title: Microarray analysis of changes in gene expression within the amacrine cell layer of chicks following optical defocus

city: Tuebingen

first: Regan

last: Ashby

address: Calwerstrasse 7/1

department: Section of Neurobiology of the Eye

institute: University of Tuebingen

summary: Ocular growth is regulated locally by signals produced in the retina that ultimately act on the growth of the scleral tissue. Consequently, a number of studies have investigated changes in retinal gene expression during manipulation of ocular growth in an attempt to elucidate the biochemical pathways underlying eye growth. However, due to the highly heterogenous nature of the retina, important changes in gene expression can be masked. Therefore, this study has investigated changes in gene expression specifically within the retinal amacrine cell layer, the most likely generator of growth signals, during manipulations of ocular growth.

overall_design: Chicks were monocularly treated with either -7D (n=3, growth stimulant) or +7D (n=3, growth suppressant) lenses for 24hrs, with untreated age-matched chicks serving as a control (n=3). Total RNA from the amacrine cell layer was isolated from laser-capture microdissected (Zeiss, Bernried, Germany) 10µm thick sections. Labeled cRNA was prepared from three separate samples per condition and hybridized to Affymetrix GeneChip Chicken Genome arrays.

first: R

middle: S

first: M

last: Feldkaemper


title: Wild type 2 hour exposure to caspofungin

status: Public on Jun 19 2010

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

summary:
We did transcription profiling on the effect of wsc1 deletion, gene involved in cell wall stress response
Keywords: cell wall stress response

overall_design: S. cerevisiae (BY4741) was grown on YEPD. For caspofungin experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with 15ng/ml of caspofungin. Cells were collected at 2 hours of growth, frozen at -80 °C and processed for RNA extraction. The total RNA from two different cultures was analyzed, and, in addition, for each sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to four DNA microarrays analyzed for each condition.

first: Clara

last: Bermejo

first: Raul

last: Garcia

first: Andrea

last: Straede

first: Jose

middle: M

last: Rodriguez-Peña

first: Cesar

last: Nombela

first: Jürgen

middle: J

last: Heinisch


title: Molecular remodeling of ion channels, exchangers and pumps in atrial and ventricular myocytes in ischemic cardiomyopathy: left ventricle DCM

status: Public on Jun 17 2010

city: Baltimore

first: Nikolai

last: Soldatov

state: MD

address: 5600 Nathan Shock Drive

country: USA

institute: National Institute on Aging, NIH

summary:
We wanted to see whether the set of affected genes in ischemic cardiomyopathy (ICM) is the same or different as compared to dilated cardiomyopathy (DCM). To find this out, we placed the single DCM sample on the same microarray slide with the ICM samples. Analysis of microarray data with ICM samples only showed 63 affected genes, while that carried out with 2 ICM samples PLUS one DCM sample reduced this number to just four genes. From this result we conclude that ICM and DCM affect different sets of genes in ventricular myocytes.

Keywords: Expression profiling by array

overall_design:
From the associated publication:
To find out whether the splice microarray results reported in Table 3 are disease-type specific, we supplemented the same splice microarray of ICM ventricular myocytes with one additional sample prepared from left ventricle of a 41-years old dilated cardiomyopathy male donor. The top-list ANOVA gene score annotation for combined altered CE&P genes in ventricular myocytes (Table 3) was reduced from 63 to just 4 genes (FXYD1 (Gfold = +2.4), HCN2 (-1.5), GLRA1 (-1.8) and GJC1 (-2.3)).


title: Analysis of micorRNA expression during  the HBV acute and chronic infections

city: Hefei

first: Wei

last: Lan

state: Anhui

address: 96#, Jinzhai Road

department: School of Life Science

country: China

institute: University of Science and Technology of China

summary: Recent implication of microRNAs (miRNAs) in the intricate cross-talk between the host and the pathogen in viral infections reveals a new layer of mechanism for host-virus interactions. In the present study, we investigated human miRNAs which may be involved in the acute and chronic HBV infections via microarray profiling. We determined the global miRNA expression profiles elicited in the uninfected control model (HepG2), the acute infection model (HepG2 transfected with a 1.3 full-length HBV genome) and the chronic infection model (HepG2.2.15) using CapitalBio corporation’s mammalian miRNA arrays.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Three cellular models were used in this study: the human hepatoblastoma cell line HepG2 as a blank control representing the condition without virus infection; HepG2 transfected with a 1.3 full-length HBV genome as an acute infection model; and HepG2.2.15, a well-established cell line derived from HepG2 transfected with a full-length HBV genome and constitutively expressing HBV, as a chronic infection model.

first: Zhen-Zhen

last: Zhang

first: Xiang

last: Liu

first: De-Qiang

last: Wang

first: Mai-Kun

last: Teng

first: Li-Wen

last: Niu

first: Zhi

last: Liang

first: Ai-Long

last: Huang


title: Androgen Regulated Genes in Intact Human Prostate Tissues: Relation to Benign Prostatic Hyperplasia and Prostate Cancer

status: Public on Jun 14 2010

city: Nashville

first: Simon

last: Hayward

state: TN

department: Urologic Surgery

institute: Vanderbilt University Medical Center

summary: To investigate gene expression profiling in intact human prostate tissue xenografts in mice, following the addition or subtraction of androgens.

overall_design: 58 prostate samples were implanted into castrated or testosterone-treated mice for 5 different lengths of time. Samples were compared to a control pool created by combining day zero tissue samples from all patients

first: Harold

middle: D

last: Love

first: S

middle: E

last: Booton

first: Braden

last: Boone

first: Joan

middle: P

last: Breyer

first: Tatsuki

last: Koyama

first: Monica

last: Revelo

first: Scott

middle: B

last: Shappell

first: Jeffrey

middle: R

last: Smith

middle: W


title: Physiological and transcriptional response of Lactobacillus casei ATCC 334 to acid stress

status: Public on Jun 16 2010

city: Logan

first: Jeff

last: Broadbent

state: UT

department: NFS

institute: Utah State University

summary:
This study investigated features of the acid tolerance response (ATR) in Lactobacillus casei ATCC 334. To optimize ATR induction, cells were acid adapted for 10 or 20 min at different pH values (range, 3.0 to 5.0) and then acid challenged at pH 2.0. Adaptation over a broad range of pHs improved acid tolerance, but the highest survival was noted in cells acid adapted for 10 or 20 min at pH 4.5. Analysis of cytoplasmic membrane fatty acids (CMFAs) in acid-adapted cells showed that they had significantly (P < 0.05) higher total percentages of saturated and cyclopropane fatty acids than did control cells. Specifically, large increases in the percentages of C(14:0), C(16:1n(9)), C(16:0), and C(19:0(11c)) were noted in the CMFAs of acid-adapted and acid-adapted, acid-challenged cells, while C(18:1n(9)) and C(18:1n(11)) showed the greatest decrease.
Comparison of the transcriptome from control cells (grown at pH 6.0) against that from cells acid adapted for 20 min at pH 4.5 indicated that acid adaption invoked a stringent-type response that was accompanied by other functions which likely helped these cells resist acid damage, including malolactic fermentation and intracellular accumulation of His. Validation of microarray data was provided by experiments that showed that L. casei survival at pH 2.5 was improved at least 100-fold by chemical induction of the stringent response or by the addition of 30 mM malate or 30 mM histidine to the acid challenge medium. To our knowledge, this is the first report that intracellular histidine accumulation may be involved in bacterial acid resistance.

platform_organism:
Lactobacillus helveticus
Lacticaseibacillus paracasei ATCC 334

overall_design: This study includes 5 samples that were analyzed (this includes a control).  Four replicates were done on the full experiment.  The control was cells that received no acid treatment prior to RNA isolation

first: Rebecca

middle: L

last: Larsen

first: Virginia

last: Deibel

first: Jim

last: Steele


title: arrayCGH profiles of endometrial cancer with and without prior prolonged tamoxifen treatment for primary breast cancer

city: Amsterdam

first: Petra

last: Nederlof

address: Plesmanlaan 121

department: Pathology

country: Netherlands

institute: The Netherlands Cancer Institute

summary:
Full title: comparison of the genomic (arrayCGH) profiles of endometrial cancer with and without prior prolonged tamoxifen treatment for primary breast cancer

Purpose: Tamoxifen has been a very effective treatment for breast cancer for several decades, however, at the same time increases the risk of endometrial cancer, especially after prolonged exposure. In addition, tamoxifen has been associated with a higher proportion of unfavorable uterine tumor subtypes (carcinosarcomas and serous adenocarcinomas) with worse survival. We investigated whether endometrial tumors, which developed after prolonged tamoxifen treatment for breast cancer, are genetically different from endometrial tumors without preceding tamoxifen exposure.

Experimental design: Array CGH was used on archival formalin-fixed paraffin embedded (FFPE) endometrial tumors to determine genomic aberrations. We compared the genomic profiles of 52 endometrial tumors from breast cancer patients after long-term (>=2 years) tamoxifen use (endometrioid adenocarcinomas n=26, carcinosarcomas n=14 and serous adenocarcinomas n=12) with endometrial tumors from unexposed breast cancer patients (n=45). Genomic profiles were correlated with tamoxifen exposure, tumor subtypes and histopathological characteristics of the endometrial tumors.

Results: The common uterine corpus cancers of the endometrioid subtype show few genomic aberrations. Tumors with many genomic aberrations were in general ER-negative. In contrast, carcinosarcomas and serous adenocarcinomas showed many aberrations, however they were indistinguishable from each other. Tumors that developed after prolonged tamoxifen use did not show more or different aberrations than unexposed tumors. This was true for all tumor subtypes.

