title: Expression analysis of Arabidopsis transgenic plants carrying DEX-inducible MKK4DD in Col or sid2 background treated with DEX or control

status: Public on Jul 29 2014

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

country: China

institute: Huazhong Agricultural University

summary: Effector-Triggered Immunity (ETI) and Pattern-Triggered Immunity (PTI) are well-defined modes of plant immunity triggered by recognition of pathogen effector proteins and microbe-associated molecular patterns, respectively. While ETI and PTI network extensively share signaling components, the shared components are used in different ways, resulting in distinct network properties in the model plant Arabidopsis: immunity is highly robust against network perturbations in ETI but relatively sensitive in PTI. However, the molecular mechanism how the shared network leads to the different properties is not known. Here we show that sustained MAPK activation compensate salicylic acid (SA) signaling.

overall_design: A 12 DNA microarray study using total RNA from Arabidopsis transgenic plants carrying DEX-inducible MKK4DD in Col or sid2-2 background treated with DEX or control.


title: Comparative genomic hybridization of a Burkholderia cenocepacia collection

status: Public on Jul 31 2014

city: East Lansing

first: erick

last: cardenas

state: Michigan

address: 540 Plant and Soil Sciences Building

country: USA

institute: Michigan State University

summary: Individual normalized intensity of Burkholderia cenocepacia and Burkholderia seminalis hybridized in a B. cenocepacia array

sample_organism:
Burkholderia cenocepacia
Burkholderia seminalis

overall_design: A collection of 199 Burkholderia isolates were hybridized against an array targeting five B. cenocepacia strains in order to understand the gene distribution within this species. Burkholderia cenocepacia (n=191) as well as Burkholderia seminalis (n=8, as controls) were used in this analysis.

first: Erick

last: Cardenas

first: Linda

middle: M

last: Kalikin

first: Amanda

last: Geaslin

first: Jean-Marie

last: Rouillard

first: Jiangchao

last: Zhao

first: Patrick

middle: S

last: Chain

first: Erdogan

last: Gulari

first: James

last: Tiedje

first: John

middle: J

last: Lipuma


title: Flcn and BHD renal tumorigenesis

status: Public on Jul 28 2014

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Targeted disruption of Flcn in mouse kidney proximal tubule gives insights into human BHD renal tumorigenesis

overall_design: Mouse Tumor kidney tissue vs. normal kidney tissue


title: Differential Responses of Plasmacytoid Dendritic Cells to Influenza and Distinct Viral Pathogens

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Plasmacytoid dendritic cells (pDCs) are key components of the innate immune response that are capable of synthesizing and rapidly releasing vast amounts of type I interferons (IFNs), particularly IFN-alpha. Here we investigated whether pDCs, often regarded as a mere source of IFN, discriminate between various functionally discrete stimuli and to what extent this reflects differences in pDC responses other than IFN-alpha release. To examine the ability of pDCs to differentially respond to various doses of intact and infectious HIV, hepatitis C virus, and H1N1 influenza virus, whole-genome gene expression analysis, enzyme-linked immunosorbent assays, and flow cytometry were used to investigate pDC responses at the transcriptional, protein, and cellular levels. Our data demonstrate that pDCs respond differentially to various viral stimuli with significant changes in gene expression, including those involved in pDC activation, migration, viral endocytosis, survival, or apoptosis. In some cases, the expression of these genes was induced even at levels comparable to that of IFN-alpha. Interestingly, we also found that depending on the viral entity and the viral titer used for stimulation, induction of IFN-alpha gene expression and the actual release of IFN-alpha are not necessarily temporally coordinated. In addition, our data suggest that high-titer influenza A (H1N1) virus infection can stimulate rapid pDC apoptosis.

overall_design: pDCs from 3 separate donors (biological replicates) were stimulated with PBS (control 1) (n=3), conditioned medium (control 2) (n=3), or HCV JFH-1 at 1.00x10^4 (n=3), 1.00x10^5 (n=3), or 1.00x10^6 (n=3) RNA copies/ml. pDCs from 3 separate donors (biological replicates) were stimulated with PBS (control) (n=3) or influenza virus A/PR/8/34 (H1N1; Charles River Laboratories) at 4 (n=3), 32 (n=3), 256 (n=3), or 2,048 (n=3) HAU/ml. pDCs from 3 separate donors (biological replicates) were stimulated with PBS (control) (n=3) or HIV-1 IIIB (Advanced Biotechnologies) at 1.00x10^2 (n=3), 1.00x10^3 (n=3), 1.00x10^4 (n=3), or 1.00x10^5 (n=3) 50% tissue culture infective doses (TCID50)/ml. pDCs from 10 separate donors (biological replicates) were treated with PBS (control) (n=10), HCV at 1.00x10^6 RNA copies/ml (n=10), HIV-1 BaL at 1.00x10^5 TCID50/ml (Advanced Biotechnologies) (n=10), HIV-1 IIIB at 1.00x10^5 TCID50/ml (Advanced Biotechnologies) (n=10), or influenza virus A/PR/8/34 (H1N1; Charles River Laboratories) at 4 HAU/ml (n=10).


title: Dynamic transcriptome structure of E. coli K-12 MG1655 across growth

status: Public on Jul 22 2014

city: Seattle

first: Aaron

last: Brooks

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

summary:
High-resolution transcriptional profiling of E. coli across nine timepoints of growth in rich media (LB). Samples collected from lag phase to stationary phase of growth. High-resolution tiling array to detect conditional operon isoforms.
Custom Agilent array designed to detect condition-specific transcriptional isoforms. Array designed for E coli K12 MG1655 genome. Tiled using 23bp sliding window. Includes >10,000 probes surrounding predicted operon break sites at 6 bp resolution.

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

overall_design: Nine growth time points in the experiment. Two-color arrays. Each time point compared to mid-exponential phase of growth.

middle: N

first: Min

last: Pan

first: Nitin

last: Baliga


title: Transcriptome profiling of Hansenula polymorpha in response to sulfur starvation and cadmium stress

city: Daejeon

first: Min Jeong

last: Sohn

address: 52 Eoeun-dong, Yuseong-gu

department: Protein therapeutics research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Transcriptome profiling analysis of the Hansenula polymorpha MET4 gene deletion strain have been carried out to obtain comprehensive information on the HpMet4p-mediated regulatory networks in association with the cadmium (Cd) detoxification and sulfur regulation in H. polymorpha.

overall_design: Total RNA samples were collected from H. polymorpha wild type, and HpMET4  deletion strain, under sulfur starvation or Cd (0.6 mM) stress conditions. The differential fluorescence intensities of each RNA sample were measured after labeling with Cy3 or Cy5. For all analyses, we performed dye swapping experiments to avoid dye bias. Thus, four intensity values were generated for each ORF and averaged for analysis.

first: MinJeong

first: Vera

last: Ubiyvovk

first: Doo-Byoung

last: Oh

first: Ohsuk

last: Kwon

first: SangYup

last: Lee

first: Andrei

middle: A

last: Sibirny

first: SangKi

last: Rhee

first: HyunAh

last: Kang


title: Transcriptional profiling of E. coli cultures exposed to tellurite 0.5 µg/ml

status: Public on Jul 30 2014

city: Santiago

first: David

middle: Enrique

last: Loyola

state: Santiago

address: Avenida Libertador Bernardo O'Higgins 340

country: Chile

institute: OMICS Solutions, Centro Nacional de Genómica y Bioinformática

summary: E. coli cultures were exposed to tellurite 0.5 µg/ml during 15 min. Total RNA was extracted and cDNA labeled probes were generated by reverse transcription using Alexa 555 and Alexa 647 fluorophores. These probes were used to hybridize genomic slides containing genomic arrays to determine global transcriptional changes.

overall_design: Two-conditions experiment, antibacterial vs. Untreated control cells. Biological replicates: 2 control, 2 toxicants exposed cells, independently grown and harvested. One replicate per array. Dye swap conditions.

first: Roberto

middle: C

last: Molina-Quiroz

middle: E


title: Agrobacterium tumefaciens ExoR controls acid response genes and impacts exopolysaccharide synthesis, horizontal gene transfer and virulence gene expression.

status: Public on Jul 26 2014

city: Bloomington

last: Buechlein

state: IN

address: 1001 E 3rd St

department: Center for Genomics and Bioinformatics

institute: Indiana University

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

overall_design: Refer to individual Series


title: Comparison of Expression Profiles for Agrobacterium tumefaciens exoRexoA double mutant to exoA mutant

summary: Agrobacterium tumefaciens is a facultative plant pathogen and the causative agent of crown gall disease. The initial stage of infection involves attachment to plant tissues and, subsequently, biofilms may form at these sites. This study focuses on the periplasmic ExoR regulator, which was identified based on the severe biofilm deficiency of A. tumefaciens exoR mutants. Genome-wide expression analysis was performed to elucidate the complete ExoR regulon. Overproduction of the exopolysaccharide succinoglycan is a dramatic phenotype of exoR mutants.  Comparative expression analyses revealed that the core ExoR regulon is unaffected by succinoglycan synthesis. Several findings are consistent with previous observations: genes involved in succinoglycan biosynthesis, motility, and type VI secretion are differentially expressed in the ΔexoR mutant. In addition, these studies revealed new functional categories regulated by ExoR including genes related to virulence, conjugation of the pAtC58 megaplasmid, ABC transporters, and cell envelope architecture. To address how ExoR exerts a broad impact on gene expression from its periplasmic location, a genetic screen was performed to isolate suppressor mutants that mitigate the exoR motility phenotype and identify downstream components of the ExoR regulatory pathway. This suppression analysis identified the acid-sensing two-component system ChvG-ChvI, and the suppressor mutant phenotypes suggest that all or most of the characteristic exoR properties are mediated through ChvG-ChvI. Subsequent analysis indicates that exoR mutants are simulating a response to acidic conditions, even in neutral media. This work expands the model for ExoR regulation in A. tumefaciens and underscores the global role this regulator plays on gene expression.

