title: Transcriptomic effects of estradiol treatment on cultured human uterine smooth muscle cells

status: Public on Jun 02 2014

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

summary: The myometrium is an important reproductive tissue composed primarily of smooth muscle cells. Contractility of the myometrial smooth muscle cells during the estrous cycle and pregnancy is modulated by estrogen. Despite much research, little is known about the molecular mechanism by which estrogen regulates myometrial contractility. This study investigates global gene expression profile of cultured human uterine smooth muscle cells (hUtSMCs) following 17β-estradiol (E2) treatment using cDNA microarray technology. In response to E2 treatment 540 genes were identified as significantly differentially expressed. Gene ontology analysis identified several significant biological processes for these genes including muscle contraction, gland development, cell migration, cell adhesion, apoptosis, response to external stimulus and phosphorylation. In this study evidence is presented that in human smooth muscle cells 17β-estradiol, contrary to expectations, altered expression of several genes that may favor myometrial relaxation. Genes related to focal adhesion function were downregulated suggesting a loosening of SMC connections to the ECM while upregulation of MMP9 is also associated with weakened ECM interactions. The hUtSMC system is an additional useful model to investigate steroid effects on smooth muscle cells in isolation from other myometrial cell types.

overall_design: In this study human myometrial smooth muscle cells (hUtSMC) purchased from Lonza were cultured and treated with 17beta estradiol. RNA was isolated after 6h, 24h and 72h from both treated and untreated control cells. The experiment was repeated at least 3 times.

first: Sreenath

last: Chandran

first: Margaret

last: O'Brien

first: Terry

last: Smith


title: aCGH assay in a Chinese family with syndactyly type 1-c

status: Public on Jun 01 2014

city: Chongqing

first: Hong

last: Guo

address: 30# Gaotanyan St. Shapingba District

department: Medical Genetics

country: China

institute: Third Military Medical University

type: Genome variation profiling by genome tiling array

summary: Syndactyly type 1 (SD1) is an autosomal dominant limb malformation characterized in its  classical form by complete or partial webbing between the third and fourth fingers and/or the second  and third toes. Four subtypes (a, b, c and d) are defined based on variable phenotypes, but the disease  genes remain unidentified. SD1-a have been mapped to chromosome 3p21.31 and SD1-b to 2q34-q36.  SD1-c and SD1-d are very rare and no gene loci are known for them. We performed linkage and  haplotype analyses in two Han Chinese families with SD1-c, and refined the disease locus to 2q31-  2q32. In the large family A, mutation of c.917G>A (p.R306Q) in the homodomain of HOXD13 was  indentified. Family B was confirmed with genetic homogeneity and the mutation was c.916C>G  (p.R306G). CNV analysis by array CGH excluded possible microdeletion or microduplication.

overall_design: SD1c patient sample in the SD1c family vs common control outside the family, healthy control sample in the SD1c family vs common control outside the family

first: Yun

last: Bai


title: MH003A:FOXO3 in control of circadian rhythms via direct regulation of Clock. Part 1: overexpression of FoxO6

status: Public on Jun 03 2014

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Circadian rhythms are responsive to a variety of external cues, light and metabolism being the most important. In mammals, the light signal is sensed by the retina and transmitted to the SCN master clock, where it is translated into the molecular oscillator via regulation of clock gene transcription. The signalling pathways governing the molecular translation from metabolic signals to circadian output in peripheral oscillators, in contrast, are less understood. FOXO transcription factors are known to translate external metabolic cues to internal transcriptional programs. In the past couple of years it has become evident that both FOXO transcription factors and the circadian clock are of key importance in the underlying mechanisms of ageing and the regulation of metabolism. We now show FOXO3 to be a crucial modulator of circadian rhythmicity via direct transcriptional regulation of Clock, a core component of the molecular oscillator, and identify FOXO3 as a novel link in the circadian feedback loop, which is required for circadian rhythms in liver. We propose that FOXO3 directly feeds back into the circadian oscillator in response to metabolic cues.

overall_design: We performed a microarray study on synchronized NIH 3T3 cells upon transient overexpression of FoxO6 (oeO6). Cells were harvested for RNA isolation 24h (time1), 30h(time2), 36h(time3) and 42h(time4) after synchronization. Experimental samples were hybridized against a reference pool of cRNA, which was derived from unsynchronized NIH 3T3 cells. Experiments were performed 4 times, of each sample group two samples were labeled with cy5 and co-hybridized with reference RNA labeled with cy3, and two samples were labeled and hybridized in the opposite way. Microarrays used were Mouse Whole Genome Gene Expression Microarrays V1 (Agilent Technologies, Belgium)

first: Ines

last: Chaves

first: Gijsbertus

middle: T

last: van der Horst

first: Raymond

last: Schellevis

first: Romana

middle: M

last: Nijman

middle: G

last: Koerkamp

first: Frank

middle: C

last: Holstege

first: Marten

middle: P

last: Smidt

first: Marco

middle: F

last: Hoekman


title: Acyclic nucleoside phosphonates: a study on cytochrome P450 gene expression

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
Focused on the cytochromes P450 (CYPs), we studied gene expression changes in mice treated with acyclic nucleoside antivirals adefovir and tenofovir. Positive control group was treated by prototypic CYP inducers phenobarbital and beta-naphthoflavone.
Expression profiling with Steroltalk cDNA arrays revealed major changes in CYP mRNA expression in the inducers-treated group but only minor changes in CYP expression in the adefovir and tenofovir groups.

overall_design: 3 groups representing treatments with adefovir, tenofovir and phenobarbital + beta-naphthoflavone. 4-5 animals in each group + a dye swap. Pooled samples from 10 animals treated with saline was used as a reference. Daily application of antivirals for three days, samples were collected after 24 hours from the last treatment.

first: Jana

last: Nekvindova

first: Juan

middle: A

last: Contreras

first: Klementina

last: Tacer

first: Eva

last: Anzenbacherová

first: Zdenek

last: Zidek

first: Damjana

last: Rozman

first: Antonin

last: Holy

first: Pavel

last: Anzenbacher


title: Autophagy regulator DRAM1 functions downstream of MYD88 in defense against tuberculosis (array)

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

institute: Institute of Biology, Leiden University

summary: MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. We infected these MyD88 mutants and wildtype individuals with S Mycobacterium marinum to compare the resulting immune response by transcriptome profiling on total RNA isolated from single embryos. Autophagy regulator dram1 was identified as one of the MyD88-dependent genes.

overall_design: This microarray study was designed to determine the effect of a truncation of the MyD88 protein on the innate immune response of zebrafish embryos during infection with Mycobacterium marinum. Embryos used in this study are derived from an incross between parents heterozygous for the mutation. Both homozygous mutants and their wildtype siblings were selected by genotyping after being injected with the bacteria or PBS as control. RNA was isolated from single embryos at 4 days post infection (4 dpi) and each treatment group consisted of three embryos: (1) Homozygous mutants mock-injected with PBS/2%PVP 4 dpi, (2) wildtype siblings mock-injected with PBS/2%PVP 4dpi, (3) M. marinum-infected homozygous mutants 4dpi, (4) M. marinum-infected wildtype siblings 4dpi. Embryos were grown at 28.5–30°C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of Mycobacterium marinum Mma20 bacteria into the caudal vein, or were mock-injected with buffer (PBS/2%PVP) as a control.  After injections embryos were transferred into fresh egg water and incubated for 4 days at 28°C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. The treatment groups were analyzed using a common reference approach.

first: M

last: van der Vaart

first: H

last: Spaink

first: A

middle: H


title: Real-time quantitative PCR analysis of human colonic HT-29 cells under insulin stimulation

city: BERN

first: Brigitte M.

last: FREY

state: BERN

address: Freiburgstrasse 15

department: Nephrology hypertension

country: Switzerland

institute: DKF

summary:
Compared mRNA expression between control and insulin treated cells. HT29 cells were treated with 100nM Insulin for 24h.
The RT2 Profiler PCR Arrays PAHS-30C (SA Biosciences, MD, USA) was designed to analyze 84 genes related to human insulin signaling pathway. The RT-PCR was carried out using an ABI PRISM® 7000 Sequence Detection System (Applied Biosystems, Foster City, CA).The expression of HSD11B2 for the 3 experiments concerned was monitored in parallel by real time PCR which confirming significant downregulation by insulin.

overall_design: qPCR gene expression profiling.  RNA from 3 separated experiments was collected.

first: Thomas

last: Andrieu

first: Brigitte

last: Frey


title: MicroRNAs in an Experimental Model of Physiologic Left Ventricular Hypertrophy: a Microarray-based Analysis

city: Porto Alegre

first: Nidiane

middle: Carla

last: Martinelli

state: Rio Grande do Sul

address: AV ALEGRETE, 414/202

department: Cardiology Division at Hospital de Clínicas de Porto Alegre

country: Brazil

institute: Federal University of Rio Grande do Sul

summary: BACKGROUND - MicroRNAs (miRs) are a class of small non-coding RNAs that regulate gene expression. Transgenic models have proved that a single miR can induce pathological cardiac hypertrophy and failure. The roles of miRs in the genesis of physiologic left ventricular hypertrophy (LVH), however, are not well elucidated.  OBJECTIVE - To evaluate miRs expression in an experimental model of exercise-induced LVH. METHODS - Male Balb/c mice were divided into sedentary (SED) and exercise (EXE) groups. Voluntary exercise was performed in odometer-monitored metal wheels during 35 days. Analyses were performed after 7 and 35 days of training, and consisted of transthoracic echocardiography, maximal exercise test, miRs microarray (miRBase v.16) and real-time qRT-PCR analysis. RESULTS - Left ventricular weight/body weight ratio increased by 7% in the EXE group at day 7 (p<0.01) and by 11% at 35 days of training (p<0.001) After 7 days of training, microarray identified 35 deregulated miRs: 20 had an increase in their expression and 15 were down-regulated (p=0.01). At day 35 of training, 25 miRs were deregulated: 15 were up-regulated and 10 had decreased their expression compared to the SED group (p<0.01). qRT-PCR confirmed an increase in miR-150 levels at both time points and a decrease in miR-26b, miR-27a and miR-143 after 7 days of voluntary exercise.  CONCLUSIONS – We unraveled new miRs that can modulate physiological cardiac hypertrophy, particularly miR-26b, -150, 27a and -143. Our data also indicate that previously established regulatory gene pathways involved in pathological LVH are not deregulated in physiologic LVH.

