title: Global analysis of cell cycle gene expression of the legume symbiont Sinorhizobium meliloti

status: Public on Jan 22 2014

city: Dallas

first: Nicole

middle: Janell

last: De Nisco

state: Texas

address: 6000 Harry Hines Blvd, NA5.146, NA5.146

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

summary:
In α-proteobacteria, strict regulation of cell cycle progression is necessary for the specific cellular differentiation required for adaptation to diverse environmental niches. The symbiotic lifestyle of Sinorhizobium meliloti requires a drastic cellular differentiation that includes genome amplification. To achieve polyploidy, the S. meliloti cell cycle program must be altered to uncouple DNA replication from cell division. In the α-proteobacterium Caulobacter crescentus, cell cycle regulated transcription plays an important role in control of cell cycle progression but this has not been demonstrated in other α-proteobacteria. Here we describe a robust method for synchronizing cell growth that enabled the first global analysis of S. meliloti cell cycle regulated gene expression. The objective of the microarray-based cell cycle gene expression analysis was to determine which genes were transcriptionally regulated as a funciton of a cell cycle in order to understand the contribution of transcriptional regulation to the timing of cell cycle events. The microarray analysis identified 462 genes with cell cycle regulated transcripts, including several key cell cycle regulators, and genes involved in motility, attachment, and cell division. Only 28% of the 462 S. meliloti cell cycle regulated genes were also transcriptionally cell cycle regulated in C. crescentus. Furthermore, CtrA and DnaA binding motif analysis revealed little overlap between the cell cycle-dependent regulons of CtrA and DnaA in S. meliloti and C. crescentus. The predicted S. meliloti cell cycle regulon of CtrA, but not that of DnaA, was strongly conserved in more closely related α-proteobacteria with similar ecological niches as S. meliloti, suggesting that the CtrA cell cycle regulatory network may control functions of central importance to the specific lifestyles of α-proteobacteria.
Gene expression levels were quantified in synchronously growing S. meliloti cultures across 8 time points and compared to gene expression levels in unsynchronized culture via a two-color custom agilent array

overall_design: A two-color array format was used with time point from synchronous culture being competed with a sample from unsynchronized culture (control same for all arrays) to determine the cell cycle-phase specific induction or repression  of genes relative to batch culture which contains cells in all phases of the cell cycle. For each of the 8 cell cycle time points, four biological replicates were used resulting in 4 arrays per time point and a total of 32 arrays. The arrays also contained duplicates of each probe resulting in two technical replicates per biological replicate per time point.

middle: J

last: DeNisco

first: Ryan

last: Abo


title: Comparison of gene expression profiles in blood, hippocampus and prefrontal cortex in rats

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
The comparability of gene expression between blood and brain tissues is a central issue in neuropsychiatric research where the analysis of molecular mechanisms in the brain is of high importance for the understanding of the diseases and the discovery of biomarkers. However, the accessibility of brain tissue is limited. Therefore, knowledge about how easily accessible peripheral tissue, e.g. blood, is comparable to and reflects the mechanisms of the brain will help to advance neuropsychiatric research.
In our study, we have compared the expression of blood, hippocampus and prefrontal cortex in genetically identical rats by using a genome-wide Affymetrix gene expression microarray covering 29,215 transcripts. We find 56.8% of genes co-expressed in blood and at least one brain tissue and 55.3% of all genes co-expressed in all three tissues simultaneously. Around one third of the genes is expressed selectively in one tissue.
This study provides a baseline analysis of absolute gene expression and its differences in blood, PFC and HC brain tissue in genetically identical rats. Our data might be used for first information on gene expression levels of genes of interest in blood and brain under baseline conditions.

overall_design: Gene expression profiling of hippocampus, prefrontal cortex and blood of three Wistar rats.

first: Stephanie

middle: H

last: Witt

first: Wolfgang

last: Sommer

first: Anita

last: Hansson

first: Marcella

last: Rietschel

first: Christian

middle: C


title: Expression profiles of E11.5 wildtype and Shox2 knockout embryonic forelimbs

status: Public on Jan 16 2014

summary:
The development of vertebrate extremities is a complex process which requires a highly coordinated network of different transcriptional activities. The homeodomain transcription factor Shox2 is a key player in limb formation controlling neural, muscular and skeletal development.
Here, we compared gene expression profiles of wildtype and Shox2 knockout limbs using microarray experiments to identify Shox2 target genes.

overall_design: Forelimbs of E11.5 mouse embryos were dissected and genotyped for RNA extraction. RNA from 3-4 embryos of 2 different pregnancies was used for hybridisation to 2 arrays per genotype (wildtype and Shox2 knockout) and compared.

first: Anne

last: Glaser

first: Norbert

last: Gretz


title: HK2/AA Stimulation

status: Public on Jan 09 2014

city: Cardiff

first: Robert

middle: Hywel

last: Jenkins

state: Cardiff

address: Heath Park

department: Institute of Molecular and Experimental Medicine

country: United Kingdom

institute: Cardiff University

summary: Aristolochic acid nephropathy (AAN) is characterised by rapidly progressive tubulointerstitial nephritis culminating in end stage renal failure and urothelial malignancy.  microRNAs (miRs) are small endogenous post-transcriptional regulators of gene expression implicated in numerous physiological and pathological processes.  We aimed to characterise the mechanism of AA induced cell cycle arrest and its regulation by miRs.  The microarray experiment was performed to identify differentially regulated microRNAs in human proximal tubulal epithelial cells treated with aristolochic acid (AA).

overall_design: Analysis or differential miR expression in human proximal tubular epithelial cell line (HK-2) treated with 5ug/ml aristolochic acid, control (n=3) vs aristolochic acid (n=3)

first: Donald

last: Fraser

first: Timothy

last: Bowen


title: Cardiac responses to elevated seawater temperature in Atlantic salmon

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Long-term exposure of Atlantic salmon to 19°C resulted in cardiac gene and protein expression changes indicating that the unfolded protein response, vascularization, remodeling of connective tissue and altered innate immune responses were part of the cardiac acclimation or response to elevated temperature

overall_design: Heart tissue from Atlantic salmon (RNA poooled from N=3 fish per 3 replicate tanks) reared under normal (14 deg C) and elevated (19 deg C) temperatures were sampled after 21 (short-term) and 56 days (long-term acclimation), and gene expression changes between the elevated and the control temperature were assessed using microarray analysis.

first: Krasnov

last: Aleksei

first: Sven

middle: M

last: Jorgensen


title: Age-related epigenetic drift in the pathogenesis of MDS and AML part 2

city: Smithville

first: Yue

last: Lu

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

country: USA

institute: MD Anderson Cancer Center

summary:
Genomic DNA is isolated from spleen (RUNX1 model and normal control) and bone marrow (NHD13 model and normal control).
We used MCAM to identify genes that have methylation changes.

overall_design: Two-condition experiment, MDS model mouse vs. normal control.

first: Nianxiang

last: Zhang

first: Shinji

last: Maegawa

first: Jean-Pierre

last: Issa


title: Murine pulmonary arterial smooth muscle cells: Wild-type vs. NOX1 deficiency (miRNA profiling)

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: NOX1 is a catalytic subunit of nonphagocytic NADPH oxidase, mainly localized to smooth muscle cells in the vasculature. We investigated the pathology underlying the pulmonary arterial hypertension-like phenotype demonstrated in mice deficient in the Nox1 gene (Nox1-KO). Spontaneous enlargement and hypertrophy of the right ventricle, accompanied by hypertrophy of pulmonary vessels, were demonstrated in Nox1-KO at 9-18 weeks of age. Since an increased number of α-smooth muscle actin-positive vessels was observed in Nox1-KO, pulmonary arterial smooth muscle cells (PASMCs) were isolated and characterized by flow cytometry and TUNEL staining. In Nox1-/Y PASMC, the number of apoptotic cells was significantly reduced without any change in the expression of endothelin-1, and hypoxia-inducible factors HIF-1a and HIF-2a, factors implicated in the pathogenesis of PAH. microRNA expression profiling of mouse pulmonary arterial smooth muscle cells in wild-type and NOX1-KO was analyzed.

overall_design: Pulmonary arterial smooth muscle cells were harvested form 3 mice.

first: Kazumi

last: Iwata

first: Yabe

middle: N

last: Chihiro


title: Age-related epigenetic drift in the pathogenesis of MDS and AML part 1

summary:
Genomic DNA is isolated from bone marrow (MDS patient) and whole blood (normal control).
We used MCAM to identify genes that have methylation changes.

overall_design: Two-condition experiment, MDS patient vs. normal control.


title: Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes

status: Public on Jan 08 2014

city: Frankfurt

first: Peter

last: Mombaerts

address: Max-von-Laue-Str. 3

institute: Max Planck Research Unit for Neurogenetics

summary: We developed a systematic statistical method, tTREAT, to identify differentially expressed genes with respect to a predefined FC threshold. The tTREAT approach aims to reduce false discoveries.

overall_design: We applied statistical tests relative to a Fold Change threshold to a dataset about mouse odorant receptor gene expression generated by the NanoString technology. We used mouse strains ∆P and ∆H that lack the P element and the H element respectively. We also used a mouse strain generated by chromosome engineering (∆Olfr7∆) whereby a 2.4 Mb region is deleted, thus lacking 99 odorant receptor genes. We sought to understand the regulation of the expression of odorant receptor genes by comparing mutant mice to wildtype mice.

first: Evelien

last: Vaes

first: Mona

last: Khan


title: Age-related epigenetic drift in the pathogenesis of MDS and AML

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Host plant peptides elicit a transcriptional response to control the Sinorhizobium meliloti cell cycle during symbiosis

status: Public on Jan 21 2014

city: Cambridge

first: Jon

last: Penterman

state: MA

address: 31 Ames Street

department: Department of Biology

institute: MIT

summary: We profiled gene expression in synchronized cultures of Sinorhizobium meliloti treated with or without the nodule-specific cysteine-rich peptide 247. We compared gene expression between the two conditions at 5 timepoints (15, 30, 60, 90, 120) following the addition of the peptide

overall_design: A population of synchronized Sinorhizobium meliloti was subjected to two treatments (no treatment and treated with sublethal levels of the NCR247 peptide). A series of timepoints was taken to profile the gene expression in both populations.