overall_design: Three biological replicates, Independent RNA preparations, One dye-swap

first: Clay

last: Fuqua

first: Brynn

last: Heckel

first: Amelia

middle: D

last: Tomlinson

first: Elise

middle: R

last: Morton

first: Jeong-Hyeon

last: Choi


title: Affymetrix SNP array data for diffuse large B cell lymphoma samples

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

country: Germany

institute: University Hospital Essen

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

summary: The pathogenesis of diffuse large B cell lymphomas (DLBCL) is only partly understood. We analyzed 148 DLBCL by high resolution single nucleotide polymorphism (SNP)-chips to characterize genomic imbalances. Seventy-nine cases were of the germinal center B-cell like (GCB) type of DLBCL, 49 of the activated B-cell like (ABC) subtype and 20 were type 3 DLBCL. Twenty-four regions of recurrent genomic gains and 38 regions of recurrent genomic losses were identified over the whole cohort, with a median of 25 imbalances per case for ABC-DLBCL and 19 per case for GCB-DLBCL. Several recurrent copy number changes showed differential frequencies in the GCB- and ABC-DLBCL subgroups, including gains of HDAC7A predominantly in GCB-DLBCL (38% of cases) and losses of BACH2 and CASP8AP2 predominantly in ABC-DLBCL (35%), hinting at disparate pathogenetic mechanisms in these entities. Correlating gene expression and copy number revealed a strong gene dosage effect in all tumors, with 34% of probesets showing a concordant expression change in affected regions. Two new potential tumor suppressor genes emerging from the analysis, CASP3 and IL5RA, were sequenced in 10 and 16 candidate cases, respectively. However, no mutations were found, pointing to a potential haploinsufficiency effect of these genes, considering their reduced expression in cases with deletions. This work thus describes differences and similarities in the landscape of genomic aberrations in the DLBCL subgroups in a large collection of cases, confirming already known targets, but also discovering novel copy number changes with possible pathogenetic relevance.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved lymph node biopsies of tumor samples.

first: René

first: Markus

last: Kreuz


title: Microarray analysis of leaf rust-induced bread wheat genes

status: Public on Jul 20 2014

city: Giza

first: Sameh

middle: El-Sayed

last: Hassanein

state: Giza

address: Gamaa st., Giza, Egypt

department: Bioinformatics and Computer Networks

country: Egypt

institute: Agricultural Genetic Engineering Research Institute

summary:
One week old bread wheat plantlets were artifically infected with Puccinia triticinae (the causal organism of wheat leaf rust) and samples were collected after one week from infection.
Samples were collected after one week from infection, non infected as well. Two loacl varities were used MISR 1 and GEMMZA 7.

overall_design: Four chamber slide was used and single dye (Cy3) was detedcted. Non infected samples from both varities were hybridized in two chamber seperately and the other two chamber were assigned for the two infected samples.

first: Ahmed

last: Shokry

first: Hussien

middle: F

last: Almeldin

first: Yasser

middle: B

last: Morsy

first: Hala

last: Eissa


title: Folsomia candida soil analysis expression assay

status: Public on Jul 19 2014

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

summary: The present invention relates to methods for determining soil quality, and especially soil pollution, using the invertebrate soil organism Folsomia candida also designated as springtail. Specifically, the present invention relates to a method for determining soil quality comprising: contacting Folsomia Candida with a soil sample to be analysed during a time period of 1 to 5 days; isolating said soil contacted Folsomia Candida; extracting RNA from said isolated soil contacted Folsomia Candida; determing a gene expression profile based on said extracted RNA using microarray technology; comparing said gene expression profile with a reference gene expression profile; and determing soil quality based expression level differences between said gene expression profile and said control expression profile.

overall_design: A direct design was used where springtails were exposed to 3 field soils (2 polluted and 1 clean) and cadium and microarrays were directly contrased to those from animals exposed to clean LUFA2.2 soil. 4 biological replicates were used with each containing 25 grams of soil and 30 adult, randomly selected, age sychronized springtails

first: N

last: van Straalen

first: T

last: Roelofs


title: Dioxin (TCDD) Induces Epigenetic Transgenerational Inheritance of Adult Onset Disease and Sperm Epimutations

city: Pullman

first: Michael

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by genome tiling array

summary: Environmental compounds can promote epigenetic transgenerational inheritance of adult-onset disease in subsequent generations following ancestral exposure during fetal gonadal sex determination. The current study examined the ability of dioxin (2,3,7,8-tetrachlorodibenzo[p]dioxin, TCDD) to promote epigenetic transgenerational inheritance of disease and DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to dioxin during fetal day 8 to 14 and adult-onset disease was evaluated in F1 and F3 generation rats. The incidences of total disease and multiple disease increased in F1 and F3 generations. Prostate disease, ovarian primordial follicle loss and polycystic ovary disease were increased in F1 generation dioxin lineage. Kidney disease in males, pubertal abnormalities in females, ovarian primordial follicle loss and polycystic ovary disease were increased in F3 generation dioxin lineage animals. Analysis of the F3 generation sperm epigenome identified 50 differentially DNA methylated regions (DMR) in gene promoters. These DMR provide potential epigenetic biomarkers for transgenerational disease and ancestral environmental exposures. Observations demonstrate dioxin exposure of a gestating female promotes epigenetic transgenerational inheritance of adult onset disease and sperm epimutations.

overall_design: Methylated sperm DNA was isolated from rats ancestrally exposed to dioxin (Hip). Three independent samples from the treatment group were obtained.  Differential DNA methylation between treatment groups was determined using Nimblegen microarrays. Treated samples were paired with control samples and hybridized together on arrays (Hip1/Cip1, Hip2/Cip2, and Hip3/Cip3), resulting in three arrays for the treatment.

first: Mohan

last: Manikkam

first: Rebecca

last: Tracey

first: Carlos

last: Guerrero-Bosagna


title: Microbial community structure and functions are resilient to metal pollution along two forest soil gradients

city: Krakow

first: Hamed

last: Azarbad

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

summary: Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level significantly impacted microbial community structure (p = 0.037), but not bacterial taxon richness. Metal pollution altered the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal resistance genes showed significant correlations with metal concentrations in soil, although no clear impact of metal pollution levels on overall functional diversity and structure of microbial communities was observed. While screens of phylogenetic marker genes, such as 16S rRNA, provided only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appeared to be a more promising strategy. This study showed that the effect of metal pollution on soil microbial communities was not straightforward, but could be filtered out from natural variation and habitat factors by multivariate statistical analysis and spatial sampling involving separate pollution gradients.

overall_design: 12 samples were collected from two long-term polluted areas (Olkusz and Miasteczko Śląskie) in Southern Poland. In the study presented here, a consecutively operated, well-defined cohort of 50 NSCLC cases, followed up more than five years, was used to acquire expression profiles of a total of 8,644 unique genes, leading to the successful construction of supervised

first: Wilfred

last: Roling


title: The effects of phthalates on S. tropicalis development

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

summary: Phthalates are added to polymers in order to increase their flexibility, but leach out of the  matrix. Given that these plasticizers are mainly found in water bound to particles, aquatic species are exposed to phthalates. Silurana tropicalis eggs were exposed to high concentrations of three pththalates: dicyclohexyl phthalate (DCHP; 19 mg/L), dimethyl phthalate (DMP; 34 mg/L), and monomethyl phthalate (MMP; 1500 mg/L), along to their respective controls: 0.82% DMSO for DCHP, and water controls for DMP and MMP. The exposure lasted 3 days during embryogenesis. Four pooled of 10 larvae were sampled per treatment and analyzed for gene expression changes using a microarray approach.

overall_design: Four microarrays per group (control and treatment); each phthalate had its on control. There were three phthalates tested that included DCHP, MMP, and DMP.

first: Valérie

last: Langlois

first: Justine

last: Mathieu-Denoncourt


title: Hydrocarbons (Jet Fuel JP-8) Induce Epigenetic Transgenerational Inheritance of Obesity, Reproductive Disease and Sperm Epimutations

summary: Environmental compounds have been shown to promote epigenetic transgenerational inheritance of disease. The current study was designed to determine if a hydrocarbon mixture involving jet fuel (JP-8) promotes epigenetic transgenerational inheritance of disease. Gestating F0 generation female rats were transiently exposed during the fetal gonadal development period. The direct exposure F1 generation had an increased incidence of kidney abnormalities in both females and males, prostate and pubertal abnormalities in males, and primordial follicle loss and polycystic ovarian disease in females. The first transgenerational generation is the F3 generation, and the jet fuel lineage had an increased incidence of primordial follicle loss and polycystic ovarian disease in females, and obesity in both females and males. Analysis of the jet fuel lineage F3 generation sperm epigenome identified 33 differential DNA methylation regions, termed epimutations. Observations demonstrate hydrocarbons can promote epigenetic transgenerational inheritance of disease and sperm epimutations, potential biomarkers for ancestral exposures.

overall_design: Methylated sperm DNA was isolated from rats ancestrally exposed to jet fuel (Jip). Three independent samples from the treatment group were obtained.  Differential DNA methylation between treatment groups was determined using Nimblegen microarrays. Treated samples were paired with control samples and hybridized together on arrays (Jip1/Cip1, Jip2/Cip2, and Jip3/Cip3), resulting in three arrays for the treatment.


title: mRNA profiling in enterovirus type 71-infected SH-SY5Y cells after transfection with miR-1246 inhibitor

city: Beijing

first: li

last: juan

address: East Street Fengtai District

institute: Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary: Today, the pathogenesis of human enterovirus type 71 (HEV71) infection in human central neural system remains unclear. HEV71 is the major pathogen of hand-foot-and-mouth disease (HFMD), and has been associated with severe neurological disease and even death in infants and young children. We employed the human whole genome microarray analyze the mRNA profiling in human neuroblastoma cells SH-SY5Y infected with HEV71 after transfection. Firstly, SH-SY5Y cells were transfected wtih miR-1246 inhibitor and negtive control respectively using HiPerFect Transfection Reagent according to the manufacturer’s instructions. Then the cells were infected with HEV71 after transfection. After 12 hours infection, the cells were harvested to microarray analysis. The results showed the altered expression of mRNAs including up-regulated genes and down-regulated genes.  Overall, this finding will help to understand the functional genes in HEV71-infected human neuroblastoma cells and miR-1246-virus-host interaction.

overall_design: SH-SY5Y cells were transfected wtih miR-1246 inhibitor and negtive control respectively using HiPerFect Transfection Reagent according to the manufacturer’s instructions. Then the cells were infected with HEV71 after transfection. After infection, the cells were harvested to microarray analysis. Total RNA of cells infected with HEV71 was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each pooling RNA sample separately on the GeneChip_ Porcine Genome Array at CapitalBio Corporation (Beijing, China).