overall_design:
Experimental model of left ventricular hypertrophy induced by voluntary exercise
Male Balb/c mice, 8-10 weeks old, 4 groups analyzed, each group consisted of a pool from 4 animals

first: Carolina

middle: R

last: Cohen

first: Kátia

last: dos Santos

first: Andréia

last: Biolo

first: Luzia

last: Frick

first: Daiane

middle: N

last: Silvello

first: Stéfanie

last: Schneider

first: Michael

middle: E

last: Andrades

first: Nadine

last: Clausell

first: Ursula

last: Matte

first: Luis

last: Rohde


title: Using C. intestinalis to study Islet in ascidian palp morphogenesis

status: Public on May 23 2014

city: Berkeley

first: Justin

last: Choi

state: CA

address: 255 Life Sciecnces Addition

department: Functional Genomics lab

country: USA

institute: UC Berkeley

summary:
In Ciona intestinalis, the palps consist of three conical protrusions within a field of thickened epithelium that form late in embryogenesis as tailbuds mature into larvae. The palp protrusions express the LIM-homeodomain transcription factor Islet. Protrusion occurs through differential cell elongation, likely mediated by Islet, as we find that ectopic expression of Islet is sufficient to promote cell elongation. FGF signaling is required for both Islet expression and palp morphogenesis. Importantly, we show that Islet expression can rescue the palp-deficient phenotype that results from inhibition of FGF signaling. We conclude that Islet is a key regulatory factor governing morphogenesis of the palps. It is conceivable that Islet is also essential for the cellular morphogenesis of placode-derived sensory neurons in vertebrates.
Islet expression can rescue the palp-deficient phenotype that results from inhibition of FGF signaling, and conclude that Islet is a key regulatory factor governing morphogenesis of the palps.

overall_design: Three biological replicates were analyzed for both sample types (Fox positive and Negative).

first: Eileen

last: Wagner

first: Alberto

last: Stolfi

first: Yoon

first: Mike

last: Levine


title: Genome-wide analysis of gene expression variation in CD4+ T cells from patients with active rheumatoid arthritis (RA).

status: Public on May 26 2014

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

summary: Analysis of the regulatory architecture of gene expression variation in CD4+ T cells from patients with active RA. We have integrated gene expression with genotyping data in order to identify eQTLs that characterize the gene expression of CD4+ T cells in active RA.

overall_design: CD4+ T cell RNA was extracted from 26 patients with active RA. All samples were used to study the genetic regulatory mechanisms of CD4+ T cells in active Rheumatoid Arthritis.

first: Aterido

last: Adrià

first: Julià

last: Antonio

first: Marsal

last: Sara


title: High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation [microarray]

status: Public on Jun 06 2014

city: QINGDAO

first: Muyan

last: Chen

address: 5 YUSHAN ROAD

institute: Ocean University of China

summary: The regulatory role of miRNA in gene expression is an emerging hot new topic in the control of hypometabolism. Sea cucumber aestivation is a complicated physiological process that includes obvious hypometabolism as evidenced by a decrease in the rates of oxygen consumption and ammonia nitrogen excretion, as well as a serious degeneration of the intestine into a very tiny filament. To determine whether miRNAs play an important regulatory roles in this process, the present study analyzed profiles of miRNA expression in the intestine of sea cucumber (Apostichopus japonicus), using Solexa deep sequencing technology. We identified 309 sea cucumber miRNAs, including 19 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA) after at least 15 days of continuous torpor, were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 42 differentially expressed miRNAs (RPM (reads per million) >10, |FC| (|fold change|) ≥1, FDR<0.01) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-200-3p, miR-2004, miR-2010, miR-22, miR-252a, miR-252a-3p and miR-92 were significantly over-expressed during deep aestivation compared with non-aestivation animals. Preliminary analyses of their putative target genes suggest that these miRNAs could play important roles in global transcriptional depression during aestivation.

overall_design: In the present study,we present for the first time, using Solexa sequencing technology, an analysis of the global profile of small RNAs in non-aestivation (NA) and deep aestivation (DA) sea cucumbers. We focus on intestine in the present study because it is the major site responsible for the strong metabolic rate depression seen under deep aestivating conditions and the global expression profile of mRNA from the this organ has also been constructed applying RNA-seq technology in our previous study (Zhao and Chen, unpublished data). A preliminary analysis of the functional relevance of miRNA expression in relation to hypometabolism during aestivation is presented. A miRNA microarray and RT-qPCR were both used to supplement and confirm differentially expressed miRNAs. Our findings provide important new insights into the molecular mechanisms of sea cucumber aestivation.


title: MicroRNA expression array of 1833 cells: control vs. HMGA2 shRNA

city: Chicago

first: Miao

last: Sun

institute: University of Chicago

summary: HMGA2 has been implicated in tumor progression. Identification of microRNAs regulated by HMGA2 helps us to understand how HMGA2 regulates tumor metastasis via its downstream target mircoRNAs and genes.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Total RNA was extracted from 1833 cells with control or depleted HMGA2 expression, respectively. Exiqon miRCURY LNA 5th generation expression array was performed to identify the microRNAs regulated by HMGA2.

first: Marsha

last: Rosner


title: Gene expression profiling of Wt1 mutant renal anlagen

city: Nice

first: Andreas

last: Schedl

address: Parc Valrose

department: iBV

country: France

institute: University of Nice

summary:
Wt1 is required for renal development and homozyogus knockout mice show renal agenesis caused by apoptosis of the metanepric mesnchyme.
To identify genes regulated by WT1, we performed comparative gene expression profiling on kidney rudmients of Wt1 heterozygous and homozygous mutant E10.25 embryos.

overall_design: To identify deregulated genes, timed matings were performed and embryos isolated at E10.25, a time point before the onset of apoptosis in Wt1 mutants.  The region containing the metanephric mesenchyme was microdissected, RNA isolated and after labeling, hybridized to Mouse Genome Survey Microarrays. Deregulated genes were identified using GeneSpring (GSX) software.

first: Rita

last: Lecca

first: Danielle

last: Badro

first: André

last: Brändli


title: Gene expression of T47D-MTVL human breast cancer cells upon H1.4 knock-down or overexpression

status: Public on May 16 2014

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

institute: IBMB-CSIC

summary: Gene expression of T47D-MTVL human breast cancer cells expressing Dox-inducible shRNAs against histone H1.4 (sh120) or multiple H1 variants (sh225), or overexpressing WT or K26A mutant HA-tagged H1.4.

overall_design:
T47D-MTVL, breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter, is stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.
Stable breast cancer-derived cell lines expressing an shRNA against one of each of the histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox, in duplicate, and RNA extracted for microarray hybridization. Cell lines used: inducible shRNA against  H1.4 or  multiple H1 variants, and random shRNA-expression vector. Stable breast cancer-derived cell lines expressing  the histone H1.4 isoform, WT or K26A, HA-tagged, in duplicate, and RNA extracted for microarray hybridization. Cell lines used: overexpressing  H1.4 WT or  K26A mutant.

first: Jean-Michel

last: Terme

first: Lluís

last: Millán-Ariño


title: Expression analysis of WASH knockout LT-HSC cells

status: Public on May 17 2014

city: Beijing

first: Pengyan

last: Xia

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of biophysics, Chinese Academy of Sciences

summary: Investigation of whole genome gene expression level changes in WASH knockout LT-HSCs, compared to the WASH WT strain.  To find the reason that causes LT-HSC abnormal.

overall_design: Gene expression profiling using sorted LT-HSC samples from C57/BL6 strain. Total RNA extracted from WASH     control (isolated RNA from WT, IRWT) and knockout mice (IRKO) were quantified by the NanoDrop ND-1000 and     RNA integrity was assessed by standard denaturing agarose gel electrophoresis.Each chip measures the     expression level of 44, 170 genes from Mus Musculus.

first: Shuo

last: Wang


title: miRNA expression profiling of ALL samples

city: Singapore

first: Chong-Lei

last: Bi

address: #12-02, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

summary: We performed a comprehensive genome-wide miRNA expression profiling (MEP) of adult ALL samples with known genetic and clinical characteristics (n=65) in comparison with normal, non-malignant samples, with the objective of understanding the pathogenetic role of miRNA deregulation in ALL.

overall_design: Total RNA, including miRNA, were extracted using Trizol and profiled using Agilent human miRNA V2.

first: Kow-Yin

last: Kham

first: Yeow-Liang

last: Seah

first: Eng-Juh

last: Yeoh

first: Xue-Ling

last: Boo

first: Gao-Feng

last: Huang

first: Jun-Li

last: Yan

first: Bao-Hong

last: Lin

first: Wee-Joo

last: Chng


title: Hong Shan Capsule (HSC) offers radioprotection and modulates acute lethal total-body irradiation-induced alterations of gene expression in rats

status: Public on May 15 2014

city: ShangHai

first: Jian-Zhong

last: Li

address: Guo He Road 325#

institute: Second Military Medical University

summary:
To further investigate the potential molecular basis of the protective effects of HSC on irradiation (6.5Gy)  damage, gene expression analysis was conducted on rats liver tissues using microarrays.Pre-treatment with HSC prevented differential expression of 66% (1,398 genes) of 2,126 genes differentially expressed in response to radiation.
Pathway enrichment analysis indicated that these genes were mainly involved in a total of 32 pathways, such as olfactory transduction,  uroactive ligand-receptor interaction, pathways in cancer, calcium signaling pathway, vascular smooth muscle contraction, cytokine-cytokine receptor interaction, mitogen-activated protein kinase (MAPK) signaling pathway, peroxisomal proliferator-activated receptor (PPAR）signaling pathway, gonadotropin-releasing hormone (GnRH) signaling pathway, Wnt signaling pathway, janus kinase-signal transducers and activators of transcription (Jak-STAT) signaling pathway, Notch signaling pathway.Our analysis indicated that the pretreatment of rats with HSC attenuated radiation-induced these pathways, such as multiple MAPK pathways, suggesting that the protective effect of HSC acts mainly through the attenuation of these pathways.

overall_design: The rats were randomly assigned to one of the three following treatment groups (10-12 animals per group): normal control, radiation and HSC dose (10g/kg body weight/day) + radiation. HSC dissolved in double distilled water were administered intragastrically to the male animals for 3 consecutive days before irradiation. Radiation induced gene expression in rat liver was measured at 24 hours after 6.5 Gy exposure.

