title: Lack of the pif1 helicase enhances zinc tolerance in S. cerevisiae

status: Public on Jun 01 2010

city: Cerdanyola

first: Antonio

last: Casamayor

address: Edifici IBB, Campus UAB

institute: Universitat Autonoma de Barcelona

summary: The Saccharomyces cerevisiae gene PIF1 encodes a conserved eukaryotic DNA helicase required for both mitochondrial and nuclear DNA integrity. Our previous work revealed that a pif1D strain is tolerant to zinc overload. We demonstrate here that this effect is independent of the Pif1 helicase activity and is only observed when the protein is absent from the mitochondria. pif1 cells accumulate abnormal amounts of mitochondrial zinc and iron. Transcriptional profiling reveals that pif1 cells under standard growth conditions overexpress aconitase-related genes. When exposed to zinc, pif1 cells show lower induction of genes encoding iron (siderophores) transporters and higher expression of genes related to oxidative stress responses than wild type cells. Coincidently, pif1 mutants are less prone to zinc-induced oxidative stress and display a higher reduced/oxidized glutathione ratio. Strikingly, although pif1 cells contain normal amounts of the Aco1 protein, they completely lack aconitase activity. Loss of Aco1 activity is also observed when the cell expresses a non-mitochondrially targeted form of Pif1. We postulate that lack of Pif1 forces aconitase to play its DNA protective role as nucleoid protein and that this would trigger a domino effect on iron homeostasis resulting in increased zinc tolerance.

overall_design:
Four samples were analyzed: WT and pif1 mutant both, in the presence and in the absence of 5 mM ZnCl2 for 1 h.

We compared the expression profile of:
1) WT+Zn vs WT-Zn,
2) pif1 mutant+Zn vs pif1 mutant-Zn,
3) pif1 mutant vs WT, and
4) pif1 mutant+Zn vs WT+Zn.

A Dye-swap was carried out for each comparison of samples.

Total number of chips analyzed: 8.

first: Maria

last: Guirola

first: Lina

last: Barreto

first: Miriam

last: Romagosa

first: Silvia

last: Atrian

first: Joaquin

last: Ariño


title: Expression data from porcine hepatic and adipose tissue of males and females fed with two feeding levels

status: Public on May 22 2010

city: Madrid

first: Ana

middle: I

last: Fernandez

state: Madrid

address: Ctra. Coruña Km 7.5

department: Mejora Genética Animal

country: Spain

institute: INIA

summary:
Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot,  we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death.
Breed, gender and diet are factors affecting porcine metabolism. The aim of this study has been to investigate the gene expression patterns of the major sites for lipid metabolism, liver and fat, conditional on gender and on a moderate feeding restriction in Iberian pigs, as a model of obese porcine breed. Our results show that tissue effect account for more differentially expressed genes than gender or feeding restriction. The results obtained from the comparison between tissues support the studies showing adipose tissue is not only a fat-storage depot,  we report a high number of upregulated genes in adipose tissue which represent relevant biological functions such as carbohydrate and energy metabolisms and endocrine function. Besides, key genes implicated in lipid metabolism are specifically overrepresented in liver or fat, particularly the differentially expressed genes related to fatty acid synthesis support previous studies showing that in pig, as in cattle or sheep, this process largely occurs in fat. We identified metabolic differences between genders such as oxidation capacity or response to toxins, reflected at gene expression level in liver but no in adipose tissue, contrarily to previous studies. Finally, our results seem to indicate that a moderate feeding restriction does not have large effects on liver or fat gene expression of obese pigs. Although the list of differentially expressed genes due to the effect of feeding restriction is limited, we could identify expression differences in genes related to antiageing mechanisms associated with feeding restriction as enhancement of immune response and anticoagulation and the balance between prosurvival and cell-death.

overall_design: 16 liver and subcutaneous backfat samples from eight animals at slaughter, 211 days old, four males and four females, four under high feeding level and four under 20% restriction

last: Fernández

first: Cristina

last: Óvilo

first: Almudena

first: Amanda

last: Fernández-Rodríguez

first: Dafne

last: Pérez-Montarelo

first: Carmen

last: Barragán

first: Clemente

last: López-Bote

first: Miguel

middle: A

last: Toro

first: MCarmen

last: Rodríguez

first: Luis

last: Silió


title: Identification of novel SNP candidates associated with chemo-responsiveness in colorectal cancers

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary:
Identificaiton of novel single-nucleotide polymorphism (SNP) candidates associated with chemo-responsiveness in colorectal cancers using microarray
Response rates of 104 colorectal cancer patients to established regiments (FL, CAPE, FLOX, FLIRI) were evaluated by histoculture drug response assay. Affymetrix SNP 5.0 chips were used to determine genotypes of the same colorectal cancer patients. SNPs associated with chemosensitivity to standard regimens were identified by genome-wide association study. FL: 5-FU + Leucovorin; CA: Capecitabine, FLOX: 5-FU + Leucovorin + Oxaliplatin, FLIRI: 5-FU + Leucovorin + Irinotecan

overall_design:
Response rates of 104 colorectal cancer patients to established regiments (FL, CAPE, FLOX, FLIRI) were evaluated by histoculture drug response assay. Affymetrix SNP 5.0 chips were used to determine genotypes of the same colorectal cancer patients. SNPs associated with chemosensitivity to standard regimens were identified by genome-wide association study. FL: 5-FU + Leucovorin; CA: Capecitabine, FLOX: 5-FU + Leucovorin + Oxaliplatin, FLIRI: 5-FU + Leucovorin + Irinotecan

Histoculture drug response assay results provided as % inhibition rate of tumor growth (1 - (tumor cell count in drug treatment)/(tumor cell count in control treatment)) * 100. Cell count is measured by UV spectrometer at 540 nm. The  value is between 0% (No inhibition) to 100% (Complete inhibition). For example, a patient with FL 60 was more responsive to  FL treatment than a patient with FL 20.

first: J

first: Y

middle: S

first: S

middle: Y


title: rilkit-eqtl analysis (random pair design). Tools to optimize the use of RIL populations for natural diversity studies and QTL cloning

status: Public on Jun 30 2011

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

summary: gnp07_rilkit - rilkit-eqtl analysis (random pair design). To provide quantitative geneticists studying natural variation in our RIL populations with information and resources necessary to speed up QTL cloning and candidate genes identification. This articulates around the creation of two major resources and their integration into databases to make the information accessible to users: A. Whole transcriptome survey, B. Production of complementary material. Comparison of 164 Cvi/Col(8RV) Recombinant Inbred Lines (RILs) and 164 Bur/Col (20RV) RILs.

overall_design: 162 dye-swaps. Genotype and ecotype comparison.

first: Ludivine

last: Taconnat

first: Christine

last: Camilleri

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Role of HB6 in plant development

status: Public on Aug 01 2010

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

summary:
rs09-07_hb6 - hb6 - The aim is to determine downstream target of HB6 transcription factor involved in plant development - Transcriptome on Arabidopsis HB6 over-expressing plants and BPM Knock down plants during development

Keywords: wt vs mutant comparison

overall_design: 6 dye-swap - CATMA arrays

first: Pascal

last: Genschik

first: Jean-Pierre

middle: P

last: Renou

first: Esther-

last: Lechner

middle: L


title: Expression data from porcine ovary tissue of sows from two prolificacy levels

status: Public on Apr 21 2010

first: Amanda

last: Fernández Rodríguez

address: Ctra Coruña km 7.5

summary: Previous results from a genome scan in a F2 Iberian by Meishan intercross showed several chromosome regions associated with litter size traits. In order to identify candidate genes underlying these QTL we have performed an ovary gene expression analysis during pregnancy. F2 sows were ranked by their estimated breeding values for prolificacy, the six sows with higher EBV (HIGH prolificacy) and the six with lower EBV (LOW prolificacy) were selected. Samples were hybridized to Affymetrix porcine expression microarrays. The statistical analysis with a mixed-model approach identified 221 differentially expressed probes, representing 189 genes. These genes were functionally annotated in order to identify the genetic pathways overrepresented. Among the most represented functional groups the first one was immune system response activation against external stimulus. The second group was made up of genes which regulate the maternal homeostasis by complement and coagulation cascades. The last group was involved on lipid and fatty acid enzymes of metabolic processes, which participate in steroidogenesis pathway. In order to identify powerful candidate genes for prolificacy, the second approach of this study was merging microarray data with position information of QTL affecting litter size, previously detected in the same experimental cross. According to this, we have identified 27 differentially expressed genes co-localized with QTL for litter size traits, which fulfill the biological, positional and functional criteria.

overall_design: Twelve ovary samples: six high prolific sows and low prolific sows, slaughtered after 30 days of pregnancy. Each sample is the average between right and left ovary from each sow.

last: Fernández-Rodríguez

first: María

last: Muñoz-Muñoz

first: Ramona

middle: N

last: Pena

first: Almudena

last: Fernández

first: Cristina

last: Óvilo

first: AnaI


title: Chromosomal aberrations in Tak1-/- mice

status: Public on Mar 31 2010

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

summary:
Characterization of chromosomal aberrations in liver tumors of Tak1-/- mice of different ages
The aim of the project is to dissect signaling mechanisms which could be of importance during the process of liver carcinogenesis.