Conclusion: Endometrial carcinomas that develop after prolonged tamoxifen use can not be distinguished from non-users on basis of their tumor genomic profile.

overall_design: 52 endometrial tumors from breast cancer patients after long-term (>=2 years) tamoxifen use (endometrioid adenocarcinomas n=26, carcinosarcomas n=14 and serous adenocarcinomas n=12) and 45 endometrial tumors from unexposed breast cancer patients

first: R

last: Fles

first: W

last: Hoogendoorn

first: P

first: F

last: van Leeuwen

first: H

middle: H

last: van Boven


title: 72hr Toxoplasma gondii bradyzoite induction

status: Public on Jun 15 2010

city: Philadelphia

first: Paul

last: Davis

state: PA

address: 433 S. University Ave.

department: Biology

institute: University of Pennsylvania

summary: Two samples, 0hr and 72hr, were used to generate tachyzoite and bradyzoite transcriptional data from tissue-cultured Toxoplasma gondii strain Prugniaud, respectively.

overall_design: Samples are single replicates, and a subset of a larger timeseries.  Non-control sample was exposed to alkaline conditions, media pH 8.2, for 72hr.

first: Amit

last: Bahl

first: David

last: Roos


title: Subtype classification, grading, and outcome prediction of urothelial carcinomas by combined mRNA profiling and aCGH

city: Lund

last: Lindgren

address: Building 404 A3, Scheelevägen 2, Medicon Village

department: Dept of Laboratory Medicine

country: Sweden

institute: Lund University

type: Genome variation profiling by genome tiling array

summary:
[original title] Combined gene expression and genomic profiling define two intrinsic molecular subtypes of urothelial carcinoma and gene signatures for molecular grading and outcome.

In the present investigation we sought to refine the classification of urothelial carcinoma by combining information on gene expression, genomic, and gene mutation levels. For these purposes we performed gene expression analysis of 144 carcinomas, and whole genome array-CGH analysis and mutation analyses of FGFR3, PIK3CA, KRAS, HRAS, NRAS, TP53, CDKN2A, and TSC1, in 103 of these cases. Hierarchical cluster analysis identified two intrinsic molecular subtypes, MS1 and MS2, which were validated and defined by the same set of genes in three independent bladder cancer data sets. The two subtypes differed with respect to gene expression and mutation profiles, as well as with the level of genomic instability. The data shows that genomic instability was the most distinguishing genomic feature of MS2 tumors, and that this trait was not dependent on TP53/MDM2 alterations. By combining molecular and pathological data it was possible to distinguish two molecular subtypes of Ta and T1 tumors, respectively. In addition, we define gene signatures validated in two independent data sets that classify urothelial carcinoma into low (G1/G2) and high grade (G3) tumors as well as non-muscle and muscle-invasive tumors with high precisions and sensitivities, suggesting molecular grading as a relevant complement to standard pathological grading. We also present a gene expression signature with independent prognostic impact on metastasis and disease specific survival. We conclude that the combination of molecular and histopathological classification systems may provide a strong improvement for bladder cancer classification and produce new insights into the development of this tumor type.

overall_design: 144 bladder cancer tumor samples and 12 normal samples were analyzed on 2-color cDNA or oligo microarrays using the Stratagene Universal Human Reference RNA as the common reference sample. 24 samples are hybridized to both the cDNA and oligo platform and these were used for merging of data from the two different gene expression platforms into a single expression matrix and for subsequent evaluation steps. The merged gene expression matrix used for analyses is supplied as a supplementary file (at the foot of this record). 103 of the samples were also analyzed on a BAC array containing ~32 000 BAC clones. Arrays were produced at the Swegene Centre for Integrative Biology at Lund University (SCIBLU).

first: Attila

last: Frigyesi

first: Sigurdur

last: Gudjonsson

first: Gottfrid

last: Sjödahl

first: Christer

last: Hallden

first: Gunilla

last: Chebil

first: Srinivas

last: Veerla

first: Tobias

last: Ryden

first: Wiking

last: Månsson

first: Fredrik

last: Liedberg

first: Mattias

last: Höglund


title: Dynamic changes in gene expression in vivo predict prognosis of tamoxifen-treated patients with breast cancer

city: Carrington Crescent

first: Andrew

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

summary: Tamoxifen is the most widely prescribed anti-estrogen treatment for patients with ER-positive breast cancer. However, there is still a need for biomarkers that reliably predict endocrine sensitivity in breast cancers and these may well be expressed in a dynamic manner.   In this study we assessed gene expression changes at multiple time points (days 1, 2, 4, 7, 14) after tamoxifen treatment in the ER-positive ZR-75-1 xenograft model that displays significant changes in apoptosis, proliferation and angiogenesis within 2 days of therapy.   Hierarchical clustering identified six time-related gene expression patterns, which separated into three groups: two with early/transient responses, two with continuous/late responses and two with variable response patterns. The early/transient response represented reductions in many genes that are involved in cell cycle and proliferation (e.g. BUB1B, CCNA2, CDKN3, MKI67, UBE2C), whereas the continuous/late changed genes represented the more classical estrogen response genes (e.g.TFF1, TFF3, IGFBP5). Genes and the proteins they encode were confirmed to have similar temporal patterns of expression in vitro and in vivo and correlated with reduction in tumour volume in primary breast cancer. The profiles of genes that were most differentially expressed on days 2, 4 and 7 following treatment were able to predict prognosis, whereas those most changed on days 1 and 14 were not, in four tamoxifen treated datasets representing a total of 404 patients.   Both early/transient/proliferation response genes and continuous/late/estrogen-response genes are able to predict prognosis of primary breast tumours in a dynamic manner. Temporal expression of therapy-response genes is clearly an important factor in characterising the response to endocrine therapy in breast tumours which has significant implications for the timing of biopsies in neoadjuvant biomarker studies.

overall_design: Tamoxifen treated ZR-75 xenograft samples compared to a pooled control. 5 timepoints, replicates and dye swaps, giving a total of 32 arrays

first: Karen

last: Taylor

first: Liang

last: Liang

first: Dana

last: Faratian

first: Morwenna

last: Muir

first: Graeme

last: Walker

first: Barbara

last: Kuske

first: J

last: Dixon

middle: A

last: Cameron

last: Harrison

first: Simon

last: Langdon


title: Trout macrophages: Control vs. Escherichia coli PGNs from strains O111:B4 and K12

city: Chile

first: Sebastian

last: Boltana

state: Bio BIO

address: Edmundo Larenas s/n, Barrio Universitario. Biotechnology Center

department: Oceanografia

country: Chile

institute: Universidad de Concepcion

summary: We evaluated both the transcriptomic and inflammatory response in trout (O. mykiss) macrophages in primary cell culture stimulated with DAP-PGN (DAP; meso-diaminopimelic acid, PGN; peptidoglycan) from two strains of Escherichia coli (PGN-K12 and PGN-O111:B4) over time. Transcript profiling was assessed using function-targeted cDNA microarrays hibridation (n = 36) to differential responses to both PGNs that are both time and treatment dependen over trout macrophages. Wild type E. coli (K12) generated an increase in transcript number/diversity over time whereas PGN-O111:B4 stimulation resulted in a more specific and intense response. In line with this gene Ontology analysis (GO) highlights a specific transcriptomic remodelling for PGN-O111:B4 whereas results obtained for PGN-K12 shows a high similarity with a general LPS response where multiple functional classes are related to ribosome biogenesis or cellular metabolism

overall_design: Two-condition experiment, PGN vs. control cells. Biological replicates: 18 control, 18 treated. Dye-swap.

last: Mackenzie


title: gene expression analysis in different tissues of Flax (Linum usitatissimum L.)

city: Villeneuve d'Ascq

first: Stephane

last: Fenart

address: Cité Scientifique

country: France

institute: University Lille 1

summary: We developped a new oligo microarray platform to analyse flax transcriptome. Here, we validated this microarray on several tissues of flax, at different developmental stages.

overall_design: 30 chips study using total RNA from 9 different tissue samples of Flax (Leaf sample at green capsule stage, stem inner tissue at vegetavie stage, stem outter tissue at vegetative stage, stem inner tissue at green capsule stage, stem outter tissue at green capsule stage, roots, embryos of 10, 20 and 40 days after flowering) for an overall survey of microarry accuracy and total RNA from 6 stem tissue at green capsule stage (3 of the cultivar 'Belinka' and 3 of the cultivar 'Drakkar') for an analysis of biological replicates reproducibility.


title: Time course of manganese treatment in LB

status: Public on Jun 12 2010

city: Stanford

first: Sharon

last: Hoover

state: CA

address: 337 Campus Drive, Lokey 105

department: Department of Biology

institute: Stanford University

summary: The SOS response to DNA damage in bacteria is a well-known component of the complex transcriptional responses to genotoxic environmental stresses such as exposure to reactive oxygen species, alkylating agents, and many of the antibiotics targeting DNA replication. However, bacteria such as Bacillus subtilis also respond to conditions that perturb DNA replication via a transcriptional response mediated by the replication initiation protein DnaA. In addition to regulating the initiation of DNA replication, DnaA directly regulates the transcription of specific genes. Conditions that perturb DNA replication can trigger the accumulation of active DnaA, activating or repressing transcription of genes in the DnaA regulon. We report here that simply growing B. subtilis in LB medium altered DnaA-dependent gene expression in a manner consistent with the accumulation of active DnaA, and that this was part of a general transcriptional response to manganese limitation. The SOS response to DNA damage was not induced under these conditions. One of the genes positively regulated by DnaA in Bacillus subtilis encodes a protein that inhibits the initiation of sporulation, Sda. Sda expression was induced as cells entered stationary phase in LB but not in LB supplemented with manganese, and induction of Sda inhibited sporulation-specific gene expression and the onset of spore morphogenesis. In the absence of Sda, manganese-limited cells initiated spore development but failed to form mature spores. These data highlight that DnaA-dependent gene expression may influence the response of bacteria to a range of environmental conditions, including conditions that are not obviously associated with genotoxic stress.

overall_design: Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays).


title: Entrapment Neuropathy Results in Different MicroRNAs Expression Patterns from Denervation Injury in Rats

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary:
To compare the microRNAs (miRNAs) expression profile in the innervated soleus muscle and L4-L6 DRG neuronsafter sciatic nerve entrapment with a non-constrictive silastic tube, subsequent surgical decompression, and denervation injury.
The experimental soleus muscles and dorsal root ganglions (DRGs)  from each experimental group (sham control, denervation, entrapment, and decompression) were analyzed with an Agilent® rat miRNA array to detect dysregulated miRNAs

overall_design: Three-condition experiment, DRGs and soleus muscles of the rats receiving sciatic nerve denervation 6 months, sciatic nerve entrapment 6 months, and sciatic nerve entrapment 6 months then decompression for 3 months v.s. soleus muscle (sham control), Biological replicates: 1 control replicates, 3 experiment replicates


title: CGH array in neuroblastoma and small cell lung carcinoma cell lines

status: Public on Jun 10 2010

city: Bologna

first: Stefania

last: Purgato

address: via Selmi 3

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

summary: In the present study we investigated the structure of MYCN amplifications, examples of both dmin and hsr, in eight neuroblastoma (NB) and two small cell lung carcinoma (SCLC) cell lines.

