title: Transcription factor HMGA2 controls the K-RAS mediated transformation-specific genetic program

city: Berlin

first: Oleg

last: Tchernitsa

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite

summary:
A genome-wide survey of transcriptional targets responding to chronic KRAS/MAPK (mitogen-activated protein kinase) pathway activation in rat ovarian surface epithelial cells (ROSE 199) has identified multiple differentially expressed transcriptional regulators including the architectural transcription factor high mobility group AT hook 2
(HMGA2). To elucidate the role of HMGA2 in the transcriptional network affected by oncogenic signaling, we used an integrated approach combining RNAi-mediated silencing, microarray-based expression profiling, computational prediction of transcription factor binding sites in target gene promoters and phenotypic analysis. Knocking-down HMGA2 resulted in the reversion of epithelial-mesenchymal transition, loss of anchorage independence and in a substantial restoration of the gene expression pattern characteristic of non-transformed ROSE cells. Computational prediction of transcription factor binding sites in the promoters of HMGA2-regulated genes and expression profiling revealed a preferential role of activator complex-1 (AP-1) components Fra-1 and JunB in target gene regulation. Forced expression of HMGA2 did not transform normal ovarian epithelial cells, suggesting that HMGA2 up-regulation is not sufficient for inducing the transformed phenotype, but mediates cancer-specific phenotypic traits in cells expressing mutated KRAS and, hence, oncogene addiction.

overall_design:
The Ras signaling target array was designed and produced as described
(Tchernitsa et al., 2005). Briefly, we selected 121 genes recovered from subtracted cDNA libraries representing sequences differentially expressed in parental and KRAStransformed ROSE 199 cells (Tchernitsa et al., 2004). In addition, we selected genes from subtracted libraries representing sequences differentially expressed in normal 208F fibroblasts and the HRAS-transformed derivative FE-8 (Zuber et al., 2000). Previously described Ras pathway targets and 13 different genes described as housekeeping genes in many different tissues and cell lines were included to permit normalization of hybridization intensities on microarrays. The total number of gene probes is 325 on the array.
Unmodified 70-mer DNA oligonucleotides were chosen as probe sets for the array. The oligonucleotide design was performed with software available on the web (http://oligo.lnatools.com/expression/) using the following parameters: option for LNA frequency=0, melting temperature between 74°C and 76°C, GC content between 45- 55%, absence of strong secondary structures and proximity to 3’ end of coding sequence. Oligonucleotides were synthesized at Illumina, Inc (San-Diego, USA) at the 50 nmol scale. Each of the 325 oligonucleotides was spotted four
times at a different location on the slides. Thus, the array contains 1,300 features.
Overall the study contains six samples. We studied for conditions:
First condition is influence of empty plasmid on ROSE199 cells. No additional hybridization replica. Sample 199_199emptyvector
Second condition is influence of siEGFP (used as a scramble duplex) on ROSEA25 cell line. As there was no influence of siEGFP on A25cell line and genes differentially expressed between ROSE199 and ROSEA25 were previously described in our several publication here we also used only one hybridization replica. Sample ROSE199_ROSEA25siEGFP.
Third condition is influence of HMGA2 expression vector on ROSE199 cells. One dye swap replica was done. Samples: ROSE199_ROSE199HMGA2 and 199HMGA2_199.
Forth condition is influence of siHMGA2 duplex on ROSEA25 cell line compared to ROSE199 cell line. One replica with dye swap. Samples ROSE199_ROSEA25siGMGA2 and ROSEA25siHMGA2_ROSE199.

first: Anastassia

last: Malek


title: Screening of the Paramecium tetraurelia megabase chromosome for autogamy-specific genes

status: Public on Mar 01 2010

city: Gif sur Yvette

first: nicolas

last: Agier

state: Ile de France

address: Avenue de la terrasse

department: transcriptomique

country: France

institute: CNRS

summary: Total RNA was extracted at different stages (TV, T0, T11 and T20) during autogamy of strain d4-2. Genes specifically induced during autogamy were identified following analysis of microarray hybridization data

overall_design:
3 technical replicates of the time course were hybridized
Subset one and three were labelled with Cy3
Subset two was labelled with Cy5

first: Jacek

middle: K

last: Nowak

first: Marek

last: Juszczuk

first: Robert

last: Gromadka

first: Maria

last: Jerka-Dziadosz

first: Marie-hélène

last: Mucchielli

first: Nicolas

first: Thomas

last: Tang

first: Lawrence

last: Aggerbeck

first: Olivier

last: Arnaiz

first: Jean

last: Cohen

first: Christopher

last: Herbert

first: Hervé

last: Delacroix

first: Linda

last: Sperling

first: Mireille

last: Bétermier

last: Zagulski


title: Small RNAs in different tissues and phloem of oilseed rape under nutrient stress conditions

status: Public on Feb 24 2010

city: Madrid

first: Anja

last: Buhtz

address: Campus de Montegancedo, M40,km38

country: Spain

institute: Centro de Biotecnologia y Genomica de Plantas

summary:
The objective of this study was to identify nutrient-responsive small RNAs in different tissues and in phloem sap of rape plants. miRNA microarrays containing all currently known plant miRNAs (Sanger miRBase versions 10.0, 10.1 and 11.0), and a set of unknown small RNAs cloned earlier from Brassica phloem sap (Bn_PsRNA) were used. The phloem, leaf and root response to nutrient deficiency were analyzed by removing either sulfate, copper or iron from the growth medium. The small RNA profile from phloem and inflorescence stems of plants grown under full nutrition conditions was also analyzed and compared.
The study demonstrates that the phloem sap sRNA profile is distinct from that of the inflorescence stems, leaves and roots. Furthermore, we could identify phloem-enriched small RNAs and showed that some of them specifically accumulate in the phloem in response to nutrient deprivation.

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

overall_design: For the identification of nutrient-responsive small RNAs in Brassica napus, three tissues (leaf, root, phloem sap) were analyzed under different nutrient stresses (sulfur, iron or copper starvation) and were compared to the corresponding tissue from plants grown under full nutrition conditions. Nine dual-color arrays (provided by LC Sciences, MRA-1038) were performed. In addition, a microarray hybridization experiment comparing phloem sap to the surrounding inflorescence stem tissue was performed.

first: Janin

last: Pieritz

first: Franziska

last: Springer

first: Julia

last: Kehr


title: Hypoxia regulates microRNA expression

status: Public on Feb 28 2010

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

country: USA

institute: University of Minnesota

summary: We examined hypoxia responsing miRNAs in HUVEC and MA148cells.  Microarray studies revealed hypoxia can change microRNA expression in HUVEC and MA148 cells.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: 8 HUVEC samples (4 controls and 4 experimentals) and 4 MA148 samples (2 controls and 2 experimentals)

first: Yan

last: Zeng

first: Goutam

last: Ghosh

first: Indira

last: Subramanian

first: Sundaram

last: Ramakrishnan


title: Host cell transcripts during malaria liver stage infection reveals a coordinated and sequential set of biological events

city: Seattle

last: Phan

state: WA

address: 307 Westlake Av N

institute: SBRI

summary:
After entering their mammalian host via the bite of an Anopheles mosquito, Plasmodium sporozoites migrate to the liver where they traverse several hepatocytes before invading the one inside which they will develop and multiply into thousands of merozoites. Although this constitutes an essential step in malaria infection, the requirements of Plasmodium parasites in liver cells and how they use the host cell for their own survival and development are poorly understood.
To gain new insights into the molecular host-parasite interactions that take place during malaria liver infection, we have used high-throughput microarray technology to determine the transcriptional profile of P. yoelii-infected hepatocytes that were collected from P. yoelii-infected mice 24 and 40 h after infection. This in vivo microarray expression was compared with the microarray analysis of in vitro infected hepatoma cells infected with closely related rodent malaria parasite P. berghei. Differential expression patterns for host genes  identify genes and pathways involved in the host response to rodent Plasmodium parasites.

Keywords: gene expression

platform_organism:
Plasmodium yoelii
Mus musculus

overall_design: Total RNA from sorted liver stage (LS) infected hepatocytes were isolated from PyGFP-infected BALB/c mice as described in Tarun et al (2008). RNA from LS-infected hepatocytes were isolated at two time points post-infection (pi): 24 hr pi (LS24) and 40 hr pi (LS40). As control, RNA from hepatocytes isolated from mock-infected mice (infected with salivary gland extract) at the same time points was also isolated following the same procedure. Total RNA was then subjected to two rounds of linear amplification using the Amino Allyl Message Amp II aRNA Amplification Kit (Ambion) according to manufaturer’s directions. The quality of total and amplified RNAs were examined with the Agilent 2100 BioanalyzerTM (Agilent Technologies) and the quantity of the RNA samples was assessed using a Nanodrop ND-1000 spectrophotometer  prior to microarray hybridization. For each timepoint two independent biological replicates were obtained.

first: Sónia

last: Albuquerque

first: Céline

last: Carret

first: Ana

middle: R

last: Grosso

first: Alice

middle: S

last: Tarun

first: Xinxia

last: Peng

first: Stefan

middle: H

last: Kappe

first: Miguel

last: Prudêncio

first: Maria

middle: M

last: Mota


title: Cellular and molecular evidence for a role of tumor necrosis factor alpha in the ovulatory mechanism of trout

status: Public on Feb 23 2010

city: Barcelona

first: Diego

last: Crespo

state: Barcelona

address: Avenida Diagonal 645

department: Physiology

institute: University of Barcelona

summary: The relevance of immune-endocrine interactions to the regulation of ovarian function in teleosts is virtually unexplored. As part of the innate immune response during infection, a number of cytokines such as tumor necrosis factor α (TNFα) and other immune factors, are produced and act on the reproductive system. However, TNFα is also an important physiological player in the ovulatory process in mammals. In the present study, we have examined for the first time the effects of TNFα in vitro in preovulatory ovarian follicles of a teleost fish, the brown trout (Salmo trutta). In control and recombinant trout TNFα (rtTNFα)-treated granulosa cells, we examined the percentage of apoptosis by flow cytometry analysis and cell viability by propidium iodide (PI) staining. Furthermore, we determined the in vitro effects of rtTNFα on follicle contraction and testosterone production in preovulatory trout ovarian follicles. In addition, we analyzed the gene expression profiles of control and rtTNFα-treated ovarian tissue by microarray and real-time PCR (qPCR) analyses.Treatment with rtTNFα induces ovarian cell apoptosis, decreases granulosa cell viability and stimulates the expression of genes known to be involved in the normal ovulatory process in trout. In addition, rtTNFα causes a significant increase in follicle contraction and testosterone production. Also, using a salmonid-specific microarray platform (SFA2.0 immunochip) we observed that rtTNFα induces the expression of genes known to be involved in inflammation, proteolysis and tissue remodeling. In view of these results, we propose that TNFα could have an important role in the biomechanics of follicle weakening, ovarian rupture and oocyte expulsion during ovulation in trout, primarily through its stimulation of follicular cell apoptosis and the expression of genes involved in follicle wall proteolysis and contraction.

