title: DNA methylation in newborn cordblood

status: Public on Jan 14 2015

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

summary: There is extensive variation in DNA methylation between individuals and ethnic groups. These differences can arise from a combination of genetic and non-genetic influences and potential modifiers include nutritional cues, early life experience, and social and physical environments. Here we have assayed genome-wide DNA methylation in neonatal cord blood from African American, European American, and other ancestral groups. This is part of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood). Our overarching goal is to determine the different environmental and maternal factors that can modify DNA methylation in newborns.

overall_design: This is a cross-sectional study of a total of 216 racially diverse participants of CANDLE. Cordblood was collected at birth. DNA methylation was measured using the Illumina HumanMethylation27 BeadChip. Based on maternal self-report, the samples are 112 African Americans, 91 European Americans and 13 other racial or mixed race group.

first: Frances

last: Tylavsky

first: Ronald

last: Adkins

first: Julia

last: Krushkal


title: Expression profiling of B.subtils ftsZ depletion cells with ftsZ induced or uninduced for 1 or 2hrs.

status: Public on Jan 01 2015

city: Houston

first: Jue

middle: D.

last: Wang

state: TX

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

summary: The past twenty years have seen tremendous advances in our understanding of the mechanisms underlying bacterial cytokinesis, particularly the composition of the division machinery and the factors controlling its assembly. At the same time, however, we understand very little about the relationship between cell division and other cell cycle events in bacteria. Here we report that inhibiting division in Bacillus subtilis and Staphylococcus aureus quickly leads to an arrest in the initiation of new rounds of DNA replication followed by a complete arrest in cell growth. Arrested cells are metabolically active but unable to initiate new rounds of either DNA replication or division when shifted to permissive conditions. Inhibiting DNA replication results in entry into a similar quiescent state, in which cells are unable to resume growth or division when returned to permissive conditions. Our findings suggest the presence of two cell cycle control points: one linking division to the initiation of DNA replication and another linking the initiation of DNA replication to division. Significantly, this evidence contradicts the prevailing view of the bacterial cell cycle as a series of coordinated but uncoupled events. Importantly, the terminal nature of the cell cycle arrest validates the bacterial cell cycle machinery as an effective target for antimicrobial development.

overall_design: Four-condition experiment: ftsZ induced for 1hr, ftsZ depleted for 1hr, ftsZ induced for 2hrs, ftsZ depleted for 2hrs. Biological replicates: 3-4 for each sample. Reference: a mixture of wt RNA from different growth phases and wt backgrounds.

first: Allison

last: Kriel

first: Heidi

last: Arjes


title: Comparison of miRNA profiles of Chronic Myelogenous Leukemia with normal PBSC CD34+ cells

status: Public on Dec 31 2014

city: Beijing

first: Lisheng

address: 27 Taiping Road

department: Experimental Hematology

country: China

institute: Beijing Institute of Radation Medicine

summary: We isolated the CD34+ cells from bone marrow samples of CML patients and mobilized peripheral blood of healthy donors. The miRNA expression profiles were assayed by using the Agilent microarrays and compared.

overall_design: The mononuclear cells of both CML Bone marrow and mobilized peripheral blood from healthy donors will be isolated. Furthermore, the CD34+ cells populations (>95% CD34+ cells) will be purified by microBeads kit from Miltenyi Biotec. We will extract the total RNAs including miRNAs  by using the miRNeasy Mini Kit. These samples will be labeled and assayed for miRNA profiles using the G4470B human miRNA microarray 8x15K version 2. The differences of microRNA profiles will be compared.

first: Ravi

last: Bhatia

first: Sierra

middle: M

last: Li

first: Keh-Dong

last: Shiang


title: Extensive remodeling of DC function by rapid maturation-induced epigenetic gene silencing [ChIP-chip]

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

type: Genome binding/occupancy profiling by genome tiling array

summary: Dendritic-cell (DC) maturation involves substantial remodeling of their gene-expression program. Most research has focused on inducible gene-expression networks promoting the acquisition of new functions, such as cytokine production and enhanced T-cell-stimulatory capacity. In contrast, mechanisms that modulate DC-function by inducing gene silencing remain poorly understood. Here we describe a novel primary epigenetic-silencing response that makes major contributions to the DC-maturation process. The repressed genes function in pivotal processes - including antigen-presentation, extracellular-signal detection, signal-transduction and lipid-mediator biosynthesis - underscoring the central contribution of the silencing mechanism to rapid reshaping of DC-function. Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this transcription factor in marking genes poised for inducible repression

overall_design: Analysis of H4Ac changes triggered by 1 hour LPS treatement of Mo-DC. 3 biological replicates

first: Queralt

last: Seguín-Estévez

first: Isabelle

last: Dunand-Sauthier

first: Sylvain

last: Lemeille

first: Christian

last: Iseli

first: Vassilios

last: Ioannidis

first: Emmanuèle

last: Barras

first: Antoine

last: Geinoz

first: Christoph

middle: D

last: Schmid

first: Philippe

last: Rousseau

first: Ioannis

last: Xenarios

first: Hans

last: Acha-Orbea

first: Walter

last: Reith


title: Probing the Existence of an Alternative Gibberellin Receptor(s) in Rice Aleurone Cells

status: Public on Dec 19 2014

city: Nagoya

first: Kenji

last: Yano

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and BIothechnology Center

country: Japan

institute: Nagoya University

summary: Many years after the discovery of GID1 as the GA receptor, the belief in the existence of GA-binding protein (GBP)  in aleurone cells still persists. Actually, some recent reviews and textbooks still contain information about the possibility of an alternative GA perception mechanism mediated by GBPs. Thus, to finally clarify this issue, we examined the expression of GA-regulated genes using rice embryoless half-seeds of four kinds of GA signaling mutants, each one independently carrying mutated GID1, DELLA, and GA-related F-box, which are all encoded by single genes in rice, allowing for convenient study of the GA perception system. The comprehensive microarray analysis using these rice mutants revealed that all genes tested to be responsive to GA in the wild-type (WT) aleurone cells consistently did not respond to GA in the gid1 or slr1 mutant.

overall_design: All microarray experiments were performed according to the manufacturer’s manual. The Feature Extraction software (Agilent Technologies) was used to delineate and measure the Cy3 and Cy5 signal intensities of each spot in the array. The resulting data were normalized using the Variance-stabilizing normalization (VSN) algorithm.

first: Makoto

last: Matsuoka


title: Host-specific transcriptomic pattern of Trichoderma virens during interaction with maize or tomato roots

city: Haifa

first: Benjamin

middle: A

last: Horwitz

state: Israel

address: Dept Biology Technion

department: Biology

country: Israel

institute: Technion

summary:
To test the hypothesis that gene expression by the fungal partner in this beneficial interaction is modulated by the plant host, Trichoderma virens was co-cultured with maize or tomato in a hydroponic system allowing interaction with the roots. The transcriptomes for T. virens alone were compared with fungus-inoculated tomato or maize roots by hybridization on oligonucleotide microarrays
Based on the relevant role of Trichoderma virens as a biological control agent this study provides a better knowledge of its crosstalk with plants in a host-specific manner.

overall_design: Trichoderma virens was co-cultured for three days with maize or tomato in a hydroponic system allowing interaction with the roots. 3 experiments were performed for each treatment, and compared to 5 experiments with T. virens grown under the same conditions without plants.

first: Maria

middle: E

last: Moran-Diez

first: Naomi

last: Trushina

first: Charles

last: Kenerley


title: Long Non-coding RNA expression profiles in Hereditary Haemorrhagic Telangiectasia

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

summary: Hereditary Haemorrhagic Telangiectasia (HHT) is an autosomal dominantly inherited vascular disease characterized by the presence of mucocutaneous telangiectasia and arteriovenous malformations in visceral organs. HHT is predominantly caused by mutations in ENG and ACVRL1, Which both belong to the TGF-β signalling pathway. Further knowledge on how a disturbance of the TGF-β signalling pathway leads to HHT manifestations is needed in order to identify potential therapeutic targets. As long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression and constitute a sizable fraction of the human transcriptome, we wanted to assess whether lncRNAs play a role in the molecular pathogenesis of HHT. Here we used microarray analysis to profile lncRNAs to compare the expression of HHT telangiectasial and HHT non-telangiectasial nasal tissue from the same patient in a paired design. The microarray probes were re-annotated using the GENCODE v.16 dataset, identifying 4,810 probes mapping to 2,811 lncRNAs. By comparing HHT telangiectasial tissue versus HHT non-telangiectasial tissue, we identified 42 lncRNAs that are differentially expressed (q<0.001). Using GREAT, a tool that assumes cis-regulation, we showed that differently expressed lncRNAs are enriched for genomic loci involved in key pathways concerning HHT. Our study identified lncRNAs that are aberrantly expressed in HHT telangiectasia and indicates that lncRNAs may contribute to regulate protein-coding loci in HHT. Which suggest that the lncRNA component of the transcriptome deserves more attention in HHT. A deeper understanding of lncRNAs and their role in telangiectasia formation possesses potential for discovering therapeutic targets in HHT.

overall_design: Gene expression profiling of 80 paired nasal samples from patients with hereditary Haemorrhagic Telangiectasia (HHT), representing telangiectasial and non-telangiectasial (normal) tissue respectively. The patients were divided into HHT1 or HHT2 in regard to the germline mutation in ENG (HHT1) or ACVRL1 (HHT2). Additional controls were healthy siblings (not carrying the germline mutation) and external controls. The study was conducted using Agilent-028004 SurePrint G3 Human GE 8x60K Microarray platform.

first: Pernille

last: Torring

first: Klaus

last: Brusgaard

first: Anette

last: Kjeldsen

first: Lilian

middle: B

last: Ousager

first: Qihua

last: Tan

middle: J


title: Genome-wide transcript analysis of ErbB2-induced tumors from different tumor-initiating cells

status: Public on Dec 24 2014

city: Iowa City

first: Weizhou

last: Zhang

state: IA

address: 100 Medical Laboratories

department: Pathology

institute: The University of Iowa

summary:
ErbB2-induced mouse mammary tumors can originate from different mammary epithelial cells, including both basal epithelial cells and luminal progenitors. Here we used the tumors from basal cells or luminal progenitors
to compare the difference in transcripts.

overall_design: RNA was isolated from  basal cell- or luminal progenitor-derived tumors for Illumina whole mouse transcript array analysis. Three paired tumors were analyzed.

first: Nicholas

last: Borcherding


title: Activation of plant defence in Brassica napus L. cv. Westar and transgenic MINELESS plants after attack by Mamestra brassicae (cabbage moth)