first: Graham

last: Walker


title: Esophageal Cancer Project

status: Public on Mar 11 2014

city: shenzhen

first: Lin

last: Li

address: Beishan Industrial Zone

country: China

institute: BGI

type: Genome variation profiling by genome tiling array

summary: Esophageal cancer is one of the most aggressive cancers and the sixth leading cause of cancer death worldwide. Approximately 70% of the global esophageal cancers occur in China and over 90% histopathological forms of this disease are esophageal squamous cell carcinoma (ESCC). Currently, there are limited clinical approaches for early diagnosis and treatment for ESCC, resulting in a 10% 5-year survival rate for the patients. Meanwhile, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we show a comprehensive genomic analysis in 158 ESCC cases, as part of the International Cancer Genome Consortium (ICGC) Research Projects (http://icgc.org/icgc/cgp/72/371/1001734). We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases and additional 70 ESCC cases were subjected to array comparative genomic hybridization (a-CGH) analysis.


title: Biphasic euchromatin-to-heterochromatin transition  on the KSHV genome following de novo infection

status: Public on Jan 01 2014

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

type: Genome binding/occupancy profiling by genome tiling array

summary:
The establishment of latency is an essential step for the life-long persistent infection and pathogenesis of Kaposi’s sarcoma-associated herpesvirus (KSHV). While the KSHV genome is chromatin-free in the virions, the viral DNA in latently infected cells has a chromatin structure that is characterized by a specific pattern of activating and repressive histone modifications that ultimately promote latent gene expression while suppressing lytic gene expression. To investigate the molecular events involved in the establishment of the latent chromatin structure during the pre-latency phase of KSHV infection, we performed a comprehensive epigenetic study to analyze the recruitment of chromatin regulatory factors onto the KSHV genome at various time-points following de novo infection of SLK and TIME cells. This showed that the KSHV genome undergoes a biphasic chromatinization following de novo infection. Initially, a transcriptionally active chromatin (euchromatin), characterized by high levels of the H3K4me3 and acetylated H3K27 (H3K27ac) activating histone marks, was deposited on the viral episome and was accompanied by the temporary induction of a limited number of lytic genes. Interestingly, transient expression of the RTA protein facilitated the increases of H3K4me3 and H3K27ac occupancy on the KSHV episome during de novo infection. Between 24-72 hours post-infection, as the levels of these activating histone marks declined on the KSHV genome, the levels of the repressive H3K27me3 and H2AK119ub histone marks increased concomitantly with the decline of lytic gene expression. Importantly, this transition to heterochromatin was dependent on both the Polycomb Repressive Complex 2 and 1. In contrast, upon infection of human gingiva-derived epithelial cells, the KSHV genome underwent a continuously transcription-active euchromatinization, resulting in efficient lytic gene expression. Our data demonstrate that the KSHV genome undergoes a temporally ordered biphasic euchromatin-to-heterochromatin transition in endothelial cells, leading to latent infection, whereas KSHV preferentially adopts a transcriptionally active euchromatin in oral epithelial cells, resulting in lytic gene expression. Our results suggest that the differential epigenetic modification of the KSHV genome in distinct cell types is a potential determining factor for latent infection vs. lytic replication of KSHV.
Please see above.

overall_design: 16 hybridizations:  ChIP and Input DNA

first: Zsolt

last: Toth

first: Jae

middle: U

last: Jung


title: Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix exon-level)

status: Public on Jan 07 2014

city: Malaga

first: James

middle: R

last: Perkins

address: Pl. Hosp. Civil

department: Hospital Civil

country: Spain

institute: Hospital Carlos Haya

summary: RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level

overall_design: 6 biological replicates (3 case – SNT subjected L5-DRG tissue, 3 control – naïve L5-DRG tissue). Each sample was made from pooling 4 distinct animals. Sample preparation and hybridization were performed by UCL genomics, following Affymetrix instructions. The 6 replicates were also used for RNA-seq, see GSE53762.

first: Ana

last: Antunes-Martins

first: Margarita

last: Calvo

first: John

last: Grist

first: Werner

last: Rust

first: Ramona

last: Schmid

first: Tobias

last: Hildebrandt

first: Matthias

last: Kohl

first: Christine

last: Orengo

first: Stephen

middle: B

last: McMahon

first: David

middle: L

last: Bennett


title: Knockdown of a zebrafish aryl hydrocarbon receptor repressor (ahrra) affects expression of genes related to photoreceptor development and hematopoiesis.

status: Public on Jan 15 2014

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: The aryl hydrocarbon receptor repressor (AHRR) is a bHLH-PAS protein closely related to the aryl hydrocarbon receptor (AHR). AHRR is a transcriptional repressor of AHR and hypoxia-inducible factor (HIF) and is regulated by an AHR-dependent mechanism. Zebrafish possess two AHRR paralogs; AHRRa regulates constitutive AHR signaling during development, while AHRRb regulates polyaromatic hydrocarbon-induced gene expression. However, very little is known about the endogenous roles of AHRRs in development and physiology. The objective of this study was to elucidate the role of AHRRs during zebrafish development using a loss-of-function approach followed by microarray analysis. Zebrafish embryos were microinjected with morpholino oligonucleotides (MO) against AHRRa or AHRRb to disrupt endogenous signaling during development. At 72 hours post-fertilization (hpf), embryos were sampled for microarray analysis.  Agilent microarray analysis revealed altered expression of 279 and 116 genes with knockdown of AHRRa and AHRRb, respectively. In AHRRa-morphant embryos, 97 genes were up-regulated and 182 genes were down-regulated. Among the differentially expressed genes were a large number related to photoreceptor development, including cone-specific genes such as short-wave, medium-wave and long-wave sensitive opsins (opn1sw1, opn1sw2, opn1mw1, opn1lw2), phosphodiesterases (pde6H, pde6C), retinol binding protein (rbp4l), phosducin, and arrestin. These results suggest that AHRRa may be involved in photoreceptor development. In addition, AHRRa knockdown also caused up-regulation of embryonic hemoglobin (hbbe3), suggesting a role for AHRR in regulating hematopoiesis. Knockdown of AHRRb caused up-regulation of 31 genes and down-regulation of 85 genes, without enrichment of genes related to any specific biological process.  Overall, these results suggest that AHRRs play multiple roles during development.

overall_design: Three different treatment conditions (Control-MO, AHRRa-MO and AHRRb-MO) and two replicates per treatment

first: Mathew

last: Jenny

first: Mark

middle: E

last: Hahn


title: Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix transcript-level)


title: Role of epigenetic modifiers on the bovine fibroblast innate immune response

city: Burlington

last: Kerr

state: VT

address: 500 Main Street 205 Terrill Hall

department: Animal Science

institute: University of Vermont

summary: The innate immune signaling pathway plays a crucial role in the recognition and early response to pathogens associated with disease. Genetic analysis has been unable to completely account for individual variability in the strength of the innate immune response. The aim of this study was to determine the role of the epigenetic markers (DNA methylation or histone acetylation) in controlling bovine gene expression in relation to the response to lipopolysaccharide (LPS). To determine the impact epigenetics may have in controlling innate immunity, dermal fibroblasts from fifteen dairy heifers having previously displayed a differential response to LPS were exposed to 5-aza-2’-deoxyctidine (AZA) and trichostatin A (TSA); de-methylating and hyper-acetylating agents, respectively. The AZA-TSA

overall_design: Fibroblast cultures (n=3) were examined under either control conditions or for gene expression following epigenetic modification with the de-methylating agent 5-aza-2'-deoxycytidine and hyper-acetylation agent trichostatin-A. Finally, expression was investigated for responsiveness to lipopolysaccharide (LPS)

first: Benjamin

last: Green


title: Expression data from rhesus macaque tongue

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression.  Our study evaluates the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease.
Microarrays were used to characterize changes in gene expression in the tongue mucosa that occur during chronic SIV infection.

overall_design: Dorsal tongue tissues from healthy uninfected macaques and macaques with chronic stage SIV infection were used for RNA extraction and hybridization on Affymetrix microarrays.

middle: D


title: Understanding cross-communication between aboveground and below ground plant via transcriptome analysis of a sucking insect whitefly-infested pepper plants

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

summary: Transcriptome analysis in response to infestation of whitefly in peppr leaf and root

overall_design: Microarry study using total RNA from whitefly infestation, BTH, whitefly + BTH, and control in both leaf and root of pepper

first: Yong-Soon

last: Park

first: Choong-Min

last: Ryu


title: Transcriptomic profiling of Ewing's sarcoma cell lines after knockdown of TRIP6

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

summary: This study aimed to explore the role of the Zyxin-related protein TRIP6 (thyroid receptor interacting protein 6) in Ewing's sarcoma (ES). By interrogation of published miccroarray data, we observed that of all seven Zyxin-proteins only TRIP6 is highly overexpressed in ES compared to normal tissues. RNA interference experiments and subsequent microarray and gene-set enrichment analyses indicated that TRIP6 expression is associated wth a pro-proliferative and pro-invasive transcriptional signature. Consistently, functional assays demonstrated that TRIP6 promotes migration, invasion, long-term proliferation and clonogencity of ES cells.

overall_design: A673 and SK-N-MC Ewing sarcoma cells were transfected with specific siRNA against TRIP6 (siTRIP6_4 or siTRIP6_5) or negative control siRNA (siControl) or Mock-transfected.

first: Olivia

last: Prazeres da Costa


title: Transcriptome analysis to elucidate puffing disorder in Citrus

first: Abhaya

last: Dandekar

address: One Shields Ave

department: Plant Sciences

summary: To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from navel orange displaying, and not displaying, the puff disorder.

overall_design:
Symptomatic and healthy “Navel” orange fruits were harvested from an orchard located in in Pauma Valley, San Diego County, California, USA. Sampling for all analysis (healthy or disordered Navel orange) was performed at the same time, from trees grown under the same agronomic, soil, and environmental conditions. Healthy and disordered fruits were analyzed at the mature stage. All transcriptome analysis was performed on mature fruit. For each type of fruit, three tissues (flavedo, albedo, and juice sacs) from three different trees (biological replicates) were separately analyzed. Four symptomatic fruits comprised one biological replicate each. Two healthy fruits comprised two biological replicates of control samples. A 1 cm-thick equatorial disc and four sections (N, S, E, and W) were cut per fruit. Each section of flavedo, albedo, and juice sac tissue was dissected.
gene expression variation underlying quality trait, different genotypes

first: Ana

last: Ibáñez

first: Russell

last: Reagan

first: Sandra

last: Uratsu

first: Federico

last: Martinelli

first: Ying

last: Chen

last: Rocke


title: Comparison of transcriptomes in five varieties of citrus fruit

summary: To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from five types of citrus fruit including, mandarin orange, navel orange, valencia orange, grapefruit and lemon.

