clinica e Sperimentale

country: Italy

institute: Universita di Perugia

summary: A deficit in synaptic plasticity is one of the many changes that occurs with age.  Specifically the archetypal model of plasticity, long-term potentiation (LTP), is reduced in hippocampus of middle-aged and aged animals.  Several factors are likely to contribute to this deficit including morphological changes like a net loss of neurons and loss of synapses with the consequent changes in receptor signalling.  However it is also clear that ageing is associated with development of oxidative stress, and also inflammatory stress which is typified by increased activation of microglia.  Recent evidence has indicated that probiotics exert anti-inflammatory in the gut.  Specifically VSL#3, a proprietary probiotic comprising 8 Gram-positive bacterial strains, decreased markers of inflammation in the colon in an animal model of colitis. We considered that its anti-inflammatory effects might extend to brain and therefore that treatment of aged rats with VSL#3 might attenuate the age-related deficit in LTP.  The evidence indicates that LTP was impaired in control-treated aged rats but sustained in aged rats which received VSL#3.  This was accompanied by a modest decrease in markers of microglial activation and an increase in BDNF and synapsin . The microarray analysis demonstrated that VSL#3 treatment   induces  changes also in the expression of  some brain genes.

overall_design: four sample groups each representing a certain treatment condition of young or adult male Han Wistar rats

first: Julie-Ann

last: O'Reilly

first: James

middle: P

last: Barrett

first: Claire

middle: L

last: McDonald

first: Sabrina

last: Ciapriani

first: Marina

last: Lynch


title: Gene expression profiles of rat enamel organs (secretory--stage and maturation stage)

first: Michael

last: Paine

address: 2250 Alcazar Street

institute: USC

summary: We conducted the genome-wide mRNA expression profiling in parallel with miRNA expression profiling using RNA samples extracted from rat incisor enamel organs, so as to refine the number of predicted gene targets for miRNA regulators.

overall_design: RNA samples were obtained from the incisor enamel organs of four rats (both secretory- and maturation-stage RNA samples). Gene expression profiling was done separately for each of the four pairs of RNA samples.

first: Kaifeng

last: Yin


title: Carbon starvation induces autophagy and recycling of nutrients in the ectomycorrhizal fungus Paxillus involutus

status: Public on Apr 01 2014

city: LUND

first: Magnus

last: Ellström

address: Sölvegatan 37

department: MEMEG

institute: Lund University

summary: Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus.

overall_design: A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 527890) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) grown on Minimum Melin Norkrans medium (MMN) amended with ammonium (C/N ratio 3) and harvested at different times of carbon starvation.)

first: Tomas

last: Johansson

first: Anders

last: Tunlid


title: Bone marrow-derived stromal cells  from double transgenic rats (of Sprague-Dawley origin) harboring the human angiotensinogen and human renin genes, and control rats

status: Public on Mar 31 2014

city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

summary: Hypertension and persistent activation of the renin-angiotensin system (RAS) are predisposing factors for development of acute kidney injury (AKI). Although bone marrow-derived stromal cells (BMSCs) have shown therapeutic promise in treatment of AKI, the impact of pathological RAS on BMSC functionality has remained unresolved. RAS and its local components in the bone marrow are involved in several key steps of cell maturation processes. This may also render BMSC population vulnerable to alterations even in the early phases of RAS pathology.  We isolated TG-BMSCs from young, end organ disease-free rats with increased RAS activation (human angiotensinogen/renin double transgenic rats; dTGR) that eventually develop hypertension and die of end-organ damage and kidney failure at 8-weeks-of-age. Control cells were isolated from wild-type Sprague-Dawley rats (SD-BMSCs). Cell phenotype, mitochondrial reactive oxygen species (ROS) production and respiration were assessed, and gene expression profiling was carried out using microarrays. Cells’ therapeutic efficacy was evaluated in a rat model of acute ischemia-reperfusion-induced AKI. Serum urea and creatinine were measured at 24h and 48h. Acute tubular damage was scored and immunohistochemistry was used for evaluation for markers of inflammation (MCP-1, ED-1), and kidney injury (KIM-1, NGAL).  TG-BMSCs showed distinct mitochondrial morphology, decreased cell respiration, and increased production of ROS. Gene expression profiling revealed a pronounced pro-inflammatory phenotype. In contrast to the therapeutic effect of SD-BMSCs, administration of TG-BMSCs in the AKI model resulted in exacerbation of kidney injury and high mortality.   Our results demonstrate that early persistent RAS activation can dramatically compromise therapeutic potential of BMSCs by shift into a pro-inflammatory phenotype with mitochondrial dysfunction.