first: Jian

middle: Z


title: microRNA Expression Profile on Stimulated Peripheral Blood Mononuclear Cells from HIV-1 infected Elite Controllers, Viremic Patients, Treated Patients and Uninfected Donors

status: Public on May 06 2014

first: Mireia

last: Arnedo

state: Other

address: Casanovas, 143. CELLEX, A41

department: AIDS Unit

institute: Institut Investigacions Biomediques Agusti Pi i Sunyer (IDIBAPS)

summary:
Background: The emerging relationship between microRNAs (miRNA) and viral-control is a topic of interest in the field of HIV. Host-genome might play an important role in the control of viremia. The aim of this study was to assess the specific miRNA profile that could contribute to the control of HIV replication in Elite Controllers
Results: After adequate normalization, expression profile of 286 human miRNAs (hsa-miR) was evaluated in phytohaemagglutinin-stimulated PBMCs from 29 individuals classified in 4 groups: 8 elite controllers (EC; viral load <50 cp/ml without treatment), 8 viremic progressors (VP; VL>5000 cp/ml without treatment), 8 patients under antiretroviral treatment (ART; VL<200cp/ml) and 5 uninfected individuals (HIV-) through TaqMan® Array Human microRNA Cards v3.0.  A differential expression pattern consisting of 23 miRNAs overcame significantly different when comparing EC and VP. Profiling analysis segregated the population in two different blocks: while EC and HIV- clustered together in the same block (EC/HIV-_block 1), VP and ART individuals clustered together in a second block (VP/ART_block 2). Two inversely expressed miRNA patterns were determined within those two blocks: a set of 4 miRNAs (hsa-miR-221, -27a, -27b and -29b) was up-expressed in EC/HIV-_block and down-expressed in VP/ART_block while 19 miRNAs were down-expressed in block 1 and up-expressed in block 2. Differential miRNAs were successfully validated through individual RT-qPCR assays.
Conclusions: Profile in EC resembled HIV- and differentially clusters with VP and ART. Therefore, differential clustering does not rely on undetectable viremia.

overall_design: Peripheral blood mononuclear cell were collected and processed from five uninfected controls, eight HIV-1-infected viremic patients, eight HIV-1-infected elite controllers with undetectable viral load without treatment and eight HIV-1-infected antiretroviral-treated individuals with undetectable viral load.

first: L

last: Egaña-Gorroño

first: T

last: Escribà

first: N

last: Boulanger

first: AC

last: Guardo

first: A

last: León

first: ME

last: Bargalló

first: F

last: Garcia

first: JM

last: Gatel

first: M

last: Plana


title: miRNA expression profiles in rat Acute Respiratory Distress Syndrome (ARDS)

status: Public on May 07 2014

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

summary: Rat model of ARDS was induced by saline lavage and mechanical ventilation. miRNA from rat lungs were used for dual color DNA microarray hybridization with 3DNA 50 kit version 2.

overall_design: Two-condition experiment, CON vs. ARDS lung tissues. replicates: 6 control, 6 ARDS. One replicate per array.

first: Chaoqun

first: Lin

last: Liu


title: High-density deletion bin map of wheat chromosome 7B

status: Public on May 09 2014

city: Aas

first: Tatiana

last: Belova

address: arboretveien 6

department: department of plant science

country: Norway

institute: cigene

summary:
Using 270K Nimblegen Comparative Genomic Hybridization (CGH) array on a set of cv. Chinese Spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8% of chromosome 7B physical length) were mapped into nine deletion bins.
In our study we have developed 270K CGH Nimblegen array containing wheat 7B chromosome specific probes and genotyped wheat 7B deletion stocks which have terminal deletions in 7B.  Our main aim was to identify absent probes (sequences) in deletion lines.
Initially, spatial normalization and M-A loess normalization was performed for comparison test/reference and then clustering analysis (Mcust) was carried out. Further analysis was done on scaffolds (i.e. on larger sequences instead of probes; probes are designed from scaffolds)

sample_organism:
Triticum aestivum
Triticum turgidum subsp. durum

overall_design:
Hybridization of DNA from 13 wheat lines, including 11 Chinese Spring cytogenetic stocks (Del7BL-9, DT7BL, DT7BS, Del7BL-13, Del7BL-14, Del7BL-5, Del7BL-1, Del7BL-7Del1DS-3, Del7BL-2,Del7BS-2, Del7BL-3) and 2 replicates of Langdon (LDN) tetraploid wheat.
A set of 49,500 7B chromosome specific features (ISBP probes and random genomic features) and 18,000 control probes with each probe replicated four times on the 270K chip.

first: Lars

last: Grønvold

first: Ajay

last: Kumar

first: Shahryar

last: Kianian

first: Xinyao

last: He

first: Morten

last: Lillemo

first: Nathan

last: Springer

first: Sigbjørn

last: Lien

first: Odd-Arne

last: Olsen

first: Simen

last: Sandve


title: Progression to Latent Infection Following Exposure to Mtb

status: Public on Apr 19 2014

city: Covington

first: Deepak

last: Kaushal

state: LA

address: 18703 Three Rivers Rd

department: Microbiology & Immunology

institute: Tulane National Primate Research Center

summary:
These results were obtained in a controlled longitudinal experiment in which a group of rhesus macaques were exposed to a low dose of Mtb to study their progression to latent infection or active disease. Subsets of the animals were euthanized at scheduled time points, and granulomas taken from their lungs were assayed for gene expression.
The clinical profiles associated with the animals following Mtb exposure revealed considerable variability, and we developed models for the disease trajectory for each subject using a Bayesian hierarchical B-spline approach. Disease severity estimates were derived from these fitted curves and included as covariates in linear models to identify genes significantly associated with disease progression. Our results demonstrate that the incorporation of clinical data increases the value of information extracted from the expression profiles and contributes to the identification of predictive biomarkers for TB susceptibility.

overall_design: Samples from 21 animals were included in this study.   18 rhesus macaques were exposed to Mtb and euthanisized according to a pre-defined schedule, and at least two granulomas were extracted from their lungs during necropsy.  The remaining three animals were healthy controls and samples represent control lung tissues.  The samples were arrayed using an extended loop design with animals grouped according to similar clinical profiles.  Biological replication is provided in the form of at least two granuloma samples per animal.

first: Michelle

last: Lacey


title: Gene expression profiles in rat Acute Respiratory Distress Syndrome (ARDS)

status: Public on Apr 24 2014

summary: Rat model of ARDS was induced by saline lavage and mechanical ventilation. Total RNA from rat lungs were used for dual color DNA microarray hybridization with 3DNA 50 kit version 2.

overall_design: Two-condition experiment, CON vs. ARDS lung tissues. replicates: 5 control, 7 ARDS. One replicate per array.

last: Huang


title: Analysis of the Caulobacter crescentus Zur regulon reveals novel insights in zinc acquisition by TonB-dependent outer membrane proteins

status: Public on Apr 29 2014

city: São Paulo

first: Ricardo

middle: Ruiz

last: Mazzon

state: SP

address: Avenida Professor Lineu Prestes, 1374

department: Microbiology

institute: Institute of Biomedical Sciences from University of São Paulo

summary:
Intracellular zinc concentration needs to be maintained within strict limits due to its toxicity at high levels, and this is achieved by a finely regulated balance between uptake and efflux. Many bacteria use the Zinc Uptake Regulator Zur to orchestrate zinc homeostasis, but little is known regarding the transport of this metal across the bacterial outer membrane. In this work we determined the C. crescentus Zur regulon by global transcriptional and in silico analyses.
Among the genes directly repressed by Zur are those encoding a putative high affinity ABC uptake system (znuCBA), three TonB-dependent receptors (znuD, znuE and znuF) and one new putative transporter of a family not yet characterized (zrpW). Zur is also directly involved in the activation of a RND and a P-type ATPase efflux systems, as revealed by β-galactosidase and site-directed mutagenesis assays.
Several genes belonging to the Fur regulon were also downregulated in the zur mutant, suggesting a putative cross-talk between Zur and Fur regulatory networks. Interestingly, a phenotypic analysis of the znuD and znuE mutants has shown that these genes are essential for growth under zinc starvation, suggesting that C. crescentus uses these TonB-dependent outer membrane transporters as key zinc scavenging systems.

overall_design:
The DNA microarray experiments were performed as described in (da Silva Neto et al., 2013). Briefly, cDNA was generated from 12.5 µg of total RNA and labeled with either Cy3 or Cy5 fluorescent dyes (FairPlay III Microarray Labeling System, Stratagene).
Labeled cDNA samples were hybridized to a Caulobacter DNA oligo microarray (Agilent), and the arrays were scanned with an Agilent High Resolution Microarray Scanner. RNA from three independent biological cultures was used for DNA microarray analysis.
We considered as differentially expressed genes those showing a minimum of 2-fold change relative to the control, considering at least three out of the four last probes for each gene (that are downstream of the translational start site) in at least two of three biological replicates. The values for the relative expression of each gene were obtained as the average of the four last probes.

first: José

last: da Silva Neto

first: Vânia

middle: S

last: Braz

first: Marilis

middle: V

last: Marques


title: The RUNX2 Cistrome in Osteoblasts: Characterization, Downregulation Following Differentiation and Relationship to Gene Expression [gene expression]

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

summary: RUNX2 is a transcription factor that is first expressed in early osteoblast-lineage cells and represents a primary determinant of osteoblastogenesis.  While numerous target genes are regulated by RUNX2, little is known of sites on the genome occupied by RUNX2 or of the gene networks that are controlled by these sites.  To explore this, we conducted a genome-wide analysis of the RUNX2 cistrome in both pre-osteoblastic MC3T3-E1 cells (POB) and their mature osteoblast progeny (OB), characterized the two cistromes and assessed their relationship to changes in gene expression.  We found that although RUNX2 was widely bound to the genome in POB cells, this binding profile was reduced upon differentiation to OBs.  Numerous sites were lost upon differentiation, new sites were also gained; many sites remained common to both cell states.  Additional features were identified as well including location relative to potential target genes, abundance with respect to single genes, the frequent presence of a consensus TGTGGT RUNX2 binding motif, co-occupancy by C/EBPβ and the presence of a typical epigenetic histone enhancer signature. This signature was changed quantitatively following differentiation. While RUNX2 binding sites were associated extensively with adjacent genes, the distal nature of the majority of these sites prevented assessment of whether they represented direct targets of RUNX2 action. Changes in gene expression, however, revealed an abundance of genes that contained RUNX2 binding sites and were regulated in concert.  These studies establish a basis for further analysis of the role of RUNX2 activity and its function during osteoblast lineage maturation.