sample_organism:
Citrus x limon
Citrus sinensis
Citrus x paradisi
Citrus reticulata

overall_design:
Mature, healthy fruits of five different citrus cultivars (“Valencia” and “Navel” orange [Citrus sinensis], mandarin [Citrus reticulata], lemon [Citrus × limon], grapefruit [Citrus × paradisi]) were purchased from a food market located in Davis, CA, USA. For all five types of fruit, three tissues (flavedo, albedo, and juice sacs) were compared separately. Each of the three tissues from each of the five types of fruit were sampled in three biological replicates, for a total of 45 samples. Samples were prepared from a 1 cm-thick equatorial disc and four sections (N, S, E, and W) were cut. Each section of flavedo, albedo, and juice sac tissue was dissected.
gene expression variation underlying quality trait, different genotypes

first: David


title: Expression profile pAP1-AP1-GR ap1cal inflorescences - time series (days)

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

institute: Center for Research in Agricultural Genomics

summary: This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a pAP1:AP1-GR ap1 cal line to induce a synchronized response  activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (Agilent, custom-commercial)

overall_design: Four sets of biologically independent tissue samples were collect before DEX-induction (day 0, 0d), as well as at 2 days, 4 days and 8 days after the treatment. Samples for each timepoint and biological replicate were co-hybridized as indicated; one sample was labeled with Cy3 and the other with Cy5. The dyes used for labeling RNA from a given timepoint were switched for two of the replicate experiments, to reduce dye-related artifacts. This experimental setup resulted in a total of 3 hybridizations per set (0days vs 2days, 2days vs 4days, and 4days vs 8days), and an even number (2) of hybridizations of each dye polarity per comparison.

first: Jose

first: Jian

last: Jin

first: Tomás

last: Matus

first: Oriol

last: Casagran


title: Expression data from rhesus macaque tongue epithelium

first: Michael

last: George

summary:
A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression.  Our study evaluates the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease.
Microarrays were used to characterize changes in gene expression in the dorsal tongue epithelium that occur during chronic SIV infection.

overall_design: Epithelial cells were laser microdissected from dorsal tongue tissue sections from healthy uninfected macaques and macaques with chronic stage SIV infection and used for RNA extraction and hybridization on Affymetrix microarrays.


title: Microarray profiling, C elegans: Neuronal miRISC IP vs Total RNA

city: Boulder

first: Minh

last: Than

state: CO

address: Campus Box 347

department: Molecular, Cellular, and Developmental Biology

institute: University of Colorado, Boulder/HHMI

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Identifying the physiological functions of microRNAs (miRNAs) is often challenging because miRNAs commonly impact gene expression under specific physiological conditions through complex miRNA::mRNA interaction networks and in coordination with other means of gene regulation, such as transcriptional regulation and protein degradation. Such complexity creates difficulties in dissecting miRNA functions through traditional genetic methods using individual miRNA mutations. To investigate the physiological functions of miRNAs in neurons, we combined a genetic “enhancer” approach complemented by biochemical analysis of neuronal miRNA-induced silencing complexes (miRISCs) in C. elegans. Total miRNA function can be compromised by mutating one of the two GW182 proteins (AIN-1), an important component of miRISC. We found that combining an ain-1 mutation with a mutation in unc-3, a neuronal transcription factor, resulted in an inappropriate entrance into the stress-induced, alternative larval stage known as dauer, indicating a role of miRNAs in preventing aberrant dauer formation. Analysis of this genetic interaction suggests that neuronal miRNAs perform such a role partly by regulating endogenous cyclic guanosine monophosphate (cGMP) signaling, potentially influencing two other dauer-regulating pathways. Through tissue-specific immunoprecipitations of miRISC, we identified miRNAs and their likely target mRNAs within neuronal tissue. We verified the biological relevance of several of these miRNAs and found that many miRNAs likely regulate dauer formation through multiple dauer-related targets. Further analysis of target mRNAs suggests potential miRNA involvement in various neuronal processes, but the importance of these miRNA::mRNA interactions remains unclear. Finally, we found that neuronal genes may be more highly regulated by miRNAs than intestinal genes. Overall, our study identifies miRNAs and their targets, and a physiological function of these miRNAs in neurons. It also suggests that compromising other aspects of gene expression, along with miRISC, can be an effective approach to reveal miRNA functions in specific tissues under specific physiological conditions.

overall_design: Each array was used for one biological replicate, where the red channel is used for IP RNA and the green channel is used for Total RNA. IP RNA indicates the transcripts associated with a neuronally expressed, GFP-tagged, miRISC. Five biological replicates were done on asynchronous worms. Please note the two different microarray platforms that were used.

middle: T

first: Brian

middle: A

last: Kudlow

first: Min

last: Han


title: Analysis of genome-wide copy number variations in Oryza sativa L.

city: Hangzhou

first: Ping

last: Yu

address: 359 Tiyuchang Road

institute: China National Rice Research Institute

summary:
We describe a more detailed survey undertaken to detect candidate CNVs in a panel of 20 Asian cultivated rice and the genome-wide characteristics of CNVs in subspecies and groups.
These resources allowed us to analyze genetic structure as indicated by CNVs, to implicate the biological roles of CNVs, and to identify candidate CNVs that are likely to occur independently in groups and contribute to differences between the subspecies.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: a panel of 20 accessions

first: Xinghua

last: Wei


title: Transcriptome analysis of Azospirillum lipoferum 4B during its interaction with rice roots

city: Villeurbanne

first: Benoît

last: DROGUE

state: Rhône-Alpes

address: Boulevard du 11 novembre

department: Université Lyon 1

country: France

institute: Université de Lyon

summary: Investigation of whole genome gene expression level changes in a Azospirillum lipoferum 4B associated to artificial roots, Oryza sativa japonica cv. Cigalon roots and Oryza sativa japonica cv. Nipponbare roots, compared to the strain grown in liquid culture.

overall_design: For each of the four condition, two replicates were analysed on an A. lipoferum 4B whole genome expression array designed by Roche Nimblegen, Inc. (Madison, WI, USA), based on the genome sequence (Wisniewski-Dyé et al. 2011), as follows: two replicates of 5 probes (length, 60 nucleotides) per gene, covering 6,242 genes and using a total of 62,178 probes.

last: Drogue

first: Hervé

last: Sanguin

first: Stephanie

last: Borland

first: Claire

last: Prigent-Combaret

first: Florence

last: Wisniewski-Dyé


title: Metabolomic and transcriptomic analysis for rate-limiting metabolic steps in xylose utilization by recombinant Candida utilis

city: Yokohama-shi

first: Hideyuki

last: Tamakawa

address: 1-13-5, Fukuura, Kanazawa-ku

department: Central Laboratories for Key Technologies

institute: KIRIN Co., Ltd.

summary: We previously reported that a recombinant Candida utilis strain expressing a Candida shehatae xylose reductase K275R/N277D, a C. shehatae xylitol dehydrogenase, and xylulokinase from Pichia stipitis produced ethanol from xylose. However, its productivity was low. In this study, metabolomic (CE-TOF MS) and transcriptomic (microarray) analyses were performed to characterize xylose metabolism by the engineered C. utilis and to identify key genetic changes contributing to efficient xylose utilization. Metabolomic analysis revealed that the xylose-fermenting strain accumulated more pentose phosphate pathway intermediates, more NADH, and more glycolytic intermediates upstream of glyceraldehyde 3-phosphate than wild-type. Transcriptomic analysis of the strain grown on xylose indicated a significant increase in expression of genes encoding tricarboxylic acid cycle enzymes, respiratory enzymes, and enzymes involved in ethanol oxidation. To decrease the NADH/NAD+ ratio and increase ethanol yield from the fermentation of xylose, ADH1 encoding NADH-dependent alcohol dehydrogenase was overexpressed. The resultant strain exhibited a 17% increase in ethanol production and a 22% decrease in xylitol accumulation relative to the control.

overall_design: Gene expression in Candida utilis cells grown on glucose or xylose was measured at 10.5 and 24 hours, respectively. Two or three independent experiments were performed at each time for each experiment.

first: Yasuyuki

last: Tomita

first: Aki

last: Yokoyama

first: Yuki

last: Konoeda

first: Shigehito

last: Ikushima

first: Satoshi

last: Yoshida


title: AHX and AOH effect on Oryza sativa

city: Shizuoka

first: JAE-HOON

last: CHOI

address: 836 Ohya

department: Graduate School of Science and Technology

institute: Shizuoka University

summary: Fairy rings are zones of stimulated grass growth by the interaction between the fungi and the plant. In the previous research, we reported the identification of the “fairy”, 2-azahypoxanthine (AHX), produced by the fairy ring-forming fungus and the mechanism of its growth-promoting activity using DNA microarray. We discovered AOH, a common metabolite of AHX in plants.  We investigate expression profiling of rice seedlings treated with AHX or AOH for the mechanism of their growth-promoting activity.

overall_design: Three-condition experiment, control vs. AHX-treated rice (50 and 200 mM) and AOH-treated rice (50 and 200 mM).

first: Jae-Hoon

last: Choi

first: Hiroyuki

last: Tobina

first: Reiko

last: Motohashi

first: Hirokazu

last: Kawagishi


title: Identification of Hr38 as a neural activity-induced gene

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: Silkworms show a reproductive behavior induced by sex pheromone. To elucidate the neral mechanism of sex pheromone induced sexual behavior in the silkworm, we attempted to use the neural activity-induced gene as a neural activity marker. Since no neural activity-induced gene was identified in the silkworm, we conducted screening of neural activity-induced gene using the male silkworm brain. By the screening, we identified Bhr38 as a novel neural activity-induced gene, and succeded to comprehensively map the active neruons in the silkworm brain in response to the sex pheromone exposure. Further, we found that Dhr38, the Drosophila homologue of Bhr38, also expressed in a neural activity dependent manner. These results strongly suggest that Hr38 is a highly conserved neural activity-induced gene.

overall_design: The male silkworms were exposed to the female odor for 30 min (group P). Non-treated male silkworms were used as the control group group C. Ten brains were collected for each sample and stored at -80°C until use. Total RNA was isolated by the TRIzol reagent and subjected to microarray experiments using the custam made (8x16k) Oligo Microarray (Agilent Technologies, Inc.).

first: Taketoshi

last: Kiya


title: Microarray identification of conserved microRNAs in Pinellia pedatisecta

first: Bo

last: Wang

state: zhejiang

address: Xiasha

institute: Zhejiang Sci-Tech University

summary: An in situ synthesized custom miRNA microarray was employed to detect miRNAs from P. pedatisecta, A total of 99 miRNAs belonging to 22 miRNA families were identified.