Keywords: Array comparative genomic hybridization analysis (aCGH).

overall_design: Comparison of chromosomal aberrations in Tak1-/- in comparison to wt mice

first: J

last: Haybaeck

first: M

last: Heikenwälder

first: T

last: Lüdde

first: K

last: Bettermann


title: Genome-wide Patterns of Population Structure and Admixture among Hispanic/Latino Populations

status: Public on Apr 08 2010

city: New York

first: Harry

last: Ostrer

state: NY

address: 550 First Avenue, MSB 136

department: Department of Pediatrics

country: USA

institute: NYU Langone Medical Center

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

summary: Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped using Illumina technology.

overall_design: To investigate variations of continental ancestry between different Hispanic/Latino groups (using self-reported country-specific identification of individual, both parents, and all four grandparents) and within them from healthy controls represented in the New York Health Project Biorepository. Genotyped on the Illumina 610-Quad, which is identical to  HumanHap550-v3 SNPs plus an additional ~60,000 SNPs for CNV, no CNV data is provided or was analyzed.

first: Christopher

last: Velez


title: Molecular Mechanisms Mediating Preconditioning Following Chronic Ischemia Differ from those in Classical Second Window

status: Public on Mar 29 2010

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

institute: The Catholic University of Korea

summary: Ischemic preconditioning represents the most powerful mechanism of cardioprotection. The mechanisms mediating the second window of preconditioning (SWOP) differ from those mediating first window preconditioning. We hypothesized that chronic ischemia induced by repetitive ischemic stimuli would be mediated by yet different molecular mechanisms. Accordingly, conscious, chronically instrumented pigs (n=5/group) were submitted to a protocol of classical SWOP (two 10-min episodes of coronary artery occlusion followed by 24 hr reperfusion) and compared to pigs submitted to repetitive occlusion/reperfusion (RCO) by repeating 6 episodes of SWOP 12 hrs apart, and to a model of repetitive coronary stenosis (RCS), in which 6 episodes of 90 min coronary stenosis were performed 12 hrs apart. Microarray analysis was performed on the three models. There was an 85% homology in gene response between both models of RCO and RCS, whereas SWOP was qualitatively different. Both models of RCO and RCS but not SWOP showed a down-regulation of genes encoding proteins involved in oxidative metabolism, and an up-regulation of genes involved in protein synthesis and unfolded protein response, autophagy, heat shock response, protein secretion, and a strong activation of the NF-κB signaling pathway. Two thirds of the genes regulated in the three models showed a gradual pattern of up- or down-regulation, in which RCO was quantitatively intermediary between RCS and SWOP. Therefore, the regulated genes in response to chronic, repetitive episodes of ischemia differ radically from classical first or second window preconditioning.

overall_design: Four groups of pigs were used for the study, i.e., control (n=5), SWOP (n=5), RCO (n=5), and RCS (n=5). SWOP was induced by two episodes of 10 min coronary artery occlusion (CAO), each followed by 10 min coronary artery reperfusion (CAR). RCO was induced by the same stimulus as SWOP (two cycles of 10 min CAO and 10 min CAR), but repeated six times every 12 hrs. RCS was induced by 90 min low-flow ischemia repeated six times every 12 hrs.

first: Christophe

last: Depre

first: Bin

last: Tian

first: Lin

last: Yan

first: Athanasios

last: Peppas

first: Stephen

middle: F

last: Vatner

first: Dorothy

middle: E


title: Baculovirus-encoded protein expression for epigenomic profiling in Drosophila cells

status: Public on Jul 12 2010

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

type: Genome binding/occupancy profiling by genome tiling array

summary:
Baculovirus-encoded proteins can be efficiently produced following infection of different Drosophila cell lines. Epitope-tagged proteins produced in baculovirus-infected cells provide genome-wide profiles of the histone variant H2Av that are comparable to those produced by stably transformed cell lines.

Keywords: Chromatin affinity-purification on microarray

overall_design: All experiments were done using strepavidin or FLAG pulldown DNA cohybridized with total input DNA to the same array. Two channels per array, Cy5 and Cy3, were used in each experiment.

first: Terri

middle: D

last: Bryson

middle: M

last: Weber

first: Steven


title: Gene expression following myocardial infarction with and without stem cell transplantation

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

summary:
Background: Bone marrow-derived multipotent progenitor cell (MPC) transplantation leads to short term functional and bioenergetic improvement in a porcine model of postinfarction Left Ventricular (LV) remodeling despite a low engraftment rate. However, the long term outcome after MPC transplantation is unknown.
Methods and Results: The objectives of this study were to determine the long term functional outcome after MPC transplantation in a porcine model of postinfarction LV remodeling and to elucidate its mechanisms. Myocardial infarction (MI) was created by ligating the first and second diagonal branches of the Left anterior descending artery after open thoracotomy. Intramyocardial injection of 50 million lacZ labeled MPC was performed in the periscar region (Cell, n=7)  with 5 equal injections immediately after MI, while in control animals (CONT, n=7; only 6 were profiled by microarray) saline was injected. Outcome was assessed temporally for 4 months with MRI and P-31 MRS. Engraftment was studied on histology and gene chip (Affymetrix) array analysis was used to study differential expression of genes in the two groups at 4 months. MPC treatment resulted in improvement of ejection fraction as early as 10 days after MI (32.2±5.5 vs. 43.4±5.1 in CONT and Cell respectively, p <0.05). This improvement was seen each month and persisted up to 4 months (35.7±5.0 vs. 51.2±4.8 in CONT and Cell respectively, p<0.005). PCr/ATP ratio improved with MPC transplantation (1.88±0.11 vs. 2.13±0.13 in CONT and Cell respectively, p<0.05). Under increased workload with inotropic stimulation, the bioenergetic differences were even more pronounced. There was no significant difference in scar size (scar/LV area*100) at 10 days post infarction (9.7±2.3 vs. 8.3±1.5 in CONT and Cell respectively).  However, at 4 months there was a significant decrease in scar size in the MPC treated animals (8.6±2.4 vs. 4.6±1.0 in CONT and Cell respectively, p <0.05). No significant engraftment of MPC was observed on histology at 4 months. Gene chip array analysis identified several genes which were differentially expressed in the two groups. MPC transplantation was associated with a downregulation of mitochondrial oxidative enzymes, increased levels of MEF2a (Myocyte Enhancer Factor 2a) and ZFP91 (Zinc finger protein 91).
Conclusion: MPC transplantation results in long term improvement in ventricular function and myocardial energetics that is associated with a decreased scar size and differential expression of genes.

overall_design: 13 swine were randomized after myocardial infarction to receive either 50 million stem cells (n=7) or saline only (n=6). The pigs were followed for a total of 4 months after transplantation with MRI occurring at baseline, 10 days, 1 month and then subsequently each month for 4 months. At the end of the study open-chest NMR spectroscopy was performed and then after sacrifice histology and microarray analysis was done on the tissue samples.


title: Expression data from static and cyclic stretched porcine aortic heart valves

status: Public on May 07 2010

city: Philadelphia

first: Marina

last: Bakay

state: PA

address: 3615 Civic Center Boulevard

department: Pediatrics

institute: Children's Hospital of Philadelphia

summary:
We explored the hypothesis that Serotonin (5HT) receptor signaling, that can be enhanced with 5HT transporter blockade with Fluoxetine (Fluox), in the aortic valve may vary based upon the biomechanical activity of the aortic valve leaflet.
We used Affymetrix microarrays to study gene expression profiling of Porcine Aortic Valves (PAV) incubated under organ culture conditions for 24 hours in either a static state or with 10% cyclic stretch, simulating physiologic leaflet motion. PAV in the bioreactor with or without stretch were exposed to 5HT along or the combination 5HT plus Fluox.

overall_design: Fresh porcine aortic valves were obtained from a local abattoir. The three leaflets were excised from each valve and a rectangular section of tissue 15x10 mm was isolated from the central region of each valve cusp. These samples were randomized and assigned to one of four groups. The experimental groups were: 1) Static conditions with no agents added; 2) Cyclic stretch conditions with no agents added; 3) Static conditions with 5HT plus Fluox added; and 4) Cyclic stretch conditions with 5HT plus Fluox added.

first: Robert

last: Levy

first: Jeanne

last: Connolly

first: Ajit

last: Yoganathan

first: Kartik

last: Balachandran


title: laccases-Differential expression in laccase mutants of Arabidopsis thaliana

status: Public on May 01 2010

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

summary:
ra08-03_kim - laccases - Are laccases involved in lignification - all plants were harveted at the same developmental stage in the same growth chamber between 10h30 and 11h.

Keywords: wt vs mutant comparison

overall_design: 8 dye-swap - CATMA arrays

first: Lise

last: Jouanin

first: Jean-Pierre

last: Renou

first: Marie-Laure

last: Martin-Magniette


title: Genotyping and analysis of chromosome copy number variation (CNV) from pediatric primary intracranial germ cell tumor

status: Public on Feb 26 2010

city: Taipei

first: Yu Hsuan

last: Wu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang-Ming University

summary: Intracranial pediatric germ cell tumors (GCTs) have different histological differentiations, prognosis and clinical behaviors. Prognosis of patients with germinoma and mature teratoma is good, while patients with other types of GCTs, termed as nongerminomatous malignant germ cell tumors (NGMGCTs), require more extensive drug and irradiation treatment regimen. The mechanisms underlying different prognosis of various GCT subgroups remain elusive. We presented CNVs correlating with GCTs malignancy and clinical risk.

overall_design: 16 central nervous system GCT cases with different histological subtypes are subjected to genotyping and CNVs analysis. The histological subtypes are germinoma, mixed GCT of germinoma and mature teratoma, immature teratoma, mixed GCTs of NGMGCTs category, yolk sac tumor, immature teratoma, and embryonal carcinoma.

first: Yu-Hsuan

first: Hsei-Wei

last: Wang


title: Expression data from mediastinal lymph nodes and blood samples of piglets experimentally infected with PCV2

status: Public on Dec 31 2009

city: Bellaterra

first: Anna

last: Tomas

state: Barcelona

address: campus UAB

department: Viral infections

institute: CReSA

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

overall_design: Refer to individual Series


title: Murine hepatocellular carcinoma of MCL1-/- transgenic mice and age matched alb cre mice - 12 months old.

first: Stefan

last: Zoller

summary:
aCGH analysis of murine transgenic liver tissues affected with HCC, hybridized with age (12 months) and sex matched alb cre mice.

Keywords: Array comparative genomic hybridization analysis (aCGH).

overall_design:
Independent HCC of MCL1-/- mice were hybridized with pooled wt mice.
Mcl‑1flox/flox mice (C57BL/6 background) were obtained from the Dana Farber Cancer Institute, Boston, USA (Opferman JT et al., Nature 2003) and bred to heterozygous Albumin-Cre mice (C57BL/6 background) which led to hepatocyte-specific deletion of Mcl-1. The mice develop severe chronic liver damage (Vick B et al., Hepatology, 2009).

first: J

last: Haybaeck

first: M

last: Heikenwälder

first: S


title: Expression data from blood samples of piglets experimentally infected with porcine circovirus type 2 (PCV2)

summary:
This study aimed to characterize differences in gene expression in piglets inoculated with porcine circovirus type 2 (PCV2), the essential causative agent of postweaning multisystemic wasting syndrome (PMWS). Comparisons between control and PCV2-inoculated pigs were done at five different time points: 0, 7, 14, 21 and 29 days post-inoculation.