overall_design: RNA was isolated and applied to gene expression microarrays in undifferentiated MC3T3-E1 cells as well as post 15 day osteogenic differentiation MC3T3-E1 cells.  The samples were completed in biological triplicate.

first: Nancy

last: Benkusky

first: J

middle: W

last: Pike


title: Study of extremely low frequency electromagnetic field (ELF-EMF) responses of human HaCaT keratinocytes: Control vs. ELF-EMF

status: Public on Mar 29 2014

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

summary: Use DNA microarray technology to discover transciprtional insights of HaCaT for continuous exposure to ELF-EMF

overall_design: We used a loop design in this study (details in the 'loop_design.tiff' supplementary file), cDNA microarray experiment consisted of ten RNA samples, including ELF-EMF exposed, UVB irradiated (positive control), and sham exposed samples.

first: Chao-Ying

first: Ian

last: Hsu


title: Coral-Zooxanthellae Meta-Transcriptomics Reveals Integrated Response to Pollutant Stress

status: Public on Mar 26 2014

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

summary:
Short title: Coral Meta-Transcriptomics Reveal Pollutant Stress

Background: Corals represent symbiotic meta-organisms that require harmonization among the coral animal, photosynthetic zooxanthellae and associated microbes to survive environmental stresses. We investigated integrated-responses among coral and zooxanthellae in the scleractinian coral Acropora formosa in response to an emerging marine pollutant, the munitions constituent, 1,3,5-trinitro-1,3,5 triazine (RDX; 5 day exposures to 0 (control), 0.5, 0.9, 1.8, 3.7, and 7.2 mg/L, measured in seawater).

Results: RDX accumulated readily in coral soft tissues with bioconcentration factors ranging from 1.1 to 1.5). Next-generation sequencing of a normalized meta-transcriptomic library developed for the eukaryotic components of the A. formosa coral holobiont was leveraged to conduct microarray-based global transcript expression analysis of integrated coral / zooxanthellae responses to the RDX exposure. Total differentially expressed transcripts (DET) increased with increasing RDX exposure concentrations as did the proportion of zooxanthellae DET relative to the coral animal. Transcriptional responses in the coral demonstrated higher sensitivity to RDX compared to zooxanthellae where increased expression of gene transcripts coding xenobiotic detoxification mechanisms (ie. cytochrome P450 and UDP glucuronosyltransferase 2) were initiated at the lowest exposure concentration. Increased expression of these detoxification mechanisms was sustained at higher RDX concentrations as well as production of a physical barrier to exposure through a 40% increase in mucocyte density at the maximum RDX exposure. At and above the 1.8 mg/L exposure concentration, DET coding for genes involved in central energy metabolism, including photosynthesis, glycolysis and electron-transport functions, were decreased in zooxanthellae although preliminary data indicated that zooxanthellae densities were not affected. In contrast, significantly increased transcript expression for genes involved in cellular energy production including glycolysis and electron-transport pathways was observed in the coral animal.

Conclusions: Transcriptional network analysis for central energy metabolism demonstrated highly correlated responses to RDX among the coral animal and zooxanthellae indicative of potential compensatory responses to lost photosynthetic potential within the holobiont. These observations underscore the potential for complex integrated responses to RDX exposure among species comprising the coral holobiont and highlight the need to understand holobiont-species interactions to accurately assess pollutant impacts.

overall_design: Fragments of the living branched coral Acropora formosa were obtained from Oceans, Reefs and Aquaria (http://www.orafarm.com). Ten gallon aquaria were used to expose 5 coral fragments to control or RDX exposure conditions (0.49, 0.93, 1.77, 3.67 and 7.18 mg/L, measured concentrations). The microarray hybridization experiment included 3 biological replicates for the 0.5, 2, and 8 mg/L RDX conditions and 4 biological replicates for the control.

first: Fares

last: Najar

first: Tanwir

last: Habib

first: Guilherme

last: Lotufo

first: Alan

middle: M

last: Piggot

first: Bruce

last: Fouke

first: Jennifer

middle: G

last: Laird

first: Mitchell

last: Wilbanks

first: Arun

last: Rawat

first: Karl

middle: J

last: Indest

last: Roe

first: Edward

last: Perkins


title: Pten null prostate epithelium promotes localized myeloid-derived suppressor cell expansion and immune suppression during tumor initiation and progression [microdissected tissue]

status: Public on Apr 03 2014

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

summary: Chronic inflammation is known to associate with prostate cancer development, but how epithelium-associated cancer initiating events cross-talk to inflammatory cells during prostate cancer initiation and progression is largely unknown. Using the Pten null murine prostate cancer model, we show an expansion of Gr-1+CD11b+ myeloid-derived suppressor cells (MDSCs) occurring intra-prostatically immediately following epithelium-specific Pten deletion without expansion in hematopoietic tissues.  This MDSC expansion is accompanied by sustained immune suppression. Prostatic Gr-1+CD11b+ cells, but not those isolated from the spleen of the same tumor bearing mice, suppress T cell proliferation and express high levels of Arginase 1 and iNOS. Mechanistically, loss of PTEN in the epithelium leads to a significant upregulation of genes within the inflammatory response and cytokine-cytokine receptor interaction pathways, including Csf-1 and IL-1β, two genes known to induce MDSC expansion and immunosuppressive activities. Treating Pten null mice with the selective CSF-1 receptor inhibitor GW2580 decreases MDSC infiltration and relieves the associated immunosuppressive phenotype. Our study indicates that epithelium-associated tumor initiating events trigger the secretion of inflammatory cytokines and promote localized MDSC expansion and immune suppression, thereby promoting tumor progression.

overall_design: Laser-capture microdissection was used to extract epithelial cells from murine benign and Pten null prostate tumors.  Their transcript levels were measured by the custom Agilent 4x44K whole mouse genome expression oligonucleotide microarrays.  Each cohort had three biological replicates.

first: Alejandro

last: Garcia

first: Marcus

last: Ruscetti

first: Teresita

middle: L

last: Arenzana

first: Daniella

last: Bianchi-Frias

first: Elysia

last: Sybert

first: Saul

last: Priceman

first: Lily

last: Wu

first: Pete

last: Nelson

first: Stephen

middle: T

last: Smale

first: Hong


title: Pten null prostate epithelium promotes localized myeloid-derived suppressor cell expansion and immune suppression during tumor initiation and progression

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

overall_design: Refer to individual Series


title: Bacillus subtilis strains at low-pressure: 5 kPa versus 101 kPa growth

status: Public on Mar 14 2014

city: Merritt Island

first: Samantha

last: Waters

state: Florida

address: Space Life Sciences Lab 505 Odyssey Way

department: Microbiology and Cell Science

institute: University of Florida

summary: Comparing the transcriptional responses of Bacillus subtilis strains WN624 and WN1106 at 5 kPa and 101 kPa. WN1106 is a 5 kPa-evolved strain with increased fitness compared to ancestor-WN624 strain at 5 kPa. This experiment probed the difference in response when the strains are grown at 5 kPa.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Two-condition experiment, 5 kPa vs. 101 kPa, for both strains. And two component condition of WN1106 compared to WN624 at either 5 kPa or 101 kPa. 4 pressure comparisons.

first: Jose

middle: A

last: Robles-Martínez

first: Wayne

last: Nicholson


title: Disruption of the Transcriptional Regulator Cas5 Results in Enhanced Killing of Candida albicans by Fluconazole

status: Public on May 24 2014

city: Memphis

first: Erin

last: Vasicek

state: TN

address: 881 Madison Ave

institute: University of Tennessee Health Science Center

summary: Azole antifungal agents such as fluconazole exhibit fungistatic activity against Candida albicans.  Strategies to enhance azole antifungal activity would be therapeutically appealing.  In an effort to identify transcriptional pathways that influence fluconazole susceptibility, we sought to identify transcription factors (TFs) involved in this process.  From a collection of C. albicans strains disrupted for genes encoding TFs (Homann et al., PLoS Genet. 2009;5:e1000783), four exhibited a marked reduction in minimum fungicidal concentration (MFC) in both RPMI and YPD media.  One of these, UPC2, has been previously characterized with regard to its role in azole susceptibility.  Of mutants representing the three remaining TF genes of interest, one (CAS5) was unable to recover from fluconazole exposure at concentrations as low as 2 µg/mL after 72 hours in YPD medium. This mutant also showed reduced susceptibility and a clear zone of inhibition by Etest, was unable to grow on solid media containing 10 µg/mL fluconazole, and exhibited increased susceptibility by time-kill analysis.  CAS5 disruption in highly azole-resistant clinical isolates exhibiting multiple resistance mechanisms did not alter susceptibility.  However, CAS5 disruption in strains with specific resistance mutations in ergosterol biosynthesis or efflux pumps resulted in a moderate reduction in MIC and MFC.  Genome-wide transcriptional analysis was performed in the presence of fluconazole and was consistent with the suggested role of CAS5 in cell wall organization while also suggesting a role in iron transport and homeostasis.  These findings suggest that Cas5 regulates a transcriptional network that influences susceptibility of C. albicans to fluconazole.  Further delineation of this transcriptional network may identify targets for potential co-therapeutic strategies to enhance the activity to the azole class of antifungals.

overall_design: We examined the genome-wide gene expression profiles of the wild-type parent strain SC5314 and its cas5Δ/Δ derivative in response to fluconazole in order to identify genes whose expression in response to fluconazole is influenced by Cas5.

first: Elizabeth

last: Berkow

first: Vincent

last: Bruno

first: Aaron

middle: P

last: Mitchell

first: Nathan

last: Wiederhold

first: Katherine

last: Barker

first: P

middle: D

last: Rogers


title: Hippocampal neurons, nylon-2 experiments

status: Public on Mar 12 2014

city: Bethesda

first: Philip

last: Lee

address: 35 Lincoln Drive

department: NICHD

institute: NIH

summary: Ongoing neuronal activity during development and plasticity acts to refine synaptic connections and contributes to the induction of plasticity and ultimately long term memory storage.  Activity-dependent post-transcriptional control of mRNAs occurs through transport to axonal and dendritic compartments, local translation, and mRNA stability.  We have identified a mechanism that contributes to activity-dependent regulation of mRNA stability during synaptic plasticity.  In this study we demonstrate rapid, post-transtriptional control over process-enriched mRNAs by neuronal activity.  Systematic analysis of the 3'-UTRs of destablized transcripts, identifies enrichment in sequence motifs corresponding to miRNA binding sites.  The miRNAs that were identified, miR-326-3p/miR-330-5p, miR-485-5p, miR-666-3p, and miR-761 are predicted to regulate networks of genes important in plasticity and development.  We find that these miRNAs are developmentally regulated in the hippocampus, many increasing by postnatal day 14.  We further show that miR-485-5p controls NGF-induced neurite outgrowth in PC12 cells, tau expression, and axonal development in hippocampal neurons.  miRNAs can function at the synapse to rapidly control and affect short- and long-term changes at the synapse.  These processes likely occur during refinement of synaptic connections and contribute to the induction of plasticity and learning and memory.

overall_design:
12 hippocampal cell culture samples analysed, 3 coverslips pooled per sample. Treatments are as follows:

Block:  an inhibitor cocktail containing 50 µM D-APV, 40 µM CNQX, and 100 nM TTX for 3 hrs
Activity:  50 µM bicuculline (BiC)/500 µM 4-Aminopyridine
ActD:  25 µM actinomycin D

middle: R

first: Jonathan

last: Cohen

first: R

last: Fields


title: DRG axons and cell bodies experiments

overall_design:
4 samples analysed, 3 coverslips pooled per sample.