overall_design: in the study present here, the microarray design was based on 2521 well-characterized miRNAs from 43 plant species  on Sanger miRBase Release 16, and  Eighteen 5S rRNAs that served as internal reference were chosen from A. thaliana, C. reticulata, and O. sativa with an equal amount. Eight quality control probes were synthesized to perfect match (PM) or one nucleotide mismatch (MM) with eight external spiked-in synthetic RNA (20mer).

first: Tao

last: Xu


title: Molecular impact of juvenile hormone agonists on neonatal Daphnia magna

status: Public on Dec 31 2013

city: Okazaki

first: Kenji

last: Toyota

address: 5-1 Higashiyama

institute: National Institute for Basic Biology

summary: Daphnia magna has been used extensively to evaluate organism- and population-level responses to pollutants in acute toxicity and reproductive toxicity tests.  We have previously reported that exposure to juvenile hormone (JH) agonists results in a reduction of reproductive function and production of male offspring in a cyclic parthenogenesis, D. magna. Recent advances in molecular techniques have provided tools to better understand the responses to pollutants in aquatic organisms including D. magna. DNA microarray was used to evaluate gene expression profiles of neonatal daphnids exposed to JH agonists; methoprene (125, 250 and 500 ppb), fenoxycarb (0.5, 1 and 2 ppb), and epofenonane (50, 100 and 200 ppb). Exposure to these JH analogs resulted in chemical specific patterns of gene expression. The heat map analyses based on hierarchical clustering revealed a similar pattern between treatments with a high dose of methoprene and with epofenonane. In contrast, treatment with low to middle doses of methoprene resulted in similar profiles to fenoxycarb treatments. Hemoglobin and JH epoxide hydrolase genes clustered to be JH-responsive genes. These data suggest that fenoxycarb has high activity as a JH agonist, methoprene shows high toxicity and epofenonane works through a different mechanism compared with other JH analogs, agreeing with data of previously reported toxicity tests. In conclusion, D. magna DNA microarray is useful for classification of JH analogs and identification of JH-responsive genes.

overall_design: Juvenile hormone agonists induced gene expression in daphnids neonates was measured at 48 hours after exposure to methoprene (125, 250, 500 ppb), fenoxycarb (0.5, 1, 2 ppb), epofenonane (50, 100, 200) and DMF as a control.  Three independent experiments were performed at each chemicals.

first: Yasuhiko

last: Kato

first: Hitoshi

last: Miyakawa

first: Ryohei

last: Yatsu

first: Yukiko

last: Ogino

first: Shinichi

last: Miyagawa

first: Hajime

last: Watanabe

first: Hiroyo

last: Nishide

first: Ikuo

last: Uchiyama

first: Norihisa

last: Tatarazako

first: Taisen

last: Iguchi


title: Soybean toxin (SBTX) impairs fungal growth by interfering with molecular transport, carbohydrate/amino acid metabolism and drug/stress responses

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

summary: Soybean toxin (SBTX) is an antifungal protein from soybeans with broad growth and filamentation inhibitory activity against many fungi, including human and plant pathogenic species such as Candida albicans, Candida parapsilosis, Aspergillus niger, Penicillium herquei, Cercospora sojina, and Cerospora kikuchii. Understanding the mechanism by which SBTX acts on fungi and yeasts may contribute towards the design of novel antifungal drugs and/or for the development of transgenic plants resistant to pathogens. To gain new insights into the mode of action of SBTX, the polymorphic yeast C. albicans was chosen as a model organism, and changes in the gene expression profile of strain SC5314 upon exposure to SBTX were examined. Genes that were differentially regulated in the presence of SBTX were involved in glucose transport and starvation-associated stress responses, as well as in the control of both the induction and repression of C. albicans hyphal formation. Transmission electron microscopy showd that C. albicans cells exposed to SBTX displayed severe signs of starvation and were heavily granulated. Our data were indicative of C. albicans cells starving despite sufficient nutrient availability in the medium, and it can therefore be speculated that SBTX blocks nutrient uptake systems. Because neither the starvation signal nor the alkaline response pathway lead to the induction of hyphae, we hypothesise that conflicting signals are transmitted to the complex regulatory network controlling morphogenesis, eventually preventing the filamentation signal from reaching a significant threshold.

overall_design: For transcriptional profiling, the cells were growth in the presence or absence of SBTX (200 µg∙mL-1) in SDB/4.The cultures were grown until they reached an OD600 of approximately 0.5, after 16 and 18 h, for untreated and SBTX-treated cells. The cells were harvested by centrifugation (3000•g at 25°C), snap-frozen in liquid nitrogen and stored at -80°C. Each pair of samples (untreated and SBTX-treated cells) constituted a single experiment, and two biologically independent experiments were carried out.

first: Janne

middle: K

last: Morais

first: Oliver

last: Bader

first: Ilka

last: Vasconcelos


title: Molecular immune response of the American lobster (Homarus americanus) to the White Spot Syndrome Virus

city: Charlottetown

first: Fraser

last: Clark

state: PEI

address: 550 University Ave

department: Pathology and Microbiology

country: Canada

institute: University of Prince Edward Island

summary: Transcriptomic profiling of Homarus americanus after in vivo challenge with White Spot Syndrome Virus

overall_design: Two condition (control and infected) time series experiment; Biological replicates: 3 x 6 h control, 3 x 168 h control, 4 x 6 h infected, 4 x 12 h infected, 4 x 24 h infected, 4 x 48 h infected, 4 x 96 h infected, 4 x 168 h infected

first: K

middle: F

first: Spencer

middle: J

last: Greenwood

first: Adam

last: Acorn

first: Philip

last: Byrne


title: Complementary Strand MicroRNAs Mediate Acquisition of Metastatic Potential in Colonic AdenocarcinomamRNA and microRNA profile in colon cancer

city: Tampa

first: Dung-Tsa

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

institute: Moffitt Cancer Center

summary: With broad high-throughput evaluation of microRNA expression across the spectrum of colon cancer stages, we identidied a microRNA signature that is associated with more aggressive disease

overall_design: microRNA was extracted from FFPE colon tissues for microRNA array analysis

first: Timothy

last: Yeatman


title: Curcumin intake affects miRNA signature in murine melanoma with mmu-miR-205-5p most significantly altered.

city: Saarbrücken

first: Christina

last: Backes

address: Campus, Building E 2.1

department: Chair for Clinical Bioinformatics

institute: Saarland University

summary: Melanoma is the most aggressive form of skin cancer with estimated 48,000 deaths worldwide. The polyphenol curcumin derived from the plant Curcuma longa is well known for its anti-inflammatory and anti-cancerogenic properties. Accordingly, dietary intake of this compound may be suitable for melanoma prevention. However, how this compound affects basic cellular mechanisms in developing melanoma still remains elusive. Therefore, the aim of this study was to investigate for the first time the impact of oral curcumin administration on the miRNA signature of engrafting melanoma. For this purpose, the effects of a 4% curcumin diet on murine B78H1 melanoma were tested in a flank model. Curcumin diet or standard chow (control) was administered two weeks prior to tumor initiation until termination of the experiment. Highly significant chip-based miRNA array analysis was deployed to detect alterations in the miRNA signature of the tumors. Curcumin treatment significantly reduced the growth of the flank tumors. Furthermore the miRNA expression signature in tumors was substantially altered by curcumin intake with mmu-miR-205-5p over 100 times higher expressed when compared to controls. Putative targets of curcumin-induced up-regulated miRNAs were enriched in o-glycan biosynthesis, endoplasmatic reticulum protein processing and different cancer-related pathways. These findings demonstrate a profound alteration of the miRNA expression signature in engrafting curcumin-treated melanoma with mmu-miR-205-5p being up-regulated most significantly.

overall_design: Treatment of male C57BL/6 mice with induced flank tumors (injection of B78H1 cells) either with standard mouse chow (control n=6) or chow enriched with 4% of curcumin (treatment group n=7 )


title: Dlx1 and Rgs5 in the Ductus Arteriosus: Vessel-specific Genes Identified by Transcriptional Profiling of Laser-capture Microdissected Endothelial and Smooth Muscle Cells

city: Leiden

first: Regina

last: Bokenkamp

address: Albinusdreef 2

department: Dept of Pediatric Cardiology

country: Netherlands

institute: LUMC

summary:
Closure or patency of the ductus arteriosus is a critical event in neonatal life. We aimed to identify genes that are specifically expressed in the ductus arteriosus versus (the non-closing) aorta
Gene expression profiling of laser-captured microdissected cells offers the opportunity to study gene expression profiles in cells of different embryonic origin

overall_design: Comparative microarray analysis of laser-capture dissected endothelial and smooth muscle cells of the rat ductus arteriosus and aorta at embryonic age E18 and E21.

first: R

last: Van Brempt


title: microRNA expression of pancreatic tumors

city: seoul

first: minhee

last: park

address: shinchondong

institute: student

summary:
Solid-pseudopapillary neoplasm of pancreas (SPN), ductal adenocarcinoma (PCA), neuroendocrine tumor (NET) and non-neoplastic pancreas.
comparison with gene expression of tumors and non-tumors

overall_design: To investigate the specific microRNA expression of SPN compared to other types of pancreatic tumor, we analyzed large-scale microRNA expressioin analysis to identify the molecular signature that may affect SPN tumorigenesis with mRNA expression profiles. Differentially expressed microRNAs were analyzed on SPNs, PCAs, NETs and Non-neoplastic tissues.

first: Hoguen

last: Kim

first: Minhee

last: Park

first: Minhyung


title: Homarus americanus larval development and metamorphosis

first: Dan

last: Hines

state: PE

institute: AVCLSC

summary: Transcriptional profiling of larval stage I - IV of Homarus americanus, for assessment of stage specific developmental gene expression. Individuals from each stage were gathered in July of 2009 and 2010. A reference design was used to permit comparison of all stages. Study aims included assessment of global gene expression of larval development of healthy larvae, and identifying novel molecular pathways involved in H. americanus development.

overall_design: Four condition experiment, stage I - IV individuals: 10 biological replicates per stage. Stages collected independantly from each other; sampling conducted over 2 seasons. Reference sample prepared from pooled RNA of  4 individuals per stage.