overall_design: A comparison of transcriptome of a bone marrow-derived stromal cells from a double-transgene rats compared to those from control rats

first: Kankuri

last: Esko

first: Mervaala

last: Elina Ester

first: Storvik

last: Markus

first: Ahola

last: Anni Maija

first: Levijoki

last: Jouko

first: Müller

last: Dominik

first: Finckenberg

last: Piet

last: Eero


title: Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) patient neonate lung gene expression analysis

status: Public on Mar 01 2014

city: Houston

first: Partha

last: Sen

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: Analysis of genes dysregulated in the lungs of neonates with ACDMPV neonate lungs compared to control lungs

overall_design: Total RNA extracted by eight ACDMPV lungs compared to total RNA extracted from five control lungs

first: John

last: Belmont

first: Molly

last: Bray


title: Expression analysis in pancreatic and liver tissues of diabetic db/db mice in response to dietary supplementation with selenate

status: Public on Mar 07 2014

city: Beijing

first: Chaoqun

last: Wang

address: No.2 Yuanmingyuan west Road

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

summary:
Investigation of gene expression level changes in pancreatic and liver tissues of diabetic db/db mice supplemented with selenate, compared to the diabetic db/db mice administered placebo.
Fasting blood glucose levels increased continuously in diabetic  db/db mice administered placebo (DMCtrl) but decreased gradually in selenate-supplemented diabetic db/db mice (DMSe) and approached normal values when the experiment ended. The size of pancreatic islets increased, causing the plasma insulin concentration to double in DMSe mice compared with that in DMCtrl mice.

overall_design: Two six chip studies using total RNA respectively isolated from pancreatic and liver tissues of three selenate-supplemented diabetic db/db mice, and three diabetic db/db mice administered placebo.

first: Kui

last: Li


title: Bacillus subtilis KS002 Targocil stimulon

status: Public on Feb 01 2014

city: Ithaca

middle: D.

last: Helmann

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

summary: Transcriptional response of Bacillus subtilis KS002 to targocil

overall_design: Strain KS002 (Bacillus subtilis PY79 ΔtagGHBs::cat, amyE::Phyperspank tarGHSa spc) is a targocil sensitive B. subtilis strain, with TarGH from Staphylococcus aureus as the only WTA exporter, IPTG dependent (Schirner, Stone and Walker, ACS Chem Bio 2011). Strain KS002 was treated with or without targocil for 30 min. Each experiment was conducted three times using three independent total RNA preparations (biological triplicates). For each paried comparison, one sample was labeled with Alexa Fluor 555 and the other was with Alexa Fluor 647. For each comparison, one replicate was performed with dyeswap with the same RNA.

first: Yun

last: Luo

first: Kathrin

last: Schirner

middle: D


title: Fuzzy Logic Selection as a New Reliable Tool to Identify Gene Signatures in Breast Cancer - the INNODIAG Study

status: Public on Jan 12 2014

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

institute: INSA

summary: Based on fuzzy logic selection and classification algorithms, our selection method measures the contribution of each gene for each of two pre-defined classes in order to find the best discrimination. This algorithm extracts and ranks the most pertinent markers, since it is based on feature weighting according to optimal error rate, sensitivity and specificity. We applied the fuzzy logic selection on four breast cancer microarray databases to obtain new gene signatures based on histological grade. To validate these gene signatures, we designed probes for the selected genes on Nimblegen custom microarrays and tested them on a series of 151 consecutive invasive breast carcinomas displaying clinicopathological features similar to those observed in routine practice.

overall_design: 151 frozen breast cancer tumors from the tumor bank of the Claudius Regaud Institute (ICR Toulouse, France) were selected. This cohort consisted of consecutive invasive breast carcinoma patients treated at Claudius Regaud Institute between 2009 and 2011. All patients included in this cohort signed an informed consent. Clinico-pathological characteristics of the series were similar to those observed in routine clinical practice (i.e. majority of pre-menopausal patients presenting with T1c, node negative, ER+ invasive ductal carcinoma of intermediate grade).