first: LiJuan

last: Xu

first: ChengFeng

last: Qin


title: Sustained versus Transient MAPK Activation Underlies Differential Properties of the Plant Immune Signaling Network

first: Kenichi

last: Tsuda


title: Gene expression profile of glycolaldehdye-treated yeast cells vs glycolaldehdye-nontreated cells

city: Saga

first: Lahiru

middle: Niroshan

last: Jayakody

state: Kyushu

address: Honjo-machi Honjo

department: Bioscience and Biotechnology

country: Japan

institute: Saga University

summary: Gene expression profile of yeast under the glycolaldehdye stress (newly discovered fermentation inhibitor) was evaluated in the experiment

overall_design: Two-condition design, 10 mM glycolaldehdye-treated and nontreated yeast cells, three replicates were run for each condition

first: Hiroshi

last: Kitagaki


title: Identification of Novel Auto-antibodies in Type 1 Diabetic Patients using a High-density Protein Microarray

city: Pohang, Gyungbuk

first: Sehyun

last: Chae

address: San 31, Hyoja-Dong, Nam-Gu

department: Department of Interdisciplinary Bioscience and Bioengineering(I-BIO)

institute: POSTECH

summary: Type 1 diabetes mellitus (T1DM) results from immune mediated destruction of pancreatic beta cells. However, clinical and immunologic phenotypes of T1DM are variable. Several auto-antibodies including GADA, IA-2A, and ZnT8A, were identified in T1DM, but the prevalence of these auto-antibodies varied for a broad spectrum of T1DM. Here, we systemically profiled auto-antibodies from serum samples of 16 T1DM, 16 type 2 diabetes (T2DM) patients, and 27 healthy controls with normal glucose tolerance (NGT) using protein microarrays containing 9,480 proteins. Among 9,480 different proteins on the array, we identified novel auto-antibody candidates (EEF1A1-AAb and UBE2L3-AAb) by M-test coupled with PLS-DA. These auto-antibodies were highly present in T1DM than controls and detected in 40% of T1DM without GADA. Furthermore, these auto-antibodies might help to differentiate subtype of T1DM when combined with GADA. These novel auto-antibodies provide new diagnostic information of T1DM, as well as new insights into the pathogenesis of T1DM.

overall_design:
Auto-antibodies from serum samples were profiled using a high-density, fluorescence-based protein microarray containing duplicate spots of 9,480 human proteins derived from the Ultimate ORF collection
The cohort of patients and controls consisted of 16 T1DM, 16 T2DM patients, and 27 healthy controls with NGT. This cohort was used to screen candidate auto-antibodies using protein microarrays (ProtoArray platform version 5.0, Invitrogen Corp., Carlsbad, CA). Serum samples were drawn from T1DM patients who have 1) fasting C-peptide level <0.3 nmol/L or serum C-peptide <0.6 nmol/L after glucagon loading, 2) initiation of insulin treatment within six months after diagnosis, and 3) duration of diabetes ≤12 months. Mean age of T1DM in the first cohort was 42 ± 16 years. The control serum samples were obtained from T2DM patients who were treated only with oral anti-diabetic drug at least 5 years and from NGTs who had no history of diabetes, no first-degree relatives with diabetes, a fasting plasma glucose concentration of <6.1 mmol/l, and a HbA1c value of <5.8%.

first: BoKyung

last: Koo

first: Kristine

middle: M

last: Kim

first: Daehee

last: Hwang

first: Eugene

last: Yi

first: KyongSoo

last: Park


title: Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features [aCGH]

city: Stanford

first: Joanna

last: Przybyl

address: 300 Pasteur Drive

department: Department of Pathology

institute: Stanford University

type: Genome variation profiling by genome tiling array

summary: Synovial sarcoma (SynSa) is an aggressive mesenchymal tumor, comprising approximately 10% of all soft tissue sarcomas. Over half of SynSa patients develop metastasis or local recurrence, but the underlying molecular mechanisms of the aggressive clinical behavior remain poorly characterized.  Sixty four frozen tumor specimens from 54 SynSa patients were subjected to array comparative genomic hybridization (aCGH) and gene expression profiling. The examined set of tumor specimens included 16 primary tumors from untreated patients who did not develop metastasis/local recurrence (SynSa1 group), 26 primary tumors from untreated patients who developed metastases or local recurrence during follow-up (SynSa2 group), and 22 metachronous metastatic/recurrent SynSa tumors (SynSa3 group).    AURKA and KIF18A, which play important roles in various mitotic events, were the two most up-regulated genes in SynSa2 and SynSa3 groups compared to the SynSa1 group. Expression profiles of SynSa2 and SynSa3 tumors did not show any significant differences. Analysis of genomic index (GI) based on aCGH profiles demonstrated that the SynSa1 group consisted of tumors with significantly less complex genomes compared to SynSa2 and SynSa3 groups. There was no significant difference in genome complexity between SynSa2 and SynSa3 tumors.  Primary SynSa tumors from patients who develop metastases or local recurrence share common molecular features with metastatic/recurrent tumors. Presented data suggest that the aggressive clinical SynSa behavior is determined early in tumorigenesis and might be related to impaired regulation of mitotic mechanisms.  Introduction: Synovial sarcoma (SynSa) is an aggressive mesenchymal tumor, comprising approximately 10% of all soft tissue sarcomas. Over half of SynSa patients develop metastasis or local recurrence, but the underlying molecular mechanisms of the aggressive clinical behavior remain poorly characterized.  Materials and methods: Sixty four frozen tumor specimens from 54 SynSa patients were subjected to array comparative genomic hybridization (aCGH) and gene expression profiling. The examined set of tumor specimens included 16 primary tumors from untreated patients who did not develop metastasis/local recurrence (SynSa1 group), 26 primary tumors from untreated patients who developed metastases or local recurrence during follow-up (SynSa2 group), and 22 metachronous metastatic/recurrent SynSa tumors (SynSa3 group).   Results: AURKA and KIF18A, which play important roles in various mitotic events, were the two most up-regulated genes in SynSa2 and SynSa3 groups compared to the SynSa1 group. Expression profiles of SynSa2 and SynSa3 tumors did not show any significant differences. Analysis of genomic index (GI) based on aCGH profiles demonstrated that the SynSa1 group consisted of tumors with significantly less complex genomes compared to SynSa2 and SynSa3 groups. There was no significant difference in genome complexity between SynSa2 and SynSa3 tumors.  Conclusions: Primary SynSa tumors from patients who develop metastases or local recurrence share common molecular features with metastatic/recurrent tumors. Presented data suggest that the aggressive clinical SynSa behavior is determined early in tumorigenesis and might be related to impaired regulation of mitotic mechanisms.

overall_design: Genomic DNA was extracted from the frozen tumor specimens using High Pure PCR Template Preparation Kit (Roche). DNA of sufficient quality was obtained from 61 tumor specimens. Agilent SurePrint G3 Human CGH 4x180K  array

first: Raf

last: Sciot

first: Agnieszka

last: Wozniak

first: Patrick

last: Schöffski

first: Vanessa

last: Vanspauwen

first: Ignace

last: Samson

first: Janusz

last: Siedlecki

first: Piotr

last: Rutkowski

first: Maria

last: Debiec-Rychter


title: Assessing the Potential Ecological Impacts of Perfluorinated Chemicals (PFCs) in the liver and testis of male largemouth bass (Micropterus salmoides) in Minnesota Lakes

first: Christopher

last: Martyniuk

summary: This study used an emerging analytical technology (cDNA microarrays) to assess the potential effects of PFC exposure on largemouth bass in TCMA lakes.  Microarrays simultaneously measure the expression of thousands of genes in various tissues from organisms exposed to different environmental conditions.  From this large data set, biomarkers (i.e., genes that are expressed in response to an exposure to known stressors) and bioindicators (e.g., suites of genes that correspond to changes in organism health) can be simultaneously measured to clarify the relationship between contaminant exposure and organism health.  Based on current scientific literature, we hypothesized that gene expression patterns would be altered in fish exposed to PFCs (as compared with fish from reference lakes), and that the magnitude of these changes would correspond to the concentrations of PFCs present throughout TCMA lakes. Patterns of gene expression in largemouth bass observed across the TCMA lakes corresponded closely with PFC concentration. Concentrations of PFCs in largemouth bass varied significantly across the sampled lakes, where the lowest concentrations were found in Steiger and Upper Prior Lakes and the highest concentrations were found in Calhoun and Twin Lakes.  Patterns of gene expression were most different (relative to controls) in fish with the highest PFC tissue concentrations, where fish from Twin and Calhoun Lakes were observed to have between 5437 and 5936 differentially expressed genes in liver and gonad tissues.  Although gene expression patterns demonstrated a high degree of correlation with PFC concentrations, microarray data also suggest there are likely additional factors influencing gene expression patterns in largemouth bass in TCMA lakes.

overall_design:
Seven or Eight biological replicates performed per lake; 5 lakes examined.
(i) Expression profiles of male liver compared. Upper Prior Lake (reference) compared to Medicine Lake.
(ii) Expression profiles of male testis compared. Upper Prior Lake (reference) compared to Medicine Lake.
(iii) Expression profiles of male testis compared. Steiger Lake (reference) compared to Lake Calhoun and Twin Lake.
(iv) Expression profiles of male liver compared. Steiger Lake (reference) compared to Lake Calhoun and Twin Lake.

first: Randy

last: Lehr

first: Cristina

last: Colli-Dula

first: Nancy

last: Denslow

first: Mike

last: Feist


title: Transcriptome analysis of the immature lifestages in feeding Rhipicephalus microplus cattle ticks

city: Pretoria

first: Christian

last: Stutzer

state: Gauteng

address: Lynnwood road

department: Biochemistry

country: South Africa

institute: University of Pretoria

summary: Transcriptional profiling of whole nymphs and larvae from Rhipicephalus microplus at day 4 and 7 post infestation, respectively. This enabled the identification of transcripts that are stage-specific or shared among the stages tested.

overall_design: Reference pool design: Each tissue tested was compared to a reference pool comprising ticks (immature to adult stages) sampled on day 4, 5, 7, 13, 15 and tissues collected on day 20 post infestation. Biological replicates: 2; Technical replicates: 2.