first: Daniel


title: Gene expression profiling in porcine chronic myocardial ischemia treated with intramyocardial injections of secretome

city: Vienna

first: Mariann

last: Gyongyosi

address: Wahringer Gurtel 18-20

country: Austria

institute: Medical University of Vienna

summary:
Closed-chest reperfused MI was induced in pigs by 90-min occlusion, followed by reperfusion of the mid LAD (day 0) and by cardiac MRI with late enhancement (LE) at day 3. At day 30 the animals received either porcine APOSEC (n=8) or placebo medium (n=8) in a randomized manner, injected into the border zone of MI using 3D NOGA percutaneous intramyocardial guidance. At day 60, control cardiac MRI with LE and measurements of myocardial viability via diagnostic NOGA were performed.  Gene expression profiling of the infarct core, border zone and normal myocardium was performed using microarray analysis, confirmed by quantitative real-time PCR.   Percutaneous endomyocardial injections of APOSEC led to a significant (p<0.05) decrease in infarct size and in improvement of cardiac index and myocardial viability compared to medium treatment. Trend towards higher LV ejection fraction was observed in APOSEC vs. the Medium placebo group (45.4±5.9% vs 37.4±8.9%, p=0.052). Transcriptome analysis revealed significant downregulation of caspase-1 and other inflammatory genes in the APOSEC-affected areas. PCR showed higher expression of myogenic factor, Mefc2 (p<0.05) gene with downregulated caspase-3 (p<0.05) in the APOSEC-pigs.
We have investigated the effects of catheter-based endomyocardial injections of APOSEC (secretome of apoptotic peripheral white blood cells) on porcine chronic post-infarction (MI) left ventricular (LV) dysfunction and gene expression profile.

overall_design: Pigs randomized to receive eithersecretome (n=8) or medium (placebo control, n=8)

first: Noemi

last: Pavo

first: Matthias

last: Zimmermann

first: Dietmar

last: Pils

first: Michael

last: Mildner

first: Z

last: Petrasi

first: O

last: Petnehazy

first: J

last: Fuzik

first: A

last: Jakab

first: C

last: Gabriel

first: W

last: Sipos

first: G

last: Maurer

first: M

last: Gyöngyösi

first: H

last: Ankersmit


title: Comparative genomic analysis of Aggregatibacter actinomycetemcomitans strains during short term persistent infections using a pan-genome microarray

city: Seattle

first: Weerayuth

last: Kittichotirat

state: WA - Washington

address: 960 Republican st

department: Microbiology

institute: University of Washington

summary: To analyze the gain and lost of genes in Aggregatibacter actinomycetemcomitans during short-term persistent infection in the same host

overall_design: The microarray was used to compare gene contents of 4 different pairs of Aggregatibacter actinomycetemcomitans strains (SCC393 vs A160, SCC1398 vs SCC4092, SCC2302 vs AAS4a, and S23A vs I23C), where each pair was isolated from an individual over time. Two biological duplicates were carried out for each strain.

first: Ruoxing

last: Sun

first: Justin

last: Wang

first: Minnie

last: Jan

first: Sirkka

last: Asikainen

first: Roger

last: Bumgarner

first: Casey

last: Chen


title: Transcriptome Profiling of Zymomonas mobilis Under ethanol stress

city: Chengdu

first: Mingxiong

last: He

state: Sichuan

address: Section 4-13, Renming Nanlu

department: Biomass Energy Technology Research Centre

institute: Biogas Institute of Ministry of Agriculture

summary: Investigation of the expression profiling of the ethanologenic Zymomonas mobilis in response to ethanol stress.

platform_organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

overall_design: A six chip study using total RNA recovered from three separate wild-type cultures of Zymomonas mobilis ATCC31821 and three separate cultures of a triple treated with 5% ethanol. Each chip measures the expression level of 1800 genes from Zymomonas mobilis ATCC31821 and the associated plasmids, with three-fold technical redundancy.


title: Expression analysis of Klebsiella pneumoniae MGH 78578 and capsule deletion mutant

city: Zhunan

first: Tzu-Wen

last: Huang

address: 35 Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

summary:
To investigate the whole-genome gene expression difference between the wild-type and capsule deletion mutant in Klebsiella pneumoniae MGH 78578.
The mutants analyzed in this study are further described in Huang T.W., Stapleton J.C., Chang H.Y., Tsai S.F., Palsson B.O., Charusanti P. Capsule removal via lambda-Red knockout system perturbs biofilm formation and fimbriae extression in Klesiella pneumoniae MGH 78578 (manuscript submission)

sample_organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

overall_design: A six chip study using total RNA recovered from three separate wild-type cultures and three separate cultures of a capsule deltion mutant of Klebsiella pneumoniae MGH 78578. The capsule gene cluster (KPN_02493 to KPN_02515) was entirely removed in the capsule deletion mutant. Each chip measures the expression level of 5,305 genes from Klebsiella pneumoniae MGH 78578 and the associated five plasmids (pKPN3, pKPN4, pKPN5, pKPN6 and pKPN7) with 50-mer oligo tiling array with 30-mer spacer.


title: Gene expression profile in bone metastatic prostate cancer cell line, PC3, following growth in bone marrow conditioned medium (BMCM)

city: Birmingham

first: Victor

last: Thannickal

state: AL

address: BMR2 470, 901 19th Street S

department: Medicine

institute: University of Alabama at Birmingham

summary: To determine initial genetic changes in the prostate cancer cells following migration to skeleton

overall_design: PC3 cells grown in three dimensional spheroids on hubiogel matrices were cultured for 10 days in BMCM obtained from immunocompetent C57/BL6 mouse. Total RNA was isolated from these PC3 spheroids and subjected to cDNA microarray analysis.

first: Diptiman

last: Chanda

first: Selvarangan

last: Ponnazhagan


title: NanoString analysis of a rat liver mRNA panel following TCDD treatment

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

institute: Ontario Institute for Cancer Research

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

summary: Profiling of mRNA abundances with high-throughput platforms such as microarrays and RNA-Seq has become an important tool in both basic and biomedical research. However these platforms remain prone to systematic errors, and have challenges in clinical and industrial application. As a result it is standard practice to validate a subset of key results using alternate technologies. Similarly, clinical and industrial applications typically involve transitions from high-throughput discovery platform to medium-throughput validation ones. These medium-throughput validation platforms have high technical reproducibility and reduced sample input needs, and low sensitivity to sample-quality (e.g. for processing FFPE specimens). Unfortunately, while medium-throughput platforms have proliferated, there are no comprehensive comparisons of them. Here we fill that gap by comparing two key medium-throughput platforms – NanoString’s nCounter Analysis System and ABI’s OpenArray System – to gold-standard quantitative real-time RT-PCR.

overall_design: TCDD-sensitive (Long-Evans) and TCDD-resistant (Han/Wistar) rats were used in both time-course and dose response studies to asses the transcriptomic response to TCDD-insult. The time-course experiment saw animals recieve a single dose of 100ug/kg TCDD or corn oil vehicle followed by euthanasia and tissue collection at various time-points. Animals in the dose-response experiment recieved a single dose of TCDD at varying concentrations or corn oil vehicle, followed by euthanasia and tissue collection 19 hours post-treatment. Each treatment group contained 4-5 biologicial replicates.

first: John

last: Watson

first: Daryl

last: Waggott

first: Ashley

last: Smith

first: Alexander

middle: H

last: Wu

first: Allan

last: Okey

first: Raimo

last: Pohjanvirta

first: Paul

middle: C

last: Boutros


title: Nuclear phosphatidylinositol-5-phosphate regulates ING2 stability at discrete chromatin targets in response to DNA damage [ChIP-chip]

city: Stanford

first: Dennis

middle: Jacob

last: Bua

address: Gilbert Building, Room 109, 371 Serra Mall

department: Biology

institute: Stanford University

summary: ING2 (inhibitor of growth family member 2) is a component of a chromatin-regulatory complex that represses gene expression and is implicated in cellular processes that promote tumor suppression.  However, few direct genomic targets of ING2 have been identified and the mechanism(s) by which ING2 selectively regulates genes remains unknown. Here we provide evidence that direct association of ING2 with the nuclear phosphoinositide phosphatidylinositol-5-phosphate (PtdIns(5)P) regulates a subset of ING2 targets in response to DNA damage.  At these target genes, the binding event between ING2 and PtdIns(5)P is required for ING2 promoter occupancy and ING2-associated gene repression.  Moreover, depletion of PtdIns(5)P attenuates ING2-mediated regulation of these targets in the presence of DNA damage.  Taken together, these findings support a model in which PtdIns(5)P functions as a sub-nuclear trafficking factor that stabilizes ING2 at discrete genomic sites.

overall_design: FLAG-ING2 ChIP-chip of stably-transduced HT1080 cells in the presence of vehicle (DMSO) or etoposide.  Each condition is tested in duplicate.

first: Gloria

last: Mas Martin

first: Olivier

last: Binda

first: Or

last: Gozani


title: Strigolactone and cytokinin act antagonistically in regulating rice mesocotyl elongation in darkness

city: Chikusa

first: Takaki

last: Yamauchi

address: Furo-cho

institute: Nagoya University

summary:
Strigolactones have been defined as a new group of phytohormones that regulate shoot branching. Tthe phenotypes of strigolacton-related rice (Oryza sativa) dwarf (d) mutants demonstrated that SLs inhibit mesocotyl elongation by controlling cell division. Moreover, the trans-zeatin, one of active cytokinins, content of mesocotyls was increased in the SL-deficient d10-1 and SL-insensitive d14-1 mutants.
To examine if there are genes related to cytokinin-biosynthesis or -degradation among the strigolactone-responsive genes expressed in the mesocotyl, we carried out microarray analyses using d10-1, d14-1 and the wild-type grown under dark conditions, with or without pretreatment of a synthetic strigolactone analog, GR24.

overall_design: Gene expression profiles in 4-day-old mesocotyls of dwarf (d) mutants (d10-1 and d14-1) and wild-type germinated under dark conditions with or without treatment of 1 μM GR24 were analyzed. Three biological replicates were prepared for each conditions, and a total of eighteen samples were analyzed.

first: Zhongyuan

last: Hu

first: Jinghua

last: Yang

first: Yusuke

last: Jikumaru

first: Tomoko

last: Tsuchida-Mayama

first: Hiroaki

last: Ichikawa

first: Itsuro

last: Takamure

first: Yoshiaki

last: Nagamura

first: Nobuhiro

last: Tsutsumi

first: Shinjiro

last: Yamaguchi

first: Junko

last: Kyozuka

first: Mikio

last: Nakazono


title: Transcriptome analysis of Aggregatibacter actinomycetemcomitans strains isolated from the same individual during short term persistent infections using a pan-genome microarray

first: Weerayuth

last: Kittichotirat

summary: To characterize the differences in pattern of gene expression between different pairs of Aggregatibacter actinomycetemcomitans strains (SCC393 vs A160, SCC1398 vs SCC4092, and S23A vs I23C), where each pair was isolated from an individual over time.