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

summary: Plants within the Brassicaceae family have a unique defence mechanism known as the “glucosinolate-myrosinase” system. Upon tissue disruption by insect herbivores, glucosinolates are hydrolysed by the enzyme myrosinase (EC 3.2.1.147) into a variety of degradation products, which can deter insect herbivory. This process has been termed as “The Mustard Oil Bomb”. Seeds of Brassica napus have been genetically modified to remove myrosinase containing myrosin cells. The modified plants have been named MINELESS due to a lack of toxic mines in seeds. This study aimed to get insights into defence responses of B. napus wild-type and MINELESS seedlings, after being challenged by larvae of the generalist herbivore Mamestra brassicae. The microarray analysis showed 494 and 159 genes to be differentially regulated after M. brassicae feeding on wild-type and MINELESS seedlings, respectively. Many of the observed transcriptional responses i B. napus and the MINELESS mutant are related to those found in Arabidopsis thaliana plants when they are exposed to insects.

overall_design: Mamestra brassicae larvae were maintained and propagated on wild-type (Brassica napus) and MINELESS (Brassica napus) seedling for 10 days. The 10-days old M. brassicae larvae were transferred to 6-7 days old seedlings of wild-type and MINELESS, respectively. In order to retain the larvae, pots (4 seedlings in each pot) were enclosed in cages. Controls were treated in the same way, without insects. Pots with control (non-infested) and M. brassicae infested seedlings were kept under the same conditions in greenhouse. Control and M. brassicae challenged seedlings were harvested after 24h of induction. Cages and larvae were removed and seedlings were harvested and flash frozen in liquid nitrogen. Each biological replica of untreated plants (controls) comprised 4 pots (4 seedlings in each pot), while for M. brassicae challenged seedlings, each biological replica comprised 6 pots (4 seedlings in each pot). Differences in transcriptional responses were measured by comparing genes expression of M. brassicae challenged seedlings against non-infested control seedlings.

first: Ishita

last: Ahuja

first: Marianne

last: Trælnes

first: Nicole

last: van Dam

first: Pankaj

last: Barah

first: Torfinn

last: Sparstad

first: Atle

last: Bones


title: Early SIV infection and effects of pathogenic and commensal enteric bacteria on expression in ileum tissue

city: Davis

first: Satya

last: Dandekar

state: CA

address: One Shields Ave

institute: UC Davis

summary:
We used the ileal loop model to assess the effects of enteric bacteria organisms on host gene expression in intestinal tissue independent of and following early SIV infection. SIV infection in the gut causes rapid and severe immune dysfunction and damage to the intestinal structure, this may alter the intimate interaction with lumenal organisms. This study was performed to determine whether early SIV infection, prior to the depletion of CD4+ T cells, can alter interaction of the host with pathogenic Salmonella serovar Typhimurium (ST) or commensal Lactobacillus plantarum (LP), and to further understand the earliest changes to the intestinal mucosa following SIV infection.
We used microarray analysis to detail the global program of gene expression underlying changes in the ileum following early SIV infection, and if these changes in any way alter the host interaction/ response to pathogenic and commensal enteric bacteria.

overall_design:
A subset of animals were infected with SIVmac251 for 2.5 days, following which they underwent a loop surgery where the ileum was sectioned off with surgical ties and bacteria (ST or LP) or their respective media controls (LB or MRS) were injected intralumenally. Following 5 hours of incubation the loops were excised and frozen. Tissue sections were cut and RNA extracted for gene expression analysis.
Rhesus Macaques infected with SIVmac251 for 2.5 days compared to uninfected controls. Comparisons are of ileum loop sections injected with Salmonella serovar Typhimurium, Lactobacillus Plantarum or respective media controls LB or MRS.

first: Irina

last: Grishina


title: Transcription analysis of E. coli O103:H25 in co-culture with Bacteroides thetaiotaomicron CCUG 10774

status: Public on Dec 18 2014

city: Oslo

first: Hildegunn

last: Iversen

address: P.O.Box 8146 Dep

department: Department of Food Safety and Infection Biology

institute: Norwegian School of Veterinary Science

summary: Investigation of whole genome gene expression level changes in E. coli O103:H25 in co-culture with Bacteroides thetaiotaomicron CCUG 10774 compared to when E. coli is cultured individually.

overall_design: A study using total RNA recovered from three separate co-cultures (E. coli O103:H25 and B. thetaiotaomicron 1:100) at OD=0.5, compared to when E. coli is cultured individually (5 separate samples including 1-3 technical replicates of each sample). Three separate samples are also recovered when E. coli is cultured in supernatant from Bacteroides thetaiotaomicron at OD=0.5 compared to when E coli is cultured alone. A comparison is also done after treatment with Mitomycin C (MMC). MMC is added at OD=0.5. There are 3 separate samples from each group that are compared (co-culture versus E. coli grown individually, E. coli in supernatant from B. thetaiotaomicron versus E. coli grown individually).

first: Iversen

last: Hildegunn


title: Reactive leaf volatiles act as powerful inducers of abiotic stress-related gene expression [NimbleGen]

status: Public on Dec 20 2014

city: Kobe

first: Yasuo

last: Yamauchi

state: Hyogo

address: Rokkodai 1-1, Nada

institute: Kobe University

summary: Abiotic stresses cause serious damage to plants; therefore, plants undergo a complicated stress response through signal transduction originating from environmental stimuli. Here we show that a subset of short-chain leaf volatiles with an α,β-unsaturated carbonyl bond in their structure (reactive short-chain leaf volatiles, RSLVs) like (E)-2-hexenal and (E)-2-butenal can act as signal chemicals that strongly induce the gene expression of abiotic-related transcription factors, such as heat stress-related transcription factors (HSFA2, MBF1c) and other abiotic stress-related transcription factors (DREB2A, ZATs). RSLV-induced expression of HSFA2 and MBF1c was eliminated in HSFA1s-, known as heat stress response master regulators, knockout mutant, whereas those of DREB2A and ZATs were not, suggesting that the RSLV signaling pathway is composed of HSFA1-dependent and -independent pathways. RSLV treatment induced production of chaperon proteins, and the RSLV-treated Arabidopsis thus demonstrated enhanced abiotic stress tolerance. Because oxidative stress treatment enhanced RSLV production, we concluded that commonly found RSLVs produced by environmental stresses are powerful inducer of abiotic stress-related gene expression as oxidative stress signals.

overall_design: A four chips study of Columbia-0 following 10 µM 2E-hexenal treatment for 30 min. Datasets including acetonitrile (control) and 2E-hexenal treated samples (triplicates).

first: Mikiko

last: Kunishima

first: Masaharu

last: Mizutani

first: Yukihiro

last: Sugimoto


title: 7q11.23 dosage-dependent dysregulation in the human pluripotent state primes aberrant transcriptional programs in disease-relevant lineages (microarray)

status: Public on Dec 15 2014

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology & University of Milano, Italy

summary: We apply the cellular reprogramming experimental paradigm to two disorders caused by symmetrical copy number variations (CNV) of 7q11.23 and displaying a striking combination of shared as well as symmetrically opposite phenotypes: Williams Beuren syndrome (WBS) and 7q microduplication syndrome (7dup). Through a uniquely large and informative cohort of transgene-free patient-derived induced pluripotent stem cells (iPSC), along with their differentiated derivatives, we find that 7q11.23 CNV disrupt transcriptional circuits in disease-relevant pathways already at the pluripotent state. These alterations are then selectively amplified upon differentiation into disease-relevant lineages, thereby establishing the value of large iPSC cohorts in the elucidation of disease-relevant developmental pathways. In addition, we functionally define the quota of transcriptional dysregulation specifically caused by dosage imbalances in GTF2I (also known as TFII-I), a transcription factor in 7q11.23 thought to play a critical role in the two conditions, which we found associated to key repressive chromatin modifiers. Finally, we created an open-access web-based platform (accessible at http://bio.ieo.eu/wbs/ ) to make accessible our multi-layered datasets and integrate contributions by the entire community working on the molecular dissection of the 7q11.23 syndromes.

overall_design: We differentiated a representative subset of patient-derived iPSC lines into three disease-relevant lineages: dorsal telencephalic progenitors (Neural Progenitor Cells, NPC), Neural Crest Stem Cells (NCSC) and Mesenchymal Stem Cells (MSC). We profiled NCSC and NPC through microarray (current dataset), and MSC through RNA-seq.

first: Antonio

last: Adamo

first: Sina

last: Atashpaz

first: Pierre-Luc

last: Germain

first: Matteo

last: Zanella

last: D'Agostino

first: Veronica

last: Albertin

first: Josh

last: Chenoweth

first: Lucia

last: Micale

first: Carmela

last: Fusco

first: Christian

last: Unger

first: Bartolomeo

last: Augello

first: Orazio

last: Palumbo

first: Brad

last: Hamilton

first: Massimo

last: Carella

first: Emilio

last: Donti

first: Giancarlo

last: Pruneri

first: Angelo

last: Selicorni

first: Elisa

last: Biamino

first: Paolo

last: Prontera

first: Ronald

last: McKay

last: Merla


title: Genetic and Phenotypic Intra-Species Variation in Candida albicans: Differential expression analysis

status: Public on Dec 11 2014

city: Cambridge

first: Christina

last: Cuomo

state: MA

address: 7 Cambridge Center

institute: Broad Institute

type: Expression profiling by high throughput sequencing

summary: Differential expression of isolates of Candida albicans grown in YPD using RNA-Seq.

overall_design:
We examined transcript level changes in YPD for five strains; P94015 (two replicates) and P60002 were compared to three other strains as controls (SC5314, P87, GC75).