first: Tatiana

last: Kempowsky-Hamon


title: VeraCode GoldenGate Methylation Assay microarray data for purified human leukocytes, reconstruction mixtures and human whole blood samples

status: Public on Feb 04 2014

city: Boston

first: William

last: Accomando

address: Kresge Bldg 911, 677 Huntington Ave

department: Epidemiology

institute: Harvard School of Public Health

summary: The objective of the study was to utilize DNA methylation to quantify human leukocyte subsets in human blood. This file contains data from an Illumina custom VeraCode GGMA microarray for human leukocyte subtypes (purified from whole blood samples via magnetic activated cell sorting (MACS) and purity confirmed by flourescence activated cell sorting (FACS)) as well as for complex mixtures of DNA from those samples, and for human whole blood samples.

overall_design: Bisulfite converted DNA from the  samples were hybridized to an Illumina Custom VeraCode GGMA microarray.

last: Wiencke

first: Karl

last: Kelsey


title: A diet enriched with biologically active substances as a protecting factor against carcinogenesis process induced by 1,2-dimethylhydrazine in rat liver

status: Public on Feb 27 2014

city: Warsaw

first: Hanna

last: Oszkiel

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: WARSAW UNIVERSITY OF LIFE SCIENCES – SGGW  (WULS-SGGW)

summary: The aim of this study was to evaluate the ability of a diet enriched with biologically active compounds to protect against 1,2-dimethylhydrazine - induced carcinogenesis in 14-month old rats liver.

overall_design: Rats from control and experimental groups after 14 months of experiment were given 5 times 1,2-dimethylhydrazine (DMH) by intraperitoneal treatment  at a dose of 30mg/kg of body weight once a week to induce the process of carcinogenesis. RNA from their livers were hybridized to Agilent two color microarrays with a common reference. Then, the transcriptomic profile of these livers were compared to the transcriptomic profile of 14-month rats received the same control diet and diet enriched with biologically active substances, but without 1,2-dimethylhydrazine - induction (data from GEO Submission - GSE51657).

first: Jacek

last: Wilczak

first: Alicja

last: Majewska

first: Michał

last: Jank


title: Molecular and physiological adaptations of Lactococcus lactis at near-zero growth rates

status: Public on Jan 01 2014

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

summary: This paper describes the molecular and physiological adaptations of Lactococcus lactis during the transition from a growing to a near-zero growth state using carbon-limited retentostat cultivation. Metabolic and transcriptomic analyses revealed that metabolic patterns shifted between homolactic and mixed-acid fermentation during the retentostat cultivation, which appeared to be controlled at the transcription level of the corresponding pyruvate-dissipation enzyme pathway encoding genes. Furthermore, during extended retentostat cultivation, cells continued to consume several amino acids, but also produced specific amino acids subsets, which may derive from the conversion of glycolytic intermediates. Under conditions of extremely low carbon availability, carbon catabolite repression was progressively relieved and alternative catabolic functions were found to be highly up-regulated, which was confirmed by enhanced initial acidification rates on various sugar substrates in cells obtained from near-zero growth cultures. Moreover, the expression of genes involved in multiple stress response mechanisms was gradually induced during extended retentostat cultivation, supporting the strong molecular focus on maintenance of cellular function and viability. The present integrated transcriptome and metabolome study provides molecular understanding of the adaptation of Lactococcus lactis KF147 to near-zero growth rate conditions, and expands our earlier analysis of the quantitative physiology of this bacterium at near-zero growth rates.

overall_design: loop design of the samples including two shortcuts

first: Onur

last: Ercan

first: Eddy

middle: J

last: Smid

last: Kleerebezem


title: Metabolic programs orchestrated by the activated Ha-ras and Îroteins in mouse liver tumors [protein]

status: Public on Feb 10 2014

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

institute: Novartis

summary: The process of hepatocarcinogenesis in the diethylnitrosamine (DEN) initiation/phenobarbital (PB) promotion mouse model involves the selective clonal outgrowth of cells harboring oncogene mutations in Ha-ras, B-raf, or Ctnnb1. Here, we have characterized mouse liver tumors harboring either Ctnnb1 or Ha-ras mutations via integrated molecular profiling at the transcriptional and translational and post-translational levels. In addition, metabolites of the intermediary metabolism were quantified by high resultion 1H magic angle nuclear magnetic resonance (HR-MAS NMR). We have identified tumor characteristic genotype-specific differences in mRNA and miRNA expression, protein levels, and post-translational modifications and in metabolite levels that facilitate the molecular and biochemical stratification of tumor phenotypes. Bioinformatic integration of these data at the pathway level led to novel insights into tumor genotype-specific aberrant cell signaling and in particular to a better understanding of alterations in pathways of the cell intermediary metabolism, which are driven by the constitutive activation of the β-Catenin and Ha-ras oncoproteins in tumors of the two genotypes.