Mouse DRG neuron cell bodies and axons were separated in multicompartment cell cultures allowing electrical stimulation of axons, growing under a high-resistance partition between compartments, through platinum electrodes in the lid of the culture dish (Reference:  http://www.ncbi.nlm.nih.gov/pubmed/9295372)

middle: E


title: Pten null prostate epithelium promotes localized myeloid-derived suppressor cell expansion and immune suppression during tumor initiation and progression [cell lines]

first: Linh

last: Tran

summary: Chronic inflammation is known to associate with prostate cancer development, but how epithelium-associated cancer initiating events cross-talk to inflammatory cells during prostate cancer initiation and progression is largely unknown. Using the Pten null murine prostate cancer model, we show an expansion of Gr-1+CD11b+ myeloid-derived suppressor cells (MDSCs) occurring intra-prostatically immediately following epithelium-specific Pten deletion without expansion in hematopoietic tissues.  This MDSC expansion is accompanied by sustained immune suppression. Prostatic Gr-1+CD11b+ cells, but not those isolated from the spleen of the same tumor bearing mice, suppress T cell proliferation and express high levels of Arginase 1 and iNOS. Mechanistically, loss of PTEN in the epithelium leads to a significant upregulation of genes within the inflammatory response and cytokine-cytokine receptor interaction pathways, including Csf-1 and IL-1β, two genes known to induce MDSC expansion and immunosuppressive activities. Treating Pten null mice with the selective CSF-1 receptor inhibitor GW2580 decreases MDSC infiltration and relieves the associated immunosuppressive phenotype. Our study indicates that epithelium-associated tumor initiating events trigger the secretion of inflammatory cytokines and promote localized MDSC expansion and immune suppression, thereby promoting tumor progression

overall_design: Custom Agilent 4x44K whole mouse genome expression oligonucleotide microarrays were used to measure transcript levels in murine Pten null prostate cancer cell lines. Benign mouse prostate epithelia as wild type control against cell lines.  Each cohort had three biological replicates.

first: Alejandro

last: Garcia

first: Marcus

last: Ruscetti

first: Teresita

last: Arenzana

first: Daniella

last: Bianchi-Frias

first: Elysia

last: Sybert

first: Saul

last: Priceman

first: Lily


title: Analysis of gene expression during glucocorticoid-induced apoptosis of rat primary thymocytes

city: Durham

first: Arpit

last: Tandon

state: NC

address: 2605, Meridian Parkway

institute: SRA International

summary: Glucocorticoids induce rapid apoptosis of rat primary thymocytes through mechanisms requiring altered gene expression. The determination of genes regulating glucocorticoid-induced apoptosis of lymphocytes has received considerable attention. However, the role of specific non-coding microRNAs in the regulation of glucocorticoid-induced apoptosis of lymphocytes is poorly   defined. Using deep sequencing analysis, we have identified microRNAs differentially expressed during glucocorticoid-induced apoptosis of rat primary thymocytes. We have also identified numerous loci that harbor probable novel microRNAs. Furthermore, we have validated the glucocorticoid-responsive expression of 2 novel microRNAs in the apoptotic rat primary thymocyte. These 2 novel microRNAs are predicted to target numerous messenger RNAs throughout the genome. Using whole genome expression analysis, we now seek to correlate the altered expression of these novel microRNAs with the expression of their predicted target mRNAs during glucocorticoid-induced apoptosis.

overall_design: Changes in gene expression during glucocorticoid-induced apoptosis of rat primary thymocyes (3 biological replicates) were measured after 6 hours of 100nM dexamethasone treatment in-vitro.

first: Lindsay

last: Smith

first: Ruchir

last: Shah

first: Deepak

last: Mav

first: John

last: Cidlowski


title: Regulatory Mechanisms That Prevent Re-initiation of DNA Replication Can Be Locally Modulated at Origins by Nearby Sequence Elements

status: Public on Mar 15 2014

city: Santa Barbara

first: Chris

last: Richardson

address: UCSB

department: Molecular, Cellular, and Developmental Biology

institute: UCSB

summary: Eukaryotic cells must inhibit re-initiation of DNA replication at each of the thousands of origins in their genome because re-initiation can generate genomic alterations with extraordinary frequency. To minimize the probability of re-initiation from so many origins, cells use a battery of regulatory mechanisms that reduce the activity of replication initiation proteins. Given the global nature of these mechanisms, it has been presumed that all origins are inhibited identically. However, origins re-initiate with diverse efficiencies when these mechanisms are disabled, and this diversity cannot be explained by differences in the efficiency or timing of origin initiation during normal S phase replication. This observation raises the possibility of an additional layer of replication control that can differentially regulate re-initiation at distinct origins. We have identified novel genetic elements that are necessary for preferential re-initiation of two origins and sufficient to confer preferential re-initiation on heterologous origins when the control of re-initiation is partially deregulated. The elements do not enhance the S phase timing or efficiency of adjacent origins and thus are specifically acting as re-initiation promoters (RIPs). We have mapped the two RIPs to ~60 bp AT rich sequences that act in a distance- and sequence-dependent manner. During the induction of re-replication, Mcm2-7 reassociates both with origins that preferentially re-initiate and origins that do not, suggesting that the RIP elements can overcome a block to re-initiation imposed after Mcm2-7 associates with origins. Our findings identify a local level of control in the block to re-initiation. This local control creates a complex genomic landscape of re-replication potential that is revealed when global mechanisms preventing re-replication are compromised. Hence, if re-replication does contribute to genomic alterations, as has been speculated for cancer cells, some regions of the genome may be more susceptible to these alterations than others.

overall_design:
142 array CGH experiments are presented.  Each experiment is done in experimental replicate.
Cells grown as described in Richardson CD and Li JJ PLoS Genetics 2014.  Ch1 samples taken from replicating (S phase) or re-replicating (M phase + 3/6 hour induced).  Ch2 samples taken from M phase arrested DNA.


title: Systematic identification of 3'UTR regulatory elements in activity-dependent mRNA stability in hippocampal neurons

first: Philip

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus


title: Gene expression analysis from erythroid progenitors of patients with Diamond-Blackfan anemia

status: Public on Feb 28 2014

city: Boston

first: Vijay

last: Sankaran

state: MA

address: 300 Longwood Avenue

institute: Boston Children's Hospital

summary: Gene expression analysis from erythroid progenitors (CD34+/CD71(high)/CD45- mononuclear cells from the bone marrow) of patients with Diamond-Blackfan anemia (due to RPS19 mutations) and control individuals.

overall_design: Case-control microarray gene expression analysis

first: Hanna

last: Gazda


title: Hippocampal neurons, nylon-1 experiments

last: Lee

first: Jonathan

last: Cohen

first: R


title: Gene expression analysis of bovine oocytes at optimal coasting time combined with GnRH antagonist during the no-FSH period

status: Public on Feb 25 2014

city: Quebec

first: Remi

last: Labrecque

state: QC

address: 2440, boulevard Hochelaga

department: Animal Science

country: Canada

institute: Laval University

summary: The objective of the study was to analyze the effect of a GnRH antagonist used during the FSH withdrawal period (coasting) on transcriptome changes in in vivo bovine oocytes at the GV stage. Oocytes were collected from super-stimulated animals after a coasting duration of 68hrs (optimal condition, control) and also from the same animal who received the GnRH antagonist (treated) during the whole coasting period.

overall_design: 68hrs of coasting (control) was compared with the 68hrs + GnRH antagonist (treatment), for each cow individually. Overall, 6 hybridizations were done, corresponding to the three biological replicates and one comparison using a dye-swap set-up.

first: Christian

last: Vigneault

first: Patrick

last: Blondin

first: Marc-André

last: Sirard


title: Hippocampal neurons, Illumina experiments

last: Fields


title: microRNA expressions in gastric cancer

status: Public on Jan 25 2014

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

summary:
The study was undertaken to identify microRNAs differently expressed by intestinal type of gastric cancer using miRNA microarray.
The miRNA expression in the intestinal type of gastric cancer depending on H. pylori infection suggest that different gastric cancer pathogenesis could be exist between H. pylori-positive and -negative gastric cancer.

overall_design: Total RNA was extracted from cancerous region and non-cancerous regions in formalin fixed paraffin embedded tissues of intestinal type gastric cancer patients who were H. pylori-positive (n=8) or -negative (n=8). Corresponding author: Nayoung Kim, M.D., Department of Internal Medicine, Seoul National University Bundang Hospital (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com).

first: Hyun

last: Chang

first: Jung

first: Nayoung


title: A Genomics-Based Analysis of Relative Potencies of Dioxin-Like Compounds in Primary Rat Hepatocytes

status: Public on Jan 01 2014

city: Midland

first: Craig

last: Rowlands

state: MI

address: 1803 Bldg Washington Street

department: Toxicology & Environmental Research & Consulting

institute: The Dow Chemical Company

summary: A toxicogenomics approach was used to qualitatively and quantitatively compare gene expression changes in rat primary hepatocytes exposed to 2,3,4,7,8-pentachlorodibenzofuran (4-PeCDF) or 2,3,7,8-tetrachlorodibenzofuran (TCDF). Hepatocytes from five individual rats were exposed for 24 hours to 11 concentrations of each chemical ranging from 0.00001 nM to 100 nM and a vehicle control.