first: Willem

last: van Zyl

first: Christine

last: Maritz-Olivier


title: A PBMC Transcriptional Module Related to Vascular Function

status: Public on Jul 21 2014

city: Indianapolis

first: Leni

last: Moldovan

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

summary: Peripheral blood mononuclear cells (PBMCs), including rare circulating stem and progenitor cells (CSPCs), have important yet poorly understood roles in the maintenance and repair of blood vessels and perfused organs. Our hypothesis was that the identities and functions of CSPCs in cardiovascular health could be ascertained by analyzing the patterns of their co-expressed markers in unselected PBMC samples. Because gene microarrays had failed to detect many stem cell-associated genes, we performed quantitative real-time PCR to measure the expression of 45 primitive and tissue differentiation markers in PBMCs from healthy and hypertensive human subjects. We compared these expression levels to the subjects’ demographic and cardiovascular risk factors, including vascular stiffness. The tested marker genes were expressed in all of samples and organized in hierarchical transcriptional network modules. An index of gene expression in one of these modules (metagene), defined as the average standardized relative copy numbers of 15 pluripotency and cardiovascular differentiation markers, was negatively correlated (all p<0.03) with age (R2=-0.23), vascular stiffness (R2=-0.24), and central aortic pressure (R2=-0.19) and positively correlated with body mass index (R2=0.72, in women). The co-expression of three neovascular markers was validated at the single-cell level using mRNA in situ hybridization and immunocytochemistry. The overall gene expression in this cardiovascular module was reduced by 72±22% in the patients compared with controls. However, the  compactness of both modules was increased in the patients’ samples, which was reflected in reduced dispersion of their nodes’ degrees of connectivity, suggesting a more primitive character of the patients’ CSPCs. In conclusion, our results show that the relationship between CSPCs and vascular function is encoded in modules of the PBMCs transcriptional network. Furthermore, the coordinated gene expression in these modules can be linked to cardiovascular risk factors and subclinical cardiovascular disease; thus, this measure may be useful for their diagnosis and prognosis.

overall_design: PBMCs were isolated from 26 healthy subjects and 20 hypertensive patients by density gradient centrifugation. Total RNA was extracted from ~ 10^6 cells, reverse transcription was done using 150 ng RNA, and the real-time PCR was done in duplicate for each sample.

first: Mirela

last: Anghelina

first: Taylor

last: Kantor

first: Desiree

last: Jones

first: Enass

last: Ramadan

first: Yang

last: Xiang

first: Kun

last: Huang

first: Arunark

last: Kolipaka

first: William

last: Malarkey

first: Nima

last: Ghasemzadeh

first: Peter

last: Mohler

first: Arshed

last: Quyyumi

first: Nicanor

middle: I


title: Expression analysis of Arabidopsis plants infected with Pseudomonas syringae pv. tomato DC3000 (Pto) strains

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

summary: Effector-Triggered Immunity (ETI) and Pattern-Triggered Immunity (PTI) are well-defined modes of plant immunity triggered by recognition of pathogen effector proteins and microbe-associated molecular patterns, respectively. While ETI and PTI network extensively share signaling components, the shared components are used in different ways, resulting in distinct network properties in the model plant Arabidopsis: immunity is highly robust against network perturbations in ETI but relatively sensitive in PTI. However, the molecular mechanism how the shared network leads to the different properties is not known. Here we show that salicylic acid (SA) reponsive genes can respond in the absense of SA during ETI.

overall_design: A 24 DNA microarray study using total RNA from Arabidopsis wildtype Col-0 and sid2-2 mutant infected with Pto hrcC-, Pto EV, Pto AvrRpt2 or water.


title: Pesticide and Insect Repellent Mixture (Permethrin and DEET) Induces Epigenetic Transgenerational Inheritance of Disease and Sperm Epimutations

first: Michael

last: Skinner

summary: Environmental compounds are known to promote epigenetic transgenerational inheritance of disease. The current study was designed to determine if a “pesticide mixture” (pesticide permethrin and insect repellent N,N-Diethyl-meta-toluamide, DEET) promotes epigenetic transgenerational inheritance of disease and associated DNA methylation epimutations in sperm. Gestating F0 generation female rats were exposed during fetal gonadal sex determination and the incidence of disease evaluated in F1 and F3 generations. There were significant increases in the incidence of total diseases in animals from pesticide lineage F1 and F3 generation animals. Pubertal abnormalities, testis disease, and ovarian disease (primordial follicle loss and polycystic ovarian disease) were increased in F3 generation animals. Analysis of the pesticide lineage F3 generation sperm epigenome identified 363 differential DNA methylation regions (DMR) termed epimutations. Observations demonstrate that a pesticide mixture (permethrin and DEET) can promote epigenetic transgenerational inheritance of adult onset disease and potential sperm epigenetic biomarkers for ancestral environmental exposures.

overall_design: Methylated sperm DNA was isolated from rats ancestrally exposed to pesticides (Pip). Three independent samples from the treatment group were obtained.  Differential DNA methylation between treatment groups was determined using Nimblegen microarrays. Treated samples were paired with control samples and hybridized together on arrays (Pip1/Cip1, Pip2/Cip2, and Pip3/Cip3), resulting in three arrays for the treatment.

first: Mohan

last: Manikkam

first: Rebecca

last: Tracey

first: Carlos

last: Guerrero-Bosagna


title: Expression profiles in different stages of the immune response to Salmonella enterica Pullorum in the chicken spleen

status: Public on Jul 23 2014

city: Yangzhou

first: Teng

last: Ma

state: Jiangsu

address: 88 South University ave.

department: College of Animal Science and technology

institute: Yangzhou University

summary: Salmonella enterica Pullorum（S. Pullorum） is one of the most important pathogens in poultry. A better understanding of the immune response and molecular modulation resulting from infection by S. Pullorum will facilitates the control of this pathogen. In this study, we determined the relationships among identified differential expressed genes (DEGs) and pathways via deeply mining microarray data from Guangxi Huang Chicken challenged with S. Pullorum.

overall_design: The chicks were then sacrificed via cervical dislocation immediately after anesthesia with 150 mg/kg sodium pentobarbital. This process was repeated at 2 hours post-infection (hpi), 4 hpi, 8 hpi, 24 hpi, 3 days post-infection (dpi), 5dpi, 7dpi, 12dpi, and 21dpi.The spleens were used to carrying out the microarray experiment. After total RNA extraction and quality control for each splenic sample were performed according to the standard protocol provided by Agilent Technologies, two random mRNA samples collected from the challenged group were equally mixed to hybridize with one chicken whole genome expression chip (Agilent.SingleColor.26441） for each time point. In the challenged group, there were three biological replications (chips) for every time point. However, in the control group at each time point only one chip was used to hybridize with equally mixed mRNA sample containing the three control samples.

first: Hongzhi

last: Wang

first: Fei

last: Zhai

first: Lu

last: Xu

first: Xiaomin

last: Guo

first: Zhiteng

last: Li

first: Fang

last: Wan

first: Dengke

last: Hua

first: Rong

last: Chen

first: Aiqin

last: Dai

first: Mingxiu

last: Xia

first: Jing

last: Liu

first: Guobin

last: Chang

first: Guohong


title: Comparison of Expression Profiles for Agrobacterium tumefaciens ExoR mutant to Wild Type

first: Aaron

last: Buechlein

summary: Agrobacterium tumefaciens is a facultative plant pathogen and the causative agent of crown gall disease. The initial stage of infection involves attachment to plant tissues and, subsequently, biofilms may form at these sites. This study focuses on the periplasmic ExoR regulator, which was identified based on the severe biofilm deficiency of A. tumefaciens exoR mutants. Genome-wide expression analysis was performed to elucidate the complete ExoR regulon. Overproduction of the exopolysaccharide succinoglycan is a dramatic phenotype of exoR mutants.  Comparative expression analyses revealed that the core ExoR regulon is unaffected by succinoglycan synthesis. Several findings are consistent with previous observations: genes involved in succinoglycan biosynthesis, motility, and type VI secretion are differentially expressed in the ΔexoR mutant. In addition, these studies revealed new functional categories regulated by ExoR including genes related to virulence, conjugation of the pAtC58 megaplasmid, ABC transporters, and cell envelope architecture. To address how ExoR exerts a broad impact on gene expression from its periplasmic location, a genetic screen was performed to isolate suppressor mutants that mitigate the exoR motility phenotype and identify downstream components of the ExoR regulatory pathway. This suppression analysis identified the acid-sensing two-component system ChvG-ChvI, and the suppressor mutant phenotypes suggest that all or most of the characteristic exoR properties are mediated through ChvG-ChvI. Subsequent analysis indicates that exoR mutants are simulating a response to acidic conditions, even in neutral media. This work expands the model for ExoR regulation in A. tumefaciens and underscores the global role this regulator plays on gene expression.

overall_design: Four biological replicates, Independent RNA preparations, Two dye-swaps

first: Clay

last: Fuqua

first: Brynn

last: Heckel

first: Amelia

last: Tomlinson

first: Elise

last: Morton

first: Jeong-Hyeon

last: Choi


title: Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (II)

status: Public on Jul 18 2014

city: Madison

first: Robert

last: Landick

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5‑hydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts.

overall_design: E.coli ethanologen strain GLBRCE1 or GLBRCE1 lacking the plasmid-borne PET cassette (GLBRCE1_pBBR) was grown in AFEX corn stover hydrolysate (ACSH)  Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH, and cultures were diluted into ACSH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2.  One biological replicate was grown in each medium.  RNA samples were obtained at 3 time points, corresponding to exponential (Exp), transitional (Trans), and stationary (Stat) growth phases.

first: David

middle: H

last: Keating

first: Yaoping

last: Zhang

first: Irene

last: Ong

first: Sean

last: McIlwain

first: Eduardo

last: Morales

first: Jeffrey

last: Grass

first: Mary

last: Tremaine

first: William

last: Bothfeld

first: Alan

last: Higbee

first: Arne

last: Ulbrich

first: Allison

last: Balloon

first: Michael

middle: S

last: Westphall

first: Josh

last: Aldrich

last: Lipton

first: Joonhoon

last: Kim

first: Oleg

last: Moskvin

first: Yury

middle: V

last: Bukhman

first: Joshua

last: Coon

first: Patricia

middle: J

last: Kiley

first: Donna

last: Bates


title: Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (IV)

first: Robert

last: Landick

overall_design: E.coli ethanologen strain GLBRCE1 was grown in 4 media, AFEX corn stover hydrolysate (ACSH), synthetic hydrolysate (SynH), synthetic hydrolysate with added lignotoxins (SynH_LT), or synthetic hydrolysate containing acid or amide lignotoxins only (SynH_Acids_Amides).  Fermentations were carried out in 3 L bioreactors (Applikon Biotechnology) containing 2.45 L of ACSH or SynH media, and cultures were diluted into ACSH or SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2.  Two biological replicates (independent cultures) were grown in each medium.  RNA samples were obtained at 6 time points, corresponding to early exponential (Exp1), Mid-exponential (Exp2), Late-exponential (Exp3), transitional (Trans), stationary (Stat1) and late stationary (Stat2) growth phases.