Sample name|title|strain|SRA accession
Candida albicans strain P94015 replicate 1|Candida albicans strain P94015 in YPD|P94015|SRX186183
Candida albicans strain P94015 replicate 2|Candida albicans strain P94015 in YPD|P94015|SRX337483
Candida albicans strain P94015 replicate 2|Candida albicans strain P94015 in YPD|P94015|SRX337482
Candida albicans strain P94015 replicate 2|Candida albicans strain P94015 in YPD|P94015|SRX337481
Candida albicans strain SC5314 |Candida albicans strain SC5314 in YPD|SC5314|SRX131011
Candida albicans strain SC5314 |Candida albicans strain SC5314 in YPD|SC5314|SRX129863
Candida albicans strain P87|Candida albicans strain P87 in YPD|P87|SRX129856
Candida albicans strain P87|Candida albicans strain P87 in YPD|P87|SRX131022
Candida albicans strain GC75|Candida albicans strain GC75 in YPD|GC75|SRX131009
Candida albicans strain GC75|Candida albicans strain GC75 in YPD|GC75|SRX129858
Candida albicans strain P60002|Candida albicans strain P60002 in YPD|P60002|SRX186182

SRX186183, SRX186182 processed with Base caller: GAPipeline RTA1.13.48 Sequencer Application 1.5.15.1
SRX337483, SRX337482, SRX337481 processed with Base caller: GAPipeline RTA1.17.20 Sequencer Application 2.0.5
SRX131011, SRX129863, SRX129856,SRX131022, SRX131009, SRX129858 processed with Base caller: GAPipeline RTA1.12.4.2 Sequencer Application 1.4.8
Aligner: Trinity (version r2012-05-18) alignReads.pl (parameters --aligner bowtie (version 1) and --SS_lib_type RF)
Estimate counts: Trinity run_RSEM.pl (RSEM version1.1.18) on properly mapped paired reads (parameters --paired --no_group_by_component --SS_lib_type RF)
Normalized counts: Trinity summarize_RSEM_fpkm.pl on RSEM output
Differential expression: edgeR (version 3.4.2) with TMM normalization, strains SC5314, GC75 and P87 were used as the wild type comparison  in differential expression analysis.
genome build A21-s02-m01-r01
Log2FC and FDR (as qvalue) from Edge R along with FPKM counts of strains grown in YPD

first: Diego

last: Martinez

first: Matthew

middle: P

last: Hirakawa

first: Sharadha

last: Sakthikumar

first: Richard

last: Bennett


title: An in vivo screen identifies compounds that disrupt heterochromatin integrity

status: Public on Dec 17 2014

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

type: Expression profiling by genome tiling array

summary: Heterochromatin plays a key role in gene repression, maintaining genome integrity and chromosome segregation. Fission yeast, Schizosaccharomyces pombe, utilizes conserved components to direct heterochromatin formation using siRNA generated by RNA interference (RNAi) to guide a histone H3 lysine 9 methyltransferase to cognate chromatin. To identify compounds that inhibit heterochromatin formation, an in vivo phenotypic screen for loss of silencing was performed.  A tester strain harbouring a silent dominant selectable kanMX reporter gene within fission yeast centromeric heterochromatin was used to screen a diverse library of chemicals. HMS-I1 and HMS-I2 were identified as compounds that reproducibly increased G418 resistance due to loss of kanMX silencing, and decreased the level of repressive H3K9 methylation on centromeric repeats. The pattern of changes induced by HMS-I1 and HMS-I2 were consistent with inhibition of the histone deacetylases (HDACs) Clr3 and/or Sir2. Chemical-genetic interactions and expression profiling indicated that both HMS-I1 and HMS-I2 affect the activity of the Clr3-containing Snf2/HDAC repressor complex (SHREC). Exposure to HMS-I1 was also found to alleviate silencing of reporter genes in an Arabidopsis transgenic plant line and a mouse cell line. HMS-I2 also disrupted reporter gene silencing in Arabidopsis. In vitro assays indicate that HMS-I1 impairs the activity of human HDAC6 and HDAC10.  As HMS-I1 and HMS-I2 bear no resemblance to known inhibitors of chromatin-based activities they represent potentially novel and valuable reagents for experimental and therapeutic purposes. Our findings highlight the use of in vivo chemical screening conducted in fission yeast to identify compounds that disrupt heterochromatin across plant, fungi and animal kingdoms.

overall_design: 16 RNA samples: 2 replicates of WT untreated (vehicle DMSO) (KE1-A, KE2-A), HMS-I1 treated (KE1-B, KE2-B), HMS-I2 treated (KE1-C, KE2-C), and 2 additional replicates of WT (KE05_wt_1, KE10_wt_2), 4 replicates of clr2∆ (KE01_2118_1, KE06_2118_2, KE03_0080_1, KE08_0080_2) and mit1∆ (KE02_1295_1, KE07_1295_2, KE04_1278_1, KE09_1278_2).

first: Emilie

last: Castonguay

first: Alexander

last: Kagansky

first: Daniel

last: St. Cyr

first: Araceli

middle: G

last: Castillo

first: Rachel

last: White

first: Sharon

first: Carolina

last: Bonilla

first: William

middle: C

last: Earnshaw

first: Mike

last: Tyers

first: Robin

last: Allshire


title: THE CAPACITY OF ASPERGILLUS NIGER TO SENSE AND RESPOND TO CELL WALL STRESS REQUIRES AT LEAST THREE TRANSCRIPTION FACTORS: RLMA, MSNA AND CRZA

city: Leiden

first: Benjamin

middle: M.

last: Nitsche

state: The Netherlands

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: Transcriptomics signatures of Aspergillus niger were used to predict regulator proteins mediating the survival responses against these stressors and the phenotypes of selected null mutant strains were studied. This integrated approach allowed us to reconstruct a model for the cell wall salvage gene network of A. niger that ensures survival of the fungus upon cell surface stress. The model predicts that (i) caspofungin and aureobasidin A induce the cell wall integrity pathway as main compensatory response including RhoB, RhoD, MkkA and RlmA as regulator proteins. (ii) RlmA is the main transcription factor required for the protection against calcofluor white but cooperates with MsnA and CrzA to ensure survival of A. niger when challenged with caspofungin or aureobasidin A. All three transcription factors are important for these compensatory responses and involve induction of glucan and chitin synthesising genes amongst others. (iii) Membrane stress provoked by aureobasidin A via disturbance of sphingolipid synthesis induces cell wall stress in A. niger, but membrane stress provoked by fenpropimorph via disturbance of ergosterol synthesis does not. The present work uncovered different defence strategies of A. niger to protect itself against cell wall stress conditions. At least three transcription factors - RlmA, MsnA and CrzA – are employed in a well-balanced manner. The data also predicts a fourth transfactor, SrbA, which seems to be specifically important during fenpropimorph-induced cell membrane stress. Future studies will disclose how these regulators are interlocked in different signalling pathways to secure survival of A. niger under different cell wall stress conditions.

overall_design: This data set consists of 16 samples from 8 conditions (biological duplicates for each condition). The conditions cover treatment (4 conditions) and controls (3 conditions) of the Aspergillus niger wild type to 4 cell wall stresss inducing agents. Additionally, the data set comprises data (1 condition) for an Aspergillus niger mutant strain in which the RlmA transcription factor has been deleted. RlmA is responsible for the induction of cell wall stress response genes within the cell wall integrity pathway.

first: Markus

middle: R

last: Fiedler

first: Annett

last: Lorenz

first: Cees

last: van den Hondel

first: Arthur

middle: F

last: Ram

first: Vera

last: Meyer


title: microbial functional genes are fundamentally different from bacterial phylogenetic distributions in arctic soils

status: Public on Dec 10 2014

city: Nanjing

first: zhang

middle: kao

last: ping

address: 71 East Beijing Road

institute: Chinese Academy of Sciences

summary: Understanding biological diversity and distribution patterns at multiple spatial scales is a central issue in ecology. Here, we investigated the biogeographical patterns of functional genes in soil microbes from 24 arctic heath sites using GeoChip-based metagenomics and principal coordinates of neighbour matrices (PCNM)-based analysis. Functional gene richness varied considerably among sites, while the proportions of each major functional gene category were evenly distributed. Functional gene composition varied significantly at most medium and broad spatial scales, and the PCNM analyses indicated that 14-20% of the variation in total and major functional gene categories could be attributed primarily to relatively broad-scale spatial effects that were consistent with broad-scale variation in soil pH and total nitrogen. The combination of variance partitioning and multi-scales analysis indicated that spatial distance effects contributed 12% to variation in functional gene composition，whereas environmental factors contributed only 3%. This relatively strong influence of spatial as compared to environmental variation in determining functional gene distributions contrasts sharply with typical microbial phylotype/species-based biogeographical patterns in the Arctic and elsewhere. Our results suggest that the distributions of soil functional genes cannot be predicted from phylogenetic distributions because spatial factors associated with historical contingencies are relatively important determinants of their biogeography.

overall_design: 72 heath tundra surface soil samples across the Canadian, Alaskan and European Arctic including three vegetation type (Empetrum spp., Cassiope spp., Dryas spp.)

first: Yu

last: Shi

first: Paul

last: Grogan

first: Huaibo

last: Sun

first: Jinbo

last: Xiong

first: Yunfeng

last: Yang

first: Jizhong

last: Zhou

first: Haiyan

last: Chu


title: canine hemangiosarcoma cell lines and tissues

status: Public on Dec 08 2014

city: Minneapolis

first: Jong-Hyuk

last: Kim

state: MN

address: 425 East River Rd.

department: Dept of Veterinary Clinical Science

institute: University of Minnesota

summary: Cell lines and tumor tissues from canine hemangiosarcoma derived cell lines and hemangiosarcoma tissue samples

overall_design: Comparions of gene expression between IL-8 high and low groups defined by IL-8 median value

first: Jong

middle: H

first: Milcah

last: Scott


title: Kinetic transcriptome study reveals an essentially intact cellulase induction system in a cellulase hyper-producer Trichoderma reesei strain

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

country: France

institute: IFPEN

summary: The filamentous fungus Trichoderma reesei is the main industrial cellulytic enzymes producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome sequencing, transcriptome) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG14 and RUT C30. In this follow-up work, we examined how these mutations affect phenotype at the level of the transcriptome and cultivation behavior.  We performed kinetic transcriptome analysis of the NG14 and RUT C30 strains of early cellulase production induced by lactose using bioreactor cultivations close to industrial conditions. RUT C30 exhibited both earlier onset of cellulase production and higher steady-state productivity. A rather low  number of genes were regulated, most of them being specific to the NG14 strains. Clustering of these genes highlighted similar behavior for some functional categories, and allowed to distinguish between induction-related genes and productivity-related genes. The lower number of genes regulated in RUT C30 could not formally be linked to the relief in catabolic repression that is characteristic of this strain. Cross-comparison of our transcriptome data with mutations previously identified revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting these clusters contain genes playing a role in strain performance. This is the first kinetic transcriptome study carried out in industry-relevant conditions with two related strains of T. reesei showing distinctive performances. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggest that the induction mechanism is essentially intact and that there is room for further improvement of T. reesei. We also provide some potential target for further genetic improvement of these strains.

overall_design: Two biological pool by condition in dye switch. For the two biological replicates on each four experiments we apply on the pretreated results the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes from the limma R package (Smyth 2004). We select the list of statistically regulated genes using a 5% significance threshold.