Keywords: time course

overall_design: Seven-day-old caesarean-derived, colostrum-deprived piglets were distributed into two groups: control (n=4) and inoculated with 105.2 TCID50 of the Burgos PCV2 isolate (n=4). Pigs were bled at 0, 7, 14, 21, and 29 days post-inoculation.

first: Lana

middle: T

last: Fernandes

first: Armand

last: Sanchez

first: Joaquim

last: Segales


title: photomorphogenesis-Expression profile of DET1-1 mutant during photomorphogenesis

summary:
rs09-01_det1 - photomorphogenesis - - Identification of the genes deregulated in det1-1 when seedlings grow in light or in dark (dark increase morphological differences between det1-1 and wild-type) - Expression profile of seedlings grown in dark then exposed to light - etiolated seedlings (5days) are briefly exposed to light to induce developmental transition between skoto- and photomorphogenesis without visible change in plant morphology and differences between col0 and the mutant det1-1 grown in light or in dark

Keywords: treatment variations

first: Chris

last: Bowler

first: Frédy

last: Barneche


title: Differential gene expression in high and low sulfide-producing yeast strains during wine fermentation

status: Public on Dec 03 2009

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

institute: IDAEA-CSIC

summary: Comparison between two commercial wine yeast strains (UCD522 and P29) differing in their production of H2S during wine fermentation.

overall_design:
Due to the characteristics of the strains (commercial, non-standard wine strains), the experiment was duplicated using two completely different platforms and techniques (cDNA-based and in situ synthesized oligonucleotide-based).
UCD522 and P29 wine microfermentations were performed in parallel and yeast samples were taken at the stage of fastest fermentation rate. Two biological replicates per yeast strain.

first: Enric

last: Bartra

first: Marta

last: Casado

first: David

last: Carro

last: Piña

first: Company

last: Oryzon Genomics


title: Rim15 and Igo1/Igo2 are required for proper transcriptional reprogramming during entry into G0 phase in budding yeast

status: Public on May 14 2010

city: Princeton

first: Soyeon

last: Lippman

state: NJ

address: 301 Lewis Thomas Lab

institute: Princeton University

summary: Transcriptional profiling of yeast strains (WT, rim15Δ, and igo1Δigo2Δ) treated with 100nM rapamycin at 20, 60, 120, 180min post treatment with respect to immediately before treatment as reference. Goal of the experiment was to test whether Rim15 and Igo1/2 are implicated in proper regulating of gene expression during nutrient limitation and TORC1 inhibition by rapamycin. At 180 minutes after rapamycin treatment, 478 genes were upregulated more than 2.8 fold in the wild-types cells; whereas the upregulation of 54 were diminished in rim15 mutant and upregulation of 103 genes diminished in cells lacking Igo1 and Igo2. Moreover, induction of the all Rim15-dependent genes were attenuated in igo1/igo2 cells, indicating that transcriptional control of Rim15 requires Igo1 and Igo2. Almost all of Rim15 dependent genes are involved in stress response, carbohydrate metabolism and respiration, as expected by the role of Rim15 during nutrient limitation.

overall_design: WT and mutants treated with rapamycin. Two channel experiment with channel 1 for reference and channel 2 for drug treated condition.

first: James

last: Broach

first: Nicolas

last: Talarek

first: Elisabetta

last: Cameroni

first: Claudio

last: De Virgilio


title: ChIP-chip of MG1655 with antibody against E. coli RNAP beta subunit under various conditions

status: Public on Nov 04 2009

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

summary: We integrated RNAP binding regions (RBRs) and mRNA transcript abundance to determine segments of contiguous transcription originating from promoter regions. To measure RBRs at a genome scale, we employed a ChIP-chip method to E. coli K-12 MG1655 grown in the presence or absence of rifampicin under multiple growth conditions using antibody against E. coli RNAP beta subunit.

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

overall_design: A twelve ChIP-chip study using immunoprecipitated DNA (IP-DNA)  from four separate culture conditions with and/or without rifampicin treatment.  The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome (NimbleGen). Experiments were conducted as biological duplicates or triplicates (different cultures).

first: Byung-Kwan

last: Cho

first: Karsten

last: Zengler

first: Yu

last: Qiu

first: Young-Seoub

last: Park

first: Eric

last: Knight

first: Christian

last: Barrett

first: Yuan

last: Gao

middle: O


title: Transcriptional profiling of response to acute caloric restriction in liver and fat of pigs differing in feed efficiency

status: Public on Jan 10 2010

city: Ames

first: Sender

last: Lkhagvadorj

state: IA

address: 2255 Kildee

department: Animal Science

institute: Iowa State University

summary: Residual feed intake (RFI) is a measure of feed efficiency, where low RFI denotes high feed efficiency. Caloric restriction (CR) is associated with feed efficiency in livestock species and to human health benefits such as longevity and cancer prevention. We have developed pig lines that differ in RFI and are interested to identify the genes and pathways that underlie feed efficiency. Prepubertal Yorkshire gilts with low RFI (n=10) or high RFI (n=10) were fed ad libitum or at 80% of maintenance for eight days. We measured serum metabolites and generated transcriptional profiles of liver and subcutaneous adipose tissue. 6,114 genes in fat and 305 genes in liver were differentially expressed (DE) in response to CR and 311 in fat and 147 in liver were DE due to RFI differences.  Pathway analyses of CR-induced DE genes indicated a switch to a conservation mode of energy by down-regulating lipogenesis and steroidogenesis in both liver and fat. Interestingly, CR in pigs altered expression of genes in immune and cell cycle/apoptotic pathways in fat, which may explain part of the CR-driven lifespan enhancement. In-silico analysis of transcription factors revealed ESR1 as a putative regulator of the adaptive response to CR and several targets of ESR1 in our DE fat genes were annotated as cell cycle/apoptosis genes. Lipid metabolic pathway was overrepresented by down-regulated genes due to both CR and low RFI. We propose a common energy conservation mechanism, which may be controlled by PPARA, PPARG, and/or CREB in both CR and feed efficient pigs.

overall_design: Prepubertal Yorkshire gilts with low RFI (n=10) or high RFI (n=10) were fed ad libitum or at 80% of maintenance for eight days in 2 x 2 complete factorial arrangement.

first: Long

last: Qu

first: Weiguo

last: Cai

first: Oliver

last: Couture

first: C

middle: R

last: Barb

first: Gary

middle: J

last: Hausman

first: Dan

last: Nettleton

first: Lloyd

last: Anderson

first: Jack

middle: C

last: Dekkers

first: Christopher

middle: K

last: Tuggle


title: Expression data from OBGF400 cell line (porcine olfactory bulb neuroblast origin)

status: Public on Oct 30 2009

city: Urbana

first: Gail

last: Scherba

state: IL

address: 2001 S. Lincoln Street

department: Pathobiology

institute: University of Illinois

summary:
The phenotypically characterized hTERT immortalized porcine olfactory bulb neuroblast cell line (OBGF400) was subjected to an extensive whole genome-scaled expression profile for establishing their use as an in vitro neuronal disease model system.
Microarrays were used to provide a comprehensive knowledge underlying the genomic complexity and overall gene expression capacity of the immortalized OBGF400 cells. The analysis revealed the elaborate signaling mechanisms of this unique subpopulation of porcine neuronally committed progenitors that mirrors the intricate organization of postnatal neurongenic zones.

overall_design: Total cellular RNA extracts from independent OBGF400 (neuroblasts) and PK15 (non-neuronal, epithelial origin) cell cultures (9 each) were pooled into a total of 3 biological replicates per cell line. The concentrations and purity of the pooled RNA preparations were determined using the BioAgilent RNA assay prior to hybridization on Affymetrix GeneChip® Porcine Genome Expression Arrays. To ascertain the genes that were preferentially expressed by the OBGF400 neuroblasts, we used the PK15 cellular array in an effort to exclude somatic cell background.

first: Astrid

middle: U

last: Uebing-Czipura

first: Harry

last: Dawson

first: Mark

last: Rutherford


title: Expression data from prepubertal and adult derived porcine oocytes

first: Rebecca

last: Krisher

address: 1207 West Gregory Drive

summary:
Oocyte developmental potential is progressively obtained as females approach puberty.  Therefore, oocytes derived from prepubertal females are less developmentally competent, indicated by decreased embryonic development, compared to oocytes derived from adult females.
To investigate mechanisms involved in establishing oocyte cytoplasmic maturation and developmental competence, Affymetrix GeneChip microarrays were used.

Keywords: oocyte developmental competence, maternal age

overall_design: Porcine oocytes obtained from prepubertal and adult females were collected for RNA extraction and hybridization on Affymetrix microarrays.  Oocytes were aspirated from 2 to 6 mm ovarian follicles and matured in vitro.  Analysis of the first extruded polar body ensured that all oocytes used in the analyses had completed nuclear maturation.

first: Melissa

last: Paczkowski

first: Chris

last: Bidwell


title: Differential endometrial gene expression in pregnant and non-pregnant sows

status: Public on Oct 20 2009

city: Frederiksberg

first: Esben

last: Oestrup

address: Groennegaardsvej 7

department: Department of Basic Animal and Veternary Sciences

country: Denmark

institute: University of Copenhagen

summary: In an attempt to unveil part of the molecular processes controlling porcine placentation we have investigated the pregnancy induced gene expression in the porcine endometrium at Day 14 after insemination using the Affymetrix GeneChip® Porcine Genome Array.

overall_design: At Day 14 after insemination, samples were obtained from the endometrium of pregnant sows and sows inseminated with inactivated semen for RNA extraction and hybridization on Affymetrix microarrays. The uteri were removed and each uterine horn was flushed with PBS containing 1% fetal calf serum, and subsequently opened longitudinally at the anti-mesometrial side. The sites of embryonic attachment were macroscopically visual in the endometrium on the mesometrial side in form of hyperemic zones. Samples of the endometrium (lamina epithelialis, lamina propria and tela submucosa, but not tunica muscularis) were isolated from proximal (the end close to the ovaries), intermedial, and distal (next to the corpus uteri)) sections of each uterine horn. Samples were taken from the endometrium of the non-pregnant animals at comparable locations.

last: Østrup

first: Stefan

last: Bauersachs

first: Helmut

last: Blum

first: Eckhard

last: Wolf

first: Poul

last: Hyttel


title: Expression data from mediastinal lymph nodes of piglets experimentally infected with porcine circovirus type 2 (PCV2)

first: Anna

last: Tomas

summary:
This study aimed to characterize differences in gene expression in piglets inoculated with porcine circovirus type 2 (PCV2), the essential causative agent of postweaning multisystemic wasting syndrome (PMWS). Comparisons between control and PCV2-inoculated pigs were done at five different time points: 1, 2, 5, 8, and 29 days post-inoculation.