overall_design: Male C3H/HeJ mice received a single i.p. injection of DEN (10 or 90µg/g body weight) at 2, or 6 weeks of age. After a treatment-free interval of 2 weeks, the C3H/HeJ mice were either kept on a diet containing 0.05% PB or on a PB-free control diet for 28 to 36 weeks before they were sacrificed. Ha-ras- or Ctnnb1-mutated tumors and control tissues were isolated and either flash frozen in liquid nitrogen and stored at -80°C, or prepared for immunohistochemistry.

first: Elif

middle: B

last: Unterberger

first: Michael

last: Schwarz

first: Johannes

last: Eichner

last: Römer


title: Circadian transcriptome of fast tibialis anterior (TA) and slow soleus (SOL) skeletal muscles from muscle-specific Bmal1 KO and control Cre- littermates

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary:
To investigate the role of the circadian clock gene Bmal1 in skeletal muscle, we compared the circadian transcriptomes of fast tibialis anterior (TA) and slow soleus (SOL) skeletal muscles from muscle-specific Bmal1 KO (mKO) and their control Cre- littermates (Ctrl).
Keyword: Circadian Transcriptome, time course

overall_design: 72 samples were analyzed, comprised of 4 experimental groups (Ctrl SOL, mKO SOL, Ctrl TA, mKO TA), with 3 biological replicates for each time point sampled every 4 hours for 24 hours. SOL and TA muscles were collected from the same animals, as indicated by Source Animal ID data column

first: Kenneth

middle: A

last: Dyar

first: Stefano

last: Ciciliot

first: Lauren

last: Wright

first: Rasmus

last: Biensø

first: Marcia

middle: I

last: Paz

first: Alberto

last: Casarin

first: Vanessa

last: Pertegato

first: Leonardo

last: Salviati

first: Vanina

last: Romanello

first: Francesca

last: Solagna

first: Lisa

last: Agatea

first: Guidantonio

middle: M

last: Tagliazucchi

first: Mattia

last: Forcato

first: Anders

last: Gudiksen

last: Albiero

first: Vishal

last: Patel

first: Pierre

last: Baldi

first: Kristin

last: Eckel-Mahan

first: Paolo

last: Sassone-Corsi

first: Rosario

last: Rizzuto

first: Henriette

last: Pilegaard

first: Bert

last: Blaauw

last: Schiaffino


title: CGH array of opportunistic strains

status: Public on Dec 18 2013

city: Paterna

first: Roberto

last: Pérez

address: Av Agustín Escardino 7

institute: Centro Superior de Investigaciones Científicas

summary: Genomic comparation of 3 opportunistic strains (60, 102 and D14) and one laboratory strain (W303) with the type strain S288C

overall_design: Comparison of each strain with the type strain. Biological replicates:2-3. One or two non-dye swap and one dye swap replicates were merged. One replicate per array

last: Pérez-Torrado

first: Silvia

last: Llopis


title: Neuroligin-associated microRNA-932 targets actin and regulates memory

city: Brisbane

first: Alexandre

middle: Santos

last: Cristino

state: Queensland

address: 79 QBI Building

department: The Queensland Brain Institute

country: Australia

institute: The University of Queensland

summary: Increasing evidence suggests microRNAs (miRNAs) control levels of mRNA expression during development of the nervous system and during sensory elicited remodelling of the brain. We used an associative olfactory learning paradigm (proboscis extension response) in the honeybee Apis mellifera to detect gene expression changes in the brain. Transcriptome analysis of bees trained to associate an odor with a reward and control bees exposed to air without reward, helped us abstract mRNA-miRNA interactions for empirical testing. Functional studies, feeding cholesterol-conjugated antisense RNA to bees resulted in the inhibition of miR-210 and of miR-932 that is embedded within the neuroligin 2 (Nlg2) gene involved in synapse development. Loss of miR-932 prevents long-term memory formation but not learning. We validated 3’UTR target site interactions of miR-932 and show miR-932 dysregulates actin, a key cytoskeletal molecule involved in neuronal development and activity-dependent plasticity of the brain.

overall_design: The analysis used Air group (no odor learning) as control sample for comparison to two groups of odor-conditioned bees: linalool and floral mix.