overall_design: Ten cell lines were analyzed for gene amplification: STA-NB3 (NB), STA-NB4 (NB), STA-NB8 (NB), STA-NB10DM (NB), STA-NB10HSR (NB), STA-NB13 (NB), STA-NB15 (NB), SK-N-BE (NB), GLC8 (SCLC), GLC14 (SCLC). NimbleGen human reference sample was used as reference DNA.

first: Clelia

middle: T

last: Storlazzi


city: Trieste

first: Danilo

last: Licastro

department: Genomica Funzionale

institute: CBM

summary:
The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs).
The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR.

overall_design: 12 Samples, 4 groups 3 samples per group.


title: The Smc3 deacetylase Hos1 closes the cohesin acetylation cycle

city: London

first: Lidia

last: Lopez-Serra

address: 44 Lincoln's Inn Fields

institute: London Research Institute/Cancer research UK

type: Genome binding/occupancy profiling by genome tiling array

summary: Cohesion between sister chromatids is mediated by the chromosomal cohesin complex. In budding yeast, cohesin is loaded onto chromosomes during the G1 phase of the cell cycle. During S-phase, the replication fork-associated acetyltransferase Eco1 acetylates the cohesin subunit Smc3 to promote establishment of sister chromatid cohesion. At the time of anaphase, Smc3 loses its acetylation again, but the Smc3 deacetylase and possible importance of Smc3 deacetylation are unknown. Here, we show that the class I histone deacetylase family member Hos1 is responsible for Smc3 deacetylation. Cohesin is protected from deacetylation while bound to chromosomes, but is deacetylated as soon as it dissociates from chromosomes following separase cleavage at anaphase onset. Non-acetylated Smc3 is required as a substrate for cohesion establishment in the following cell cycle. Our results complete the description of the Smc3 acetylation cycle and provide unexpected insight into the importance of de novo Smc3 acetylation for cohesion establishment.

overall_design: The Affymetrix Saccharomyces cerevisiae Chip Tiling 1.0F Arrays were used to analyze the binding pattern of both the wild type and the K112N/K113N mutated version of Smc3 along the genome of Saccharomyces cerevisiae.

first: Vanessa

last: Borges

first: Chris

last: Lehane

first: Helen

last: Flynn

first: Mark

last: Skehel

first: Tom

last: Ben-Shahar

first: Frank

last: Uhlmann


title: Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15

city: New York

first: Andrew

last: Sharp

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

type: Methylation profiling by genome tiling array

summary: Methylation profiles of chr12-16 were generated by meDIP and array hybridisation in 3 cases with maternal uniparental disomy of chromosome 15, and three cases of paternal uniparental disomy of chromosome 15. Comparison of these profiles reveals differentially methylated (imprinted) regions on chromosome 15.

overall_design: Methylated DNA was enriched by immunoprecipitation using antibodies against 5-methylcytosine. meDIP and input DNA was labeled with cy5 and cy3 respectively and hybridized to Nimblegen arrays comprising 2.1 million 50-85mers covering human chromosomes 12-16 at a mean density of ~1 probe per 100bp. Resulting log2 fluorescence ratios correspond to methylation levels. Six samples were analyzed, with technical replicates for each DNA.

first: Eugenia

last: Migliavacca

first: Yann

last: Dupre

first: Elisavet

last: Stathaki

first: Mohammad

last: Sailani

first: Alessandra

last: Baumer

first: Albert

last: Schinzel

first: Deborah

last: Mackay

first: Gilda

last: Cobellis

first: David

middle: O

last: Robinson

first: Han

middle: G

last: Brunner

first: Bernhard

last: Steiner

first: Stylianos

last: Antonarakis


title: Transposon site hybridization (TraSH) screen in the lungs

status: Public on Jun 09 2010

first: Kaitian

last: Peng

address: 299 Campus Drive, Fairchild, D327

summary:
We wanted to identify Francisella tularensis bacterial mutants that are negatively selected in vivo in the lungs of mice. Mice were infected with a Francisella transposon mutant library where each gene in the genome has been mutated via the insertion of a kanamycin resistance cassette with 2 outward facing T7 promoters. 2 days post infection, infected lungs were harvested and the bacteria present in the infected lungs were collected. Bacterial genomic DNA was isolated and subjected to an in vitro T7 transcription reaction, reverse transcribed and the resulting cDNA was hybridized to our Francisella microarray.
Infection: The goal of the study was to identify Francisella genes that are negatively selected in the lungs of mice post infection with a Francisella transposon mutant library. Resulting bacterial cDNA was hybridized to the Francisella microarray.


title: Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns

first: Johan

last: Staaf

address: Medicon Village

institute: SCIBLU - Swegene Centre for Integrative Biology at Lund University

summary:
Introduction: Five different molecular subtypes of breast cancer have been identified through gene expression profiling. Each subtype has a characteristic expression pattern suggested to partly depend on cellular origin. We aimed to investigate whether the molecular subtypes also display distinct methylation profiles.
Methods: We analysed methylation status of 807 cancer-related genes in 189 fresh frozen primary breast tumours and four normal breast tissue samples using an array-based methylation assay.
Results: Unsupervised analysis revealed three groups of breast cancer with characteristic methylation patterns. The three groups were associated with the luminal A, luminal B and basal-like molecular subtypes of breast cancer, respectively, whereas cancers of the HER2-enriched and normal-like subtypes were distributed among the three groups. The methylation frequencies were significantly different between subtypes, with luminal B and basal-like tumours being most and least frequently methylated, respectively. Moreover, targets of the polycomb repressor complex in breast cancer and embryonic stem cells were more methylated in luminal B tumours than in other tumours. BRCA2-mutated tumours had a particularly high degree of methylation. Finally, by utilizing gene expression data, we observed that a large fraction of genes reported as having subtype-specific expression patterns might be regulated through methylation.
Conclusions: We have found that breast cancers of the basal-like, luminal A and luminal B molecular subtypes harbour specific methylation profiles. Our results suggest that methylation may play an important role in the development of breast cancers.
DNA methylation profiling of breast cancer samples and normal breast tissue samples. The Illumina GoldenGate Methylation Cancer Panel I was used to obtain DNA methylation profiles across approximately 1500 CpGs. Samples included 189 breast cancer samples and 4 normal breast tissue samples.

overall_design: Bisulphite converted DNA from the samples were hybridised to the Illumina GoldenGate Methylation Cancer Panel I

first: Karolina

last: Holm

first: Cecilia

last: Hegardt

last: Vallon-Christersson

first: Göran

last: Jönsson

first: Håkan

last: Olsson

first: Ake

last: Borg

first: Markus

last: Ringnér


title: CGH analysis of Rheumatoid arthritis (RA) patient genomes

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

summary: To identify susceptibility genes concerning copy number variations (CNVs) in rheumatoid arthritis (RA), a case-control genome-wide CNV analyses was carried out by Roche Nimblegen array-based CGH. In this study, 15 RA patients and 1 control (Non-RA) were included.

overall_design: Comparative genomic hybrydiztion of 15 Rheumatoid arthritis patients and 1 control (non Rheumatoid arthritis) with Sample LX (non Rheumatoid arthritis)as reference.

first: Xiaolan

last: Lu

first: Jinxia

last: Shi

first: Zuowei

first: Zhanguo

last: Li

first: Baoli

last: Zhu


title: Broth-cultured vs swarming-phase P. mirabilis

status: Public on Jun 07 2010

city: Ann Arbor

first: Melanie

last: Pearson

state: MI

address: 1150 W Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan Medical School

summary: Swarming motility by the urinary tract pathogen Proteus mirabilis has been a long-studied, but little understood phenomenon.  On agar, a P. mirabilis colony grows outward in a bullseye pattern formed by consecutive waves of rapid swarming followed by consolidation into shorter cells.  To examine differential gene expression in these growth phases, a microarray, constructed based on the completed genome sequence and annotation, was undertaken.  RNA from 1) broth-cultured, or 2) swarming cells was extracted to assess transcription during each of these growth states.

overall_design: Five independent arrays (biological replicates) were analyzed for broth-cultured versus swarming P. mirabilis HI4320.

first: David

last: Rasko

first: Harry

last: Mobley


title: Monosomic chr5 derivative of laboratory strain of Candida albicans 3153A

city: Atlanta

first: Hong

last: Qin

state: GA

address: 350 Spelman Ln SW, Box 1183

institute: Spelman College

summary:
Differential expression between monosoic derivative and parental strain of Candida albicans.

The important human pathogen Candida albicans possesses an unusual form of gene regulation, in which the copy number of an entire specific chromosome or a large portion of a specific chromosome changes in response to a specific adverse environment, thus, assuring survival. In the absence of the adverse environment, the altered portion of the
genome can be restored to its normal condition. One major question is how C. albicans copes with gene imbalance arising by transitory aneuploid states. Here, we compared transcriptomes from two copies of chromosome 5 (Ch5) in a normal diploid strain 3153A and from a single copy of Ch5 in representative derivative Sor55. Statistical analysis revealed that at least 40% of transcripts from the monosomic Ch5 are fully compensated to a disomic level, thus, indicating the existence of a genome-wide mechanism maintaining cell homeostasis. However, a minor portion of transcripts diminished twofold in accordance with what would be expected for Ch5 monosomy. Another minor portion of transcripts, unexpectedly, increased up to twofold and higher then the disomic level, demonstrating indirect control by monosomy. We suggest that C. albicans unusual regulation of gene expression by the loss and gain of entire chromosomes is coupled with
widespread compensation of gene dosage at the transcriptional level.

overall_design: The laboratory strain 3153A is a prototrophic laboratory stain of Candida albicans. The strain Sor55 is a representative derivative of 3153A, monosomic for Ch5. Three replicate hybridizations were performed for of each strain.  Normalization were done using non-chr5 genes to avoid the potential dosage effects on chr5 genes.

first: Anatoliy

last: Kravets

first: Ausaf

last: Ahmad

first: Qinshan

last: Gao

first: Gabor

last: Bethlendy

first: Elena

last: Rustchenko-Bulgac


title: Global analysis of DNA methylation patterns on the latent KSHV episome in PEL and de novo infected endothelial cells

city: Hamburg

first: Thomas

last: Guenther

department: Mechanisms of Antiviral Defense

country: Germany

institute: Heinrich-Pette-Institut

summary:
Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis of epigenetic modifications during latent infection with Kaposi's sarcoma associated herpesvirus (KSHV), the etiologic agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). Using high resolution tiling microarrays in conjunction with immunprecipitation of methylated DNA (MeDIP) and modified histones (ChIP), we have determined global patterns of epigenetic modifications across the KSHV genome in several tumor-derived cell lines as well as de novo infected endothelial cells, revealing highly distinct landscapes of epigenetic modifications associated with latent KSHV infection. We find that KSHV genomes are subject to profound methylation at CpG dinucleotides, leading to the establishment of characteristic global DNA methylation patterns. However, such patterns evolved slowly and thus are unlikely to govern latency early during the infection process. In contrast, we observed that latent histone modification patterns were rapidly established upon a de novo infection. Our analysis furthermore demonstrates that such patterns are not characterized by the absence of activating histone modifications, since both H3K9/K14-ac and H3K4-me3 marks were prominently detected at several loci, including the promoter of the lytic cycle transactivator Rta. While these regions were furthermore largely devoid of the constitutive heterochromatin marker H3K9-me3, we observed rapid and widespread deposition of H3K27-me3 across latent KSHV genomes, a bivalent modification which is able to repress transcription despite of the simultaneous presence of activating marks. Our findings suggest that the epigenetic patterns identified here induce a poised state of repression during viral latency, which can be rapidly reversed once the lytic cycle is induced.