Keywords: longitudinal

overall_design: Seven-day-old caesarean-derived, colostrum-deprived piglets were distributed into two groups: control (n=8) and inoculated with 105.2 TCID50 of the Burgos PCV2 isolate (n=16). One control and 3 inoculated pigs were necropsied on days 1, 2, 5, and 8 post-infection (p.i.), the remaining pigs (4 of each group) were necropsied on day 29 p.i.

first: Lana

last: Fernandes

first: Armand

last: Sanchez

first: Joaquim

last: Segales


title: Expression data from estrogen disrupted endometrium

status: Public on Oct 01 2009

city: new haven

first: morgan

middle: dean

last: ashworth

state: CT

address: 333 cedar street

department: OB/GYN reproductive immunology

institute: yale school of medicine

summary:
Placentation of the conceptus to the surface epithelium is governed through a tightly regulated temporal and spatial window.  Premature exogenous steriod exposure causes a shift in the maternal tissue's receptivity and prevents proper placentation.

We used Affymetrix microarrays to detail the aberrant changes in uterine gene expression during this window, while removing all conceptus contribution to this dysfunction.

overall_design: Porcine endometrium was selected at chronological stages of psuedopregnancy and psuedopregnancy post endocrine disrupted early for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of normal endometrium at days 13 and 15 of the pseudo pregnant, and endometrium at days 13 and 15 of the endocrine disrupted pseudo pregnant in order to identify the temporal resolution of expression profiles. In brief, days 13 through 15 accounts for the window of attachment during pregnancy in the pig, so we created pseudo pregnant endometrium and obtained samples from days 13 (PIG13UN_TX)and 15 (PIG15UN_TX) of pseudo pregnancy.  In the same, we created pseudo pregnant endometrium that was subjected to endocrine disruption of the pseudo pregnancy and collected samples on days 13 (PIG13_TX)and 15 (PIG15_TX) of pseudo pregnancy.

first: M

last: Ashworth

first: J

middle: W

last: Ross

last: Ritchey

first: F

last: White

first: R

last: Geisert


title: Fatigue-related HIV disease gene-networks identified in CD14+ cells isolated from HIV-infected patients

status: Public on Oct 08 2009

first: Lawrence

last: Adams

address: 1959 NE Pacific Street

department: BNHS

institute: University of Washington

summary: HIV-related fatigue is multi-causal in origin and potentially related to mitochondrial dysfunction caused by toxicity from nucleoside reverse transcriptase inhibitor (NRTI) antiretroviral therapy. CD14+ cells are undifferentiated macrophages, vulnerable to HIV infection, and easily accessible for gene expression experiments in a purified cell population. We utilized a novel mitochondrially-specific gene expression microarray to assess mitochondrial and nuclear genes in CD14+ cells of low- and high-fatigued, NRTI-treated HIV/AIDS patients (n=5 each). Novel Bayesian and liquid association network methods identified 33 genes predictive of low versus high fatigue and 32 genes predictive of healthy versus HIV infection. Sulfotransferase 2B1 (SULT2B1) is relevant to both the cholesterol and testosterone pathway, and like several inner mitochondrial membrane genes also identified, predictive of fatigue status, while outer mitochondrial membrane genes were predictive of HIV status. A surprising finding was that adenylate cyclase 2 (ADCY2) was a predictor of both HIV and fatigue; it had the highest Kendall’s Tau association value in the HIV group, but in reverse, the lowest Tau value in the fatigue group. Assaying CD14+ cells may provide an alternative to muscle biopsy and a minimally invasive procedure to evaluate patient mitochondrial function, and Bayesian and network tools are useful to identify the link between subjective symptom perceptions and underlying biologically pathways. Fatigue status in HIV patients treated with NRTIs was found to be linked to RNA expression differences related to mitochondrial function. Additional studies are needed to confirm the relevance of our findings in CD14+ cells in other tissues (e. g. skeletal muscle) and to understand the significance of key genes such as SULT2B and ADCY2 in fatigue and HIV disease.

overall_design: The design was a comparison of HIV high fatigue to HIV low fatigue. Low fatigue was determined as 3-7 on the Revised Piper Fatigue Score and High fatigue was a score of 7 or greater. Five HIV negative control samples were used to compare normal fatigue and non-disease status.

first: Joachim

middle: G

last: Voss

first: Adrian

last: Dobra

first: Caryn

last: Morse

first: Joseph

last: Kovacs

first: Rahgavan

last: Raju

first: Marinos

last: Dalakas


title: Comparison between skeletal transcriptomes of Korean native pig and Yorkshire

status: Public on Oct 21 2009

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

institute: Korea University

summary: The pig could be a useful model to characterize molecular aspects determining several delicate phenotypes because they have been bred for those characteristics. The Korean native pig (KNP) is a regional breed in Korea that was characterized by relatively high intramuscular fat content and reddish meat color compared to other western breeds such as Yorkshire (YS). YS grew faster and contained more lean muscle than KNP. We compared the KNP to Yorksire to find molecular clues determining muscle characteristics. The comparison of skeletal gene expression profiles between these two breeds showed molecular differences in muscle. We found 82 differentially expressed genes (DEGs) defined by fold change (more than 1.5 fold difference) and statistical significance (within 5% of false discovery rate). Functional analyses of these DEGs indicated up-regulation of most genes involved in cell cycle arrest, down-regulation of most genes involved in cellular differentiation and its inhibition, down-regulation of most genes encoding component of muscular-structural system, and up-regulation of most genes involved in diverse metabolism in KNP. Especially, DEGs in above-mentioned categories included a large number of genes encoding proteins directly or indirectly involved in p53 pathway. Our results indicated a possible role of p53 to determine muscle characteristics between these two breeds.

overall_design: Comparing gene expression profiles to discover differentially expressed genes from skeletal muscles of two different pig breeds.


title: Gene regulation in Bacillus subtilis by the compatible solute glycine betaine

status: Public on Aug 01 2009

city: Greifswald

first: Leif

last: Steil

address: Friedrich-Ludwig-Jahn Str. 15A

department: Genetics and Functional Genomics

country: Germany

institute: University of Greifswald

summary: Glycine betaine (GB) is a potent osmoprotectant for salt stressed Bacillus subtilis cells, which possess three high-affinity uptake systems for GB. OpuA is the dominant transporter for this compatible solute. Northern blot analysis, primer extension experiments and opuA-treA reporter gene fusion studies demonstrated that opuA expression is strongly induced at high osmolality from a single SigA-type promoter. Promoter mutations that improve the match of the opuA promoter to the consensus sequence substantially increase basal-level expression but reduce inducibility by high salinity. Expression of opuA is sensitively controlled by GB, which causes significant repression of opuA transcription at low and high salinity. GB influences the kinetics as well as the final level of high salinity induction of opuA in a concentration-dependent fashion. The repressing effect of GB on opuA transcription requires the intracellular presence of GB, regardless whether it is taken up via OpuA or other transporters or synthesized from choline. Genome-wide transcriptional profiling of salt-stressed B. subtilis cells demonstrated that the repressive effect of GB targets only a subset of high-salinity induced genes. This group of GB-responsive genes comprises in essence the full set of genes with demonstrated functions in either the uptake or synthesis of compatible solutes.

overall_design: Four different samples (untreated, GB, NaCl, and GB + NaCl treated) were analyzed and each sample was hybridized in triplicate.

first: Tamara

last: Hoffmann

first: Annette

last: Wensing

first: Margot

last: Brosius

first: Uwe

last: Völker

first: Erhard

last: Bremer


title: Transcriptome analysis of E.coli MG1655 under multiple growth conditions

first: Bernhard

last: Palsson

type: Expression profiling by genome tiling array

summary: Investigation of comprehensive information about the expression level of RNA transcripts across the entire E.coli genome in mulitple growth conditions, including log-phase; stationary phase, heat shock and  nitrogen-limiting condition.

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

overall_design: A fourteen chip study using total RNA recovered from four separate culture conditions of E.coli K12 MG1655.  E.coli strains were harvested at mid-exponential phase with exception of stationary phase experiments. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome (NimbleGen). Experiments were conducted as three or more biological replicates (different cultures)

first: Byung-Kwan

last: Cho

first: Karsten

last: Zengler

first: Yu

last: Qiu

first: Young-Seoub

last: Park

first: Eric

last: Knight

first: Christian

last: Barrett

first: Yuan

last: Gao


title: Effect of the different protein diets on the intestinal ecosystem

status: Public on Nov 03 2009

city: Yaan

first: yunzi

last: sun

state: Sichuan

address: No36,Xingkang Road

department: Institute of Animal Nutrition,

country: China

institute: Sichuan Agricultural University

summary: This study examines the evidence that dietary can regulate genes in the intestinal epithelium and it discusses the physiologic relevance of such alterations in gene expression.

overall_design: Seven RNA samples were analyzed  using Affymetrix GeneChip® Porcine Genome Array (Affymetrix, Santa Clara, CA, USA) containing 23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 S. scrofa genes.


title: Circadian and diurnal expression data of Synechococcus

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

country: Japan

institute: Waseda University

summary:
In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild type, kaiABC-null and kaiC-overexpressor strains under LL and continuous dark (DD) conditions.
In the wild type strain more than 30% of transcripts significantly oscillated in a circadian fashion, peaking at subjective dawn and dusk. Such circadian control was nullified in kaiABC-null strains. Although KaiC has been proposed to globally repress gene expression, our analysis revealed that dawn expressing genes were upregulated by kaiC-overexpression, such that the clock was arrested at subjective dawn. Transfer of cells to continuous dark (DD) conditions from LL immediately suppressed expression of most of genes, while the clock keeps time even in the absence of transcriptional feedback. Thus, the Synechococcus genome seems primarily regulated by the light/dark cycles and dramatically modified by the protein-based circadian oscillator.

Keywords: timecourse data (~48 hours under continuous light or darkness) from Synechococcus elongatus PCC 7942 (wild type, kaiABC-null, and inducible kaiC-overexpressor) strains

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Wild type (WT), kaiABC-null (Dkai), and inducible kaiC-overexpressor (oxC) S. elongatus PCC 7942 strains were analyzed under continuous light (LL), continuous dark (DD) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: Two independent experiments in WT under LL (hours 0 to 52) and DD (hours 0 to 48); Two independent experiments in Dkai under LL (hours 0 to 48); Two independent experiments in oxC under LL in the presence or absence of an inducer, IPTG, from hour 25 to 33 in LL; a single experiment in WT under DD in the presence of an transcriptional inhibitor, rifampicin.

first: Hiroshi

last: Ito

first: Jun

last: Tomita

first: Yoriko

last: Murayama

first: Kazuki

last: Terauchi


title: Murine hepatocellular carcinoma of AlbLTa/b transgenic mice and age matched C57BL/6 mice - 18 months old.

status: Public on Jul 29 2009

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

institute: ETH Zurich

summary:
aCGH analysis of murine transgenic liver tissues affected with HCC, hybridized with age (18 months) and sex matched C57BL/6 mice.  Moreover, 18months old C57BL/6 livers were hybridized with independent 18 months old C57BL/6 livers for control.