middle: S

first: Angel

last: Barchuk

first: Zila

last: Simoes

first: Judith

last: Reinhard

first: Charles

last: Claudianos


title: Affymetrix SNP array data for dog OCD samples

status: Public on Dec 20 2013

city: Cambridge

first: Hyun Ji

last: Noh

state: MA

address: 7 Cambridge Center

department: Genome Sequencing and Analysis

country: USA

institute: Broad Institute

summary: Obsessive-compulsive disorder (OCD), a severe mental disease manifested in time-consuming repetition of behaviors, affects 1-3% of the human population. While highly heritable, complex genetics has hampered attempts to elucidate OCD etiology. Dogs suffer from naturally occurring compulsive disorders that closely model human OCD, manifested as an excessive repetition of normal canine behaviors that only partially responds to drug therapy. The limited diversity within dog breeds makes identifying underlying genetic factors easier. We use genome wide association of 87 Doberman Pinscher cases and 63 controls to identify genomic loci associated with OCD and sequence these regions in 8 affected dogs from high-risk breeds and 8 breed-matched controls. We find 119 variants in evolutionarily conserved sites that are specific to dogs with OCD. These case-only variants are significantly more common in high OCD risk breeds compared to breeds with no known psychiatric problems. Four genes, all with synaptic function, have the most case-only variation: neuronal cadherin (CDH2), catenin alpha2 (CTNNA2), ataxin-1 (ATXN1), and plasma glutamate carboxypeptidase (PGCP). Two different case-only variants targeted the same approximately 500-bp highly conserved regulatory element between the cadherin genes CDH2 and DSC3. We functionally test these variants in a human neuroblastoma cell line and show that they cause significant changes in gene expression, likely due to disrupted transcription factor binding. This work demonstrates how we can use the unique genetics of dog breeds, and mechanistic similarities between human and dog diseases, to find genes and regulatory pathways underlying complex psychiatric disorders.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions.
Genome wide association analysis was performed for 87 doberman pinshcers OCD cases and 63 breed-matched controls.

first: Hyun

first: Ruqi

last: Tang

first: Elinor

middle: K

last: Karlsson

first: Kerstin

last: Lindblad-Toh


title: Affymetrix SNP array data for Pit Bull Terrier

status: Public on Dec 23 2013

summary: The data were used to define the homozygous regions in OCD-risk breeds, together with published Gentrain dataset.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions.
Homozygosity analysis was performed.


title: Cooperative function of the three different kinds of nucleoid-associated proteins encoded on the IncP-7 plasmid pCAR1 [pCAR1 plasmid chip]

status: Public on Dec 07 2013

city: Tokyo

first: Hideaki

last: Nojiri

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

department: Biotechnology Research Center

institute: The University of Tokyo

type: Expression profiling by genome tiling array

summary: Nucleoid-associated proteins (NAPs) are known to fold bacterial DNA and influence global transcription. Incompatibility P-7 plasmid pCAR1 carries three genes encoding NAPs: H-NS family protein Pmr, NdpA-like protein Pnd, and HU-like protein Phu. Because previous reports about plasmid-encoded NAPs mainly focused on H-NS homologs, functions and importance of different kinds of NAPs encoded on a plasmid remained unknown. Here, we assessed the effects of single or double disruption of pmr, pnd, and phu in a host P. putida KT2440. When pmr and pnd or pmr and phu were disrupted simultaneously, stability and conjugation frequency of pCAR1 decreased significantly. In the comprehensive phenotypes comparisons, host availabilities of some compounds, which were reduced by pCAR1carriage, were restored by NAP-gene(s)-disruption. Transcriptome analyses showed that Pmr and Pnd have different regulons, whereas Phu mainly supports their gene regulation. These cooperative functions of the three NAPs were not simply due to protein-protein interactions because hetero-oligomers of them were not detected in pull-down assays. Our present study is the first report about the cooperative function of plasmid-encoded different kinds of NAPs, which show no homology with each other.

overall_design: The NAPs-dependent change of RNA maps in early exponential phases.

first: Chiho

last: Suzuki

first: Ryusuke

last: Hirotani

first: Yurika

last: Takahashi

first: Kazuhiro

last: Matsui

first: Toshiharu

last: Takeda

first: Choong-Soo

last: Yun

first: Masaki

last: Shintani

first: Kazunori

last: Okada

first: Hisakazu

last: Yamane


title: Study of gene expression markers for predictive significance for bevacizumab benefit in patients with metastatic colon cancer: A translational research study of the Hellenic Cooperative Oncology Group (HeCOG)

city: Thessaloniki

first: elena

last: fountzilas

address: School of Medicine, Pathology Department

department: Medical Oncology

country: Greece

institute: Aristotle University of Thessaloniki, Greece

summary:
Background. Bevacizumab, an antibody neutralizing Vascular Endothelial Growth Factor (VEGF), is licensed for the management of patients with advanced colon cancer. However, tumor biomarkers identifying the molecular tumor subsets most amenable to angiogenesis modulation are lacking.