overall_design: Reproductively mature female brown trout (Salmo trutta) from a cultured stock at the Piscifactoria de Bagà (Generalitat de Catalunya, Bagà, Spain) were kept under natural conditions of temperature and photoperiod. Fish at the preovulatory stage (according to the position of the germinal vesicle (GV) in oocytes that were cleared using a solution previously described), were anesthesized in 3-aminobenzoic acid ethyl ester (0.1 g/l; Sigma, Alcobendas, Spain) dissolved in fresh water, and the fish were sacrificed by concussion prior to the collection of the ovaries. The dissected ovaries were immediately used for the various in vitro assays. After dissection, brown trout preovulatory ovaries were placed in Hank´s balanced salt solution (HBSS) and individual ovarian follicles were manually separated with forceps from each ovary on ice, as previously described. To collect ovarian tissue for RNA extraction, preovulatory follicles from each of a total of three females were incubated (400 follicles/50 ml) in HBSS-BSA in the absence or presence of rtTNFα (100 ng/ ml, dissolved directly in HBSS-BSA), at 15ºC for 24 h with gentle shaking (100 rpm). At the end of the incubation follicles (previously de-yolked by gentle pressure) were removed, flash frozen in liquid nitrogen and stored at -80ºC until assayed.

first: Emilie

last: Bonnet

first: Nerea

last: Roher

first: Simon

last: MacKenzie

first: Aleksei

last: Krasnov

first: Frederick

middle: W

last: Goetz

first: Julien

last: Bobe

first: Josep

middle: V

last: Planas


title: Transcriptome profiling of Listeria monocytogenes during growth on a RTE-meat matrix

status: Public on Feb 25 2010

city: Mississippi State

first: Chinling

last: Wang

state: MS

address: College of Veterinary Medicine P.O. box 6100

department: Basic Sciences

institute: Missippi State University

summary: The gene expression profiles of L. monocytogenes strain F2365 grown in BHI agar (reference) or on a turkey deli meat (query) was examined. Aminosilane-coated cDNA microarray slide was used. The data from the normalized ratio of query to reference signal for each spot were transformed using a log2 scale. The expression level of genes obtained from the mean of each gene on the twelve slides was considered significantly different over 1.5 fold changes. Thirty nine and forty five genes in L. monocytogenes grown on a turkey meat matrix were upregulated and downregulated, respectively.

overall_design: To examine the gene expression profiles of L. monocytogenes grown in BHI agar or on a turkey deli meat, L. monocytogenes strains 4b F2365 aminosilane-coated cDNA microarray slide was used. Cy3 and Cy5 dyes were used for cDNA labelling. Data were obtained from three biological and four technical replicates (n = 12). Each biological replicate included a flip dye assay. TM4 package developed by TIGR was used to analyze the data.

first: Dongryeoul

last: Bae


title: Culex quinquefasciatus Jpal-per strain vs. Ogasawara strain

city: Shinjyuku-ku, Tokyo

first: Osamu

last: Komagata

address: Toyama 1-23-1

country: Japan

institute: National Institute of Infectious Diseases, Japan

summary: A pyrethroid-resistant strain of Culex quinquefasciatus, JPal-per, exhibits 2500-fold greater larval resistance to permethrin than the insecticide-susceptible strain Ogasawara. An increased microsome monooxygenase metabolism is involved in the resistance mechanism. Microarray analysis revealed altered expressions of cytochrome P450 genes in the fourth instar larvae of JPal-per compared to those in OGS. An oligo DNA array was designed for 62 different cDNA segments encoding unique P450 isoforms of the Cx. pipiens complex. Other probes for non-P450 Cx. pipiens complex genes were also mounted on the array.

overall_design: Two strains with two color experiment, total 10 replicates, 5 biological replicates (each strain), 5 dye-swap experiments.

first: Shinji

last: Kasai

first: Takashi

last: Tomita


title: Ethylamine versus succinate cells of Methylobacterium extorquens

status: Public on Feb 22 2010

first: Ludmila

last: Chistoserdova

address: 616 NE Northlake Place

department: Chemical Engineering

institute: University of Washington

summary: In order to provide global information on gene expression during growth on C2 compounds, microarray analysis of M. extorquens AM1 cells was carried out, comparing ethylamine-grown cells to succinate-grown cells. This comparison has confirmed previous observations on the inducible nature of some of the enzymes involved in C2 metabolism, such as methylamine (and ethylamine) utilization system (mau), putative enzymes for converting acetaldehyde into acetate and acetyl-CoA, and enzymes of the ethylmalonyl-CoA pathway that has been proposed to operate for assimilation of acetyl-CoA into cell biomass.

overall_design: RNA from ethylamine-grown cells was compared to RNA from succinate-grown cells. Four biological replicates were carried out.

first: Yoko

middle: O

last: Miller


title: Global gene expression of Poncirus trifoliata, Citrus sunki and their hybrids under infection of Phytophthora parasitica

status: Public on Feb 20 2010

city: Cordeirópolis

first: Leonardo

middle: Pires

last: Boava

state: São Paulo

address: Via Anhanguera, km158

country: Brazil

institute: Centro de citricultura 'Sylvio Moreira' /IAC

summary:
A microarray containing 62,876 unigenes selected from CitEST database and prepared by Nimblegen Systems was used for identifying candidate resistance genes against P. parasitica at 48 hours after inoculation
Four resistant and four susceptible F1 hybrids were selected from the population derived from the cross between Citrus sunki Hort. ex. Tan. and Poncirus trifoliate (L.) Raf cv. Rubidoux, respectively susceptible and resistant to P. parasitica. It was proposed that differentially expressed genes between resistant and susceptible hybrids and their parents provide essential candidates for identifying transcripts involved in disease resistance

sample_organism:
Citrus trifoliata
Citrus sunki
Citrus sunki x Citrus trifoliata

platform_organism:
Citrus sinensis
Citrus trifoliata
Citrus reticulata

overall_design: A total of 62,876 unigenes (18,712 unigenes of Citrus sinensis; 31,583 unigenes of Citrus reticulata and 12,581 unigenes of Poncirus trifoliate) selected from CitEST database assembled from the EST submitted to NCBI (Genebank accession number EY649559 to EY842485) were used to construct genome-wide oligonucleotide cDNA microarrays by Roche NimbleGen Systems using a multi-step approach to select probes with optimal predicted hybridization characteristics. Three probes were selected per unigene, comprising a probe set, and each probe set is represented on the final array by two replicates. All probes were designed as ‘‘perfect match’’ (PM) oligonucleotides (oligos).

first: M

last: Cristofani-Yaly

first: V

last: Mafra

first: K

last: Kubo

first: L

middle: T

last: Kishi

middle: A

last: Takita

last: Ribeiro-Alves

last: Machado


title: Microbial adaptation to environmental niches can be reproduced by experimental evolution

status: Public on Mar 03 2010

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

summary: Experimental evolution is a powerful approach to study how ecological forces shape microbial genotypes and phenotypes, but to date strains were predominantly adapted to conditions specific to laboratory environments. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and in the dairy environment and it is generally believed, that dairy strains originate from the plant niche. Here we investigated the adaptive process from the plant to the dairy niche and show that during the experimental evolution of a L. lactis plant isolate in milk, several mutations are selected that affect amino acid metabolism and transport. Three independently evolved strains were characterized by whole genome re-sequencing, revealing 4 to 28 mutational changes in the individual strains. Two of the adapted strains showed clearly increased acidification rates and yields in milk, and contained three identical point mutations. Transcriptome profiling and extensive phenotyping of the wild-type plant isolate compared to the evolved mutants, and a "natural" dairy isolate confirmed that major physiological changes associated with improved performance in the dairy environment relate to nitrogen metabolism. The deletion of a putative transposable element led to a significant decrease of the mutation rate in two of the adapted strains. These results specify the adaptation of a L. lactis strain isolated from mung bean sprouts to growth in milk and they demonstrate that niche-specific adaptations found in environmental microbes can be reproduced by experimental evolution.

overall_design: Multiple loop design with 12 samples and 16 dual label arrays. Each sample is hybrdized at least on two different arrays and with both dyes.

first: Herwig

last: Bachmann

first: Marjo

last: Starrenburg

first: Michiel

last: Kleerebezem

first: Johan

last: van Hylckama Vlieg


title: Response to nicotine (250 µM) in heads of the tobacco aphid Myzus persicae

city: Ithaca

first: John

middle: Sawyer

last: Ramsey

state: NY

address: Comstock Hall

institute: Cornell University

summary: Response of the aphid head transcriptome to nicotine in artificial diets (250 µM nicotine, 24 hours feeding)

overall_design: Two condition experiment: heads of aphids feeding on control diet vs heads of aphids feeding on 250 µM nicotine containing diet

first: Georg

last: Jander


title: MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori

status: Public on Feb 21 2010

city: Beibei

first: Qingyou

last: Xia

state: Chongqing

address: Tiansheng Road

department: College of Biotechnology

country: China

institute: Southwest University

summary:
Background: MicroRNAs (miRNAs) repress target genes at the post-transcriptional level, and function in the development and cell-lineage pathways of host species. Tissue-specific expression of miRNAs is highly relevant to their physiological roles in the corresponding tissues. However, to date, few miRNAs have been spatially identified in the silkworm.
Results: We establish for the first time the spatial expression patterns of nearly 100 miRNAs in multiple normal tissues (organs) of Bombyx mori females and males using microarray and Northern-blotting analyses. In total, only 10 miRNAs were universally distributed (including bmo-let-7 and bmo-bantam), while the majority were expressed exclusively or preferentially in specific tissue types (e.g. bmo-miR-275 and bmo-miR-1). We additionally examined the developmental patterns of miRNA expression during metamorphosis of the body wall, silk glands, midgut and fat body. In total, 63 miRNAs displayed significant alterations in abundance in at least 1 tissue during the developmental transition from larvae to pupae (e.g. bmo-miR-263b and bmo-miR-124). Expression patterns of five miRNAs were significantly increased during metamorphosis in all four tissues (e.g. bmo-miR-27 and bmo-miR-305).
Conclusions: In this study, we conducted preliminary spatial measurements of several miRNAs in the silkworm. Periods of rapid morphological change were associated with alterations in miRNA expression patterns in the body wall, silk glands, midgut and fat body during metamorphosis. Accordingly, we propose that this ubiquitous or tissue-specific expression of miRNAs supports their critical roles in tissue specification. The results obtained should facilitate future functional analyses.