overall_design: The microarray was used to examine the transcriptome of Aggregatibacter actinomycetemcomitans strains SCC393, A160, SCC1398, SCC4092, S23A, and I23C, where biological triplicates were produced for strains SCC1398, SCC4092, S23A, and I23C and biological duplicates were produced for strains SCC393, and A160

first: Ruoxing

last: Sun

first: Justin

last: Wang

first: Minnie

last: Jan

first: Sirkka

last: Asikainen

first: Roger

last: Bumgarner

first: Casey

last: Chen


title: microRNA expression patterns related to merkel cell polyomavirus infection in human merkel cell carcinoma

city: Stockholm

first: Hong

last: Xie

address: KUS-Solna, CCK R8:04

country: Sweden

institute: Karolinska Institutet

summary: We performed miRNA expression profiling in  a series of human Merkel Cell carcinoma samples using a microarray approach. Significant differentially expressed miRNAs among groups were identified using SAM analysis.

overall_design: Agilent microarray platform containing 723 human miRNAs was used to determine miRNA expression profiles in 16 human Merkel cell carcinoma (MCC) samples. To validate the microarray platform, the expression levels of selected miRNAs were evaluated using qRT-PCR.

first: Linkiat

last: Lee

first: Stefano

last: Caramuta

first: Anders

last: Höög

first: Viveca

last: Björnhagen

first: Catharina

last: Larsson

first: Weng-Onn

last: Lui


title: Spatial transcriptomes of iron-deficient and cadmium-stressed rice

city: Tsukubashi

first: Yuko

last: Ogo

state: Ibaraki

address: 3-1-3 Kannondai

institute: NARO

summary: Several metals are essential nutrients for plants but metals are toxic in excess, deleteriously affecting crop yield and quality. Various kinds of genes involved in metal homeostasis have been investigated in detail over the past few decades and the mechanisms of how metals are absorbed from soil and distributed in plants have been elucidated. However, numerous genes related to metal homeostasis remain to be investigated and a comprehensive analysis of the expressions of these genes is required. In the present study, we investigated the spatial gene expression profile of iron (Fe)-deficient and cadmium (Cd)-stressed rice by a combination of laser capture microdissection and microarray analysis.

overall_design: We performed comprehensive microarray analysis of a rice root using laser microdissection and collected a total of 13 samples (3 replicates for each sample, 39 total microarray data). Roots of normal, Fe-deficient (-Fe) and Cd-stressed (+Cd) rice were separated into the vascular bundle (VB), cortex (Cor), and epidermis plus exodermis (EP). In addition, vascular bundles from new leaves (newDC) and old leaves (oldDC) at the lowest node, which are important for metal distribution, were separately analyzed.

first: Y

last: Kakei

first: R

middle: N

last: Itai

first: T

last: Kobayashi

first: H

last: Nakanishi

last: Takahashi

first: M

first: N

last: Nishizawa


title: Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation

status: Public on Dec 23 2013

city: New York

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots.

overall_design: We examined the abundance of NATs in etiolated seedlings and seedlings undergoing de-etiolation in continuous white light for 1/6h. Seedlings were further dissected into cotyledons, hypocotyls and roots. RNAs from 3 biological replicates of each of the 3 organs were separately hybridized to ATH NAT arrays to profile light-regulated NAT pairs.

first: Pil

last: Chung

first: In-Cheol

last: Jang

first: Jun

last: Liu


title: Effect of 17 β-estradiol on developing zebrafish embryos

city: houston

first: Ruixin

last: Hao

state: TX

address: 3605 Cullen Blvd, Room 3005

department: Department of biology and biochemistry

institute: University of Houston

summary: Estrogen signaling is important for vertebrate embryonic development. Here we have used zebrafish (Danio rerio) as a vertebrate model to identify estrogen regulated genes during the first 4 days of development. Zebrafish embryos were exposed to 1 µM 17β-estradiol from 3 hours post fertilization to 4 days post fertilization, harvested daily and subjected to RNA extraction for transcriptome analysis using microarrays. Estrogen responsive genes were analyzed with hierarchical clustering followed by gene function and tissue expression analysis. Markedly distinct sets of genes were up and down-regulated by estrogen treatment at different time points. Among these genes, only the well-known estrogenic marker vtg1 was co-regulated at all time points. Despite this, the biological functional categories targeted by estrogen were similar throughout zebrafish development. Estrogen responsive genes were enriched mainly in the liver, pancreas and brain. In conclusion, our data shows that in zebrafish distinct cohorts of E2 responsive genes are expressed in a tissue specific manner at different developmental stages. However, the biological pathways that are affected are conserved.

overall_design: 30 embryos were pooled as one sample and exposed to 1 μM E2 or vehicle (0.1% DMSO) at approximately 3 hours post fertilization (hpf). At different time points, 1 dpf (24 hpf), 2 dpf (48 hpf), 3 dpf (72 hpf) and 4 dpf (104 hpf), embryos were collected for total RNA extractions. Time points 1 and 2 dpf were performed in biological triplicates of independent pools of RNA while time points 3 and 4 dpf were performed in quadruplicates.

first: Maria

last: Bondesson

first: Amar

middle: V

last: Singh

first: Jan-Åke

last: Gustafsson


title: Copy number analysis of recurrent metastatic melanoma lesions

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
In this study, we sought to indentify stable individual traits in developing metastatic melanoma, assess their stability in time, and analyze typical dynamics and common trends of genomic changes in individual cases of late stage metastatic cancer.
To this end, we compared consecutive recurrent metastases developed by a special group of eight individuals with advanced metastatic melanoma, all developing several recurrent metastases over several months to years of natural disease evolution.

overall_design: Twenty-six recurrent melanoma metastases were surgically isolated from 8 patients experiencing relapse after one or more successful treatment intervention(s) with no signs of residual disease. Patients experiencing recurrent metastases were labeled with capital letters; “A”, “B”, “C”, etc., their subsequent metastases as “A/1”, “A/2”, “B/1”, “B/2”, etc., while synchronous metastases in a given patient  were labeled as “A/1a”, “A/1b” etc. Another 22 melanoma cell lines isolated and maintained as above were expanded from melanoma patients with rapid disease curse, for whom only one metastasis was available. As no extended follow up was possible in these cases, the cell lines are considered representative of random time points in the natural course of metastatic melanoma. These cell lines were labeled with Arabic numbers, as “1”, “2”, ”3”, etc.

first: Tara

last: Spivey

first: Hui

first: Jinguo

last: Chen

first: Michele

last: Maio

first: Paul

last: Robbins

first: Ena

first: Francesco

middle: M

last: Marincola


title: Expression of Arabidopsis cis-NAT pairs in inflorescences, leaves and roots

summary: We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To detect the expression levels of these NAT pairs, we designed an Agilent custom array, ATH NAT array, and analyzed RNA samples from Arabidopsis inflorescences, leaves and roots, with 3 biological replicates each.

overall_design: Expression levels of cis-NAT pairs were investigated in WT inflorescences, leaves and roots with 3 biological replicates.

last: Xu


title: A novel chordoma xenograft allows in vivo drug testing and reveals the importance of NF-kB signaling in chordoma biology

status: Public on Dec 22 2013

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

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

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

overall_design: Refer to individual Series

last: Meltzer

first: David

last: Loeb


title: Glanville fritillary larvae from three larval families (full-sib) exposed to alternative temperature treatments during final instar stage.

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

summary:
We combined heritability analysis of larval development rate with a global expression analysis of this phenotype to investigate genotype by environment interactions across three ecologically relevant temperatures in the Glanville fritillary butterfly (Melitaea cinxia). We focused upon the development of final instar caterpillars which is greatly affected by temperature, and during this stage the caterpillars build up most of the resources for adult life.
Second generation, lab reared larvae, initially collected from the Åland metapopulation, were reared in standard lab condition until 6th larval instar. At the beginning of the final (7th) instar stage the larvae were separated into of three temperature conditions:
Cold treatment (temperature profile: 8°C 18:00-9:59, 14°C 10:00-11:59, 20°C 12:00-15:59 and 14°C 16:00-17:59)
Standard treatment (temperature profile: 15°C 17:00-6:59, 18°C 7:00-8:59, 22°C 9:00-10:59 and 26°C 11:00-16:59)
Hot treatment (temperature profile: 8°C 20:00-7:59, 15°C 8:00-9:59, 35°C 10:00-17:59 and 15°C 18:00-19:59)
The temperature profiles mimic the diurnal thermal variation of the natural habitat (Åland islands) of samples. Cold treatment mimics a cool and cloudy summer, Standard represents an average temperature profile in the Åland islands and Hot treatment mimics an exceptionally hot and sunny summer, with cold night-time temperatures.
The experiment contained several larval families (full-sib) of which three were selected for gene expression analysis. Samples were snap-frozen in liquid nitrogen during mid-development (after 6, 5 and 4 days, for Cold, Standard and Hot respectively). Additional larvae from the same treatments were assayed for survival and growth. Gene expression was analyzed using a mixed model approach to identify genes with potential heritable expression variation (variation among families), genes with plastic expression responses (treatment induced changes) and genes with treatment dependent expression that varies among families (family by treatment interactions).

overall_design: Full-sib larvae from three families (N170, N74 and O171) were exposed to three temperature treatments (Cold, Standard and Hot) during final (7th) instar stage. A total of 35 samples were used to analyze family, treatment and family by treatment interactions in gene expression, using a mixed model approach. This included 3 biological replicates in Cold and Hot treatments from each family and 5-6 biological replicates in Standard (5 in O171) per family. Techinal replicates from each family and additional techical replicates in family O171 (including dye swap replicates) were used to assess robustness of the findings.

first: Christopher

last: Wheat

first: Eveliina

last: Kallioniemi

first: Marjo

last: Saastamoinen

first: Ilkka

last: Hanski

first: Mikko

last: Frilander


title: A novel chordoma xenograft allows in vivo drug testing and reveals the importance of NF-kB signaling in chordoma biology [expression array]

summary: Chordoma is a rare primary bone malignancy that arises in the skull base, spine and sacrum and originates from remnants of the notochord. These tumors are typically resistant to conventional chemotherapy, and to date there are no FDA-approved agents to treat chordoma. The lack of in vivo models of chordoma has impeded the development of new therapies for this tumor. Primary tumor from a sacral chordoma was  xenografted into NOD/SCID/IL-2R γ-null mice. The xenograft is serially transplantable and was characterized by both gene expression analysis and whole genome SNP genotyping. The NIH Chemical Genomics Center performed high-throughput screening of 2,816 compounds using two established chordoma cell lines, U-CH1 and U-CH2B. The screen yielded several compounds that showed activity and two, sunitinib and bortezomib, were tested in the xenograft. Both agents slowed the growth of the xenograft tumor. Sensitivity to an inhibitor of IκB, as well as inhibition of an NF-κB gene expression signature demonstrated the importance of NF-κB signaling for chordoma growth. This serially transplantable chordoma xenograft is thus a practical model to study chordomas and perform in vivo preclinical drug testing.