first: Dante

last: Poggi-Parodi

first: Frédérique

first: Thomas

last: Portnoy

first: Aurélie

last: Pirayre

first: Bernhard

last: Seiboth

first: Christian

last: Kubicek

first: Stéphane

last: Le Crom

first: Antoine

last: Margeot


title: Waterborne beclomethasone diproprionate affects fish while its metabolite beclomethasone is not taken up

city: Göteborg

first: Bethanie

last: Carney Almroth

address: Medicinaregatan 38

department: Biological and Environmental Sciences

institute: University of Gothenburg

summary: Investigation of transcriptome expression changes in liver tissue of rainbow trout exposed beclomethasone diproprionate (1 µg/L nominal concentration) in a flow through set up for 2 weeks

overall_design: A four chip (x12) study using total RNA prepared from liver.

last: Almroth

first: Lina

last: Gunnarsson

first: Filip

last: Cuklev

first: Jerker

last: Fick

first: Erik

last: Kristiansson

first: D

last: Larsson


title: Gene expression profiles in kidney of Japanese flounder injected with formalin-killed bacterial cells

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

summary: In order to identify the genes induced by different bacterial cells, which may contain different types of pathogen associated molecular patterns (PAMPs), high-throughput gene expression analyses using Agilent custom-oligo DNA microarray containingon 9,573 probes constructed for Japanese flounder Paralichthys olivaceus were conducted.  A number of genes showed significant changes in mRNA levels.  However, there are no significant difference in a manner of the changes among the different bacterial cell treatments.  The genes significantly induced by the treatments included well-known immune-related genes such as granulocyte-colony stimulation factor, haptoglobin, hepcidin.

overall_design: The kidney were isolated from the formalin killed cells (FKCs) intraperitoneal injected Japanese flounder, Paralichthys olivaceus using the four formalin-killed cells, Edwardsiella tarda  strain 54, Lactococcus garviae strain EH8706, Streptococcus iniae strain 02 and Vibrio anguillarum strain H775-3, respectively. Fishes were administered by an intraperitoneal injection using the 1.0 x 10^7 to 1.0 x 10^8 cells of FKCs. After 6 hours from a injection, fish kidney was isolated. We also isolated phosphate-bufferd seline injected fish kidney as a control. We analyzed a four samples in control. We also analyze a three samples in FKC injected fish (16 hybridization).

first: Yoshiaki

last: Suzuki

first: Yuriko

last: Kawana

first: Takashi

last: Aoki

first: Ikuo

last: Hirono


title: MicroRNA profiling of malignant pleural mesothelioma tumor tissue

status: Public on Dec 02 2014

city: Zürich

first: Michaela

last: Kirschner

address: Rämisstr. 100

department: Division of Thoracic Surgery

institute: University Hospital Zürich

summary: We used microarrays to identify prognostic microRNAs with differential expression in tumor tissue from long and short survivors of extrapleural pneumonectomy surgery.

overall_design: Total RNA was isolated from laser-capture microdissected archived FFPE tumor samples from malignant pleural mesothelioma patients. RNA was hybridized on Agilent microRNA microarrays. We sought to identify microRNAs with differential expression between long and short survivors of extrapleural pneumonectomy surgery.

first: Yuen

middle: Y

last: Cheng

first: Glen

last: Reid


title: Kc167 ORC Localization in hydroxyurea (HU)

status: Public on Dec 05 2014

city: Durham

first: Jason

middle: Alan

last: Belsky

state: NC

address: LSRC Room C333

department: Pharmacology and Cancer Biology

institute: Duke University

summary: Determination of the genome-wide distribution of ORC by chromatin immunoprecipitation in the Drosophila Kc167 cell line at the beginning of S phase.  Kc167 cells were arrested at the G1/S transition with hydroxyurea (HU).  Goal was to test whether the ORC binding distribution remained the same between G1 and S.

overall_design: ChIP-Chip of ORC in HU compared to input genomic DNA.  Biological Replicates: 1

first: David

last: MacAlpine


title: Genome-wide DNA methylation differences between ex vivo differentiated cells that recapitulate the fetal-to-adult hemoglobin switch

city: Montreal

first: Guillaume

last: Lettre

state: Québec

address: 5000 rue Bélanger

country: Canada

institute: Montreal Heart Institute

summary: The aim of this study is to characterize de genome-wide DNA methylation changes that occur during the fetal-to-adult hemoglobin switch in erythroblasts. We differentiated CD34+ hematopoietic progenitor cells collected for either fetal liver or bone marrow into erythroblasts. After differentiation, cells produce respectively fetal hemoglobin and adult hemoglobin in majority. We compared genome-wide DNA methylation states of fetal-stage erythroblasts to those of adult-stage erythroblasts.

overall_design: Human erythroblasts were generated from either fetal liver or bone marrow CD34+ cells. Bisulfite converted DNA from 12 samples from each condition (total=24) was hybridized to the Illumina 450K HumanMethylation Beadchip.

first: Samuel

last: Lessard

first: Mélissa

last: Beaudoin

first: Karim

last: Benkirane


title: Kc167 Mcm2-7 Localization in Late S Phase

summary: Determination of the genome-wide distribution of the Mcm2-7 helicase by chromatin immunoprecipitation in the Drosophila Kc167 cell line at the end of S phase.  Kc167 cells were synchronized by first arresting at the G1/S transition with hydroxyurea (HU), and then releasing from the HU arrest point for 6 hours.  Goal was to evaluate changes in the genome-wide Mcm2-7 distribution throughout the cell cycle, and how this relates to the excess Mcm2-7 loaded onto chromatin in G1.

overall_design: ChIP-Chip of Mcm2-7 in late S phase compared to input genomic DNA.  Biological Replicates: 2

middle: M


title: The peroxisome proliferator-activated receptor-gamma agonist pioglitazone modulates aberrant T cell responses in systemic lupus erythematosus

city: Ann Arbor

first: Celine

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary:
Previous studies indicate that peroxisome proliferator-activated receptor-gamma (PPAR-g) agonists suppress autoimmune responses and renal inflammation in murine lupus. However, the mechanisms implicated in this process remain unclear. We tested the effect of the PPAR-g agonist pioglitazone in human lupus and control PBMCs with regards to gene regulation and various functional assays.
We used microarrays to analyze the effect of Pioglitazone on peripheral blood cells (PBMCs) from healthy and lupus patients.

overall_design:
Human PBMCs were isolated; RNA from healthy and lupus PBMCs was extracted and processed for hybridization on Affymetrix microarrays.

Samples are paired as follows: 1-2, 3-4, 5-6, 7-8, 9-10, 11-12, 13-14, 15-16, 19-20.

first: Wenpu

last: Zhao

first: Joseph

last: McCune

first: Matthias

last: Kretzler

first: Mariana

last: Kaplan

first: E

last: Lewis


title: Evaluation of ORC and Mcm2-7 Distribution Throughout the Drosophila Kc Cell Cycle

summary: This SuperSeries is composed of the SubSeries listed below and previous submissions made by modENCODE (GSE17282, GSE17283, and GSE41349).

overall_design: Refer to individual Series


title: Molecular investigation of the high radiation resistance of edible cyanobacterium Arthrospira sp PCC 8005

status: Public on Dec 01 2014

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

summary: Arthrospira is an edible cyanobacterium used in the food supplement “Spirulina”. The aim of this work was to characterise its response to ionising radiation. Live cells of Arthrospira sp. PCC 8005 were irradiated with 60Co gamma rays. Arthrospira sp. PCC 8005 recovered and resumed photosynthetic proliferation after exposure to a dose of even 6400 Gy, which is a dose about 1000x higher than the lethal dose for most plant, animal and human cells. Biochemical, proteomic and transcriptomic analysis after irradiation with 3200 or 5000 Gy showed a strong reduction in photosynthesis activity and reduced pigment content. Irradiated cells showed reduced transcription for carbon fixation, and for pigment, lipid and secondary metabolite synthesis; while induced transcription of thiol-based antioxidant systems, photosensing and signalling pathways. Cells irradiated with 3200 or 5000 Gy did not show clear dsDNA damage, but transcriptomics did show significant activation of ssDNA repair systems and mobile genetic elements at RNA-level. Irradiated cells also expressed a group of conserved proteins of which the function in radiation resistance remains to be elucidated. This study revealed for the first time the high radiation resistance of Arthrospira, and the molecular systems involved, paving the way for its further exploitation for radiation protection.

overall_design: Arthrospira was exposed to two different doses of irradiation, 3200Gy and 5000Gy. Each of those irradiated experiment was performed in biological triplicate. For each of both conditions, a separate control (reference) was run in triplicate. This sums up to a total of 12 arrays.

first: Hanene

last: Badri

first: Pieter

last: Monsieurs

first: Ilse

last: Coninx

first: Ruddy

last: Wattiez

first: Natalie

last: Leys


title: Real-time quantitative PCR analysis for miRNA in mouse CD8+ pMel-1 T cells

first: Regina

last: Lin

address: 207 Research Drive, #305

department: Immunology

summary: Mouse CD8+ pMel-1 transgenic T cells were primed by either splenic B cells or LPS-matured bone marrow-derived dendritic cells for 3 days in vitro. CD8+TCRb+ cells were then sorted for miRNA expression profiling by RT-qPCR.

overall_design: qPCR miRNA expression profiling.

first: Qi-Jing

last: Li


title: Detection of juvenile hormone-like function of diofenolan in Daphnia magna using in vivo short-term screening assay, TG211 Annex 7 reproduction test and microarray analysis

city: Okazaki

first: Kenji

last: Toyota

address: 5-1 Higashiyama

institute: National Institute for Basic Biology

summary: Juvenile hormone (JH) and JH agonists have been reported to induce male offspring production in various daphnids including Daphnia magna. We have recently established a short-term in vivo screening method to detect chemicals having JH activity, induction of male offspring, using adult D. magna. Diofenolan has been developed to be a JH agonist in insects, but no male induction in daphniids has been studied. In this study, we found the male offspring induction by diofenolan with a short-term in vivo screening method, and the most potent male offspring production activity among JH analogs studied using the OECD TG211 Annex 7. Transcriptome analysis of diofenolan-exposed D. magna showed up-regulation of JH-responsive genes. These results clearly demonstrated that diofenolan has JH activities in D. magna using the short-term in vivo screening assay, OECD TG211 Annex 7 and microarray analysis.

overall_design: Juvenile hormone agonists induced gene expression in daphnids neonates was measured at 48 hours after exposure to diofenolan (10 ng/L) and DMF as a control.  Four independent experiments were performed at each chemicals.