overall_design: To determine the global spatial expression patterns of miRNAs in silkworm, we designed a DNA oligonucleotide-based microarray examining 92 unique miRNAs with 106 antisense probes. To determine the extent of tissue-specific changes during the specific developmental events, we assessed changes in miRNA expression in four individual tissues and organs (body wall, silk glands, midgut and fat body) from the larval to pupal stages.

first: Shiping

last: Liu

first: Song

last: Gao

first: Danyu

last: Zhang

first: Jiyun

last: Yin

first: Zhonghuai

last: Xiang


title: Response to nicotine (100 µM) in heads of the tobacco aphid Myzus persicae

summary: Response of the aphid head transcriptome to nicotine in artificial diets (100 µM nicotine, 24 hours feeding)

overall_design: Two condition experiment: heads of aphids feeding on control diet vs heads of aphids feeding on 100 µM nicotine containing diet


title: Comparative genome sequencing of wild type rhesus cytomegalovirus (RhCMV) with a recombinant RhCMV lacking ORF 178

status: Public on Feb 19 2010

city: Beaverton

first: Rebecca

last: Richards

state: OR

address: 505 NW 185th Ave

department: Microbiology and Immunology

institute: Vaccine and Gene Therapy Institute

type: Genome variation profiling by genome tiling array

summary: Recombinant RhCMV was created to study super-infection of Rhesus macaques.  These viruses (RhCMV Δ178;RhCMV Δ182-189;RhCMV Δ178Δ182-189) were co-hybridized with a wild-type BAC-derived RhCMV to a RhCMV tiling array to ensure that there were no additional mutations beyond the intended deleted regions.

overall_design: Comparison of wild-type BAC-derived RhCMV Δ178, RhCMV Δ182-189, and RhCMV Δ178Δ182-189


title: Gene profiling of v-Src transformed primary chicken cells

city: Hamilton

first: Bart

middle: Michal

last: Maslikowski

state: Ontario

address: 1280 Main St. West

department: Biology

country: Canada

institute: McMaster University

summary:
Cell transformation by the Src tyrosine kinase is characterized by extensive changes in gene expression.  To describe these changes, investigators have relied extensively on the study of immortalized rodent cell lines or heterogeneous tumor samples that limit the identification of differentially expressed genes or may not represent the full spectrum of biological processes regulated during transformation.  In this study, we took advantage of transformation-deficient and temperature sensitive mutants of the Rous sarcoma virus to characterize the patterns of gene expression in two types of primary cells, namely chicken embryo fibroblasts (CEF) and chicken neuro-retinal (CNR) cells.

Keywords: viral transformation of primary cells, transformation, transformation deficient mutant, temperature sensitive mutant, v-Src

overall_design:
Chicken embryo fibroblasts (CEF) were infected with the wild-type strain Schmidt-Ruppin A RSV  or non-transforming strain NY315 RSV or the non-transforming control virus RCASBP(A) to assess genes involved in v-Src-dependent transformation of CEF.
Chicken embryo fibroblasts (CEF) were infected with the temperature sensitve strain NY72-4 RSV and cultured either at non-permissive temperature (41.5˚C) or permissive temperature (37˚C) to assess genes involved in v-Src-dependent transformation of CEF.
Chicken neuroretina cells (CNR) were infected with the temperature sensitve strain NY72-4 RSV and cultured either at non-permissive temperature (41.5˚C) or permissive temperature (37˚C) to assess genes involved in v-Src-dependent transformation of CNR and compared to CEF.

last: Maślikowski

first: Benjamin

middle: D

last: Néel

first: Ying

last: Wu

first: Lizhen

last: Wang

first: Natalie

last: Rodrigues

first: Germain

last: Gillet

first: Pierre-André

last: Bédard


title: CpG site methylation of HCV-cirrhotic, HCV-HCC, and normal liver tissues

city: Columbus

first: Kellie

middle: J.

last: Archer

state: OH

address: 1841 Neil Ave

department: Division of Biostatistics

institute: Ohio State University

summary:
In this study we used a high-throughput method for assaying methylation of CpG sites simultaneously in a single sample for identifying differences in methylation observed in tissues ranging from normal liver to pre-neoplastic (cirrhosis) and neoplastic (HCC) states.
Since there are important clinical and prognostic differences among HCC patients due to etiology, this study was designed to focus on HCC due to HCV-infection, a more common etiology of HCC among Western countries

overall_design: cross-sectional: 20 cirrhosis, 20 HCC, and 16 normal patients, 87 arrays

middle: J

first: Valeria

last: Mas

first: Daniel

middle: G

last: Maluf

first: Robert

last: Fisher


title: Breast cancer endothelial interaction

status: Public on Feb 18 2010

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
MATERIALS AND METHODS: The genomic effects of tumor-endothelial interactions in cancer are not yet well characterized. To study this interaction in breast cancer, we set up an ex vivo coculture model with human benign and malignant breast epithelial cells with endothelial cells to determine the associated gene expression changes using DNA microarrays.
RESULTS: The most prominent response to coculture was the induction of the M-phase cell cycle genes in a subset of breast cancer cocultures that were absent in cocultures with normal breast epithelial cells. In monoculture, tumor cells that contained the stem cell-like CD44(+)/CD24(-) signature had a lower expression of the M-phase cell cycle genes than the CD44(-)/CD24(+) cells, and in the CD44(+)/CD24(-) cocultures, these genes were induced. Pretreatment gene expression profiles of early-stage breast cancers allowed evaluating in vitro effects in vivo. The expression of the gene set derived from the coculture provided a basis for the segregation of the tumors into two groups. In a univariate analysis, early-stage tumors with high expression levels (n = 137) of the M-phase cell cycle genes had a significantly lower metastasis-free survival rate (P = 1.8e - 5, 50% at 10 years) and overall survival rate (P = 5e - 9, 52% at 10 years) than tumors with low expression (n = 158; metastasis-free survival, 73%; overall survival, 84%).
CONCLUSIONS: Our results suggest that the interaction of endothelial cells with tumor cells that express the CD44(+)/CD24(-) signature, which indicates a low proliferative potential, might explain the unexpected and paradoxical association of the CD44(+)/CD24(-) signature with highly proliferative tumors that have an unfavorable prognosis.

overall_design: Computed

first: Martin

last: Buess


title: Transcriptional profiling of Deinococcus radiodurans comparing wild type cells with treated cells at four time points

status: Public on Feb 27 2010

city: chongup

first: sun

middle: wook

last: Jeong

state: Chonbuk

address: Sinjeongdong 1266

department: Radiation biotechnology

country: South Korea

institute: Korea atomic energy research institute

summary: Transcriptional profiling of Deinococcus radiodurans comparing control untreated wild type cells with wild type cells treated with 100 µM CdCl2.

sample_organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

overall_design: Two-condition experiment, wild type vs. 100uM CdCl2. Biological replicates: 4 time courses (0.25, 0.5, 1, 2h), dye-swapped, independently grown and harvested. Two replicate per array.

first: Min-ho

last: Joe

first: Sun-wook

last: Jung


title: The matricellular protein CCN1 activates a pro-inflammatory genetic program in murine macrophages

city: Chicago

first: Lester

middle: F

last: Lau

state: IL

address: 900 S. Ashland Avenue

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary:
Effects of the matricellular protein CCN1 on macrophage inflammatory gene expression was tested in a macrophage cell line I-13.35.

CCN1 (CYR61) is a matricellular protein that is highly expressed at sites of inflammation and wound repair. In these contexts, CCN1 can modify the activities of specific cytokines, enabling TNF-alpha to be cytotoxic without blocking NFkB activity and enhancing the apoptotic activity of FasL and TRAIL. Here we show that CCN1 supports the adhesion of macrophages through integrin alphaMbeta2 and syndecan-4, activates NFkB-mediated transcription, and induces a pro-inflammatory genetic program characteristic of classically activated M1 macrophages that participates in Th1 responses. The effects of CCN1 include upregulation of cytokines (TNFa, IL-1a, IL-1b, IL-6, IL-12b), chemokines (MIP-1a, MCP-3, Gro1, Gro2, IP-10), regulators of oxidative stress and complement (iNOS, C3), and downregulation of specific receptors (TLR4, IL-10rb) and anti-inflammatory factors (TGF-b1). CCN1 regulates this genetic program through at least two distinct mechanisms: an immediate-early response resulting from direct activation of NFkB by CCN1, leading to the synthesis of cytokines including TNFa and IP-10; and a delayed response resulting from CCN1-induced TNFa, which acts as an autocrine/paracrine mediator to activate the expression of other cytokines including IL-1b and IL-6. These results identify CCN1 as a novel component of the extracellular matrix that activates pro-inflammatory genes in macrophages, implicating its role in regulating macrophage function during inflammation.

overall_design: Macrophage cell line I-13.35 (from Tlr4-defective C3H/HeJ) was treated with purified recombinant CCN1 protein for 6 hr. Total RNA was isolated, converted to cRNA probes, and hybridized to a oligonucleotide array representing 113 murine inflammation-related genes (from SA Biosciences at www.sabiosciences.com, Cat. Number OMM-011.) The array is a nylon membrane based DNA microarray on which 60-mer oligonucleotides probes were printed.  Gene expression profile of resting cells incubated in serum-free medium (containing albumin, BSA) was used as a control for basal levels of gene expression.