This dataset contains our MeDIP data; the ChIP-on-chip data are deposited in a separate dataset.

overall_design: Analysis and comparison of latent DNA methylation patterns in KSHV positive BCBL1, AP3, HBL6 and SLKP cells and de novo infected SLK cells. An in vitro methylated bacmid containing the complete KSHV genome (termed BacM) was used as a positive control for the MeDIP procedure. All probe signals were background corrrected by subtracting the ratios from a negative control sample containing the unmethylated KSHV bacmid (Bac). A further negative control (SLK) from KSHV negative cells was used to identifiy and permanently flag probes with show extensive crosshybridization. The negative controls Bac and SLK are hence not represented by a seperate data column in the matrix, but the raw data files are nevertheless included in this dataset.

last: Günther

first: Adam

last: Grundhoff


title: Global analysis of histone modification patterns on the latent KSHV episome

summary:
Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis of epigenetic modifications during latent infection with Kaposi's sarcoma associated herpesvirus (KSHV), the etiologic agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). Using high resolution tiling microarrays in conjunction with immunprecipitation of methylated DNA (MeDIP) and modified histones (ChIP), we have determined global patterns of epigenetic modifications across the KSHV genome in several tumor-derived cell lines as well as de novo infected endothelial cells, revealing highly distinct landscapes of epigenetic modifications associated with latent KSHV infection. We find that KSHV genomes are subject to profound methylation at CpG dinucleotides, leading to the establishment of characteristic global DNA methylation patterns. However, such patterns evolved slowly and thus are unlikely to govern latency early during the infection process. In contrast, we observed that latent histone modification patterns were rapidly established upon a de novo infection. Our analysis furthermore demonstrates that such patterns are not characterized by the absence of activating histone modifications, since both H3K9/K14-ac and H3K4-me3 marks were prominently detected at several loci, including the promoter of the lytic cycle transactivator Rta. While these regions were furthermore largely devoid of the constitutive heterochromatin marker H3K9-me3, we observed rapid and widespread deposition of H3K27-me3 across latent KSHV genomes, a bivalent modification which is able to repress transcription despite of the simultaneous presence of activating marks. Our findings suggest that the epigenetic patterns identified here induce a poised state of repression during viral latency, which can be rapidly reversed once the lytic cycle is induced.

This dataset contains our ChIP-on-chip data; the MeDIP data are deposited in a separate dataset.

overall_design: Analysis of histone modification patterns of the KSHV genome in the KSHV positive primary effusion lymphoma (PEL)-derived BCBL1 cell line, long-term in vitro infected SLK cells (SLKP), and de novo infected SLK cells at 5 days post infection (SLK5dpi).


title: Comparative gene expression analysis of thoracic spinal cord from G93A SOD1 mutant rats and from wild type littermates following mild compression injury

status: Public on Jun 05 2010

first: ANDREA

last: MALASPINA

state: England

address: 4 Newark Street

department: Neuroscience

institute: Institute of Cell and Molecular Science

summary: In this study we investigate how the molecular response to a mechanical stress applied to the spinal cord can be modified by a G93A SOD1 gene mutation, a genetic defect known to cause an invariably fatal form of motor neuron disease.  In a 7-day post-injury time period, we perform a 4 time points gene expression profiling of injured spinal cords obtained from pre-symptomatic rats over-expressing the G93A SOD1 gene mutation and from wild type (WT) littermates. The hypothesis tested in this investigation is that the presence of a known genetic defect in a pre-symptomatic rat with a macroscopically normal spinal cord modifies the molecular response to mechanical stress as part of an increase genetically-induced vulnerability to this kind of stress. A better understanding of the molecular mechanisms underlying this susceptibility to trauma may open the way to the uncovering of molecular events which are crucially linked to neurodegenerastion.

overall_design: Total RNA was isolated from the spinal cords of both wild type (WT) and mutant (G93A SOD1 gene mutation) rats sacrificed after mild compression spinal cord injury (SCI) at 30 minutes, 4 hours, 24 hours and 7 days from the experimental injury. Total RNA was also isolated from the spinal cords of both wild type (WT) and mutant (G93A SOD1 gne mutation) rats sacrificed after sham operation at 30 minutes and 4 hours after surgery. RNA samples from rats spinal cords of the same genetic type sacrificed at the same time points after sham operation or compression SCI were pooled together, for a tota of 12 pooled samples.

first: Andrea

last: Malaspina

first: John

middle: V

last: Priestley


title: DNA methylation epigenotypes in Breast Cancer Molecular Subtypes

status: Public on Jun 08 2010

city: Adelaide

first: Naiara

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

summary: Analysis of luminal A, luminal B, cerbB2+ and basal-like breast cancer subtypes' methylation profiles. The hypothesis tested in the present study was that tumor subtype specific aberrant methylation profiles might be inductors of some transcriptional changes taking place in breast cancer molecular subtypes. Results clearly demonstrate the differences in the methylation profiles of basal-like and HER2-overexpressing tumors and provide compelling evidence to support the utilization of this biomarker for prognostication and therapeutic stratification of patients with breast cancer.

overall_design: DNA methylation profiling analysis at 1537 CpG loci was performed in 28 paired breast cancer/adjacent tissues representing the four major breast cancer subtypes, plus four more non-affected tissue of which two were peritumoral, i.e. surrounding the tumor, and two corresponded to the adjacent area, i.e. more than 2 cm away from the tumor.


title: miRNA Expression in Senescent and Immortalized BJ fibroblasts

city: Chapel Hill

first: Laura

last: Bonifacio

state: NC

address: 308 Beard Hall

department: Medicinal Chemistry and Natural Products

institute: UNC Eshelman School of Pharmacy

summary: Limited data exists regarding changes of microRNA (miRNA) expression during senescence in human cells and no reports correlate telomerase expression with regulation of senescence-related miRNAs.  We used miRNA microarrays to provide a detailed account of miRNA profiles for early passage and senescent human foreskin (BJ) fibroblasts as well as early and late passage immortalized fibroblasts (BJ-hTERT) that stably express the human telomerase reverse transcriptase subunit hTERT.  The revelation that miRNA expression changes with extended passaging in BJ-hTERT cells will contribute to a comprehensive understanding of the connections between telomerase expression, senescence and processes of cellular aging.

overall_design: Four samples were assessed for miRNA expression by array:  BJ fibroblast early passage, BJ fibroblast senescent, BJ-hTERT early passage, and BJ-hTERT late passage.  Total RNA from each sample was arrayed in duplicate and results were compared to expression in early passage BJ fibroblasts. The duplicate sample of early passage BJ cells was not included in the final analysis.

first: Michael

last: Jarstfer


title: Speciation

first: Gavin

last: Sherlock

address: 300 Pasteur Drive

department: Genetics

summary:
Background: The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation.  Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities.  However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms.  The Saccharomyces sensu stricto yeasts have small genomes, can be easily cultured, and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation.  Among them, only a single D-M pair has been found, between S. bayanus and S. cerevisiae, comprising the mitochondrially targeted product of a nuclear gene, AEP2, and a mitochondrially encoded locus, OLI1, the 5' region of whose transcript is bound by Aep2.  Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts.
Methods: We report here the first detailed genome-wide analysis of rare F2 progeny from an otherwise sterile hybrid, and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus.  Instead, our analyses suggest that more complex interactions may be responsible for their post-zygotic separation.  These interactions most likely involve multiple loci having weak effects, as there were multiple significant pairwise combinations of loci, with no single combination being completely excluded from the viable F2s.
Conclusions: The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions, suggests that initial speciation events might not always be mediated by D-M pairs.  An alternative explanation may be that "death by a thousand cuts" leads to speciation, whereby an accumulation of polymorphisms can lead to an incompatibility between the species "transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility.  After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation. Genotypes for hybrids between S. cerevisiae and S. paradoxus.
A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.