first: Ryoko

last: Abe

first: Haruna

last: Watanabe

first: Tomohiro

last: Oka

first: Hitoshi

last: Miyakawa

first: Shinichi

last: Miyagawa

first: Hiroyo

last: Nishide

first: Ikuo

last: Uchiyama

first: Taisen

last: Iguchi

first: Norihisa

last: Tatarazako


title: Small RNA profiling of Arabidopsis in response to fungal elicitors

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

summary: This experiment describes small RNA gene expression after treatment of Arabidopsis seedlings with elicitors obtained from the fungus F. oxysporum

platform_organism:
Arabidopsis thaliana
Caenorhabditis elegans
Drosophila melanogaster

overall_design: Total RNA was isolated from Arabidopsis plants that had been treated with elicitors obtained from the fungus F. oxysporum, and mock-inoculated plants, at different times of treatment (from 5 min to 120 min of treatment). Three independent biological replicates were prepared for each time point and condition. Samples harvested at 5, 30, 60 and 120 min of elicitor treatment were used for microarray experiments. Elicitor-induced alterations we identified by determining the ratio of the hybridization signal intensities between treated and control plants.

first: Patricia

last: Baldrich

first: Christelle

last: Siré

first: Ana

last: Moreno

first: Blanca

last: SanSegundo

first: Tara

last: Mastro

first: Jose

middle: L


title: miRNA expression profiles in the liver of a NASH-HCC model mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: To identify miRNAs that play important roles in the liver carcinogenesis from NASH, miRNA expression profiles were examined. Some miRNAs showed aberrant expression in HCC (Hepatocellular carcinoma) from NASH (non-alcoholic steatohepatitis). These miRNAs were  regulated by DNA methylation, and could be potential therapeutic targets for HCC (Hepatocellular carcinoma) from NASH (non-alcoholic steatohepatitis).

overall_design: STAM mice, a model for HCC (Hepatocellular carcinoma) from NASH (non-alcoholic steatohepatitis) were used. miRNA expression profiles in HCC and non-tumor liver tissues in STAM mice were examined. For in vitro study, miRNA expression profiles in HepG2 cells treated with 5-Aza-CdR and/or SAHA were examined.

first: Yoshimasa

last: Saito


title: Genome-wide transcript profiling of Candida albicans PGA22 overexpression

status: Public on Nov 30 2014

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

institute: Institut Pasteur

summary: Transcript profiling from 3 biological replicates of C. albicans strains expressing PGA22 under the control of a tetracycline derivative-inducible promoter grown during 16h in the presence or absence of 50 µg/mL doxycycline (Dox)

overall_design: Two-condition experiment, untreated (-Dox) and Dox-treated (50 µg/mL during /16h in Yest Peptone Dextrose medium), 3 biological replicates


title: Determinants of excess genetic risk of acute myocardial infarction – a matched case-control study

city: Prague

first: Michal

last: Kolář

address: Pod Vodárenskou věží 2

country: Czech Republic

institute: Institute of Computer Science, Academy of Sciences of the Czech Republic

summary: Peripheral blood samples of patients with acute myocardial infarction were matched with those of control patients to identify possible differences in corresponding gene expression profiles. The controls were matched to cases based on gender, age, status of diabetes mellitus and smoking status. Six months cardiovascular survival status of the cases was used to identify two distinct subgroups among the cases. Linear models for microarray data (‘limma’) were employed to identify differential gene expression. Shrunken centroids technique helped in identifying the subsets of differentially expressed genes with predictive properties in independent samples. Predictive properties were evaluated using bootstrap sampling. Using the limma modeling with the log-fold change threshold of one (clinical significance) and Storey’s q-value approach (statistical significance), sixty transcripts were found to be both clinically and statistically differentially expressed among the cases not surviving the follow-up period relative to controls, while no such transcripts were observed among other surviving cases. The two subgroups of cases exhibited fourteen differentially expressed transcripts. Predictive modeling indicated sixteen out of sixty transcripts to best discriminate between the controls and cases who died during the follow-up period from cardiovascular causes, while for the surviving cases the already non-significant set of transcripts could not be further reduced. Eleven out of fourteen transcripts were found to best discriminate between the two groups of cases using shrunken centroids. The study identified genes, which were differentially expressed during the acute myocardial infarction, including those associated with short-term fatality of the cases.

overall_design: The genome-wide study used matched case-control design, with 97 samples of 90 patients in three disease groups. Matched control samples were used and several (7) technical replicates were performed.

first: Zdenek

last: Valenta

first: Ivan

last: Mazura

last: Kolar

first: Hana

last: Grunfeldova

first: Petra

last: Feglarova

first: Jan

last: Peleska

first: Marie

last: Tomeckova

last: Kalina

first: Jana

last: Zvarova


title: miRNAs expression profiles in HepG2 cells treated with SAHA and/or 5-Aza-CdR


title: Effects of TiO2 and Ag nanoparticles on polyhydroxybutyrate biosynthesis by activated sludge bacteria

status: Public on Dec 03 2014

city: Berkeley

first: Yvette

last: Piceno

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

institute: LBNL

summary: Manufactured nanomaterials (MNMs) are increasingly incorporated into consumer products that are disposed into sewage. In wastewater treatment, MNMs adsorb to activated sludge biomass where they may impact biological wastewater treatment performance, including nutrient removal. Here, we studied MNM effects on bacterial polyhydroxyalkanoate (PHA), specifically polyhydroxybutyrate (PHB), biosynthesis because of its importance to enhanced biological phosphorus (P) removal (EBPR). Activated sludge was sampled from an anoxic selector of a municipal wastewater treatment plant (WWTP), and PHB-containing bacteria were concentrated by density gradient centrifugation. After starvation to decrease intracellular PHB stores, bacteria were nutritionally augmented to promote PHB biosynthesis while being exposed to either MNMs (TiO2 or Ag) or to Ag salts (each at a concentration of 5 mg L-1). Cellular PHB concentration and PhyloChip community composition were analyzed. The final bacterial community composition differed from activated sludge, demonstrating that laboratory enrichment was selective. Still, PHB was synthesized to near-activated sludge levels. Ag salts altered final bacterial communities, although MNMs did not. PHB biosynthesis was diminished with Ag (salt or MNMs), indicating the potential for Ag-MNMs to physiologically impact EBPR through the effects of dissolved Ag ions on PHB producers.

platform_organism: Bacteria Archaea

overall_design: 18 samples; Triplicate PHB-enriched bacterial communities recovered from activated sludge were exposed to nanoparticle (TiO2 or Ag) or AgNO3 (as a silver control) or were not exposed to an nanoparticles (control) to determine if the naoparticles affected PHB production.

first: John

last: Priester

first: Laurie

last: Van de Werfhorst

first: Yuan

last: Ge

first: Adeyemi

last: Adeleye

first: Shivira

last: Tomar

first: Lauren

last: Tom

first: Gary

last: Andersen

first: Patricia

middle: A

last: Holden


title: Real-time quantitative PCR analysis of human embryonic stem cells, human neural stem cells and human foreskin fibroblast.

status: Public on Nov 29 2014

city: MADRID

first: María José

last: Pino-Barrio

state: MADRID

address: Avda Complutense, 40.

department: Hematopoietic Innovative Therapies Division.

institute: CIEMAT

summary: To address the question of whether v-myc modifies the stemness and potency of hNSCs, we first studied the expression of 90 genes related to stemness, self-renewal and differentiation in several v-myc immortalized cell lines (hNS1, hVM1, hCTX), non-immortalized neurospheres (hNPC derived from 9.5 and 10 weeks-old fetuses), hESCs (H9 and HS181) and human foreskin fibroblasts (hFF-1).

overall_design: A hierarchical clustering was performed to group the cell lines under study in accordance with their gene expression profiles. The gene expression data were analyzed by Principal Component Analysis (PCA) to verify gene expression differences and generate discrete groups among the studied cell lines, according to the genes that contributed most to each separation (component).

first: María

first: Elisa

last: García-García

first: Pablo

last: Menéndez

first: Alberto

last: Martínez-Serrano


title: Genome-wide omparism of Terc deficient ntESCs

city: Taipei

first: Li-Ying

last: Sung

address: 4F, No. 81, Chang-Xing St.

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

summary: Haplo-insufficiency of telomerase genes in humans leads to telomere syndromes such as dyskeratosis congenital and idiopathic pulmonary fibrosis. Generation of pluripotent stem cells from telomerase haplo-insufficient donor cells would provide unique opportunities towards the realization of patient-specific stem cell therapies. Recently, pluripotent human embryonic stem cells (ntESCs) have been efficiently achieved by somatic cell nuclear transfer (SCNT). We tested the hypothesis that SCNT could effectively elongate shortening telomeres of telomerase haplo-insufficient cells in the ntESCs using relevant mouse models. Indeed, telomeres of telomerase haplo-insufficient (Terc+/-) mouse cells are elongated in ntESCs. Moreover, ntESCs derived from Terc+/- cells exhibit naïve pluripotency as evidenced by generation of Terc+/-ntESC clone pups by tetraploid embryo complementation (TEC), the most stringent test of naïve pluripotency. These data suggest that SCNT could offer a powerful tool to reprogram telomeres and to discover the factors for robust restoration of telomeres and pluripotency of telomerase haplo-insufficient somatic cells.

overall_design: RNAs from Terc+/+, +/- and -/- contain 3 biological repeatsin each group.

first: Wei-Fang

last: Chang

first: Qian

last: Zhang

first: Chia-Chia

last: Liu

first: Jun-Yang

last: Liou

first: Chia-Chun

first: Huan

last: Ou-Yang

first: Renpeng

last: Guo

first: Haifeng

last: Fu

first: Winston

middle: T

last: Cheng

first: Shih-Torng

last: Ding

first: Chuan-Mu

last: Chen

first: Maja

last: Okuka

first: David

last: Keefe

first: Eugene

first: Lin

first: Jie

last: Xu


title: Gene expression analysis in Jatropha curcas under drought stress and recovery

city: Nagoya

first: Joyce

last: Cartagena

address: Furo-cho, Chikusa-ku

institute: Nagoya University

summary:
Jatropha is known for its ability to grow in marginal lands and drought prone areas receiving limited amounts of rainfall. Accordingly, gene discovery in Jatropha will be useful for providing a source of genetic information for the improvement of drought tolerance in crops. In this study, a Jatropha oligomicroarray was developed to evaluate the gene expression profile of Jatropha plants during drought stress response and recovery from stress.
When the gene expression patterns were compared between those differentially expressed during exposure to drought stress and re-watering, it was possible to identify 333 genes that are involved in the response to dehydration, while 592 genes were found to be significant during recovery, and 375 genes are associated in both dehydration and recovery. Furthermore, representative genes from the three gene categories were compared to those found in other plant species and a basic understanding on how Jatropha copes with drought and its mechanism for survival in dry conditions is discussed. Taken together, the oligomicroarray that we developed in this study is a useful tool for analyzing expression profiles of Jatropha genes to better understand molecular mechanism underlying drought stress responses as well as other aspects of molecular studies in Jatropha.

overall_design: All plants were given equal amounts of water every two days. For drought stress treatment, one-month old seedlings were used. Control plants were continuously given equal amounts of water while the drought-treated plants were withheld from watering. After three weeks without watering, leaf tissues were collected from drought-treated plants for isolation of total RNA. Three independent experiments with three biological samples each were simultaneously carried out.