first: Tao

last: Bai

first: Chih-Chiun

last: Chen


title: Complete Genomes of a Hunter-Gatherer and a Bantu from Southern Africa

first: Jeffrey

last: Kidd

address: 1705 NE Pacific St

department: Department of Genome Sciences

summary: The genetic structure of the indigenous hunter-gatherer peoples of Southern Africa, the oldest known lineage of modern man, holds an important key to understanding humanity's early history. Previously sequenced human genomes have been limited to recently diverged populations. Here we present the first complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and of a Bantu from Southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, and 13,146 novel amino-acid variants. These data allow genetic relationships among Southern African foragers and neighboring agriculturalists to be traced more accurately than was previously possible. Adding the described variants to current databases will facilitate inclusion of Southern Africans in medical research efforts.

overall_design: Copy number differences between NA18507 and KB1 were predicted from the depth of whole-genome shotgun sequence reads. These predictions were then validated using array-CGH using a a genome-wide design as well as a custom design targeted at specific regions of copy number difference

first: Can

last: Alkan

first: Evan

middle: E

last: Eichler


title: A restricted repertoire of cytosine methylation changes in neonates following intrauterine growth restriction

city: Bronx

first: Reid

last: Thompson

address: 1301 Morris Park Avenue

department: Molecular Genetics

institute: Albert Einstein College of Medicine

type: Methylation profiling by genome tiling array

summary: Perturbations of the intrauterine environment can affect fetal development during critical periods of plasticity, and can increase susceptibility to a number of age-related diseases (e.g. type 2 diabetes mellitus; T2DM), manifesting sometimes decades later.  We hypothesized that this biological memory is mediated by permanent alterations of the epigenome in stem cell populations.  Our studies focused specifically on DNA methylation in CD34+ hematopoietic stem and progenitor cells from cord blood, and utilized a two-stage design involving genome-wide discovery followed by quantitative, single-locus validation.  We found that changes in cytosine methylation occur in response to intrauterine growth restriction (IUGR), but that they are of a substantially lesser degree and involve many fewer loci than the epigenomic dysregulation observed in cancer.  This is consistent with a comparable study of individuals born following maternal starvation during the Dutch famine.  We also identify specific loci that are targeted for dysregulation of DNA methylation, in particular the hepatocyte nuclear factor 4α (HNF4A) gene, a well-known diabetes candidate gene not previously associated with growth restriction in utero, and other loci encoding HNF4A-interacting proteins.   Our results give some insights into the potential contribution of epigenomic dysregulation in mediating the long-term consequences of IUGR, and demonstrate the value of this approach to studies of the fetal origin of adult disease.

overall_design: Direct comparison of DNA methylation in 10 neonatal CD34+ samples isolated from umbilical cord blood belonging to two groups: IUGR (n=5) and their age-matched controls (n=5).  Each microarray consists of a two-color comparison of a methylation-sensitive representation of the genome (HpaII) with an internal methylation-insensitive control/reference (MspI).

first: Francine

middle: H

last: Einstein

first: Melissa

last: Fazzari

first: Amit

last: Verma

first: Tushar

last: Bhagat

first: Nir

last: Barzilai

first: John

last: Greally


title: Genomic DNA hybridizations of Col-0, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana

status: Public on Feb 17 2010

city: Austin

first: Thomas

middle: E.

last: Juenger

state: TX

address: 1 University Station, C0930

department: Section of Integrative Biology

institute: University of Texas at Austin

summary:
These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana.  The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies.
Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range.  Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin.  These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance.  Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India).  The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content.

overall_design: Each accession has 6 replicates, single channel on the ATH1 array.  Samples were processed in two balanced batches (bioprime random labeling, hybridization,scanning).  A total of 18 arrays


title: cRNA hybridizations of Tsu-1 and Kas-1 accessions of Arabidopsis thaliana under well-watered and mild soil drying

summary:
These data provide a basis for exploration of gene expression differences between physiologically extreme accessions of Arabidopsis thaliana.
Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range.  Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin.  These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance.  Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India).  The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content.   Microarray transcript profiling of leaf RNA identified a large number (5,996) of genes exhibiting robust constitutive differences in expression including many genes involved in general growth and development as well as abiotic stress pathways.  Interestingly, mild soil drying resulted in only subtle physiological responses but resulted in gene expression changes in hundreds of transcripts, including 352 genes exhibiting differential responses between accessions.  Our results highlight the value of genomic studies of natural accessions as well as identify a number of candidate genes for the observed constitutive and induced physiological differences between Tsu-1 and Kas-1.

overall_design: The basic experimental design involves two accessions (Tsu-1 and Kas-1) crossed with two environmental levels (well-watered soil and mild soil drying) and 3 biological replicates per accession/treatment combination (2 x 2 x 6 =24 arrays total)


title: Molecular Remodeling of Ion Channels in Human Atrial and Ventricular Myocytes Associated with Ischemic Cardiomyopathy

city: Baltimore

first: Nikolai

middle: M

last: Soldatov

state: MD

address: 5600 Nathan Shock Drive

institute: National Institute on Aging, NIH

summary: Ischemic cardiomyopathy (ICM) leads to congestive heart failure and can cause sudden cardiac death due to arrhythmia. Existing molecular knowledge base of ICM is rudimentary because of lack of specific attribution to cell type and function. This study was designed to investigate cell-specific molecular remodeling of ion channels, exchangers and pumps, which are signaling molecules (SM) involved in electrical, signaling and mechanical functions of the heart. Atrial and ventricular myocytes were isolated by laser-capture microdissection from left atrium and ventricle of healthy and ICM human hearts. SM and their splice variants altered by ICM in cardiomyocytes were identified by splice microarray and validated by RT-PCR. Molecular profiling of ICM-related changes showed that SM in atrial and ventricular myocytes remodel following their unique programs. ICM affected 63 genes in ventricular myocytes and 12 genes in atrial myocytes. Only few of the identified genes were previously linked to human cardiac disfunctions.

overall_design: In our experiments we used 3 healthy hearts rejected from transplantation procedure and explanted ICM hearts from three male patients. Tissue samples were dissected from left ventricle and left atrial appendages. Atrial and ventricular myocytes were laser-capture  microdissected from serial 7-8-µm thick cryostat sections. Individual cellular total RNA samples were analyzed on custom-built Human Ion Channel Splice Arrays slides (ExonHit) manufactured on the Ion Channel Splice Array sv1.1 platform representing 287 human SM, including 248 alternatively spliced ones in total 1655 splicing events and supplemented with capabilities to recognize connexins and ryanodine receptors.

first: Naomi

last: Gronich

first: Azad

last: Kumar

first: Yuwei

last: Zhang

first: William

last: Wood

first: Kevin

last: Becker

first: Igor

middle: R

last: Efimov


title: RNAs expression profiling in a resistant and a susceptible grapevine cultivar to Plasmopara viticola

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

summary: Plasmopara viticola (Berk. and Curt.) Berl. and de Toni is the agent of the destructive disease known as grapevine downy mildew, for the control of which intensive fungicide treatments are required. Natural sources of resistance are available in several wild Vitis species, which are being used in traditional breeding approaches. However, molecular switches, signals and effectors involved in resistance are poorly understood. In this paper we report a microarray analysis of early transcriptional changes associated to P. viticola infection in both susceptible Vitis vinifera and resistant Vitis riparia plants (12 and 24 h post inoculation). To provide a biological basis to the choice of time points for transcriptome analyses, we performed microscopic examinations of infected tissues at 12, 24, 48 and 96 hpi.  Data suggest that resistance in V. riparia is mainly a post-infectional event and involves a large reprogramming of host metabolism. Transcripts of signal transduction-related genes are specifically and often strongly accumulated in response to infection. Well known defence genes also show marked transcript increases, especially  pathogenesis-related proteins PR-10 and stylbene synthases, and genes related to an hypersensitive reaction. On the other hand, V. vinifera mounts a much weaker transcriptional response, involving mainly defence genes,  not effective enough in preventing pathogen infection.

sample_organism:
Vitis vinifera
Vitis riparia

overall_design: Leaves from one resistant (V. riparia cv. Gloire de Montpellier) and one susceptible (V.vinifera cv. Pinot Noir) grapevine cultivars grown in vitro were infected with the oomycete Plasmopara viticola, and transcriptome changes were investigated at 12h and 24h after infection. Three biological replicates were considered and each hybridization was performed twice. One color labeling was performed

first: Marianna

last: Polesani

first: Luisa

last: Bortesi

first: Anita

last: Zamboni

last: Fasoli

first: Claudia

last: Zadra

first: Arianna

last: Lovato

first: Massimo

last: Delledonne

first: Mario

last: Pezzotti

first: Annalisa

last: Polverari


title: Effects of Caveolin 1 knockout in mice

status: Public on Feb 15 2010

city: St. Lucia

first: Milena

last: Gongora

state: QLD

address: bld 80, services rd

country: Australia

institute: Institute for Molecular Biosciences

summary: In conjunction with other techniques, the role of caveolin-1 in lipid metabolism was assayed by comparing the gene expression of three tissues in Cav1+/+ and Cav1-/- mice. The tissues assayed were liver, adipose tissue, and mouse embryonic fibroblasts (MEFs) primary cell line, collected 24 hours after plating.    The MEFs were selected to give insights into the fundamental cellular functions of Cav1.    The adipose tissue and liver were selected because they are the most important tissues or organs involved the control of the lipid metabolism in mammals. Both of them were study during fasting because lipid metabolism become essential for maintaining of mammal metabolism homeostasis and tissue/organ functions in animals.

overall_design: Pairwise comparisons of WT-KO for each of the three tissues.

first: M

first: Manue

last: Fernandez-Rojo

first: Robert

last: Parton

first: Sean

last: Grimmond


title: Topo mutants psoralen photobinding

status: Public on Feb 16 2010

city: Burjassot

first: Jose

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary: We present a DNA array-based method for the genome-wide analysis of Psoralen photobinding in Saccharomyces cerevisiae cells. PB was found reduced in subtelomeric regions and increased in the subset of genes with smallest nucleosomal density.