platform_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

overall_design: Genotyping design

first: Katy

last: Kao


title: Gene Expression Profiling Identifies Inflammation and Angiogenesis as Distinguishing Features of Canine Hemangiosarcoma

status: Public on Jun 04 2010

city: Denver

first: Beth

last: Tamburini

state: CO

address: 1400 Jackson Street, K503

department: Immunology

institute: University of Colorado Denver

summary:
The etiology of hemangiosarcoma remains incompletely understood. Its common occurrence in dogs suggests predisposing factors favor its development in this species. These factors could represent a constellation of heritable characteristics that promote transformation events and/or facilitate the establishment of a microenvironment that is conducive for survival of malignant blood vessel-forming cells. The hypothesis for this study was that characteristic molecular features distinguish hemangiosarcoma from non-malignant endothelial cells, and that such features are informative for the etiology of this disease. We first evaluated mutational events in candidate genes that might drive hemangiosarcoma. Each of 10 tumor and four non-tumor samples had wild type sequence for these genes. Thus, we used gene expression profiling as a global approach to test the hypothesis. Hemangiosarcoma cells clustered separately from non-malignant endothelial cells based on robust signatures that included genes involved in inflammation, angiogenesis, adhesion, invasion, metabolism, cell cycle, signaling, and patterning. The data do not distinguish whether functional or ontogenetic plasticity creates this phenotype, although they suggest that the cells that give rise to hemangiosarcoma modulate their microenvironment to promote tumor growth and survival.
Keywords: Hemangiosarcoma, microarray, heritability, GSEA, canine

overall_design: 10 dogs with hemangiosarcoma were compared to 3 dogs without hemangiosarcoma and 21 dogs with other tumors

first: Tzu

last: Phang

first: Susan

last: Fosmire

last: Trapp

first: Miguel

last: Gonzalez

first: Jill

last: Slansky

first: Leslie

middle: C

last: Sharkey

first: Gary

last: Cutter

first: Donald

last: Bellgrau

first: Robert

last: Gemmill

first: Lawrence

last: Hunter

first: Jaime

middle: F

last: Modiano


title: Gene expression profiles of wild-type Yersinia pestis CO92 and its Braun lipoprotein mutant at flea and human temp

city: Galveston

first: Ashok

middle: K

last: Chopra

state: TX

address: 301 University Blvd.

department: Microbiology & Immunology

institute: University of Texas Medical Branch

summary: Braun/murein lipoprotein (Lpp) is one of the major outer membrane components of gram-negative bacteria belonging to the enterobacteriaceae family that that is involved in inflammatory responses and septic shock. We previously characterized a delta-lpp isogenic mutant of Yersinia pestis CO92 and found that this mutant was defective in surviving in macrophages and was attenuated in a mouse inhalation model of plague when compared to the highly virulent wild-type (WT) bacterium. To better understand how deletion of the lpp gene might affect Yersinia virulence, we performed global transcriptional profiling of the genes in the WT Y. pestis CO92 and its delta-lpp mutant by using microarrays. The organisms were cultured at both 26 and 37 degrees Celsius to simulate the flea vector and mammalian host environments, respectively. Our data revealed vastly different effects of lpp mutation on the transcriptomes of Y. pestis grown at 37 versus 26°C. While the absence of Lpp resulted mainly in the down-regulation of metabolic genes at 26°C, the Y. pestis CO92 lpp mutant cultured at 37°C exhibited profound alterations in stress response and virulence genes, compared to the WT bacterium. We further investigated one of the stress-related genes (htrA) down-regulated in the lpp mutant relative to WT Y. pestis, as HtrA was previously shown to be important for intracellular survival of Y. enterocolitica in macrophages. Indeed, complementation of the delta-lpp mutant with the htrA gene in trans restored intracellular survival of the Y. pestis lpp mutant. Our results support a role for Lpp in Y. pestis CO92 adapatation to the host environment, possibly via transcriptional activation of htrA.

overall_design: WT Y. pestis CO92 was obtained from the Centers for Disease Control and Prevention (CDC, Atlanta, GA) and maintained in our restricted access biosafety level (BSL)-2 laboratory. The creation and characterization of the strain deficient in the expression of the lpp gene were described in detail previously. All Yersinia strains were grown in brain, heart, infusion broth (BHI, Difco, Voigt Global Distribution Inc, Lawrence, KS) at 26-28°C. Prior to RNA isolation, bacteria were grown in BHI broth overnight at 26°C. The overnight culture was diluted 1:20 in BHI broth and grown at 26°C for an additional 6 h. In another set of experiment, after 2 h of cultivation at 26°C, the temperature was shifted to 37°C for 4 h to facilitate activation of the T3SS and production of Yops. Bacteria were harvested and RNA isolated using RiboPure (Ambion/Applied Biosystems, Austin, TX). Microarray for Y. pestis are available to our laboratory through the NIAID's Pathogen Functional Genomics Resource Center at The Institute for Genomic Research (TIGR). RNA was processed and hybridized by the Molecular Genomics Core Facility at UTMB.

first: Cristi

last: Galindo

first: Jian

last: Sha


title: Gene expression analysis of 3 MCL and 3 CLL cell lines

status: Public on Jun 03 2010

city: Heidelberg

first: Alexandra

last: Farfsing

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: Microarray-based gene expression analysis identified genes differentially expressed in 3 MCL and 3 CLL cell lines compared to the lymphoblastoid non-tumor cell line LCL_WEI.

overall_design: In this study, a set of 3 CLL and 3 MCL cell lines was used to acquire expression profiles of a total of 16 441 transcripts, leading to the identification of differentially expressed genes compared to the a non-tumor B-cell line LCL-WEI by Significance Analysis of Microarray data.

first: Felix

last: Engel


title: Protective unfolded protein response in human pancreatic beta cells transplanted into mice

status: Public on Jun 02 2010

city: Boston

first: Lorella

last: Marselli

state: MA

address: One Joslin Place

department: Joslin Diabetes Center and the Department of Medicine

institute: Harvard Medical School

summary: Islet transplantation exposes beta cells to mild hyperglycemia and to the abnormal environment of the transplant site. These conditions may affect beta cells and induce the expression of genes involved in beta cell damage. Gene expression profile of human beta cells exposed to mild hyperglycemia by transplantation into ICR-SCID mice was evaluated and compared with the gene profile of beta cells obtained from non-diabetic subjects. We found that the transplanted beta cells showed an unfolded protein response (UPR). There was upregulation of many genes of the IRE-1 pathway that provide protection against the deleterious effects of ER stress. Among them, increased expression of genes coding XBP-1; the chaperone proteins PDIA4, Bip, and Grp94; and the ER degradation proteins EDEM1 and EDEM2. ERdj4 and DNA-JC3 were also upregulated. JUK had downregulated expression. The PERK and ATF-6 arms of the ER stress response had many downregulated genes in transplanted islets. The PERK's substrates, EIF2A and NRF2, showed markedly reduced expression, as downregulated was the expression of CReP. Other downregulated genes included HERP2, IRS-2, CHOP and C/EBP-beta. In the transplanted beta cells there was significantly decreased expression of ATF-6, as well as the downstream gene products CHOP and HERP2. There was increased expression of HRD1, which exerts an antiapoptotic effect by degrading unfolded proteins. In conclusion human beta cells in a transplant site had UPR changes in gene expression that protect against the proapoptotic effects of unfolded proteins.

overall_design: Frozen sections were obtained from pancreases of non-diabetic subjects at surgery and from human islets transplanted into ICR-SCID mice for 4 weeks. β cell enriched samples were obtained by laser capture microdissection. RNA was extracted, amplified and subjected to microarray analysis.

first: Jeffrey

last: Kennedy

first: Hitoshi

last: Katsuta

first: Min-Ho

last: Jung

first: Allison

last: Goldfine

first: Ulysses

middle: J

last: Balis

first: Dennis

last: Sgroi

last: Bonner-Weir

first: Gordon

last: Weir


title: Genome-wide transcriptome analysis of two maize inbred lines under drought stress during the seedling stage

city: Beijing

first: Guoying

last: Wang

address: Zhongguancun Nandajie 12

department: Institute of Crop Sciences

institute: Chinese Academy of Agricultural Sciences

summary: To understand the transcriptome changes during drought tolerance in maize, the drought-tolerant line Han21 and drought-sensitive line Ye478, which show substantial differences in drought tolerance at the seedling stage, were selected for this study. Using the GeneChip Maize Genome Arrays, we applied genome-wide gene expression analysis to the two genotypes under gradual drought stress and re-watering. We identified 2172 common regulated transcripts in both lines under drought stress, with 1084 common up-regulated transcripts and 1088 common down-regulated transcripts. Among the 2172 transcripts, 58 potential protein kinases and 117 potential transcription factors were identified. The potential components of the ABA signaling pathway were identified from the common regulated transcripts. We also identified 940 differentially regulated transcripts between the two lines. Among the 940 transcripts, the differential expression levels of 29 transporters and 15 cell wall-related transcripts may contribute to the different tolerances of the two lines. Additionally, we found that the drought-responsive genes in the tolerant Han21 line recovered more quickly when the seedlings were re-watered, and 311 transcripts in the tolerant Han21 line were exclusively up-regulated at the re-watering stage compared to the control and stress conditions. Our study provides a global characterization of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize.

overall_design: In two independent experiments, we generate maize gene expression profiles during drought stress and re-watering through comparing genome-wide expression patterns of drought stress treatment and re-watering treatment by using 17,555 Affymetrix maize whole genome array.

first: Jun

last: Zheng

first: Junjie

last: Fu

first: Mingyue

last: Gou

first: Junling

last: Huai

first: Yunjun

last: Liu

first: Min

last: Jian

first: Quansheng

last: Huang

first: Xiying

last: Guo

first: Zhigang

last: Dong

first: Hongzhi


title: Comparison of gene expression between a human epididymal cell line derived from the caput epididymidis of a fertile patient and another one derived from the caput epididymidis of an obstructive azoospermic patient

status: Public on Jun 01 2010

city: Pointe-Claire

first: Daniel

last: Cyr

state: Québec

address: 245, Boulevard Hymus

country: Canada

institute: INRS-Institut Armand-Frappier

summary: Transcriptional profiling of human epididymal cell lines FHCE1 and IHCE1 respectively derived from the caput epididymidis of a fertile and an obstructive azoospermic patient. These two cell lines are comprised of homogenous populations of principal cells immortalized with the SV40 Large T antigen. Goal was to determine if cell junctions are impaired in this type of male infertility.

overall_design: Two-condition experiment, FHCE1 vs. IHCE1 cells. Replicates: 3 replicates from each cell line.

first: Evemie

last: Dubé

first: Louis

last: Hermo

first: Peter

last: Chan


title: Broth-cultured vs consolidation-phase P. mirabilis

first: Melanie

middle: M

last: Pearson

summary: Swarming motility by the urinary tract pathogen Proteus mirabilis has been a long-studied, but little understood phenomenon.  On agar, a P. mirabilis colony grows outward in a bullseye pattern formed by consecutive waves of rapid swarming followed by consolidation into shorter cells.  To examine differential gene expression in these growth phases, a microarray, constructed based on the completed genome sequence and annotation, was undertaken.  RNA from 1) broth-cultured, or 2) consolidation-phase cells was extracted to assess transcription during each of these growth states.