Keywords: Array comparative genomic hybridization analysis (aCGH).

overall_design: Independent HCC of AlbLTab mice were hybridized with independent C57BL/6 mice.

first: M

last: Heikenwälder

first: S

first: J

last: Haybaeck

first: U

last: Wagner


title: Preliminary characterization of gene expression in European wild boar naturally infected with Brucella suis

status: Public on Sep 29 2009

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

institute: Instituto de Investigacion en Recursos Cinegéticos

summary: Brucella suis infects macrophages and dendritic cells. Wild boars act as reservoirs and carriers of Brucella suis biovar 2, and there is evidence that wild boar can be the main source of infection for domestic pigs through the venereal route. Transmission through this route could be an important path for disesease dissemination. The result from this study will contribute to the overall understanding of the molecular pathogenic mechanisms involved during Brucella suis infection in European wild boar.

overall_design: In this study we preliminarily characterized differential gene expression in European wild boar naturally infected with Brucella suis biovar 2 using Microarray hybridization and Real Time RT-PCR analysis. Since Brucella suis acts by infecting macrophages, we used spleen cells to analyze the gene expression response to Brucella suis infection.

first: Clara

last: Marín

first: Pilar

last: Muñoz

first: José

last: Blasco

last: Gortázar

first: Katherin

last: Kocan

first: Jose

last: de la Fuente


title: Illumina HapMap YRI (Human610-Quadv1)

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

summary: HapMap samples

overall_design: 77 samples from Human610-Quadv1_YRI_Final_Call_Report.csv


title: Discovery of novel hypermethylated gene loci in prostate cancer using genome wide coverage CpG island microarrays

status: Public on Mar 27 2009

city: Toronto

first: Ken

last: Kron

address: 60 Murray Street

country: Canada

institute: Mount Sinai Hospital

type: Methylation profiling by genome tiling array

summary: In order to identify methylation changes in prostate cancer, we performed a genome-wide analysis of DNA methylation using Agilent human CpG island arrays. We then chose specific genes to validate methylation both in the same cases as were hybridized to the array (using quantitative EpiTYPER analysis) and in an independent series of prostate cancer samples (using MethyLight quantitative methylation specific PCR). We specifically chose low grade (Gleason score 6 cases) and high grade (Gleason score 8 cases) to discover methylated genes/loci that may be involved in the progression to a higher grade of prostate cancer.

overall_design: We collected 20 specimens consisting of 10 Gleason 6 and 10 Gleason 8 prostate cancers, and compared these to a reference lymphocyte pool (6 age matched, healthy men) to determine cancer associated methylation changes as well as disease progression associated methylation changes. We performed the differential methylation hybridization procedure as described by Yan et al. (Methods, 2002) on each case to enrich for methylated DNA. Each specimen in the reference pool underwent the same enrichment with amplicons being pooled at the end of the procedure. Each prostate cancer case was subsequently co-hybridized to the microarray with the reference pool.

first: Vaijayanti

last: Pethe

first: Laurent

last: Briollais

first: Bekim

last: Sadikovic

first: Hilmi

last: Ozcelik

first: Alia

last: Sunderji

first: Vasundara

last: Venkateswaran

first: Jehonathan

last: Pinthus

first: Neil

last: Fleshner

first: Theodorus

last: van der Kwast

first: Bharati

last: Bapat


title: Expression data from porcine hepatic tissue of males and females fed with two feeding levels

status: Public on Jul 24 2009

city: Madrid

first: Ana

middle: I

last: Fernandez

address: Ctra. Coruña Km 7.5

department: Mejora Genética Animal

institute: INIA

summary: Liver plays major roles in vital functions including responses to energy deprivation. It is known that body composition and fuel metabolism differs between genders. However there are many unclear aspects related to metabolic pathways affected by feeding level and gender, which could be addressed by transcriptome analyses. To date, no published study in porcine liver has investigated the effects of both gender and feeding level on global gene expression level.We performed a gene expression analysis, using microarrays, in hepatic samples of pigs of the obese Iberian breed to analyze feeding level and gender effects. Results showed that feeding level leads to small expression differences, while gender leads to larger ones. Biological interpretation of the differentially expressed genes conditional on feeding level showed an overrepresentation of genes implicated in general metabolic processes, responses to stimulus and stress, oxidoreductase activity, calcium ion binding and lipid, organic acid and carbohydrate metabolisms. We validated the expression difference of PHYHD1 by qRT-PCR; however we could not validate the expression differences of other relevant genes. Curiously, validation of PGK1, considered reference gene, confirmed expression differences conditional on feeding level and gender. The annotation of the differentially expressed probes for gender effect allowed to observe sex-chromosome enrichment and dosage compensation phenomena in liver. Biological interpretation showed overrepresentation of genes related with oxidoreductase and transferase activities, lipid, organic acid, carbohydrate and steroid metabolisms and genes related with metabolites generation and energy and electron transport. Aside from 13 consistently across tissue differentially expressed genes between gender, gender hepatic expression dimorphism of key genes involved in lipid, carbohydrate and protein metabolisms and antioxidant capacity were also detected. A deeper qRT-PCR analysis showed a downregulation in entire males of all major genes implicated in hepatic degradation processes of androstenone and skatole. We have identified changes in hepatic gene expression conditional on feeding and gender. Reduction of around 25% in feeding level do not lead to great differences but gender effect leads not only to a larger number of differentially expressed probes, but much larger expression differences. Validation of microarray results is needed mainly for small expression differences.

overall_design: Eight liver samples from eight animals at slaughter, 211 days old, four males and four females, four under high feeding level and four under 25% restriction.

last: Fernández

first: Cristina

last: Óvilo

first: Almudena

first: Amanda

last: Fernández-Rodríguez

first: Dafne

last: Pérez-Montarelo

first: Carmen

last: Barragán

first: Clemente

last: López-Bote

first: Miguel

middle: A

last: Toro

first: MCarmen

last: Rodríguez

first: Luis

last: Silió


title: Illumina HapMap CEU (Human610-Quadv1)

last: Illumina Inc.

summary: HapMap samples

overall_design: 73 samples from Human610-Quadv1_CEU_Final_Call_Report.csv


title: Porcine placenta, Erhualian pigs and Large White pigs, gestation day 75 and 90

status: Public on Jun 20 2009

city: Wuhan

first: Shuhong

last: Zhao

address: Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

summary: From gestation day 75 to gestation day 90, an important stage for the placental and fetal development, the fetuses grow rapidly and need adequate nutrition. The Meishan pigs and the Large White pigs employ different ways in supplying the enough nutrients and oxygen to the fetus. The Meishan pigs increased the vascular density and the Large White pigs have the second increase in the surface of placenta. To understand the molecular basis related to late gestation placenta development in Chinese indigenous and Western breeds with different placental efficiency, samples were collected and used to hybridized. The results offered new data on understanding the molecular basis of placenta efficiency, and indicated that Erhualian pigs had the more  efficient than the Large White pigs.

overall_design: Placenta efficiency (the body weight of a piglet divided by the mass of its placenta) of Erhualian pigs is markedly higher than Large White pigs. so placenta samples (female) from 6 Erhuanlian pregnant gilts at gestation day 75 (E75) and day 90 (E90) and 6 Large White pregnant gilts at gestation day 75 (L75) and day 90 (L90) were collected. RNAs from two female piglet placentas from each gilt were combined to 12 pools and hybridized to the porcine Affymetrix GeneChip.

first: Quan-Yong

last: Zhou

first: Shu-Hong


title: Illumina HapMap CHB and JPT (Human610-Quadv1)

summary: HapMap samples

overall_design: 75 samples from Human610-Quadv1_CHB+JPT_Final_Call_Report.csv


title: The Impact of Environment on Microbial Diversity and Global Transcriptional Responses in the Developing Pig Gut

status: Public on Dec 01 2009

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

country: United Kingdom

institute: University of Aberdeen

summary: The study investigated the impact of environment on the composition of the gut microbiota and mucosal immune development and function at gut surfaces in early and adult life. Piglets of similar genotype were reared in indoor and outdoor environments and in an experimental isolator facility. Mucosa-adherent microbial diversity in the pig ileum was characterized by sequence analysis of 16S rRNA gene libraries. Host-specific gene responses in gut ileal tissues to differences in microbial composition were investigated using Affymetrix microarray technology and Real-time PCR.

overall_design: Animals were reared on the sow at an outdoor or indoor facility. Additional piglets from the indoor facility were transferred to individual isolator units at 24 hours of age, and given a daily dose of antibiotic cocktail for the duration of the study. Piglets were weaned at day 28. From day 29 onwards, piglets were fed creep feed ad libitum. Ileal tissue samples were excised from N=6 piglets per group at day 5, 28 and 56.

first: Imke

last: Mulder


title: Induced Pluripotent Stem Cells from the Pig Somatic Cells

status: Public on Jul 10 2009

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

summary: We have derived induced porcine pluripotent stem cells (iPPSCs) from porcine fetal fibroblasts by  lentiviral transduction of four human (h) reprogramming genes, hOCT4, hSOX2, hKLF4 and hc-MYC , the same combination of factors used for deriving induced pluripotent stem cell (iPSC) lines in both mouse and human. The obtained iPPSC lines resemble human embryonic stem cells (ESC) in their gross morphology and dependence on FGF2, on the other hand, the iPPSCs share characteristics like growth rate and cell surface markers with mESC . Additionally, the iPPSCs express pluripotency- associated genes similar to mouse and human iPSCs as well as ESC, along with the pig epiblast cells. Some of the iPPSC lines retained a stable karyotype and phenotype even in culture for a prolonged period of time (passage 39). The iPPSCs can be induced to differentiate along lineages representative of the three embryonic germ layers both in vitro and in vivo  demonstrating the pluripotency of these cells.