overall_design: Total five microarray experiments were conducted, two of which are for chordoma xenograft sammples and three for chrodoma primary tumor. RNA extracted from xenograft samples and from chordomas was hybridized to Illumina arrays.


title: A novel chordoma xenograft allows in vivo drug testing and reveals the importance of NF-kB signaling in chordoma biology [SNP array]

overall_design: The copy number and allelic balance pattern of a novel human chordoma xenograft samples was determined with Illumina BeadChips.


title: Expression profiling of cisplatin resistant derivatives of ovarian cancer cell line A2780

summary: The goal of this study was to determine genes with altered expression after selection of ovarian cancer cells for survival in increasing concentrations of cisplatin.

overall_design: A series of progressively cispatin resistant derivatives of A2780 ovarian cancer cell lines was hybridized to spotted cDNA microarrays using two color technology using the parental A2780 cells as a reference.  Duplicate hybridizations were carried out for each resistant derivative.

first: Tamas

last: Gonda


title: Multiple mechanisms mediate the taurine-induced proliferation of neural stem/progenitor cells from the subventricular zone of the adult mouse

status: Public on Dec 21 2013

city: México DF

first: Reyna

last: Hernandez-Benitez

address: Circuito Exterior S/N Ciudad Universitaria

department: Neurociencias

country: Mexico

institute: Instituto de Fisiología Celular UNAM

summary: Taurine was previously reported to increase the proliferation of neural precursor cells (NPCs) from subventricular zone of the mouse brain. The results of a study that aimed to understand the mechanisms of this effect are presented here. A gene expression profile analysis indicated that genes regulated by taurine have roles in proliferation, cellular adhesion, cell survival, and mitochondrial functioning. Together with additional functional analyses, the results suggest that taurine provides more favorable conditions for cell proliferation by improving mitochondrial functioning.

overall_design: The total RNA from the control and taurine NPC cultures was used to produce tagged complementary DNA (cDNA) probes. Hybridation analysis used the mouse 65-mer oligo library from Sigma-Genosys to compare the expression of 23,232 gene-specific oligonucleotide probes for mouse.

first: Gerardo

last: Ramos-Mandujano


title: Whole Genome CGH array on patients with acute myeloid leukemia-M5 (AML-M5)

status: Public on Dec 18 2013

city: Oklahoma city

first: Xianfu

last: Wang

state: OK

address: 1122 Ne 13th ST

department: Pediatrics

institute: OUHSC

summary:
Unbalanced chromosomal abnormalities might play a major role in the leukemogenesis of AML-M5
Oligonucelotide array CGH were performed on 24 patients with AML-M5

overall_design: To assess the possible existence of unbalanced chromosomal abnormalities and delineate the characterization of copy number alterations (CNAs) of acute myeloid leukemia-M5 (AML-M5)

first: Rui

last: Zhang

first: Ji-Yun

last: Lee

first: Rurong

last: Tang

first: Shibo

last: Li

first: Yan


title: Using transcriptomic tools to evaluate biological effects across effluent gradients at a diverse set of study sites in Minnesota, USA

status: Public on Dec 13 2013

city: Duluth

first: Jason

last: Berninger

state: MN

address: 6201 Congdon Blvd

department: NHEERL

institute: US EPA

summary:
To assess the impact of a municiple effluent across different environments, a gradient design (upstream, downstream, and at effluent) was set up across three waste water treatment plant outflows in three different regions of MN.  These three sites represents vastly different land use and contamination profiles.  The upstream location at each site was used as a point of comparison to reduce site specific differences in water.  Fish were exposed at three sites in three locations for 4 days.  The objectives of the study were to 1). determine if biological impact of the effluent could be detected at the downstream site; 2). If the use of the upstream site would allow point source influence to be detected over the ambient level of biological activity; 3). if using functional analyses of transcriptomic results would show similarities between effleunt and downstream sites.
The current series contains n=53 microarrays associated with fish exposed at three locations (upstream, effluent, downstream) at 3 different site R, H, E for 4 days until tissues were collected

overall_design: At the specific locations (UP, EF, DS), sexually mature female fathead minnows (SI-SM2) were exposed to location specific water in mini-mobile environmental monitoring units (MMU)14  for a period of 4d, at each of three sites (R, H, E) during the summer and fall of 2010 (SI-SM3).  The MMUs allowed for consistency in aeration, temperature, and feeding.  In the case of the riverine R and H sites, the MMU was supplied with a continuous flow of location-specific water.  Due to logistical constraints, exposures at the lake site (E) were conducted under static renewal conditions within the MMUs.  However, the cumulative number of daily water exchanges were equivalent to those in the flow-through studies.  After exposure fish were anesthetized (buffered MS-222), and necropsied at a facility near the site, specific tissues were excised and flash frozen in liquid nitrogen, and stored at -80°C. Gonads were removed from female and flash-frozen for gene expression analyses using microarray. Ovarian transcripts from six females per location (three locations per site, three sites) were analyzed using a custom 15,000 feature microarray (GEO Platform Accession GPL9248). Data sets for this phase (n=53 microarrays)  were normalized independently using Fastlo (Ballman et al., 2004) implemented in R (http://www.r-project.org/), but analyzed using parallel approaches.

middle: P

first: Dalma

last: Martinović-Weigelt

first: Natàlia

last: Garcia-Reyero

first: Lynn

last: Escalon

first: Edward

last: Perkins

first: Gerald

last: Ankley

first: Daniel

middle: L

last: Villeneuve


title: Adaptation of Propionibacterium freudenreichii to the colon environment

status: Public on Dec 11 2013

city: Rennes

first: Hélène

last: Falentin

address: 65 rue de St Brieuc

department: Microbiologie

institute: INRA

summary:
Mechanisms allowing P. freudenreichii adaptation to digestive stresses have been only studied in vitro so far. Our aim was therefore to study P. freudenreichii metabolic adaptation to intra-colonic conditions in situ.
We maintained a pure culture of P. freudenreichii CIRM-BIA1, contained in a dialysis bag, within the colon of vigilant piglets during 24 hours. A transcriptomic analysis identified the metabolic pathways induced by this environment, in comparison with control propionibacteria maintained in spent culture medium.

overall_design: 12 cutures in a dialysis bag in the colon of piglets during 24H compared to 12 cultures propionibacteria maintained in spent culture medium

first: Taous

last: Saraoui

first: Sandrine

last: Parayre

first: Grégory

last: Guernec

first: Valentin

last: Loux

first: Jérôme

last: Montfort

first: Aurélie

last: Lecam

first: Gaëlle

last: Boudry

first: Gwenaël

last: Jan


title: Nuclesome Distribution data for KSHV reactivation

status: Public on Nov 19 2013

city: Tallahassee

first: Jonathan

middle: Hancock

last: Dennis

address: 319 Stadium Dr.

department: Biological Science

institute: The Florida State University

summary: iSLK.219 cells at 0, 6, 12, 24, and 48 hours post KSHV reactivation.  Nucleosome occupancy plays a key role in regulating access to the eukaryotic genomes.  Although various chromatin regulatory complexes are known to regulate nucleosome occupancy, the role of DNA sequence in this regulation remains unclear, particularly in mammals.  To address this problem, we measured nucleosome distribution at high temporal resolution in human cells at hundreds of genes during the reactivation of Kaposi’s sarcoma-associated herpesvirus (KSHV).  We show that nucleosome redistribution peaks at 24 hours post KSHV reactivation and that the nucleosomal redistributions are widespread and transient. To clarify the role of DNA sequence in these nucleosomal redistributions, we compared the genes with altered nucleosome distribution to a sequence-based computer model and in vitro assembled nucleosomes.  We demonstrate that both the predicted model and the assembled nucleosome distributions are concordant with the majority of nucleosome redistributions at 24 hours post KSHV reactivation.  We suggest a model in which loci are held in unfavorable chromatin architecture and “spring” to a transient intermediate state directed by DNA sequence information.  We propose that DNA sequence plays a more considerable role in the regulation of nucleosome positions than was previously appreciated.  The surprising findings that nucleosome redistributions are widespread, transient, and DNA-directed shift the current perspective regarding regulation of nucleosome distribution in humans.

first: Brittany

middle: S

last: Sexton


title: Autoimmune antigen and serum factor antigen reactivity in a cohort of patients with systemic lupus erythematosus (SLE) and healthy controls from the ABCoN cohort.

status: Public on Sep 24 2013

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

summary:
The aim of the study was to test the hypothesis that SLE patient sera contains IgG reactivity to serum factor antigens concomitant with prototypical autoimmne antigens.
We diluted patient sera 1:250 and incubated dilutions on a nitrocellulose-platform array printed with whole protein antigens.

platform_organism:
Gallus gallus
Homo sapiens
Bos taurus

overall_design: In this study, serum from 45 individuals (subsetted into high and low interferon signature as well as healthy control categories) was profiled for IgG autoantibody reactivity to whole protein autoimmune and serum factor antigens. SLE and specifically IFN high patient sera was found using the significance analysis of microarrays (SAM) algorithm to be significantly more reactive with prototypical autoimmune antigens and select serum factor array antigens.

first: Paul

last: Utz


title: Autoimmune antigen and serum factor antigen reactivity in a cohort of patients with mycobacterium infection shown previously to be positive and negative for IgG autoantibodies to IFN-gamma.

summary:
The aim of the study was to test wether our microarray platform is capable of detecting previously described IgG autoantibodies to IFN-gamma.
We diluted patient sera 1:250 and incubated dilutions on a nitrocellulose-platform array printed with whole protein antigens.

overall_design: In this study, serum from 10 individuals (subsetted into two groups: individuals positive or negative for previously described IFN-gamma-targeted autoantibodies) was profiled for IgG autoantibody reactivity to whole protein autoimmune and serum factor antigens. We found that IFN-gamma-targeted IgG autoantibodies were recognized in the IFNg-pos samples and also identified other array targets significantly associated with anti-IFNg positive individials using the significance analysis of microarrays (SAM) algorithm.