Patients and Methods. We profiled expession of 24526 genes by means of whole genome 24K DASL (c-DNA-mediated, Annealing, Selection and Ligation) arrays, (Illumina, CA) in 16 bevacizumab-treated patients with advanced colon cancer (Test set). Genes with correlation to 8-month Progression-free status were studied by means of qPCR in two independent colon cancer cohorts: 49 patients treated with bevacizumab+chemotherapy (Bevacizumab qPCR set) and 72 patients treated with chemotherapy only (Control qPCR set). Endpoints were best tumor response before metastasectomy (ORR) and progression-free survival (PFS).

Results. Five genes were significantly correlated to 8-month progression-free status in the Test set: overexpression of KLF12 and downregulation of AGR2, ALDH6A1, MCM5, TFF2. In the two independent datasets, irinotecan- or oxaliplatin-based chemotherapy was administered as first-line treatment and metastasectomies were subsequently applied in 8-14% of patients.  No prognostically significant gene classifier encompassing all five genes could be validated in the Bevacizumab or Control qPCR sets. The complex gene expression profile of all-low tumor (ALDH6A1+TFF2+MCM5) was strongly associated with ORR in the Bevacizumab qPCR set (ORR 85.7%, p=0.007), but not in the Control set (ORR 36.4%, p=0.747). The Odds Ratio for response for the all-low tumor (ALDH6A1+TFF2+MCM5) profile versus any other ALDH6A1+TFF2+MCM5 profile was 15 (p=0.018) in the Bevacizumab qPCR set but only 0.72 (p=0.63) in the Control set. The tumor expression profile of (KLF12-high+TFF2-low) was significantly associated with PFS only in the Bevacizumab qPCR set:  bevacizumab-treated patients with (KLF12-high + TFF2-low) tumors had superior PFS (median 14 months, 95% CI 2-21) compared to patients with any other (KLF12+TFF2) expression profile (median PFS 7 months, 95% CI 5-10, p=0.021). The Hazard Ratio for disease progression for (KLF12-high + TFF2-low) versus any other KLF12+TFF2 expression profile was 2.92 (p=0.03) in the Validation and 1.29 (p=0.39) in the Control set.

Conclusions. Our <three-stage> hypothesis-generating study failed to validate the prognostic significance of a five-gene classifier in mCRC patients. Exploratory analyses suggest two gene signatures  that are potentially associated with bevazicumab benefit in patients with advanced colon cancer.

overall_design: 18 tumor tissue samples were analysed, no replicates

first: George

last: Pentheroudakis

first: Vassiliki

last: Kotoula

first: Elena

last: Fountzilas

last: Kouvatseas

last: Basdanis

first: Ioannis

last: Xanthakis

first: Thomas

last: Makatsoris

first: Elpida

last: Charalambous

first: Demetris

last: Papamichael

first: Epaminontas

last: Samantas

first: Pavlos

last: Papakostas

first: Bafaloukos

last: Dimitrios

first: Evangelia

last: Razis

first: Christos

last: Christodoulou

last: Varthalitis


title: Cooperative function of the three different kinds of nucleoid-associated proteins encoded on the IncP-7 plasmid pCAR1 [KT2440 chromosome chip]

first: Hideaki

last: Nojiri

overall_design: The NAPs-dependent change of chromosomal RNA maps in early exponential phases.

first: Chiho

last: Suzuki

first: Ryusuke

last: Hirotani

first: Yurika

last: Takahashi

first: Kazuhiro

last: Matsui

first: Toshiharu

last: Takeda

first: Choong-Soo

last: Yun

last: Shintani

last: Okada

last: Yamane


title: Expression data of CD9 positive germ cells from young and aged Sprague Dawley germ cell specific GFP rats

status: Public on Dec 05 2013

city: Montreal

first: Bernard

last: Robaire

address: 3655 Sir William Osler

institute: McGill University

summary:
Male fertility and testis function changes with age and so it was sought to determine if these changes are accompanied by changes in gene expression in the spermatogonial cells at the foundation of spermatogenesis
A full genome microarray was used to determine if distinct pathways of genes were altered in expression in CD9-positive germ cells with age

overall_design: Testes from young (4 months) and aged (21 months) Sprague Dawley rats were subjected to dissociation to isolate a singel cell suspension of germ cells. These cells were used to isolate CD9 positive spermatogonial cells. RNA was isolated from these cells for hybridization on agilent miroarrays.