overall_design: The open reading frames of the human (h) SOX2, hKLF4, and hc-MYC have been cloned into the BamHI and EcoRI sites of the lentiviral vector, FUGW and the hOCT4 cDNA into the pSIN18.cPPT.hEF1a.EGFP.WPRE vector at its BamHI and SalI sites. Pseudovirus was produced in human 293FT cells (Invitrogen) by transfection with each lentiviral vector (FUGW or pSIN18) along with VSV-G envelope vector (pMD2.G) and packaging vector (psPAX2) by using Lipofectamine-Plus reagents (Invitrogen). The target cells were porcine fibroblasts expressing enhanced green fluorescent protein (EGFP-PFF) derived at day 34 of pregnancy. Titered virus was used to infect the target cells (1 x 10^5 /35mm dish). On the second day following infection (day 2), the cells were dispersed with trypsin and transferred to 10 cm plates preseeded with irradiated mouse embryonic fibroblasts (MEF), and after day 3 the cells were maintained on a culture medium standardized for human ESC containing 4 ng/ml human FGF2.

first: Bhanu-Prakash

middle: V

last: Telugu

first: Shrikesh

last: Sachdev

last: Roberts


title: Ischemia reperfusion injury (IRI) in organ transplantation and the effects of carbon monoxide treatment

status: Public on Jan 20 2009

city: Vienna

first: Florian

middle: Leopold

last: Klinglmueller

address: Spitalgasse 23

department: Medizinische Statistik und Informatik

country: Austria

institute: Medizinische Universitaet Wien

summary:
Ischemia reperfusion injury (IRI) in organ transplantation remains a significant problem with limited alternative therapeutic options. Organs that undergo significant damage during IRI, particularly those enduring long warm ischemia times, undergo significant delayed graft function (DGF) after reperfusion and tend to have greater complications long term with the onset of chronic rejection. The gas molecule carbon monoxide (CO) has emerged as an agent that can suppress IRI in rodent models of solid organ transplantation. Since the use of CO is a potential therapeutic modality in humans, we tested if CO can prevent DGF in a pig model of kidney transplantation

Keywords: stress response, treatment response

overall_design: 18 Samples from pig kidneys, two naïve controls, two timepoints, two conditions, 4 replicates

first: Leo

last: Otterbein

first: Martin

last: Bilban


title: Functional Modeling of Pressure Induced Gene Expression Reveals Mechanosensitive Signaling Pathways

status: Public on Mar 14 2009

city: STARKVILLE

first: CAROL

middle: ANDREA

last: PREGONERO

state: MS

address: 130 Creelman Street

department: AG & BIO ENGINEERING

institute: MISSISSIPPI STATE UNIVERSITY

summary:
Multiple molecular and cellular mechanisms are associated with the initiation and progression of aortic valve disease. Alterations in ECM remodeling, increased expression of pro-inflammatory cytokines, calcification, lipid deposition and changes in valve cell phenotype have demonstrated roles in development of aortic valve disease. Mechanical stimulation has a significant role in determining the physiological properties of valve tissue and an altered hemodynamic environment may result in pathological changes.
We used microarrays to detail the global  of gene expression profiles underlying valve remodeling during valve exposure to of two levels of cyclic mechanical pressure (normotensive 0-80mmHg and hypertensive 0-120mmHg ) on porcine valve tissue transcriptome using Sus Scrofa cDNA  microarrays from Affymetrix and we identified distinct classes of up-regulated genes during this process. Hybridizations were carried out with RNA isolated from six independetn samples of valve tissue exposed to normotensive and hypertensive pressure for 24 hours at 1hz frecuency.    Differentially expressed genes were identified by The t test with the option of unequal variance was used to calculate P values for each gene. The fold change and Q values for each gene were calculated with SAM program with permutation of 500 . Biological modeling of the differentially expressed genes (DE) was carried out based on GO groups and network analysis in ingenuity Pathway Analysis (IPA).

Keywords: Response of valve leaflets to hypertensive pressure

overall_design: The experimental design included three biological samples of porcine valve leaflets  exposed to cyclic pressures of 0-80 or 0-120 mmHg for 24 hours, representing normotensive and hypertensive diastolic transvalvular pressure, respectively. Using Affymetrix porcine microarrays, we compared global gene expression profiles of aortic valve leaflets exposed to elevated and normal physiological pressure conditions . The effects of cyclic pressure on the transcriptome was determined by comparing the quantity and magnitud of change in gene expression levels of valve leflets, as well evaluating  the molecular function each gene  has in the cell,in the presence of  hypertennsive (experimental) and normotensve pressurec (control).

first: Carol

last: Pregonero

first: Juliet

last: Tang

first: James

last: Warnock

first: Shane

last: Burgess

first: Fiona

last: McCarthy

first: Bindu

last: Nanduri

first: Huaijun


title: Porcine spleen_Haemophilus Parasuis infected_7days

status: Public on Mar 26 2009

first: Shuhong

last: Zhao

summary: Haemophilus parasuis(HPS) is a prominent swine pathogen that causes Glässer's disease characterized by fibrinous polyserositis, meningitis and arthritis; however, the molecular mechanisms underlying disease pathogenesis remains poorly understood, particularly the host counteraction to HPS invasion by the immune system. Here, we  investigated the global expression changes in spleen following HPS infection using the Affymetrix Porcine Genechip.Our findings indicate  previously unrecognized gene transcription changes in case of HPS infection in vivo and many presumed cascades in the study are clearly merit further investigation. Our data should provide new clues for immune response in mammals and identification of candidate genes related to HPS resistance.

overall_design: All animal tissue collection procedures were performed according to  protocols approved by The Hubei Province, PR China for Biological Studies Animal Care and Use Committee. Piglets at 30 days old were determined to be HPS-free by serum indirect haemagglutination test before artificial bacterial challenges. Each piglet was intratracheally challenged with 5×108 colony-forming units (CFU) per millilitre of HPS strain 0165 (serotype 5) . A total of 5 piglets were challenged, and 5  pigs were used as controls. These two groups were raised in isolated facilities. Six microarrays were used in the experiment, corresponding to the RNAs from spleen tissues of three most severe piglets with fibrinous polyserositis, meningitis and arthritis after HPS infection and three controls.

first: Hongbo

last: Chen

first: Changchun

last: Li

first: Mingdi

last: Fang

first: Mengjin

last: Zhu

first: Xinyun

first: Rui

last: Zhou

first: Kui


title: MPA and NQO studies (Sevilla)

status: Public on Dec 30 2008

city: Cerdanyola

first: Antonio

last: Casamayor

address: Edifici IBB, Campus UAB

institute: Universitat Autonoma de Barcelona

summary: RNA polymerases deal with obstacles during transcription elongation that need to be removed. One important type of hindrance consists of DNA lesions, which are removed by transcription-coupled repair (TCR). To improve our knowledge of transcription elongation and its coupling to TCR, we performed DNA microarray experiments and used the yeast library of nonessential knock-out mutations to screen for genes conferring resistance to the transcription-elongation inhibitor micophenolic acid and the DNA-damaging agent 4- nitroquinoline-N-oxide.

overall_design: A single sample for each treatment was analyzed.

first: Laia

last: Viladevall

first: Anna

last: Barceló

first: Joaquin

last: Ariño

first: Andres

last: Aguilera


title: Impact of breed and sex on porcine endocrine transcriptome: A Bayesian biometrical analysis

status: Public on Feb 12 2009

city: Bellaterra

first: Miguel

last: Perez-Enciso

address: Veterinary School

institute: Universitat Autonoma Barcelona

summary:
Background: Transcriptome variability is due to genetic and environmental causes, much like any other complex phenotype. Ascertaining the transcriptome differences between individuals is an important step to understand how selection and genetic drift may affect gene expression. To that end, extant divergent livestock breeds offer an ideal genetic material.

Results: We have analyzed with microarrays five tissues from the endocrine axis (hypothalamus, adenohypophysis, thyroid gland, gonads and fat tissue) of 16 pigs from both sexes pertaining to four extreme breeds (Duroc, Large White, Iberian and a cross with SinoEuropean hybrid line). Using a Bayesian linear model approach, we observed that the largest breed variability corresponded to the male gonads, and was larger than at the remaining tissues, including ovaries. Measurement of sex hormones in peripheral blood at slaughter did not detect any breed-related differences. Not unexpectedly, the gonads were the tissue with the largest number of sex biased genes. There was a strong correlation between sex and breed bias expression, although the most breed biased genes were not the most sex biased genes. A combined analysis of connectivity and differential expression suggested three biological processes as being primarily different between breeds: spermatogenesis, muscle differentiation and several metabolic processes.

Conclusion: These results suggest that differences across breeds in gene expression of the male gonads are larger than in other endocrine tissues in the pig. Nevertheless, the strong presence of breed biased genes in the male gonads cannot be explained solely by changes in spermatogenesis nor by differences in the reproductive tract development.

overall_design:
Sixteen animals, four from each of four breeds, Large White (LW), Duroc (DU), Youli (YL) and Iberian (IB) piglets were sampled. These breeds represent a wide genetic variability in current pig breeding schemes. There were two males and two females per breed except in Youli, represented by three males and one female. Animals were bought from three breeding companies and transferred to the University experimental farms at weaning, i.e., aged one month approximately. Pigs were housed simultaneously, fed the same diets during the fattening period, that lasted two months, and were weighed at weekly intervals. At the time of slaughter, the average ages were 87, 83, 80 and 89 days for Large White, Duroc, Youli and Iberian pigs, respectively. Their mean live weights at that time were 27.2 (LW), 23.1 (DU), 18.9 (YL) and 17.4 kg (IB).