overall_design: The analysis includes 3 repeats of the wild type strain (JCW25) at 30ºC and 3 more at 37ºC, 3 repeats of the double top1 (delta) top2ts mutant at 37ºC and 3 repeats of naked genomic DNA treated with trimethyl psoralen (TMP) in the same way to be used as a control of unspecific binding.

first: Ignacio

last: Bermudez


title: A saturated fatty acid rich diet can induce an 'obese-like' gene expression profile in adipose tissue

status: Public on Feb 14 2010

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: We investigated the effect of a saturated (SFA) and a monounsaturated (MUFA) rich diet on insulin sensitivity and adipose tissue gene expression profiles of subjects at risk for metabolic syndrome. A controlled-feeding trial was performed with 20 moderately overweight subjects. Subjects received a SFA-rich or a MUFA-rich diet for 8 weeks. Subcutaneous adipose tissue samples were obtained and insulin sensitivity was measured. Whole genome micro-array analysis was performed on the adipose tissue samples. Consumption of a SFA-rich diet resulted in a pro-inflammatory 'obese-like' gene expression profile while consumption of a MUFA-rich diet caused a more anti-inflammatory profile. This suggests that replacement of dietary SFA by MUFA could prevent adipose tissue inflammation and may reduce the risk for inflammation related diseases such as the metabolic syndrome.

overall_design: In a parallel controlled feeding trial, subcutaneous adipose tissue samples were collected from moderately overweight human subjects at baseline and after 8 weeks consumption of either SFA-rich or MUFA-rich diets. RNA was isolated from the samples using Trizol and the Qiagen RNeasy Micro kit (Qiagen, Venlo, the Netherlands). RNA was was labeled using a one-cycle cDNA labeling kit (MessageAmpTM II-Biotin Enhanced Kit, Ambion, Inc.) and hybridized to Affymetrix NuGO_Hs1a52018 arrays.

first: Susan

last: van Dijk

first: Edith

last: Feskens

first: Marieke

middle: B

last: Bos

first: Dianne

middle: W

last: Hoelen

first: Rik

last: Heijligenberg

first: Mechteld

last: Bromhaar

first: Lisette

middle: C

last: de Groot

first: Jeanne

last: de Vries

first: Michael

last: Müller

first: Lydia

last: Afman


title: HSD17B10, RPL8, IFITM2 and IFITM3 as predictive markers of response to chemotherapy in conventional osteosarcomas.

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

institute: ICO (Integrated Center of Oncology Nantes)

summary:
The aim of this study was to identify molecular markers able to classify osteosarcoma patients as good or poor responders before therapy.
Methods: Gene expression profiling of 20 non-metastatic high-grade osteosarcoma patients was performed using cDNA nylon microarray which contained 8,032 unique sequenced-verified cDNA clones, representing 5,776 distinct genes. Expression of selected genes was validated using RTQ-PCR. For correlated genes, corresponding proteins were explored. Immunohistochemistry (IHC) on sections of tissue microarrays (TMA) were performed on a cohort of 50 patients, out of which 30 were new patients. Furthermore, fluorescent in situ hybridization (FISH) was performed on gene which could not be tested using IHC.
Results: We have found that HSD17B10 gene expression was upregulated in the group of poor responders and that IHC expression of HSD17B10 in biopsy done before treatment was correlated to response to chemotherapy in 50 patients. Other relevant results include correlation of IFITM2, IFITM3 and RPL8 gene expression to response to chemotherapy. RPL8 gene expression also had a prognostic value for event-free survival. Moreover, a significant statistical correlation was found between polysomy 8 of RPL8 and good response to chemotherapy.
Conclusion:  These data suggest that HSD17B10 gene may be a biological marker and a therapeutic target in conventional osteosarcoma. This study highlights the prognostic and the predictive value of RPL8. RPL8 and IFITM2 may be useful in the assessment of patients with osteosarcoma at diagnosis and for stratifying patients taking part in randomized trials.
Keywords: Gene-expression profiling

overall_design: Gene expression profiling of 20 non-metastatic high-grade osteosarcoma patients was performed using spotted cDNA nylon membrane

first: Sébastien

last: Salas

first: Pascal

last: Jézéquel

first: Loïc

last: Campion

first: Frédéric

last: Chibon

first: Catherine

last: Bartoli

last: Charbonnel

first: Brigitte

last: Porsche

first: Jean-Claude

last: Gentet

first: Gérard

last: Bollini

first: Alexandre

last: Rochwerger

first: Florence

last: Duffaud

first: Dominique

last: Figarella-Branger

first: Corinne

last: Bouvier


title: Microarray-CGH of wine yeast strains

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

summary: Gene copy number comparison between similar wine yeast strains of Saccharomyces cerevisiae from different geographic origins.

overall_design: Microarray-CGH of wine strains EC1118, L-957 and LV CB compared to a common reference. Reference DNA was from laboratory strain S288C.

first: Francisco

middle: S

last: Salinas


title: Lignocellulosic biomass deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus

city: Raleigh

first: Amy

last: VanFossen

state: NC

address: 840 Main Campus Dr.  Rm3305

department: Chemical and Biomolecular Engineering

institute: NC State Unversity

summary: The ideal microorganism for consolidated biomass processing to biofuels has the ability to breakdown of lignocellulose. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on lignocellulose samples as well as model hemicellulose components. Identification of the enzymes utilized by the cell in lignocellulose saccharification was done using whole-genome transcriptional response analysis and comparative genomics.

overall_design: C. saccharolyticus was subcultured (overnight) seven times on the substrate of interest in modified DSMZ 640 medium before inoculating a 1-liter batch containing 0.5 gram substrate per liter. Cells were grown at 70 °C until mid-logarithmic phase (3-5*107) and harvested by rapid cooling to 4 °C and centrifugation and then stored at -80 °C. To elucidate the transporters plus the central carbon metabolic pathways and their regulation utilized on the different sugars, transcriptome analysis was performed after growth on switchgrass, poplar, glucose and xylose.

middle: L


title: MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori)

city: Beibei

first: Qingyou

last: Xia

address: Tiansheng Road

institute: Southwest University

summary:
Background: MicroRNAs (miRNAs) are expressed by a wide range of eukaryotic organisms, and function in diverse biological processes. Numerous miRNAs have been identified in Bombyx mori, but the temporal expression profiles of miRNAs corresponding to each stage transition over the entire life cycle of the silkworm remain to be established. To obtain a comprehensive overview of the correlation between miRNA expression and stage transitions, we performed a whole-life test and subsequent stage-by-stage examinations on nearly one hundred miRNAs in the silkworm.
Results: Our results show that miRNAs display a wide variety of expression profiles over the whole life of the silkworm, including continuous expression from embryo to adult (bmo-miR-184), up-regulation over the entire life cycle (bmo-let-7 and miR-100), down-regulation over the entire life cycle (miR-124), expression associated with embryogenesis (miR-29 and miR-92), up-regulation from early 3rd instar to pupa (miR-275), and complementary pulses in expression between miR-34b and miR-275. Stage-by-stage examinations revealed further expression patterns, such as emergence at specific time-points during embryogenesis and up-regulation of miRNA groups in late embryos (miR-1 and bantam), expression associated with stage transition between instar and molt larval stages (miR-34b), expression associated with silk gland growth and spinning activity (miR-274), continuous high expression from the spinning larval to pupal and adult stages (miR-252 and miR-31a), a coordinate expression trough in day 3 pupae of both sexes (miR-10b and miR-281), up-regulation in pupal metamorphosis of both sexes (miR-29b), and down-regulation in pupal metamorphosis of both sexes (miR-275).
Conclusions: We present the full-scale expression profiles of miRNAs throughout the life cycle of Bombyx mori. The whole-life expression profile was further investigated via stage-by-stage analysis. Our data provide an important resource for more detailed functional analysis of miRNAs in this animal.

overall_design: In the study presented here, we performed a whole-life test and subsequent stage-by-stage examinations on nearly one hundred miRNAs in the silkworm, leading to a comprehensive overview of the correlation between miRNA expression and stage transitions. In all, 59 unique developmental timepoints were inspected in this study.

first: Shiping

last: Liu

first: Liang

last: Zhang

first: Qibin

last: Li

first: Ping

last: Zhao

first: Jun

last: Duan

first: Daojun

last: Cheng

first: Zhonghuai

last: Xiang


title: Madin Darby Canine Kidney (MDCK) Cells: Early & Late Passage

status: Public on Feb 13 2010

city: Newark

first: Saleena

last: Ghanny

address: 185 South Orange Ave

institute: Rutgers University

summary: The paracellular passage of ions in epithelial systems is dictated by the repertoire of tight junction (TJ) proteins, the number and architecture of apicolateral TJ strands, and the interaction of TJ proteins with the cytoskeleton.  To investigate the relative contribution of these factors and to explore their regulation, we examined a passage number dependent phenotypic change in Madin Darby Canine Kidney (MDCK) cells iteratively passaged at low density in which dilution potentials of the monolayer abruptly decreased but transepithelial resistance (TER) progressively increased.  Here, we report that the phenotypic transition involved a decrease surface expression of peanut agglutinin (PNA), a decrease in steady state levels of claudin-1 and a slight decrease in E-cadherin expression in the context of an apparently claudin-2-negative system.  Late passage cells grew in more densely packed monolayers and exhibited characteristics of a competent, functional cultured monolayer including inducible vectorial ion transport in response to norepinephrine (NE) and sphere formation in three dimensional laminin gel culture.  Microarray analysis of gene expression levels in early and late passage cells revealed an increase in transcript abundance for SGK and GLUT-3, and a reduction Id-3.  The steady state protein expression levels of GLUT-3, however, were found to be equivalent.  These findings suggest that the expression of claudin-2 in MDCK cells could be contingent on signaling via lateral cell contacts and that claudin-1, in the context of sustained claudin-8 expression, could function as a negative regulator of overall TER.

overall_design: 3 biological replicates of early and late passage were run on Affymetrix chips.  the replicates were averaged then compared.