title: Comparative genome-wide identification of transcriptional start sites in two environmentally relevant cyanobacteria reveals unexpected diversity in the transcriptome architecture

status: Public on Dec 07 2013

city: Freiburg

first: Karsten

last: Voigt

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

summary: Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present the comprehensive comparison of the structure and composition of the transcriptomes of two closely related Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We used large-scale strand-specific cDNA sequencing, microarray RNA profiling and computational analyses to characterize the transcriptomes of Prochlorococcus sp. MED4 and Prochlorococcus sp. MIT9313, representatives of the two major ecotypes adapted to high and low light conditions, respectively. We present genome-wide maps of transcriptional start sites (TSS) for both organisms. Our data suggest antisense transcription for three quarters of all genes. A direct comparison revealed very little conservation in the use of TSS and the nature of non-coding transcripts between both strains. We conclude that the major transcriptional output from these highly streamlined genomes consists of antisense RNA and that a hitherto unrecognized high degree of variability exists in the transcriptional architecture of these rapidly evolving prokaryotes. Furthermore, we detected extremely short 5’ untranslated regions with a median length of only 27 nt and 29 nt for MED4 and MIT9313, respectively, and noticed the absence of the Shine-Dalgarno motif, which is suggestive of alternative mechanisms for the initiation of translation. For 8 % of all protein-coding genes, the median length to the initiator codon is 10 nt or shorter, suggesting that leaderless translation and ribosomal protein S1-dependent translation constitute the primary avenues for protein synthesis in Prochlorococcus.

sample_organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

overall_design: Prochlorococcus cells were either grown under standard growth conditions or various stress conditions (darkness, high light, iron or nitrogen depletion, cold or heat stress). Stress conditions were subsequently pooled and hybridized on one microarray.

first: Cynthia

last: Sharma

first: Jan

last: Mitschke

first: S

last: Lambrecht

first: Björn

last: Voß

first: Wolfgang

middle: R

last: Hess

first: Claudia

last: Steglich


title: Wild type cells in different times after transfer to no phosphate medium

status: Public on Sep 07 2013

city: rehovot

first: Noam

last: Vardi

address: herzel 235

department: molecular genetics

country: Israel

institute: Weizmann Institute of Science

summary: Wild type cells were grown in SC medium and then transferred to no phosphate medium

overall_design: Cells were grown to logarithmic phase in SC medium (OD=0.5), washed and transferred to no phosphate medium (OD = 0.05). During the experiment (t=0.25, 0.5, 1, 2, 4, 8 and 25 hours) cells were harvested, pelleted and frozen for further analysis. Cell were also grown in a chemostat in a  dilution rate of 0.3[1/hr] and phosphate concentration in the feeding vessel of 0.3mM, allowed to reach steady state and then harvested, Total RNA was extracted using MasterPure™ Kit (Epicentre). The samples were amplified, labeled, hybridized to yeast dual color expression microarrays and scanned, all using standard Agilent protocols, reagents, and instruments. The scanned images were analyzed using SpotReader software (Niles Scientific).

last: Levy

first: N

first: M

last: Carmi

last: Barkai


title: How does exposure of yellow perch (Perca flavescens) to nickel and cadmium affect the transcriptome-results from a 1000 candidate-gene microarray

status: Public on Sep 19 2013

city: Québec

first: Berenice

last: BOUGAS

state: QC

address: 1030 avenue de la médecine, IBIS, Pavillon Marchand

institute: Laval university

summary:
Our main objectives were: 1) to identify transcriptional signatures specific to the exposure to two metals: Ni and Cd; 2) to investigate the mechanisms of toxicity for these two metals; and 3) to develop a predictive tool to identify the sublethal effects of Ni and Cd contaminants in fish sampled from natural environments.
The molecular mechanisms underlying nickel (Ni) and cadmium (Cd) toxicity and their specific effects on fish are poorly understood. Documenting gene transcription profiles offers a powerful approach towards identifying the molecular mechanisms affected by these metals and to discover biomarkers of their toxicity. However, confounding environmental factors can complicate the interpretation of the results and the detection of biomarkers for fish captured in their natural environment. In the present study, a 1000 candidate-gene microarray, developed from a previous RNA-seq study on a subset of individual fish from contrasting level of metal contamination, was used to investigate the transcriptional response to metal (Ni and Cd) and non metal (temperature, oxygen, and diet) stressors in yellow perch (Perca flavescens). Specifically, we aimed at 1) identifying transcriptional signatures specific to Ni and Cd exposure, 2) investigating the mechanisms of their toxicity, and 3) developing a predictive tool to identify the sublethal effects of Ni and Cd contaminants in fish sampled from natural environments. A total of 479 genes displayed significantly different transcription levels when temperature varied while 287 and 177 genes were differentially transcribed at different concentrations of Ni and Cd, respectively. These metals were found to mainly affect the transcription level of genes involved in iron metabolism, transcriptional and translational processes, vitamin metabolism, blood coagulation, and calcium transport. In addition, a linear discriminant analysis (LDA) made using gene transcription levels yielded 94% correctly reassigned samples regarding their level of metal contamination, which indicates the potential of the microarray to detect perch response to Cd or Ni effects.

overall_design: Comparison between fish exposed to three temperatures (11, 20, 28°C) using a loop design, comparison between control fish and fich exposed to restrictive diet using a pairwise design, comparison between fish exposed to hypoxia and control fish, comparison between fish exposed to two concentrations of cadmium and control fish using a loop design, and comparison between fish exposed to two concentrations of nickel and control fish using a loop design.

last: Bougas

first: Eric

last: Normandeau

first: Fabien

last: Pierron

first: Peter

middle: G

last: Campbell

first: Louis

last: Bernatchez

first: Patrice

last: Couture


title: Commitment to the phosphate starvation response after replenishment of phosphate

summary: Diploid wild type cells in a chemostat, in different times after changing the feeding medium from low to high Pi.

overall_design: Diploid cells were also grown in a chemostat at a dilution rate of 0.3[1/hr] and phosphate concentration in the feeding vessel of 0.3mM Pi. Cells were allowed to reach steady state and then feeding medium was replaced to 7.3mM Pi. Samples from the chemostat were harvested in different times after the transfer (t= 0.35, 2, 5, and 10 days). Total RNA was extracted using MasterPure™ Kit (Epicentre). The samples were amplified, labeled, hybridized to yeast dual color expression microarrays and scanned, all using standard Agilent protocols, reagents, and instruments. The scanned images were analyzed using SpotReader software (Niles Scientific).


title: Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes

status: Public on Sep 01 2013

city: Ikoma

first: Diana

middle: Mihaela

last: Buzas

state: Nara

address: 8916-5 Takayama

department: Biological Sciences

institute: NAIST

summary: Background. Polycomb Repressive Complex 2 (PRC2) is an essential regulator of gene expression that maintains genes in a repressed state by marking chromatin with trimethylated Histone H3 lysine 27 (H3K27me3). In Arabidopsis, loss of PRC2 function leads to pleiotropic effects on growth and development thought to be due to ectopic expression of seed and embryo-specific genes. While there is some understanding of the mechanisms by which specific genes are targeted by PRC2 in animal systems, it is still not clear how PRC2 is recruited to specific regions of plant genomes.Results. We used ChIP-seq to determine the genome-wide distribution of hemagglutinin (HA)-tagged FERTLIZATION INDEPENDENT ENDOSPERM (FIE-HA), the Extra Sex Combs homolog protein present in all Arabidopsis PRC2 complexes. We found that the FIE-HA binding sites co-locate with a subset of the H3K27me3 sites in the genome and the associated genes were more likely to be de-repressed in mutants of PRC2 components. The FIE-HA binding sites are enriched for three sequence motifs including a putative GAGA factor binding site that is also found in Drosophila Polycomb Response Elements (PREs).Conclusions. Our results suggest that PRC2 binding sites in plant genomes share some sequence features with Drosophila PREs. However,

overall_design: RNA was extracted from intermediate phenotype siFIE plants, clf-7 swn-28 and Col using Qiagen Plant RNeasy mini kit. For each sample, three pools of 10-12 plants were used. The siFIE plants were analysed for FIE mRNA by RT-qPCR; the maximum level of FIE mRNA was found to be 10% of wildtype.


title: Steady state chemostat cultures grown in different dilution rates and levels of phosphate feeding

summary: Wild type steady state chemostats cultures, in dilution rate of 0.3[1/hr] or 0.1[1/hr], and phosphate concentration in the feeding vessel of 0.3 or 0.1mM Pi

overall_design: Wild type cells were grown in a chemostat at a dilution rate of 0.3[1/hr] or 0.1[1/hr], and phosphate concentration in the feeding vessel of 0.3 or 0.1mM Pi. Cells were allowed to reach steady state and then harvested. Total RNA was extracted using MasterPure™ Kit (Epicentre). The samples were amplified, labeled, hybridized to yeast dual color expression microarrays and scanned, all using standard Agilent protocols, reagents, and instruments. The scanned images were analyzed using SpotReader software (Niles Scientific).


title: Myeloid derived suppressor cells enhance stemness of cancer cells by inducing miRNA101 and suppressing the corepressor CtBP2

status: Public on Aug 23 2013

city: Ann Arbor

first: Ilona

last: Kryczek

address: 1150 W. Medical Center Dr.

country: USA

institute: University of Michigan

summary: The work identifies an immune associated cellular, molecular and clinical network involving MDSCs-microRNA101-CtBP2-stem cell core genes, which extrinsically controls cancer stemness and impacts patient outcome.

overall_design: Primary ovarian cancer cells (5 x105) were co-cultured with freshly sorted ovarian cancer associated-MDSCs, peripheral blood lin-CD45+CD33+ cells (5 x105) or medium in a transwell (Corning) for 24 hours.  Then, RNA was extracted from the cancer cells by Trizol reagent. The RNAs were applied for microRNA profiling using OpenArray system (Applied Biosystems, Cat# 4470187) (Mestdagh et al., 2008) at University of Michigan Sequencing Core

first: Tracy

middle: X

last: Cui

first: Lili

last: Zhao

first: Ende

first: Rork

last: Kuick

first: Michael

last: Roh

first: Linda

last: Vatan

first: Wojciech

last: Szeliga

first: Yujun

last: Mao

first: Dafydd

last: Thomas

last: Kotarski

first: Rafat

last: Tarkowski

first: Max

last: Wicha

first: Kathleen

last: Cho

first: Thomas

last: Giordano

first: Rebecca

last: Liu

first: Weiping

last: Zou