Animals were euthanized, after 24h fasting, by an overdose of intravenous sodium thiobarbital. At necropsy, tissue samples were collected, snap frozen in liquid nitrogen and stored at -80 ºC. The average time gap between euthanasia and tissue collection was ~ 15 minutes, maximum time was 25 minutes. The tissues collected were hypothalamus (HYPO), adenohypophysis (AHYP), which was separated from the neurohypophysis, thyroid gland (THYG), gonads (GONA) from both sexes, and back fat tissue (FATB). The hypothalamus included the mamillary body and grey tubercle but excluded the chiasma opticum. Throughout this work, each sample was identified by the acronym of the tissue followed by the animal id, e.g., FATBLWF1 refers to back fat tissue from female 1 Large White.

last: Pérez-Enciso

first: Andre

middle: L

last: Ferraz

first: Ana

last: Ojeda

first: Manel

last: López-Béjar


title: Gene Expression and Comparative Genomic Hybridization of Ductal Carcinoma In Situ of the Breast

status: Public on Nov 24 2008

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

type:
Expression profiling by array
Genome variation profiling by array

summary:
Background
The dramatic increase in incidence of ductal carcinoma in situ (DCIS) associated with mammographic screening for breast cancer has given emphasis to the challenges of managing this important clinical entity. Unlike invasive breast cancer, there is no established histopathologic grading system for DCIS, nor are there biological markers of prognosis to guide clinical management. The aim of this study is to use molecular profiling to identify robust and clinically applicable indicators of DCIS malignant potential.
Methods
Areas of intraduct carcinoma, atypical ductal hyperplasia and benign epithelium were isolated from 46 well-characterised invasive breast cancers by laser capture microdissection. Microarray based gene expression profiling was used to identify genes differentially expressed between DCIS associated with grade 1 and grade 3 invasive carcinoma (‘grade associated genes’). The expression profile of these genes was then determined in all samples and used to define ‘molecular grade’ categories. The genomic basis of gene expression derived categories was examined by array-based comparative genomic hybridisation (CGH).
Results
DCIS samples could be divided into two subgroups, designated low and high molecular grade (MG) on the basis of expression at 173 grade associated oligonucleotide probes. The low MG subgroup included 21 DCIS samples of low (n=10) and intermediate (n=11) nuclear grade as well as all samples of ADH (n=4) and benign epithelium (n=7). The high MG subgroup included 27 DCIS samples of intermediate (n=7) and high (n=19) nuclear grade. Array CGH revealed distinct differences in the character and degree of genomic aberration associated with MG and  the clinical significance of MG was verified by a strong correlation with survival in two independent invasive breast cancer gene expression datasets (n=295 and n=186).  MG categories were strongly associated with histopathologic and biomarker features of DCIS. Using a classification tree model, DCIS MG could be accurately predicted in 44/46 (95.7%) of samples using a combination of nuclear grade and Ki67 score.
Conclusions
Molecular profiling indicates a binary grading scheme for DCIS that is both biologically relevant and clinically informative. The low and high MG DCIS classification could be recapitulated by a novel combination of routinely accessible features. This practical approach has potential to immediately improve clinical evaluation and management of DCIS.
Keywords: Paired gene expression and CGH

overall_design: Paired CGH and Gene Expression on DCIS of the breast

first: Lucy

last: Webster

first: Rosemary

last: Balleine

first: Elizabeth

last: Salisbury

first: Robert

last: Walker

first: Karen

last: Byth

first: Christine

last: Clarke

first: Paul

middle: S

last: Meltzer


title: Gene expression data from Muscle Longissimus dorsi sample of F2 animals, T-test paired and SAM

status: Public on Jan 01 2009

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary:
To identify biological processes as well as molecular markers for drip loss, the transcriptomes of logissimus dorsi from 6 sib pair of F2 animals
Keywords: T-test paired and SAM

overall_design: 12 F2 animals of a resource population based on the breeds Duroc and Pietrain known to differ in meat quality and quantity traits were hybridized to Affymetrix Porcine Genome Arrays

first: Siriluck

last: Ponsuksili


title: Transcript profiling in Arabidopsis gollum mutant: Role of the Gollum gene in the plant development

status: Public on Nov 01 2008

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

summary:
rs07-08_gollum - trancript profiling in arabidopsis gollum mutant. Elucidate the role of Gollum gene in the plant development by a RNAi approach. Seeds of WT and RNAi lines were sowed on soil and conserved 2 days at 4°C. The pots were transferred to the greenhouse under long-day conditions (16h light, 22°C). The leaves of one-month old plants were harvested and total RNA were extracted.
Keywords: wt vs mutant comparison

overall_design: 3 dye-swap - wt vs mutant comparison

first: Pascal

last: Ratet

first: Samuel

last: Mondy

first: Ludivine

last: Taconnat

first: Jean-Pierre

last: Renou

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Gene expression data from Muscle Longissimus dorsi sample of F2 animals

summary:
In this study, we used correlation analysis of the expression profiles and drip loss to produce a list of functional candidate genes under the assumption that genes with strong correlation between their expression values and drip belong to pathways or networks relevant for the control of the trait.
Expression QTL analyses for transcripts showing trait dependent expression were done in order to identify genes which show trait associated expression, map to pQTL regions, and exhibit cis regulation.
Keywords: Corrrelation and association

overall_design: 74 F2 animals of a resource population based on the breeds Duroc and Pietrain known to differ in meat quality and quantity traits were hybridized to Affymetrix Porcine Genome Arrays.


title: Transcriptional profiling of Rapamycin treatment in yeast cells lacking the Ptc1 protein phosphatase.

status: Public on Dec 31 2008

first: Antonio

last: Casamayor

summary: We are interested in the study of the already reported sensitivity of yeast cells lacking the type 1 protein phosphatase Ptc1 to the drug rapamycin. In order to carry out our studies, we analyzed the changes in the transcription profile that a short-term incubation with rapamycin (200 ng/mL) has in both, wild type and ptc1 cells. It has been shown that inhibition of the TOR pathway by treatment with rapamycin has profound effects on the global transcriptional profile. We confirmed the previously described transcription changes induced by the drug in wild type cells. Under our working conditions rapamycin increased, in wild type cells, at least 2-fold the expression of 667 genes, whereas it decreased the mRNA level of 721 genes (13.8% and 14.9% of genes with measurable expression level, respectively). Gene ontology analysis shows that, as previously documented, many induced genes falls into the NCR, Msn2/Msn4 regulated stress response or Retrograde response categories, whereas genes encoding cytoplasmic, but not mitochondrial, ribosomal proteins and the so called RIBI regulon where largely repressed. Deletion of PTC1 decreases the number of genes induced or repressed at least 2-fold by rapamycin treatment. Remarkably, lack of Ptc1 seems to lead to a general attenuation of changes triggered by rapamycin.

overall_design:
The wt and the ptc1 mutant strains were analyzed in this series.
We compared the expression profile of each strain treated with Rapamycin (200 ng/ml for 1h) with that of the same strain mock-treated (90% ethanol, 10% Tween-20).
A Dye-swap was carried out for each RNA sample.
Total number of chips analyzed: 4

first: Asier

last: Gonzalez

first: Amparo

last: Ruiz

first: Joaquin

last: Arino


title: Comparison of corneal and conjunctival keratinocyte clones

status: Public on Aug 29 2008

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

summary:
Integrity of the cornea, the most anterior part of the eye is indispensable for vision. 45 million individuals are bilaterally blind and another 135 millions have severely impaired vision in both eyes because of loss of corneal transparency; treatments range from local medications to corneal transplants and more recently to stem cell therapy. The corneal epithelium is a squamous epithelium that is constantly renewing with a vertical turnover of seven to fourteen days in many mammals3. Identification of slow cycling cells (label-retaining cells or LRCs) in the limbus of the mouse has led to the notion that the limbus is the niche for the stem cells responsible for the long-term renewal of the cornea4; hence, the corneal epithelium is supposedly renewed by cells generated at and migrating from the limbus, in striking opposition to other squamous epithelia in which each resident stem cell has in charge a limited area of epithelium. Here, we show that the corneal epithelium of the mouse can be serially transplanted, is self-maintained and contains oligopotent stem cells with the capacity to generate goblet cells if provided with a conjunctival environment. In addition, the entire ocular surface of the pig, including the cornea, contains oligopotent stem cells (holoclones) with the capacity to generate individual colonies of corneal and conjunctival cells; hence, the limbus is not the only niche for corneal stem cells and corneal renewal is not different from other squamous epithelia.

Keywords: Cell type comparison

overall_design: Expression profile difference between keratinocyte clones from conjunctiva and cornea (3 individual clones in each group)

first: Michael

last: Nicolas

first: Ariane

last: Rochat

first: Yann

last: Barrandon

first: Otto

last: Hagenbüchle


title: KNP_vs_YS_Fat

status: Public on Oct 15 2008

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

institute: Korea University

summary:
Anim Genet. 2009 Feb;40(1):115-8. Epub 2008 Oct 17.

Differentially expressed transcripts in adipose tissue between Korean native pig and Yorkshire breeds.

Moon JK, Kim KS, Kim JJ, Choi BH, Cho BW, Kim TH, Lee CK.

Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, South Korea.

We measured and compared the transcripts of adipose tissue from Korean native pig (KNP) and Yorkshire (YS) breeds to investigate breed-specific transcription changes. We employed both the Affymetrix porcine genome array and quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We found eight genes showing significant changes between the two breeds. Based on a literature review, these genes were indicative of differences in extracellular structure density and differences in the potential to metabolize xenobiotic chemicals and lipids. The differentially expressed genes indicated that KNP has a lower extracellular structure density and a lower potential to metabolize xenobiotic chemicals than YS.

PMID: 18945290

overall_design:
Gene expression comparison between KNP and YS pigs grown at identical conditions.
Sample size: n=4 (total n=8)
Adipose tissue: backfat in the middle of pig.
Age: KNP (7 month-old), YS (6 month-old)

first: Jin-Kyoo

last: Moon


title: Gene expression profiles of fasting induced changes in liver and fat tissues of pigs expressing the MC4R D298N variant

status: Public on Apr 20 2009

city: Ames

first: Sender

last: Lkhagvadorj

address: 2255 Kildee

department: Animal Science

institute: Iowa State University

summary: Transcriptional profiling coupled with blood metabolite analyses were used to identify porcine genes and pathways that respond to a fasting treatment or to a D298N missense mutation in the melanocortin-4 receptor (MC4R) gene. Gilts (12 homozygous for D298 and 12 homozygous for N298) were either fed ad libitum or fasted for 3 days. Fasting decreased body weight and backfat and increased serum concentrations of non-esterified fatty acid and urea. In response to fasting, 7,029 genes in fat and 1,831 genes in liver were differentially expressed (DE, q value less than 0.05). MC4R genotype did not affect gene expression, body weight, backfat depth, and any measured serum metabolite concentration. Pathway analyses of fasting-induced DE genes indicated that both liver and fat down-regulated energetically costly processes such as lipid and steroid synthesis and up-regulated efficient energy utilization pathways. Fasting increased expression of genes in involved in glucose sparing pathways in liver and extracellular matrix pathways in adipose tissue. Within the DE genes, transcription factors (TF) that regulate many DE genes were identified, confirming the involvement of TF that are known to regulate fasting response and implicating additional TF that are not known to be involved in energy homeostatic responses. Interestingly, estrogen receptor 1 transcriptionally controls fasting induced genes in fat that are involved in cell matrix morphogenesis. Our findings indicate a transcriptional response to fasting in two key metabolic tissues of pigs that was corroborated by changes in blood metabolites; and involvement of novel putative transcriptional regulators in the immediate adaptive response to fasting.