first: Erik

last: Young

first: Daragh

last: Quinn

first: Virginie

last: Aris

first: Patricia

last: Soteropoulos

first: Richard

last: Davies


title: Analyses of the SAGE expression of Human Embryonic Stem Cells

city: Singapore

first: Zhenyang

last: Lai

address: Science Drive 4

department: Department of Biologcial Sciences

country: Singapore

institute: National University of Singapore

summary: A plethora of research has focused on the human embryonic stem cells (hESC) ever since they were first reported mainly due to their distinct features of self renewal and pluripotency. Probing of the hESC transcriptome using global expression profiling tools such as DNA microarray, Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) and Expressed Sequence Tag (EST) analysis have contributed significantly in our current understanding of hESCs. In fact, a large number of markers to assess the pluripotent and differentiation status of hESCs have been presented by such studies. However, till date clarity is lacking in identifying a robust set of markers to assess the true state of the hESCs. In this paper, we report the generation of long SAGE libraries for partially differentiated and differentiated HES3 along with a deeper profiling of our previously reported HES3 undifferentiated library. Clustering analysis of these libraries in concert with long and short SAGE libraries available in public databases using Hierarchical Cluster Analysis (HCA) as well as a poison-based approach helped in identification of expression patterns distinct from those reported for the well established pluriptency/differentiation markers. Almost all the previous studies reporting a robust set of markers have focused on a gene by gene comparison in listing out the upregulated and downregulated genes rather than look at the expression patterns in establishing a list of markers. In this analysis, however, we report a new set of markers as well as add confidence to some previously reported markers based on their novel expression patterns as identified by SAGE analysis and also confirm it by real-time PCR analysis. For the real-time PCR confirmation, instead of taking two extreme data sets such as undifferentiated and a late stage embryoid body, we profiled a time series of embryoid body stages so that we could identify those genes which show a dramatic increase or decrease upon differentiation and hence would serve as more reliable markers.

overall_design: The hESC lines HES3 from ES Cell International, Singapore (http://www.escellinternational.com) were cultured on mouse embryonic fibroblast feeders (MEFs) as described previously.  Selection of cells for library construction was done by micro-dissection following our established protocols. Spontaneous differentiation was induced by prolonged culture without changing the feeder layer.  Briefly the HES3 cell line was grown to 18 passages (P18) on MEFs, after which no sub-culturing was performed. The medium was changed daily for 25 days and the differentiated cell population was harvested at the end of the culture period by micro-dissection. Cell differentiation was confirmed by Immuno-cytochemistry for markers to the three germ layers, as well as RT-PCR for the differentiation markers. For construction of the partially differentiated library, colonies which had started differentiation, as suggested by the morphological changes towards the centre and periphery of the colonies were used. Entire HES3 colonies (24P) which had started differentiation were harvested by micro-dissection and used for library construction. MmeI was used as tagging enzyme and libraries were constructed using the LS-SAGE kit from Invitrogen (http://www.invitrogen.com). Cloning of concatemerized ditags and sequencing of tags were done as outlined earlier. The 10 bp SAGE tags were extracted using Microsoft Excel for direct comparisons between libraries.

first: Shubha

last: Vij

first: Rajeev

middle: K

last: Sukumaran

first: Yue

last: Wang

first: Woon-Khiong

last: Chan

first: Ariff

last: Bongso


title: Gene expression analysis of glioblastoma spheroid cultures II

city: Heidelberg

first: Aurelie

last: Ernst

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: Microarray-based gene expression analysis identified genes differentially expressed in 10 glioblastoma spheroid cultures compared to a non-neoplastic spheroid culture isolated from the bulbus olfactorius

overall_design: In this study, a set of 10 glioblastoma spheroid cultures was used to acquire expression profiles of a total of 17 093  transcripts, leading to the identification of differentially expressed genes compared to a  non-neoplastic brain spheroid culture

first: Aurélie

first: Felix

last: Engel


title: Array CGH analysis of glioblastoma spheroid cultures

summary:
The goal of this study was to investigate genomic aberrations of glioblastoma spheroid cultures.

Keywords: Comparative genomic hybridization

overall_design: We performed array comparative genomic hybridization of spheroid cultures derived from 20 glioblastomas using as a reference DNA from healthy donors.


title: Time resolved response of E. coli to 5 different stress conditions

city: Potsdam

first: Szymon

last: Jozefczuk

address: Am Mühlenberg 1

institute: Max Planck Institute

summary: Environmental fluctuations lead to a rapid adjustment of the physiology of Escherichia coli, necessitating changes on every level of the underlying cellular and molecular network. Thus far, the vast majority of global analyses of E. coli stress responses have been limited to just one level, gene expression. Here we incorporate the metabolite composition together with gene expression data in order to provide a more comprehensive insight on system level stress adjustments by describing detailed time-resolved E. coli response to five different perturbations (cold, heat, oxidative stress, lactose diauxie, and stationary phase). The metabolite response is more specific as compared to the general response observed on the transcript level and is reflected by much higher specificity during the early stress adaptation phase and when comparing the stationary phase response to other perturbations. Despite these differences, the response on both levels still follows the same dynamics and general strategy of energy conservation as reflected by rapid decrease of central carbon metabolism intermediates coinciding with down regulation of genes related to cell growth. Application of co-clustering and canonical correlation analysis on combined metabolite and transcript data identified a number of significant condition dependent associations between metabolites and transcripts. The results confirm and extend existing models about co-regulation between gene expression and metabolites demonstrating the power of integrated systems oriented analysis.

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

overall_design: Four different environmental perturbations, comprising oxidative stress, glucose-lactose diauxic shift, heat, and cold treatments and using an unperturbed culture as a control have been used for transcript profiling. microarray-based transcript profiling was carried out for samples from time points 10-50 min post-perturbation plus two control time points prior to each perturbation for all conditions except the oxidative stress experiment in which all samples (12 time points) were used for transcript profiling covering the entire growth curve, including the stationary phase. Each experimental condition was independently repeated three times.

first: Dirk

last: Steinhauser

first: Sebastian

last: Klie

first: Lothar

last: Willmitzer


title: Array CGH analysis of glioblastomas

summary:
The goal of this study was to investigate genomic aberrations of glioblastoma patients.

Keywords: Comparative genomic hybridization

overall_design: We performed array comparative genomic hybridization of 7 glioblastomas using as a reference DNA from healthy donors.


title: Array CGH analysis of single spheroids from glioblastoma spheroid cultures

overall_design: We performed array comparative genomic hybridization of spheroid cultures derived from 2 glioblastoma spheroid cultures using as a reference DNA from healthy donors.


title: Array CGH analysis of glioblastoma cell lines

summary:
The goal of this study was to investigate genomic aberrations of glioblastoma cell lines.

Keywords: Comparative genomic hybridization

overall_design: We performed array comparative genomic hybridization of 8 glioblastoma cell lines


title: Array CGH analysis of glioblastoma serum grown adherent cultures

summary:
We performed array comparative genomic hybridization of spheroid cultures derived from 13 glioblastomas.

Keywords: comparative genomic hybridization

overall_design: Comparative genomic hybridization of spheroid cultures derived from glioblastomas using as a reference DNA from healthy donors.


title: Thymine starvation and limitation in Escherichia coli thyA- cells

status: Public on Feb 12 2010

city: Princeton

first: Dipen

last: Sangurdekar

state: NJ

address: 132 Carl Icahn laboratory, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Transcriptional profiling of responses of E. coli thymine auxotrophs to i) growth under sub-optimal thymine concentration (TLM) and ii) lethal conditions under complete thymine starvation (TLD).

overall_design: Thymine limitation: Time series following shift to limiting thymine concentrations (15, 30, 45, 60 and 90 mins) - single replicate. Thymine starvation: Time series following shift to zero thymine medium (15, 30, 45, 60 and 90 mins) - 2 biological replicates at each time point.

middle: P

first: Bree

last: Hamann

first: Arkady

last: Khodursky


title: UTX Chromatin Immunoprecipitation on human HG18 Nimblegen 2 array promoter set

city: Stanford

first: Jordon

address: 269 Campus Dr.

department: Dermatology

institute: Stanford University

type: Genome binding/occupancy profiling by genome tiling array

summary:
UTX binding sites were located genome wide in primary human fibroblasts (foot and lung)
Tiled promoters with a probe per 100bp of refseq known genes 3kb upstream and 700 bp downstream of transcriptional start

overall_design: 8 samples (2 cell types (foot and lung primary human fibroblasts) x 2 set promoter arrays x 2 channels (channel 1 = ChIP = Cy5, channel 2 = input (10% of total genomic DNA hybed) = Cy3)


title: Role of Hfq in Iron Dependent and Independent Gene Regulation in Neisseria meningitidis

status: Public on Feb 11 2010

city: Boston

first: Ryan

last: McClure

state: MA

address: 650 Albany St.

department: Microbiology

institute: Boston University

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

summary: In Neisseria meningitidis iron responsive gene regulation is mediated primarily by the Ferric Uptake Regulator (Fur) protein.  When complexed with iron, Fur represses gene expression by preventing transcription initiation. Fur can also indirectly activate gene expression via the repression of regulatory small RNAs (sRNA).  One such Fur-and iron-regulated sRNA, NrrF, was previously identified in N. meningitidis and shown to repress expression of the sdhA and sdhC genes encoding subunits of the succinate dehydrogenase complex. In the majority of Gram-negative bacteria sRNA-mediated regulation requires a cofactor RNA-binding protein (Hfq) for proper gene regulation and stabilization.   In this study we examined the role of Hfq in NrrF-mediated regulation of the succinate dehydrogenase genes in N. meningitidis and the effect of an hfq- mutation on iron-responsive gene regulation more broadly.  We first demonstrated that the stability of Nrrf as well as the regulation of sdhC and sdhA in vivo was unaltered in the hfq- mutant.   Secondly, we established that iron responsive gene regulation of the Fur-regulated sodB gene was dependent on Hfq.  Finally, we demonstrate that in N. meningitidis Hfq functions to control expression of both ORFs and intergenic regions via iron independent mechanisms.  Collectively these studies demonstrate that in N. meningitidis iron and NrrF mediated regulation of sdhC and sdhA can occur independently of Hfq, although Hfq functions more globally to control regulation of other N. meningitidis genes primarily by iron-independent mechanisms.