first: David

last: Keating

first: Yaoping

last: Zhang

first: Irene

last: Ong

last: McIlwain

middle: A


title: microRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity

status: Public on Jul 17 2014

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

summary: In the present study we analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition, simulated by a ground-based Rotating Wall Vessel (RWV) bioreactor. Our results show that 42 miRNAs were differentially expressed in MMG-incubated PBLs compared with 1g-incubated ones. Among these, miR-9-5p, miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p were the most dysregulated. To improve the detection of functional miRNA-mRNA pairs we performed gene expression profiles on the same samples assayed for miRNA profiling and we integrated miRNA and mRNA expression data. The functional classification of miRNA-correlated genes evidenced significant enrichments in the biological processes of immune/inflammatory response, signal transduction, regulation of response to stress, regulation of programmed cell death and regulation of cell proliferation. We identified the correlation between miR-9-3p, miR-155-5p, miR-150-3p and miR-378-3p expression with that of genes involved in immune/inflammatory response (eg. IFNG and IL17F), apoptosis (eg. PDCD4 and PTEN) and cell proliferation (eg. NKX3-1 and GADD45A). Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation.

overall_design: microRNA expression profiling were carried out on total RNA extracted from PBLs of twelve healthy donors at the end of 24h-incubation time in MMG and in 1g conditions. Analyses were performed by using the “Human miRNA Microarray kit (V2)” (Agilent Technologies), that allows the detection of 723 known human (miRBase v.10.1) and 76 human viral miRNAs.By comparing the expression profile of MMG-incubated vs. 1g-incubated PBLs of the same donor, we found 42 differentially expressed miRNAs, 25 up-regulated and 17 down-regulated.

first: Cristina

last: Girardi

first: Cristiano

last: De Pittà

first: Silvia

last: Casara

first: Enrica

last: Calura

first: Chiara

last: Romualdi

first: Lucia

last: Celotti

first: Maddalena

last: Mognato


title: Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification (III)

middle: C

overall_design: Fermentations were carried out in 0.5L bioreactors (Sartorius) containing 0.3L of  SynH, SynH lacking osmoprotectants, SynH+LT, or SynH lacking osmoprotectants but containing lignotoxins and cultures were diluted into SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2.  Two biological replicates (independent cultures) were grown in each medium.  RNA samples were obtained at 4 time points, corresponding to exponential (Exp), transitional (Trans), early stationary (Stat1), and late stationary (Stat2) growth phases.

first: Sean

first: Eduardo

last: Morales

first: Jeffrey

last: Grass

first: Mary

last: Tremaine

first: William

last: Bothfeld

first: Alan

last: Higbee

first: Arne

last: Ulbrich

first: Allison

last: Balloon

first: Michael

last: Westphall

first: Josh

last: Aldrich

last: Lipton

first: Joonhoon

last: Kim

first: Oleg

last: Moskvin

last: Bukhman


title: Comparison between all runs of a serial repitching in brewery B

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

institute: Universität Hannover

summary: The aim of this study was to identify differently expressed genes between all 6 runs of brewery B. A run describes the industrial fermentation of brewery wort. By the end of fermentation the yeast slurry is cropped. These cells are reused for inoculation of another cylindro-conical vessel (CCVs).

overall_design: Results from two loops of two different breweries are summarized in this study. The samples were taken from two serial repitchings of a two breweries. Microarrays were hybridized in a loop approach.

first: Franziska

last: Bühligen

first: Lindner

last: Patrick

first: Ingo

last: Fetzer

first: Thomas

last: Scheper

first: Hauke

last: Harms

first: Susann

last: Müller


title: Comparison between all runs of a serial repitching in brewery A

summary: The aim of this study was to identify differently expressed genes between all 6 runs of brewery A. A run describes the industrial fermentation of brewery wort. By the end of fermentation the yeast slurry is cropped. These cells are reused for inoculation of another cylindro-conical vessel (CCVs).


title: N-starvation and supplementation in weedy red rice

status: Public on Jul 16 2014

city: Fayetteville

first: Nilda

last: Burgos

address: 1366 W Altheimer Dr

institute: University of Arkansas

summary: Background: Weedy rice (Oryza sativa L.) is a worldwide problem in rice production, being highly tolerant to sub-optimal nutrient levels hence competitive in nutrient acquisition.  To understand the function of genes that are potentially involved in the high nutrient acquisition ability of weedy rice, we compared the transcriptomes of strawhull weedy red rice  (tolerant to N deficit) with the rice cultivar ‘Wells’ (intolerant to N deficit),  by examining profiles in flag leaves at panicle initiation under low and optimum N levels. Strawhull weedy red rice and cultivar ‘Wells’ were grown in nutrient solution with NH4NO3 concentration manipulated to simulate optimum and deficient N conditions. Changes in gene expression in leaf tissues were analyzed at three conditions: N deficiency, and at 24- and 48-h NH4NO3 supplementation after N starvation. Differential gene expression on weedy red rice was evaluated using oligonucleotide arrays representing 44,974 rice gene models. Overall, comparative real-time PCR analysis of 21 candidate genes identified from the microarray data between weedy red rice and cultivar ‘Wells’  supported our hypothesis that key genes involved in N assimilation are expressed differentially at N- deficient conditions between  the tolerant and intolerant strains.  Results: Eight candidate genes showed significant differences in expression at one of the time points: N and starch metabolism-related [alanine aminotransferase (OsAlaAT) locus ID Os10g25140.1; soluble starch synthase 2-1(OsSSSII1), Os10g30156.1; and soluble starch synthase 2-3(OsSSSII3), Os06g12450.1]; cell structure-related  [alpha-L-fucosidase 2 precursor (OsFUCA2), Os06g06250.1]; signal transduction [two-component response regulator-like(OsPRR1), Os02g40510.1 and EF hand family protein (OsPOLC2_JUNOX), Os02g50060.1]; and transcription factors [zinc finger, C2H2 type family protein(OsC2H2Znf), Os11g06840.1 and Myb-like DNA-binding domain (OsMYB), Os01g62660.1]. Genome-wide gene expression analysis of weedy rice showed that nitrite reductase (Os01g25484.1; Os01g25484.2; Os01g25484.3) was most highly induced at N starvation and was most deeply repressed at 24 h of N-stress recovery. A few other genes, namely SANT/MYB (Os01g47370.1), chaperonin (Os02g54060.1; Os02g54060.2), protein phosphatase (Os09g15670.1), polyamine transporter (Os01g61044.1), trehalose-6-phosphate synthase (Os02g54820.2), uracil phosphoribosyltransferase (Os05g38170.1), an MIKCc type-box transcription factor (Os02g52340.1), a cell homeostasis-related uncharacterized protein (Os02g16880.1), a protease inhibitor (Os07g18990.1), dehydrin (Os11g26760.1), and cytochrome P450 (Os11g05380.1) were also strong indicators of starvation and recovery. Conclusions: Weedy rice has N-stress adaptive mechanisms that are probably distinct to the mechanisms in most cultivars. This mechanism potentially contributes to its high vigor and competitive advantage over most rice cultivars under sub-optimal nutrient levels.   Expression of key genes involved in  nitrate assimilation, trehalose synthesis, and protein modification  appeared to be critical for adaptation to N stress in weedy rice. N-stress tolerance of weedy red rice appeared to be due at least in part to the ability to sustain C fixation and starch synthesis during N starvation.

overall_design: Plants were subjected to four treatments: T1 – Full N; T2 – NH4NO3starvation until NSI <95%; T3 - 24-h NH4NO3 readdition post-starvation; and T4 – 48-h NH4NO3 readdition post-starvation. The 24- and 48-h time points for NH4NO3 supplementation were selected to assess both the early and late molecular responses. There were four replications, with three plants per replication per N treatment.

first: Marites

last: Sales

first: Joon

last: Song

first: Yuan

last: Ren

first: Benildo

middle: G

last: de los Reyes


title: Toxicogenomic effects of nano- and bulk TiO2 particles in the soil nematode Carnorhabditis elegans using juglone as a positive control for oxidative stress

city: Montreal

first: Sylvie

last: Rocheleau

state: Quebec

address: 6100 Royalmount Avenue

country: Canada

institute: National Research Council Canada

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

overall_design: Refer to individual Series


title: Environmentally induced epigenetic transgenerational inheritance of ovarian disease

first: Michael

last: Skinner


title: Validation of the C. elegans model using juglone as a positive control for oxidative stress

summary: To confirm the suitability of C. elegans as a model organism, preliminary gene expression experiments were performed using juglone (5-hydroxy-1,4-naphthoquinone; 97% pure; Sigma-Aldrich, St-Louis, MO), an ROS-generator, as a positive control of oxidative stress (d'Arcy Doherty et al. 1987; Leiers et al. 2003). Reproduction tests were initially performed to establish the sub-lethal effect concentrations used in the microarray experiments.

overall_design: The effects of juglone on C. elegans gene expression were then measured after 24 h of exposure to 0.2, 2, and 20 μM juglone as compared to negative control (K-medium).  Four replicates for each concentration and 12 replicates for negative controls were analyzed as single color microarray.

first: Luke

last: Masson

first: Melanie

last: Arbour

first: Miria

last: Elias

first: Geoffrey

last: Sunahara


title: Comparison between brewery A and brewery B

first: Frank

last: Stahl


title: gntR1 mutant gene expression profiles and Chip-chip analysis of GntR1

status: Public on Jul 15 2014

city: Shinjuku-ku

first: Norihiko

last: Takemoto

state: Tokyo

institute: Research Institute of National Center for Global Health and Medicine

type: Genome binding/occupancy profiling by array


title: WT vs gntR1 mutant gene expression profiles

summary: The transcriptional regulator GntR1 downregulates the genes for gluconate catabolism and pentose phosphate pathway in Corynebacterium glutamicum. Gluconate lowers the DNA binding affinity of GntR1, which is probably the mechanism of gluconate-dependent induction of these genes. In addition, GntR1 positively regulates the ptsG, a gene encoding for a major glucose transporter, and the pck, a gene encoding phosphoenolpyruvate carboxykinase. Here, we searched for the new target of GntR1 at genome-wide scale by chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis. This analysis identified 56 in vivo GntR1 binding sites, of which 7 sites were previously reported. The newly identified GntR1 sites include the upstream regions of carbon metabolism genes such as pyk, maeB, gapB, and icd. Binding of GntR1 to the promoter region of these genes was confirmed by electrophoretic mobility shift assay. The activity of the icd, gapB, and maeB promoters were reduced by the mutation at GntR1 binding site in contrast to the pyk promoter activity increased, indicating that GntR1 is a transcriptional activator of icd, gapB, and maeB and is a repressor of pyk. Thus, it is likely that GntR1 stimulates glucose uptake by inducing the phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS) gene while repressing pyk to increase PEP availability in the absence of gluconate. Repression of zwf and gnd may reduce NADPH supply which may be compensated by the induction of maeB, and icd. Upregulation of icd, gapB, and maeB and downregulation of pyk by GntR1 probably supports gluconeogenesis.