overall_design: Gilts (n=24; 12 wildtype and 12 homozygous for D298N) were either fed ad libitum or fasted for 3 days in a completely randomized complete block design with a 2x2 factorial treatment structure.

first: Christopher

last: Tuggle

first: Jack

last: Dekkers

first: Lloyd

last: Anderson

first: Dan

last: Nettleton

first: Long

last: Qu

first: Weiguo

last: Cai

first: Oliver

middle: P

last: Couture


title: Gcn2p regulates a G1/S cell cycle checkpoint in response to DNA damage

status: Public on Oct 22 2007

city: Valencia

first: Jose

middle: Ramón

last: Murguía

state: Valencia

address: Ingeniero fausto Elio

institute: IBMCP

summary:
In Saccharomyces cerevisiae, the Gcn2p kinase controls a gene expression program in response to nutrient deprivation. Upon amino acid deprivation Gcn2p phosphorylates the translation initiation factor 2a subunit (eIF2a). Phosphorylation of eIF2a  transiently inhibits translation initiation, and favours selective translation of the GCN4 transcription factor mRNA. High levels of Gcn4p then activate the expression of genes encoding amino acid biosynthesis pathways. Besides nutrient deprivation, Gcn2p can also be activated by other stresses such as DNA damage. Previous studies in our lab suggested that Gcn2p regulated other cellular pathways apart from translation initiation. To gain insights into these new regulatory roles of Gcn2p, we generated a strain called (GCN2c) expressing a constitutively active Gcn2p kinase mutant. In the GCN2c strain, phosphorylation of eIF2a and translation of a GCN4-lacz reporter was constitutively high in the absence of amino acid starvation. We investigated the transcriptional profile of the GCN2c mutant strain by cDNA microarrays. As expected, numerous amino acid biosynthetic genes were upregulated, being dependent of Gcn4p. Most interestingly, expression of genes encoding proteins involved in DNA replication/repair was decreased, suggesting that Gcn2p could regulate cell cycle progression from G1 to S phase. Accordingly, the Gcn2c strain exhibited, i) slow growth, ii) a delayed entry into S phase, and iii) hypersensitivity to hydroxyurea. In addition, MMS treatment induced a G1 checkpoint and a growth defect which was dependent on Gcn2p and Gcn3p. Considering that MMS delays cell cycle progression by generating DNA lesions, the findings suggest that DNA damage induces a G1/S checkpoint by a novel pathway involving the protein kinase Gcn2p.
Keywords: mutant analysis

overall_design: Four biological replicates were used to assess diferentially expression between wilt type yeast strain and GCN2c overexpressing strain. Differentially expressed genes were identified using one-class significant analysis of microarrays (SAM; Tusher et al, 2004)

first: Mauricio

last: Menacho-Marquez

first: Jorge

last: Pérez

first: Joaquín

last: Ariño

first: José

last: Gadea

middle: R


title: Genome-wide expression profiling of the cryptolepine-induced toxicity in Saccharomyces cerevisiae

status: Public on Aug 08 2008

city: Barcelona

first: Benjamin

last: Pina

address: Jordi Girona, 18

institute: IDAEA-CSIC

summary: We have used the budding yeast Saccharomyces cerevisiae to identify genes that may confer sensitivity in vivo to the antimalarial and cytotoxic agent cryptolepine. To this end, five S. cerevisiae strains, which differ in the condition of genes related to cell membrane integrity and to DNA damage repair, were exposed to several concentrations of cryptolepine. Results showed a relatively mild toxicity of cryptolepine for wild type strains, which increased by either increasing cell permeability (∆erg6 or ISE2 strains) or disrupting DNA damage repair (∆rad52 strains). These results are compatible with the ability of cryptolepine to intercalate into DNA and therefore, promote DNA lesions. The effects of low concentrations of cryptolepine (IC20 and IC40) were then analysed by comparison between gene expression profiles of treated and untreated ∆erg6 yeast cells. Significant changes in expression levels were observed for 349 genes (117 up-regulated and 232 down-regulated). General stress-related genes constituted the only recognizable functional cluster whose expression was increased upon cryptolepine treatment, making up about 20% of up-regulated genes.  In contrast, analysis of characteristics of down-regulated genes revealed a specific effect of cryptolepine on genes related to iron-transport or acid phosphatases, as well as a significant proportion of cell wall components. In particular, the effects of cryptolepine treatment on transcription of iron transport-related genes were compatible with of a loss-of-function of the iron sensor Aft1p, indicating a possible disruption of the iron metabolism is S. cerevisiae. As iron metabolism is one of the putative antimalarial effects of cryptolepine, this finding exemplarises the utility of S. cerevisiae in drug-developing schemes. These results are analyzed in the context of the known cryptolepine activities as antimalarial and cytotoxic drug.

overall_design: Eight sets of microarray data were produced, corresponding to treatments with two different cryptolepine concentration (7.5 and 17µM, equivalent to IC20 and IC40), each performed by duplicated, and  each RNA preparation labeled and hybridized twice, swapping dyes between treated and untreated samples. Data is presented as treated to untreated fluorescence ratios.

first: Marta

last: Rojas

first: Colin

last: Wright

last: Portugal


title: Differential gene expression during porcine conceptus trophoblastic elongation and attachment to the uterine epithelium

status: Public on Sep 10 2008

first: Jason

last: Ross

address: 2356E Kildee Hall

summary: The objective of the present investigation was to utilize the GeneChip® Porcine Genome Array from Affymetrix possessing 20, 201 unique probe sets to identify differentially expressed genes during rapid trophoblastic elongation and attachment to the uterine surface in the pig.  Identification and characterization of conceptus gene expression patterns during rapid trophoblastic elongation and attachment in the pig will provide a better understanding of the events required for successful implantation and embryonic survival.

overall_design: Four chips were used for each morphological stage of development (spherical, tubular, Day 12 filamentous and Day 14 filamentous).  RNA utilized for each chip represented a unique pool of conceptus total RNA for the respective morphological stage of development.  Prior to target labeling, RNA was further purified (RNeasy MinElute Cleanup, Qiagen, Valencia, CA).  Target labeling, GeneChip® hybridization, scanning and quantification were conducted by The University of Tulsa Microarray Core Facility.   Affymetrix GeneChip Operating Software (GCOS version 1.1.1, Affymetrix, Santa Clara, CA) was used to quantitate each GeneChip®.  The summary intensities for each probe were loaded into DNA-Chip Analyzer (dChip), version 1.3 for normalization, standardization, and analysis.

first: Morgan

middle: D

last: Ashworth

first: Daniel

last: Stein

first: Rodney

last: Geisert


title: Contribution of germline to sex-biased expression in Drosophila melanogaster

status: Public on May 01 2008

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary:
The effect of germline tissue on somatic sex-biased expression is examined.  Expression is assayed in various adult tissues with germline ablated directly or genetically. The effect of germline signalling on sex-biased expression in the Drosophila head is also examined.
Keywords: Expression profiling

overall_design: Two-color microarray experiments in a loop design are used.  Additional descriptive information is available at Parisi et.al (2004) Genome Biol. 2004;5(6):R40. PMID: 15186491

first: Michael

last: Parisi


title: Stress-related gene expression of HK-2 cells exposed to GF/FAF HSA, GF HSA, AngII or AngII+Cand

status: Public on Feb 28 2008

city: Liverpool

first: Rana

last: Rustom

address: Duncan Street

department: Metabolic and Cellular Medicine

institute: University of Liverpool

summary:
Proteinuria is pathogenic to proximal tubular cells (PTC) and linked with progression to renal failure. Angiotensin II (AngII) is also independently involved in the pathogenesis of progressive renal injury in varied kidney disease. The effects of human serum albumin (HSA) overload, AngII and candesartan, a specific inhibitor of AngII type 1 recptor, on the changes in gene protein expression stimulated by oxidative stress in PTC were assesed using cDNA microarrays.
Keywords: stress response

overall_design: Cells were growth arrested for 48 h in serum-free DMEM/Ham's F-12 medium with 5.5 mM glucose, 2 mM L-glutamine,100 U/ml penicillin, 100 ug/ml streptomycin, 20 mM Hepes. Media were refreshed and cells were incubated for 24h in conditioned media alone, or with media supplemented with 30mg/ml of different HSA preparations, 1 uM AngII or AngII in the presence of candesartan. After further 24 h under standard cell culture conditions (37C, 5% CO2) cells were subjected to RNA extraction.

first: Liliana

last: Shalamanova

first: Frank

last: McArdle

first: Malcolm

middle: J

last: Jackson


title: IPEC-J2 cells treated with cholera toxin for 8h

status: Public on Apr 01 2008

city: St. Paul

first: Cheryl

last: Dvorak

address: 1971 Commonwealth Avenue

department: Veterinary and Biomedical Sciences

institute: University of Minnesota

summary:
The molecular mechanisms involved in host pathogen interactions at mucosal surfaces needs to be better understood in order to develop immune-mediated methods of protection against pathogens. Cholera toxin (CT) has the rare ability for a protein of inducing robust mucosal immunity in the gut and is therefore an excellent model with which to determine mechanisms of adjuvanticity and immunogenicity at intestinal mucosal surfaces. Jejunal epithelial cells are one of the first sites of antigen encounter. Therefore a porcine intestinal epithelial cell line, IPEC-J2, was cultured in 6-well transwell plates in the presence or absence of 50 ng/ml cholera toxin for up to 8 hours and the cell layer was harvested for gene expression analysis using the Affymetrix porcine genome array and real-time PCR analysis. Affymetrix analysis identified, and real-time PCR analysis of 15 genes confirmed, an increase in gene expression for 59 genes and a decrease in gene expression for 14 genes under CT treatment. An 8 hour time course of expression revealed that by 2-4 hours after CT treatment, all 10 upregulated genes were differentially expressed and by 4-6 hours after CT treatment 3 of the 5 downregulated genes were differentially expressed. These data suggest that the potent mucosal adjuvanticity and immunogenicity of CT derives from rapid alterations in gene expression at the site of first antigen encounter with the immune system. Characterization of early immune gene expression may elucidate potential biological mechanisms for mucosal immune induction leading to the development of effective vaccines against enteric pathogens.
Keywords: Treatment comparison, cholera toxin vs untreated at 8h time point

overall_design: Confluent IPEC-J2 cell monolayers were treated with or without 50 ng/ml cholera toxin in transwell dishes for 8h. The experiment was repeated 3 times for a total of 6 chips, 3 cholera toxin treated and 3 untreated. Gene expression was compared between cholera toxin treated and untreated cells.

middle: M

last: Murtaugh