overall_design: Five independent arrays (biological replicates) were each analyzed for broth-cultured vs consolidation-phase P. mirabilis.

first: David

last: Rasko

first: Harry

last: Mobley


title: An initial map of chromosomal segmental copy number variations in chickens

status: Public on Jun 11 2010

city: Nashville

first: Xiaofei

last: Wang

state: TN

address: 3500 John A Merritt blvd

department: Biological Sciences

institute: Tennessee State University

summary: Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory regions. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as model animal for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosome regions that segregate for important agricultural and disease phenotypes. NimbleGen 385k whole genome tiling arrays were used to map CNVs in the chicken. This study has identified 96 CNVs in three lines of chickens (broiler, Leghorn and Rhode Island red). These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Smaller sized CNVs mostly affect none coding sequences while larger CNV regions involve genes, for example prolactin receptor, aldose reductase and zinc finger proteins, suggesting chicken CNVs potentially affect agricultural or disease related traits.

overall_design: Blood DNA isolated from Cornish Rock, Leghorn and Rhode Island Red birds. Cy5 labeled DNA from a Cornish Rock male used as reference was mixed with Cy3 labeled DNA samples was then hybridized to the 385K chicken tiling array. Fluorescence intensity data were normalized with qspline algorithm and ratio data were analyzed with the circular binary segmentation algorithm from Olshen et al. Copy number variation calls were made if the averaged Log2 ratio of a segment was shifted by 0.3 from the baseline.

first: Sameul

last: Nahashon


title: The expression profiles of log-phase and stationary-phase cells of Shigella flexneri grown at 30 degrees and 37 degrees Celsius

first: Li

last: Zhu

address: 20 Dongdajie, Fengtai District

department: State Key Laboratory of Pathogens and Biosecurity

institute: Beijing Institute of Biotechnology

summary: To obtain a global view of the response of S. flexneri at the expression level induced by temperature up-shift, we compared the expression profiles of log-phase and stationary-phase cells grown at 30 degrees and 37 degrees Celsius.

overall_design: A virulent S. flexneri serotype 2a strain 2457T was grown aerobically in 100 mL LB medium at 30°C and 37°C. Cells were harvested in the log phase (OD600nm=1.0) and stationary phase (about 9 hrs).

first: Hengliang


title: Global coordinated bistable activation of the core region of the ICEclc genomic island in Pseudomonas knackmussii

city: Lausanne

first: Jan

middle: Roelof

last: van der Meer

address: Bâtiment Biophore, Quartier UNIL-Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

summary: To further characterize the organization of the transcriptional units and the global behaviour of the genomic island ICEclc in Pseudomonas knackmussii, we have employed Agilent DNA custom microarray in the 8X15K format.

overall_design: ICEclc-specific gene expression in Pseudomonas knackmussii strain B13 was measured during exponential phase growth on 10mM 3-chlorobenzoate (3CBA) as sole carbon and energy source and during the following stationary phase. Both growth phases were performed in triplicate.

first: Nicolas

last: Pradervand

last: Johnson


title: Gene expression analysis of JVM-2 and Granta-519 after CCDC50 gene modulation

first: Alexandra

last: Farfsing

summary: Microarray-based gene expression analysis identified genes differentially expressed in JVM-2 and Granta-519 after CCDC50 gene modulation.

overall_design: In this study, JVM-2 and Granta-519 cells, silenced for CCDC50 using siCCDC50 was compared to genome wide expression changes when compared to cellular transfections with a siRNA non-template control by Significance Analysis of Microarray data. Further, Ooverexpression of CCDC50 using the vector pCMV_CCDC50 was compared to cellular transfections 9with an empty vector pCMV in the cell lines JVM-2 and Granta-510

first: Felix

last: Engel


title: CGH of common Candida albicans strains

first: Anna

last: Selmecki

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: The purpose of this review is to describe the tools used to detect genome changes, to highlight recent advances in our understanding of large scale chromosome changes that arise in C. albicans and to discuss the role of specific stresses in eliciting these genome changes. The types of genomic diversity that have been characterized suggest C. albicans can undergo extreme genomic changes in order to survive stresses in the human host. We propose that C. albicans and other pathogens may have evolved mechanisms not only to tolerate, but also to generate, large-scale genetic variation as a means of adaptation.

overall_design: Strains included in this series are described in a Eukaryotic Cell review of genomic plasticity of Candida albicans.  These strains are well-characterized and some of them are frequently utilized by the Candida community to generate mutant strains.  Each strain was analyzed once and all strains were competed against the same reference strain, SC5314 (the first sequenced C. albicans strain).

first: Anja

last: Forche

first: Judith

last: Berman


title: Expression profiling data from mid-log phase cultures of wild type Vibrio campbellii BAA-1116

city: Washington

first: Baochuan

last: Lin

state: DC

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

summary:
Small RNA and regulatory RNA discovery has been based on (i) computational predictions mainly in intergenic regions, (ii) microarray experiments, (iii) shotgun cloning of cDNA libraries, (iv) classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels and (v) copurification with proteins like Hfq, CsrA and RNA polymerase.
In this study, we attempted to experimentally validate in silico small and regulatory RNA predictions for V. campbellii BAA-1116 using a microarray expression profiling strategy. Specifically, we investigated transcripts from mid-log phase cultures grown in nutrient rich media and examined their hybridization to tiled probes targeting annotated V. campbellii BAA-1116 intergenic regions.

Keywords: small RNA discovery

sample_organism: Vibrio campbellii CAIM 519 = NBRC 15631 = ATCC 25920

overall_design: Five replicates of wild type V. campbellii BAA-1116 were grown to Mid-log phase, and total RNA was extracted from 1.0E+9 cells. Messenger RNA was isolated from the total RNA extracts treated with DNase, labeled with biotin, fragmented and hybridized to V. campbellii BAA-1116 whole genome microarray (520694F, Affymetrix).

first: Ana

last: Silverira

first: Kelly

last: Roberson

last: Vasconcelos

first: Fabiano

last: Thompson

first: Zheng

first: Gary

last: Vora


title: Human esophageal adenocarcinomas

first: Paul

last: Grosu

address: 33 Avenue Louis Pasteur

institute: Microsoft/Merck

summary: The incidence of esophageal and junctional adenocarcinoma has increased 6 fold in the last 30 years and 5 year survival remains less than 14%. Most patients present with advanced disease and current staging is limited in its ability to predict survival. We aimed to generate and validate a molecular prognostic signature for esophageal adenocarcinoma. Gene expression profiling was performed and the resulting signatures correlated with clinical features for 91 snap frozen esophageal and junctional resection specimens. Gene expression profiles were obtained from 76/91 of the samples (82%). 119 genes were  significantly associated with survival and 270 genes with the number of involved lymph nodes. Three genes were prognostic at the protein level in the external validation dataset. This three gene signature outperformed all the pathological features at predicting survival in this independent cohort (p<0.001).

overall_design: Total RNA isolated from human tissue sections was used to make fluorescently labeled cRNA that was hybridized to DNA oligonucleotide. Briefly, 4 µg of total RNA was used to synthesize dsDNA through reverse transcription. cRNA was produced by in vitro transcription and labeled postsynthetically with Cy3 or Cy5. Two populations of labeled cRNA, a reference population and an experimental population, were compared with each other by competitive hybridization to microarrays. Two hybridizations were done with each cRNA sample pair using a fluorescent dye reversal strategy. Human microarrays contained oligonucleotide probes corresponding to approximately 21,000 genes. All oligonucleotide probes on the microarrays were synthesized in situ with inkjet technology (Agilent Technologies, Palo Alto, CA). After hybridization, arrays were scanned and fluorescence intensities for each probe were recorded. Ratios of transcript abundance (experimental to control) were obtained following normalization and correction of the array intensity data. Gene expression data analysis was done with the Rosetta Resolver gene expression analysis software (version 7.0, Rosetta Biosoftware, Seattle, WA).

first: C

last: Peters

first: J

last: Rees

middle: S

last: Hardwick

first: S

last: Vowler

last: Zhang

first: V

last: Save

first: M

last: O'Donovan

first: D

last: Rassl

last: Caldas

last: Alderson

first: R


title: Control of oligodendroglial cell number by the miR-17~92 family of miRNA cluster (miRNA Exiqon Part)

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: The generation of myelinating cells in the central nervous system (CNS) requires the initiation of specific gene-expression programs in oligodendrocytes. We reasoned that miRNAs could play an important role in this process by regulating critical developmental genes. Microarray profiling of cultured oligodendrocytes identifies the miR-17~92 family of miRNA cluster as highly enriched miRNAs in oligodendrocytes.We specifically deleted the miR-17~92 cluster in oligodendrocytes using the 2´3´-cyclic nucleotide 3´-phosphodiesterase (CNP)-Cre mice. Absence of miR-17~92 leads to a reduction of oligodendrocyte number in vivo and we find that the expression of these miRNAs in primary cultures of oligodendrocytes promotes cell proliferation by influencing Akt signalling. Together, these results suggest that the miRNA pathway is essential in determining oligodendroglial cell number and that the miR-17~92 cluster is crucial in this process.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: miRNA microarray profiling was used for the identification of miRNAs enriched in oligodendrocytes. Total RNA lysates from primary oligodendroctes compared to primary astrocytes were analysed regarding their miRNA levels. Three independent samples for each of the two cell types were used. The study was initially designed with a comparison of oligodendrocytes, astrocytes and microglia. However, only the comparison of oligodendrocytes and astrocytes is discussed in the present study.

first: Holger

last: Budde

first: Sebastian

last: Schmitt

first: Dirk

last: Fitzner

first: Lennart

last: Opitz

last: Salinas-Riester

first: Mikael

last: Simons


title: Comparative transcriptome analysis of the CO2 sensing pathway via differential expressions of carbonic anhydrase in Cryptococcus neoformans