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

first: Tanaka

last: Yuya

first: Terukazu

last: Ito

first: Haruhiko

last: Teramoto

first: Masayuki

last: Inui

first: Hideaki

last: Yukawa


title: Chip-chip analysis of C. glutamicum GntR1

summary: The transcriptional regulator GntR1 downregultates the genes for gluconate catabolism and pentose phosphate pathway in Corynebacterium glutamicum. Gluconate lowers the DNA binding affinity of GntR1, which is probably the mechanism of gluconate-dependent induction of these genes. In addition, GntR1 positively regulates the ptsG, a gene encoding for a major glucose transporter, and the pck, a gene encoding phosphoenolpyruvate carboxykinase. Here, we searched for the new target of GntR1 at genome-wide scale by chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis. This analysis identified 56 in vivo GntR1 binding sites, of which 7 sites were previously reported. The newly identified GntR1 sites include the upstream regions of carbon metabolism genes such as pyk, maeB, gapB, and icd. Binding of GntR1 to the promoter region of these genes was confirmed by electrophoretic mobility shift assay. The activity of the icd, gapB, and maeB promoters were reduced by the mutation at GntR1 binding site in contrast to the pyk promoter activity increased, indicating that GntR1 is a transcriptional activator of icd, gapB, and maeB and is a repressor of pyk. Thus, it is likely that GntR1 stimulates glucose uptake by inducing the phosphoenolpyruvate (PEP): carbohydrate phosphotransferase system (PTS) gene while repressing pyk to increase PEP availability in the absence of gluconate. Repression of zwf and gnd may reduce NADPH supply which may be compensated by the induction of maeB, and icd. Upregulation of icd, gapB, and maeB and downregulation of pyk by GntR1 probably supports gluconeogenesis.

overall_design: ChIP-chip analyses using strain carrying FLAG-tagged gntR1 in the background of the wild type. Biological replicates: 2 replicates.


title: Environmentally Induced Transgenerational Epigenetic Reprogramming of Primordial Germ Cells and Subsequent Germline

city: Pullman


title: Environmentally Induced Transgenerational Epigenetic Reprogramming of Primordial Germ Cells and Subsequent Germline [NimbleGen]

summary: A number of environmental factors (e.g. toxicants) have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. Transgenerational inheritance requires the germline transmission of altered epigenetic information between generations in the absence of direct environmental exposures. The primary periods for epigenetic programming of the germ line are those associated with primordial germ cell development and subsequent fetal germline development. The current study examined the actions of an agricultural fungicide vinclozolin on gestating female (F0 generation) progeny in regards to the primordial germ cell (PGC) epigenetic reprogramming of the F3 generation (i.e. great-grandchildren). The F3 generation germline transcriptome and epigenome (DNA methylation) were altered transgenerationally. Interestingly, disruptions in DNA methylation patterns and altered transcriptomes were distinct between germ cells at the onset of gonadal sex determination at embryonic day 13 (E13) and after cord formation in the testis at embryonic day 16 (E16). A larger number of DNA methylation abnormalities (epimutations) and transcriptional alterations were observed in the E13 germ cells than in the E16 germ cells. These observations indicate that altered transgenerational epigenetic reprogramming and function of the male germline is a component of vinclozolin induced epigenetic transgenerational inheritance of disease. Insights into the molecular control of germline transmitted epigenetic inheritance are provided.

overall_design: The F0 generation females were exposed to a vehicle (dimethylsulfoxide DMSO) as control or to vinclozolin, as described in the Methods. The F1 generation offspring were bred to generate the F2 generation and the F2 generation offspring were bred to generate the F3 generation offspring.  The timed pregnant F2 generation females were used to isolate the F3 generation control and vinclozolin lineage fetal gonads at the E13 and E16 time points. The F3 generation E13 PGC and E16 prospermatogonia were isolated. DNA was isolated from the freshly isolated cells to examine DNA methylation by methylated DNA immunoprecipitation (MeDIP) followed by analysis on a genome-wide promoter tiling array (Chip) using a comparative hybridization MeDIP-Chip analysis between control and vinclozolin lineage samples  as described in Methods. This allowed a comparison of the epigenome alterations in F3 vinclozolin lineage germ cells at E13 and E16. Three separate experimental comparisons of control and vinclozolin-lineage animals involving different germ cell isolations were analyzed with three different MeDIP-Chip analyses at each time point.

first: Carlos

last: Gurerrero-Bosagna

first: Md

last: Haque

first: Eric

last: Nilsson

first: John

last: McCarrey


title: Protein expression of bladder cancer

city: Daejeon

first: Myung-Shin

last: Lee

address: Yongdu-dong, Jung-gu

department: Microbiology and Immunology

institute: Eulji University School of Medicine

summary: Expression profiling of a total of 656 proteins in 3 high grade non-muslce invasive bladder cancer cases/normal urothelial mucosa pairs

overall_design: In the study presented here, a consecutively operated, well-defined 3 HG NMIBC cases was used to acquire expression profiles of a total of 656 unique proteins, leading to the successful construction of supervised

first: Jingsung

last: Park


title: Toxicogenomic effects of nano- and bulk TiO2 particles in the soil nematode Carnorhabditis elegans

first: Sylvie

last: Rocheleau

summary: The toxicity and toxicogenomics of selected anatase and rutile nanoparticles (NP) and bulk titanium dioxide (TiO2) particles were evaluated in the soil nematode Caenorhabditis elegans. Results indicated that bulk or nano-TiO2 particles were slightly toxic to soil nematode C. elegans, as measured by reproduction EC50 values ranging from 4 to 32 mg/L. Whole-genome microarray results indicated that the regulation of glutathione-S-transferase gst-3, cytochrome P450 cypp33-c11, stress resistance regulator scl-1, oxidoreductase wah-1, and embryonic development pod-2 genes were significantly affected by nano-sized and bulk TiO2 particles. More specifically, it was determined that anatase particles exerted a greater effect on metabolic pathways, whereas rutile particles had a greater effect on developmental processes. The up-regulation of the pod-2 gene corroborated the phenotypic effect observed in the reproduction test. Our results demonstrated that C. elegans is a good genomic model for nano-TiO2 toxicity assessment.

overall_design: TiO2 genomic experiments were performed using three separate biological replicates for each concentration.

first: Luke

last: Masson


title: Environmentally Induced Epigenetic Transgenerational Inheritance of Ovarian Disease [NimbleGen]

first: Michael

last: Skinner

address: Abelson 507

institute: WSU

summary: The actions of environmental toxicants and relevant mixtures in promoting the epigenetic transgenerational inheritance of ovarian disease was investigated with the use of a fungicide, a pesticide mixture, a plastic mixture, dioxin and a hydrocarbon mixture. After transient exposure of an F0 gestating female rat during embryonic gonadal sex determination, the F1 and F3 generation progeny adult onset ovarian disease was assessed. Transgenerational disease phenotypes observed included an increase in cysts resembling human polycystic ovarian disease (PCO) and a decrease in the ovarian primordial follicle pool size resembling primary ovarian insufficiency (POI). The F3 generation granulosa cells were isolated and found to have a transgenerational effect on the transcriptome and epigenome (differential DNA methylation). Epigenetic biomarkers for environmental exposure and associated gene networks were identified. Epigenetic transgenerational inheritance of ovarian disease states was induced by all the different classes of environmental compounds, suggesting a role of environmental epigenetics in ovarian disease etiology.

overall_design: Granulosa cells from large antral follicles were collected and evaluated from F3 generation rats that were ancestrally exposed to one of the five different treatments: Vinclozolin, Pesticide (includes permethrin and DEET), Plastics (includes BPA, DBP and DEHP), Low-dose Plastics (50% of Plastics dose), Dioxin, Hydrocarbon (Jet fuel JP8), or DMSO vehicle as Control. Vinclozolin lineage alterations in differentially DNA methylated regions (DMR) in the granulosa cells was investigated by using a methylated DNA immunoprecipitation (MeDIP) procedure followed by comparative hybridization on a genome wide promoter tiling array (Chip), termed an MeDIP-Chip assay. The DNA fractions from four animals of the same treatment group were pooled to create three different pooled DNA samples from each of the two treatment groups (experimental vs. control). These DNA samples were then used for methylated DNA immunoprecipitation (MeDIP) using Nimblegen microarrays. Each MeDIP sample was then used to preform three different comparative (amplified MeDIP vs. amplified MeDIP) hybridization experiments (3 sub-arrays), each encompassing DNA samples from 24 animls (3 treatment and 3 control groups).

first: G

last: Larson

first: M

last: Manikkam

last: Guerrero-Bosagna

first: Marina

last: Savenkova


title: Collier/OLF/EBF-dependent transcriptional dynamics control muscle specification from cardiopharyngeal progenitors

city: New York

first: Lionel

last: Christiaen

state: NY

address: 1009 Silver Center 100 Washington Square East

department: Biology

institute: NYU

summary:
In vertebrates, pluripotent pharyngeal mesoderm progenitors produce the cardiac precursors of the second heart field as well as the branchiomeric head muscles and associated stem cells. However, the cellular and molecular mechanisms underlying the transition from multipotent progenitors to distinct heart and muscle precursors remain obscured by the complexity of vertebrate embryos. Here, using the ascidian Ciona intestinalis as a simple chordate model for cardiopharyngeal development, we show that bipotent progenitors are transcriptionally primed to activate both heart and pharyngeal muscle regulatory programs, which become restricted to the corresponding precursors following a conserved pattern of asymmetric divisions. Localized expression of COE (Collier/OLF1/EBF) then orchestrates the transition to a pharyngeal muscle fate both by promoting an MRF (Myogenic Regulatory Factor)-associated core myogenic program in myoblasts and by maintaining an undifferentiated state in their sister precursors through Notch-mediated lateral inhibition. Using single cell lineage tracing, we show that the latter are stem-like muscle precursors, which form most of the juvenile body wall muscles following proliferation, self-renewal, re-activation of MRF, and migration. We discuss the implications of our findings for the development and evolution of the cardiopharyngeal mesoderm in chordates.
We combined fluorescence-activated cell sorting (FACS) and whole genome transcription profiling following perturbations of COE function to characterize the transcriptional dynamics underlying the specification of heart and ASM precursors in the ascidian cardiopharyngeal lineage.