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Takaki

last: Yamauchi

first: Shusei

last: Sato

first: Hideki

last: Hirakawa

first: Takashi

last: Tsuge


title: Diverse dog breeds genotyped on Affymetrix Canine v2 Arrays

status: Public on Nov 20 2014

city: Cambridge

first: Hyun Ji

last: Noh

address: 7 Cambridge Center

department: Genome Sequencing and Analysis

institute: Broad Institute

summary: Diverse dataset of 1247 dogs from many breeds and wolves used to investigate the origins of dog domestication

sample_organism:
Canis lupus
Canis lupus familiaris

overall_design: DNA for 1228 dogs from 35 breeds and 19 wolves was extracted from whole blood samples and genotyped on the Affymetrix Canine v2 Arrays. Genotypes were called using Affymetrix's snp5-probeset-genotype software and the BRLMM-P calling algorithm. The included breed designations are owner reported.

first: Kerstin

last: Lindblad-Toh


title: Effect of embryonic and maternal genotype on foetal growth in rabbit

status: Public on Oct 21 2014

city: Valencia

first: M. Desemparats

last: Saenz-de-Juano

state: Valencia

address: Camino de Vera s/n

department: Animal Science

institute: Universidad Politécnica Valencia

summary: The aim of this work was to evaluate the influence of maternal and embryonic genotype of two lines of rabbit selected by growth rate (line R) and litter size at weaning (line A) on foetal and placental growth. Embryos were recovered at 48 h of gestation from line R (46) and line A (40) donors and transferred to nulliparous recipient does (26 R and 24 A). Each recipient doe received six embryos into one oviduct from line R and six embryos form line A into the other. Laparoscopy was performed at day 14 to determine implantation rate. Recipient females were slaughter at day 14, 24 and 30 (12, 24, 14, respectively) to determine the number of live fetuses and the weight of live foetuses, foetal placenta and maternal placenta. To analyze endocrine levels, blood serum was collected from 14 females at 14, 21 and 28 days of gestation. A transcriptome analysis was performed to search for differences between foetal placentas at day 14 and 24 of development. Foetal survival at Days 14, 24 and 30, and weight at Day 14 was higher for line A embryos, being the weight higher for AA genotype (0.29±0.01g vs. 0.19±0.01g ,for RR genotype). Only the R embryonic genotype showed higher foetal weight at Day 30 (53.4 ± 1.74 vs. 48.5 ± 1.81, for line R and line A foetuses). However, foetal and maternal placentas were higher for RR genotype on Day 24 and 30. No differences in foetal placenta at transcriptome level were found. Additionally, both progesterone and IGF-I levels were similar between lines. In conclusion, line R presented reproductive troubles, with higher gestational losses at embryonary level at Day 14 and 24, and uterine environment problems at least at last part of gestation which reduced survival rate of A line foetuses.

overall_design: Embryos were recovered at 48 h of gestation from line R and line A donors and transferred to nulliparous recipient does. Recipient females were slaughter at Day 14 and 24, and a transcriptomic comparison analysis was performed from foetal placenta tissue.

first: C

last: Naturil

first: M

middle: D

first: J

middle: S

last: Vicente


title: Cytokines & Chemokines PCR Array on human DC

status: Public on Oct 23 2014

city: Leiden

first: Rob

last: Mariman

address: Zernikedreef 9

institute: TNO

summary: Stimulation of human DC with LPS, VSL#3, or a combination of both resulted in their maturation, evident from enhanced expression of activation markers on the cell-surface, as well as the induction of various chemokines and cytokines.

overall_design: 24 samples were analyzed (4 experimental conditions and 6 biological replicates)


title: Transcriptional analysis of adaptation to high glucose concentration in Zymomonas mobilis

status: Public on Oct 14 2014

city: chengdu

first: kun

last: zhang

state: sichuan

address: section 29，Wangjiang Rd.

department: College of Life Sciences

institute: Sichuan University

summary: High glucose concentrations were desirable for ethanol fermentation of Zymomonas mobilis, but it can lead to decrease in ethanol production and productivity. Sorbitol as a compatible solute can be absorbed or synthesized to counteract the detrimental osmotic stress caused from external high glucose concentrations by Z. mobilis. Currently, molecular mechanisms of tolerance to high glucose concentrations and sorbitol promoting ethanol fermentation are still unclear for Z. mobilis. To better understand mechanisms with which high concentrations of glucose and sorbitol affect physiology and metabolism of Z. mobilis ATCC31821 (ZM4), the global transcriptional responses of ZM4 to the challenge of high glucose concentration and sorbitol were profiled using whole genome microarray analysis. Swings J, Deley J. Bacterial Rev. 1977, 41(1): 1-46. Loos H, Kramer R, Sahm H and Sprenger GA. J Bacteriol. 1994, 176(24):7688–7693.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: Gene expression analysis was performed using twelve independent microarray experiments (four time point reactions × three biological replicates), representing four patterns of growth conditions  from ZM4 cultures. Each microarray measures the expression level of 1,918 genes from ZM4 ATCC31821 and the associated plasmids, with three-fold technical redundancy.

first: Feng

last: Hong

first: Kun

last: Zhang


title: Transcriptional effects of glucocorticoid receptor alpha and beta signaling in zebrafish

status: Public on Nov 18 2014

first: Marcel

last: Schaaf

address: Einsteinweg 55

institute: Leiden University

summary: The glucocorticoid receptor (GR) regulates gene expression upon activation by glucocorticoid (GC) hormones. In zebrafish, two GR splice variants exist: the canonical GR α-isoform (GRα), and the GR β-isoform (GRβ). The exact function of GRb remains elusive. We have investigated the transcriptional role of GRa and GRb in the zebrafish embryo model by injecting mebryos with two splice-blocking morpholinos (one leading to knockdown of both GR α- and β-isoforms, and another targeting the alternative splicing of the GR pre-mRNA in favor of the GR β-isoform) and with GRβ mRNA (resulting in specific GRβ overexpression). Transcriptome profiling was performed on total RNA isolated from 30 hpf embryos. Our results show that GRb does not act as a dominant-negative inhibitor of GRa, and that GRa regulates two distinct gene clusters, which are mainly involved in the metabolism of the embryo.

overall_design: This microarray study was designed to determine the effect of knockdown and overexpression of GRa and GRb. For this purpose, wild type (AB/TL) zebrafish embryos were injected at the 1-2 cell stage with a standard control morpholino (SC-MO), a splice-blocking morpholino leading to knockdown of both GR α- and β-isoforms (MO1), a splice-blocking morpholino targeting the alternative splicing of the GR pre-mRNA in favor of the GR β-isoform (MO2), or GRb mRNA. At 24 hpf, each group was treated with dexamathasone (or vehicle) for 6 hr. This resulted in 8 treament groups: SC-MO/veh, SC-MO/dex, MO1/veh, MO1/dex, MO2/veh, MO2/dex, GRb mRNA/veh, GRb mRNA/dex. After the incubation period, embryos were collected and RNA was isolated from 20 embryos per treatment group (30 hpf). Three individual experiments were performed, and the resulting triplicate samples were analyzed by microarray, using a common reference approach.

first: A

last: Chatzopoulou

first: H

last: Spaink

last: Meijer

middle: J


title: Arabidopsis thaliana Col-0 Al stress 6hrs

status: Public on Oct 11 2014

city: Gifu

first: Mutsutomo

last: Tokizawa

address: yanagido 1-1

department: Faculty of Applied Biological Sciences

institute: Gifu University

summary: Transcriptional profiling of roots in Arabidopsis Col-0  with 10 µM AlCl3 6hrs vs w/o AlCl3 6hrs

overall_design: 10 µM AlCl3 pH5.0 6hrs vs. noAlCl3 pH5.0 6hrs

first: Yasufumi

last: Kobayashi

first: Hiroyuki

last: Koyama


title: Attachment of Bacillus subtilis to the hyphae of Aspergillus niger results in altered metabolism and defense mechanisms in both partner

status: Public on Oct 07 2014

city: Utrecht

first: miaomiao

last: Zhou

address: Uppsalalaan 8

department: fungal physiology

institute: centre of fungal biodiversity, Utrecht, KNAW

summary: Interaction of microbes affects the growth, metabolism and differentiation of members of the community. While direct and indirect competitions, like spite and nutrient consumption have negative effect on each other, microbes also evolved in nature not only to fight, but in some cases to adapt or support each other while increasing the fitness of the community. Presence of bacteria and fungi in the soil results in interactions and various examples were described, including mutualism. Bacilli attach to the plant root and form complex communities in the rhizosphere. Bacillus subtilis, when grown in the presence of Aspergillus niger interacts with the fungal partner, attaches and grows on the hyphae. Using dual transcriptome experiment, we show that both fungi and bacteria alter their metabolisms during the interaction. Interestingly, the transcription of genes related to the antifungal and antibacterial defense mechanism of B. subtilis and A. niger, respectively, are decreased upon attachment of bacteria to the mycelia. Our microarray experiments provide a novel insight into the mutual interaction of a bacterium and a fungus.

overall_design: Aspergillus niger were grown with and without Bacillus subtilis. Biological triplicates were made for both conditions, Affymetrix microarray experiments were performed on these samples.