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

summary: Carbon dioxide (CO2) sensing, transport, and metabolism play a pivotal role in survival and proliferation of pathogenic microbes infecting human host from natural environments due to the drastic difference of CO2 levels. Carbonic anhydrases (CAs) are not only key CO2-metabolic enzymes catalyzing reversible interconversion between CO2 and bicarbonate (HCO3-), but also important CO2-signaling modulators. Cryptococcus neoformans that causes fatal fungal meningitis contains two functional CAs, Can1 and Can2, among which Can2 plays essential roles for growth and sexual differentiation of the pathogen. However, downstream genes and signaling network regulated by CAs have not been studied thus far. In this study, we constructed a C. neoformans strain where CAN2 expression is controlled by the CTR4 (copper transporter) promoter and elucidated its transcriptome patterns by using DNA microarray analysis to elucidate downstream target genes of Can2. Expectedly, the CAN2 promoter replacement strain showed growth defects in a CO2-dependent manner when CAN2 is repressed. The CA-transcriptome analysis discovered a number of Can2-dependent genes, including those involved in fatty acid biosynthesis (FAS1), sexual differentiation (GPB1), capsule structure organization (CAS3), iron-metabolism (CFO2), and a number of stress-regulated genes, including an oxidative stress-responsive Atf1 transcription factor, although a majority of them do not have any orthologs in other fungi. The present study revealed other roles of Atf1 in capsule and melanin production and diverse stress responses, including thermotolerance and antifungal drug resistance, of C. neoformans. This study provides further insights into the signaling network of CA/CO2-sensing pathway in pathogenic fungi.

overall_design: 17 slides are used in this analysis, 3 or 2 biological replicate experiments are performed, total RNAs are extracted from 2 strains (H99 Wild type strain, CTR4::CAN2) at 2 time points (0hr time, 12hr time) in 2 conditions (BCS, CuSO4). We use the mixed all of total RNAs from this experiment as a control RNA. We use Cy5 as Sample dye and Cy3 as a control dye. Several experiment samples are dye swaped.

first: Young-Joon

last: Ko

first: Min-Su

last: Kim

first: Shinae

last: Maeng

first: Anna

last: Floyd

first: Joseph

last: Heitman


title: Expression profiling of E.coli K-12 wild-type vs. delta dksA cells upon amino acid starvation

city: Houston

first: Jue

middle: D.

last: Wang

address: 1 Baylor Plaza, Rm T932

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Actively dividing cells perform robust and accurate DNA replication during fluctuating nutrient availability, yet factors that prevent disruption of replication remain largely unknown. Here we report that DksA, a nutrient-responsive transcription factor, ensures replication completion in Escherichia coli. In the absence of DksA, replication is rapidly arrested upon amino acid starvation. This replication arrest occurs independently of exogenous DNA damage, yet it induces the DNA damage response and recruits the main recombination protein RecA. This microarray experiment compares the transcriptional responses to amino acid starvation in wild-type and delta dksA cells. The SOS-regulated genes are highly induced in delta dksA cells.

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

overall_design: Four-condition experiment: wt, wt+SHX, delta dksA, delta dksA+SHX. Biological replicates: 3 for each sample. Reference: a mixture of the same amount of the four RNA samples.

first: Yan

last: Zhang

middle: D


title: Sigma B in Listeria monocytogenes strains from different lineages

city: Ithaca

first: Haley

middle: Franks

last: Oliver

address: 410 Stocking

department: Food Science

institute: Cornell University

summary: Listeria monocytogenes strains classify into at least three distinct phylogenetic lineages.  Correlations exist between lineage classification and source of bacterial isolation, e.g., human clinical and food isolates usually classify into either lineage I or II, however, human clinical isolates are over-represented in lineage I while food isolates are over-represented in lineage II.  σB, a transcriptional regulator previously demonstrated to contribute to environmental stress response and virulence in L. monocytogenes lineage II strains, was hypothesized to provide differential capabilities for L. monocytogenes survival in various niches (e.g., food vs. human clinical).  To determine if σB contributions to stress response and virulence differ across diverse L. monocytogenes strains, ΔsigB mutations were created in strains from lineages I, II, IIIA, and IIIB.  Paired parent and ΔsigB mutant strains were tested for acid and oxidative stress survival, Caco-2 cell invasion efficiency, and virulence using the guinea pig listeriosis infection model.  Parent and ΔsigB mutant strain transcriptomes were compared using whole-genome expression microarrays.  σB contributed to virulence in each strain.  However, while σB contributed significantly to acid and oxidative stress survival and Caco-2 cell invasion in lineage I, II, and IIIB strains, σB contributions were not significant for these phenotypes in the lineage IIIA strain.  A core set of 63 genes was positively regulated by σB in all four strains; different total numbers of genes were positively regulated by σB in each strain.  Our results suggest that σB universally contributes to L. monocytogenes virulence, but specific σB-regulated stress response phenotypes vary among strains.

overall_design: Independent RNA isolations were performed for four wildtype and ΔsigB strains from cells grown to early stationary phase. Three biological replicates were used in competitive whole-genome microarray experiments. For each set of hybridizations, RNA from a L. monocytogenes wildtype strain was hybridized with RNA from its isogenic ΔsigB null mutant.  Four wildtype and ΔsigB isogenic pairs were compared independently.

first: Renato

last: Orsi

first: Martin

last: Wiedmann

first: Kathryn

last: Boor


title: C. perfringens 13 strain: growth with 1 mM homocysteine vs growth with 0.5 mM cystine

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: Transcriptionnal profiling of C. perfringens 13 strain comparing growth in minimal medium with 1 mM homocysteine with growth in minimal medium with 0.5 mM cystine.

overall_design: two-condition experiment, homocysteine vs cystine, 4 biological replicates for each condition

first: Gaëlle

last: André

first: Marc

last: Monot


title: Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora

city: Provo

first: Chin-Yo

last: Lin

state: UT

address: 753 WIDB

department: Microbiology and Molecular Biology

institute: Brigham Young University

summary:
This research investigates the molecular mechanisms of trait deterioration of two experimental lines of entamopathogenic nematodes, an inbred line (L5M) and its original parental line (OHB), created by sub-culturing different experimental lines of the nematode-bacterium complex over 20 passages in insect hosts. These lines differed in their virulence, heat tolerance and fecundity .
Transcriptional profiles of the two experimental lines were determined and select differentially expressed genes were validated by quantitative PCR.

overall_design: Samples from four biological replicates each of the parental strain (OHB) and the laboratory strain (L5M) were hybridized to the custom H. bacteriophora arrays.

first: Bishwo

middle: N

last: Adhikari

first: Byron

last: Adams


title: Gene expression analysis of 6 MCL and 18 CLL patient samples

first: Alexandra

last: Farfsing

summary: Microarray-based gene expression analysis identified genes differentially expressed in 6 MCL and 18 CLL patient samples compared in independent analyses to CD19 selected healthy donor B-cell samples.

overall_design: In this study, a set of 18 CLL patient samples and 6 MCL patient samples was used to acquire expression profiles of a total of 16 441 transcripts, leading to the identification of differentially expressed genes compared to healthy CD19 positive sorted B-cells by Significance Analysis of Microarray data.

first: Felix

last: Engel


title: Eukaryotic Initiation Factor 4E-BP Protien Family: Sentinels at a Translational Checkpoint in Lung Tumor Defense

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

institute: Karolinska Institutet

summary: The usurping  of translational control by sustained activation of translation initiation factors is oncogenic. Here we show that the primary negative regulators of these oncogenic initiation factors - the 4E-BP protein family - operate as guardians of a translational control checkpoint in tumor defense. When challenged with the tobacco carcinogen NNK, 4ebp1-/-/4ebp2-/- mice showed increased sensitivity to tumorigenesis compared to their wild type counterparts. The 4E-BP deficient state per se creates pro-oncogenic, genome-wide skewing of the molecular landscape - with translational activation of genes governing angiogenesis, growth and proliferation; and translational activation of the precise cytochrome p450 enzyme isoform (CYP2A5) that bioactivates NNK into mutagenic metabolites. Our study provides in vivo proof for a translational control checkpoint in tumor defense.

overall_design: Comparisons of Total RNA and polysomal RNA from lungs derived from WT and 4ebp1-/-/4ebp2-/- Balb/c mice

first: Peter

last: Bitterman


title: Germination of Leafy Spurge (Euphorbia esula) Seeds under Constant and Alternating Temperature

city: Fargo

first: Michael

middle: E

last: Foley

state: ND

address: 1605 Albrecht Blvd

institute: USDA-ARS

summary: Transcriptome changes were investigated for Euphorbia esula (leafy spurge) seeds with a focus on the effect of constant and diurnal fluctuating temperature on dormancy and germination. Leafy spurge seeds do not germinate when incubated for 21 days at 20°C constant temperatures, but nearly 30% germinate after 21 days under fluctuating temperatures 20:30°C (16:8 h). Incubation at 20°C for 21 followed by 20:30°C resulted in approximately 63% germination in about 10 days. A cDNA microarray representing approximately 22,000 unique sequences was used to profile transcriptome changes.

platform_organism:
Manihot esculenta
Euphorbia esula

overall_design: Labeled cDNA was prepared from total RNA using the Alexa Fluor cDNA labeling kit (Invitrogen, Carlsbad, CA) according to manufacture's protocols. Labeled cDNAs were hybridized to a custom made 23 K element microarray that contained 19,808 unigenes from the leafy spurge EST database and an additional 4,129 unigenes from a cassava EST database. A rolling circle dye swap hybridization scheme was used to compare gene expression between samples. There were three biological and two technical replications for each treatment. Microarray hybridization was visualized using a GenPix 4000B scanner (Axon Instruments/Molecular Devices Corp., Sunnyvale, CA) and spot intensities and background was quantified using GenPix Pro software. Hybridization intensities were log2 transformed, and arrays were centered and normalized against each other.

first: David

middle: P

last: Horvath

first: James

last: Anderson

first: Wun

last: Chao


title: Screening for chromosomal aberrations by array CGH in 74 patients with congenital hypothyroidism

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

institute: MPIMG

summary: Congenital Hypothyroidism occurs in 1:3500 live births and is therefore the most common congenital endocrine disorder. A spectrum of defective thyroid morphology, termed thyroid dysgenesis, represents 80% of permanent CH cases. Although several candidate genes have been implicated in thyroid development, comprehensive screens failed to detect mutation carriers in a significant number of patients with non-syndromic TD. Due to the sporadic occurrence of TD, de novo chromosomal rearrangements are conceivably representing one of the molecular mechanisms participating in its aetiology. Recently, the use of array CGH technique has provided the ability to map these variations genomewide with high resolution. We performed an array CGH screen of 74 TD patients to determine the role of copy number variants (CNV) in the aetiology of the disease. We identified novel CNVs in 8.75% of all patients that have not been described as frequent variations in the healthy population. Affected patients presented with athyreosis or thyroid hypoplasia and in one case with associated heart malformation.

overall_design:
We selected 74 patients with thyroid dysgenesis for array CGH analysis. All individuals were detected in neonatal screening programs and abnormal thyroid gland morphology was subsequently confirmed by ultrasound examination.  Intragenic mutations in NKX2-1, FOXE1 and NKX2.5 had been previously excluded in phenotype characteristic individuals. PAX8 mutations were excluded in all patients with hypoplastic thyroids by direct sequencing of the coding exons 1-11. The study was approved by the local ethics committee.