overall_design: RNA was isolated from wild-type MC58 Neisseria meningitidis, from an hfq- mutant, and from a complemented hfq-  mutant under both iron-replete and iron-deplete conditions.  Three biological replicates were analyzed for each strain and condition were analyzed.

first: J

last: Mellin

first: Caroline

last: Genco


title: Gene expression analysis of glioblastoma spheroid cultures I

summary: Microarray-based gene expression analysis identified genes differentially expressed in 10 glioblastoma spheroid cultures compared to normal brain.

overall_design: In this study, a set of 10 glioblastoma spheroid cultures was used to acquire expression profiles of a total of 16 441  transcripts, leading to the identification of differentially expressed genes compared to normal brain by Significance Analysis of Microarray dada.


title: Pyruvate carboxylase and carbon metabolism in Listeria monocytogenes

status: Public on Feb 10 2010

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

institute: University of Wuerzburg

summary:
Transcriptional profile of wild type L. monocytogenes (EGDe) and a pycA mutant strain was compared on growth in BHI.
The human pathogen L. monocytogenes is a facultatively intracellular bacterium that  survives and replicates in the cytosol of many mammalian cells. The listerial  metabolism, especially under intracellular conditions , is still poorly understood. Recent  studies analyzed the carbon metabolism of L. monocytogenes by the 13C-isotopologue  perturbation method in a defined minimal medium containing [U-13C6]glucose. It was  shown that these bacteria produce oxaloacetate mainly by carboxylation of pyruvate due  to an incomplete tricarboxylic acid cycle. Here we report that a pycA insertion mutant  defective in pyruvate carboxylase (PYC) still grows, albeit at a reduced rate, in BHI  medium, but is unable to multiply in a defined minimal medium with glucose or glycerol 36 as carbon source. Transcriptional profiling was performed on the pycA mutant and the wild type strain grown in BHI to get a closer insight into the effect of the pycA mutation in Listeria monocytogenes.

overall_design: RNA from the two strains were isolated after growth in BHI and and compared using whole genome oligonucleotide microarrays

first: Jennifer

last: Schär

first: Regina

last: Stoll

first: Daniela

middle: I

last: Loeffler

first: Eva

last: Eylert

first: Kristina

last: Schauer

first: Biju

last: Joseph

first: Wolfganga

last: Eisenreich

first: Thilo

last: Fuchs

first: Werner

last: Goebel


title: Expression and function of miRNAs in gastric carcinoma

city: Bunkyo-ku

first: rie

last: wada

state: Tokyo

address: Yushima 1-5-45

department: Molecular Oncology

institute: Tokyo Medical and Dental University

summary: To clarify the role of micro (mi) RNAs in gastric carcinogenesis, we studied the expression and function of miRNAs in gastric carcinoma (GC) cells. Initially, we performed microarray analysis using total RNA from three human GC cell lines and non-cancerous gastric tissue. Among the down-regulated miRNAs in GC cells,miR-212 expression was decreased in all eight GC cell lines examined and a significant decrease of miR-212 expression in human primary GC tissues was also observed in 6 of 11 cases. Transfection of the precursor miR-212 molecule induced decreased growth of a GC cell line. Using three different databases, methyl-CpG-binding protein MeCP2 was postulated to be a target of miR-212. As seen on reporter assaying, miR-212 repressed the construct with the MECP2 3'-UTR. Ectopic expression of miR-212 repressed expression of the MeCP2 protein,but not the MECP2 mRNA level. These data suggest that down-regulation of miR-212 may be related to gastric carcinogenesis through its target genes, such as MECP2.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We used three GC cell lines (MKN7, MKN74 and NUGC4) and one non-cancerous gastric tissue. miRNA microarray analysis was performed with mirVana miRNA Bioarrays V1 (Ambion) according to the manufacturer’s instructions.

first: Rie

last: Wada

first: Yoshimitsu

last: Akiyama

first: Yutaka

last: Hashimoto

first: Hiroshi

last: Fukamachi

first: yasuhito

last: Yuasa


title: Genomic markers that predict survivorship in colorectal cancer

city: Cambridge

first: George

last: Poulogiannis

address: Tennis Court Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

summary:
Genomic instability, including microsatellite instability (MSI) and gross chromosomal abnormalities, has been described in sporadic colorectal cancer (CRC) and MSI has been suggested to have prognostic significance. However, there are few prognostically relevant biomarkers. Here we explore the potential of the analysis of DNA copy number changes at 1Mb resolution to predict survivorship in sporadic CRC.

Keywords: Comparative Genomic Hybridization

overall_design:
Single hybridization per case. 109 colorectal tumours were analyzed. Target (tumor) labeled with Cy5 and reference with Cy3. Mixture of 20 normal male or female genomic DNA was used in sex-mismatched hybridization. 30 of the tumors were also later hybridized to a second 1Mb resolution array also containing Chr18 sequences for a total of 139 samples.

Definitions:
MSI	Microsatellite instability
MSI-H	Microsatellite instability at high frequency
MSI-L	Microsatellite instability at low frequency

first: Koichi

last: Ichimura

first: Rifat

last: Hamoudi

first: Feijun

last: Luo

first: Suet

middle: Y

last: Leung

first: Siu

middle: T

last: Yuen

first: David

middle: J

last: Harrison

first: Andrew

last: Wyllie

first: Mark

last: Arends


title: intDCs versus LCs

city: Vienna

first: Jennifer

last: Jurkin

address: Lazarettgasse 19

department: Institut of Immunology

country: Austria

institute: Medical University of Vienna

summary:
miRNA profiling of CD34+ derived, in vitro-generated Langerhans cells (LCs) and interstitial-type dendritic cells (intDCs).
Epidermal Langerhans cells (LCs) form a network of dendritic cells (DCs) in basal/suprabasal layers of the skin and are characterized by a unique phenotype (CD207+ CD1abright CD324+ CD11b-). Due to their specific location at body surfaces, LCs are constantly exposed to environmental stimuli. Conversely, interstitial-type DCs (intDCs) are located in adjacent tissues and can be discriminated from LCs phenotypically (CD207- CD1adim CD324- CD11b+). These DCs constitute a second line of defense against pathogens that have crossed the epithelial barrier. During development both DC subsets originally arise from myeloid progenitor cells via monocyte-committed intermediates in response to specific microenvironmental signals. Additionally certain pools of DCs can be replenished by tissue resident cells or monocytes in response to specific microenvironmental signals (2, 4, 5). In vitro generated GM-CSF/IL-4-dependent DCs derived either from CD14+ monocytes or via CD14+CD11b+ monocyte intermediates from CD34+ progenitor cells share many characteristics with intDCs in vivo. On the other hand, LCs generated from CD34+ cells under serum-free TGF-beta1-dependent conditions phenotypically resemble epidermal-resident LCs. Since these two DC subsets are of considerable interest for clinical cell therapy studies, an improved understanding of their development and function is of substantial relevance. To identify differentially expressed miRNAs in DC subsets, we performed a miRNA screen. Therefore, we generated LCs or intDCs from human CD34+ cord blood haematopoietic progenitor cells as described. For intDCs, CD34+ cells (1 x 104 to 2 x 104/ml per well) were cultured in 24-well tissue culture plates in serum free CellGro® DC medium (CellGenix, Freiburg, Germany) supplemented with GM-CSF (100 ng/ml), SCF (20 ng/ml), FL (50 ng/ml) and TNFalpha (2.5 ng/ml) for 3-5 days and subsequently with GM-CSF (100 ng/ml) and IL-4 (2.5 ng/ml) for 4-5 days. For LCs, CD34+ cells (1 x 104 to 2 x 104/ml per well) were cultured in 24-well tissue culture plates in serum free CellGro® DC medium (CellGenix, Freiburg, Germany) supplemented with GM-CSF (100 ng/ml), SCF (20 ng/ml), FL (50 ng/ml), TNFalpha (2.5 ng/ml) and TGF-beta1 (0.5 ng/ml). The well-established immunophenotype of LCs (CD1ahi CD11b- CD207+ CD324+) and intDCs (CD1a+ CD11b+ CD207- CD324-) was confirmed by FACS. These two DC subsets were purified and submitted to differential miRNA profiling.

overall_design:
Two conditioned experiment LCs vs. intDCs. Biological replicates: 3 LCs, 3 intDCs, independently differentiated, harvested and purified.  3 replicates  each were pooled and hybridized on one array.
Supplementary files linked below.

first: Herbert

last: Strobl

first: Berhard

last: Gesslbauer


title: Genome-wide Promoter Mapping of Histone H3 Lysine 4 and Lysine 27 Methylation in Preimplantation Embryos

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: First lineage specification in the mammalian blastocyst embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to the embryo proper and extraembryonic tissues. We show histone methylation asymmetry on promoters in the first two developmental lineages, and highlight epigenetic skewing associated with derivation of embryonic stem (ES) cells.

overall_design: Comparison of histone methylation patterns on promoters in the ICM, TE and in ES cells derived from ICM. ChIP-chip experiments using anti-H3K4me3 or anti-H3K27me3 antibodies. Two or three replicates per sample.

last: Dahl

last: Reiner


title: Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds

city: Urbana

first: Kirstin

last: Replogle

address: 1206 W Gregory Drive

institute: University of Illinois

summary: We have performed a comparison of global patterns of gene expression between two bird species, the chicken and zebra finch, especially with regard to sex bias of autosomal vs. Z chromosome genes, dosage compensation and evolution of sex bias. Both species appear to lack a Z chromosome-wide mechanism of dosage compensation, because both have a similar pattern of significantly higher expression of Z genes in males relative to females. Unlike the chicken Z chromosome, which has female-specific expression of the non-coding RNA MHM (male hypermethylated), and acetylation of histone 4 lysine 16 (H4K16) near MHM, the zebra finch Z chromosome appears to lack the MHM sequence and acetylation of H4K16. The zebra finch also does not show the reduced male to female (M:F) ratio of gene expression near MHM similar to that found in the chicken. Although the M:F ratios of Z chromosome gene expression are similar across tissues and ages within each species, they differ between the two species. Z genes showing the greatest species difference in M:F ratio were concentrated near the MHM region of the chicken Z chromosome. The current study shows that the zebra finch differs from the chicken because it lacks a specialized region of greater dosage compensation along the Z chromosome, and shows dosage compensation for a different set of Z genes than the chicken. These patterns suggest that different avian taxa may have evolved specific compensatory mechanisms.