overall_design: 115 microarrays representing primary hepatocytes from 5 rats, each exposed to 11 doses of each chemical (PeCDF and TCDF) and vehicle controls. Arrays were completed with a one-color design.

first: Alan

last: Dombkowski


title: Relapse from nicotine abstinence increases the pacemaking frequency of cholinergic habenular neurons

status: Public on Dec 30 2013

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary:
The discovery of genetic variants in the CHRNA5-CHRNA3-CHRNB4 gene cluster associated with heavy smoking and higher relapse risk has led to the identification of the midbrain habenula- interpeduncular axis as a critical relay circuit in the control of nicotine addiction
Here we profile the cholinergic neurons of the medial habenula and identify the unique transcirptional features of this population of neurons.

overall_design:
For each cell population, three independent TRAP replicates were collected, and total RNA from both the immunoprecipitate and unbound fractions were seperately amplified and hybridized.
For each tissue, several representative unnbound fractions are provided to serve as controls.  Biological replicates are GCRMA normalized within groups.
Following averaging of replicates, we recommend further global normalization between groups, using affymetrix biotinylated controls, to correct for any broad biases in scanning and hybridization.
Finally for many analyses, we also recommend filtering to remove those probesets with low IP/UB fold change values from each cell type(see PMID:20962086).
Researchers can contact us for spreadsheets where these additional steps have been completed.

first: Andreas

last: Görlich

first: Beatriz

last: Antolin-Fontes

first: Jessica

last: Ables

first: Silke

last: Frahm

first: Ines

last: Ibanez-Tallon


title: Long term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster

status: Public on Dec 18 2013

city: Sao Paulo

first: Maria

last: Vibranovski

address: Rua do Matao, 277

department: Genetics and Evolutionary Biology

institute: Universidade de Sao Paolo

summary: Recent studies have revealed key roles of non-coding RNAs in sex-related pathways, but little is known about the evolutionary forces acting on these non-coding RNAs. We used whole-genome tiling arrays to profile the transcriptome of Drosophila melanogaster tissues and found that 15% of male-biased transcribed fragments (transfrags) are intergenic non-coding RNAs (incRNAs), suggesting a potentially important role for incRNAs in sex-related biological processes. Statistical analysis revealed a paucity of male-biased incRNAs and coding genes on the X chromosome, suggesting that similar evolutionary forces could be affecting the genomic organization of both coding and non-coding genes. Expression profiling across germline and somatic tissues further suggests that both male meiotic sex chromosome inactivation (MSCI) and sexual antagonism contribute to the chromosomal distribution of male-biased incRNAs. Comparative sequence analysis shows that the evolutionary age of male-biased incRNAs is a significant predictor of their chromosomal locations. In addition to identifying abundant sex-biased incRNAs in fly genome, our work unveils a global picture of the complex interplay between non-coding RNAs and sexual chromosome evolution.

overall_design: We used whole-genome tiling arrays to assess sex-biased transcription in D. melanogaster adult whole bodies, and testis, ovary, and accessory gland samples. Gut and thorax, tissues expected to exhibit little or no sex-biased expression, were included as controls. Expression was measured in 2-4 replicates for each tissue.

first: Ge

last: Gao

first: Li

last: Zhang

first: Zheng

last: Li

first: Ming

last: Liu

first: Yong

first: Xinmin

first: Wenxia

first: Qichang

last: Fan

first: Nicholas

last: VanKuren

first: Manyuan

last: Long

first: Liping

last: Wei


title: UV-B regulation of microRNAs in maize

status: Public on Oct 31 2013

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

summary: Differential expression of microRNAs was studied in maize leaves after an 8-h-exposure under UV-B light. As a control, plants were kept in the greenhouse in the absence of UV-B

platform_organism:
Physcomitrium patens
Pinus taeda
Gossypium hirsutum
Populus trichocarpa
Arabidopsis thaliana
Brassica napus
Glycine max
Medicago truncatula
Solanum lycopersicum
Oryza sativa
Saccharum officinarum
Sorghum bicolor
Triticum aestivum
Zea mays
Vitis vinifera
Selaginella moellendorffii

overall_design: 4-week maize plants were grown in the greenhouse in the absence of UV-B. Then, they were divided in two groups. One group was treated with UV-B lights provided once for 8 h, starting 3 h after the beginning of the light period, using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) at a UV-B intensity of 2 W m-2, UV-A: 0.65 W m-2. The bulbs were covered with cellulose acetate to exclude wavelengths <280 nm. For the second control group, plants were exposed for 8 h under the same lamps covered with polyester film (no UV-B treatment, UV-B: 0.04 W m-2, UV-A: 0.4 W m-2). Lamp output was recorded using a UV-B/UV-A radiometer (UV203 A+B radiometer, Macam Photometrics, Ltd, Livingston, UK) to insure that both the bulbs and filters provided the designated UV dosage in all treatments. Leaf samples were collected immediately after irradiation. RNA was extracted immediately after the treatments, and used for the microRNA microarray experiments.


title: Model steatogenic compounds (amiodarone, valproic acid, and tetracycline) alter lipid metabolism by different mechanisms in mouse liver slices

status: Public on Dec 23 2013

city: Wageningen

first: Ewa

last: Szalowska

address: Akkermaalsbos 2

institute: RIKILT-Wageningen UR


title: Model steatogenic compounds (amiodarone, valproic acid, and tetracycline) alter lipid metabolism by different mechanisms in mouse liver slices [Cholestatic compounds exposures]

summary:
Although drug induced steatosis represents a mild type of hepatotoxicity, it can progress into more severe non-alcoholic steatohepatitis. Current models used for safety assessment in drug development and chemical risk assessment do not accurately predict steatosis in humans. Therefore, new models need to be developed to screen compounds for steatogenic properties. We have studied the usefulness of mouse precision-cut liver slices (PCLS) as an alternative to animal testing to gain more insight into the mechanisms involved in the steatogenesis. To this end, PCLS were incubated 24h with the model steatogenic compounds, amiodarone (AMI), valproic acid (VA), and tetracycline (TET). Transcriptome analysis using DNA microarrays was used to identify genes and processes affected by these compounds. AMI and VA upregulated lipid metabolism, whereas processes associated with extracellular matrix remodelling and inflammation were downregulated. TET downregulated mitochondrial functions, lipid metabolism, and fibrosis. From the transcriptomics data it was hypothesized that all 3 compounds affect peroxisome proliferator activated-receptor (PPAR) signalling. Application of PPAR reporter assays classified AMI and VA as PPARγ and triple PPARα/ (β/δ)/γ agonist, respectively, whereas TET had no effect on any of the PPARs. Some of the differentially expressed genes were considered as potential candidate biomarkers to identify PPAR agonists (i.e. AMI and VA) or compounds impairing mitochondrial functions (i.e. TET). Finally, comparison of our findings with publicly available transcriptomics data showed that a number of processes altered in the mouse PCLS was also affected in mouse livers and human primary hepatocytes exposed to known PPAR agonists. Thus mouse PCLS are a valuable model to identify mechanisms of action of compounds altering lipid metabolism. Two sets of candidate biomarkers could be used to screen compounds interfering with lipid metabolism by different mechanisms.
Cholestatic compounds exposures

overall_design: Mouse precision cut liver slices (PCLS) were prepared from livers obtained from 5 different C57BL/6 male mice (24 weeks old). PCLS were cultured for 24 hours at 80% of oxygen; 5% CO2 and the remaining gas volume was filled up to 95% with N2. PCLS were exposed to model steatogenic, cholestatic, and necrotic compounds selected based on published reports. As steatogenic model compounds amiodarone (AMI), valproic acid (VA), and tetracycline (TET) were selected. As model cholestatic compounds cyclosporin A (CsA), chlorpromazine (CPZ), and ethinyl estradiol (EE) were applied. As necrotic compounds acetaminophen (APAP), isoniazid (ISND), and paraquat (PQ) were applied. To select a non-toxic dose eventually to be used for exposure experiments and subsequent gene expression profiling experiments, the following concentrations ranges were tested: AMI 0-100 μM,   VA 0-500 μM, TET 0-100 μM , CsA 0-100 μM,  CPZ 0-80 μM,  EE 0-100 μM,  PQ 0-10 μM,  APAP 0-3000 μM and ISND 0-1000 μM. CsA, CPZ, AMI, PQ, EE were dissolved in DMSO, VA and TET were dissolved in ethanol (EtOH), and ISND was dissolved in PBS. The compounds were added to the culture medium at a final concentration of 0.1% vol/vol in an appropriate solvent (DMSO, EtOH, or PBS). Slices incubated with the solvents at 0.1% vol/vol served as controls. The viability of the slices was assessed by measuring the ATP content normalized on protein.   Dose selection for the three steatogenic, cholestatic, and necrotic exposures were performed in 5 independent experiments with slices obtained from 5 mice.  Concentrations that did not cause a decrease of the ATP level normalized on protein, compared to controls, were selected. For transcriptome analysis, PCLS were cultured at the same conditions as described above. The selected concentrations for steatogenic, cholestatic, and necrotic drugs were tested again in liver slices obtained from 5 different mice to re-confirm that the selected concentrations for the exposure experiments were not toxic.  The concentrations used in the exposure experiments were for the steatogenic compounds: 50 μM for AMI, 200 μM for VA, and 40 μM for TET. For the cholestatic exposures 40 μM CsA, 20 μM CPZ, and 10 μM EE. For the necrotic compounds: 1000 μM APAP, 1000 μM ISND, and 5 μM PQ.  Thereafter, RNA was extracted from three slices per each condition and after processing, the samples were hybridized on the HT Mouse Genome 430 PM array plate(s) using the Affymetrix GeneTitan system (CA, USA).