first: Catriona

last: Paul


title: Global transcriptome analysis reveals major roles for protein quality control, autophagy, and reactive oxygen species scavenging during the acquisition of desiccation tolerance in the resurrection plant Boea hygrometrica

first: Xin

last: Deng

address: No.20 Nanxincun, Xiangshan

country: China

institute: Institute of Botany, the Chinese Academy of Science

summary: Transcriptional profiling of resurrection plant Boea hygrometrica comparing control untreated plants with plants treated with dehydration. Goal was to determine the different effects of desiccation with different rates, and drought acclimation on global gene expression in Boea hygrometrica .

overall_design: 8 conditions comparison: untreated plants vs. plants treated with rapid dehydration for 2h (RWC~80%) and 48h (RWC<10%), untreated plants vs.plants treated with slow dehydration for 5d (RWC~80%) and 14d (RWC<10%), untreated plants vs. drought acclimated plants treated with rapid dehydration for 2h (RWC~80%) and 48h (RWC<10%). Biological replicates: 3 control replicates, 3 treated replicates.


title: Expression analysis of shoots in Olea europaea cultivar ‘Arbequina’ collected at different growth time

status: Public on Nov 09 2013

city: Vairao

first: Antonio

last: Muñoz

state: Porto

address: Rua Padre Armando Quintas, 7 (Campus Agrario)

country: Portugal

institute: CIBIO-InBIO (University of Porto)

summary: Genetic changes involved in the juvenile-to-adult transition in the shoot apex of Olea europaea L. occurs years before the first flowering.

overall_design:
For the study of the genetic-expression pattern over development, 21 seedlings originating from open pollination of olive cultivar ‘Arbequina’ were grown in a greenhouse in Centro IFAPA “Churriana” Málaga, Spain. At the sixth month the apical shoot was removed and kept for genomic analysis. Any lateral shoot was removed to force the growth along just one axis. Every three months a new (1 cm long) apical-shoot tip was taken, which included the meristem down to two very small young leaves. When the apical-shoot tip is removed the two lateral buds immediately below are activated, one of them is removed, and the other one becomes the new apical-shoot tip. Seedlings reaching 50 nodes or 1 m high were allowed to form a top canopy. From then, the samples were taken from apical shoots of higher branches.  We analyzed samples taken from the seedling/tree No 11, in a dense time-course study by microarray analysis. According to the nature of the samples, i.e. the main apical shoots, we had to use single samples during the first 6 to 15 months of growth. This limits the use of the statistics for this period but is compensated for by providing a series of consecutive data that make it possible to ascertain the time course of gene expression over plant development.
Roots samples were obtained from seedling and adult trees from the previous breeding program. Juvenile samples were taken from 9 two-month-old seedling plants from a “Picual x Arbequina” cross. Adult samples were taken from six-month old plants coming from vegetative propagation of adult “Picual” and “Arbequina” trees. Both types of plants had similar size at the time of sampling. The root and meristem samples were all taken in early spring.

last: Muñoz-Merida

first: Jaime

last: Jiménez-Ruiz

first: Francisco

last: Luque


title: Yale Triple Negative Breast Cancer Cohort

status: Public on Aug 15 2013

city: Heidelberg

first: Robert

last: Lindner

state: BW

address: INF 364

country: Germany

institute: University of Heidelberg

summary: Triple negative breast cancer (TNBC) is characterized by high proliferation, poor differentiation and a poor prognosis due to high rates of recurrence. Despite lower overall incidence African American (AA) patients suffer from higher breast cancer mortality in part due to the higher proportion of TNBC cases among AA patients compared to European Americans (EA). It was recently shown that the clinical heterogeneity of TNBC is reflected by distinct transcriptional programs with distinct drug response profiles in preclinical models. In this study, we used gene expression profiling and immunohistochemistry to eluicidate potential differences between TNBC tumors of EA and AA patients on a molecular level.

overall_design: WG-DASL experiment of 90 FFPE samples of ER, PR and HER2 (triple) negative breast cancer samples diagnosed between 1987 and 2007. Invasive disease was identified on H&E sections by the study pathologist and one to three 1.5 mm cores were punched from the top down in the designated tumor areas of each FFPE block. The cores were deparaffinized with xylene at 50°C for 3 minutes. RNA was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Applied Biosystems) following the manufacturer's protocol. The isolated RNA was hybridized to Whole-Genome DASL (HumanRef8 V 3.0, Illumina) at the Yale Center for Genome Analysis. 90 primary tumor RNA samples from 90 patients were adequate for analysis and passed Quality control.