first: Miaomiao

first: Isabelle

last: Benoit

first: Marielle

last: van den Esker

first: Jan

last: Dijksterhuis

first: Oscar

middle: P

last: Kuipers

first: Ronald

last: de Vries

first: Akos

last: Kovács


title: Aspergillus nidulans strains TNO2a3 and ∆ptpB (AN4896) grown on casaminoacids as sole carbon source transfer to glucose

status: Public on Oct 03 2014

city: Ribeirão Preto

first: Leandro

middle: Jose

last: Assis

state: São pAULO

address: Av. do Cafe S/N

department: FCFRP

country: Brazil

institute: USP

summary: Transcriptome of A. nidulans TNO2a3 and ∆ptpB strains when grown on minimal media plus casaminoacids and transferred to minimal media plus glucose as a sole carbon source for 4 hours

overall_design: Three conditions minimal media plus casaminoacids during 24 hours (reference) and minimal media plus glucose for 4 hours. Three strains TNO2a3 and ∆ptpB. Three biological repetitions of each timepoint of TNO2a3 / ∆ptpB

last: José de Assis

first: Neil

last: Brown

first: Gustavo

last: Goldman


title: Ecotoxicogenomic assessment of diclofenac toxicity in soil

status: Public on Oct 01 2014

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

institute: MicroLife Solutions

summary: Diclofenac is widely used as nonsteroidal anti-inflammatory drug leaving residues in the environment. To investigate effects on terrestrial ecosystems, we measured dissipation rate in soil and investigated ecotoxicological and transcriptome-wide responses in Folsomia candida. Exposure for 4 weeks to diclofenac reduced both survival and reproduction of F. candida in a dose-dependent manner. At concentrations ≥200 mg/kg soil diclofenac remained stable in the soil during a 21-day incubation period. Microarrays examined transcriptional changes at low and high diclofenac exposure concentrations. The results indicated that development and growth were severely hampered and immunity-related genes, mainly directed against bacteria and fungi, were significantly up-regulated. Furthermore, neural metabolic processes were significantly affected only at the high concentration. We conclude that diclofenac is toxic to non-target soil invertebrates, although its mode of action is different from the mammalian toxicity. The genetic markers proposed in this study may be promising early markers for diclofenac ecotoxicity.

overall_design: A direct design was used where springtails were exposed to 3two concentrations of diclofenac (EC10 and EC50 on reproduction) and microarrays were directly contrased to those from animals exposed to clean LUFA2.2 soil. 4 biological replicates were used with each containing 25 grams of soil and 30 adult, randomly selected, age sychronized springtails

first: Guangquan

last: Chen

first: Michiel

middle: W

last: den Braver

first: Cornelis

last: van Gestel

first: Nico

last: van Straalen

first: Dick

last: Roelofs


title: Accelerated senescence and enhanced disease resistance in hybrid chlorosis lines derived from interspecific crosses between tetraploid wheat and Aegilops tauschii

status: Public on Aug 12 2014

city: Kobe

first: Shigeo

last: Takumi

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

summary:
Hybrid chlorosis, one of the hybrid incompatibilities, has frequently been reported in inter- and intraspecific crosses of allopolyploid wheat. In our previous study, hybrid chlorosis was observed in the wheat triploids between a tetraploid wheat cultivar Langdon and four Ae. tauschii accessions and in their derived synthetic hexaploids. However, the molecular mechanisms underlying hybrid chlorosis are not well understood. Here, we performed cytological and comparative gene expression analyses in leaves to characterize the abnormal growth in wheat synthetics showing mild and severe chlorosis symptom. In addition, disease resistance was comparatively assessed. A number of carbohydrate metabolism- and defense-related genes were markedly up-regulated in the hybrid chlorosis lines, and abnormal chloroplasts were formed in the mesophyll cells before the leaves turned to be yellowish. The mild chlorosis plants showed increased resistance to a wheat blast fungus, although little significant differences of agricultural traits were found between the wild-type and mild chlorosis-showing plants.
These observations suggest that the senescence processes might be accelerated in the hybrid chlorosis lines of wheat synthetics. Moreover, the negative effects on biomass can be minimized and the substantial fitness may be obtained under pathogen-polluted conditions in the mild chlorosis-showing wheat synthetics.

overall_design: Expression patterns were compared between a wild-type synthetic wheat line (as a reference) and two hybrid chlorosis-showing hybrid chlorosis lines. Total RNA samples were isolated from the 3-week-old leaf tissues. Two independent experiments were conducted in each line.

first: Hiroki

last: Nakano


title: Blood gene expression reveals reduced circadian rhythmicity in individuals resistant to sleep deprivation

status: Public on Oct 02 2014

city: RTP

first: Keith

last: Shockley

address: 111 TW Alexander Drive

country: USA

institute: NIEHS

summary:
To address whether changes in gene expression in blood cells with sleep loss are different in individuals resistant and sensitive to sleep deprivation (SD).
Blood draws every 4 hours during a 3-day study: 24-hour normal baseline, 38 hours of continuous wakefulness and subsequent recovery sleep, for a total of 19 time-points per subject, with every 2-hr psychomotor vigilance test (PVT) assessment when awake. Fourteen subjects who were previously identified as behaviourally resistant (n=7) or sensitive (n=7) to SD by PVT.  Intervention consisted of 38 hours continuous wakefulness. We found 4,481 unique genes with a significant 24-hour diurnal rhythm during a normal sleep-wake cycle in blood (false discovery rate [FDR] <5%). Biological pathways were enriched for biosynthetic processes during sleep. After accounting for circadian effects, two genes (SREBF1 and CPT1A, both involved in lipid metabolism) exhibited small, but significant, linear changes in expression with the duration of SD (FDR<5%). The main change with SD was a reduction in the amplitude of the diurnal rhythm of expression of normally cycling probe sets. This reduction was noticeably higher in behaviourally resistant subjects than sensitive subjects, at any given p-value. Furthermore, blood cell type enrichment analysis showed that the expression pattern difference between sensitive and resistant subjects is mainly found in cells of myeloid origin, such as monocytes. Individual differences in behavioural effects of sleep deprivation are associated with differences in diurnal amplitude of gene expression for genes that show circadian rhythmicity.

overall_design: Blood draws were done every 4 hours during a 3-day (+1 baseline day) study: 24-hour normal baseline (6 time points: day 1 8hr, 12hr, 16hr, 20hr, day 2 0hr, 4hr), 38 hours of continuous wakefulness (10 time points: day 2 8hr, 12hr, 16hr, 20hr, day 3 0hr, 4hr, 8hr, 12hr, 16hr, 20hr) and subsequent recovery sleep (3 time points: day 4 0hr, 4hr, 8hr), for a total of 19 time-points per subject, with every 2-hr psychomotor vigilance test (PVT) assessment when awake. The missing/failed samples were as following: Resistant subjects (total 10 samples): BH006 day 2 20hr, 12hr, BH003 day 2 12hr, 4hr, BH003 day 3 4hr, BH008 day 4 0hr, BH008 day 1 16hr, BH008 day 3 16hr 20hr, BH010 day 4 0hr; Sensitive subjects (total 7 samples): BH004 day 2 12hr and 1 more missing sample, BH026 day 2 4hr, BH007 day 2 20hr and 1 more missing sample, BH016 day 2 4hr, BH015 day 3 0hr.

first: Allan

middle: I

last: Pack

first: Alexei

last: Podtelezhinikov


title: The expression profile of cytochromes P450 (CYPs) and aldo-keto reductases (AKRs) in post-treatment breast carcinomas

status: Public on Aug 31 2014

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

institute: National Institute of Public Health

summary:
Metabolism of anticancer drugs markedly affects their antitumor effects. The major goal of our study was to investigate associations of gene expression of enzymes metabolizing taxanes and/or anthracyclines with therapy response and survival of breast carcinoma patients
AKR1A1 was significantly overexpressed and AKR1C1-4, KCNAB1, CYP2C19, CYP3A4, and CYP3A5 downregulated in tumors compared with control non-neoplastic tissues after correction for multiple testing. Significant associations of CYP2B6 levels in tumors with expression of hormonal receptors were found. Significantly higher intratumoral levels of AKR1C1, AKR1C2, and CYP2W1 were found in responders to NACT compared with non-responders. Patients with high AKR1C2 and CYP3A4 levels had significantly longer disease-free survival than patients with low levels.

overall_design: Transcript levels of twenty-four selected human metabolic genes (CYPs and AKRs) were determined by qPCR in post-treatment tumor and non-neoplastic tissue samples from 68 breast carcinoma patients treated by anthracycline and/or taxane based neoadjuvant chemotherapy. EIF2B1, MRPL19, IPO8, and UBB were used as reference genes for data normalization.

first: Viktor

last: Hlavac

first: Radka

last: Vaclavikova


title: Gene expression in natural subyearling fall Chinook salmon in the Snake and Clearwater Rivers

status: Public on Jun 20 2014

city: Cook

first: Helena

last: Christiansen

state: WA

address: 5501A Cook-Underwood Rd

department: Western Fisheries Research Center

institute: U.S. Geological Survey

summary: We used gene expression accompanied by physical characteristics and gill Na+/K+-ATPase activity to analyze physiological differences associated with two life history variations of juvenile fall Chinook Salmon in the Snake River basin. Subyearlings originating in the Snake River typically migrate seaward as subyearlings, whereas many subyearlings from the Clearwater River delay seaward migration during summer and complete seaward migration the following spring as yearlings.  We examined gill Na+/K+-ATPase activity and gene expression of subyearlings at different times during rearing and seaward emigration.   Natural-origin Snake River subyearlings rearing under an increasing photoperiod and seasonally increasing temperatures showed a typical increasing pattern of parr to smolt gill  Na+/K+-ATPase activity development, which then declined into autumn.  In contrast, Clearwater River subyearlings that had experienced cooler temperatures showed no pattern of increasing gill Na+/K+-ATPase activities and were not different from parr.  Liver transcription of genes involved in DNA repair and binding, the cell cycle, metabolism (steroid, fatty acid and other metabolic pathways) iron homeostasis, heme and oxygen binding, the immune response, and male sexual development were enriched amongst genes differentially expressed between Snake River parr versus smolts.  Gene expression results confirmed that Clearwater River subyearlings were parr-like in their physiological status.  By autumn, subyearlings had low gill Na+/K+-ATPase activities despite their large size and external smolt characteristics.  We suggest that environmental factors like temperature and photoperiod influence subyearling physiological status in each river that ultimately dictates juvenile life history pathways.

overall_design: Non-migrating and migrating natural subyearling fall Chinook salmon were collected from the Snake River. Non-migrating natural subyearling fall Chinook salmon were collected from the Clearwater River. Twelve fish were collected at each of four different time points for a total of 48 fish. Total RNA was extracted from the liver of each fish. Equal amounts of RNA from three fish were pooled to create four pools of RNA per time point. Each RNA pool was hybridized to an array for a total of 16 arrays with four arrays per time point.

middle: E

first: Kenneth

last: Tiffan


title: Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism

status: Public on Mar 13 2014

first: miaomiao

last: Zhou

summary: The genome of the filamentous fungus Aspergillus niger is rich in genes encoding pectinases, a broad class of enzymes that have been extensively studied due to their use in industrial applications.  The sequencing of the A. niger genome provided more knowledge concerning the individual pectinolytic genes, but relatively little is still known about the regulatory genes involved in pectin degradation. Understanding regulation of the pectinolytic genes provides a tool to optimize the production of pectinases in this industrially important fungus. This study describes the identification and characterization of one of the activators of pectinase-encoding genes, RhaR. Inactivation of the gene encoding this regulator resulted in down-regulation of genes involved in the release and catabolism of L-rhamnose from the pectinolytic substructure rhamnogalacturonan I.