first: Bart

last: van der Burg

first: Hai-Yen

last: Man

first: Peter

last: Hendriksen

first: Ad

last: Peijnenburg


title: Model steatogenic compounds (amiodarone, valproic acid, and tetracycline) alter lipid metabolism by different mechanisms in mouse liver slices [Necrotic compounds exposures]

summary:
Although drug induced steatosis represents a mild type of hepatotoxicity, it can progress into more severe non-alcoholic steatohepatitis. Current models used for safety assessment in drug development and chemical risk assessment do not accurately predict steatosis in humans. Therefore, new models need to be developed to screen compounds for steatogenic properties. We have studied the usefulness of mouse precision-cut liver slices (PCLS) as an alternative to animal testing to gain more insight into the mechanisms involved in the steatogenesis. To this end, PCLS were incubated 24h with the model steatogenic compounds, amiodarone (AMI), valproic acid (VA), and tetracycline (TET). Transcriptome analysis using DNA microarrays was used to identify genes and processes affected by these compounds. AMI and VA upregulated lipid metabolism, whereas processes associated with extracellular matrix remodelling and inflammation were downregulated. TET downregulated mitochondrial functions, lipid metabolism, and fibrosis. From the transcriptomics data it was hypothesized that all 3 compounds affect peroxisome proliferator activated-receptor (PPAR) signalling. Application of PPAR reporter assays classified AMI and VA as PPARγ and triple PPARα/ (β/δ)/γ agonist, respectively, whereas TET had no effect on any of the PPARs. Some of the differentially expressed genes were considered as potential candidate biomarkers to identify PPAR agonists (i.e. AMI and VA) or compounds impairing mitochondrial functions (i.e. TET). Finally, comparison of our findings with publicly available transcriptomics data showed that a number of processes altered in the mouse PCLS was also affected in mouse livers and human primary hepatocytes exposed to known PPAR agonists. Thus mouse PCLS are a valuable model to identify mechanisms of action of compounds altering lipid metabolism. Two sets of candidate biomarkers could be used to screen compounds interfering with lipid metabolism by different mechanisms.
Necrotic compounds exposures


title: Model steatogenic compounds (amiodarone, valproic acid, and tetracycline) alter lipid metabolism by different mechanisms in mouse liver slices [Steatogenic compounds exposures]

summary:
Although drug induced steatosis represents a mild type of hepatotoxicity, it can progress into more severe non-alcoholic steatohepatitis. Current models used for safety assessment in drug development and chemical risk assessment do not accurately predict steatosis in humans. Therefore, new models need to be developed to screen compounds for steatogenic properties. We have studied the usefulness of mouse precision-cut liver slices (PCLS) as an alternative to animal testing to gain more insight into the mechanisms involved in the steatogenesis. To this end, PCLS were incubated 24h with the model steatogenic compounds, amiodarone (AMI), valproic acid (VA), and tetracycline (TET). Transcriptome analysis using DNA microarrays was used to identify genes and processes affected by these compounds. AMI and VA upregulated lipid metabolism, whereas processes associated with extracellular matrix remodelling and inflammation were downregulated. TET downregulated mitochondrial functions, lipid metabolism, and fibrosis. From the transcriptomics data it was hypothesized that all 3 compounds affect peroxisome proliferator activated-receptor (PPAR) signalling. Application of PPAR reporter assays classified AMI and VA as PPARγ and triple PPARα/ (β/δ)/γ agonist, respectively, whereas TET had no effect on any of the PPARs. Some of the differentially expressed genes were considered as potential candidate biomarkers to identify PPAR agonists (i.e. AMI and VA) or compounds impairing mitochondrial functions (i.e. TET). Finally, comparison of our findings with publicly available transcriptomics data showed that a number of processes altered in the mouse PCLS was also affected in mouse livers and human primary hepatocytes exposed to known PPAR agonists. Thus mouse PCLS are a valuable model to identify mechanisms of action of compounds altering lipid metabolism. Two sets of candidate biomarkers could be used to screen compounds interfering with lipid metabolism by different mechanisms.
Steatogenic compounds exposures


title: Response of Sweet Orange (Citrus sinensis) to Candidatus Liberibacter asiaticus Infection

status: Public on Oct 01 2013

city: Lake Alfred

first: Valente

last: Aritua

address: 700 Experiment Staion Road

department: Plant Pathology

summary:
Citrus greening or huanglongbing (HLB) is a devastating disease of citrus. HLB is associated with the phloem-limited fastidious prokaryotic alpha-proteobacterium Candidatus Liberibacter spp. In this report, we used sweet orange (Citrus sinensis) leaf tissue infected with 'Ca. Liberibacter asiaticus' and compared this with healthy controls.
Investigation of the host response was examined with citrus microarray hybridization based on 30,171 sets expressed sequence tag sequences from several citrus species and hybrids. The microarray analysis indicated that HLB infection significantly affected expression of 624 genes whose encoded proteins were categorized according to function.
The categories included genes associated with sugar metabolism, plant defense, phytohormone, and cell wall metabolism, as well as 14 other gene categories.

overall_design: Young, healthy Valencia sweet orange (C. sinensis) plants were graft inoculated with budwood from Ca. L. asiaticus-infected citrus plants. Prior to the innocualtion, the plants were confirmed to be Ca. L. asiaticus-free in ordinary and quantitative PCR tests. The presence of the bacteria in the inoculated plants was confirmed in both conventional and quantitative PCR with specific primers to Ca. L. asiaticus.  The stem and root samples used for RNA extraction and hybridization on Affymetrix microarrays were obtained from three symptomatic and three healthy control trees of similar size, approximately 1 year after inoculation.

first: Nain

last: Wang


title: MYBL2 Is a Sub-haploinsufficient Tumor Suppressor Gene in Myeloid Malignancy (RNAi)

status: Public on Sep 15 2013

city: Essen

first: Stefan

last: Heinrichs

address: Virchowstr. 179

department: Institute of Transfusion Medicine

country: Germany

institute: University Hospital Essen

summary: A dosage-dependent role for tumor suppressor genes in the initiation of myeloid malignancies remains controversial. Here we show that MYBL2 is expressed at sharply reduced levels in CD34+ cells from most patients with myelodysplastic syndrome (MDS; 65%; n=26). In a murine competitive reconstitution model, Mybl2 knockdown by RNAi to 20-30% of normal levels in multipotent hematopoietic progenitors led to clonal dominance by these “sub-haploinsufficient” cells, affecting all blood cell lineages. By 6 months post-transplantation, the reconstituted mice had developed a myeloproliferative/myelodysplastic disorder originating from the cells with aberrantly reduced Mybl2 expression. Thus, downregulation of MYBL2 activity to levels below those predicted by classical haploinsufficiency drives the clonal expansion of hematopoietic progenitors in a large fraction of human MDS cases.

overall_design: Cryopreserved CD34+ bone marrow were cultured for 24 hours, transduced with shRNA-encoding vectors and selected with Puromycin for 48 hours. Vectors shRNA 1-8 are specifically targeting MYBL2, vectors shRNA A-D encoded an irrelevant control shRNAs and one culture was left untreated (no shRNA). Cells were harvested after Puromycin selection and total RNA was prepared using Trizol (LifeTechnologies).


title: Effects of gentamycin on gene expression of kidney in SD rats

status: Public on Sep 13 2013

city: Shanghai

first: min

last: hong

address: 199 Guoshoujing Rd., Zhangjiang Hi-tech Park

department: general toxicology

institute: National Shanghai Center for Drug Safety Evaluation and Research

summary: To investigate the gene expression profile of genamycin induced nephrotoxicity in a time-series aspect, SD rats were administrated once daily with saline, genamycin 80 mgkg for 28 consecutive days by intramuscular injection folled by 28 days recovery. Kidney samples were collected for microarray analysis and histological examination. There were 4360 and 4323 regulated genes for females and males, respectively, however, the overlapping expression genes coregluated at each time point were few, with 2 for females and 12 for males. By Principle Component Analysis and Hierarchical Cluster, the gene expression patterns were apparently associated with the disease stage of the nephrotoxicity,while GO Annotation showed the biological processes were specific to each course of this nephrotoxicity.Our studymapped the different gene expression patterns at the initiation, development and recovery stage of gentamycin-induced nephrotoxicity

overall_design: Gene expression in kidney from SD rats administrated once daily with saline or 80 mg/kg genamycin by intramuscular injection for 28 consecutive days follwed by 28 days recovery were measured using Aglient Rat Whole Genome 4*44 k array

first: Yunliang

last: Qiu

first: Min

last: Hong

first: Wenxin

last: Dong

first: Jing

last: Ma

first: Ching-hung

last: Hsu


title: MYBL2 Is a Sub-haploinsufficient Tumor Suppressor Gene in Myeloid Malignancy (RNA)

overall_design: Total RNA was prepared from CD34+ bone marrow cells obtained from MDS patients or healthy controls.


title: MYBL2 Is a Sub-haploinsufficient Tumor Suppressor Gene in Myeloid Malignancy

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

overall_design: Refer to individual Series


title: Systems Biology Analysis of Zymomonas mobilis ZM4 Ethanol Stress Responses

status: Public on Sep 04 2013

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

summary:
Background

Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of its ethanol stress response have not been elucidated fully.

Methodology/Principal Findings

In this study, ethanol stress responses were investigated using systems biology approaches. Medium supplementation with an initial 47 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 55% of the predicted ZM4 proteome. Proteins related to metabolism and stress response such as chaperones and key regulators were more abundant in the early ethanol stress condition. Transcriptomic studies indicated that the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Transcriptomic data were used to update Z. mobilis ZM4 operon models. Furthermore, correlations among the transcriptomic, proteomic and metabolic data were examined. Among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher.

Conclusions

Our study has provided insights into the responses of Z. mobilis to ethanol stress through an integrated “omics” approach for the first time. This systems biology study elucidated key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress.

sample_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: A sixteen array study using total RNA recovered from wild-type cultures of Zymomonas mobilis subsp mobilis ZM4 at different time points of 6, 10, 13.5, and 26h post-inoculation with 6% (v/v) treatment compred to that of control without ethanol supplementation. Two biological replicates for treatment and control condition.

last: Yang

first: Chongle

last: Pan

first: Timothy

last: Tschaplinski

first: Gregory

last: Hurst

first: Nancy

last: Engle

first: Stanton

last: Martin

first: Brian

middle: H

last: Davison

first: Miguel

last: Rodriguez

first: Steven

last: Brown


title: Hepatic transcriptome of rats treated with vehicle or fipronil (3 mg/kg/d per os for 14 days)

status: Public on Aug 22 2013

city: Villenave d'Ornon

first: Pascal

middle: GP

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

summary: Fipronil (CAS #: 120068-37-3), a widely used insecticide, has been described as a thyroid disruptor in rat inducing a marked increase in thyroxine (T4) clearance resulting in a decrease in T4 plasma concentration. These effects seem to require the bioactivation of fipronil via its biotransformation into fipronil sulfone by cytochromes P450 (CYP). Here, we hypothesized that fipronil-induced thyroid disruption may, at least in part, result from the induction of hepatic enzymes involved in the metabolism of thyroid hormones. Thus, we used microarrays to perform a genome-wide analysis of the effects of fipronil on gene expression in rat liver.