first: Catherine

last: Sullivan

first: Onyinye

last: Offor

first: Kimberly

last: Lezon-Geyda

first: Neal

last: Fischbach

first: Mansi

last: Shah

first: Veerle

last: Bossuyt

first: Vincent

last: Schulz

first: David

last: Tuck

first: Lyndsay

middle: N

last: Harris


title: Identification of ATF2 target genes

status: Public on Nov 10 2013

city: Manchester

first: steve

last: lyons

address: Wilmslow Rd

department: Cell Regulation

country: United Kingdom

institute: CRUK Manchester

summary:
In order to identify transcriptional targets of ATF2, we used a recombinant adenovirus to express constitutively active ATF2 in murine hepatoblasts. Expression of GFP was the control condition.
Total RNA was harvested from cells 8 hours post infection. Reverse transcription was performed using Ovation Pico WTA kit (NuGen, 3300-12). Labelling, Encore Biotin Module (NuGen, 4200-12)

overall_design: three replicates GFP control and C2ATF2

first: Steve

last: Lyons


title: Gene expression profiles of tumor-positive sentinel lymph node biopsies from cutaneous melanoma patients

status: Public on Aug 01 2013

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

summary: Sentinel lymph node, the first node draining the primary tumor, is a key component of tumor microenvironment promoting immune tolerance. In melanoma, sentinel node is one of the most important prognostic factors and the most frequent site of regional metastasis. To unravel the immunomodulatory pathways that are triggered by melanoma cells in the draining node that allow tumor spreading, transcriptional profiles associated to disease progression were analyzed in archival sentinel node biopsies (SNB).    Gene expression profiles of melanoma-positive and negative SNB selected to maximize the differences in terms of disease stage and course, revealed subgroups correlating with regional node involvement and disease progression within positive biopsies. Transcriptional profiles revealed that genes showing differential expression between tumor-positive SNB with/without disease progression were mainly related to inflammatory response and that were mostly down regulated in patients with poor prognosis.    TNFRSF8 encoding CD30 showing up regulation in SNB from patients with progressing disease displayed higher expression by immunohistochemical staining compared to SNB from non progressing patients. Subpopulations of CD30 positive CD4/CD8 double negative and CD4 Foxp3/PD-1 CD147 positive T cells were identified by flow cytometry analysis in metastatic nodes, suggesting a potential role of regulatory and tolerogenic T cells in melanoma progression.

overall_design: Cutaneous melanoma patients undergoing SNB biopsy in 2001-2004 with available 5–year follow-up clinical data were selected. Data relative to 752 cases was extracted, 80% (n= 603) with a negative SNB and 20% (n=149) with SNB positivity for melanoma metastases. The latter underwent regional lymphadenectomy by CLND and 30% (n=44) resulted positive for melanoma metastases at non-sentinel regional lymph nodes while 70% (n=105) resulted negative. Analysis of follow-up data showed that disease recurrence at 5 yrs occurred in 9% SNB negative patients, 14% of the patients with positive SNB resulting negative at CLND, and in 57% of the patients with positive SNB resulting positive at CLND, consistent to the range of previously reported rates (Santinami M 2009, Balch CM 2009).  In order to exploit gene expression profiles to unravel molecular modifications occurring in SNB from patients with progressing disease we selected two groups of cases representing the extremes of the survey, i.e. patients positive at CLND (stage IIIB-C) recurring within 5 years follow-up (SNB-PP), and patients negative at CLND (stage IIIA-B) and non-relapsing at 5 years (SNB-PN). In addition, a group of negative SNB patients without disease recurrence at 5 years was selected and analysed for comparison as tumor negative SNB (SNB-N).

first: L

first: M

last: Rodolfo


title: The influence of long-term use of diet enriched with biologically active substances on transcirptomic profile in rats liver

status: Public on Oct 25 2013

first: Hanna

last: Oszkiel

summary: The aim of the study was to identify genes which are differentially expressed in the liver from rat fed with control diet and rat fed with diet enriched with biologicaly active compounds after 3 and 14 months of experiment

overall_design: RNA from rats fed with control diet and rats fed with diet enriched with biologicaly active compunds were hybridized to Agilent two color microarrays with a common reference

first: Jacek

last: Wilczak

first: Alicja

last: Majewska

first: Michał

last: Jank