overall_design: We used whole genome transcription profiling of FACS-purified cell populations isolated from 21 hpf larvae expressing FoxF>COE, FoxF>COE::WRPW or the FoxF>NLS::lacZ control. To gain insights into the transcriptional dynamics underlying fate specification in the cardiopharyngeal lineage, we also purified B7.5-lineage cells from control embryos and larvae collected every two hours from 8 to 28 hpf. This time window encompasses all developmental transitions from early TVC specification till ASM ring formation and initial differentiation.

first: Florian

last: Razy-Krajka

first: Karen

last: Lam

first: Wei

last: Wang

first: Alberto

last: Stolfi

first: Marine

last: Joly

first: Richard

last: Bonneau


title: Human Peripheral blood mononuclear cells (PBMCs): Control vs. Kashin-Beck Disease

city: Xi'an

first: Xi

address: No.76 Yanta West Road

institute: Xi‘an Jiaotong University Health Science Center

summary: Objective:To identify an accurate blood-based gene signature for early detection of Kashin-Beck disease (KBD). Methods: Gene expression analysis was conducted of peripheral blood samples from 100 patients with KBD and 100 controls randomly chosen from two KBD-endemic areas

overall_design: Two-condition experiment, Control vs. KBD PBM cells. Biological replicates: 100 control replicates, 100 KBD replicates.

first: Yujie

last: Ning

first: Feng

last: Zhang

first: Fangfang

last: Yu

first: Wuhong

last: Tan

first: Yanxia

last: Lei

first: Hanjie

first: Zheng

last: Li

first: Mikko

last: Lammi

first: Xiong

last: Guo


title: Comparison of the expression profiles of 630E strain and hfQ mutants

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur


title: Comparison of the expression profiles of 630E strain and a hfQ mutant after 7.5h of growth in Tyt

summary: Clostridium difficile is an emergent human pathogen and the most common cause of nosocomial diarrhea. Our recent deep-sequencing data strongly suggest the importance of RNA-based mechanisms for the control of gene expression in C. difficile. The RNA chaperon protein Hfq is a key component of post-transcriptional regulatory network in various bacterial systems. In an effort to understand the function of Hfq in C. difficile, we have constructed and characterized an Hfq-depleted strain in this bacterium. We present evidence that Hfq is necessary for the normal cell growth, for the establishment of bacillary form and might be involved in metabolic adaptations, stress response and sporulation, important during C. difficile infection cycle. In accordance to these phenotypic changes, our transcriptome analysis revealed pleiotropic effects of Hfq on gene expression in C. difficile. This microarray analysis showed altered expression of genes encoding cell wall and membrane transport components, sporulation proteins, as well as stress response, transcriptional regulator genes and genes of unknown function. Remarkably, a great number of genes belonging to the regulon dependent on sporulation-specific sigma K factor were generally up-regulated in the strain depleted for Hfq. Many important metabolic pathways were also affected by Hfq depletion. Finally, the altered accumulation of several previously identified sRNAs suggests potential involvement of Hfq in these regulatory RNA function. Altogether, these results provide evidence for the pleiotropic role of Hfq protein in C. difficile physiology expanding our knowledge of Hfq-dependent regulation in Gram-positive bacteria.

overall_design: Two-conditions experiments, 630E strain vs. hfQ mutant grown in TYt, 4 biological replicates for each condition.

first: Pierre

last: Boudry

first: Marc

last: Monot


title: Involvement of miRNAs in the regulation of muscle wasting during catabolic conditions

first: Gerolamo

last: Lanfranchi

summary: Loss of muscle proteins and the consequent weakness has important clinical consequences in diseases such as cancer, diabetes, chronic heart failure and in ageing. In fact, excessive proteolysis causes cachexia, accelerates disease progression and worsens life expectancy. Muscle atrophy involves a common pattern of transcriptional changes in a small subset of genes named atrophy-related genes or atrogenes. Whether microRNAs play a role in the atrophy program and muscle loss is debated. To understand the involvement of miRNAs in atrophy we performed miRNA expression profiling of mouse muscles under wasting conditions such as fasting, denervation, diabetes and cancer cachexia. We found that the miRNA signature is peculiar of each catabolic condition. We then focused on denervation and we revealed that changes in transcripts and microRNAs expression did not occur simultaneously but were shifted. Indeed, while the transcriptional control of the atrophy-related genes peaks at 3 days, the changes of miRNA expression maximised at 7 days after denervation. Among the different miRNAs, microRNA-206 and 21 were the most induced in denervated muscles. We characterized their pattern of expression and defined their role in muscle homeostasis. Indeed, in vivo gain and loss of function experiments revealed that miRNA-206 and miRNA-21 were sufficient and required for atrophy program. In silico and in vivo approaches identified the transcription factor YY1 and the translational initiator factor eIF4E3 as downstream targets of these miRNAs. Thus miRNAs are important for the fine-tuning of the atrophy program and their modulation can be a novel potential therapeutic approach to counteract muscle loss and weakness in catabolic conditions.

overall_design: To determine which miRNAs are relevant for the atrophic process, we performed miRNA expression profiles of muscles from different atrophic models (starvation, denervation and streptozotocin-induced diabetes). We checked whether there was a common signature of miRNA expression in different atrophying conditions and we found that every catabolic situation require a peculiar pattern of miRNA. We further focus on the condition of denervation and identified the most up-regulated miRNAs in this condition, miRNA-206 and miRNA-21.

first: Ricardo

last: Soares

first: Cristiano

last: De Pittà

first: Francesco

last: Chemello

first: Stefano

last: Cagnin

first: Matteo

last: Silvestrin

first: Marco

last: Sandri


title: Comparison of the expression profiles of 630E strain and an Hfq antisense after 7.5h of growth in Tyt

summary: Transcriptional profiling of C. difficile 630E strain vs. an Hfq antisense after 7.5h of growth inTYt.

overall_design: Two-conditions experiments, 630E strain vs. Hfq antisense grown in TYt, 4 biological replicates for each condition.


title: The overall effect of parasitization by Nasonia vitripennis on its host Sarcophaga crassipalpis

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Nasonia vitripennis injects venom into its host organism Sarcophaga crassipalpis together with the eggs in order to make it suitable for the offspring to survive. The venom is known to suppress the hosts immune system, elevate the lipid levels, slow down development, et cetera.This microarray can uncover new transcriptomal effects on the host organism after natural envenomation that have not been discovered by bioassays. Since transcriptomal effects will vary during time, two different time points have been selected, 3 and 25 hours after parasitization.

overall_design: 16 individuals per sample, 4 replicates per group, loopdesign, 4 control individuals per time point, dye swap

first: Ellen

middle: L

last: Danneels

last: Formesyn

first: Peter

last: Verleyen

first: Tom

last: Wenseleers

first: Liliane

last: Schoofs

first: Dirk

last: de Graaf


title: Differentially expressed genes involved in the regulation of muscle wasting during catabolic conditions

overall_design: To determine which transcripts could be real mRNA targets of miRNAs relevant for the atrophic process, we performed gene expression expression profiles of muscles from different atrophic models (starvation, denervation and streptozotocin-induced diabetes).For this purpose, we defined the gene expression signature on the same atrophic samples used to assess miRNA expression profile (see GSE51648), and then we compared miRNA and mRNA expression levels.


title: Electrochemical selection and characterization of a high current-generating Shewanella oneidensis mutant with altered cell-surface morphology and biofilm-related gene expression

status: Public on Jul 14 2014

city: Hachioji

first: Atsushi

last: Kouzuma

address: 1432-1 Horinouchi

institute: Tokyo University of Pharmacy and Life Sciences

summary: Shewanella oneidensis MR-1 exhibits extracellular electron transfer (EET) activity that is influenced by various cellular components, including outer-membrane cytochromes, cell-surface polysaccharides (CPS), and regulatory proteins. Here, a random transposon-insertion mutant library of S. oneidensis MR-1 was screened after extended cultivation in electrochemical cells (ECs) with a working electrode poised at +0.2 V (vs. Ag/AgCl) to isolate mutants that adapted to electrode-respiring conditions and identify as-yet-unknown EET-related factors. Several mutants isolated from the enrichment culture exhibited rough morphology and extraordinarily large colonies on agar plates compared to wild-type MR-1. One of the isolated mutants, designated strain EC-2, produced 90% higher electric current than wild-type MR-1 in ECs and was found to have a transposon inserted in the SO_1860 (uvrY) gene, which encodes a DNA-binding response regulator of the BarA/UvrY two-component regulatory system. However, an in-frame deletion mutant of SO_1860 (∆SO_1860) did not exhibit a similar level of current generation as that of EC-2, suggesting that the enhanced current-generating capability of EC-2 was not simply due to the disruption of SO_1860. In both EC-2 and ∆SO_1860, the transcription of genes related to CPS synthesis was decreased compared to wild-type MR-1, suggesting that CPS negatively affects current generation. In addition, transcriptome analyses revealed that a number of genes, including those involved in biofilm formation, were differentially expressed in EC-2 compared to those in ∆SO_1860. The present results indicate that the altered expression of the genes related to CPS biosynthesis and biofilm formation is associated with the distinct morphotype and high current-generating capability of strain EC-2, suggesting an important role of these genes in determining the EET activity of S. oneidensis.

overall_design: Total 6 samples, 3 biological replicates for each sample

first: Hitomi

last: Oba

first: Kazuya

last: Watanabe


title: Comparison of exon-wise expression profiling between normal and cancer tissues of human stomach

status: Public on Jul 12 2014

city: Goyang

first: Sung-Ho

last: Goh

state: Gyeonggido

address: Research Bldg. 5th Fl., 323 Ilsanro

department: Functional Genomics Branch

institute: National Cancer Center

summary: Gastric cancers account for the fourth most frequent cancer death worldwide. Although many differential gene expression profiles are reported for gastric cancers, their variation at the post-transcriptional level has not been provided yet. In this study, we compared the gene expressions of normal stomach vs. stomach cancer in an exon-wise manner and compared alternatively spliced transcripts. The RNA from normal and cancer tissues of gastric cancer patients were subjected to Exon 1.0 ST microarrays.