Genomic DNA of all subjects as well as of healthy controls was isolated from peripheral blood leucocytes using the Qiagen DNA blood mini kit (Qiagen, Hilden, Germany). Array-comparative genomic hybridization was carried as described previously {Erdogan, 2006 #142; Pinkel, 1998 #151}. In brief, sonicated patient- and control DNA was labeled by random priming with Cy3-dUTP and Cy5-dUTP (Bioprime Array CGH, Invitrogen, Carlsbad, CA), respectively, and hybridized onto a submegabase resolution tiling path BAC array,  consisting of ~ 36 000 BAC clones obtained from several sources as described elsewhere {Fiegler, 2003 #198; Ishkanian, 2004 #196; Krzywinski, 2004 #197} . Step-by-step protocols are also provided at http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/.  Arrays were scanned with the G2565BA Agilent Microarray Scanner System (resolution 10 µm; PMT 100 % for Cy3/Cy5, respectively) (Agilent Inc. Santa Clara, CA) and analyzed using GENEPIX Pro 5.0 Software. Analysis and visualization of array CGH data were performed with our software package CGHPRO {Chen, 2005 #143}. For the assessment of copy number gains and losses, we used conservative log2 ratio thresholds of 0.3 and -0.3, respectively. Deviant signal intensity ratios involving three or more consecutive BAC clones were considered to be potentially pathogenic, unless they were covered by more than one known DNA copy number variant, as listed in the Database of Genomic Variants (http://projects.tcag.ca/variation/) or covered by > 50% of their length at least once in our reference set of 600 samples. Potentially pathogenic CNVs were verified by array CGH on a 244k oligonucleotide array from Agilent following the manufacturer’s instructions (Protocol-No. G4410-90010). Confirmed CNVs were tested for inheritance by co-hybridization of parental DNA on BAC arrays as described above. All chromosome coordinates are referring to the UCSC Genome Browser Assembly May 2004 (hg17/ NCBI Build 35; available at: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=99195739&clade=vertebrate&org=Human&db=hg17). Cytoscape {Shannon, 2003 #201} was used for the elucidation of potential interactions between genes within the intervals of interest.

first: Anne

last: Thorwarth


title: Neuronal microRNA response to Alzheimer's disease amyloid beta

status: Public on May 30 2010

city: Camperdown

first: Nicole

last: Schonrock

state: New South Wales

address: 100 mallett street

department: Medicine

institute: Brain and Mind Research Institute, University of Sydney

summary: In neurodegenerative disorders such as Alzheimer’s disease (AD), brain miRNA profiles are altered; thus miRNA dysfunction could be both a cause and a consequence of disease. Our study dissects the complexity of human AD pathology, in the absence of a post mortem delay, and provides the first miRNA profiling analysis addressing the contribution of amyloid-β (Aβ), a known causative factor of AD, to the de-regulation of neuronal miRNA expression. We used murine primary hippocampal neurons to show that Aβ is a powerful regulator of mature miRNA expression and a prominent miRNA down-regulation is evoked in response to Aβ peptides. Our study provides insight into a previously unexplored mechanism of how Aβ may impact the pathology of AD and identification of key miRNAs affected by Aβ will allow further analysis on target genes and biological pathways contributing to AD pathomechanisms.

overall_design: Mouse primary hippocampal neurons were grown for 23 DIV before being treated for 24 hours with either 5uM amyloid beta (1-42) aged for 24 hours at 37 degrees with shaking, or a PBS control. Total RNA was extracted using the Qiagen miRNeasy Kit and expression of 380 microRNA was analysed using rodent TaqMan low density microRNA microarrays (Applied Biosystems).

first: Jurgen

last: Gotz


title: Rbf1 induced gene expression in Ustilago maydis

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

institute: Karlsruhe Institute of Technology

summary: In the phytopathogenic Basidiomcete Ustilago maydis, sexual and pathogenic development are tightly connected and controlled via the b-mating type locus. The b-mating type locus encodes two homeodomain transcription factors, bE and bW, which form an active heterodimeric complex when they are derived from different b-alleles. Rbf1 encodes a zinc-finger transcription factor that is expressed upon formation of an active bE/bW heterodimer. To identify gene regulated by rbf1 independently from b, the b mating type locus was replaced by a copy of rbf1 under control of the arabinose-inducible crg1 promoter (strain CP27). Samples were taken 5h after induction of rbf1 gene expression. Strain JB2, carrying a deletion of the b-locus, was used as control.

overall_design: Strains were grown to an OD600 of 0.4-0.6 at 28°C in liquid array medium: 6.25% (w/v) salt solution, 30 mM L-glutamine, 1% (w/v) glucose, pH 7.0 (filter-sterilized). For induction of the bE and bW genes, cells were inoculated in liquid array medium containing 1% (w/v) arabinose instead of glucose as a carbon source. For induction, cells were washed once with inducing medium. Experiments were performed in two biological replicates for each time point.

first: Mario

last: Scherer

first: Chetsada

last: Pothiratana


title: Analysis of cardiac gene expression in response to isoproterenol-induced heart failure (part 2)

status: Public on May 31 2010

city: Duesseldorf

first: Antje

last: Lindecke

address: Universitaetsstr. 1

department: BMFZ

institute: Universitaet Duesseldorf

summary:
Myoglobin knockout mice (myo-/-) adapt to the loss of myoglobin by the activation of a variety of compensatory mechanisms on the structural and functional level. In order to analyze to what extent myo-/- mice would tolerate cardiac stress we used the model of chronic isoproterenol application to induce cardiac hypertrophy in myo-/- mice and wild type (WT) controls. After 14 d of isoproterenol infusion cardiac hypertrophy in WT and myo-/- mice reached a similar level. WT mice developed lung oedema and left ventricular dilatation indicating the development of heart failure. In contrast, myo-/- mice displayed conserved cardiac function and no signs of heart failure. Analysis of the cardiac gene expression profile using 40 k mouse oligonucleotide arrays showed that isoproterenol affected the expression of 180 genes in WT but only 92 genes of myo-/- hearts.
Only 40 of these genes were regulated in WT and myo-/- hearts. Whereas in WT hearts a prononced induction of genes of the extracellular matrix occurred suggesting a higher level of remodelling, in myo-/- hearts genes of carbon metabolism and genes linked to inhibition of apoptosis and muscular repair were altered. Interestingly, a subset of genes which was altered in myo-/- mice already under basal conditions was differentially expressed in WT hearts under isoproterenol treatment. In summary, our data show, that the genetic background (WT, myo-/-) has a major impact on cardiac gene expression even in the context of an aggressive hypertrophy model such as chronic isoproterenol stimulation.

Keywords: gene expression profiling of isoproterenol induced heart failure in WT and myo-/- mice

overall_design: We analysed the cardiac gene expression profiles in a total of 32 hearts subdivided into 4 groups (8 WT vehicle, 8 WT ISO, 8 myo-/- vehicle, 8 myo-/- ISO).

first: Andrei

last: Molojavyi

first: Claudia

last: Kessels

first: Sarah

last: Kocks

first: Karl

last: Köhrer

first: Axel

last: Gödecke


title: Gene expression profile of recurrent and non-recurrent HNSCC

city: Sao Paulo

first: Anna

last: Coló

address: Rua Professor Antonio Prudente, 211

country: Brazil

institute: Hospital A.C. Camargo

summary:
Head and neck squamous cell carcinomas (HNSCCs) is the seventh most common solid malignancy in the United States, accounting for more than 47,000 new cancer cases.
HNSCC shows significant diversity in its clinical behavior after treatment, which cannot be predicted using the current clinical or pathological markers. Despite tumor complexity, many studies have tried unsuccessfully to test single genes to be used as prognostic markers in HNSCC. A group of tumor samples can be characterized in terms of the behavior of modules. These modules include clusters of coexpressed genes, such as genes that belong to the same pathway or functional category.
Cancer is a multifaceted phenomenon that involves activation and/or disruption of various cellular processes. Thus, the identification of pathways or group of genes such as those involved in the development of lymph node metastasis and recurrent disease may help understanding the complex biology of cancer.

overall_design:
Samples were obtained during surgery and neck dissection of 47 patients with primary untreated HNSCC at the Head and Neck Surgery Department from the Hospital AC Camargo (São Paulo, Brazil) between 1998 and 2003. Diagnosis of HNSCC was determined by biopsy. All patients signed a pre-informed consent and the study was approved by our institutional review board. After surgery, all patients were treated with adjuvant radiotherapy. Recurrence were diagnosed by imaging or biopsy. Tumor samples were snap-frozen in liquid nitrogen. Before RNA extraction, diagnosis was confirmed by hematoxylin-eosin staining. Frozen samples were hand dissected for removal of normal cells, necrosis, and infiltrating inflammatory cells.
Total RNA was extracted using TRIzol. RNA quality was accessed by spectrophotometry and gel electrophoresis. To be considered as high-quality, the RNA had to have a 260/280 ratio higher than 1.7 and a 18S/28S rRNA ratio ~2. Amplifictaion of the mRNA was done using a T7-based protocol and cDNA was indirectly labeled with Alexa Dye 555 or 647. Samples and a common RNA reference were hybridized overnight at 42oC in dye-swap to a 4,800-element in-house printed microarray, enriched with cancer-related ESTs derived from the Human Cancer Genome Project. After washing, slides were scanned on a confocal laser scanner and data were extracted.

first: Alex

last: Carvalho

first: Luiz

last: Reis

first: André

last: Kowalski

first: Ana

last: Simões

first: Eduardo

last: Neves

first: Lucas

last: Fahham

first: Louise

last: Mota

first: Waleska

last: Martins

first: Hugo

last: Campos

first: Bianca

last: Barreto

last: Pagotto

last: Marques

first: Mariana

first: Chamberlein

last: Neto