overall_design: Experimental groups: Post-hatch Days 1, 25, 45, and 90+ for both Females and Males (d1_F, d1_M, d25_F, d25_M, d45_F, d45_M, adult_F, adult_M). Biological replicates: 6 per group. One test developmental stage subject and one universal SoNG reference (pooled Taeniopygia guttata brain) per array.

first: Yuichiro

last: Itoh

first: Yong-Hwan

last: Kim

first: Juli

last: Wade

middle: F

last: Clayton

first: Arthur

last: Arnold


title: MicroRNA Expression Profile Reveals Important Clinical Tools for the Pathology of Lung Cancer

city: beijing

first: wu

last: jp

address: 18 Life Science Parkway

institute: National Engineering Research Center

summary:
We investigated whether the miRNA expression could distinguish lung cancers from normal tissues, examining 116 pairs of primary lung cancers with their corresponding adjacent normal lung tissues collected a minimum of 5 cm from the tumor. Our analysis identified a five microRNA classifier could distinguish malignant lung cancer lesions from adjacent normal tissues.  SCLC could be distinguished from non small lung cancer by microRNAs profiling.  Survival associations were examined with the SCC and adenocarcinoma subtypes.  High hsa-miR-31 expression was associated with poor survival in SCC, and the association was confirmed in 20 independent SCC patients by qRT-PCR assays.  Overall these findings may help advance the use of microRNA profiling in personalized diagnosis of lung cancers.
Key Words: microRNA; lung cancer; microarray; diagnosis; prognosis

overall_design: cancer vs adjacent normal tissues


title: ArrayCGH mapping of the recurrent 3q26.3-q27 amplifications in lung Squamous Cell Carcinoma (SCC)

city: ILLKIRCH

first: Thomas

last: Hussenet

address: 1 rue Laurent Fries

department: Cancer Biology Department

institute: IGBMC

summary:
To prospectively identify new oncogenes implicated in lung Squamous Cell Carcinoma pathogenesis, we investigated chromosome 3 aberrations in advanced tumours using arrayCGH. Chromosome 3 aberrations are indeed among the most frequent alterations in lung SCC and correlate with SCC patient's poor prognosis. We have precisely mapped regions of recurrent losses at 3p and gains at 3q25-qter in a series of lung SCC (GSE14859) amd moreover uncover 3q26.3-q27 high level amplifications in 20% of tumours. These amplicons were precisely mapped in these tumors using arraCGH with a 3q26.3 dedicated tiling array. Keywords : ArrayCGH, lung Squamous Cell Carcinoma, 3q26.3, SOX2

Keywords: ArrayCGH

overall_design: Profiling of 5 advanced (stage III) lung SCC using a chromosome 3 array providing 3q26.3-q27 tiling coverage. Replicates : each array contains three replicates per clone and each sample is hybridized to two arrays, results are subsequently averaged.

first: Stanislas

last: du Manoir


title: Expression profiling of P. stutzeri A1501 treated with 20mM ammonia shock for 10 min

city: Beijing

first: yongliang

last: yan

address: zhongguancun south 12th

institute: CAAS

summary: A whole genome DNA microarray was used to undertake a global transcriptional analysis of nitrogen fixation and ammonium repression in Pseudomonas stutzeri A1501. The aim of this study was to identify the genes that are up-regulated under nitrogen fixation conditions and rapidly down-regulated as soon as 10 min after ammonia shock. The expression changed genes may be the candidate genes for the ammonia signal transmission or be involved in the nitrogen regulatory mechanism.

overall_design: First, P. stutzeri A1501 was treated with 0.1 mM ammonia and 0.5% Oxygen tension until the nitrogenase activity was detectable. Then the cells were sudden shifted from the nitrogen fixation conditions to the ammonia repression conditions by addition of 20 mM ammonia for 10min. Subsequently, the bacterium was collected and began the RNA extraction process. Thus, we compare the expression profilings in these two conditions in order to identify the candidate genes.

first: Yongliang

last: Yan

first: Shuzhen

last: Ping

first: Yuetan

last: Dou

first: Qi

last: Jin

first: Min

last: Lin


title: Strains of increasing genetic divergence to the reference strain

status: Public on Feb 06 2010

first: Deborah

middle: R.

last: Yoder-Himes

address: 77 Louis Pasteur Ave, 1038 NRB

department: Microbiology and Molecular Genetics

institute: Harvard Medical School

summary: comparative genomic hybridization between Burkholderia cepacia sequenced strains to determine what are the limits to strain relativity in order to still provide accurate estimations of gene content

sample_organism:
Burkholderia cenocepacia J2315
Paraburkholderia xenovorans LB400
Burkholderia vietnamiensis G4
Burkholderia cenocepacia HI2424
Burkholderia ambifaria AMMD
Burkholderia orbicola

overall_design: Two color experiment, Burkholderia cenocepacia J2315 (reference), B. cenocepacia AU1054 (tester), HI2424 (tester), B. ambifaria AMMD (tester), B. vietnamiensis G4 (tester), B. xenovorans LB400 (tester): At least two replicates including a single dye swap for each reference-tester comparison

first: Seung-Dae

last: Oh

first: James

last: Tiedje

first: Konstantinos

last: Konstantinidis


title: Influence of environmental conditions and AI2 on the adhesion adaptive response of Lactobacillus acidophilus NCFM

status: Public on Feb 09 2010

city: Raleigh

first: Todd

middle: Robert

last: Klaenhammer

department: Department of Food, Bioprocessing, and Nutrition Sciences

institute: North Carolina State University

summary:
This study reports an over 20-fold increase in the adhesive ability of Lactobacillus acidophilus NCFM to Caco-2 cells following a 1 hour incubation of cells that were concentrated ten-fold, immediately prior to adhesion.  Microarray analysis of the global transcriptional response with and without exposure to the adhesion adaptive conditions revealed several genes potentially involved with adhesion to the intestinal epithelial cells and a classic stress response.  Interestingly, putative genes linked to the synthesis of an interspecies signaling molecule, autoinducer-2 (AI-2), were overexpressed.  Examination of the L. acidophilus NCFM genome revealed the complete pathway for AI-2 synthesis.  AI-2 activity was detected in L. acidophilus NCFM during stationary growth phase using the Vibrio harveyi BB170 assay system.  Using site-specific integration, an isogenic mutation was created in luxS and the resulting derivative of L. acidophilus NCFM did not produce AI-2.  A 58 % decrease in adherence to Caco-2 cells was also observed by the LuxS- mutant when the cells were used for adhesion directly from logarithmic phase cultures.  However, the LuxS- mutant strain still responded to adhesion adaptive conditions with significantly increased adherence indicating that additional factors contribute to the amplified adhesion response.
Keywords: Culture response to specific environmental conditions

overall_design: A single 20 mL culture of L. acidophilus was grown in MRS to OD600 of 0.6, divided into two 10 ml aliquots, and harvested by centrifugation for 8 min at 3,150 x g.  One aliquot was resuspended in 10 ml of fresh MRS (Sample "control"), the other resuspended in 1 ml of fresh MRS (Sample "test").  Both cultures were then incubated for 1 hr at 37°C.  Following incubation, cells were harvested by centrifugation and frozen immediately in a dry ice-ethanol bath.  RNA isolation was conducted according to the protocol described previously (Azcarate-Peril et al., 2005). Two slides, each containing the complete genome of L. acidophilus NCFM spotted in triplicate, were hybridized reciprocally to Cy3- and Cy5-labeled probes per experiment (dye swap) for each of two biological replicates.

first: Brock

last: Buck

first: Maria

middle: A

last: Azcarate-Peril


title: ChIP-chip profiling of SsrB in Salmonella enterica sv. Typhimurium

status: Public on Feb 08 2010

city: Hamilton

first: Brian

last: Coombes

address: 1200 Main St. West

department: Biochemistry & Biomedical Sciences

institute: McMaster University

summary: We performed chromatin immunoprecipitation on microarray (ChIP-chip) transcriptional profiling of the SsrB regulator of Salmonella enterica Typhimurium to better characterize its regulon and to identify the DNA-recognition element coordinating its specific interaction at cis-regulatory sites.  SsrB, the response regulator of the two component regulatory system SsrA-SsrB encoded within the Salmonella Pathogenicity Island (SPI-2), directs transcriptional activation of the closely associated type three secretion system (T3SS) also encoded at this locus.  Immunoprecipitaiton of SsrB translationally fused to a C-terminal FLAG-tag from formaldehyde cross-linked genomic DNA was performed under SPI-2 activating and non-activating conditions.  Downstream analysis and experimental work identified specific interactions within SPI-2 at the previously identified ssrA, ssaB, sseA, ssaG, ssaM promoters and identified an additional cryptic promoter driving expression upstream of ssaR.  Additionally, a previously unknown SsrB interaction site within ssaE was shown to be the major contributor driving the expression of the downstream genes and not the previously identified interaction site within the intergenic region of ssaE-sseA.  Interactions were also identified outside of SPI-2 upstream of other T3SS-associated genes encoded within other genomic islands, and for other uncharacterized genes.  Integration of this data with transcriptional microarray work, previously published DNase I footprinting data, bacteria 1-hybrid investigations and comparative genomics analyses of cis-regulatory regions within the orthologous Sodalis symbiosis region 3 (SSR-3) of Sodalis glossinidius enabled identification of a conserved 18bp palindrome which was experimentally validated as being required for transcriptional activation of SsrB dependant genes.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: SsrB-FLAG immunoprecipitations were performed under SsrB activating and non-activating conditions from formaldehyde cross-linked bacterial lysates.  Nine immunoprecipitation reactions were pooled into three replicate samples for the activating condition and three reactions were pooled into one sample for the non-activating control condition.  The immunoprecipitated DNA in addition to the non-immunoprecipitated control DNA for each of the four samples were labeled with Cy3 or Cy5 fluorophores respectively and were concurrently hybridized to four arrays on a single slide.

first: David

last: Mulder

first: Ana

middle: M

last: Tomljenovic