overall_design: Transcriptome analysis of RNAs from normal and cancer tissues of human stomach by exon array. We analyzed 30 pairs of normal-cancer stomach tissues using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by the Affymetrix Exon Array Computational Tool.

first: Il-Ju

last: Choi

first: Namshin

last: Kim


title: Human Embryonic Kidney(293T) Cells: Control vs. Transfected

city: Pune

first: Sanjay

last: Mukherjee

state: Maharashtra

address: Ganeshkhind

department: Department of Zoology

country: India

institute: University of Pune

summary: Transcriptional profiling of Human Embryonic Kidney(293T) Cells comparing control untreated 293T cells with 293T cells transfected with A) pcDNA 3.0(-) vector[Invitrogen] (Mock) and B) Expression vector pcDNA 3.0(-) containing cloned Influenza virus H5N1and H11N1-NS1 (Non-Structural1) gene.

overall_design: Two-condition experiment, 293T vs. TF-293T cells. Biological replicates: 3 control, 3 transfected, independently grown and harvested for each set of experiment.Total 4 groups 1.Control untransfected (293T) cells 2. Mock 293T cells transfected with pcDNA3.0(-) expression 3. 293T cells transfected with NS1 gene of H5N1 virus cloned in pcDNA 3.0(-) vector 4.293T cells transfected with NS1 gene of H11N1 virus cloned in pcDNA 3.0(-) vector.

first: Alok

last: Chakrabarti


title: Ustilago maydis gene expression after growth on hydrophobic surface plus/minus hydroxy fatty acids

city: Marburg

first: Regine

last: Kahmann

address: Karl-von-Frisch Str. 10

department: Organismic Interactions

institute: MPI for Terrestrial Microbiology

summary: Infection-related development of phytopathogenic fungi is initiated by sensing and responding to plant surface cues. This response results in the formation of specialized infection structures, so-called appressoria. To unravel the program inducing appressoria in the biotrophic smut fungus Ustilago maydis, we exposed cells to a hydrophobic surface and the cutin monomer 16-hydroxy hexadecanoic acid. Genome-wide transcriptional profiling under these appressorium-inducing in vitro conditions revealed dramatic transcriptional changes in almost 20% of the genes. Comparisons with the U. maydis sho1 msb2 double mutant, lacking two putative sensors for plant surface cues, revealed that these plasma membrane receptors regulate a small subset of the surface cue-induced genes. These genes comprised mainly secreted proteins including plant cell wall degrading enzymes that facilitate plant penetration and secreted effectors that are essential virulence factors, with functions after penetration. Our data also demonstrate specific effects on two transcription factors that redirect the transcriptional regulatory network towards appressorium formation and plant penetration. Thus, plant surface cues prime U. maydis for biotrophic development.

overall_design: Solopathogenic Ustilago maydis strain AM1 and its derivate AM1Δsho1Δmsb2 were grown to mid-log phase in YEPSL medium and resuspended in 2% YEPSL plus/minus 16-hydroxy hexadecanoic acid (HDA). The cell suspensions were sprayed on hydrophobic surface (Parafilm) and incubated for 12 h. As control, cells were sprayed on hydrophilic glass surface and incubated for 2 h. After RNA extraction Affymetrix microarrays were performed.

first: D

last: Lanver

first: P

last: Berndt

first: R


title: MicroRNA Expression Profiles of Patients with Biochemically Recurrent Prostate Cancer

status: Public on Jul 10 2014

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary: It is of paramount importance to unravel the molecular mechanisms underlying PCa progression to develop novel diagnostic and therapeutic approaches. MicroRNA (miRNA) profiling through microarrays is an invaluable tool to identify a miRNA signature, which is required to determine the general and specific expression alterations between distinct types of tissues.

overall_design: In this study, it is aimed to compare the miRNA profile of recurrent and non-recurrent prostate tumor tissues to explore a possible involvement of miRNAs in PCa progression.

first: Michael

last: Ittmann

first: Mustafa

last: Ozen

first: Yiqun

last: Zhang


title: Plastics Derived Endocrine Disruptors (BPA, DEHP and DBP) Induce Epigenetic Transgenerational Inheritance of Obesity, Reproductive Disease and Sperm Epimutations

last: Skinner

department: SBS

summary: Environmental compounds are known to promote epigenetic transgenerational inheritance of adult onset disease in subsequent generations (F1–F3) following ancestral exposure during fetal gonadal sex determination. The current study was designed to determine if a mixture of plastic derived endocrine disruptor compounds bisphenol-A (BPA), bis(2-ethylhexyl)phthalate (DEHP) and dibutyl phthalate (DBP) at two different doses promoted epigenetic transgenerational inheritance of adult onset disease and associated DNA methylation epimutations in sperm. Gestating F0 generation females were exposed to either the “plastics” or “lower dose plastics” mixture during embryonic days 8 to 14 of gonadal sex determination and the incidence of adult onset disease was evaluated in F1 and F3 generation rats. There were significant increases in the incidence of total disease/abnormalities in F1 and F3 generation male and female animals from plastics lineages. Pubertal abnormalities, testis disease, obesity, and ovarian disease (primary ovarian insufficiency and polycystic ovaries) were increased in the F3 generation animals. Kidney and prostate disease were only observed in the direct fetally exposed F1 generation plastic lineage animals. Analysis of the plastics lineage F3 generation sperm epigenome previously identified 197 differential DNA methylation regions (DMR) in gene promoters, termed epimutations. A number of these transgenerational DMR form a unique direct connection gene network and have previously been shown to correlate with the pathologies identified. Observations demonstrate that a mixture of plastic derived compounds, BPA and phthalates, can promote epigenetic transgenerational inheritance of adult onset disease. The sperm DMR provide potential epigenetic biomarkers for transgenerational disease and/or ancestral environmental exposures.

overall_design: Methylated sperm DNA was isolated from rats ancestrally exposed to plastics (Bip). Three independent samples from the treatment group were obtained.  Differential DNA methylation between treatment groups was determined using Nimblegen microarrays. Treated samples were paired with control samples and hybridized together on arrays (Bip1/Cip1, Bip2/Cip2, and Bip3/Cip3), resulting in three arrays for the treatment.

first: Mohan

last: Manikkam

first: Rebecca

last: Tracey

first: Carlos

last: Guerrero-Bosagna


title: Characterization of the Rel2-regulated transcriptome and proteome of Anopheles stephensi identifies new anti-Plasmodium factors

status: Public on Jul 11 2014

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

summary: Mosquitoes possess an innate immune system that is capable of limiting infection by a variety of pathogens, including the Plasmodium spp. parasites responsible for human malaria. The Anopheles immune deficiency (IMD) innate immune signaling pathway confers resistance to Plasmodium falciparum. While some previously identified Anopheles anti-Plasmodium effectors are regulated through signaling by Rel2, the transcription factor of the IMD pathway, many components of this defense system remain uncharacterized. To begin to better understand the regulation of immune effector proteins by the IMD pathway, we used oligonucleotide microarrays and iTRAQ to analyze differences in mRNA and protein expression, respectively, between transgenic An. stephensi mosquitoes exhibiting blood meal-inducible overexpression of an active recombinant Rel2 and their wild-type conspecifics. Numerous genes were differentially regulated at both the mRNA and protein levels following induction of Rel2. While multiple immune genes were up-regulated, a majority of the differentially expressed genes have no known immune function in mosquitoes. Identified sequences were assigned putative functions and gene ontology (GO) terms based on homology to previously annotated A. gambiae gene sequences. Selected up-regulated genes from multiple GO categories were tested for both anti-Plasmodium and anti-bacterial action using RNA interference (RNAi). Based on our experimental findings, we conclude that increased expression of the IMD immune pathway-controlled transcription factor Rel2 affects the expression of numerous genes with diverse functions, suggesting a broader physiological impact of immune activation and possible functional versatility of Rel2. Our study has identified multiple novel anti-Plasmodium effectors.

overall_design: Midguts from midgut-specific transgenic A. stephensi at 6 and 12 hours post-blood meal and fat bodies from fat body-specific transgenic A. stephensi at 12 and 18 hours post-blood meal were compared to wild-type A. stephensi at the same time points.  3 biological replicates and 1 pseudo-replicate per array.

first: A

last: Pike

last: Vadlamani

first: S

last: Sandiford

last: Gacita

first: G


title: Compare miRNA expression profiles of human iNSC, H9-NSC, fibroblast

city: Seoul

first: Kyung-Rok

last: Yu

address: Rm727, Bd85, Gwanak-gu

institute: Seoul National University

summary: miRNA profiling of human H9-derived neural stem cells (H9-NSCs) comparing control human adult dermal fibroblasts (hDFs), SOX2-transduced human induced neural stem cells (hDF-iNSC (SOX2)), SOX2/HMGA2-transduced human induced neural stem cells (hDF-iNSC (SOX2/HMGA2)). Goal was to determine the global miRNA expression between the groups.

overall_design: H9-NSC vs hDF vs hDF-iNSC(SOX2) vs hDF-iNSC(SOX2/HMGA2)

first: Kyung-Sun

last: Kang


title: Cdk11-Cyclin L controls the assembly of the RNA polymerase II Mediator [expression]

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

summary: The L-Mediator is a general co-activator of RNA Polymerase II transcription and is formed by the reversible association of the S-Mediator and the kinase module harbouring Cdk8. We describe the Cdk11-Lcp1 complex and show that its inactivation alter the global expression profiles in a very similar way than mutations of the kinase module. Cdk11 is broadly distributed onto chromatin and phosphorylate the Med27 and Med4 Mediator subunits on conserved residues. The inactivation of either Cdk11 or the mutation of its target residues on the Mediator leads to a strongly decreased association of the kinase module and the S-Mediator. The results show that Cdk11-Lcp1 regulates that assembly of the L-Mediator complex.

overall_design: Total RNA was isolated from two biological replicates for all conditions, and each biological replicate was hybridized in duplicate on Agilent arrays (dye-swap).

first: Julie

last: Drogat

first: Valérie

last: Migeot

first: Elise

last: Mommaert

first: Caroline

last: Mullier

first: Marc

last: Dieu

last: van Bakel

first: Damien

last: Hermand