overall_design: We aim to discover differencial expressed genes in A.niger wild type strain N402 and ΔrhaR mutant while growing on rhamnose as carbon source. Biological duplicates were made for both strain at the growth of 2 hours, Affymetrix microarray experiments were performed on these samples.

first: Birgit

last: Gruben

first: Miaomiao

first: Ad

last: Wiebenga

first: Joost

last: Ballering

first: Karin

last: Overkamp

first: Peter

last: Punt

first: Ronald

last: de Vries


title: Transcriptome analysis of blood monocytes from sepsis patients

status: Public on May 14 2014

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

summary: Blood monocytes serve as the first line of host defense and are equipped to recognize and respond to infection by triggering an immune-inflammatory response. While most information on these cells comes from in vitro studies in humans or in vivo studies in mice,  little is known about monocytes under human disease conditions. We investigated the role of monocytes during sepsis and its resolution in humans.  A transcriptomal and functional  analysis of blood monocytes from patients during gram negative sepsis and at recovery was performed. Monocytes from sepsis patients showed upregulation of a large number of pro-inflammatory  genes and cytokines/chemokines, consistent with an ongoing systemic inflammation. However, these cells showed impairment to ex vivo endotoxin (LPS) challenge, displaying a quantitative decrease in the number of LPS-inducible genes. Moreover, they downregulated the expression  of several pro-inflammatory cytokine/chemokine genes, activation marker genes and transcription factors associated with monocyte/macrophage activation, upon ex vivo LPS stimulation. Functionally, they downregulated expression of inflammatory cytokines/chemokines and antigen presentation-related molecules and functions. In contrast, genes and functions related to phagocytosis, anti-microbial activity and tissue remodeling where remained unaffected or even enhanced . Collectively, our observations suggest a genetic and functional re-programming of these cells during human sepsis progression. Understanding the molecular mechanisms which regulate this re-programming will allow  to devise strategies which could modulate the response of these cells and hence, disease progression.

overall_design: Blood monocytes from gram-negative sepsis patients during sepsis (Sepsis) and following their recovery (Recovery/Basal)  as well as healthy donor (control) were isolated. Thereafter, these cells were treated ex vivo with or without LPS for 3h and  analysed for transcriptomic study.

first: Subhra

middle: K

last: Biswas


title: Molecular rules governing de novo methylation in cancer

status: Public on Mar 26 2014

city: Jerusalem

first: Deborah

last: Nejman

address: Ein Kerem

institute: Hebrew University

type: Methylation profiling by genome tiling array

summary: De novo methylation of CpG islands is seen in many tumors, but the general rules governing this process are not known.  By analyzing DNA from tumors, as well as normal tissues, and by utilizing a wide range of published data, we have been able to identify a well-defined set of tumor targets, each of which has its own “coefficient” of methylation that is largely determined by its inherent relative ability to recruit the polycomb complex.  This pattern is initially formed by a slow process of de novo methylation that occurs during aging and then undergoes expansion early in tumorigenesis, where it may play a role as an inhibitor of development-associated gene activation.  We also demonstrate that DNA methylation patterns can be used to diagnose the primary tissue source of tumor metastases.

overall_design: CpG-methylated genomic DNA was enriched using a methyl-DNA immunoprecipitation (mDIP) assay. DNA from the input and bound (enriched) DNA for each sample were labeled and hybridized on the array to define the methylation state of each region.

first: Howard

last: Cedar


title: MicroRNA-21 dysregulates the expression of MEF2C in neurons in monkey and human SIV/HIV neurological disease

status: Public on Feb 18 2014

city: Omaha

last: Fox

state: Nebraska

address: 985800 Nebraska Medical Center - DRC 3008

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

summary: MicroRNAs (miRNAs) have important roles in regulating a plethora of physiological and pathophysiogical processes including neurodegeneration. In both human immunodeficiency virus (HIV)-associated dementia in humans and its monkey model simian immunodeficiency virus encephalitis (SIVE), we find miR-21, a miRNA largely known for its link to oncogenesis, to be significantly upregulated in the brain. In situ hybridization of the diseased brain sections revealed induction of miR-21 in neurons. miR-21 can be induced in neurons by prolonged N-methyl-D-aspartic acid receptor stimulation, an excitotoxic process active in HIV and other neurodegenerative diseases. Introduction of miR-21 into human neurons leads to pathological functional defects. Furthermore, we show that miR-21 specifically targets the mRNA of myocyte enhancer factor 2C (MEF2C), a transcription factor crucial for neuronal function, and reduces its expression. MEF2C is dramatically downregulated in neurons of HIV-associated dementia patients, as well as monkeys with SIVE. Together, this study elucidates a novel role for miR-21 in the brain, not only as a potential signature of neurological disease, but also as a crucial effector of HIV-induced neuronal dysfunction and neurodegeneration.

overall_design: Total cellular RNA was isolated from frozen (−80°C) brain specimens by using TRIzol (Invitrogen, Carlsbad, CA, USA) for the monkey samples, and RNAzol (Biotecx Laboratories, Houston, TX, USA) for the human samples, followed by column purification (miRNeasy, Qiagen, Valencia, CA, USA) as per manufacture's instructions. For the monkeys, four samples were from uninfected animals and four from SIV-infected animals that developed simian AIDS with SIV encephalitis. For the human samples, six samples were from individuals who were HIV negative with no history of dementia or neurocognitive disability and showed no significant neuropathology. Five samples were from HIV positive individuals that were neurocognitively impaired (NNTC clinical rating >6)38 and a neuropathological diagnosis of HIV encephalitis. Clinical information is provided in the supplemental material. For microarray analysis, only three of the HAD specimens were sufficient for use, but all five were used for the qRT-PCR studies.


title: Detection of aberrant DNA methylation in undifferentiated and differentiated human ES cells compared to normal fetal tissues

status: Public on Feb 04 2014

summary: Embryonic stem cells can be differentiated in vitro to produce a variety of somatic cell types. We have employed the mDIP method combined with hybridization to a tiling microarray to obtain a genome-wide methylation analysis of all UnMethylated Regions(UMRs).  We show that this differentiation is accompanied by an intrinsic process of extensive aberrant CpG island de novo methylation that includes developmental and cancer target genes.


title: Domains of genomewide gene expression dysregulation in Down syndrome [array]

status: Public on Apr 08 2014

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

summary: Trisomy 21 (T21) is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in T21, and to eliminate the noise of the genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for T21. Here we show that the differential expression between the twins is organized in domains along all chromosomes that are either up- or downregulated. These gene expression dysregulation domains (GEDDs) can be defined by the expression level of their gene content, and are well conserved in induced pluripotent stem cells derived from the twins’ fibroblasts. Comparison of the transcriptome of the Ts65Dn mouse model of DS and wild-type, also showed GEDDs along the mouse chromosomes that were syntenic in human. The GEDDs correlate with the lamina-associated (LADs) and replication domains of mammalian cells. The overall LADs position was not altered in trisomic cells. However, the H3K4me3 profile of the trisomic fibroblasts was modified and accurately followed the GEDD pattern. These results suggest that the nuclear compartments of trisomic cells undergo modifications of the chromatin environment influencing the overall transcriptome and that GEDDs may therefore contribute to some T21 phenotypes.

overall_design: LaminB1-chromatin interactions in a pair of monozygotic twins discordant for trisomy21

first: Federico

last: Santoni

first: Ximena

last: Bonilla

first: M

middle: R

last: Sailani

first: David

last: Gonzalez

first: Jop

last: Kind

first: Claire

last: Chevalier

first: Robert

last: Thurman

first: Richard

last: Sandstrom

first: Youssef

last: Hibaoui

first: Konstantin

last: Popadin

first: Emilie

last: Falconnet

first: Maryline

last: Gagnebin

first: Corinne

last: Gehrig

first: Anne

last: Vannier

first: Michel

last: Guipponi

first: Laurent

last: Farinelli

first: Daniel

last: Robyr

first: Marco

last: Garieri

first: Eugenia

last: Migliavacca

first: Christelle

last: Borel

first: Samuel

last: Deutsch

first: Anis

last: Feki

first: John

last: Stamatoyannopoulos

first: Yann

last: Herault

first: Bas

last: van Steensel

first: Roderic

last: Guigo

first: Stylianos

last: Antonarakis


title: Transcriptome analysis of zones of colonies of the ΔflbA strain of Aspergillus niger

status: Public on Feb 13 2014

first: Pauline

last: Krijgsheld

address: Padualaan 8

department: Sciences

institute: Utrecht University

summary:
Gene expression was studied at the periphery, an intermediate zone, and the centre of wild-type and ∆flbA colonies using Affymetrix A. niger whole genome microarrays.
We used Affymetrix GeneChip A. niger Geome Arrays and identifed up- and down-regulated genes that may account for the differences between wild-type and  ΔflbA colonies.

overall_design: RNA was isolated from a biological duplicate of concentric zones of 7-day old wildtype and mutant colonies. Zone 1 represented the most central zone, zone 3 an intermediate zone, and zone 5 the peripheral zone. Mycelium of the distinct zones was harvested from three colonies.

first: Han

last: Wösten


title: Host transcripts detected in exosomes derived from M.tb infected murine RAW264.7 macrophages

status: Public on Sep 15 2014

city: Notredame

first: prachi

last: singh

state: indiana

address: 130 Galvin

department: biological sciences

institute: university of notredame

summary:
Investigation to study mRNA transcripts present in exosomes from M.tb infected cells and how they compare to those derived from uninfected cells. Transcripts were also studied in donor macrophages as controls
The gene expression study identified unique transcripts as well as differentially expressed transcripts present in exosomes released from infected macrophages

overall_design: Total RNA isolated from exosomes or donor macrophages was converted to cDNA, labeled and hybridized onto whole mouse genome arrays from Nimblegen MM8_60mer_expr.ndf. Four sample each with three experimental replicates were included in the study.

first: Prachi

last: Singh

first: Jeffrey

last: Schorey


title: Expression analysis for detection of mycobacterial transcripts present in exosomes derived from M.tb infected macrophages

summary:
Mycobacterial transcripts were identified in exosomes released from M.tb infected RAW264.7 macrophages that were not present in uninfected exosomes suggesting export of mycobacterial RNA via exosomes
Mycobacterial RNA was used as positive control and RNA from exosomes released from uninfected macrophages was used as negative control

overall_design: Total RNA isolated from exosomes or mycobacteria was reverse transcribed to ds cDNA which wa slabeled with Cy3 and hybridized to custom whole M.tb genome array from Nimblegen 120910_Mtub_AD_expr.ndf

first: Jeff