overall_design: Liver gene expression was measured from female Wistar rats treated with vehicle (n = 7) or fipronil 3 mg/kg/day per os for 14 days (n = 8)

first: Julien

last: Leghait

first: Frédéric

last: Lasserre

first: Béatrice

last: Roques

first: Catherine

last: Viguié

first: Thierry

last: Pineau


title: Analysis of change in circulating microRNAs in mice during breast tumor development

status: Public on Sep 01 2013

city: Galway

first: Róisín

last: Dwyer

address: Costelloe Road

institute: National University of Ireland Galway

summary: The aim of this study was to analyse alterations in circulating microRNA expression during breast tumour progression in a murine model, and to apply significantly altered miRNAs to patient samples to identify novel circulating microRNA markers or tumour progression. Athymic nude mice (n=10) received an injection of 2 x 105 MDA-MB-231 cells. Tumour volume was monitored weekly and blood sampling performed at weeks 1 and 6 following tumour induction. A microRNA array was performed comparing circulating 384 microRNAs in animals with early (week 1, n=5) versus late (week 6, n=5) disease.

overall_design: Five animals were included in the study (n=2 samples from each, total n=10 microArrays performed), with whole blood sampled one week following tumor induction and again at 6 weeks in the presence of established disease. The change in microRNA profile was then compared at week 1 and week 6, which the "early" sample providing the baseline measurements for each animal.

first: Roisin


title: Gene expression profiles of non-genotoxic hepatocarcinogens and hepatotoxicants in rat liver

status: Public on Jul 31 2013

city: Sophia Antipolis

first: Sophie

last: Ludwig

address: 355 Rue Dostoievski BP 153

department: Toxicology Research

institute: Bayer Cropscience

summary: Liver tumors in rodents are frequently induced by non-genotoxic carcinogens. These hepatocarcinogens generally activate hepatic nuclear receptors (e.g., CAR and PXR), resulting in a cascade of signals causing modifications in the expression of genes responsible for several processes involved in carcinogenesis. Evaluation of the carcinogenic potential of chemicals is a regulatory requirement but is time-consuming and expensive. Consequently, several short-term in vivo and in vitro approaches, using molecular tools, have been proposed as predictive models for non-genotoxic hepatocarcinogens. The objective of our study was to discriminate between chemicals that are either non-genotoxic hepatocarcinogens or merely hepatotoxicants and also between CAR and PXR modulators on the basis of their gene expression profiles. Thus, we treated rats for seven days with the hepatoxicants, diclofenac and diazepam, or with several CAR and PXR modulators, which were mainly hepatocarcinogens. Different hepatic gene expression profiles were obtained not only between the hepatotoxicants and the non-genotoxic hepatocarcinogens but also between the CAR activators phenobarbital, phenytoin and 1,1-bis-(4-chlorophenyl)-2,2-dichloroethene which were grouped together, and the two PXR activators pregnenolone 16α-carbonitrile and clotrimazole. Diethylstilbestrol had an expression profile that was quite distinct from the other PXR activators, suggesting that this compound is certainly not a classic PXR modulator. Moreover, some differences were observed between phenytoin (not considered as a hepatocarcinogen), and the other two CAR activators. Our data therefore indicate that discrimination is possible between hepatocarcinogens and hepatotoxicants, between CAR and PXR modulators and also between compounds within the same class of modulators using a short-term transcriptomic approach.

overall_design: CAR or PXR inducers were administered in suspension to rats (7 weeks old at start of treatment) by oral gavage at a daily dose for 7 consecutive days. Treatment-related changes in gene expression were determined in the liver using whole genome oligonucleotide microarrays.

first: Olivier

last: Blanck


title: Expression changes in Tetrahymena thermophila TRX1 and EZL2 gene knockouts and after hydroxyurea (HU) treatment

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

summary: 12 genome-wide microarrays to investigate the Tetrahymena thermophila gene expression changes in TRX1 and EZL2 gene knockout and hydroxyurea (HU) treatment conditions.

overall_design: For the TRR1 knockout (KO) condition, wild type (WT427) cells and TRX1 KO cells were cultured using 1XSPP, 30 degrees, 100 rpm shaking, until 350,000 cells/ml. For the EZL21 knockout (KO) condition, wild type (WT427) cells and EZL2 KO cells were cultured using 1XSPP, 30 degrees, 100 rpm shaking, until 350,000 cells/ml. For the HU treatment condition, HU was used to treat the WT427 cells for 48 hours, setting wild type (WT427) as the control; cells were cultured using 1XSPP, 30 degrees, 100 rpm shaking. Each sample has two biological replicates.

first: Yifan

last: Liu


title: In silico nano-dissection: defining cell type specificity at transcriptional level in human disease (glomeruli)

status: Public on Aug 06 2013

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

summary:
To identify genes with cell-lineage-specific expression not accessible by experimental micro-dissection, we developed a genome-scale iterative method, in-silico nano-dissection, which leverages high-throughput functional-genomics data from tissue homogenates using a machine-learning framework.
This study applied nano-dissection to chronic kidney disease and identified transcripts specific to podocytes, key cells in the glomerular filter responsible for hereditary proteinuric syndromes and acquired CKD. In-silico prediction accuracy exceeded predictions derived from fluorescence-tagged-murine podocytes, identified genes recently implicated in hereditary glomerular disease and predicted genes significantly correlated with kidney function. The nano-dissection method is broadly applicable to define lineage specificity in many functional and disease contexts.

overall_design: We applied a machine-learning framework on high-throughput gene expression data from human kidney biopsy tissue homogenates and predict novel podocyte-specific genes. The prediction was validated by Human Protein Atlas at protein level. Prediction accuracy was compared with predictions derived from experimental approach using fluorescence-tagged-murine podocytes.

first: Wenjun

last: Ju

first: Casey

middle: S

last: Greene

first: Felix

last: Eichinger

first: Jeffery

last: Hodgin

first: Markus

last: Bitzer

first: Young-suk

last: Lee

first: Qian

last: Zhu

first: Masami

last: Kehata

first: Min

last: Li

first: Maria

last: Rastaldi

first: Clemens

last: Cohen

first: Olga

last: Troyanskaya

first: Matthias

last: Kretzler


title: Genes induced after BDV infection in Sprague Dawley and Lewis rats

status: Public on Jun 26 2013

city: Freiburg

first: Martin

last: Schwemmle

address: Hermann-Herder-Str. 11

institute: University Freiburg

summary: Borna Disease Virus (BDV) is a neurotropic virus that persistently infects neurons in the central nervous system of various hosts, including rats. Although BDV is known to be an IFN sensitive virus, determination of the cellular mRNA transcript levels revealed the induction of IFN-stimulated genes in organotypic rat hippocampus slice cultures, raising the question how BDV evades this innate immune response. Using rat Mx protein as a specific marker for IFN-induced gene products, we could show that neurons lack detectable levels of Mx in these BDV infected cultures, whereas astrocytes and microglial cells were Mx positive. Neurons remained Mx negative after treatment of uninfected hippocampus cultures as well as primary dissociated neuronal cultures with high concentrations of IFN-α. This non-responsiveness correlated with a lack of a detectable nuclear translocation of pSTAT1 in rat neurons. Consistently, IFN treatment of BDV-infected rat neurons did not prevent the establishment of a viral persistence in the neuronal tissue. However, IFN treatment efficiently prevented vesicular stomatitis virus (VSV) replication, indicating that these cells can mount a weak innate immune response. In contrast, IFN treatment of mouse neurons resulted in the upregulation of Mx1 proteins and inhibition of BDV replication, indicating species-specific differences in the IFN response in neurons between mice and rats. Rat neurons may therefore represent the ideal cell type for BDV to evade the innate immune in the central nervous system.

overall_design:
To determine the mRNA levels in the hippocampal slice cultures after BDV infection in Sprague Dawley and Lewis rats
Hippocampal slice cultures were prepared from newborn Lewis and SD rats (P0-P2). Half of the samples remained uninfected, whereas the other half was infected with 1000 focus forming units (FFU) of BDV strain He/80. Total RNA from a pool of 12 slice cultures was prepared

first: Yuan-Ju

last: Wu


title: SICKLE is a novel factor involved in miRNA biogenesis and is important for development and stress tolerance of Arabidopsis

status: Public on Aug 18 2013

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

type: Expression profiling by genome tiling array

type: Non-coding RNA profiling by genome tiling array

summary: To evaluate the function of SICKLE in miRNA biogenesis and stress tolerance, we use whole genome tiling array to detect the expression change of protein coding genes, miRNAs, intronic regions in sck-l mutant comparing to wildtype.

overall_design: sic-l mutant vs. wildtype. Two biological replicates each. Seedling plants were used.

first: Viswanathan

last: Chinnusamy

first: Jian-Kang


title: Time course expression study in the rat superior olivary complex

city: Oldenburg

first: Hans Gerd

last: Nothwang

state: Lower Saxony

address: Carl von Ossietzky Str. 9-11

department: Neurogenetics

institute: University of Oldenburg

summary: The superior olivary complex (SOC) is a prominent auditory brainstem center and represents one of the prime model systems to study the development of sensory circuits. We recently performed genome-wide microarray studies to analyze the SOC-related genetic program at postnatal day (P)4 and P25. Here, we extended this analysis by including two additional time points, P0 and P16. Data sets were validated by qRT-PCR. Statistical analysis were performed for the different developmental time points as well as with for differences between the SOC and our previously analyzed brain samples. This analysis revealed that after hearing-onset (P16 and P25), 918 oligos were up-regulated and 810 oligos down-regulated in the SOC compared to the two prehearing stages (P0 and P4). Of the up-regulated oligos, 530 were significantly higher expressed compared to the brain at P25. Concerning neurotransmission, SOC-related elevation was mainly observed for K+ channels, G-proteins, and myelination-related proteins, whereas Ca2+-related proteins showed a decreased expression. In the pre-hearing period, 47 oligos were up-regulated compared to the brain. Several of them were transcription factors, previously associated with other auditory structures, and might ensure coordinated development of peripheral and central auditory structures. Stage-specific comparison identified distinct genetic programs during development: Circuit formation/refinement at P4; myelination and circuit refinement/consolidation at P16; and neuroprotection at P25. Altogether, our study defines the genetic program of postnatal SOC development and provides strong functional candidates for various developmental processes.

overall_design: The genome wide expression during the postnatal development of the SOC was investigated at two different time points: at postnatal (P) day 0  (before hearing onset) and P16 (after hearing onset). Samples were hybridized onto two color platforms. At least 6 up to nine biological replicates per sample were performed.